Source: UNIVERSITY OF CALIFORNIA submitted to
NEMATODE MANAGEMENT IN ANNUAL CROPS WITH EMPHASIS ON HOST PLANT RESISTANCE.
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
REVISED
Funding Source
Reporting Frequency
Annual
Accession No.
0191017
Grant No.
(N/A)
Project No.
CA-R-NEM-6964-H
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Oct 1, 2011
Project End Date
Sep 30, 2016
Grant Year
(N/A)
Project Director
Roberts, P. A.
Recipient Organization
UNIVERSITY OF CALIFORNIA
(N/A)
RIVERSIDE,CA 92521
Performing Department
Nematology, Riverside
Non Technical Summary
Plant parasitic nematodes cause significant losses in production and quality of field and vegetable crops worldwide. These losses occur in both subsistence and highly mechanized agricultural systems. Effective management practices for nematodes can increase productivity of land and growers' income, improve quality of food and fiber and give more uniform emergence, growth and maturity of crop plants. Over the last fifty years, nematode management has been based primarily on the use of soil-applied nematicidal agents that either kill nematodes or inhibit their parasitic ability. However, a major shift away from the use of these pesticides is occurring because of problems associated with human health and environment risks, and the prohibitive cost structure of developing new nematicides and of using currently available nematicides in many low cash value production systems. Future use of nematicides will require a more judicious use of the pesticide through integration with other control strategies. Through better understanding of the ecology, biology and pathology of known or suspected nematode pathogens of plants, non-chemical management strategies may be made more effective and, where suitable, might be integrated with existing or modified nematicide use in a broad based management program. Currently the best alternative controls in field and vegetable crops are based on host plant resistance that protects both the resistant crop and the following susceptible crops in annual rotations. Natural host plant resistance is a major resource in agriculture for developing nematode management tools and programs. The potential for resistance has been achieved in some crops and situations but not in many others, reflecting that only a small portion of natural host plant resistance has been utilized. The approach in this project is to identify, analyze and implement host plant resistance traits to the root-knot nematodes, the most broadly damaging nematode parasites of crop plants. We will identify new sources of resistance in wild and domesticated plant germplasm, with emphasis on cotton, dry grain legumes (bean crops), and carrots. The resistance genes will be analyzed and mapped within the plant genome and molecular markers developed for use in resistance selection by plant breeders. This approach enables different genes to be stacked into improved crop varieties. Advanced breeding lines and new varieties will be studied in crop rotations to assess their effectiveness for protecting against nematode crop losses. Identification and characterization of resistance genes in crop plants will lead to more effective and safe approaches to managing root-knot nematodes by developing resistant varieties. The use of the resistance in crop production systems is aided by understanding the number, combinations and specific types of resistance that will be most effective. Optimal crop protection and durability of resistance are advanced by determining the most efficient ways of deploying resistant cultivars in cropping systems.
Animal Health Component
40%
Research Effort Categories
Basic
60%
Applied
40%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2121719112025%
2121499112040%
2122499108035%
Goals / Objectives
The overall project goal is to identify, analyze and implement host plant resistance to root-knot nematodes in annual cropping systems. Resistance will be studied as a primary means of nematode management in annual field and vegetable cropping systems, with emphasis on nematode and interacting pathogen resistance traits in cotton, grain legumes (especially cowpea), and carrots. These target crop plants each present excellent models for host plant resistance to nematodes, with several genes available in each case. To meet this goal, three specific objectives include: 1) examine nematode biology in nematode interactions with soil and with plant hosts, specifically including the abiotic factors temperature and moisture, and biotic factors of interacting organisms (fungi, bacteria, other nematodes) and plant host status; 2) develop, refine and implement management strategies for root-knot and comparative nematodes on field and vegetable crops, emphasizing non-host rotations, resistant and tolerant cultivars and nematicides, singly or integrated where appropriate; and 3) identify, characterize, introgress and implement host plant resistance traits, corresponding to genetic variation for parasitism in nematode populations. Resistance has a proven track record of effectiveness in managing nematodes in agriculture, resistance genes in crops are environmentally benign, the cost of resistance use is compatible with both subsistence level and high input agricultural systems, and a huge untapped resource of natural host resistance genes is available. Advances can be made through enhanced and new knowledge of the identity, genetic and molecular nature, mode of function, and effects in cropping systems of resistance genes. Gene-for-gene matching of resistance genes and nematode avirulence genes occurs, but the genetic basis for the virulence condition is poorly understood. New knowledge on these gene systems should lead to stronger and more durable forms of resistance in crop varieties. The expected outputs from the project are several-fold. New knowledge will be gained concerning the nature and effectiveness of root-knot nematode resistance in multiple crop plants. The genome location and organization of key resistance traits in cotton, legumes and carrots will be determined through genetic and physical mapping using segregating breeding populations of the target crop plants. This knowledge will enable the development of molecular markers for the resistance determinant genes. The markers will be applied to breeding populations for indirect selection of resistant progenies carrying the desired complement of resistance genes in agronomically preferred backgrounds. These outputs will be extended through the release of improved varieties with nematode resistance, coupled with performance evaluations of the resistance and guidelines for its effective use in nematode-infested fields.
Project Methods
Integrative procedures for combining resistance with crop rotation, nematicides and other control tactics will be determined using field microplot and small plot multifactorial experiments on nematode infested soils. Experiments will be designed using standard methods, to test the frequency, combinations, and sequences of resistance traits in different crops. The multiple year experiments will assess the nematode soil population density dynamics under the different cropping treatments, by assaying at the beginning and end of each crop cycle. Plant growth and yield data will be used to index effects on crop yield. Characterization of genetic determinants of resistance will be made using classical Mendelian approaches in conjunction with molecular marker and QTL mapping approaches. Crossing and selfing will be used to generate segregating plant populations, near-isogenic lines and recombinant inbred lines, for use in resistance gene mapping and marker development. Emphasis will be placed on SSR, SNP and SFP based marker analysis for gene tagging and mapping using current and novel techniques, including identification of candidate resistance genes through RNA based gene expression approaches. We will focus on using co-dominant SSR markers in cotton and carrot and SNP markers derived from ESTs in cowpea and carrot. SNP genotyping in cowpea will be conducted using the cowpea 1536-Illumina Goldengate Assay platform we recently developed, coupled with QTL analysis using MapQTL software. A high throughput SNP genotyping platform in development for carrot will be available during most of the project period. Thus, both foreground and background based genomic selection will be applied for introgression of multiple resistance traits into elite backgrounds of cowpea and carrot. Re-sequencing of key plant genotypes will be done using next generation deep-sequencing technology, such a Illumina HiSeq. Synteny relationships with the annotated soybean sequence and with other sequenced plant genomes will be used for candidate gene identification. BAC libraries in cotton and cowpea will be utilized for physical mapping and isolation of target resistance genes, and for increasing marker density in the QTL regions of interest. Molecular and genomic characterization of resistance genes will guide decisions on the priority and combinations of resistance gene introgression for crop improvement, including preferred genes for cloning. Genetic analysis will provide plant populations and genetic mapping information to develop marker-assisted breeding protocols and for map-based resistance gene-cloning. Nematode populations will be studied using similar genetic approaches to those described for plant gene analysis. Nematode populations segregating for avirulence traits will be developed by controlled matings. In parthenogenetic nematodes, isofemale line analysis will be used to study avirulence genetics.

Progress 01/01/12 to 12/31/12

Outputs
OUTPUTS: Host plant resistance to root-knot nematodes (MELOIDOGYNE spp.) and interacting organisms was studied as a major integrative tactic for nematode management programs in annual field and vegetable cropping systems. Resistance traits in cowpea (blackeye beans), carrot, and cotton were investigated at the molecular and genome organization levels, in conjunction with trait determinants of agronomic characters (e.g. cowpea seed size, carrot root shape and quality) and resistance to other biotic stresses including fungal pathogens and insects. QTL for root-knot nematode resistance were mapped in multiple cowpea populations. Field and greenhouse screens were used to phenotype recombinant inbred lines and F2 derived families. Knowledge of QTL positions flanked by mapped SNP markers was used in recurrent backcrossing to develop advanced generation blackeye dry grain breeding lines carrying the Rk2 gene, which confers stronger and broader root-knot resistance than the currently used gene Rk. Field trials on nematode infested sites confirmed that lines carrying the stronger resistance had significantly higher grain yields than lines with gene Rk only or with no resistance. A SNP marker platform using the KASP technology developed from the mapped SNP markers was applied in high-throughput genotyping of cowpea breeding lines and germplasm. New QTL for biotic stress resistance genes in the cowpea genome were identified including those for Fusarium wilt resistance and thrips resistance, leaf morphology and heat tolerance, as part of a comprehensive cowpea molecular breeding approach. Two infested field nurseries were used for selection of nematode resistance among more than 1000 fresh market carrot lines developed for high nutritional content and resistance to M. JAVANICA and M. INCOGNITA. More than 50 percent of the breeding lines showed strong dual resistance in these trials. We focused on combing the major resistance gene Mj-1 with an additive gene for enhanced M. INCOGNITA resistance, and now have lines in the homozygous condition for both genes. Populations were greenhouse screened for genetic mapping to identify the additive gene presence. QTL mapping in a population segregating for the additive gene identified a candidate gene region in the carrot genome. Molecular analysis of M. INCOGNITA and Fusarium wilt races 1 and 4 resistance in cotton was continued for marker development and mapping, using chromosome substitution lines and a newly developed interspecific RIL population. BAC clones from a BAC library of the Acala NemX resistance source which are positive for microsatellite markers that map to chromosomes 11 and 21 of the cotton genetic map were sequenced and annotated. Additional markers in the nematode and wilt resistance regions on these chromosomes were developed using the G. RAIMONDII D5 whole genome sequence, and then remapped in populations segregating for nematode resistance. QTL for resistance to Fusarium wilt Races 1 and 4 were identified using interspecific cotton mapping populations. Validations were made of transgressive resistance to M. INCOGNITA in cotton lines of an interspecific recombinant inbred population. PARTICIPANTS: Collaborators in the cowpea research included Dr. T J Close and Dr. J. D. Ehlers, University of California, Riverside; Dr. S Temple and B. Sanden, University of California Cooperative Extension, and California blackeye bean growers and processors. Collaborators in the carrot research included Dr. P. W. Simon, USDA-ARS, University of Wisconsin, Madison, and J. Nunez, University of California Cooperative Extension. Collaborators in the cotton research included Dr. M. Ulloa, USDA-ARS, Lubbock, TX, and Dr. Robert Nichols, Cotton Incorporated, Cary, North Carolina. TARGET AUDIENCES: Primary target audiences are commercial producers (growers) of cotton, grain legumes, and fresh market carrots. Secondary target audiences include public and private cotton, grain legume, and carrot breeders and seed producers. Through these secondary target audiences, the new knowledge and availability of nematode resistance genes, associated molecular markers, and advanced breeding lines or varieties carrying resistance is being applied for modern breeding of improved crop varieties. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Natural host plant resistance genes are valuable in crop plants as effective and safe approaches to managing root-knot nematodes and interacting pathogens including Fusairum wilt. Studies on their specificity, efficacy and use in cropping systems advance their utilization in agriculture. Identification and characterization of resistance genes in crop plants will lead to effective and safe approaches to managing root-knot nematodes by developing resistant varieties. New knowledge on the genetics and performance of nematode resistance is important in guiding the effective deployment of resistant varieties in crop production systems as alternatives to nematicides. Characterized resistance with genetic markers can be selected more efficiently in breeding programs and deployed in cropping systems. The study of the genetic diversity of resistance and other beneficial traits will lead to genetic improvement of important food and fiber crops including cotton, carrot, and grain legumes. The screening and selection for nematode resistance in different market classes in cowpea based on grain type should lead to release of new dry grain varieties, The high-throughput SNP genotyping capability coupled with QTL discovery for important traits including resistance to nematodes and other biotic and abiotic stresses will expedite cowpea breeding and genetic improvement programs. Additional advanced breeding lines of fresh market carrots developed with resistance to both common species of root-knot nematodes were provided to the commercial seed industry for use in finished varieties and for seed multiplication, with the goal of introducing resistant carrot varieties into the fresh carrot production system. Combinations of the new sources of resistance in carrot were shown to provide strong levels of resistance for future use in the carrot industry. Genetic analysis and marker development for nematode and wilt resistance in cotton provided new knowledge and resources in support of public and private cotton breeding programs.

Publications

  • Subbotin, S.A., R.N. Inserra, M. Marais , P. Mullin, T.O. Powers, P.A. Roberts, E. Van Den Berg, G. W. Yeates, J.G. Baldwin. 2011 Diversity and phylogenetic relationships within spiral nematodes of Helicotylenchus Steiner, 1945 (Tylenchida: Hoplolaimidae) as inferred from analysis of D2-D3 expansion segments of 28S rRNA gene sequences. Nematology 13:333-345.
  • Ehlers, J. D. and P. A. Roberts. 2012. Blackeye Varietal Improvement. p. 11-18. In University of California Dry Bean Research 2011 Progress Report, California Dry Bean Advisory Board, Dinuba, CA.
  • Roberts, P.A., W. C. Matthews, and P. W. Simon. 2012. Identification of gene sources for resistance to root-knot nematodes. Pp.53-84 in 2011 Annual Report of California Fresh Carrot Advisory Board. California Fresh Carrot Advisory Board, Dinuba, CA.
  • Hu Z, JD Ehlers, PA Roberts, TJ Close, MR Lucas, S Wanamaker, S Xu. 2012. ParentChecker: a computer program for automated inference of missing parental genotype calls and linkage phase correction. BMC Genetics 13:9.
  • Wang, C., M. Ulloa, T. R. Mullens, J. Yu and P.A. Roberts. 2012. QTL analysis for transgressive resistance to root-knot nematode in interspecific cotton (Gossypium spp.) progeny derived from susceptible parents. PLoS ONE 7(4): e34874. doi:10.1371/journal.pone.0034874
  • Pottorff, M., J.D. Ehlers, C. Fatokun, P.A. Roberts, and T.J. Close. 2012. Leaf morphology in Cowpea [Vigna unguiculata (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species. BMC Genomics 13:234 doi:10.1186/1471-2164-13-234.
  • Pottorff, M., S. Wanamaker, Y. Q. Ma, J.D. Ehlers, P.A. Roberts, and T.J. Close. 2012. Genetic and physical mapping of candidate genes for resistance to Fusarium oxysporum f.sp. tracheiphilum race 3 in cowpea [Vigna unguiculata (L.) Walp]. PLoS ONE 7(7): 1-11.
  • Lucas, M.R., J.D. Ehlers, B. L. Huynh, N.-N. Diop, P.A. Roberts, and T.J. Close. 2012. Markers for breeding heat tolerant cowpea. Molecular Breeding. Doi: 10.1007/s11032-012-9810-z.
  • Lucas, M.R., Ehlers, J.D., Roberts, P.A., Close, T.J. 2012. Markers for quantitative inheritance of resistance to foliar thrips in cowpea. Crop Science 52:2075-2081.


Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: Host plant resistance to root-knot nematodes (MELOIDOGYNE spp.) and interacting organisms was studied as a major integrative tactic for nematode management programs in annual field and vegetable cropping systems. Analyses of resistance traits were conducted in cowpea (blackeye beans), carrot, and cotton. Cowpea includes several loci with multiple resistance specificities to different root-knot nematode species and populations. A recurrent backcrossing program was advanced to the eighth generation, to introgress the Rk2 gene for stronger and broader root-knot resistance than gene Rk, into preferred California blackeye dry grain cowpeas. This resistance protects against M. JAVANICA and M. INCOGNITA populations that are virulent to gene Rk. Advanced breeding lines of improved blackeye lines with Lygus bug tolerance and new market type cowpeas including all-white and persistent green grain types with nematode resistance were screened in field and greenhouse tests; lines carrying the resistance were selected for seed multiplication. Additional refinements were made to the high density SNP marker-based consensus genetic map of cowpea, using 12 recombinant inbred line (RIL) mapping populations. A new SNP marker platform using KASPar technology was developed for high-throughput genotyping of cowpea breeding lines and germplasm. The genetic map was used to identify new resistance QTL and to validate previously identified QTL representing various biotic stress resistance genes in the cowpea genome, including the independent Rk, Rk2 and rk3 nematode resistance loci. A set of near-isogenic lines with or without the nematode resistance genes were seed-increased and field tested for M. INCOGNITA tolerance. Lines with combinations of R genes had more than double the yield of the null susceptible lines. Three infested field nurseries were used for selection of nematode resistance among 500 fresh market carrot lines developed for high nutritional content and resistance to M. JAVANICA and M. INCOGNITA. Many lines had strong dual resistance based Mj1 plus an additive gene for M. INCOGNITA resistance. Populations were greenhouse screened for genetic mapping to identify the additive gene. Co-selection for Mj1 and the additive gene using linked markers should expedite breeding for comprehensive resistance. Molecular analysis of M. INCOGNITA and Fusarium wilt resistance in cotton was continued for marker development and mapping. Fifty BAC clones from a new BAC library of the Acala NemX resistance source which map to homoeologous chromosomes 11 and 21 were fully sequenced and annotated. Sequenced BAC clones from an Acala Maxxa BAC library that also map to these target regions were annotated, revealing clusters of resistance gene motifs, especially NBS-LRR types. QTL for Fusarium wilt Race 1 resistance were identified using interspecific cotton mapping populations. Transgressive resistance to M. INCOGNITA conferring high levels of resistance was found in a cotton interspecific recombinant inbred population developed from two susceptible parents. PARTICIPANTS: Cowpea collaborators included Dr. T J Close and Dr. J. D. Ehlers, University of California, Riverside; Dr. S Temple and B. Sanden, University of California Cooperative Extension, and California blackeye bean growers and processors. Carrot collaborators included Dr. P. W. Simon, USDA-ARS, University of Wisconsin, Madison, and J. Nunez, University of California Cooperative Extension. Cotton collaborators included Dr. M. Ulloa, USDA-ARS, WICS, Shafter, CA, and Dr. Robert Nichols, Cotton Incorporated, Cary, North Carolina. TARGET AUDIENCES: Primary target audiences are commercial producers (growers) of cotton, grain legumes, and fresh market carrots. Secondary target audiences include public and private cotton, grain legume, and carrot breeders and seed producers. Through these secondary target audiences, the new knowledge and availability of nematode resistance genes, associated molecular markers, and advanced breeding lines or varieties carrying resistance is being applied for modern breeding of improved crop varieties. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Natural host plant resistance genes are valuable in crop plants as effective and safe approaches to managing root-knot nematodes. Studies on their specificity, efficacy and use in cropping systems advance their utilization in agriculture. The identification and characterization of resistance genes in crop plants will lead to effective and safe approaches to managing root-knot nematodes by developing resistant varieties. The use of the resistance in crop production systems as alternatives to nematicides is aided by understanding the nature and specificity of resistance genes. Characterized resistance with genetic markers can be selected more efficiently in breeding programs and deployed in cropping systems. The study of the genetic diversity of resistance and other beneficial traits will lead to genetic improvement of important food and fiber crops including cotton, carrot, and grain legumes. The screening and selection for nematode resistance in different market classes in cowpea based on grain type should lead to release of new dry grain varieties, The improved genetic map and high-throughput SNP genotyping platform are outputs that will expedite cowpea breeding and genetic improvement programs, especially for selection of nematode and other biotic and abiotic stress resistance traits. The advanced breeding lines of fresh market carrots developed with resistance to both common species of root-knot nematodes were provided to the commercial seed industry for use in finished varieties and for seed multiplication, with the goal of introducing resistant carrot varieties into the fresh carrot production system. Combinations of the new sources of resistance in carrot were shown to provide strong levels of resistance for future use in the carrot industry. The development and targeted sequencing of a cotton BAC library using a nematode resistant cotton genotype has provided the technical opportunity for identifying physical segments of cotton DNA that carry nematode and Fusarium wilt resistance genes. This has enabled development of closely associated DNA markers for use in marker-assisted breeding for nematode resistance. Transgressive resistance in cotton derived from combining minor effect QTL donated by susceptible parents opens up new breeding strategies for cotton improvement.

Publications

  • Ehlers, J. D., P. A. Roberts, and B. Sanden. 2011. Blackeye Varietal Improvement. p. 15-24. In University of California Dry Bean Research 2010 Progress Report, California Dry Bean Advisory Board, Dinuba, CA.
  • Xu, P., X. Wu, B. Wang, Y. Liu, J. D. Ehlers, T. J. Close, P. A. Roberts, N. N. Diop, D. Qin, T. Hu, Z. Lu, and G. Li. 2010. A SNP and SSR based genetic map of asparagus bean (Vigna. unguiculata ssp. sesquipedialis) and comparison with the broader species. PLoS ONE 6(1): e15952. doi:10.1371/journal.pone.0015952.
  • Roberts, P.A., W. C. Matthews, and P. W. Simon. 2011. Identification of gene sources for resistance to root-knot nematodes. Pp.69-90 in 2010 Annual Report of California Fresh Carrot Advisory Board. California Fresh Carrot Advisory Board, Dinuba, CA.
  • Ulloa, M., C. Wang, R. B. Hutmacher, S. D. Wright, R. M. Davis, C. A. Saski and P. A. Roberts. 2011. Mapping Fusarium wilt race 1 resistance genes in cotton by inheritance, QTL and sequencing composition. Mol Genet Genomics 286:21 - 36.
  • Barrera-Figueroa, B. E., L. Gao, N. N. Diop, Z. Wu, J. D. Ehlers, P. A. Roberts, T. J. Close, J.-K. Zhu, and R. Liu. 2011. Identification and comparative analysis of drought-associated microRNAs in two cowpea genotypes. BMC Plant Biology Vol.11:27.
  • Lucas, M. R., N. N. Diop, S. Wanamaker, J. D. Ehlers, P. A. Roberts, and T. J. Close. 2011. Cowpea - Soybean Synteny clarified through an improved genetic map. The Plant Genome. doi: 10.3835/plantgenome2011.06.0019; Published online 13 Oct. 2011.


Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: Host plant resistance to root-knot nematodes (MELOIDOGYNE spp.) was studied as a major tactic for nematode management programs in annual field and vegetable cropping systems. Analyses of resistance genes were conducted in carrot, cowpea (blackeye beans), and cotton. The resistance in cowpea is includes several loci with multiple specificities to different root-knot nematode species and populations. A recurrent backcrossing program was advanced to the seventh generation, in which the Rk2 gene, that confers stronger and broader root-knot resistance than gene Rk, is being introgressed into preferred California blackeye dry grain cowpeas. This resistance protects against M. JAVANICA and M. INCOGNITA populations that are virulent to gene Rk. Advanced breeding lines of new market type cowpeas including all-white and persistent green grain types with nematode resistance were screened in field and greenhouse tests; lines carrying the resistance were selected for seed multiplication. An improved high density SNP marker-based consensus genetic map of cowpea was developed, using 12 recombinant inbred line (RIL) mapping populations. This genetic map was used to better define previously identified QTL representing the different Rk genes in the cowpea genome, specifically Rk, Rk2 and rk3 gene loci which localize to different cowpea linkage groups. The RIL populations polymorphic for the root-knot resistance were re-phenotyped for resistance and susceptibility in field tests and in growth-pouch screens, together with F2:3 families. Additional nematode resistance genes were identified by QTL mapping, and QTL controlling tolerance to drought and insect feeding, as interacting factors, were also mapped. Two nematode infested field nurseries in Tustin, southern California were used in 2010 to select among several hundred breeding lines of fresh market type carrots with resistance to M. JAVANICA and M. INCOGNITA. More than 50% of these elite advanced inbred carrot lines had strong dual resistance to both root-knot species based on resistance gene Mj1 and an additive gene and were selected for advancement. New sources of resistance in carrot were analyzed for their uniqueness and combining ability in progenies from crosses between the sources in greenhouse tests, combined with marker analysis. Molecular analysis of M. INCOGNITA resistance in cotton was continued for marker development and mapping. A new BAC library of the Acala NemX resistance source was screened with a suite of BAC-end sequence-derived SSR markers from homoeologous chromosomes 11 and 21. Complete sequencing of BAC clones from these target regions was initiated in this BAC library and in a Maxxa BAC library, and the sequences gene annotated. Transgressive resistance to M. INCOGNITA was analyzed by QTL mapping in a recombinant inbred population developed from an interspecific cross between susceptible upland and pima allotetraploid cotton parents. PARTICIPANTS: Cowpea collaborators included Dr. T J Close and Dr. J. D. Ehlers, University of California, Riverside; Dr. S Temple and B. Sanden, University of California Cooperative Extension, and California blackeye bean growers and processors. Carrot collaborators included Dr. P. S. Simon, USDA-ARS, University of Wisconsin, Madison, and J. Nunez, University of California Cooperative Extension. Cotton collaborators included Dr. M. Ulloa, USDA-ARS, WICS, Shafter, CA, and Dr. Robert Nichols, Cotton Incorporated, Cary, North Carolina. TARGET AUDIENCES: Primary target audiences are commercial producers (growers) of cotton, grain legumes, and fresh market carrots. Secondary target audiences include public and private cotton, grain legume, and carrot breeders and seed producers. Through these secondary target audiences, the new knowledge and availability of nematode resistance genes, associated molecular markers, and advanced breeding lines or varieties carrying resistance will be applied for modern breeding of improved crop varieties. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Natural host plant resistance genes are valuable in crop plants as effective and safe approaches to managing root-knot nematodes. Studies on their specificity, efficacy and use in cropping systems advance their utilization in agriculture. The identification and characterization of resistance genes in crop plants will lead to effective and safe approaches to managing root-knot nematodes by developing resistant varieties. The use of the resistance in crop production systems as alternatives to nematicides is aided by understanding the nature and specificity of resistance genes. Characterized resistance with genetic markers can be selected more efficiently in breeding programs and deployed in cropping systems. The study of the genetic diversity of resistance and other beneficial traits will lead to genetic improvement of important food and fiber crops including cotton, carrot, and grain legumes. The screening and selection for Rk genes in cowpea led to the release in 2008 of a new blackeye dry grain variety, CB50, adapted to the San Joaquin Valley production area of California. This variety has larger and brighter white grain than the current industry standard CB46, plus good root-knot nematode and Fusarium wilt resistance. During the report period, the production acreage of CB50 has expanded to more than 1000 acres in 2010. The improved genetic fine-mapping of the different Rk genes for root-knot resistance in cowpea identified efficient molecular markers for the genes. These markers are being employed in cowpea breeding programs to expedite resistance selection in elite backgrounds. The advanced breeding lines of fresh market carrots developed with resistance to both common species of root-knot nematodes were provided to the commercial seed industry for use in finished varieties and for seed multiplication, with the goal of introducing resistant carrot varieties into the fresh carrot production system. Combinations of the new sources of resistance in carrot were shown to provide strong levels of resistance for future use in the carrot industry. The development and targeted sequencing of a cotton BAC library using a nematode resistant cotton genotype has provided the technical opportunity for identifying physical segments of the cotton DNA that carry nematode resistance gene(s). In turn, this has enabled development of closely associated DNA markers for use in marker-assisted breeding for nematode resistance, and a framework for cloning and sequencing of the genes for use in transgenic breeding approaches for cotton improvement.

Publications

  • Das, S., J.D. Ehlers, T.J. Close, and P.A. Roberts. 2010. Transcriptional profiling of root-knot nematode induced feeding sites in cowpea (Vigna unguiculata L. Walp.) using a soybean genome array. BMC Genomics 11:480, p.1-16.
  • Muchero, W., J.D. Ehlers, and P.A. Roberts. 2010. Restriction site polymorphism-based candidate gene mapping for seedling drought tolerance in cowpea [Vigna unguiculata L. (Walp.)]. Theoretical and Applied Genetics 120:509-518.
  • Muchero, W., J.D. Ehlers, and P.A. Roberts. 2010. QTL analysis for resistance to foliar damage caused by Thrips tabaci and Frankliniella schultzei (Thysanoptera: Thripidae) feeding in cowpea. Molecular Breeding 25:47-56.
  • Muchero, W., J.D. Ehlers, T.J. Close, and P.A. Roberts. 2011. Genic SNP markers and legume synteny reveal candidate genes underlying QTL for Macrophomina phaseolina resistance and maturity in cowpea [Vigna unguiculata (L) Walp.]. BMC Genomics 12:8, 1-14. R
  • Roberts, P. A., and M. Ulloa. 2010. Introgression of root-knot nematode resistance into tetraploid cottons. Crop Science 50:940-951.
  • Ulloa, M., C. Wang, and P.A. Roberts. 2010. Gene action analysis by inheritance and QTL mapping of resistance to root-knot nematodes in cotton. Plant Breeding 129:541-550.


Progress 01/01/09 to 12/31/09

Outputs
OUTPUTS: Host plant resistance to root-knot nematodes (MELOIDOGYNE spp.) was studied as a major tactic for nematode management programs in annual field and vegetable cropping systems. Analyses of resistance genes were conducted in carrot, cowpea (blackeye beans), and cotton. The resistance in cowpea is includes several loci with multiple specificities to different root-knot nematode species and populations. A recurrent backcrossing program was advanced to the sixth generation, in which the Rk2 gene, that confers stronger and broader root-knot resistance than gene Rk, is being introgressed into preferred California blackeye dry grain cowpeas. This resistance protects against M. JAVANICA and M. INCOGNITA populations that are virulent to gene Rk. Nematode resistance in cowpea crossed into new market type cowpeas including all-white and persistent green grain types was screened in filed and greenhouse tests to select progeny lines and families carrying the resistance. A new blackeye variety released as California Blackeye 50 (CB50) was greenhouse screened to confirm that it carried the Rk gene resistance, coupled with resistance to Fusarium wilt races 3 and 4. The variety CB50 was released in 2008. A high density SNP marker-based genetic map of cowpea was developed, using six recombinant inbred line (RIL) mapping populations, to construct a consensus map. This genetic map was used to identify QTL representing the different Rk genes in the cowpea genome. The RIL populations polymorphic for the root-knot resistance were phenotyped for resistance and susceptibility in field tests and in growth-pouch screens. The phenotype data were used to map the Rk, Rk2 and rk3 gene loci on different cowpea linkage groups, and new genes were identified by additional QTL. Two nematode infested field nurseries in Tustin, southern California were used in 2009 to advance several hundred breeding lines of fresh market type carrots with resistance to M. JAVANICA and M. INCOGNITA. About 30 elite advanced inbred carrot lines with strong dual resistance to both root-knot species based on resistance gene Mj1 and an additive gene were selected for advancement through selfing and crossing. Nine new sources of resistance in carrot were re-evaluated in field and greenhouse screens, and some progenies from crosses between the sources were screened for resistance in greenhouse and field tests for genetic analysis of the resistance sources. A new incompletely dominant resistance gene, Mj2, was identified in an Asian source of carrot germplasm. Molecular analysis of M. INCOGNITA resistance in cotton was continued for marker development and mapping. A new BAC library of the Acala NemX resistance source was developed, and arranged in superpools and pools for BAC pool screening with existing and new BAC-end sequence-derived SSR markers. Marker allele size and sequence information were used to study introgression of root-knot resistance into tetraploid cottons, by comparisons between resistance sources, wild diploid cottons and the domesticated upland and pima allotetraploid cottons. PARTICIPANTS: Cowpea collaborators included Dr. T J Close and Dr. J. D. Ehlers, University of California, Riverside; Dr. S Temple and B. Sanden, University of California Cooperative Extension, and California blackeye bean growers and processors. Carrot collaborators included Dr. P. S. Simon, USDA-ARS, University of Wisconsin, Madison, and J. Nunez, University of California Cooperative Extension. Cotton collaborators included Dr. M. Ulloa, USDA-ARS, WICS, Shafter, CA, and Dr. Robert Nichols, Cotton Incorporated, Cary, North Carolina. TARGET AUDIENCES: Primary target audiences are commercial producers (growers) of cotton, grain legumes, and fresh market carrots. Secondary target audiences include public and private cotton, grain legume, and carrot breeders and seed producers. Through these secondary target audiences, the new knowledge and availability of nematode resistance genes, associated molecular markers, and advanced breeding lines or varieties carrying resistance will be applied for modern breeding of improved crop varieties. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Natural host plant resistance genes are valuable in crop plants as effective and safe approaches to managing root-knot nematodes. Studies on their specificity, efficacy and use in cropping systems advance their utilization in agriculture. The identification and characterization of resistance genes in crop plants will lead to effective and safe approaches to managing root-knot nematodes by developing resistant varieties. The use of the resistance in crop production systems as alternatives to nematicides is aided by understanding the nature and specificity of resistance genes. Characterized resistance with genetic markers can be selected more efficiently in breeding programs and deployed in cropping systems. The study of the genetic diversity of resistance and other beneficial traits will lead to genetic improvement of important food and fiber crops including cotton, carrot, and grain legumes. The screening and selection for Rk genes in cowpea led to the release of a new blackeye dry grain variety adapted to the San Joaquin Valley production area of California. This variety has larger and brighter white grain than the current industry standard CB46, plus good root-knot nematode and Fusarium wilt resistance. During the report period, the formal release and production of certified seed of CB50 led to several hundred acres of the new variety being produced by growers in 2009, with an expected expansion of production in 2010. The genetic mapping of the different Rk genes for root-knot resistance in cowpea led to identification of closely linked molecular markers for the genes. These markers are now being employed in cowpea breeding programs for modern, expedited breeding for resistance and other desirable traits using marker-assisted selection techniques. The advanced breeding lines of fresh market carrots developed with resistance to both common species of root-knot nematodes provide materials for future release to the commercial seed industry, from which nematode resistant commercial carrot varieties can be developed. The new sources of resistance in carrot provide the opportunity to combine and pyramid resistance genes in breeding lines. This approach should lead to stronger and more durable forms of resistance for use in the carrot industry. The development of a cotton BAC library using a nematode resistant cotton genotype has provided the technical opportunity for identifying physical segments of the cotton DNA that carry nematode resistance gene(s). In turn, this enables development of closely associated DNA markers for use in marker-assisted breeding for nematode resistance, and the cloning and sequencing of the genes for use in transgenic breeding approaches for cotton improvement.

Publications

  • Ehlers, J. D., B.L. Sanden, C.A. Frate, A.E. Hall, and P.A. Roberts. 2009. Registration of California Blackeye 50 Cowpea. Journal of Crop Registrations 3:236-240.
  • Muchero, W., N.N. Diop, P.R. Bhat, R.D. Fenton, S. Wanamaker, M. Pottorff, S. Hearne, N. Cisse, C. Fatokun, J.D. Ehlers, P.A. Roberts, and T.J. Close. 2009. A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs. Proceedings of the National Academy of Sciences, USA 106:18159-18164.
  • Sawadogo, A., B. Thio, S. Kiemde, I. Drabo, C. Dabire, J. Ouedraogo, T. R. Mullens, J.D. Ehlers, and P.A. Roberts. 2009. Distribution and prevalence of parasitic nematodes of cowpea (Vigna unguiculata) in Burkina Faso. Journal of Nematology 41 (2):120-127.
  • Subbotin, S., Ragsdale, E. Mullens, T.R., Roberts, P.A., Mundo-Ocampo, M., and J.G. Baldwin. 2008. A phylogenetic framework for root-lesion nematodes of the genus Pratylenchus (Nematoda): evidence from 18S and D2-D3 expansion segments of 28S ribosomal RNA genes and morphological characters. Molecular Phylogenetics and Evolution 48:491-505.
  • Das, S., P. R. Bhat, C. Sudhakar, J. D. Ehlers, S. Wanamaker, P. A. Roberts, X. Cui, and T. J. Close. 2008. Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array. BMC Genomics 9:107, pages 1-12.
  • Ulloa, M., C. Wang, and P.A. Roberts. 2009. Gene action analysis by inheritance and QTL mapping of resistance to root-knot nematodes in cotton. Plant Breeding (online October at doi:10.1111/j.1439-0523.2009.01717.x.
  • Roberts, P. A., and M. Ulloa. 2010. Introgression of root-knot nematode resistance into tetraploid cottons. Crop Science 50(3):(In Press).
  • Williamson, V. M., and P. A. Roberts. 2009. Mechanisms and genetics of resistance. Pp. 301-325 in: Perry, R. N., Moens, M., and Starr, J. L. (eds). Root-Knot Nematodes. CABI: Wallingford, UK. 480 pages.


Progress 01/01/07 to 12/31/07

Outputs
Host plant resistance to root-knot nematodes (MELOIDOGYNE spp.) was studied as a major tactic for nematode management programs in annual field and vegetable cropping systems. Analyses of resistance genes are being conducted in carrot, cowpea, cotton, tomato, and lima bean. The Rk resistance gene in cowpea is a complex locus with multiple specificities to different nematode populations. Histological comparisons of infected roots of resistant and susceptible plants during three weeks after inoculation showed normal feeding site development up to 9 to 14 days, after which giant cells vacuolated and the nematode feeding decreased. No hypersensitive reaction with programmed cell death was observed. The delayed resistance reaction was confirmed by profiling reactive oxygen species (ROS) release in roots. ROS time-course was similar in both resistant and susceptible infected roots, indicating it is part of basal defense in cowpea but not related to hypersensitivity. A recurrent backcrossing program was advanced to the fourth generation, in which the Rk2 gene, that confers stronger and broader root-knot resistance than gene Rk, is being introgressed into preferred California blackeye dry grain cowpeas. This resistance protects against M. JAVANICA and M. INCOGNITA populations that are virulent to gene Rk. Nematode resistance in cowpea was also crossed into and selected in progenies of new market type cowpeas including all-white and persistent green grain types. Three nematode infested field nurseries in the San Joaquin Valley and Coachella Valley of California were used in 2007 to advance several hundred breeding lines of fresh market type carrots with resistance to M. JAVANICA and M. INCOGNITA. Twenty-seven elite advanced inbred carrot lines with strong dual resistance to both root-knot species based on resistance gene Mj1 were selected for advancement. Nine new sources of resistance in carrot were evaluated in field and greenhouse screens, and crosses between the sources were used to generate hybrid carrots for genetic analysis. Molecular analysis of M. INCOGNITA resistance in cotton was continued for marker development and mapping. Using crosses between resistant and susceptible genotypes of both pima and upland cottons, a series of transgressive segregants with extremely high levels of resistance were found in progeny tests. Analyses of these super resistant progenies with BAC end derived and other SSR markers revealed that the novel resistance was governed by combining gene rkn1 from Acala Nemx with a gene in susceptible Pima S7, named RKN2. Both genes were found to map genetically to the same region of cotton chromosome 11. A combination of SSR markers linked to both genes was shown to be effective for indirect selection of the high resistance based on the gene combination, for use in cotton marker assisted breeding.

Impacts
The identification and characterization of resistance genes in crop plants will lead to effective and safe approaches to managing root-knot nematodes by developing resistant varieties. The use of the resistance in crop production systems as alternatives to nematicides is aided by understanding the nature and specificity of resistance genes. Characterized resistance with genetic markers can be selected more efficiently in breeding programs and deployed in cropping systems. The study of the genetic diversity of resistance and other beneficial traits will lead to genetic improvement of important food and fiber crops including cotton, tomato and grain legumes.

Publications

  • Wang, C., M. Ulloa, and P.A. Roberts. 2008. A transgressive segregation factor (RKN2) in Gossypium barbadense for nematode resistance clusters with gene rkn1 in G. hirsutum. Molecular Genetics and Genomics 279:41-52.
  • Das, S., D.A. DeMason, J.D. Ehlers, T.J. Close, and P.A. Roberts. 2008. Histological characterization of root-knot nematode resistance in cowpea and its relation to reactive oxygen species modulation. Journal of Experimental Botany (In press).
  • Muchero, W., J. D. Ehlers, and P.A. Roberts. 2008. Seedling stage drought-induced phenotypes and drought-responsive genes in diverse cowpea genotypes. Crop Science (In press).
  • Roberts, P. A., W.C. Matthews, J.D. Ehlers, and D. Helms. 2008. Genetic determinants of differential resistance to root-knot nematode reproduction and galling in Lima bean. Crop Science (In press).
  • Starr, J.L., S. R. Koenning, T. L. Kirkpatrick, A. F. Robinson, P. A. Roberts, and R. L. Nichols. 2008. The future of nematode management in cotton. Journal of Nematology: (In press).


Progress 01/01/06 to 12/31/06

Outputs
Host plant resistance to root-knot nematodes (MELOIDOGYNE spp.) is being studied as a major tactic for nematode management programs in annual field and vegetable cropping systems. Analyses of resistance genes are being conducted in carrot, cowpea, cotton, tomato, and lima bean. The Rk resistance gene in cowpea is a complex locus with multiple specificities to different nematode populations. Infected and non-infected roots of resistant and susceptible plants were harvested at seven time points up to 28 days after inoculation. The sectioned and stained roots examined by light microscopy indicated that the resistance response of gene Rk is not a hypersensitive-type reaction, but is a slow response in which the nematode-induced giant cells appear normal up to nine days and then show deterioration including increased vacuoles from 14 days post-inoculation. A series of Rk near-isogenic lines in a blackeye cowpea background produced by recurrent backcrossing was compared in repeated controlled temperature experiments to determine the efficacy of each Rk gene form in protecting cowpea from nematode infection. Three nematode populations (avirulent and virulent M. INCOGNITA, and M. JAVANICA) were used. At five constant temperatures from 23C to 35C, assays of nematode reproduction indicated that the Rk gene forms (alleles or linked genes) were heat-stable, conferring strong resistance up to 35C. In work on tomato, DNA sequence comparisons in the region of the heat-stable root-knot nematode resistance gene Mi-9 from the wild relative Solanum arcanum revealed several Mi-1 homologues to be present. Virus-induced gene silencing using Mi-1 constructs was used to determine that Mi-9 is a homologue of the heat sensitive Mi-1 gene. Nematode infested field nurseries in the San Joaquin Valley of California were used in 2006 to advance two hundred breeding lines of fresh market type carrots with resistance to M. JAVANICA and M. INCOGNITA. Molecular genetic analysis of M. INCOGNITA and Fusarium wilt race 1 and race 4 resistance in cotton was continued for marker development and mapping. Using crosses between resistant and susceptible genotypes of both pima and upland cottons, the location of gene rkn1 from cultivar NemX on chromosome 11 (formerly A03) was confirmed. Additional AFLP and microsatellite (SSR), RAPD and STS molecular polymorphisms between resistant and susceptible genotypes were found linked to gene rkn1 in a high density mapping effort. One linked marker was converted to a SNP marker for use in high throughput screening of cotton for marker-assisted selection. A large collection of cotton germplasm was screened for nematode and Fusarium resistance, and several resistant genotypes were identified. Crosses were made between some of the resistant lines for use in allelism tests to compare the uniqueness of the resistance genes.

Impacts
The identification and characterization of resistance genes in crop plants will lead to effective and safe approaches to managing root-knot nematodes by developing resistant varieties. The use of the resistance in crop production systems as alternatives to nematicides is aided by understanding the nature and specificity of resistance genes. Characterized resistance with genetic markers can be selected more efficiently in breeding programs and deployed in cropping systems. The study of the genetic diversity of resistance and other beneficial traits will lead to genetic improvement of important food and fiber crops including cotton, tomato and grain legumes.

Publications

  • Wang, C. and Roberts, P.A. 2006. Development of AFLP and derived CAPS markers for root-knot nematode resistance in cotton. Euphytica 152:185-196.
  • Niu, C., Hinchliffe, D. J., Cantrell, R. G., Wang, C., Roberts, P. A. and Zhang, J. 2007. Identification of molecular markers associated with root-knot nematode resistance in upland cotton. Crop Science (In press).
  • Jablonska, B., Ammiraju, J. S. S., Bhattarai, K. K., Mantelin, S., Martinez de Ilarduya, O., Roberts, P. A. and Kaloshian, I. 2006. The Mi-9 gene from Solanum arcanum conferring heat-stable resistance to root-knot nematodes is a homologue of Mi-1. Plant Physiology 143:1044-1054.
  • Fang, J., Chao, C. T., Roberts, P. A. and Ehlers, J. D. 2007. Genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] in four West African and USA breeding programs as determined by AFLP analysis. Genetic Resources and Crop Evolution (In press)


Progress 01/01/05 to 12/31/05

Outputs
Host plant resistance to root-knot nematodes (MELOIDOGYNE spp.) is being studied as a primary means of nematode management in annual field and vegetable cropping systems. Analyses of resistance genes are being conducted in carrot, cowpea, cotton, tomato, and lima bean. The Rk resistance gene in cowpea is a complex locus with multiple specificities to different nematode populations. Infected and non-infected roots of resistant and susceptible plants were harvested and used for preparing cDNA libraries during the period of resistance expression, as an approach to develop markers for the Rk genomic region. Cowpea RNA was micro-arrayed on the Affymetrix soybean GeneChip, and SFP markers identified. A series of near-isogenic lines in a blackeye cowpea background produced by recurrent backcrossing was compared for a second year to determine the value of each Rk gene form in protecting cowpea from nematode infection in field experiments. Field experiments were conducted comparing the four near-isogenic lines over a series of replicated inoculum densities of three nematode populations (avirulent and virulent M. INCOGNITA, and M. JAVANICA). Results of cowpea yield and nematode multiplication rates provided a relative index of the protective effect of each resistance gene, using regression analysis. Recombinant inbred lines developed from crosses between root-knot susceptible and resistant Lima bean genotypes were screened to determine the relationship of resistance genes effective against nematode reproduction on roots, nematode induced root-galling, or both. One Lima genotype (L-136) was shown to be a donor of three resistance genes. These genes were compared in the field in subsets of recombinant inbred lines possessing the three genes singly and in different combinations. The relative protective value to grain yield of each gene or combination was determined. A second Lima genotype with two resistance genes was confirmed to be highly effective against M. INCOGNITA and M. JAVANICA in greenhouse pot tests. A set of recombinant inbred lines from a cross of the two resistant genotypes was screened to study the relationship between the two sets of resistance genes. The genes appear independent between the two resistance donor sources. Nematode infested field nurseries in the San Joaquin Valley of California were used in 2005 to advance two hundred breeding lines of fresh market type carrots with resistance to M. JAVANICA and M. INCOGNITA. Analysis of M. INCOGNITA and Fusarium wilt race 1 resistance in cotton was continued using crosses between resistant and susceptible genotypes of both pima and upland cottons. Both AFLP and microsatellite (SSR) molecular polymorphisms detected between resistant and susceptible genotypes were found to be linked to a major nematode resistance gene, rkn1, in NemX cotton. The gene was mapped to linkage group A03 of the cotton genome, and linked markers were developed and tested for use in marker-assisted selection.

Impacts
The identification and characterization of resistance genes in crop plants will lead to effective and safe approaches to managing root-knot nematodes by developing resistant varieties. The use of the resistance in crop production systems as alternatives to nematicides is aided by understanding the nature and specificity of resistance genes. Characterized resistance with genetic markers can be more easily selected for in breeding programs and deployed in cropping systems.

Publications

  • Petrillo, M.D. and P.A. Roberts. 2005. Isofemale line analysis of Meloidogyne incognita virulence to cowpea resistance gene Rk. J. Nematol. 37: December issue (in press).
  • Petrillo, M.D. and P.A. Roberts. 2005. Fitness of Virulent Meloidogyne incognita Isolates on Susceptible and Resistant Cowpea. J. Nematol. 37 December issue (in press).
  • Petrillo, M.D., W.C. Matthews, and P.A. Roberts. 2006. Host influence on Meloidogyne incognita virulence to resistance genes Rk and Rk2 in cowpea. J. Nematol. 38: (in press).
  • Roberts, P.A. 2006. Nematode Resistance in Vegetable Crops emphasizing Meloidogyne species. In: Management of Nematode and Insect Borne Diseases. G. Saxena and K. G. Mukerji (eds.). The Haworth Press: New York. In press.
  • Roberts, P. A., W.C. Matthews, and J. D. Ehlers. 2005. Root-knot nematode resistant cowpea cover crops in tomato production systems. Agronomy J. 97:1626-1635.
  • Starr, J. L. and Roberts, P.A. 2004. Resistance to Plant-Parasitic Nematodes. In: Nematology, Advances and Perspectives. Vol. 2. Nematode Management and Utilization. Z. X. Chen, S. Y. Chen and D. W. Dickson (eds.). CABI Publishing, Wallingford, UK. Pp. 879-907.
  • Timko, M. P., J. D.Ehlers, and P. A. Roberts. 2006. Cowpea. In: Kole, C. (ed) The Genomes: A Series on Genome Mapping, Molecular Breeding & Genomics. Science Publisher, Inc.: Enfield, New Hampshire. (In press).
  • Wang, C. and P.A. Roberts. 2006. A Fusarium wilt resistance gene in Gossypium barbadense L and its effect on root-knot nematode-wilt disease complex. Phytopathology (in press).
  • Wang, C., W.C. Matthews, and P.A. Roberts. 2006. Genetic analysis of root-knot nematode resistance in Acala NemX cotton (Gossypium hirsutum L.) using an intraspecific cross. J. Nematol. (submitted).
  • Wang, C., M. Ulloa, and P.A. Roberts. 2005. Identification and mapping of microsatellite markers linked to the root-knot nematode resistance gene rkn1 in Acala NemX cotton (Gossypium hirsutum L.) Theor. Appl. Genet. 112: (online first, Dec 14, 2005).


Progress 01/01/04 to 12/31/04

Outputs
Host plant resistance to root-knot nematodes (MELOIDOGYNE spp.) is being studied as a primary means of nematode management in annual field and vegetable cropping systems. Analyses of resistance genes are being conducted in carrot, cowpea, cotton, and lima bean. The Rk resistance gene in cowpea is a complex locus with multiple specificities to different nematode populations. Infected and non-infected roots of resistant and susceptible plants were harvested and used for preparing cDNA libraries during the period of resistance expression, as an approach to develop markers for the Rk genomic region. Histological studies of resistant and susceptible infected and non-infected roots were made at several sampling times during the first two weeks after infection. Avirulent juveniles of M. INCOGNITA developed at least partially after root penetration, indicating that the resistance mechanism operates gradually over the two weeks following infection, unlike a classical, rapid hypersensitivity response. A series of near-isogenic lines in a blackeye cowpea background was produced by recurrent backcrossing, for use in comparing the value of each Rk gene form in protecting cowpea from nematode infection in field experiments. Field experiments were conducted comparing the four near-isogenic lines over a series of replicated inoculum densities of three nematode populations (avirulent and virulent M. INCOGNITA, and M. JAVANICA). Results of cowpea growth and nematode multiplication rates provided a relative index of the protective effect of each resistance gene, using regression analyses. Recombinant inbred lines developed from crosses between root-knot susceptible and resistant Lima bean genotypes were screened to determine the relationship of resistance genes effective against nematode reproduction on roots, nematode induced root-galling, or both. One Lima genotype was shown to be a donor of three resistance genes. A second lima genotype was found to possess two resistance genes based on analyses of recombinant inbred lines derived from the resistant x a susceptible genotype cross. These genes were highly effective against M. INCOGNITA and M. JAVANICA in greenhouse pot tests. A set of recombinant inbred lines from a cross of the two resistant genotypes is being developed to study the relationship between the two sets of resistance genes. Nematode infested field nurseries in the San Joaquin Valley of California were used again to advance one hundred and fifty breeding lines of fresh market type carrots with resistance to M. JAVANICA and M. INCOGNITA. Co-dominant flanking molecular markers for the Mj-1 resistance locus were used to screen progenies in a marker-assisted selection approach in carrot breeding. Analysis M. INCOGNITAFusarium wilt resistance in cotton was continued using crosses between resistant and susceptible genotypes of both pima and upland cottons. Both AFLP and microsatellite (SSR) molecular polymorphisms detected between resistant and susceptible genotypes were found to be linked to nematode resistance genes and are being used for mapping resistance genes in the cotton genome.

Impacts
The identification and characterization of resistance genes in crop plants will lead to effective and safe approaches to managing root-knot nematodes by developing resistant varieties. The use of the resistance in crop production systems as alternatives to nematicides is aided by understanding the nature and specificity of resistance genes. Characterized resistance with genetic markers can be more easily selected for in breeding programs and deployed in cropping systems.

Publications

  • Chen, P., and Roberts, P.A. 2004. Genetic analysis of (a)virulence in Meloidogyne hapla to resistance in bean (Phaseolus vulgaris). Nematology 5:687-697.
  • Starr, J. L., and Roberts, P.A. 2004. Resistance to plant-parasitic nematodes. In: Nematology Advances and Perspectives. Vol. 2. Nematode Management and Utilization. Z. X. Chen, S. Y. Chen and D. W. Dickson (eds.). CABI Publishing, Wallingford, UK. Pp. 879-907.


Progress 01/01/03 to 12/31/03

Outputs
Host plant resistance to root-knot nematodes (MELOIDOGYNE spp.) is being studied as a primary means of nematode management in annual field and vegetable cropping systems. Analyses of resistance genes are being conducted in carrot, cowpea, cotton, lima bean and tomato. The Rk resistance gene in cowpea is a complex locus with multiple specificities to different nematode populations. Infected and non-infected roots of resistant and susceptible plants were harvested for preparing cDNA libraries during the period of resistance expression, as an approach to develop markers for the Rk genomic region. A series of near isogenic lines in a blackeye background was advanced by recurrent backcrossing, for use in comparing the value of each Rk gene form in protecting cowpea from nematode infection in field experiments. Recombinant inbred lines developed from crosses between root-knot susceptible and resistant Lima bean genotypes were screened to determine the relationship of resistance genes effective against nematode reproduction on roots, nematode induced root-galling, or both. One Lima genotype was shown to be a donor of three resistance genes that were incorporated in a newly released nematode resistant Lima variety, Cariblanco N. Nematode infested field nurseries in the San Joaquin Valley of California were used to advance one hundred and fifty breeding lines of fresh market type carrots with resistance to M. JAVANICA and M. INCOGNITA. A pair of co-dominant flanking molecular markers for the Mj-1 resistance locus was used to screen progenies in efforts to better understand the resistance genetics and for advancing the use of marker-assisted selection in carrot breeding. Analysis of root-knot nematode, M. INCOGNITA, and Fusarium wilt resistance in cotton was continued using crosses between resistant and susceptible genotypes of both pima and upland cottons. Some AFLP polymorphisms detected between resistant and susceptible genotypes were linked to nematode resistance genes and some of these are being converted to STS markers for use in cotton breeding.

Impacts
The identification and characterization of resistance genes in crop plants will lead to effective and safe approaches to managing root-knot nematodes by developing resistant varieties. The use of the resistance in crop production systems as alternatives to nematicides is aided by understanding the nature and specificity of resistance genes. Characterized resistance with genetic markers can be more easily selected for in breeding programs and deployed in cropping systems.

Publications

  • Helms, D.M., Matthews, W.C., Temple, S.R., and Roberts, P.A. 2004. Registration of 'Cariblanco N' Lima bean. Crop Science 44:352-353.
  • Roberts, P.A. 2002. Concepts and Consequences of Resistance. In: Plant Resistance to Parasitic Nematodes. J.L. Starr, R. Cook, J. Bridge (eds.). CABI Publishing, Wallingford, UK. Pp. 23-41.
  • Chen, P., and Roberts, P.A. 2003. Virulence in Meloidogyne hapla differentiated by resistance in common bean (Phaseolus vulgaris). Nematology 5:39-47.
  • Chen, P., Roberts, P.A., Metcalf, A.E., and Hyman, B.C. 2003. Nucleotide substitution patterning within the Meloidogyne rDNA D3 region and its evolutionary implications. J. Nematol. 35:404-410.
  • Ehlers, J.D., Matthews, W.C., Hall, A.E., and Roberts, P.A. 2003. Breeding and evaluation of cowpeas with high levels of broad-based resistance to root-knot nematodes. In: Advances in Cowpea Research. Vol II. C. A. Fatokun et al. (eds.). International Institute Tropical Agriculture, Ibadan, Nigeria. Pp. 41-51
  • Hall, A.E., Cisse, N., Thiaw, S., Elawad, H.O.A., Ehlers, J.D., Ismail, A.M., Fery, R.L., Roberts, P.A., Kitch, L.W., Murdock, L.L., Boukar, O., Phillips R.D., and McWatters, K.H. 2003. Development of Cowpea Cultivars and Germplasm. Field Crops Res. 82:103-134.


Progress 01/01/02 to 12/31/02

Outputs
Host plant resistance to root-knot nematodes (MELOIDOGYNE spp.) is being studied as a primary means of nematode management in annual field and vegetable cropping systems. Analyses of resistance genes are being conducted in carrot, cowpea, cotton, lima bean and tomato. Genetic analysis in cowpea showed that the Rk resistance locus has at least four forms based on the specificity of resistance to different nematode populations. The gene locus was mapped to linkage group one of cowpea and a fine-mapping of the Rk region is being conducted to generate useful molecular markers for cowpea breeding and for a positional gene cloning effort. A series of near isogenic lines in a blackeye background is being developed, for use in comparing the value of each Rk gene form in protecting cowpea from nematode infection in field experiments. A series of recombinant inbred lines was developed from crosses between root-knot susceptible and resistant Lima bean genotypes. The resistant parents represent different R gene sources. The genetic analyses of the resistance revealed several recessive and dominant genes that control nematode reproduction on roots, nematode induced root-galling, or both. Combinations of the R genes were shown to be necessary in providing Lima bean plants with adequate broad-based field resistance. Nematode infested field nurseries in the San Joaquin and Coachella Valleys of California were used to advance several hundred breeding lines of fresh market type carrots with resistance to M. JAVANICA and M. INCOGNITA. The resistance was shown to be an adequate replacement for soil fumigation treatment when combined with prior planting of non-host or resistant rotation crops and (or) use of delayed planting time of carrot in the fall. Analysis of root-knot nematode, M. INCOGNITA, and Fusarium wilt resistance in cotton was started using crosses between resistant and susceptible genotypes of both pima and upland cottons. AFLP polymorphisms are being screened in a search for gene markers for use in cotton breeding programs.

Impacts
The identification and characterization of resistance genes in crop plants will lead to effective and safe approaches to managing root-knot nematodes by developing resistant varieties. The use of the resistance in crop production systems as alternatives to nematicides is aided by understanding the nature and specificity of resistance genes. Characterized resistance with genetic markers can be more easily selected for in breeding programs and deployed in cropping systems.

Publications

  • Roberts, P.A., P.S. Simon, L.S. Boiteux, W.C. Matthews, and T.R. Mullens. 2002. Characterization of resistance to root-knot nematodes in carrot. Nematology 4:236.
  • Yu, M.H., and P.A. Roberts. 2002. Selection of root-knot nematode resistant sugarbeet from field plantings. Nematology 4:240.
  • Ammiraju, J.S.S., J.C. Veremis, X. Huang, P.A. Roberts and I. Kaloshian. 2003. Fine mapping of the heat-stable root-knot nematode resistance gene Mi-9 in Lycopersicon peruvianum. Theor. Appl. Genet. (in press).
  • Ammiraju Jetty, S.S., J.C. Veremis, P.A. Roberts, and I. Kaloshian. 2002. High resolution linkage map around novel heat-stable nematode resistance gene Mi-9. Page 204. Proc. Intl Plant, Animal and Microbe Genome Conf. X. San Diego, CA.
  • Boiteux, L.S., F.A.S. Arag, I.C. Bach, M.E. N. Fonseca, W.C. Matthews, P.A. Roberts, and P.S. Simon. 2002. A dosage-dependent response of the Meloidogyne javanica resistance locus in carrot estimated via linkage analysis with flanking codominant STS markers. Page 244. Proc. Intl Plant, Animal and Microbe Genome Conf. X. San Diego, CA.
  • Chen, P. C. 2002. Genetic variation in Meloidogyne hapla and inheritance of resistance in common bean. Ph.D. Dissertation, University of California, Riverside.
  • Roberts, P.A. and T. Mullens. 2002. Diseases caused by Nematodes. In: Compendium of Carrot and Celery Diseases. M. Davis, (ed.). American Phytopathological Society. APS Press, St. Paul, MN. Pp 45-50.