Source: UNIVERSITY OF GEORGIA submitted to
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
Funding Source
Reporting Frequency
Accession No.
Grant No.
Project No.
Proposal No.
Multistate No.
Program Code
Project Start Date
Mar 1, 2004
Project End Date
Feb 28, 2010
Grant Year
Project Director
Boerma, H. R.
Recipient Organization
Performing Department
Non Technical Summary
Soybean cultivars improved for agronomic traits, pest resistance, and seed composition are needed to keep soybean production economically viable in the southeastern U.S. Integration of DNA marker technologies with conventional breeding approaches will expedite development of high-yielding cultivars with resistance to regional pests and seed traits demanded by the market.
Animal Health Component
Research Effort Categories

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
Goals / Objectives
Our overall goal is the development of contemporary soybean cultivars which increase profitability of soybean growers, enhance the quality and reduce the cost of soybean products in human and animal diets, and reduce impact to the environment from soybean production. This goal will be accomplished through the integration of classical and molecular breeding technologies, allowing reduction of the cultivar development period and improvement of historically intractable traits. The specific objectives include: i) The development of soybean cultivars adapted to Southeastern environments with enhanced productivity, quality, and pest resistance, ii) The improvement of soybean value via enhancement of seed composition, iii) The development of germplasm and genomic resources to improve resistance to root-knot nematodes, reniform nematode, and defoliating insects, iv) The development of germplasm and cultivars with improved drought tolerance, and v) The mining of exotic germplasm for superior alleles at yield QTL.
Project Methods
Crosses will be made between cultivars, breeding lines, and improved germplasm releases that possess traits of interest. Phenotypic and/or marker-assisted selection will be used to identify individual plants and lines from segregating populations that carry superior alleles for these traits or display the desired phenotypes. Specific approaches with regard to the method of selection and the generation at which selection begins will depend on estimates of the heritability of a trait and the number of loci affecting the trait, and the availability of markers linked to known loci. "Recurrent screening" or marker-based selection will be imposed on early generations if a trait is highly heritable or has oligogenic inheritance. For traits with a more complex inheritance, selection will be delayed until later generations, when among-line variation exceeds within line variation. Marker-assisted selection will involve amplification of SSRs and SNPs from DNA extracted from quarter-seed chips, thus permitting the remaining embryo-containing portion of desirable seed to be planted.

Progress 03/01/04 to 02/28/10

OUTPUTS: pi has retired PARTICIPANTS: Not relevant to this project. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.

pi has retired


  • No publications reported this period

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

Reniform nematodes (Rotylenchulus reniformis Linford & Oliveira) are semi-endoparasites of roots, and occur commonly in tropical and subtropical regions. With RFLP markers, Pioneer Hi-Bred International, Inc. had previously identified a quantitative trait loci (QTL) on LG-B1 and another on LG-L associated with reniform nematode resistance in a cross between BSR101 and PI 437654. Recent studies have shown that soybean cyst nematode (Heterodera glycines Ichinohe) resistant cultivars derived from PI 437654 are also potentially resistant to reniform nematode. In this study we validated existing QTL and identified additional QTL conditioning resistance to reniform nematode in a population of 228 recombinant-inbred lines (RILs) from a cross of BSR101 and PI 437654 with SSR markers. A major QTL conditioning reniform reproductive index (RI) was found on Linkage Group L (LG-L) flanked by Sat_184 and Satt513. Two other QTL were identified. One was located in the interval from Satt359 to Satt484 on LG-B1 and the other on LG-G linked to Sat_168. The QTL on LG-B1 and -G acted in an epistatic manner with lines homozygous for PI 437654 alleles at both QTL providing the lowest reniform RI. The 31 RILs from BSR101 &#61620; PI 437654 that were homozygous for the PI 437654 alleles at Satt513, Satt358, and Sat_168 averaged 1,077 reniform eggs and juveniles (RI=0.63), while the 33 RILs homozygous for the BSR101 alleles averaged 10,606 (RI=6.24). By screening the RILs population of Prichard and Anand we confirmed that the QTL on LG-G and -B1 conditioned reniform RI. These results support the genetic linkage between soybean resistance to the reniform nematode and the soybean cyst nematode. Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, is a widespread disease of soybean with the potential to cause serious economic losses. A population of 117 RILs from the cross of Dillon (tan lesion) and Hyuuga (red-brown lesion, RB) was rated for ASR lesion type in the field and inoculated with P. pachyrhizi in the greenhouse. The RB resistance gene mapped between Satt460 and Satt307 on linkage group (LG) C2. When field severity and lesion density in the greenhouse were mapped, the Rpp?(Hyuuga) locus explained 22 and 15 percent of the variation, respectively (P < 0.0001). The RB lesion type was associated with lower severity, fewer lesions and reduced sporulation when compared to the tan lesion type. A population from the cross of Benning and Hyuuga was screened with SSR markers in the region on LG-C2 flanked by Satt134 and Satt460. Genotype at these markers was used to predict lesion type when the plants were exposed to P. pachyrhizi. All the lines selected for the Hyuuga markers in this interval had the RB lesion type and they averaged approximately 50 percent fewer lesions compared to lines with tan lesions. Sporulation was only detected in 6 percent of the RB lines compared with 100 percent of the tan lines. Marker-assisted selection can be used to develop soybean cultivars with the Rpp?(Hyuuga) gene for resistance to ASR.

The reduction in the use of pesticides by increasing levels of resistance in soybean cultivars to major soybean pests has dual benefits through reduced impact on the environment from soybean production and reduced cost of production to the soybean grower. Additionally, human food and animal feed products developed from these cultivars will have a reduced risk of pesticide residuals. Another beneficiary of this research will be commercial soybean breeding organizations. These organizations will benefit from the fundamental research to discover QTL for previously intractable traits and the availability of high throughput DNA markers to select for these QTL. Their ability to extend these findings to other maturity zones of the USA will accelerate soybean improvement programs across all regions of the USA.


  • Zhu, S., D.R. Walker, H.R. Boerma, J.N. All, and W.A. Parrott. 2006. Fine-mapping of a major insect resistance QTL in soybean and its interaction with minor resistance QTLs. Crop Sci. 46:1094-1099.
  • Walker, D.R., A. Scaboo, V.R. Pantalone, J.R. Wilcox, and H.R. Boerma. 2006. Genetic mapping of loci associated with seed phytic acid levels in soybean CX1834-1-2. Crop Sci. 46:390-397.
  • Walker, D.R., A.K. Walker, E.D. Wood, M.E. Bonet Talevera, F.E. Fernandez, G.B. Rowan, C.K. Moots, R.A. Leitz, P.A. Owen, W.E. Baxter, J.L. Head, and H.R. Boerma. 2006. Gametic selection by glyphosate in soybean plants hemizygous for the CP4 EPSPS transgene. Crop Sci. 46:30-35.

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

Two new maturity group VII soybean cultivars, AGS 758 RR and G00-3209 were developed and approved for release. AGS 758 RR was released based on its high seed yield and resistances to the glyphosate herbicide, race 3 of soybean cyst nematode, southern root-knot nematode, peanut root-knot nematode, Javanese root-knot nematode, and stem canker. G00-3209 was approved for release based on its superior seed yield. In 19 environments, it averaged 19% higher seed yield (8.1 bu/a) than Benning. G00-3209 averaged 14% greater seed yield (6.5 bu/a) than Haskell-RR when evaluated in 15 environments. It is unusual for new soybean cultivars to achieve yield increases of this magnitude. In the past 50 years this has occurred with well-known soybean cultivars such as Lee (released in 1954), Bragg (released in 1963), Hutcheson (released in 1987), and Cook (released in 1991). All of these cultivars were widely grown in the Southeast and subsequently used as parents for the next cycle of breeding. G00-3209 is resistant to race 3 soybean cyst nematode, southern root-knot nematode, stem canker, and red crown rot. In addition to these two new cultivars, 18 germplasm lines selected from within the cultivars Haskell, Cook, or Benning were approved for release due to their significant variation in seed protein, seed oil, seed weight, plant height, lodging resistance, or maturity when compared to the cultivar from which they were derived. These germplasm lines should be more useful as parental material than Haskell, Cook, and Benning for the development of elite breeding populations by contributing greater variation in one or more specific agronomic or seed composition trait than the cultivar from which they were derived. Furthermore, these lines should be useful to molecular geneticists in the discovery of the genes responsible for conditioning the phenotype of the selected variants within each germplasm line. We were also successful in obtaining the first U.S. field data that evaluated the level of resistance to Asian soybean rust among soybean plant introductions, breeding lines, and cultivars. We evaluated approximately 780 plant introductions that had been previously identified in the biocontainment facility at Fort Detrick MD as potentially resistant to Asian soybean rust. These plant introductions ranged from maturity group 00 to IX. In order to manage the wide range in maturity of these plant introductions, we planted the experiment at Attapulgus GA on 2 September 2005 and provided supplemental lighting to extend photoperiod for 1 month after planting. Initial rust ratings were taken in mid-November and continued until 22 December. Among these plant introductions, we identified 40 that showed the least Asian soybean rust incidence. Information on these 40 Asian soybean rust resistant plant introductions was distributed electronically and at the 2006 Soybean Breeder Workshop in Saint Louis MO.

The development of new soybean cultivars and breeding lines with superior seed yield, seed composition, and multiple pest resistances increases the competitiveness of U.S. agriculture. The increased culture of soybeans with multiple pest resistances reduces the need for pesticide application and the risk of environmental impact from soybean production. The identification of sources of resistance to Asian soybean rust will provide public and commercial soybean breeders the ability to develop productive soybean cultivars with resistance to this newly introduced soybean disease. This will result in a reduced cost of production and significantly reduce the need to apply fungicides to the U.S. soybean crop.


  • Boerma, H.R., and D.R. Walker. 2005. Discovery and utilization of QTLs for insect resistance in soybean. Genetica 123:181-189.
  • Fasoula, V.A., and H.R. Boerma. 2005. Divergent selection at ultra-low plant density for seed protein and oil content within soybean cultivars. Field Crops Res. 91:2005:217-229.
  • Missaoui, A.M., H.R. Boerma, and J.H. Bouton. 2005. Genetic variation and heritability of phosphorous uptake in Alamo switchgrass grown in high phosphorous soils. Field Crops Res. 93:186-198.
  • Walker, D.R., and H.R. Boerma. 2005. History and future of soybean biotechnology: From markers to sequences to improved varieties. Proc. of the American Seed Trade Association 60th Corn and Soybean Seed Research Conference Seed Expo, Chicago, IL, 7-9 Dec 2005.
  • Carter, Jr., T.E., J. H. Orf, L. C. Purcell, J. E. Specht, P. Chen, T. R. Sinclair, T.W. Rufty, and H.R. Boerma. 2005. Tough Times, Tough Plants-New Soybean Genes Defend Against Drought and Other Stresses. Proc. of the American Seed Trade Association 60th Corn and Soybean Seed Research Conference Seed Expo, Chicago, IL, 7-9 Dec 2005.

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

In 2004 we continued our efforts to develop improved soybean cultivars by conducting research to identify and map genes conditioning important traits, while simultaneously using integrated molecular and conventional breeding techniques to accumulate superior alleles in elite genetic backgrounds. Our focus has been largely on traits for seed composition (fatty acid composition, increased protein unaccompanied by yield reduction, elimination of lipoxygenase, and reduction of phytic acid) and improvement of resistance to pests and pathogens like insects, nematodes, frogeye leaf spot, and stem canker. We were able to better characterize the locations and contributions of two genes from the mutant line CX1834-1-2 which are responsible for reduced levels of phytic acid in soybean seed. The genotype at a locus on linkage group (LG) N explained 41% of the phenotypic variation for this trait in a F2:3 population, and the genotype at a locus on LG L explained 11%. An epistatic interaction between the two loci accounts for an additional 8 to 11%, and the low phytate trait is only observed when both loci are homozygous for the CX1834-1-2 alleles. Results from our insect resistance studies include evidence that an allele conditioning sharp tips on leaf pubescence is consistently associated with lepidopteran resistance in PI227687 and other insect resistant soybean germplasms. This relationship was investigated after a QTL was detected near the Pb allele on LG E. The trait should be relatively easy to backcross into other genetic backgrounds, since it is easy to select for phenotypically. Field testing of lines containing all factorial combinations of a Bt cry1Ac transgene and PI229358 alleles at an antibiosis/antixenosis QTL on LG M and an antixenosis QTL on LG H demonstrated that the resistance allele on LG M broadens and enhances the resistance provided by the Bt protein. The combination of the Bt gene and LG M allele were particularly effective at reducing larval weights in a laboratory strain of tobacco budworm selected for resistance to the Bt protein. When we were backcrossing the CP4 EPSPS glyphosate tolerance transgene into some Univ. of Georgia cultivars, we observed a higher than expected proportion of glyphosate tolerant plants in segregating populations. A series of experiments was conducted to confirm our hypothesis that gametic selection was occurring in hemizygous plants, and that the male gametes were sensitive to glyphosate. One of the experiments evaluated the effects of rate and timing of the glyphosate application on recovery of glyphosate sensitive progeny. Glyphosate applications at three stages of plant development (V3, V3 + 2-3 wk, and V3 + 3-4 wk) eliminated the glyphosate-sensitive phenotypic class. Two sets of reciprocal crosses between glyphosate sensitive and glyphosate tolerant parents were used in these experiments. As a result of gametic selection in hemizygous plants (such as backcrosses), gametes with the EPSPS transgene will be found at a higher frequency if glyphosate is applied before or around the time that flowering commences.

The development of soybean cultivars with improvements in seed composition, disease and pest resistance, and important agronomic traits will allow soybean producers in the Southeast to stay competitive, and will provide excellent MG VI to VIII germplasm which can be used in future crosses by both us and our colleagues. Modifications in the seed composition will keep soybean meal and oil competitive in a market driven by health concerns and the desire to improve the nutritional value of soy products, while reducing the impact of components such as phytic acid on the environment. The low profit margins of soybean producers in the Southeast make the planting of resistant material the most financially practical way to prevent yield losses caused by pests and pathogens. A large part of our research and breeding efforts are therefore focused on the development of breeding lines with resistance gene packages tailored to the South. The availability of high-yielding elite material with resistance to a number of pests and seeds with protein and fatty acid profiles meeting the needs of the producers of food products for human, poultry, and livestock consumption will benefit soybean breeders as well as producers throughout the region.


  • Narvel, J.M., T.E. Carter, Jr., L.R. Jakkula, J. Alvernaz, M.A. Bailey, M.A.R. Mian, S.H. Lee, G.J. Lee, and H.R. Boerma. 2004. Registration of NC113 soybean mapping population. Crop Sci. 44:704-706.
  • Fasoula, V.A., and H.R. Boerma. 2004. Validation and designation of quantitative trait loci for seed protein, seed oil, and seed weight from two soybean populations. Crop Sci. 44:1218-1225.
  • Walker, D.R., J.M. Narvel, H.R. Boerma, J.N. All, and W.A. Parrott. 2004. A QTL the enhances and broadens Bt resistance in soybean. Theor Appl Genet 109:1051-1057.
  • Hulburt, D.J., H.R. Boerma, and J.N. All. 2004. Effect of pubescence tip on soybean resistance to Lepidopteran insects. J. Econ. Entomology 97:621-627.
  • Lee, G.J., H.R. Boerma, M.R. Villagarcia, X. Zhou, T.E. Carter, Jr., Z. Li, and M.O. Gibbs. 2004. A major QTL conditioning salt tolerance in S-100 soybean and descendent cultivars. Theor Appl Genet 109:1610-1619.
  • Ha, B.K., J.B. Bennett, R.S. Hussey, and H.R. Boerma. 2004. Pedigree analysis of a major QTL conditioning soybean resistance to southern root-knot nematode. Crop Sci. 44:758-763.
  • Lee, S.H., D.R. Walker, P.B. Cregan, and H.R. Boerma. 2004. Comparison of four flow cytometric SNP detection assays and their use in plant breeding. Theor Appl Genet 110:167-174.
  • Boerma, H.R., and J.E. Specht (eds.). 2004. Soybeans: Improvement, Production, and Uses, 3rd edition, ASA, CSSA, and SSA, Madison WI. 1,144 pages.
  • Orf, J.H., B.W. Diers, and H.R. Boerma. 2004. Genetic improvement: Conventional and molecular-based strategies. In H.R. Boerma and J.E. Specht (ed.) Soybean improvement, production, and uses, 3rd edition, ASA, CSSA, and SSA, Madision WI. p. 417-450.
  • Boerma, H.R., and M. Curtis. 2004. Development and status of the U.S. legume crops genomics initiative. In R.F. Wilson, H.T. Stalker, E.C. Brummer (ed.) Legume Crop Genomics. AOCS Press, Champaign IL. p. 1-8.
  • Boerma, H.R., D.R. Walker, W.A. Parrott, R.S. Hussey, and J.N. All. 2004. Molecular breeding for resistance to defoliating insects and root-knot nematodes. In F. Moscardi (ed.) Proceed. World Soybean Research Conference VII. Foz do Iguassu, PR, Brazil. 29 Feb. to 5 March 2004. p. 465-470.
  • Pantalone, V.R., D.R. Walker, R.E. Dewey, and I. Rajcan. 2004. DNA marker-assisted selection for improvement of soybean oil concentration and quality. In R.F. Wilson, H.T. Stalker, E.C. Brummer (ed.) Legume Crop Genomics. AOCS Press, Champaign IL. p. 283-311.