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United States Department of Agriculture

Agricultural Research Service

Research Project: INCREASING THE COMPETITIVE POSITION OF U.S. SOYBEANS IN GLOBAL MARKETS THROUGH GENETIC DIVERSITY AND PLANT BREEDING

Location: Soybean and Nitrogen Fixation Research

2012 Annual Report


1a.Objectives (from AD-416):
Objective 1, the improvement of yield potential, will deal with QTL analysis of breeding populations derived from exotic germplasm and with a method to identify appropriate exotic germplasm for study. Objective 2, the improvement of seed composition, will focus on raising oleic acid content of soy oil, reducing phytate in the protein meal, and in determining the impact of altered seed composition on vulnerability to disease. Objective 3, the improvement of drought tolerance, will identify QTLs for drought tolerance derived from exotic germplasm and test a rapid screening method that may streamline breeding for drought tolerance.


1b.Approach (from AD-416):
The research will be accomplished by combining conventional breeding technology with Quantitative Trait Loci (QTL) analysis and near isogenic line development. Drought tolerance is treated as a topic distinct from yield, because it is the greatest agronomic limitation to soybean production in the USA.

Using molecular marker technology in combination with field and lab studies, we will assess the genetic potential of accessions in the USDA soybean germplasm collection for improving soybean yield potential, seed composition, disease resistance, and drought tolerance. We will identify the genomic location of alleles which govern these traits.


3.Progress Report:
Soybean is among the least diverse crops in the USA. Such narrow genetic diversity renders a crop vulnerable to changing pests and environmental extremes, and also limits the ability of breeders to enhance the crop. New genetics are needed to address this problem. This project will use the USDA Soybean Germplasm Collection as a source of novel diversity to identify genes and alleles which improve seed yield, seed composition, and drought tolerance.

Approximately 20,000 experimental plots were harvested in pursuit of these objectives. To improve yield potential, advanced breeding lines derived from exotic pedigree were grown in more than 8000 yield plots. 22 USDA-ARS breeding lines with Asian pedigree were evaluated across the South in USDA Regional Trials. 46 additional USDA-ARS breeding lines with Asian pedigree were grown in a separate regional Southern Diversity Trial. 9 ARS breeding lines tracing 50% of pedigree to the wild progenitor of domesticated soy were evaluated in regional Southern Diversity tests and 7 were included in USDA Regional Trials. To improve drought tolerance, more than 4000 yield plots were evaluated at a drought-prone field site. From this work, 4 advanced breeding lines were submitted to regional testing trials. DNA extraction and SNP analysis were completed for 3 QTL populations. 4000 yield plots were grown in support of the breeding effort to improve seed composition.

We are continuing a Marker Assisted Backcrossing (MAB) program to introgress two high oleic alleles (FAD2-1A and FAD2- 1B) into advanced soybean breeding lines. We expanded our ARS winter nursery in Puerto Rico to make an additional crossing cycle per year. We also added two additional loci to our MAB program (FAD3A and FAD3C mutations) which reduce linolenic acid concentration of soybean oil to about 3%. The combination of these alleles and traits will significantly improve the oxidative stability of soy oil. We are also characterizing additional high stearic mutations, employing selective genotyping.

Purple stain disease, caused by Cercospera kikuchii, is a problem in soybean for some southern states. An assay of green seed harvested 35 days after flowering was used to characterize fungal seed colonization and expression of 25 host defense genes. Reverse transcription polymerase chain reaction (q RT-PCR) technologies were employed. Expectations are that certain defense genes will differ between soybean varieties that have shown resistance in the field. Results will provide important clues which will aid soybean breeders.

The interaction of antibodies with food proteins is the basis for allergenic response in mammals. Allergenic responses are common in livestock, especially when feeding soy-protein based feed to pigs. This basis of the allergenic problem was investigated by challenging peptides from a seed storage protein of soybean (the conglycinin subunit) with sera from 30 pigs. Specific regions of the soy protein were identified as immunogenic (i.e. allergenically reactive). A previously reported allergenic region was confirmed, and a second allergenic region was discovered.


4.Accomplishments
1. Identification of a novel high-stearic soybean mutation in the delta 9–stearoyl-acyl carrier isoform B (SACPD-B) and development of perfect SNP Mmrkers for breeding. Palmitic acid, a common saturated fatty acid in foods, increases cholesterol levels and should be avoided to reduce the risk of cardiovascular disease. Stearic acid is a healthier fatty acid alternative for the diet. A novel high stearic mutation was identified and a USDA/ARS researcher at Raleigh, in collaboration with NC State University faculty, discovered the basis for the mutation. They sequenced SACPD isoforms in the genome and revealed the deletion of an ‘A’ nucleotide in exon 3 of SACPD-B in the mutant, which results in a protein whose final 28 amino acids are predicted to differ from the common SACPD-B of Williams 82. The effect of this mutation was confirmed in two populations that were also segregating for a SACPD-C point mutation previously identified in our group. Additive effects for stearic acid were +3.3 for SACPD-C and +1.9 for SACPD-B, and together can increase the stearic acid content in soybean oil to 15%, much higher than in normal soybean types. Perfect makers were developed for this new mutation and are available to applied breeders.

2. High yielding soybean breeding lines developed from wild soybean. More than 6000 scientific papers mention wild soybean, the progenitor of cultivated soy, and 100 accessions are preserved in the USDA soybean germplasm collection. However, this important genetic resource is NOT being used in applied breeding. The reason is the viny growth habit of the wild types and F2, F3, and F4 populations derived from hybridizing it with the domesticate. A USDA/ARS researcher at Raleigh, in collaboration with NC State University, developed and tested a new plant breeding methodology to produce large numbers of adapted breeding lines which are high yielding, 50% wild soybean by pedigree, and approx. 35% wild soybean based on DNA markers. These lines are being transferred to industry for applied breeding. This success is unprecedented and may fundamentally change how wild soybean is used in breeding.

3. Genes from exotic soybean increase yield of U.S. Soybean varieties. The genetic base of US soybean is too narrow and threatens to curb breeding progress in the USA. A USDA/ARS researcher at Raleigh, NC has used the rich genetic diversity of the USDA germplasm collection to combat this problem. Using exotic Japanese soybean accessions (varieties) as breeding stock, new breeding lines have been developed which yield 10% better than the original U.S. parent. By design, only one U.S. variety appears in the pedigree of the new breeding lines, thus making yield advances from exotic sources readily identified. These results clearly show that Japanese yield enhancing genes from the USDA germplasm collection are poised to rectify important production problems that threaten US agriculture. This is an unprecedented success in the use of exotic soybean in plant breeding. These new lines and the breeding methodology used to develop them will be a great new resource for the soybean industry. These new lines have been transferred to industry for applied breeding.

4. Identification of a second major allergenic region in the soybean seed storage protein conglycinin. Young pigs which are fed a post-weaning diet that includes soy protein often experience reduced growth associated with allergic response. A USDA/ARS researcher at Raleigh, NC has identified a second allergenic region of soybean seed protein, found in the alpha subunit of conglycinin, which may be an important part of the overall allergenic response of pigs to soybean. This discovery was made by challenging a protein peptide array representing this protein with sera from 30 pigs. Identification of variants of allergenic sites may be an important step in identifying a more healthful source of soy protein for young pigs, making pork production more efficient and less costly.


Review Publications
Carter Jr, T.E., Koenning, S., Burton, J.W., Rzewnicki, P.E., Villagarcia, M.R., Bowman, D.T., Arelli, P.R. 2011. Registration of ‘N7003CN’ maturity group VII soybean with high yield and resistance to race 2 soybean cyst nematode. Journal of Plant Registrations. 5(3):309-317.

Ray, J.D., Smith, J.R., Taliercio, E.W., Fritschi, F.B. 2011. Genomic location of a gene conditioning a miniature phenotype in soybean. Plant Biology. 55:26-32.

Maxwell, J.J., Lyerly, J.H., Srnic, G., Murphy, P., Cowger, C., Parks, W.R., Marshall, D.S., Brown Guedira, G.L., Miranda, L.M. 2012. MlNCD1: A novel Aegilops tauschii derived powdery mildew resistance gene identified in common wheat. Crop Science. 52:1162-1170.

Feng, L., Burton, J.W., Carter Jr, T.E., Miranda, L.M., St. Martin, S., Brownie, C. 2011. Genetic analysis of populations derived from matings of southern and northern soybean cultivars. Crop Science. 51:2479-2488.

Burton, J.W., Miranda, L.M., Carter Jr, T.E., Bowman, D. 2012. Registration of ‘NC- Miller’ soybean with high yield and high seed oil content. Journal of Plant Registrations. 6:294-297.

Hussein, A., Carter Jr, T.E., Purcell, L., King, A., Ries, L., Chen, P., Schapaugh, W., Sinclair, T., Boerma, R. 2012. Mapping of quantitative trait loci for canopy wilting trait in soybean (Glycine max L.. Journal of Theoretical and Applied Genetics. 125:837-846.

Place, G.T., Reberg-Horton, S.C., Carter Jr, T.E., Brinton, S.R., Smith, A.N. 2011. Screening Tactics For Identifying Competitive Soybean Genotypes. Communications in Soil Science and Plant Analysis. Vol. 42, Issue 21.

Ries, L.L., Purcell, L.C., Carter Jr, T.E., Edwards, J.T., King, C.A. 2011. Physiological traits contributing to differential canopy wilting in soybean under drought. Crop Science. Vol. 52. pp. 272-281.

Upchurch, R.G., Ramirez, M.E. 2011. Effects of temperature during soybean seed development on defense-related gene expression and fungal pathogen accumulation. Biotechnology Letters. 33:2397-2404. 2011.

Upchurch, R.G. 2011. Soybean fatty acid desaturase pathway: reponses to temperature changes and pathogen infection. Pp. 113-128. In D. Krezhova (ed.) Soybean-genetics and novel techniques for yield enhancement. InTech Open Access Press. Vienna, Austria. 2011.

Last Modified: 9/10/2014
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