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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Soybean Genomics & Improvement Laboratory » Research » Publications at this Location » Publication #308566

Research Project: Defining the Genetic Diversity and Structure of the Soybean Genome and Applications to Gene Discovery in Soybean, Wheat and Common Bean Germplasm

Location: Soybean Genomics & Improvement Laboratory

Title: Multi-population selective genotyping to identify soybean (Glycine max (L.) Merr.) seed protein and oil QTLs

Author
item Phansak, Piyaporn - Nakhon Sawan Field Crops Research Center
item Soonsuwon, Watcharin - Prince Of Songkla University
item Hyten, David - Dupont Pioneer Hi-Bred
item Song, Qijian
item Cregan, Perry
item Graef, George - University Of Nebraska
item Broman, Karl - University Of Wisconsin
item Specht, James - University Of Nebraska

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/25/2016
Publication Date: 4/2/2016
Citation: Phansak, P., Soonsuwon, W., Hyten, D., Song, Q., Cregan, P.B., Graef, G.L., Broman, K.W., Specht, J.E. 2016. Multi-population selective genotyping to identify soybean (Glycine max (L.) Merr.) seed protein and oil QTLs. Genes, Genomes, Genetics. doi:10.1534/g3.116.027656.

Interpretive Summary: The major use of soybean is for oil and protein meal which is an extremely important part of livestock diets. Therefore, an important objective of soybean breeding is maintaining seed protein and oil while at the same time improving seed yield. The objective of this research was to define genetic factors that impact the levels of soybean seed protein and oil. A total of 48 high seed protein soybean lines were each crossed to a soybean line with normal protein and similar maturity. A total of 224 progeny was obtained from each of the 48 crosses and the progeny were grown in the field and the seed protein and oil content of the seed produced by each progeny line was determined. The 10% of progeny lines from each cross with the highest seed protein and the 10% with the lowest seed protein were analyzed with 1536 single nucleotide polymorphism (SNP) DNA markers. An analysis of the seed protein and oil data along with the DNA marker data detected genes or other genetic factors on 18 of the 20 pairs of soybean chromosomes impacting seed protein and similarly, genetic factors on 18 of the 20 pairs of chromosomes were detected that influenced seed oil content. These genetic factors and the SNP DNA markers associated with them can be used by soybean breeders to select soybean breeding lines that carry genetic factors that result in increased soybean seed protein and oil.

Technical Abstract: Plant breeders continually generate ever-higher yielding cultivars, but also want to improve seed constituent value, which in soybean [Glycine max (L.) Merr.] is seed protein and oil. Identification of genetic loci governing those two traits would facilitate that effort, and though genome-wide association is one such approach, multiple-population selective genotyping is another, and was evaluated here, using 48 F2.3 populations (n=~224) created by mating 48 high protein germplasm accessions to cultivars of similar maturity with normal seed protein content. All F2.3 progeny were phenotyped for seed protein and oil, but only the extreme 22 high and 22 low decile progeny in each F2.3 phenotypic distribution were genotyped with a soybean 1536-SNP chip (~450 SNPs segregated in each mating). In a QTL analysis of the 48 selectively genotyped populations, LOD => 3.0 QTLs were identified in all but two of the 20 soybean chromosomes (1 & 17 for protein; 11 & 17 for oil). In a recent genome-wide association involving 151 high protein germplasm accessions using a –logP=> 3.0 criterion, 17 protein QTLs and 13 oil QTLs were detected in a respective ten and 13 chromosomes. In the SoyBase historical listings of protein and oil QTLs, those meeting a P<=0.05 F-statistic criterion map to just a respective 13 and 15 chromosomes. With the two above-described studies, a QTL for either protein or oil can now be reported as being present on each of the 20 chromosomes.