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Association mapping identifies and confirms loci for soybean seed weight
Author(s) -
Kaler Avjinder S.,
Purcell Larry C.
Publication year - 2020
Publication title -
crop science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.76
H-Index - 147
eISSN - 1435-0653
pISSN - 0011-183X
DOI - 10.1002/csc2.20349
Subject(s) - germplasm , biology , single nucleotide polymorphism , association mapping , candidate gene , quantitative trait locus , linkage disequilibrium , genetics , allele , genetic association , genome wide association study , snp , molecular breeding , gene , genotype , botany
Seed weight (SW) is a component of soybean [ Glycine max (L.) Merr.] yield and it is also an important determinant of quality for food products such as edamame, soy nuts, and tofu. A better understanding of the genetic basis of SW is important for cultivar development and for use in various food industries. The objective of this study was to identify and confirm the genomic regions, favorable alleles, and candidate genes associated with SW. Genome‐wide association mapping was conducted on 36 panels including a diverse panel of 373 accessions grown in three environments (one panel) and 35 panels obtained from the Germplasm Resources Information Network. Association mapping identified 66 significant single nucleotide polymophisms (SNPs) that probably tagged 47 putative loci associated with SW that had allelic effects ranging from –7.8 to 6.9 g per 100 seeds. Of these 47 loci, 42 significant loci–SW associations were confirmed with previously identified SW quantitative trait loci (QTLs). One SNP on Gm17 and another SNP on Gm19 were present in 16 and 8 panels, respectively. There were 121 candidate genes found within the same linkage disequilibrium blocks as the identified SNPs; 97 of these genes had biological functions associated with seed components including protein, fatty acids (oil), carbohydrates, seeds, embryos, water, and cotyledons. The entire USDA soybean germplasm collection was explored for the favorable alleles. Favorable alleles, accessions identified from the germplasm collection, and candidate genes may be important resources for breeding for SW in soybean.