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Document Type

Dissertation - University Access Only

Award Date


Degree Name

Doctor of Philosophy (PhD)


Plant Science

First Advisor

Guo-Liang Jiang


Soybean (Glycine max) is a globally important crop. Developing high yield cultivars with high concentration and quality of protein or oil is one of the major objectives of soybean breeding. Genome-wide association study (GWAS) has been proven an effective tool to dissect genetic architecture of complex traits in crops. However, its application in soybean is limited. The objectives of this study were to: i) explore the efficiency of GWAS for complex traits in soybean; ii) enhance our understanding on the genetic architecture of agronomically important traits and seed composition; iii) identify markers and genetic variants usable for soybean cultivar improvement, and iv) identify candidate genes controlling those traits for future functional validation. To these ends, we conducted GWAS with a soybean population consisting of 309 early maturing germplasm accessions genotyped with the SoySNP50K BeadChip and phenotyped in multiple environments. High heritability estimates suggested that phenotypic selection is effective for trait improvement in soybean. The high positive correlation between protein and most amino acids implied that selection of high protein could increase concentration of amino acids but it is hard to improve quality of soybean protein. Genome-wide linkage disequilibrium (LD) analysis indicated that extensive LD might be a common phenomenon in soybean. GWAS analysis identified 27, 6, 18, 27 and 22 QTLs associated with days to flowering and maturity, reproductive duration, plant height and seed weight, respectively. And 6, 6, 73, 45 and 99 QTLs associated with concentration of protein, oil, fatty acids, seed weight- and protein-based amino acids were also detected, respectively. Function-known candidate genes Dt1, GmSAT1, GmSAD-C, GmFAD3A, GmFATB and GmAK-HSDH involved in stem elongation, nitrogen fixation, and fatty acid and amino acid biosynthesis were identified. Additionally, numerous candidate genes with Arabidopsis orthologs functioning in similar traits were predicted. This study evidently demonstrated the high efficiency of GWAS for dissection of complex traits in soybean. The loci identified may provide new information on genetic variants and options to breeders for soybean cultivars improvement, and the traits-associated SNPs could be used for MAS. The candidate genes identified in this study offered promising targets for further functional validation and bioengineering.

Library of Congress Subject Headings

Soybean -- Varieties
Soybean -- Germplasm resources
Soybean -- Seeds


Includes bibliographical references



Number of Pages



South Dakota State University


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