title: Genome-wide association study for flowering time, maturity dates and plant height in early maturing soybean (Glycine max) germplasm.
abstract: BACKGROUND
  Soybean (Glycine max) is a photoperiod-sensitive and self-pollinated species. Days to flowering (DTF) and maturity (DTM), duration of flowering-to-maturity (DFTM) and plant height (PH) are crucial for soybean adaptability and yield. To dissect the genetic architecture of these agronomically important traits, a population consisting of 309 early maturity soybean germplasm accessions was genotyped with the Illumina Infinium SoySNP50K BeadChip and phenotyped in multiple environments. A genome-wide association study (GWAS) was conducted using a mixed linear model that involves both relative kinship and population structure.
  
  
  RESULTS
  The linkage disequilibrium (LD) decayed slowly in soybean, and a substantial difference in LD pattern was observed between euchromatic and heterochromatic regions. A total of 27, 6, 18 and 27 loci for DTF, DTM, DFTM and PH were detected via GWAS, respectively. The Dt1 gene was identified in the locus strongly associated with both DTM and PH. Ten candidate genes homologous to Arabidopsis flowering genes were identified near the peak single nucleotide polymorphisms (SNPs) associated with DTF. Four of them encode MADS-domain containing proteins. Additionally, a pectin lyase-like gene was also identified in a major-effect locus for PH where LD decayed rapidly.
  
  
  CONCLUSIONS
  This study identified multiple new loci and refined chromosomal regions of known loci associated with DTF, DTM, DFTM and/or PH in soybean. It demonstrates that GWAS is powerful in dissecting complex traits and identifying candidate genes although LD decayed slowly in soybean. The loci and trait-associated SNPs identified in this study can be used for soybean genetic improvement, especially the major-effect loci associated with PH could be used to improve soybean yield potential. The candidate genes may serve as promising targets for studies of molecular mechanisms underlying the related traits in soybean.
authors.affiliation: Plant Science Department, South Dakota State University, Brookings, SD, 57006, USA. jiaopingzhang@gmail.com.
authors.forename: Jiaoping
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Soybean Genomics and Improvement Laboratory, US Department of Agriculture, Agricultural Research Service (USDA-ARS), 10300 Baltimore Ave, Beltsville, MD, 20705, USA. Qijian.Song@ars.usda.gov.
authors.forename: Qijian
authors.initials: Q
authors.lastname: Song
authors.affiliation: Soybean Genomics and Improvement Laboratory, US Department of Agriculture, Agricultural Research Service (USDA-ARS), 10300 Baltimore Ave, Beltsville, MD, 20705, USA. Perry.Cregan@ars.usda.gov.
authors.forename: Perry B
authors.initials: PB
authors.lastname: Cregan
authors.affiliation: USDA-ARS, Soybean/Maize Germplasm, Pathology, and Genetics Research Unit and Department of Crop Sciences, University of Illinois, Urbana-Champaign, 1101 West Peabody Drive, Urbana, IL, 61801, USA. Randall.Nelson@ars.usda.gov.
authors.forename: Randall L
authors.initials: RL
authors.lastname: Nelson
authors.affiliation: Plant Science Department, South Dakota State University, Brookings, SD, 57006, USA. xianzhiwang1@gmail.com.
authors.forename: Xianzhi
authors.initials: X
authors.lastname: Wang
authors.affiliation: Plant Science Department, South Dakota State University, Brookings, SD, 57006, USA. jixiang.wu@sdstate.edu.
authors.forename: Jixiang
authors.initials: J
authors.lastname: Wu
authors.affiliation: Plant Science Department, South Dakota State University, Brookings, SD, 57006, USA. gjiang@vsu.edu.|Agricultural Research Station, Virginia State University, P.O. Box 9061, Petersburg, VA, 23806, USA. gjiang@vsu.edu.
authors.forename: Guo-Liang
authors.initials: GL
authors.lastname: Jiang
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D035264:Flowers / Q000235:genetics; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D015810:Linkage Disequilibrium; D010641:Phenotype; D017440:Photoperiod; D010940:Plant Proteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D011133:Polysaccharide-Lyases / Q000235:genetics; D040641:Quantitative Trait Loci; D013025:Glycine max / Q000235:genetics* / Q000254:growth & development
chemical_list: D010940:Plant Proteins; D011133:Polysaccharide-Lyases; C027349:pectin lyase