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BMC Genomics. 2015 Mar 20;16:217. doi: 10.1186/s12864-015-1441-4.

Genome-wide association study for flowering time, maturity dates and plant height in early maturing soybean (Glycine max) germplasm.

Author information

1
Plant Science Department, South Dakota State University, Brookings, SD, 57006, USA. jiaopingzhang@gmail.com.
2
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.
3
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.
4
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.
5
Plant Science Department, South Dakota State University, Brookings, SD, 57006, USA. xianzhiwang1@gmail.com.
6
Plant Science Department, South Dakota State University, Brookings, SD, 57006, USA. jixiang.wu@sdstate.edu.
7
Plant Science Department, South Dakota State University, Brookings, SD, 57006, USA. gjiang@vsu.edu.
8
Agricultural Research Station, Virginia State University, P.O. Box 9061, Petersburg, VA, 23806, USA. gjiang@vsu.edu.

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.

PMID:
25887991
PMCID:
PMC4449526
DOI:
10.1186/s12864-015-1441-4
[Indexed for MEDLINE]
Free PMC Article

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