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

Abstract

BackgroundSoybean (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.ResultsThe 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1441-4) contains supplementary material, which is available to authorized users.

Potential yield of tidal swamp-adaptive soybean promising lines

“…It means that longer days to flowering caused longer days to maturing. Some authors also reported similar result that the flowering days correlated positively with maturing days (Mahbub et al, 2015;Zhang et al, 2015). However, Kuswantoro et al (2014) reported no corelation between days to flowering and days to maturing on Korean varieties grown in Indonesia.…”

Research Article Genetic parameters and selection of soybean lines based on selection indexes.

“…Evaluating 309 soybean genotypes, Zhang et al (2015) verified heritability values of 95.6, 94.2, 92.2, and 82.8% for the number of days for flowering, number of days for maturity, number of days to flowering and maturity, and plant height at maturity, respectively. Bizari et al (2017) determined that the characters with the highest heritability value were the number of days at maturity (91.7%), followed by oil content (86.21%), agronomic value (74.97%), and grain yield (71.31%).…”

Crop rotation affects soybean performance in no-tillage system under optimal and dry cropping seasons

“…In DCS, the average of plant height was 0.71 m, which was below the acceptable value [0.96 m in average (Franchini et al, 2014) and 0.91 m in average (Rosa et al, 2015)]. Although, the plant height is determined by genetic control (Lee et al, 2015;Zhang et al, 2015), it is possible to infer that the environmental conditions, like rainfall may diminish the soybean height. This depletion observed in this research was 31.1% between the cropping seasons (Fig.…”