Genomic consequences of selection and genome-wide association mapping in soybean

BMC Genomics
Zixiang WenDechun Wang

Abstract

Crop improvement always involves selection of specific alleles at genes controlling traits of agronomic importance, likely resulting in detectable signatures of selection within the genome of modern soybean (Glycine max L. Merr.). The identification of these signatures of selection is meaningful from the perspective of evolutionary biology and for uncovering the genetic architecture of agronomic traits. To this end, two populations of soybean, consisting of 342 landraces and 1062 improved lines, were genotyped with the SoySNP50K Illumina BeadChip containing 52,041 single nucleotide polymorphisms (SNPs), and systematically phenotyped for 9 agronomic traits. A cross-population composite likelihood ratio (XP-CLR) method was used to screen the signals of selective sweeps. A total of 125 candidate selection regions were identified, many of which harbored genes potentially involved in crop improvement. To further investigate whether these candidate regions were in fact enriched for genes affected by selection, genome-wide association studies (GWAS) were conducted on 7 selection traits targeted in soybean breeding (grain yield, plant height, lodging, maturity date, seed coat color, seed protein and oil content) and 2 non-selection tra...Continue Reading

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Aug 9, 2016·Annual Review of Cell and Developmental Biology·Takehiko Ogura, Wolfgang Busch
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Apr 14, 2021·Scientific Reports·Janice KofskyBao-Hua Song

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Methods Mentioned

BETA
dissection
PCA
genotyping

Software Mentioned

XP
PowerMarker
EIGENSTRAT
R package
TASSEL
Haploview
GenomeStudio
CLR
TASSEL4
lm

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