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A high-resolution genetic linkage map of soybean based on 357 recombinant inbred lines genotyped with BARCSoySNP6K

Sungwoo Lee, Keith R. Freewalt, Leah K. McHale, Qijian Song, Tae-Hwan Jun, Andrew P. Michel, Anne E. Dorrance, M. A. Rouf Mian
Molecular breeding 2015 v.35 no.2 pp. 209
Glycine max, chromosome mapping, gene frequency, genetic markers, genome, genome assembly, genotyping, heterozygosity, inbred lines, linkage groups, loci, parents, quantitative trait loci, single nucleotide polymorphism, soybeans
The objective of this study was to construct a high-density genetic map of soybean (Glycine max L. Merr) using a high-throughput single nucleotide polymorphism (SNP) genotyping on 357 F₇recombinant inbred lines from a cross of ‘Wyandot’ × PI 567301B. Of 5,403 SNP loci scored from the Infinium BARCSoySNP6K BeadChip array, 2,585 (48 %) were polymorphic between the two parents and subsequently 2,563 SNPs remained after filtering for minor allele frequency, heterozygosity, and missing data. A total of 2,545 SNPs were mapped into 20 linkage groups corresponding to the 20 chromosomes of soybean. The total length of the map was 2,346 cM with 2,213 unique SNP loci with 86 to 162 unique loci per chromosome. Average marker interval ranged from 0.9 to 1.3 cM with an overall mean of 1.1 cM, but 22 marker intervals were still greater than 10 cM. Colinear relationship was observed between genetic (cM) and physical positions (Mb) of SNPs for most of the genome, highlighting the improvements in the updated soybean genome assembly Glyma.Wm82.a2 in comparison with the previous Glyma.Wm82.a1. This high-density genetic map shows the utility of the BARCSoySNP6K BeadChip array and will lead to a better understanding of the genetic architecture of complex traits and identification of SNPs tightly linked to QTL for many important soybean traits.