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ARS Home » Midwest Area » Wooster, Ohio » Corn, Soybean and Wheat Quality Research » Research » Publications at this Location » Publication #304994
Title: A high resolution genetic linkage map of soybean based on 357 recombinant inbred lines genotyped with BARCSoySNP6K

Author
item LEE, SUNGWOO - The Ohio State University
item FREEWALT, KEITH - The Ohio State University
item MCHALE, LEAH - The Ohio State University
item SONG, QIJIAN - The Ohio State University
item TAEHWAN, JUN - The Ohio State University
item MICHEL, ANDREW - The Ohio State University
item DORRANCE, ANNE - The Ohio State University
item Mian, Rouf

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/13/2014
Publication Date: 1/28/2015
Publication URL: http://handle.nal.usda.gov/10113/61299
Citation: Lee, S., Freewalt, K., McHale, L., Song, Q., Taehwan, J., Michel, A., Dorrance, A.E., Mian, R.M. 2015. A high resolution genetic linkage map of soybean based on 357 recombinant inbred lines genotyped with BARCSoySNP6K. Molecular Breeding. 35:58. DOI:10.1007/s11032-015-0209-5.

Interpretive Summary: High Quality high density molecular linkage maps are needed for tagging genes of interest with molecular markers to facilitate marker assisted breeding of soybean. 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 F7 recombinant inbred lines (RILs) from a cross of cultivar 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 2,545 SNP markers were mapped into 20 linkage groups corresponding to 20 chromosomes of soybean. The total length of the map was 2,346cM with 2,213 unique SNP loci. Between 86 and 162 unique loci were mapped in each chromosome and average marker interval ranged from 0.9 to 1.3cM with an overall mean of 1.1cM. Co-linear 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, Glyma2.1in comparison to Glyma1.01. 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, including resistance to soybean aphids, powdery mildew, Phomopsis seed decay, and several agronomic traits.

Technical Abstract: 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 F7 recombinant inbred lines (RILs) 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 20 chromosomes of soybean. The total length of the map was 2,346cM with 2,213 unique SNP loci. Between 86 and 162 unique loci were mapped in each chromosome and average marker interval ranged from 0.9 to 1.3cM with an overall mean of 1.1cM. Co-linear 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, Glyma2.1in comparison to Glyma1.01. 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.