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

Lee, Sung‐Woo; Freewalt, Keith; McHale, Leah K.; Song, Qijian; Jun, Tae-Hwan; Michel, Andrew P.; Dorrance, Anne E.; Mian, M. A. Rouf

doi:10.1007/s11032-015-0209-5

Cited by 27 publications

(20 citation statements)

References 22 publications

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“…Soybean seed composition is a quantitatively inherited trait controlled by multiple genes and regulators. In this regard, a large number of QTL for seed composition traits have been identified and genetically mapped with the advancement of genetic map construction (Hyten et al ., ; Lee et al ., ), the availability of a well‐annotated reference genome (Schmutz et al ., ), resources for association mapping (Song et al ., , ), and whole‐genome resequencing data (Valliyodan et al ., ; Zhou et al ., ). These QTL were detected from varying genetic backgrounds and environments, using different genotyping, QTL mapping, and statistical methods.…”

Section: Introductionmentioning

confidence: 99%

Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high‐density linkage mapping

Patil

Vuong

Kale

et al. 2018

Plant Biotechnology Journal

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SummaryThe cultivated [Glycine max (L) Merr.] and wild [Glycine soja Siebold & Zucc.] soybean species comprise wide variation in seed composition traits. Compared to wild soybean, cultivated soybean contains low protein, high oil, and high sucrose. In this study, an interspecific population was derived from a cross between G. max (Williams 82) and G. soja (PI 483460B). This recombinant inbred line (RIL) population of 188 lines was sequenced at 0.3× depth. Based on 91 342 single nucleotide polymorphisms (SNPs), recombination events in RILs were defined, and a high‐resolution bin map was developed (4070 bins). In addition to bin mapping, quantitative trait loci (QTL) analysis for protein, oil, and sucrose was performed using 3343 polymorphic SNPs (3K‐SNP), derived from Illumina Infinium BeadChip sequencing platform. The QTL regions from both platforms were compared, and a significant concordance was observed between bin and 3K‐SNP markers. Importantly, the bin map derived from next‐generation sequencing technology enhanced mapping resolution (from 1325 to 50 Kb). A total of five, nine, and four QTLs were identified for protein, oil, and sucrose content, respectively, and some of the QTLs coincided with soybean domestication‐related genomic loci. The major QTL for protein and oil were mapped on Chr. 20 (qPro_20) and suggested negative correlation between oil and protein. In terms of sucrose content, a novel and major QTL were identified on Chr. 8 (qSuc_08) and harbours putative genes involved in sugar transport. In addition, genome‐wide association using 91 342 SNPs confirmed the genomic loci derived from QTL mapping. A QTL‐based haplotype using whole‐genome resequencing of 106 diverse soybean lines identified unique allelic variation in wild soybean that could be utilized to widen the genetic base in cultivated soybean.

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Section: Introductionmentioning

confidence: 99%

Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high‐density linkage mapping

Patil

Vuong

Kale

et al. 2018

Plant Biotechnology Journal

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“…By contrast, the WP mapping population is among the few biparental soybean mapping populations featuring highresolution genetic maps (Hyten et al, 2010a;Lee et al, 2015a; Lee et al (2015b) and Jun et al (2014). No locus was signiicant for 2-yr average of speciic leaf weight (Jun et al, 2014); thus, this trait was excluded in this table.…”

Section: Discussionmentioning

confidence: 99%

Registration of Wyandot × PI 567301B Soybean Recombinant Inbred Line Population

Lee

Jun

McHale

et al. 2017

J of Plant Registrations

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A soybean [Glycine max (L.) Merr] mapping population, Wyandot × PI 567301B (Reg. No. MP‐5, NSL 519221 MAP), consisting of 357 F7–derived recombinant inbred lines (RILs) was jointly developed by the USDA‐ARS and the Ohio Agricultural Research and Development Center in Wooster, OH. The population was developed by single seed descent from a cross between ‘Wyandot’ and PI 567301B. Wyandot is a food‐grade cultivar released by The Ohio State University, and PI 567301B is a plant introduction from China that differs from Wyandot for many morphological traits. PI 567301B was also confirmed to carry resistance to seed and seedling root rot, powdery mildew, and the soybean aphid. We have used this population to map quantitative trait loci (QTL)/genes for nine traits. The 357 RILs were genotyped using BARCSoySNP6K BeadChips, and a high density linkage map with 2545 single nucleotide polymorphism (SNP) markers well distributed on the 20 chromosomes of soybean was constructed and recently published. This mapping population is among the few biparental soybean mapping populations featuring high‐resolution genetic maps. We believe that the genetic map, population, and phenotypic data we provide will be an excellent resource for teaching labs in plant breeding and genetics as well as in discovery of new QTL.

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“…Recombination rates were taken from a genetic map developed by Lee et al (2015). Briefly, a recombinant inbred line family was derived from a cross between a wild soybean line and a cultivated soybean line, and genotyped with the SoySNP6K genotyping platform.…”

Section: Relating Recombination Rate To Deleterious Predictionsmentioning

confidence: 99%

“…Comparison between the recombination rate and proportion of nonsynonymous SNPs inferred to be deleterious in soybean on chromosome 1. The cM/Mb values are calculated from a genetic map using the SoySNP6K(Lee et al 2015). Red points are the proportion of nonsynonymous variants that are inferred to be deleterious, and black points are cM/Mb values between adjacent markers.…”

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confidence: 99%

The role of deleterious substitutions in crop genomes

Kono

Mohammadi

et al. 2015

Preprint

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Populations continually incur new mutations with fitness effects ranging from lethal to adaptive. While the distribution of fitness effects of new mutations is not directly observable, many mutations likely either have no effect on organismal fitness or are deleterious. Historically, it has been hypothesized that a population may carry many mildly deleterious variants as segregating variation, which reduces the mean absolute fitness of the population. Recent advances in sequencing technology and sequence conservation-based metrics for inferring the functional effect of a variant permit examination of the persistence of deleterious variants in populations. The issue of segregating deleterious variation is particularly important for crop improvement, because the demographic history of domestication and breeding allows deleterious variants to persist and reach moderate frequency, potentially reducing crop productivity. In this study, we use exome resequencing of 15 barley accessions and genome resequencing of 8 soybean accessions to investigate the prevalence of deleterious single nucleotide polymorphisms (SNPs) in the protein-coding regions of the genomes of two crops. We conclude that individual cultivars carry hundreds of deleterious SNPs on average, and that nonsense variants make up a minority of deleterious SNPs. Our approach identifies known phenotype-altering variants as deleterious more frequently than the genome-wide average, suggesting that putatively deleterious variants are likely to affect phenotypic variation. We also report the implementation of a SNP annotation tool BAD_Mutations that makes use of a likelihood ratio test based on alignment of all currently publicly available Angiosperm genomes.

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

Cited by 27 publications

References 22 publications

Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high‐density linkage mapping

Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high‐density linkage mapping

Registration of Wyandot × PI 567301B Soybean Recombinant Inbred Line Population

The role of deleterious substitutions in crop genomes

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