A SNP-Based Genetic Linkage Map of Soybean Using the SoySNP6K Illumina Infinium BeadChip Genotyping Array

Akond, Masum; Liu, Shiming; Schoener, Lauren; Anderson, James A.; Kantartzi, Stella K.; Meksem, Khalid; Song, Qijian; Wang, Dechun; Zhang, Wen; Lightfoot, David A.; Kassem, My Abdelmajid

doi:10.5147/pggb.v1i3.154

Cited by 45 publications

(48 citation statements)

References 44 publications

(40 reference statements)

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“…Currently, only one study has reported a soybean genetic map constructed for a RIL population using a custom Illumina Infinium SoySNP6K BeadChip (Akond et al 2013), which was not the same as BARCSoySNP6K used in the present study. Although genotypic data for more than 5,000 SNPs was successfully produced, only 657 SNPs were polymorphic, met criteria of goodness-of-fit (1:1) with less than 20 % missing data, and were available for construction of the genetic map.…”

Section: Resultsmentioning

confidence: 93%

“…The final set of 550 SNPs were highly concentrated in narrow regions of 17 chromosomes and each linkage group did not exceed 40 cM with up to 94 SNPs (Akond et al 2013). Because many markers were clustered, the map represented only a small portion of the genome (Akond et al 2013). The genetic map from our study is comparable to the soybean Consensus Map4.0 and the genetic map of Williams 82 9 PI 468916 population constructed using 1,790 SNPs and 444 RILs by Hyten et al (2010b).…”

Section: Resultsmentioning

confidence: 95%

“…Although genotypic data for more than 5,000 SNPs was successfully produced, only 657 SNPs were polymorphic, met criteria of goodness-of-fit (1:1) with less than 20 % missing data, and were available for construction of the genetic map. The final set of 550 SNPs were highly concentrated in narrow regions of 17 chromosomes and each linkage group did not exceed 40 cM with up to 94 SNPs (Akond et al 2013). Because many markers were clustered, the map represented only a small portion of the genome (Akond et al 2013).…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2015

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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 F 7 recombinant inbred lines from a cross of 'Wyandot' 9 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.a2Electronic supplementary material The online version of this article (

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Section: Resultsmentioning

confidence: 93%

Section: Resultsmentioning

confidence: 95%

Section: Resultsmentioning

confidence: 99%

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

et al. 2015

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“…On the other hand, greater length for a genetic map derived from a single segregating population was reported by Hwang et al (2014), with 2241.3 cM obtained with 664 markers (171 SSRs + 493 SNPs) and 97 RILs. According to Akond et al (2013Akond et al ( , 2015, these maps are not comparable to the map construction with only one population and one type of marker. According to Akond et al (2013Akond et al ( , 2015, these maps are not comparable to the map construction with only one population and one type of marker.…”

Section: Discussionmentioning

confidence: 98%

Identification of QTLs Associated with Biological Nitrogen Fixation Traits in Soybean Using a Genotyping‐by‐Sequencing Approach

et al. 2018

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2523 RESEARCH S everal legumes, when in symbiosis with bacteria collectively known as rhizobia, have the ability to assimilate atmospheric N 2 in a process called biological N fixation (BNF). Legume-rhizobia symbioses potentially contribute both to environmental and agricultural sustainability by reducing greenhouse gas emissions, nitrogenous water pollution, and fossil energy consumption (Serraj et al., 1999;Kaewsuralikhit et al., 2005;Hungria and Mendes, 2015).Soybean [Glycine max (L.) Merr.] is the most important legume cultivated worldwide. Symbiotic associations between soybean and Bradyrhizobium japonicum, Bradyrhizobium diazoefficiens, and Bradyrhizobium elkanii strains are economically and environmentally important; for example, savings on N fertilizer in Brazil with the soybean crop are estimated at about US$15 billion per cropping season (Hungria and Mendes, 2015). ABSTRACTAlthough biological N fixation (BNF) is a key process for economic cultivation of soybean [Glycine max (L.) Merr.], the trait is often neglected in breeding programs, mainly due to difficulties in evaluating nodulation and N fixation parameters. We used a genotyping-by-sequencing approach to provide a dense genome-wide marker coverage with 1448 single nucleotide polymorphisms (SNPs) distributed broadly across the chromosomes of a soybean population. The mapping population was composted of 113 F 7:8 recombinant inbred lines, obtained by singleseed descent method, derived from crossing of soybean cultivars 'Bossier' (high BNF capacity) and 'Embrapa 20' (medium BNF capacity). The traits evaluated were nodule number (NN), nodule dry weight (NDW), average NDW (ANDW; i.e., NDW/NN), and shoot dry weight (SDW). A genetic map was constructed with 1448 SNPs that generat ed 35 linkage groups totaling 1793 cM, thus covering ?72% of the genome based on the consensus linkage map. The estimated heritability for NN, NDW, ANDW, and SDW was 0.41, 0.30, 0.30, and 49.11, respectively. Inclusive composite interval mapping identified two significant quantitative trait loci (QTLs) for ANDW at 67 cM on chromosome 13, with a logarithm of odds (LOD) score of 4.66. The additive effect of this locus was −0.31 mg nodule −1 , and it explained 18.13% of the phenotypic variation. Another QTL was identified for SDW at 24 cM on chromosome 19 and exhibited an LOD score of 3.93. The additive effect was of 0.57 g plant −1 , and it accounted for 14.93% of the phenotypic variation. Additive genetic effects contribute to the final phenotype. In the present study, Embrapa 20 was the major contributor to ANDW, and Bossier was the major contributor to SDW. The latter was previously reported using simple sequence repeat markers.

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“…DNA samples were extracted from soybean seedlings and leaves following a previously described method (Kisha, Sneller, & Diers, ). All accessions were genotyped via the Illumina SoySNP6k iSelect BeadChip, which consisted of 5,361 SNPs (Akond et al., ). Chromosomal distributions, coding and quality controlling of these SNPs were followed as previously documented (Wen et al., ).…”

Section: Methodsmentioning

confidence: 99%

Selection of soybean elite cultivars based on phenotypic and genomic characters related to lodging tolerance

Liu

Fan

et al. 2017

Plant Breeding

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Soybean lodging can result in serious yield reduction. Detecting the quantitative trait loci (QTL) associated with lodging tolerance for their further application in marker‐assisted selection (MAS) has the potential to enhance soybean breeding efficiency. In this study, a genome‐wide association analysis (GWAS) was performed to identify soybean accessions that could potentially be used to produce lodging‐tolerant varieties, based on the comprehensive evaluation of lodging scores (LS) obtained for the parental cultivar “Tokachi nagaha” and its 137 derived cultivars. Results showed that genotype, environment and genotype × environment interaction significantly influenced LS. Of the 31 significant SNPs identified, 22 were consistently detected in two or more environments and 27 SNPs were located in or close to agronomically important QTL mapped by linkage analysis. Best linear unbiased predictors (BLUPs) of LS tend to decrease with the elite alleles contained by accessions increasing. Some excellent accessions, with lower BLUPs and Di (stability coefficients) values and more elite alleles, were selected. This study contributed to understand the genetic mechanism of lodging, providing genetic and phenotypic information for MAS.

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A SNP-Based Genetic Linkage Map of Soybean Using the SoySNP6K Illumina Infinium BeadChip Genotyping Array

Cited by 45 publications

References 44 publications

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

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

Identification of QTLs Associated with Biological Nitrogen Fixation Traits in Soybean Using a Genotyping‐by‐Sequencing Approach

Selection of soybean elite cultivars based on phenotypic and genomic characters related to lodging tolerance

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