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Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research

The limited number of recombinant events in recombinant inbred lines suggests that for a biparental population with a limited number of recombinant inbred lines, it is unnecessary to genotype the lines with many markers. For genomic prediction and selection, previous studies have demonstrated that o...

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Autores principales: Song, Qijian, Yan, Long, Quigley, Charles, Fickus, Edward, Wei, He, Chen, Linfeng, Dong, Faming, Araya, Susan, Liu, Jinlong, Hyten, David, Pantalone, Vincent, Nelson, Randall L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7702105/
https://www.ncbi.nlm.nih.gov/pubmed/32772442
http://dx.doi.org/10.1111/tpj.14960
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author Song, Qijian
Yan, Long
Quigley, Charles
Fickus, Edward
Wei, He
Chen, Linfeng
Dong, Faming
Araya, Susan
Liu, Jinlong
Hyten, David
Pantalone, Vincent
Nelson, Randall L.
author_facet Song, Qijian
Yan, Long
Quigley, Charles
Fickus, Edward
Wei, He
Chen, Linfeng
Dong, Faming
Araya, Susan
Liu, Jinlong
Hyten, David
Pantalone, Vincent
Nelson, Randall L.
author_sort Song, Qijian
collection PubMed
description The limited number of recombinant events in recombinant inbred lines suggests that for a biparental population with a limited number of recombinant inbred lines, it is unnecessary to genotype the lines with many markers. For genomic prediction and selection, previous studies have demonstrated that only 1000–2000 genome‐wide common markers across all lines/accessions are needed to reach maximum efficiency of genomic prediction in populations. Evaluation of too many markers will not only increase the cost but also generate redundant information. We developed a soybean (Glycine max) assay, BARCSoySNP6K, containing 6000 markers, which were carefully chosen from the SoySNP50K assay based on their position in the soybean genome and haplotype block, polymorphism among accessions and genotyping quality. The assay includes 5000 single nucleotide polymorphisms (SNPs) from euchromatic and 1000 from heterochromatic regions. The percentage of SNPs with minor allele frequency >0.10 was 95% and 91% in the euchromatic and heterochromatic regions, respectively. Analysis of progeny from two large families genotyped with SoySNP50K versus BARCSoySNP6K showed that the position of the common markers and number of unique bins along linkage maps were consistent based on the SNPs genotyped with the two assays; however, the rate of redundant markers was dramatically reduced with the BARCSoySNP6K. The BARCSoySNP6K assay is proven as an excellent tool for detecting quantitative trait loci, genomic selection and assessing genetic relationships. The assay is commercialized by Illumina Inc. and being used by soybean breeders and geneticists and the list of SNPs in the assay is an ideal resource for SNP genotyping by targeted amplicon sequencing.
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spelling pubmed-77021052020-12-14 Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research Song, Qijian Yan, Long Quigley, Charles Fickus, Edward Wei, He Chen, Linfeng Dong, Faming Araya, Susan Liu, Jinlong Hyten, David Pantalone, Vincent Nelson, Randall L. Plant J Resource The limited number of recombinant events in recombinant inbred lines suggests that for a biparental population with a limited number of recombinant inbred lines, it is unnecessary to genotype the lines with many markers. For genomic prediction and selection, previous studies have demonstrated that only 1000–2000 genome‐wide common markers across all lines/accessions are needed to reach maximum efficiency of genomic prediction in populations. Evaluation of too many markers will not only increase the cost but also generate redundant information. We developed a soybean (Glycine max) assay, BARCSoySNP6K, containing 6000 markers, which were carefully chosen from the SoySNP50K assay based on their position in the soybean genome and haplotype block, polymorphism among accessions and genotyping quality. The assay includes 5000 single nucleotide polymorphisms (SNPs) from euchromatic and 1000 from heterochromatic regions. The percentage of SNPs with minor allele frequency >0.10 was 95% and 91% in the euchromatic and heterochromatic regions, respectively. Analysis of progeny from two large families genotyped with SoySNP50K versus BARCSoySNP6K showed that the position of the common markers and number of unique bins along linkage maps were consistent based on the SNPs genotyped with the two assays; however, the rate of redundant markers was dramatically reduced with the BARCSoySNP6K. The BARCSoySNP6K assay is proven as an excellent tool for detecting quantitative trait loci, genomic selection and assessing genetic relationships. The assay is commercialized by Illumina Inc. and being used by soybean breeders and geneticists and the list of SNPs in the assay is an ideal resource for SNP genotyping by targeted amplicon sequencing. John Wiley and Sons Inc. 2020-09-23 2020-11 /pmc/articles/PMC7702105/ /pubmed/32772442 http://dx.doi.org/10.1111/tpj.14960 Text en © 2020 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Resource
Song, Qijian
Yan, Long
Quigley, Charles
Fickus, Edward
Wei, He
Chen, Linfeng
Dong, Faming
Araya, Susan
Liu, Jinlong
Hyten, David
Pantalone, Vincent
Nelson, Randall L.
Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research
title Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research
title_full Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research
title_fullStr Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research
title_full_unstemmed Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research
title_short Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research
title_sort soybean barcsoysnp6k: an assay for soybean genetics and breeding research
topic Resource
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7702105/
https://www.ncbi.nlm.nih.gov/pubmed/32772442
http://dx.doi.org/10.1111/tpj.14960
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