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Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research

文献类型： 外文期刊

作者： Song, Qijian 1 ; Yan, Long 2 ; Quigley, Charles 1 ; Fickus, Edward 1 ; Wei, He 3 ; Chen, Linfeng 1 ; Dong, Faming 1 ; Ara 1 ;

作者机构： 1.USDA ARS, Soybean Genom & Improvement Lab, Beltsville, MD 20705 USA

2.Hebei Acad Agr & Forestry Sci, Shijiazhuang Branch, Ctr Natl Ctr Soybean Improvement, Key Lab Crop Genet & Breeding,Inst Cereal & Oil C, Shijiazhuang, Hebei, Peoples R China

3.Henan Acad Agr Sci, Inst Ind Crops, Zhengzhou, Henan, Peoples R China

4.Univ Nebraska, Dept Agron & Hort, Lincoln, NE USA

5.Univ Tennessee, Dept Plant Sci, Knoxville, TN USA

6.Univ Illinois, Soybean Maize Germplasm Pathol & Genet Res Unit, USDA ARS, Urbana, IL 61801 USA

7.Univ Illinois, Dept Crop Sci, USDA ARS, Urbana, IL 61801 USA

关键词： soybean (Glycine max); single nucleotide polymorphisms; SNP assay; BARCSoySNP6K beadchips; haplotype block; QTL mapping; genomic selection; genomic prediction; breeding selection

期刊名称：PLANT JOURNAL （ 影响因子：6.417； 五年影响因子：7.627 ）

ISSN： 0960-7412

年卷期： 2020 年 104 卷 3 期

页码：

收录情况： SCI

摘要： 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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