Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research

Abstract

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 BARC-SoySNP6K 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.

Genome-wide association study and genomic selection for yield and related traits in soybean

“…A 10 kb-genomic region spanning a significant SNP was used for candidate gene search using the G. max Williams 82.a2 reference in Soybase (https://www.soybase.org/) [34]. The SNPs associated with the combined data over three years for maturity date, plant height, seed weight, and yield were used for candidate gene discovery.…”

The Soybean High Density ‘Forrest’ by ‘Williams 82’ SNP-Based Genetic Linkage Map Identifies QTL and Candidate Genes for Seed Isoflavone Content

“…DNA concentration was quantified with a spectrophotometer (NanoDrop Technologies Inc., Centreville, DE, USA) and then normalized at 50 ng/μL for genotyping. SNP genotyping was performed in the Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA, using the Illumina Infinium SoySNP6K BeadChips (Illumina, Inc. San Diego, CA, USA) as previously described [53]. Subsequently, SNP alleles were called using GenomeStudio Genotyping Module 2.0 (Illumina, Inc. San Diego, CA).…”

Dissection The Practical Soybean Breeding Pipeline By Developing High Throughput Functional Array ZDX1

“…Here, we found that sampling SNPs located within genic regions was more informative than sampling SNPs from intergenic or random regions, and therefore marker effects do not need to be considered for each different population. Indeed, sampling SNPs from genic regions can ensure or even signi cantly improve the accuracy of prediction and reduce sequencing costs (Song et al 2020). In addition, expanding the training group can also improve the accuracy of predictions (Hao et al 2019).…”

“…Despite low SNP density, previously developed soybean arrays have been used in diversity analysis, genetic mapping, and association analysis, etc. (Shen et al 2005;Song 2014; Song et al 2020;Wang et al 2018b). More recently, high density soybean arrays have been successively developed.…”