Development, validation and genetic analysis of a large soybean SNP genotyping array

Abstract

Cultivated soybean (Glycine max) suffers from a narrow germplasm relative to other crop species, probably because of under-use of wild soybean (Glycine soja) as a breeding resource. Use of a single nucleotide polymorphism (SNP) genotyping array is a promising method for dissecting cultivated and wild germplasms to identify important adaptive genes through high-density genetic mapping and genome-wide association studies. Here we describe a large soybean SNP array for use in diversity analyses, linkage mapping and genome-wide association analyses. More than four million high-quality SNPs identified from high-depth genome re-sequencing of 16 soybean accessions and low-depth genome re-sequencing of 31 soybean accessions were used to select 180,961 SNPs for creation of the Axiom(®) SoyaSNP array. Validation analysis for a set of 222 diverse soybean lines showed that 170,223 markers were of good quality for genotyping. Phylogenetic and allele frequency analyses of the validation set data indicated that accessions showing an intermediate morphology between cultivated and wild soybeans collected in Korea were natural hybrids. More than 90 unanchored scaffolds in the current soybean reference sequence were assigned to chromosomes using this array. Finally, dense average spacing and preferential distribution of the SNPs in gene-rich chromosomal regions suggest that this array may be suitable for genome-wide association studies of soybean germplasm. Taken together, these results suggest that use of this array may be a powerful method for soybean genetic analyses relating to many aspects of soybean breeding.

Transcript Polymorphism Rates in Soybean Seed Tissue Are Increased in a Single Transformant ofGlycine max

“…This is where gene density is the highest, which has been illustrated previously by several works conducted on soybean polymorphism rates [36, 38, 47]. Our snpEff dataset summaries available in the Supporting Data of this manuscript show the same distribution pattern, with no significant alterations of SNP rates between biological replicates of progeny.…”

The Current Status of the Soybean-Soybean Mosaic Virus (SMV) Pathosystem

“…Marker assisted selection (MAS) has become very useful in the effort of tagging genes for SMV resistance. Single nucleotide polymorphism (SNP) is a powerful tool in genome mapping, association studies, and cloning of important genes (Clevenger et al, 2015) and the increasingly saturated SNPs are being established in soybean (Wu et al, 2010; Lee et al, 2015). With all these tools and resources available, pyramiding multiple SMV resistance genes in elite soybean cultivars to generate durable resistance with broad spectrum is more realistic than ever.…”

Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy

“…These infrastructure networks enable access to the necessary tools for phenotyping, in particular robot-assisted image capture (Cooper et al, 2009;Fiorani and Schurr, 2013), statistical designs and models for extracting relevant physiological variables from raw data (Cabrera-Bosquet et al, 2016), and specialized information systems managing large datasets originating from phenotyping experiments (Tardieu et al, 2017). GrowScreen-PaGe is a non-invasive, high-throughput phenotyping system developed at the Institute of Biosciences Accelerating genetic gains in legumes | 3295 (Lee et al, 2015) • 286 (14 wild, 153 landraces and 119 elite; Zhou et al, 2015b) • Illumina 384 SNP VeraCode assays (Lee et al, 2015) • NJAU 355 K SoySNP array • Illumina Infinium SoySNP6K…”

“…To overcome these constraints several high-throughput SNP genotyping platforms, such as Veracode assays, Illumina GoldenGate assays, Infinium chips and Axiom arrays, are now available, which not only increase the precision of SNP calling but also enable genotyping of larger populations at reduced cost (Table 1). Axiom arrays with >50K SNPs with uniform genome coverage were developed and are being used for germplasm characterization, trait mapping and molecular breeding in chickpea (Roorkiwal et al, 2017), pigeonpea (ICRISAT unpublished data), groundnut (Pandey et al, 2017a) and soybean (Lee et al, 2015; Table 1). …”