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Soybean Community Panel

We offer the Soybean Community panel for full-service, PlexSeq  genotyping to be used as a tool to conduct molecular breeding and production quality control tests.

 

The Soybean Community panel, which consists of 1327 SNPs, was developed by a consortium of professional researchers and breeders from the soybean community and are actively working on an update. 

 We also offer the Soybean Community panel  to the public at a discounted price and expedited turnaround through the AgriPlex Connect program.

* The following is derived from the White Paper

Introduction

The advent of targeted, Next Generation Sequencing (NGS) technology and the PlexSeq platform provides an efficient method for mid-density SNP genotyping. We introduce the 1327 SNP Soybean Community Panel, which is the combined effort with AgriPlex Genomics and the community soybean consortium to develop an informative, high-throughput, and cost-effective mid-density genotyping solution for applied molecular breeding programs and seed production Quality Assurance (QA)

The Soybean Community Panel

The Community soy 1K SNP panel at AgriPlex Genomics is made of 1327 SNPs and consists of two parts: Genomic Screen and Trait Markers.  

The Genomic Screen consists of 1242 markers. Originally, the SNPs were part of the SoySNP50K array (Song et al. 2013). Initial reduction of the array resulted in the BARCSoySNP6K (Song et al. 2020), which were reduced further to the BARCSoySNP3K. The present selection out of the 3k SNP array was made based on the following criteria: 

  • Reduce the number of SNPs in the same large linkage blocks in the North American elite population.

  • SNP selection is based upon even spacing between SNPs in the segments of the genome outside of the major haplotype blocks.

  • Location of SNPs in euchromatic vs. heterochromatic regions of the genome 

  • Minor allele frequency (MAF). The average MAF of the SNPs among 562 elites was 0.36, and the minimum allowed was MAF > 0.10. The average MAF in the Southern and Northern elites was 0.29 and 0.33, respectively.

The number of SNPs per chromosome ranges from 32 to 92 and averages at 61 SNPs per chromosome. The average distance between adjacent SNPs is 787.9 KB (Table 1). 

The Trait Markers portion of the panel is made of 84 markers that are either embedded within gene sequences of traits of interest or associated with them. Currently, the panel includes markers for diverse phenotypic characteristics (Table 2). These characteristics include:

  • Growth habit and morphological features

  • Biochemical qualities such as seed composition

  • Environmental tolerances

  • Disease resistance to life cycle attributes

The soy research and breeding community have contributed to this collection of trait markers (Appendix A). The effort to build this collection should be ongoing, enriching the panel with additional trait markers as new discoveries are made.

soybean chart sell sheet march 2023.png
Soybean trait chart (1).png

Table 1: Genomic Screen: SNPs numbers and average spacing (Mbp) along the soy chromosomes

Table 2: Selected traits, genes, and associated number of markers in the panel

The Soybean Community SNP Panel serves as a useful tool for conducting genomic selection, genomic prediction, and germplasm identification.

For the full white paper and list of References, click here.

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