b'PARTNER CONTENTNew mid-density SNP panel developed by the soy breeding community and AgriPlex GenomicsBy: Beni Kaufman, Director of Operations, AgriPlex GenomicsA griPlex Genomics, together with the soy breeding commu-nity, is pleased to introduce the development of a mid-density single nucleotide polymorphic (SNP) panel for soy, the worlds leading oilseed crop. Molecular marker technologies have evolved over the past 80 years for interrogating genetic variation. SNPs - single nucleotide changes that are heritable codominant and distributed relatively frequently throughout eukaryotic genomescan be used as mo-lecular markers for accurate, early selection of individuals of in-terest in molecular breeding, shortening the number of selection cycles required, reducing new lines time to market, and lowering overall breeding costs. Several high-density soy SNP chip arrays have been developed and commercialized over the years that can interrogate many SNPs per DNA sample. However, the advent of imputing tech-niques brought a need for informative, high-throughput, and cost-effective mid-density genotyping solutions for applied molecular breeding programs and seed production Quality Assurance.AgriPlex Genomics and more than 20 soy researchers and breeders worked together to develop the Community soy 1K SNPThe soy 1K SNP panel was made possible by the combined panel. The panel includes 1213 genomic screen markers takenefforts of the soy community and the multiplexing of AgriPlex from the existing BarCoSoySNP3K array developed through ongo- Genomics PlexSeq platform. PlexSeq saves critical time and ing work by Song (et al) over the last decade. The specific markersexpenses thanks to multiple efficiencies:selected for the soy mid-density panel were chosen: PlexSeq offers the PlexForm artificial intelligence multiplex- t o reduce the number of SNPs in the same large linkageing algorithm, which can design all possible primers around any blocks in the North American elite population, SNP of interest and identifies optimal sets of primers that can be to be evenly spaced in the segments of the genome outside ofmixed in just one PCR amplification reaction. Once the amplifica-the major haplotype blocks, tions are complete, the amplicon libraries produced from eachto be located in euchromatic regions of the genome,sample are equivalent in concentration and do not require anyby minor allele frequency (MAF). The average MAF of theadditional equalization steps. A mixture of all the libraries is sub-SNPs among 562 elites was 0.36; the minimum allowed wasjected to one bead clean-up and are loaded onto the sequencer. MAF0.10. The average MAF in the Southern and NorthernThe PlexSeq process requires minute quantities of crude DNA elites was 0.29 and 0.33, respectively. isolatable from a variety of tissues. The process is amenable to au-The number of SNPs per chromosome ranges from 32 to 92 andtomation; all steps can be conducted on liquid handlers and high-averages 61. The average distance between adjacent SNPs is 788 KB. capacity thermocyclers, enabling high throughput genotyping. Additionally, the panel includes 73 trait associated mark- AgriPlex Genomics vast collection of barcode combinations ers that are either embedded within gene sequences of traits ofpermits simultaneous sequencing of up to 55,000 individuals, interest or associated with them. This collection of trait markerslimited only by the sequencers capacity. Because the panel is a includes markers for diverse phenotypic characteristics: 21 mark- collection of PCR primers untethered to a surface, the markers in ers for biochemical composition (seed antinutritional, oil com- the panel are dynamically alterable, and customizable.position, carbohydrate and protein); 19 markers for agronomicsAgriPlex intends the soy SNP panel to be dynamic, with its ge-(pod shatter, stem termination, seed coat color, flower color, hardnomic screen and trait markers periodically updated to maximize seed, and pubescence color); 7 markers for biotic/abiotic stressrelevance and optimize its genomic selection, genomic predic-responses (salt tolerance, aphid resistance and herbicide resis- tion, and germplasm identification utility.tance), 9 markers for flowering time/maturity, and 17 markers forThe 1K soy SNP panel is available from AgriPlex Genomics as plant health (IDC tolerance, SCN resistance).an off-site service or on-site kit.JANUARY 2022SEEDWORLD.COM /15'