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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #414842
Research Project: Championing Improvement of Sorghum and Other Agriculturally Important Species through Data Stewardship and Functional Dissection of Complex Traits

Location: Plant, Soil and Nutrition Research

Title: Sorghum 2.4K SNP panel: a cost-effective, high sample throughput genotyping resource for US sorghum breeding and research community

Author
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item Gladman, Nicholas
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item Ware, Doreen

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/2/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: At SICNA 2022, the Crop Germplasm Committee (CGC) recognized the need for a domestic sorghum SNP panel. SorghumBase is pleased to share updates on its recent breeding initiatives to support the SNP panel for the US sorghum community for molecular breeding applications including marker assisted selection, diversity studies, and genetic profiling. To support this effort, SorghumBase worked with CGC to help establish the CGC Genotyping Panel working group in August 2022 with members from academia, government, and industry. In coordination with the working group, SorghumBase conducted surveys targeting the community genotyping service needs and hosted presentations focused on offerings by various commercial genotyping service providers. After the confirmation of the target genotyping platform PlexSeq (Agriplex Genomics) in coordination with the working group, SorghumBase prepared a list of ~3500 candidate SNP markers based on existing panels such as DArTag panel for CGIAR (Consultative Group on International Agricultural Research), community KASP (Kompetitive Allele Specific PCR) panel, QC (quality check) markers, and other markers associated with traits of interest for the breeders. Given its diversity, the Sorghum Association Panel (SAP) was used for the validation stage of the CMP panel design and development. SAP germplasm was provided by the USDA-ARS GRIN (Germplasm Resources Information Network). The community was invited to contribute their germplasm for genotyping that included landraces, elite breeding lines, and RILs (recombinant inbred lines). More than 15 organizations including universities, seed companies and multiple USDA sites participated by submitting over 25 94-well leaf tissue plates as per the sample preparation protocols provided by the service provider. After multiple rounds of genotyping tests and validations, ~2400 markers were shortlisted and rsIDs were assigned to support interoperability across panels and breeding resources. SorghumBase aims to host the public germplasms including SAP and select landraces based on this panel in near future.