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Research Project: Genetic Improvement and Cropping Systems of Alfalfa for Livestock Utilization, Environmental Protection and Soil Health

Location: Plant Science Research

Title: Development of a mid-density genotyping platform for alfalfa and its application in a drought tolerance breeding program

item SANDERCOCK, ALEXANDER - Cornell University
item SAPKOTA, MANOJ - Cornell University
item MEDINA, CESAR - University Of Minnesota
item Xu, Zhanyou
item Yu, Long-Xi
item ZHAO, DONGYAN - Cornell University
item MEJIA-GUERRA, KATHERINE - Cornell University
item MOLLINARI, MARCELO - North Carolina State University
item Samac, Deborah - Debby
item Irish, Brian
item HELLER-USZYNSKA, KASIA - Cornell University
item BEIL, CRAIG - Cornell University
item SHEEHAN, MOIRA - Cornell University

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 10/29/2023
Publication Date: 1/12/2024
Citation: Sandercock, A.M., Sapkota, M., Medina, C.M., Xu, Z., Yu, L., Zhao, D., Mejia-Guerra, K., Mollinari, M., Samac, D.A., Irish, B.M., Heller-Uszynska, K., Beil, C.T., Sheehan, M.J. 2024. Development of a mid-density genotyping platform for alfalfa and its application in a drought tolerance breeding program. Plant and Animal Genome Conference. San Diego, California. January 12-17, 2024.

Interpretive Summary:

Technical Abstract: Molecular breeding techniques have revolutionized breeding decisions in major crops like tomato and maize, yet many specialty crop species lack accessible genetic resources. The development of genetic resources, such as openly accessible marker panels, can improve breeding programs through lowering costs and time necessary to make selection decisions. Alfalfa (Medicago sativa L.) is a globally important perennial forage crop that is pivotal in beef and dairy production, yet breeding is still largely relying on “breeders’ eyes”. To improve breeding and assist breeders in adopting modern molecular techniques, Breeding Insight (BI) developed a 3K DArTag marker panel from whole-genome skim sequencing of 40 elite alfalfa lines used in North America. DArTag markers were selected for their genome-wide distribution and location within genic regions. The marker panel was then tested through the genotyping of an F1 and a backcross population – leading to the creation of a combined genetic map of 1,792 markers. Finally, we performed DArTag sequencing for 436 alfalfa genotypes within a breeding population to identify genomic regions associated with drought tolerance. Using GWASpoly and trait data for 16 harvest yields (May-August, 2020-2023), we discovered 24 quantitative trait loci (QTL) associated with drought tolerance. Genomic prediction was performed using RRBLUP, GBLUP and WGBLUP methods. RRBLUP and GBLUP provided moderate and comparable predictive abilities through ten-fold cross validation. WGBLUP integrated SNPs allocated within the above mentioned 24 QTL regions and provided increased predictive abilities. Thus, the open accessibility of this genetic resource marks a significant contribution to existing alfalfa breeding programs and is suited to benefit the global alfalfa breeding community.