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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: Fast and effective genotyping of alfalfa made possible using a mid-density genotyping platform

item ZHAO, DONGYAN - Cornell University
item LIN, MENG - Cornell University
item MEJIA-GUERRA, KATHERINE - Cornell University
item Samac, Deborah - Debby
item BEIL, CRAIG - Cornell University
item SHEEHAN, MOIRA - Cornell University

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 12/5/2022
Publication Date: 1/13/2023
Citation: Zhao, D., Lin, M., Mejia-Guerra, K., Samac, D.A., Beil, C., Sheehan, M. 2023. Fast and effective genotyping of alfalfa made possible using a mid-density genotyping platform. Plant and Animal Genome Conference. January 13-18, 2023. San Diego, California.

Interpretive Summary:

Technical Abstract: Genomics-assisted breeding in alfalfa has not been utilized due to the lack of a cost-effective genotyping platform. Breeding Insight (BI), a U.S. Department of Agriculture (USDA) initiative, was launched in 2018 to make high-tech breeding a reality for specialty crop and animal breeders, including alfalfa. A 3K marker panel using the DArTag technology ( was created by BI from skim-sequencing of a diversity panel of 40 alfalfa accessions, with a focus on elite breeding and stress-resistant lines commonly used in North America. The DArTag marker panel was validated using a bi-parental population, a backcross population, and a diverse set of elite lines and extant Medicago species. As expected, the missing data rate was the lowest among the cultivated alfalfa accessions. Among the 356 Medicago sativa accessions, on average 300 (10%) markers of the 3K marker panel produced <10 reads. The extant Medicago species had an average of 1,157 (39%) markers having less than 10 reads, about three times higher than the cultivated alfalfa accessions. Using this marker panel, eight linkage groups were constructed for the alfalfa bi-parental and backcross populations. Moreover, a QTL study identified the same genetic hotspots for Aphanomyces root rot resistance as previously discovered by a genotyping-by-sequencing method in the same bi-parental population. One advantage of the DArTag genotyping is that it generates a short stretch of sequence around the targeted SNP markers, which often contains additional nucleotide polymorphisms, including SNPs and indels. Haplotypes constructed from the target SNPs and additional sequence variations are better representations of genotypes in alfalfa since there are four identical copies of each chromosome. To date, BI has supported genotyping of over 4,000 samples from USDA alfalfa breeders and will genotype >7,000 more samples using the DArTag panel in the coming year, which will cover most of the alfalfa germplasm in U.S. breeding programs. The DArTag panel and these genotyping data will be valuable resources for accelerating alfalfa breeding by enabling parental and progeny genotyping, genomic prediction, QTL mapping, and GWAS.