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ARS Home » Midwest Area » St. Paul, Minnesota » Plant Science Research » Research » Publications at this Location » Publication #417318
Research Project: Expanding Resiliency and Utility of Alfalfa in Agroecosystems

Location: Plant Science Research

Title: Development of universal DaRTag markers for alfalfa (Medicago sativa) and use in mapping resistance to Aphanomyces root rot

Author
item Samac, Deborah - Debby
item LIN, MENG - Cornell University
item ZHAO, DONGYAN - Cornell University
item TANG, XUEMEI - Cornell University
item Yu, Long-Xi
item BEIL, CRAIG - Cornell University
item SHEEHAN, MOIRA - Cornell University

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 8/26/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Alfalfa (Medicago sativa) is the engine that drives dairy and beef production in the United States and alfalfa is unparalleled for providing environmental services. However, developing genomic resources for alfalfa improvement has been slow due to its large complex genome and the heterogeneity within cultivars. Breeding Insight, a USDA-Agricultural Research Service and Cornell University collaboration, is supporting breeding projects that have not benefited from the genomics and informatics revolution of molecular breeding. Through this collaboration a 3,000 SNP marker panel using the DArTag technology was created from whole-genome skim sequencing of 40 elite alfalfa lines used in North America. DaRTag is an amplicon-based genotyping platform targeting known genetic variants that provides microhaplotypes in addition to the target SNP within 81 bp sequences. Markers were selected for their genome-wide distribution and location within genic regions and can be used on any alfalfa population for molecular breeding and genomic insight. The marker panel was used to identify QTLs for resistance to Aphanomyces root rot (ARR), one of the most important diseases of alfalfa in North America. Two races of the pathogen causing ARR, Aphanomyces euteiches, are distinguished by differential cultivars. Resistant and susceptible plants were identified from the commercial cultivar 53V52 and the check cultivar WAPH-5 and were used as parents to produce F1 mapping populations. Plants were phenotyped with several race 1 and race 2 strains. Race-specific resistance involves a hypersensitive response of individual epidermal or cortical cells upon zoospore penetration and is highly heritable, suggesting that resistance is conditioned by a small number of genes, most likely of the NBS-LRR resistance genes. Markers significantly associated with resistance to race 1 were identified on chromosome 1 from both populations while resistance to race 2 was identified on chromosome 2 or 4 depending on the parental germplasm. Transcript profiling was done to gain a better understanding of the compatible and incompatible interactions and mapped to the QTLs for resistance to identify candidate genes. Markers associated with race 2 resistance can be used to identify the resistance QTL in diverse germplasm and to follow introgression of the trait into elite parents to increase resistance to the disease. Identification of two different sources of race 2 resistance will enable breeders to stack genes to improve plant health and stand life. The use of DaRTag makers to map other agronomic traits and characterize crop genetic diversity will also be presented.