Alfalfa

Current panel name: Alfalfa DArTag 3K BI Cornell University (1.0)

Panel name for soft release: Alfalfa_DArTag_BI_Cornell_University (1.0)

Version description: (1.0) original

Availability: Yes

Green and healthy alfalfa plants growing in the field

Description: Alfalfa panel version 1 for 3,000 marker loci developed by Breeding Insight at Cornell in collaboration with DArT and funded by USDA-ARS for public use. DArTag assay uses custom designed oligos to amplify targeted SNPs, and their flanking sequences, prior to Next Generation Sequencing (NGS). The sequenced amplicons are demultiplexed and targeted SNPs/haplotypes are analyzed using DArT P/L’s proprietary pipeline The marker loci were selected from a diverse set of 40 cultivated alfalfa parents and founders from North American breeding programs.  The panel is suitable for genotyping tetraploid alfalfa for breeding decisions and selection.  Usage of the panel on diploid Medicago was tested and resulted in higher missing data and fewer polymorphic data points.  Usage of the panel outside of Medicago sativa is likely to result in higher missing data and fewer data points.  Access to the panel can be found on DArT’s website (https://www.diversityarrays.com/services/targeted-genotying/).

Results and Data Sharing: DArT offers multiple data output formats. Users are encouraged to work with DArT to ensure the data type they desire is provided. Users are also strongly encouraged to request the Missing Allele Discovery Counts (MADC) file from DArT when placing orders. This file contains the read counts of each 81-bp michrohaplotype detected in each sample and at each locus. Breeding Insight requests that the MADC file and sample metadata also be sent to bi-genotyping@cornell.edu to be added to the public microhaplotype database for fixed allele naming and public data sharing. Proprietary sample metadata can be privatized in the database for IP protection.

Citation: Zhao, D., Mejia-Guerra, K., Mollinari, M., Samac, D. A., Irish, B. M., Heller-Uszynska, K., Beil, C. T., Sheehan, M. J. (2023). A public mid-density genotyping platform for alfalfa (Medicago sativa L.). Genetic Resources 4 (8), 55–63. doi: 10.46265/genresj.EMOR6509.

**Disclaimer: These materials are based upon work supported by the U.S. Department of Agriculture, under agreement numbers [8062-21000-043-004-A, 8062-21000-052-002-A, and 8062-21000-052-003-A). Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of the U.S. Department of Agriculture. In addition, any reference to specific brands or types of products or services does not constitute or imply an endorsement by the U.S. Department of Agriculture for those products or services.**