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ARS Home » Northeast Area » Geneva, New York » Grape Genetics Research Unit (GGRU) » Research » Publications at this Location » Publication #385637

Research Project: Grapevine Genetics, Genomics and Molecular Breeding for Disease Resistance, Abiotic Stress Tolerance, and Improved Fruit Quality

Location: Grape Genetics Research Unit (GGRU)

Title: Chromosome-level genome sequence assembly and genome-wide association study of Vitis rotundifolia reveal the genetics for 12 berry-related traits

item PARK, MINKYU - Florida A & M University
item VERA, DANIEL - Silico, Llc
item KAMBRIANDA, DEVAIAH - Southern University
item GAJJAR, PRANAVKUMAR - Florida A & M University
item Cadle-Davidson, Lance
item TSOLOVA, VIOLETA - Florida A & M University
item EL-SHARKAWY, ISLAM - Florida A & M University

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/25/2021
Publication Date: 1/18/2022
Citation: Park, M., Vera, D., Kambrianda, D., Gajjar, P., Cadle Davidson, L.E., Tsolova, V., El-Sharkawy, I. 2022. Chromosome-level genome sequence assembly and genome-wide association study of Vitis rotundifolia reveal the genetics for 12 berry-related traits. Horticulture Research.

Interpretive Summary: In addition to bunch grapes that are widely known for wine, juice, raisins, and table grapes, the Vitis genus includes muscadine grapes, which remain a small market in the Southeastern U.S. We sequenced the muscadine genome and identified 20 chromosomes and 26,394 genes. The muscadine genome is smaller than bunch grape genomes, but DNA markers designed to work across bunch grapes also worked well in muscadines. We tested for regions in the genome that control fruit traits across 356 muscadine vines and found 56 regions associated with the 12 fruit traits. The DNA markers enabled direct comparison of previously reported results in bunch grapes and muscadines. These results and resources provide new opportunities for the study and genetic improvement of muscadine grapes.

Technical Abstract: Vitis has two subgenera: Euvitis, which includes commercially important Vitis vinifera and interspecific hybrid cultivars, and Muscadinia. Of note, the market for Muscadinia grapes remains small, and only Muscadinia rotundifolia is cultivated as a commercial crop. To establish a basis for the study of Muscadinia species, we generated chromosome-level whole-genome sequences of M. rotundifolia. A total of 393.8 Mb of sequences were assembled from 20 haploid chromosomes, and 26,394 coding genes were identified from the sequences. Comparative analysis with the genome sequence of V. vinifera revealed a smaller size of the M. rotundifolia genome due to the differential activity of LTR retrotransposons. A genome-wide association study of 12 Muscadinia berry-related traits was performed among 356 individuals from parental and breeding populations of V. rotundifolia. For the transferability of markers between Euvitis and Muscadinia, we used 2,000 core genome rhAmpSeq markers developed to allow marker transferability across Euvitis species. A total of 1,599 (80%) rhAmpSeq markers returned data in Muscadinia. From the GWAS analyses, we identified a total of 56 loci associated with the 12 berry-related traits. The transferable markers enabled the direct comparison of the associated markers with previously reported results. The whole-genome sequences along with the GWAS results provide a new basis for the extensive study of Muscadinia species.