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Article|18 Jan 2022|OPEN
Chromosome-level genome sequence assembly and genome-wide association study of Muscadinia rotundifolia reveal the genetics of 12 berry-related traits
Minkyu Park1 , Daniel Vera2 , Devaiah Kambrianda3 , Pranavkumar Gajjar1 , Lance Cadle-Davidson4 , Violeta Tsolova1 and Islam El-Sharkawy,1 ,
1Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, 6361 Mahan Dr., Tallahassee, FL 32308, USA
2Silico LLC, 23 Essex Street #761119, Melrose, MA 02176, USA
3Plant and Soil Sciences, Southern University Agricultural Research and Extension Center, 181 B. A. Little Dr., Baton Rouge, LA 70813, USA
4USDA-ARS, Grape Genetics Research Unit, 630 West W North St., Geneva, NY, 14456, USA
*Corresponding author. E-mail: islam.elsharkawy@famu.edu

Horticulture Research 9,
Article number: uhab011 (2022)
doi: https://doi.org/10.1093/hr/uhab011
Views: 189

Received: 25 Jun 2021
Revised: 01 Sep 2021
Accepted: 25 Sep 2021
Published online: 18 Jan 2022

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 Muscadinia rotundifolia cv. Noble. 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 but highly conserved gene synteny. A genome-wide association study of 12 Muscadinia berry-related traits was performed among 356 individuals from breeding populations of M. rotundifolia. For the transferability of markers between Euvitis and Muscadinia, we used 2000 core genome rhAmpSeq markers developed to allow marker transferability across Euvitis species. A total of 1599 (80%) rhAmpSeq markers returned data in Muscadinia. From the GWAS analyses, we identified a total of 52 quantitative trait nucleotides (QTNs) associated with the 12 berry-related traits. The transferable markers enabled the direct comparison of the QTNs with previously reported results. The whole-genome sequences along with the GWAS results provide a new basis for the extensive study of Muscadinia species.