Genetic Diversity Analysis and Construction of a Core Germplasm Resource Bank of Xinjiang’s Indigenous Cultivated Grapes

Shiqing Liu, Jiancheng Wang, Xuerong Li, Xianhang Wang, Xiyong Wang, Haixia Zhong, Ilham Aibibul, Feng Sun, Hongbin Li and Wei Shi ()
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Shiqing Liu: College of Life Sciences, Shihezi University, Shihezi 832003, China
Jiancheng Wang: State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
Xuerong Li: State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
Xianhang Wang: College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling 712100, China
Xiyong Wang: State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
Haixia Zhong: Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
Ilham Aibibul: People’s Government of Lianmuqin Town, Shanshan County, Shanshan 838200, China
Feng Sun: People’s Government of Lianmuqin Town, Shanshan County, Shanshan 838200, China
Hongbin Li: College of Life Sciences, Shihezi University, Shihezi 832003, China
Wei Shi: College of Life Sciences, Shihezi University, Shihezi 832003, China

Agriculture, 2025, vol. 15, issue 8, 1-20

Abstract: This study systematically investigated the genetic characteristics and germplasm conservation strategies of Xinjiang Thompson Seedless grapes ( Vitis vinifera Thompson Seedless) and Munake grapes ( Vitis vinifera L. cv. Munake) using SSR molecular markers and whole-genome resequencing technology. A genetic diversity analysis of 165 Thompson Seedless accessions with 16 SSR markers identified 442 alleles (27.63 alleles per locus on average), with the expected heterozygosity (He = 0.76) and observed heterozygosity (Ho = 0.83) indicating moderate-to-low genetic diversity. A molecular variance analysis (AMOVA) further revealed that 96% of the genetic variation originated within populations, with minimal inter-population differentiation (Fst = 0.04). Phylogenetic reconstruction using SSR markers demonstrated significant genealogical associations between the two cultivars, supporting the hypothesis that Thompson Seedless may have originated from a domesticated lineage of Munake. The selected SSR markers exhibited high discriminatory power (PIC = 0.92), enabling the precise differentiation of accessions with closely related genetic backgrounds. Whole-genome resequencing identified 20,074,046 and 69,214,080 high-quality SNPs in 100 Thompson Seedless and 141 Munake accessions, respectively. Core germplasm banks were subsequently established: the Thompson Seedless core collection (25 accessions) captured 94% of genetic variation, reflecting genetic homogenization driven by intensive clonal cultivation, while the Munake core collection (42 accessions) retained 95% of allelic diversity and resolved regional synonym issues through highly polymorphic SNP markers. A comparative analysis revealed that Munake maintains higher genetic diversity due to natural gene flow, whereas Thompson Seedless faces heightened risks of genetic erosion from prolonged asexual propagation. These findings provide a theoretical foundation and technical framework for precise conservation, varietal improvement, and sustainable utilization of grape germplasm resources in Xinjiang.

Keywords: Thompson Seedless; Munake grapes; whole-genome resequencing; genetic diversity; SSR; SNP; germplasm resource safety; intensive cultivation (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2025
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