Characterisation of linkage disequilibrium patterns among intra-gene single-nucleotide polymorphisms in Vitis based on resequencing of 30 gene fragments

Background and Aims Linkage disequilibrium (LD) is an important tool in studies of genetics and evolution. In the cultivated species of Vitis vinifera, LD has been extensively surveyed; however, in other Vitis species, LD has not previously been reported. Patterns of LD in five populations of 48 Vitis species and 248 accessions were extensively characterised in this study. Methods and Results Patterns of LD were discerned using 6862 intra‐gene single‐nucleotide polymorphisms (SNPs) through resequencing 12.4 kb from 30 gene fragments. Most SNPs (99.9–100.0%) in Vitis presented LD associations within fragments. Similar contribution between linkage and recombination to LD was found in four of the five populations from estimation of the entire dataset. More contribution, however, from recombination to LD was observed in most of the single fragments. With moderate frequency, LD may be more stable than that with either low or high frequency. Mantel tests showed that most correlation coefficients (Rxy) were non‐significant between LD and physical distance (PD, bp); however, most significant Rxy had negative values, indicating that PD proximity may be an important contributor to LD. Conclusions Patterns of LD differed extensively among the five populations, among gene fragments and among regions within fragments. Most SNPs were depicted near each other in the principal coordinates analysis plots, suggesting that these SNPs were associated with each other. Both advantages and disadvantages of LD association should be properly evaluated for genetic conservation and grape breeding. Significance of the Study This research not only greatly adds to our knowledge of LD association and other genetic features in the genus of Vitis, but also provides valuable suggestions for genetic conservation and grape breeding.