Genetic diversity of Iranian and some European grapes as revealed by nuclear and chloroplast microsatellite and SNP molecular markers

Genetic and chloroplast haplotype variations of 35 Iranian genotypes and 10 European grape cultivars were investigated using 9 nuclear simple sequence repeats (nSSRs), 4 chloroplast simple sequence repeats (cpSSRs) and 46 single nucleotide polymorphism (SNP) markers. In total, 83 alleles were detected at nine nSSRs, giving a mean of 15.66 alleles per locus and polymorphism information content (PIC) values ≥0.75 ranged from 0.75 to 0.90. For SNP markers, PIC values varied from 0.30 to 0.39 with an average of 0.34. Analysis of molecular variance revealed 97 and 93% of partitioned genetic diversity within populations using nSSRs and SNPs markers, respectively. Un-weighted neighbour-joining (NJ) cluster analysis grouped grapes into 10 and 9 major clusters using SSR and SNP markers, respectively. Synonyms and homonyms were identified among the Iranian genotypes. Close genetic relationship among Farkhi and Bidane-Sefid genotypes may probably propose a common ancestor and mutational evolution. Most European cultivars were differentiated from Iranian genotypes, however, clustering of some Iranian genotypes with European cultivars in the same clusters suggests that clonally propagated materials have probably been exchanged from the Middle East to West or vice versa. C and D chloroplast haplotypes were the most frequent within the Iranian genotypes, while A chloroplast haplotype was exclusively observed among European cultivars.本研究采用9个核简单序列重复（nuclear simple sequence repeats, nSSRs）标记、4个叶绿体简单序列重复（chloroplast simple sequence repeats, cpSSRs）标记以及46个单核苷酸多态性（single nucleotide polymorphism, SNP）标记，对35份伊朗葡萄基因型与10份欧洲葡萄栽培品种的遗传变异及叶绿体单倍型变异展开了分析。在9个nSSR位点中共检测到83个等位基因，平均每个位点包含15.66个等位基因，多态信息含量（polymorphism information content, PIC）值介于0.75至0.90之间，均不低于0.75。对于SNP标记，其PIC值分布区间为0.30至0.39，平均值为0.34。分子方差分析结果表明，利用nSSRs与SNP标记进行分析时，种群内遗传多样性分别占总遗传变异的97%与93%。采用不加权邻接法（Un-weighted neighbour-joining, NJ）进行聚类分析，基于SSR标记与SNP标记可分别将供试葡萄材料划分为10个与9个主要类群。研究团队在供试伊朗葡萄基因型中鉴定出了同物异名与同名异物现象。Farkhi基因型与Bidane-Sefid基因型之间存在紧密的遗传亲缘关系，这提示二者可能拥有共同祖先并经历了突变演化。多数欧洲葡萄栽培品种与伊朗基因型存在显著遗传分化，但部分伊朗基因型与欧洲栽培品种聚为同一类群，这表明无性繁殖的葡萄材料可能曾在中东与西欧之间双向交流。在供试伊朗基因型中，C、D型叶绿体单倍型最为常见，而A型叶绿体单倍型仅在欧洲栽培品种中被检测到。