Park Seoyeon, Park Ye-Ok, Park Younghoon
Department of Horticultural Science, Pusan National University, Miryang 50463, Republic of Korea.
Sweet Persimmon Research Institute, Gyeongsangnam-do Agricultural Research and Extension Services, Gimhae 50871, Republic of Korea.
Plants (Basel). 2023 May 24;12(11):2097. doi: 10.3390/plants12112097.
This study investigated the genetic diversity and population structure of a persimmon ( Thunb., 2n = 6x = 90) collection in South Korea by evaluating 9751 genome-wide single-nucleotide polymorphisms (SNPs) detected using genotyping-by-sequencing in 93 cultivars. The results of neighbor-joining clustering, principal component analysis, and STRUCTURE analysis based on SNPs indicated clear separation between cultivar groups (pollination-constant nonastringent (PCNA, 40 cultivars), pollination-constant astringent (PCA, 19), pollination-variant nonastringent (PVNA, 23), and the pollination-variant astringent type (PVA, 9)) based on the astringency types, while separation between PVA and PVNA-type cultivars was unclear. Population genetic diversity based on SNPs showed that the proportions of polymorphic SNPs within each group ranged from 99.01% (PVNA) to 94.08% (PVA), and the PVNA group exhibited the highest genetic diversity (He = 3.86 and uHe = 0.397). (fixation index) values were low ranging from -0.024 (PVA) to 0.176 (PCA) with an average of 0.089, indicating a deficiency of heterozygosity. Analysis of molecular variance (AMOVA) and st among cultivar groups indicated that variation within individuals was higher than that among the groups. Pairwise st values among the groups ranged from 0.01566 (between PVA and PVNA) to 0.09416 (between PCA and PCNA), indicating a low level of cultivar type differentiation. These findings highlight the potential application of biallelic SNPs in population genetics studies of allopolyploids species and provide valuable insights that may have significant implications for breeding and cultivar identification in persimmon.
本研究通过对93个韩国柿品种（柿属，2n = 6x = 90）进行基因分型测序，评估了9751个全基因组单核苷酸多态性（SNP），从而研究了其遗传多样性和群体结构。基于SNP的邻接聚类、主成分分析和STRUCTURE分析结果表明，根据涩味类型，品种组（授粉常数非涩味（PCNA，40个品种）、授粉常数涩味（PCA，19个）、授粉变异非涩味（PVNA，23个）和授粉变异涩味类型（PVA，9个））之间有明显分离，而PVA和PVNA类型品种之间的分离不明显。基于SNP的群体遗传多样性表明，每组内多态性SNP的比例从99.01%（PVNA）到94.08%（PVA）不等，PVNA组表现出最高的遗传多样性（He = 3.86，uHe = 0.397）。固定指数（F）值较低，范围从-0.024（PVA）到0.176（PCA），平均为0.089，表明杂合性不足。品种组间的分子方差分析（AMOVA）和Fst表明，个体内的变异高于组间变异。组间的成对Fst值范围从0.01566（PVA和PVNA之间）到0.09416（PCA和PCNA之间），表明品种类型分化程度较低。这些发现突出了双等位基因SNP在异源多倍体物种群体遗传学研究中的潜在应用，并提供了有价值的见解，可能对柿树的育种和品种鉴定具有重要意义。
