Genetic structure analysis of 85 kiwifruit varieties (lines) and wild relatives by SCoT molecular markers

Abstract: 【Objective】Kiwifruit, as a dioecy plant, is a kind of wild fruit tree, native to China. It was introduced into New Zealand in the early 20th century. Frankly speaking, kiwifruit has received attention in the worldwide now. It has been reported that more than 100 varieties were bred since the 1970s in China, most of which were made from seedling breeding of wild relatives, and few varieties were produced by sexual crossbreeding. The heterosis of interspecific or subspecies was not well utilized, which resulted in the serious homogeneity between varieties. In our previous research, we found that the polymorphism of start codon targeted polymorphism (SCoT) markers was higher than that of other second generation DNA molecular markers. Qinba region is the main distribution area of Actinidia chinensis var. chinensis and A. chinensis var. deliciosa that are the two most valuable varieties of A. chinensis, which has seriously restricted the exploration and utilization of excellent kiwifruit germplasm resources due to lack of comprehensive research on kiwifruit in this region. The population structure analysis can provide the basis for protection and development of kiwifruit resources.【Methods】85 kiwifruit samples collected from Qinba region were analyzed using 20 SCoT markers to access genetic diversity and population structure.【Results】In this study, a total of 108 alleles were obtained, with an average of 5.4 loci per primer and that of 4.6 polymorphic loci, and the percentage of polymorphic bands (PPB) ranged from 66.67% to 100%, with an average of 83.77%. And the polymorphism information content (PIC) ranged from 0.46 to 0.96, with an average of 0.70. Among these, SCoT16, 25, 30, 32, 33, and SCoT 34 possessed the highest PPB in 20 SCoT markers. SCoT16 showed the highest PIC. Specific primers were found that may be used to identify six samples. The 85 kiwifruit samples could be divided into two subpopulations based on Beiyes algorithm, and the results from K = 2 to K = 5 revealed the occurrence of gene introgression among 85 samples, accounting for approximately 83.53% of the observed variations (calculated by K=2). And the Beiyes results were inconsistent with the unweighted pair-group method with arithmetic means (UPGMA) algorithm clustering and principal component analyses (PCA). The lowest genetic similarity coefficient appeared between Qihong ♀ N and wild 22 ♂ A, while that of the highest was found between Qihong2 ♂ A and Qihong5 ♂ A by UPGMA clustering, in which the average number of genetic similarity coefficient of 85 samples were 0.74 ranging from 0.54 to 0.94, and the density distribustion of genetic similarity coefficient of 85 samples was in 0.75~0.78, accounting for 31.83%. The 36 cultivars (lines) planted in production were 0.74 ranging from 0.63 to 0.90, the 46 female samples were 0.74 ranging from 0.57 to 0.90, the 36 male samples were 0.77 ranging from 0.60 to 0.94, and the 20 wild relatives were 0.73 ranging from 0.56 to 0.91. The first three principal components accounted for 13.24%, 7.68% and 0.65% of the population variation, respectively. The 85 samples were not grouped clearly, indicating that there was no significant difference in the principal components among 85 samples【. Conclusion】All three clustering methods have the trend of clustering firstly by subspecies rather than gender. The population genetic structure analyzed by Beiyes algorithm is closer to reality than UPGMA and PC analysis, which can be visualized of homogeneity or heterogeneous level of each sample. The phenomenon that different varieties may have the same name, or one variety may have two and even more names, exists. A higher level of genetic background was observed in 85 kiwifruit varieties (lines), in which the genetic differences among wild related species were larger, the six wild resources including Wild17 ♀ A, Wild22 ♂ A, Wild16 ♀ A, Wild18 ♀ A, Wild21 ♂ A and Wild19？can be used as parents for breeding new varieties or improving cultivated varieties. And the genetic differences among female resources are more abundant than those among male resources. The simple genetic basis occurs among commercial male plant fields as a source of pollen. Several varieties used in production have closer relationship, some germplasm resources of wild relatives are far from being developed and utilized, which are expected to be used as raw materials for breeding new varieties.