Analysis of genetic diversity and population structure of pear germplasm resources in Guangxi

Abstract:【Objective】Pear, one of the most economically important temperate fruit trees, belongs to the genus Pyrus. China is one of the origin centers of Pyrus plants with a wide range of germplasm resources and has a long history of cultivation. As one of the important producing areas in southern China, pear cultivation area and production of Guangxi were 2.1×104 hm2 and 5.08×105 tons in 2022, respectively. There is a rich wild pear germplasm resources in Guangxi according to the previous investigation. However, the understanding of the genetic diversity and population structure of the pear resources in Guangxi is still limited. It is of great significance for accelerating the identification, evaluation and conservation of the pear germplasm, and promoting the effective utilization of the local high- quality pear germplasm resources by clarifying the genetic diversity, population structure of the local peargermplasms in Guangxi, as well as its relationship with the nonlocal germplasms.【Methods】A total of 119 pear cultivars and landraces were collected and subjected to analyze the genetic diversity and the population structure using 15 pair of SSR primers reported in previous research. The genomic DNA was extracted by genomic DNA extraction kit of magnetic bead method, and the purity concentration and integrity of the extracts were assessed by NanoDROP and agarose gel electrophoresis. A 10 μL PCR system was adopted, including 5.0 μL of 2×Taq PCR Master Mix, 0.5 μL of each of forward and reverse primers (10 pmol·μL^-1 ), 1.0 μL genomic DNA (20 ng·μL^-1 ), and 3.0 μL of ddH2O. The DNA was amplified according to the molecular weight records using capillary electrophoresis technology. According to the polymorphic bands, the data matrix was obtained. The number of alleles (Na), the number of effective alleles (Ne), the Shannon information index (I), the expected heterozygosity (He), the observed heterozygosity (Ho), the polymorphic information content (PIC), and the inbreeding coefficient (Fis) were calculated using GenAlEx version 6.501 software. The Nei’s genetic distance among between 119 accessions of the germplasm resources were calculated using Powermarker software. The UMPGA cluster trees of the 119 pear germplasm resources based on the Nei’s genetic distance were constructed using MEGA7.0 software. The genetic structure analysis of the populations of pear was performed using STRUCTURE 2.3.4 software. The population number (K) was set to 1-20. Each K value was simulated 20 times, and the Markov Chain Monte Carlo (MCMC) was set 100 000 times. Finally, the optimal ∆K value was calculated using the online tool STRUCTURE HARVESTER. The genetic linkage map was constructed using CLUMMP and DISTRUCT software. The principal coordinate analysis (PCoA) was accomplished using GenAIEx software.【Results】A total of 190 alleles were detected in the pear germplasm resources by the 15 polymorphic SSR markers. The average number of alleles was 12.667. The average effective allele per SSR marker was 5.454. The average polymorphic information content (PIC) was 0.762. These results showed that there was a relatively high genetic diversity within this population. The average observed heterozygosity (Ho) and expected heterozygosity (He) were 0.682 and 0.788, respectively, suggesting that the presence of inbreeding would exist within the pear population. The average Shannon information index (I) was 1.876, reflecting that there was a high genetic diversity in the local pear population. Compared with the nonlocal germplasms, the genetic diversity of the local pear was higher with an average allele of 11.53, an average effective allele of 5.606, and a Shannon information index (I) of 1.894. The cluster analysis showed that the majority of the local germplasms in Guangxi and nonlocal germplasms were divided into two different groups, with a distant genetic relationship. The analysis of population genetic structure also indicated that there was a significant difference in the genetic structure between the majority of the local germplasms in Guangxi and the nonlocal germplasms. The Fis mean values of the two populations were over 0, indicating that there would be inbreeding within the population. Further research found that the 71 local germplasms in Guangxi were clustered into three groups, which could be divided into four different populations based on population genetic structure. However, there were no obvious regional differentiation characteristics between the populations. The result of the analysis of molecular variance (AMOVA) indicated that the genetic variation in the pear germplasms mainly occurred within individuals, while the genetic differentiation between the populations and individuals was relatively small.【Conclusion】The fifteen SSR primers had the characteristics of clear amplification results, good repeatability and high polymorphism, and would be suitable for pear germplasm identification, genetic linkage map construction, genetic diversity, and molecular marker-assisted breeding. Furthermore, the genetic diversity of the local pear germplasms in Guangxi was relatively rich. There would be a general inbreeding and no obvious regional differentia-tion within the populations, and the genetic background differed greatly from some cultivars or hybrids of nonlocal pear. Therefore, we proposed to strengthen the conservation and utilization of the local pear germplasm in Guangxi.