Impacts of Chronic Habitat Fragmentation on Genetic Diversity of Natural Populations of Prunus persica in China

Abstract

Wild peach is an important resource for improving existing peach varieties. However, the extant populations of wild peach show fragmented distribution due to human disturbance and geographic isolation. In this study, we used natural populations (or wild populations) of Prunus persica (Rosaceae) to assess the genetic effects of habitat fragmentation. A total of 368 individuals sampled from 16 natural populations were analyzed using 23 polymorphic simple sequence repeat (SSR) markers. Prunus persica maintained low within-population genetic variation and high level of genetic differentiation. Two genetic clusters were revealed based on three different methods (UPGMA, PCoA, and STRUCTURE). All populations showed a significant heterozygosity deficiency and most extant populations experienced recent reduction in population size. A significant isolation by distance (IBD) was observed with Mantel’s test. Compared to historical gene flow, contemporary gene flow was restricted among the studied populations, suggesting a decrease in gene flow due to habitat fragmentation. Habitat fragmentation has impacted population genetic variation and genetic structure of P. persica. For breeding and conservation purpose, collecting as many individuals as possible from multiple populations to maximize genetic diversity was recommended during the process of germplasm collection. In addition, populations from central China had higher genetic diversity, suggesting these populations should be given priority for conservation and germplasm collection.

Genetic Diversity Analysis and Core Germplasm Construction of Rubus chingii Hu

“…Regarding the observed heterozygosity, all of the observed heterozygous population SNPs loci were lower than expected, and R. chingii (0.044) had a much lower observed heterozygosity than Prunus persica (0.444) [ 66 ]. This indicates a clear lack of heterozygosity and low genetic diversity that may herald a potentially depressed breeding problem [ 66 , 67 ].…”

“…Regarding the observed heterozygosity, all of the observed heterozygous population SNPs loci were lower than expected, and R. chingii (0.044) had a much lower observed heterozygosity than Prunus persica (0.444) [ 66 ]. This indicates a clear lack of heterozygosity and low genetic diversity that may herald a potentially depressed breeding problem [ 66 , 67 ]. The high MAF (0.95) and Fis > 0 confirmed that there is less observed heterozygosity than expected, which also indicates that the population has a low outcrossing rate and low genetic variation, which may be related to the characteristics of root tiller reproduction [ 68 , 69 ].…”

“…Considering that genetic variations within and between populations do not depend on sexual and/or asexual reproduction, this means that sexual plants are as genetically diverse as asexual plants [ 71 , 72 ]. Overexploitation of nature often results in habitat loss for wild resources, while habitat fragmentation leads to smaller population sizes, which will also endanger the long-term survival of R. chingii through asexual reproduction and genetic drift [ 66 ]. Therefore, it seems that poor habitat conditions, low distribution density and severe human intervention are the main reasons for the reduction in genetic diversity [ 73 ].…”