ISSR Analysis of Genetic Diversity and Structure of Plum Varieties Cultivated in Southern China

Abstract

Plums (Prunus spp.) are important deciduous fruit crops in the world. China is a major producer of P. salicina Lindl., but the genetic relationship of Chinese plums in key production regions remain unclear. In this study, 14 University of British Columbia (UBC) inter simple sequence repeats (ISSR) primers were used to analyze 33 plum varieties cultivated in Fujian Province to determine their genetic diversity and population structure. A total of 146 bands were generated, of which 130 were polymorphic. Mean percentage of polymorphic bands was 89.04%, Shannon’s information index value was 0.38, and the Nei’s genetic index value was 0.24. Using unrooted trees (Neighbor-Joining method), 33 varieties were classified into four groups. Split graph separated them into two major groups, each with two subgroups. The two phylogenetic trees indicate that environmental or natural selection pressure is an important factor influencing their genetic relationship. Analysis of population structure revealed that they have frequent genetic exchanges among closed subpopulations; thus, genetic variation mainly occurs within the population. Additionally, based on the phylogenetic analysis and unique morphological characteristics of fruits, we propose that the Chinese landrace Nai could contribute significantly to development of the famous variety Wickson.

Genetic diversity in wild populations of the restinga ecotype of the cashew (Anacardium occidentale) in coastal Piauí, Brazil

“…These markers continue to be used especially in genetic structure studies in economically important plant species (e.g. Kumar and Agrawal 2017;Wu et al 2019). Most studies of genotyping error in dominant markers have been carried out on AFLP data.…”

“…We used ISSR molecular markers (inter-simple sequence repeat), widely deployed in studies of economically important species and their wild relatives that focus on genotype identification, genetic conservation and cultivar development (e.g. Nunes et al 2013;Martins et al 2014;Oliveira et al 2014;Rodrigues et al 2015;Carmo et al 2017;Wu et al 2019).…”

Do Grapholita funebrana Infestation Rely on Specific Plum Fruit Features?

“…Plums (Prunus domestica L. and Prunus salicina Lindl.) are widely cultivated in areas with a temperate and subtropical climate in China, India, America, Japan, and European countries [1][2][3]. In 2017, world plum production reached almost 12 million tons [4].…”

“…Due to the economic and social importance of plum production, several studies evaluated new varieties adapted to regional climatic conditions, displaying resistance or tolerance to abiotic and biotic stresses (among them diseases and pests), improved fruit quantity, and overall quality [1,3,[9][10][11][12][13]. Nevertheless, a detailed examination on the discrimination of cultivars is lacking, as prior studies have been often carried out at regional level or regarded specific quality parameters [14][15][16][17][18].…”

Genetic diversity analysis of Chinese plum (Prunus salicinaL.) based on whole-genome resequencing

“…Zhang and Zhang [8] took the lead in collecting plum germplasm resources and evaluating their genetic diversity on the basis of morphological traits and isozyme polymorphisms, whereas, morphological traits were highly susceptible to environmental factors, so the estimates of genetic diversity were not precise; while isozymes had a low degree of polymorphism and hence were not efficient enough for the characterization of germplasm genetic diversity [9]. Overcoming the above-mentioned problems, DNA-based markers became widely applied in plum genetic diversity analysis, including random amplified polymorphic DNAs (RAPDs) [5,10], simple sequence repeats (SSRs) [11][12][13], inter-simple sequence repeats (ISSRs) [2,14]. In addition, benefiting from the advances in next-generation sequencing (NGS) technologies, genotyping by sequencing (GBS), provides a great wealth of information that makes it possible to identify thousands of single nucleotide polymorphisms (SNPs), which, after adequate filtering, allow us to carry out detailed genetic diversity studies [7,[15][16][17].…”