Characterization of Genetic Diversity in Accessions of Prunus salicina Lindl: Keeping Fruit Flesh Color Ideotype While Adapting to Water Stressed Environments

Abstract

The genetic diversity of 14 Japanese plum (Prunus salicina Lindl) landraces adapted to an ecosystem of alternating flooding and dry conditions was characterized using neutral simple sequence repeat (SSR) markers. Twelve SSRs located in six chromosomes of the Prunus persica reference genome resulted to be polymorphic, thus allowing identification of all the evaluated landraces. Differentiation between individuals was moderate to high (average shared allele distance (DAS) = 0.64), whereas the genetic diversity was high (average indices polymorphism information content (PIC) = 0.62, observed heterozygosity (Ho) = 0.51, unbiased expected heterozygosity (uHe) = 0.70). Clustering and genetic structure approaches grouped all individuals into two major groups that correlated with flesh color. This finding suggests that the intuitive breeding practices of growers tended to select plum trees according to specific phenotypic traits. These neutral markers were adequate for population genetic studies and cultivar identification. Furthermore, we assessed the SSR flanking genome regions (25 kb) in silico to search for candidate genes related to stress resistance or associated with other agronomic traits of interest. Interestingly, at least 26 of the 118 detected genes seem to be related to fruit quality, plant development, and stress resistance. This study suggests that the molecular characterization of specific landraces of Japanese plum that have been adapted to extreme agroecosystems is a useful approach to localize candidate genes which are potentially interesting for breeding.

Prediction of the Potential Distributions of Prunus salicina Lindl., Monilinia fructicola, and Their Overlap in China Using MaxEnt

“…Furthermore, the occurrence and prevalence of plant pests and diseases are not only affected by climate but also closely related to host conditions, the species and quantity of natural enemies, and the frequency of orchard medication. Environmental factors affecting the distribution of host plants include climate, soil type, vegetation type, topographic factors, variety type, human activities, and socioeconomic structure [ 53 , 54 , 55 ]. Due to unknown changes in many future factors, and to reduce the complexity of the model, other factors were not included in the environmental variables in this study.…”

Molecular Genetics, Genomics, and Biotechnology in Crop Plant Breeding

“…The low-cost and easy-to-use PCR-based simple sequence repeat (SSR) makers showed its efficiency in the study of genetic diversity in landraces of Prunus salicina Lindl in the Paraná River Delta in Argentina, which has a particularly harsh agro-ecosystem, especially regarding water stress [14]. These neutral markers were found to be adequate for population genetic studies and cultivar identification.…”

An LTR retrotransposon in the promoter of a PsMYB10.2 gene associated with the regulation of fruit flesh color in Japanese plum

“…However, they found no allele significantly associated with the red flesh color. To our knowledge, only two studies have found polymorphisms, mapped in LG6 and LG3, associated with the fruit flesh color in Japanese plum 42,43 . The number of individuals used in both studies was reduced, which limits the transfer of the markers to broader and more variable collections and motivates the search for markers more tightly linked to the trait.…”