Abstract
This study reports the construction of high density linkage maps of Japanese plum (Prunus salicina Lindl.) using single nucleotide polymorphism markers (SNPs), obtained with a GBS strategy. The mapping population (An x Au) was obtained by crossing cv. “Angeleno” (An) as maternal line and cv. “Aurora” (Au) as the pollen donor. A total of 49,826 SNPs were identified using the peach genome V2.1 as a reference. Then a stringent filtering was carried out, which revealed 1,441 high quality SNPs in 137 An x Au offspring, which were mapped in eight linkage groups. Finally, the consensus map was built using 732 SNPs which spanned 617 cM with an average of 0.96 cM between adjacent markers. The majority of the SNPs were distributed in the intragenic region in all the linkage groups. Considering all linkage groups together, 85.6% of the SNPs were located in intragenic regions and only 14.4% were located in intergenic regions. The genetic linkage analysis was able to co-localize two to three SNPs over 37 putative orthologous genes in eight linkage groups in the Japanese plum map. These results indicate a high level of synteny and collinearity between Japanese plum and peach genomes.
Highlights
The genus Prunus contains more than 200 species, which include some relevant agricultural stone fruit crops such as peach, apricot, cherry, Japanese plum, myrobalan and European plum, among others [1, 2]
Genetic linkage maps are used as a tool for primary localization of important genomic regions associated with the genetic control of both qualitative and quantitative traits, which can help to support a breeding program [46]
The huge amount of genetic information that can be obtained from high throughput sequencing approaches today have allowed whole-genome sequencing and linkage analysis to become powerful methodologies for the identification of genetic polymorphisms related to complex traits in different species [47, 48]
Summary
The genus Prunus (family Rosaceae) contains more than 200 species, which include some relevant agricultural stone fruit crops such as peach, apricot, cherry, Japanese plum, myrobalan and European plum, among others [1, 2]. Japanese plum is a self-incompatible, diploid species (2n = 2X = 16) that produces an edible drupe; it has been cultivated for 4,000 years [2] for fruit production and ornamental purposes. Different centers around the world have begun to perform breeding programs to obtain new cultivars. The new cultivars show a high level of variability for some important traits such as harvest date, fruit size, flesh color and shape [3].
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