Construction of an SNP-based high-density genetic map for Japanese plum in a Chinese population using specific length fragment sequencing

Abstract

The Japanese plum (Prunus salicina Lindl.) is one of the most important stone fruit crops in China. High-density linkage map is valuable resources which enhance functional genomics and genetic breeding studies. So far several Japanese plum linkage maps have been reported using different kinds of molecular markers; however, the marker numbers and chromosome coverage are limited. Recently, a newly developed strategy which genome sequencing towards specific-locus amplified fragments (SLAF) markers, has been proven to be powerful for rapid genotyping of genome-wide markers and for high-density genetic map construction. In this study, SLAF was used to genotype markers with 114 F1 seedlings from the '09-16' × 'Fortune' cross. Suitable SLAF markers (160,344 out of 343,436,902 pair-end reads) were chosen to conduct genetic map construction, 16.31% of which were polymorphic. The overall integrated map contained 3,341 high quality SLAFs and 720 loci that were grouped in eight genetic linkage groups with a total length of 869.9 cM and an average distance of 1.21 cM, and only five gaps with a genetic distance > 5 cM between adjacent markers occurred in linkage group (LG) 3 and LG6. The number of markers with each LG ranged from 82.3 cM (LG3) to 138.3 cM (LG1). Aligning the map against the peach reference genome sequence (Prunus persica L.) indicated a strictly co-linear relationship between the LGs and peach genome, demonstrating the markers on ours LGs were well ordered. Overall, our studies identified large-scale of genetic markers and constructed high-density linkage maps for Japanese plum, which will obviously provide a solid foundation for marker-assisted selection and sequence assembly of the Japanese plum reference genome. Keywords Japanese plum. Genetic linkage map. Single nucleotide polymorphism. Specific length fragment sequencing Prunophora, genus Prunus, the Rosaceae family (Topp et al. 2012). The Japanese plum is a crop tree species native to China and it is widely cultivated from 23°N (the Guangxi and Yunnan provinces) to 45°N (Heihongjiang province). Due to its rich nutrients and unique flavour, the Japanese plum was popular in China, where the yield was the highest in the world (6,663,165 tonnes). Other major Japanese plumproducing countries include the USA (392,537 tonnes), followed by India (261,903 tonnes), Mexico (77,931 tonnes) and Japan (23,000 tonnes). In the Southern hemisphere plum production is dominated by Chile (294,873 tonnes) followed by Argentina (156,084 tonnes), South Africa (81,463 tonnes) and Australia (17,992 tonnes), also based on Japanese plum production (http://faostat.fao.org). The highest plum production in China over the last century came from native cultivars, since they had good flavour and were able to adapt to complex environments, though they had Qiu-ping Zhang and Xiao Wei contributed equally to this work. Communicated by D. Chagné

Construction of a High-Density Genetic Map and Identification of Quantitative Trait Loci Linked to Fruit Quality Traits in Apricots Using Specific-Locus Amplified Fragment Sequencing

“…Because of the lower availability of AFLP, RAPD, RFLP, and SSR markers, the map density was not high enough and the adjacent marker gaps were larger in previous apricot linkage maps ( Lalli et al, 2008 ). SNPs are the most common genetic variation in the whole genome, and they are very important genetic markers for constructing a high-density genetic map, resulting in a significant decrease in the time and cost of genotyping ( Zeballos et al, 2016 ; Zhang et al, 2020 ). Recently, some SNP markers have been used to construct genetic maps in apricots to screen for QTLs related to fruit development period-related traits and graft compatibility ( Salazar et al, 2016 ; Pina et al, 2021 ).…”

“…Compared with the published linkage maps, the genetic group constructed in our study covered a longer genetic distance and contained a higher marker density. The differences in the length and density of genetic maps may be related to the genetic distance between the parents, the number of markers, and the population size used in different studies ( Zhang et al, 2020 ). For example, Shi et al (2020) published a peach map including 7,998 SLAF markers covering the peach genome of 1098.79 cM based on an F1 peach population of 202 individuals.…”

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

“…The genus Prunus has shown conserved intraspecific and intragenic collinearity in the Rosaceae family, with the peach being considered a model species for the genus Prunus for multiple types of genetic research (Arús et al 2012;Carrasco et al 2018;Marti et al 2018). Zhang et al (2020) found that the correlation of eight chromosomes was greater than 0.8, indicating a high level of collinearity between the Japanese plum and peach genomes. A recently released plum genome has been published, and collinearity analysis has shown that the assembled genomes of the plum also exhibit a high level of genome synteny with the peach (Liu et al 2020).…”

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

“…NGS is a kind of low-cost technologies to discover large numbers of SNPs for extensive genetic studies, including within-species diversity analysis, linkage map construction, and genome-wide association studies (GWAS), which is allowing significant advances in plant genetics and breeding [6,22,23,29]. The genus Prunus has shown conserved intraspecific and intragenic collinearity in the Rosaceae family, and peach has been considered as a model species for the genus Prunus regarding multiple genetic types of research [30][31][32][33]. On these bases, for the first time, we conducted high-depth (~20×) whole-genome resequencing of 67 plum accessions using the peach genome sequence as a reference, obtaining an average of 6.9 Gb high-quality data for each acquisition, which ensured the accurate and comprehensive population genetic analysis.…”