Construction of a high-density genetic map and the X/Y sex-determining gene mapping in spinach based on large-scale markers developed by specific-locus amplified fragment sequencing (SLAF-seq)

Abstract

BackgroundCultivated spinach (Spinacia oleracea L.) is one of the most widely cultivated types of leafy vegetable in the world, and it has a high nutritional value. Spinach is also an ideal plant for investigating the mechanism of sex determination because it is a dioecious species with separate male and female plants. Some reports on the sex labeling and localization of spinach in the study of molecular markers have surfaced. However, there have only been two reports completed on the genetic map of spinach. The lack of rich and reliable molecular markers and the shortage of high-density linkage maps are important constraints in spinach research work. In this study, a high-density genetic map of spinach based on the Specific-locus Amplified Fragment Sequencing (SLAF-seq) technique was constructed; the sex-determining gene was also finely mapped.ResultsThrough bio-information analysis, 50.75 Gb of data in total was obtained, including 207.58 million paired-end reads. Finally, 145,456 high-quality SLAF markers were obtained, with 27,800 polymorphic markers and 4080 SLAF markers were finally mapped onto the genetic map after linkage analysis. The map spanned 1,125.97 cM with an average distance of 0.31 cM between the adjacent marker loci. It was divided into 6 linkage groups corresponding to the number of spinach chromosomes. Besides, the combination of Bulked Segregation Analysis (BSA) with SLAF-seq technology(super-BSA) was employed to generate the linkage markers with the sex-determining gene. Combined with the high-density genetic map of spinach, the sex-determining gene X/Y was located at the position of the linkage group (LG) 4 (66.98 cM–69.72 cM and 75.48 cM–92.96 cM), which may be the ideal region for the sex-determining gene.ConclusionsA high-density genetic map of spinach based on the SLAF-seq technique was constructed with a backcross (BC1) population (which is the highest density genetic map of spinach reported at present). At the same time, the sex-determining gene X/Y was mapped to LG4 with super-BSA. This map will offer a suitable basis for further study of spinach, such as gene mapping, map-based cloning of Specific genes, quantitative trait locus (QTL) mapping and marker-assisted selection (MAS). It will also provide an efficient reference for studies on the mechanism of sex determination in other dioecious plants.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3659-9) contains supplementary material, which is available to authorized users.

Construction of a High-Density Genetic Map and Analysis of Seed-Related Traits Using Specific Length Amplified Fragment Sequencing for Cucurbita maxima

“…Recently, a new high-throughput strategy for de novo SNP discovery called specific length amplified fragment sequencing (SLAF-seq) has been developed and successfully applied to construct high-density maps of grape (Wang et al, 2017a), gingko (Liu et al, 2017), pear (Wang et al, 2017b), tobacco (Gong et al, 2016), matsudana (Zhang et al, 2016), cauliflower (Zhao et al, 2016), soybean (Qi et al, 2014), sesame (Zhang et al, 2013), watermelon (Shang et al, 2016), and cucumber (Xu et al, 2015). This strategy has also been applied for QTL mapping of important economic and nutritional traits in sesame (Mei et al, 2017), soybean (Li et al, 2017), spinach (Qian et al, 2017), cucumber (Zhu et al, 2016), wax gourd (Jiang et al, 2015), and pumpkin (Zhong et al, 2017). However, SLAF-seq has not been successfully applied in squash.…”

Identification of a quantitative trait loci (QTL) associated with ammonia tolerance in the Pacific white shrimp (Litopenaeus vannamei)

“…The mean distance between adjacent markers was 0.58 cM on the male map, 0.53 cM on the female map, and 0.37 cM on the sex-average map (Supplementary Material, Table S3, Table S4, and Table S5). The distribution of markers among LGs was not uniform: in the male map, LG31 contained the most markers (585), while LG26 contained the least (39); in the female map, LG36 contained the most markers (540), while LG27 contained the least (21); and in the sex-average map, LG31 contained the most markers (695), while LG26 contained the least (53).…”

QTL and transcriptomic analyses for ammonia tolerance in the Pacific white shrimp (Litopenaeus vannamei)

“…The mean distance between adjacent markers was 0.58 cM on the male map, 0.53 cM on the female map, and 0.37 cM on the sex-average map (Supplementary Material, Table S3, Table S4, and Table S5). The distribution of markers among LGs was not uniform: in the male map, LG31 contained the most markers (585), while LG26 contained the least (39); in the female map, LG36 contained the most markers (540), while LG27 contained the least (21); and in the sex-average map, LG31 contained the most markers (695), while LG26 contained the least (53).…”