Construction of a highly saturated Genetic Map for Vitis by Next-generation Restriction Site-associated DNA Sequencing

Abstract

Background: High-saturate molecular linkage maps are an important tool in studies on plant molecular biology and assisted breeding. Development of a large set of single nucleotide polymorphisms (SNPs) via next-generation sequencing (NGS)-based methods, restriction-site associated DNA sequencing (RAD-seq), and the generation of a highly saturated genetic map help improve fine mapping of quantitative trait loci (QTL).

Results: We generated a highly saturated genetic map to identify significant traits in two elite grape cultivars and 176 F₁ plants. In total, 1,426,967 high-quality restriction site-associated DNA tags were detected; 51,365, 23,683, and 70,061 markers were assessed in 19 linkage groups (LGs) for the maternal, paternal, and integrated maps, respectively. Our map was highly saturated in terms of marker density and average "Gap ≤ 5 cM" percentage.

Conclusions: In this study, RAD-seq of 176 F₁ plants and their parents yielded 8,481,484 SNPs and 1,646,131 InDel markers, of which 65,229 and 4832, respectively, were used to construct a highly saturated genetic map for grapevine. This map is expected to facilitate genetic studies on grapevine, including an evaluation of grapevine and deciphering the genetic basis of economically and agronomically important traits. Our findings provide basic essential genetic data the grapevine genetic research community, which will lead to improvements in grapevine breeding.

Keywords: Genetic map; Linkage group; Restriction site-associated DNA sequencing; Single nucleotide polymorphism; Vitis.

Fig. 1

a, b Average read sequencing depth (fold) (a) and number of clean reads (b) expressed as genome equivalents of the 176 F₁ individuals (shown in the X axis)

Fig. 2

Number of markers in each of the five segregation patterns

Fig. 3

Genetic lengths and marker distribution in 19 linkage groups of the integrated map. Genetic distance is indicated by the vertical scale in centimorgans (cM). Black lines represent mapped markers. LG1–19 represent corresponding linkage groups ID

Fig. 4

Collinear analysis of the consensus between genetic and physical maps

Fig. 5

Marker density of integrated map.X-axis: physical position on 19 linkage groups. Y-axis: markers number per LG. The marker density on the genome was calculated by sliding windows using window size of 0.5 cM

Fig. 6

Distribution of marker density across the chromosome. The x-axis represents the 10 cM map interval and the y-axis represents the number of RAD markers present in the interval