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

Abstract

BackgroundHigh-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).ResultsWe 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.ConclusionsIn 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.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1575-z) contains supplementary material, which is available to authorized users.

Novel stable QTLs identification for berry quality traits based on high-density genetic linkage map construction in table grape

“…The percentage of "Gap < 5 cM" reached up to 98% (Table 2). But it needs to point out that total length of the maps in this study were over 3000 cM, which is similar to that of maps constructed by Zhu et al [52], but longer than most other published maps [7,11,25,[33][34][40][41]. Collard et al [53] have suggested that the difference in chromosome recombination events occurred during sexual reproduction in each subpopulation can be the reason for the variation in map length.…”

Construction of a High-Density Genetic Map and Mapping of Firmness in Grapes (Vitis vinifera L.) Based on Whole-Genome Resequencing

“…In general, increasing the density of markers can increase the resolution of genetic maps, thereby improving the precision of QTL mapping [54,77]. Previous QTL studies of grape traits were mainly based on lower marker numbers (<1000) with relatively high QTL intervals, which affected the accuracy of QTLs and hard-to-locate candidate genes [33,78]. With the rapid development of sequencing technologies and bioinformatics, a large number of polymorphic molecular markers to meet the needs for high-density genetic map construction can be identified, and high-resolution linkage maps have been successfully used for QTL fine mapping in many crops, such as soybean, cotton, pear, and jujube [57][58][59]76].…”

“…A (high-density) genetic map is essential for QTL mapping [21]. In the past ten years, a number of grape genetic maps have been constructed based on different mapping populations [20,[22][23][24][25][26][27][28][29][30][31][32][33]. Numerous QTLs for important economic traits, including resistance to downy mildew [10,16,22,[34][35][36][37][38], powdery mildew [34,36,[39][40][41], anthracnose [24], root-knot nematodes [42], and grape phylloxera [43,44], as well as flower sex [45,46], berry color [46,47], seedlessness [48], berry weight [18,32], soluble solid content [32], acidity [20], and muscat flavor [49], have been identified.…”

“…Next-generation sequencing is a high-throughput, low-cost technology that has been used to identify a large number of SNPs for high-density genetic map construction in various crops, such as soybean [57], cotton [58], and pear [59]. In recent years, several genetic maps for grapevine have been constructed on the basis of high-throughput sequencing technology; these maps have increased marker density and have led to the identification of some new QTLs [10,24,28,33,46]. Nearly all of the genetic maps were constructed using reduced representation methods, such as restriction site-associated DNA sequencing and genotyping-by-sequencing, which are relatively cheap as they sample only a fraction of the genome, but they also produce incomplete data [60].…”

High-density genetic linkage map construction and white rot resistance QTL mapping for Vitis based on restriction site-associated DNA sequencing

“…In recent years, the development of high-throughput sequencing technology allowed SNP markers to become widely used for grape genetic map construction and greatly improved the marker number and density of the linkage maps. Because of differences in sequencing type, genetic background of the parents, and number of individuals within the sequencing population, there was a significant difference in marker number, average length of adjacent markers, and the total genetic length in these constructed maps (Sapkota et al 2018, Chen et al 2015, Wang et al 2012, Zhu et al 2018, Barba et al 2014, Guo et al 2015, Wang et al2017). In this study, we used RAD-seq to construct a high-density linkage map, which contained 6249 markers, at a total genetic length of 3118.13 cM and an average length of adjacent markers of 0.50 cM.…”