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.
Highlights
High-saturate molecular linkage maps are an important tool in studies on plant molecular biology and assisted breeding
Only reads showing < 5 bases with a Q score > 20 were further analyzed, yielding 206,411,693 clean reads ~ 150 bp in length; 94.39% were of a high quality, with quality scores of at least 30 (Q30, indicating a 0.1% chance of an error—i.e., 99.9% confidence)
A total of 1,426,967 RAD tags were detected; average sequencing depths were 52.7 for female parents “Red Globe,” 44.77 for male parents “Venus seedless,” and 7.25 for the progeny (Fig. 1a). Of these high-quality data, 85,503,839 clean reads were obtained for Red Globe; Venus seedless, 79,625,497 reads (Fig. 1b); per the criteria of segregation distortion (P < 0.05), 70,061 genome-wide DNA markers were used to construct a genetic map
Summary
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). Considerable progress had been made in the identification of molecular markers and the construction of molecular linkage maps in grapevine. The first molecular map for the 60 F1 progeny and the parental plants (F0) generation “Cayuga White” × “Aurore” was generated using 422 randomly amplified polymorphic DNAs (RAPDs), 16 restriction fragment length polymorphisms (RFLPs), and few isoenzyme markers [7].
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