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Open Access Highly Accessed Research article

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

Nian Wang1, Linchuan Fang12, Haiping Xin1, Lijun Wang3 and Shaohua Li1*

Author Affiliations

1 Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China

2 Graduate School of Chinese Academy of Sciences, Beijing, 100049, China

3 Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China

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BMC Plant Biology 2012, 12:148  doi:10.1186/1471-2229-12-148

Published: 21 August 2012

Abstract

Background

Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development.

Results

An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations.

Conclusions

The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.

Keywords:
Grape; Genetic map; Next generation sequencing (NGS); Restriction-site associated DNA (RAD)