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

Nian Wang,Lijun Wang,Shaohua Li,Haiping Xin,Linchuan Fang

doi:10.1186/1471-2229-12-148

Abstract

BackgroundGenetic 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.ResultsAn 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.ConclusionsThe 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.

Highlights

Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding
Lodhi et al [5] developed a genetic map for Vitis with 422 random amplified polymorphic DNA (RAPD) and 16 restriction fragment length polymorphism (RFLP) molecular markers, as well as a number of isozyme markers [5], possibly the first report of a complete genetic map for grape
Two characteristics are required for an appropriate restriction enzyme: 1) because the next generation sequencing (NGS) technology can only cover 75 to 100 bp of DNA at each end concurrently, the enzyme must be able to digest the genome of interest to a suitable size (e.g. ~300–400 bp); 2) the number of digested fragments of the expected size should be sufficient for subsequent manipulation (100,000–150,000 restriction-site associated DNA (RAD) tags)

Summary

Introduction

Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. A number of new genetic maps were developed, several of them based on the framework of that map The latter studies generally made use of an F1 population as the plant material, with amplified fragment length polymorphisms (AFLP), simple sequence repeats (SSR), and single nucleotide polymorphisms (SNP) being the three major molecular marker types for map construction [6,7,8,9,10,11,12,13,14,15,16]. A high-density genetic map for grape is still lacking, and one that covers a large number of molecular markers with sufficient sequence information is needed to meet the demand for improvement

Methods

Results

Conclusion