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Article|01 Apr 2018|OPEN
Genotyping-by-sequencing application on diploid rose and a resulting high-density SNP-based consensus map
Muqing Yan1, David H. Byrne1, Patricia E. Klein1,2,, Jizhou Yang2,3, Qianni Dong1,4 & Natalie Anderson1
1Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
2Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
3Present address: Department of Computer Science, San Francisco State University, San Francisco, CA 94132, USA
4Present address: Monsanto Company, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA

Horticulture Research 5,
Article number: 17 (2018)
doi: 10.1038/hortres.2018.17
Views: 544

Received: 10 Aug 2017
Revised: 03 Oct 2017
Accepted: 22 Jan 2018
Published online: 01 Apr 2018

Abstract

Roses, which have been cultivated for at least 5000 years, are one of the most important ornamental crops in the world. Because of the interspecific nature and high heterozygosity in commercial roses, the genetic resources available for rose are limited. To effectively identify markers associated with QTL controlling important traits, such as disease resistance, abundant markers along the genome and careful phenotyping are required. Utilizing genotyping by sequencing technology and the strawberry genome (Fragaria vesca v2.0.a1) as a reference, we generated thousands of informative single nucleotide polymorphism (SNP) markers. These SNPs along with known bridge simple sequence repeat (SSR) markers allowed us to create the first high-density integrated consensus map for diploid roses. Individual maps were first created for populations J06-20-14-3דLittle Chief” (J14-3×LC), J06-20-14-3דVineyard Song” (J14-3×VS) and “Old Blush”דRed Fairy” (OB×RF) and these maps were linked with 824 SNPs and 13 SSR bridge markers. The anchor SSR markers were used to determine the numbering of the rose linkage groups. The diploid consensus map has seven linkage groups (LGs), a total length of 892.2 cM, and an average distance of 0.25 cM between 3527 markers. By combining three individual populations, the marker density and the reliability of the marker order in the consensus map was improved over a single population map. Extensive synteny between the strawberry and diploid rose genomes was observed. This consensus map will serve as the tool for the discovery of marker–trait associations in rose breeding using pedigree-based analysis. The high level of conservation observed between the strawberry and rose genomes will help further comparative studies within the Rosaceae family and may aid in the identification of candidate genes within QTL regions.