Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage

BMC Plant Biology

Research Article

Yeisoo Yu¹  Heebal Kim²  Il-Sup Nou³  Ho Jun Joh⁴  Hyeon Ju Lee⁴  Jonghoon Lee⁴  Tae-Jin Yang⁴  Murukarthick Jayakodi⁴  Jee Young Park⁴  Sang-Choon Lee⁴  Sampath Perumal⁴  Ki-Woung Yang⁵  Nur Kholilatul Izzah⁶  Kyounggu Ahn⁷  Joodeok Seo⁷  Youngdeok Suh⁷  Jaeheung Yoo⁷  Gyung Ja Choi⁸  Ji Hyun Lee⁸ 

[1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, 85721, Tucson, Arizona, USA;Department of Agricultural Biotechnology, Seoul National University, 151-921, Seoul, Republic of Korea;CHO & KIM genomics, Seoul National University Mt.4-2, Main Bldg. #514, SNU Research Park, NakSeoungDae, 151-919, Seoul, Gwanakgu, Republic of Korea;Department of Horticulture, Sunchon National University, 540-950, Suncheon, Republic of Korea;Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Republic of Korea;Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Republic of Korea;Department of Horticulture, Sunchon National University, 540-950, Suncheon, Republic of Korea;Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Republic of Korea;Indonesian Research Institute for Industrial and Beverage Crops (IRIIBC), Pakuwon, Sukabumi, Indonesia;Joeun Seed, #174, Munbang-Ri, Cheonhan-Myun, 367-833, Goesan-Gu, Chungcheongbuk-Do, Korea;Research Center for Biobased Chemistry, Korea Research Institute of Chemical Technology, 305-600, Daejeon, Yusong-Gu, Republic of Korea;

关键词: Cabbage;    Whole-genome resequencing;    Genetic linkage map;    Black rot;    QTL;   

DOI  :  10.1186/s12870-015-0424-6

 received in 2014-09-25, accepted in 2015-01-15,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundBlack rot is a destructive bacterial disease causing large yield and quality losses in Brassica oleracea. To detect quantitative trait loci (QTL) for black rot resistance, we performed whole-genome resequencing of two cabbage parental lines and genome-wide SNP identification using the recently published B. oleracea genome sequences as reference.ResultsApproximately 11.5 Gb of sequencing data was produced from each parental line. Reference genome-guided mapping and SNP calling revealed 674,521 SNPs between the two cabbage lines, with an average of one SNP per 662.5 bp. Among 167 dCAPS markers derived from candidate SNPs, 117 (70.1%) were validated as bona fide SNPs showing polymorphism between the parental lines. We then improved the resolution of a previous genetic map by adding 103 markers including 87 SNP-based dCAPS markers. The new map composed of 368 markers and covers 1467.3 cM with an average interval of 3.88 cM between adjacent markers. We evaluated black rot resistance in the mapping population in three independent inoculation tests using F2:3 progenies and identified one major QTL and three minor QTLs.ConclusionWe report successful utilization of whole-genome resequencing for large-scale SNP identification and development of molecular markers for genetic map construction. In addition, we identified novel QTLs for black rot resistance. The high-density genetic map will promote QTL analysis for other important agricultural traits and marker-assisted breeding of B. oleracea.

【 授权许可】

Unknown   
© Lee et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.