QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa.

Leaf heads of cabbage (Brassica oleracea), Chinese cabbage (B. rapa), and lettuce (Lactuca sativa) are important vegetables that supply mineral nutrients, crude fiber and vitamins in the human diet. Head size, head shape, head weight, and heading time contribute to yield and quality. In an attempt t...

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Main Authors: Xiang Yu, Han Wang, Weili Zhong, Jinjuan Bai, Pinglin Liu, Yuke He
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2013-01-01
Series:PLoS ONE
Online Access:http://europepmc.org/articles/PMC3810141?pdf=render
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author Xiang Yu
Han Wang
Weili Zhong
Jinjuan Bai
Pinglin Liu
Yuke He
author_facet Xiang Yu
Han Wang
Weili Zhong
Jinjuan Bai
Pinglin Liu
Yuke He
author_sort Xiang Yu
collection DOAJ
description Leaf heads of cabbage (Brassica oleracea), Chinese cabbage (B. rapa), and lettuce (Lactuca sativa) are important vegetables that supply mineral nutrients, crude fiber and vitamins in the human diet. Head size, head shape, head weight, and heading time contribute to yield and quality. In an attempt to investigate genetic basis of leafy head in Chinese cabbage (B. rapa), we took advantage of recent technical advances of genome resequencing to perform quantitative trait locus (QTL) mapping using 150 recombinant inbred lines (RILs) derived from the cross between heading and non-heading Chinese cabbage. The resequenced genomes of the parents uncovered more than 1 million SNPs. Genotyping of RILs using the high-quality SNPs assisted by Hidden Markov Model (HMM) generated a recombination map. The raw genetic map revealed some physical assembly error and missing fragments in the reference genome that reduced the quality of SNP genotyping. By deletion of the genetic markers in which recombination rates higher than 20%, we have obtained a high-quality genetic map with 2209 markers and detected 18 QTLs for 6 head traits, from which 3 candidate genes were selected. These QTLs provide the foundation for study of genetic basis of leafy heads and the other complex traits.
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spelling doaj.art-fd3d029f2cee49df81dc1f723f7fff252022-12-21T18:30:51ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-01810e7605910.1371/journal.pone.0076059QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa.Xiang YuHan WangWeili ZhongJinjuan BaiPinglin LiuYuke HeLeaf heads of cabbage (Brassica oleracea), Chinese cabbage (B. rapa), and lettuce (Lactuca sativa) are important vegetables that supply mineral nutrients, crude fiber and vitamins in the human diet. Head size, head shape, head weight, and heading time contribute to yield and quality. In an attempt to investigate genetic basis of leafy head in Chinese cabbage (B. rapa), we took advantage of recent technical advances of genome resequencing to perform quantitative trait locus (QTL) mapping using 150 recombinant inbred lines (RILs) derived from the cross between heading and non-heading Chinese cabbage. The resequenced genomes of the parents uncovered more than 1 million SNPs. Genotyping of RILs using the high-quality SNPs assisted by Hidden Markov Model (HMM) generated a recombination map. The raw genetic map revealed some physical assembly error and missing fragments in the reference genome that reduced the quality of SNP genotyping. By deletion of the genetic markers in which recombination rates higher than 20%, we have obtained a high-quality genetic map with 2209 markers and detected 18 QTLs for 6 head traits, from which 3 candidate genes were selected. These QTLs provide the foundation for study of genetic basis of leafy heads and the other complex traits.http://europepmc.org/articles/PMC3810141?pdf=render
spellingShingle Xiang Yu
Han Wang
Weili Zhong
Jinjuan Bai
Pinglin Liu
Yuke He
QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa.
PLoS ONE
title QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa.
title_full QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa.
title_fullStr QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa.
title_full_unstemmed QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa.
title_short QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa.
title_sort qtl mapping of leafy heads by genome resequencing in the ril population of brassica rapa
url http://europepmc.org/articles/PMC3810141?pdf=render
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