Coupling Seq-BSA and RNA-Seq Analyses Reveal the Molecular Pathway and Genes Associated with Heading Type in Chinese Cabbage

Coupling Seq-BSA and RNA-Seq Analyses Reveal the Molecular Pathway and Genes Associated with Heading Type in Chinese Cabbage

In Chinese cabbage, heading type is a key agricultural trait of significant economic importance. Using a natural microspore-derived doubled haploid plant, we generated self-crossed progeny with overlapping or outward curling head morphotypes. Sequencing-based bulked segregant analysis (Seq-BSA) reve...

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Main Authors: AiXia Gu, Chuan Meng, YueQi Chen, Lai Wei, Hui Dong, Yin Lu, YanHua Wang, XuePing Chen, JianJun Zhao, ShuXing Shen
Format: Article
Language:English
Published: Frontiers Media S.A. 2017-12-01
Series:Frontiers in Genetics
Subjects:
Chinese cabbage
heading type
plant hormone
BrGH3.12
BrABF1
Seq-BSA
Online Access:http://journal.frontiersin.org/article/10.3389/fgene.2017.00176/full
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spelling doaj-d56fbc068ef94eba9ec88439eeb9f43b2020-11-24T21:30:50ZengFrontiers Media S.A.Frontiers in Genetics1664-80212017-12-01810.3389/fgene.2017.00176292650Coupling Seq-BSA and RNA-Seq Analyses Reveal the Molecular Pathway and Genes Associated with Heading Type in Chinese CabbageAiXia Gu0Chuan Meng1YueQi Chen2Lai Wei3Hui Dong4Yin Lu5YanHua Wang6XuePing Chen7JianJun Zhao8ShuXing Shen9Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, ChinaEconomic Crop Research Institute, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, ChinaKey Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, ChinaKey Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, ChinaShijiazhuang Pomology Institute, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, ChinaKey Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, ChinaKey Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, ChinaKey Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, ChinaKey Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, ChinaKey Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, ChinaIn Chinese cabbage, heading type is a key agricultural trait of significant economic importance. Using a natural microspore-derived doubled haploid plant, we generated self-crossed progeny with overlapping or outward curling head morphotypes. Sequencing-based bulked segregant analysis (Seq-BSA) revealed a candidate region of 0.52 Mb (A06: 1,824,886~2,347,097 bp) containing genes enriched for plant hormone signal transduction. RNA Sequencing (RNA-Seq) analysis supported the hormone pathway enrichment leading to the identification of two key candidate genes, BrGH3.12 and BrABF1. The regulated homologous genes and the relationship between genes in this pathway were also revealed. Expression of BrGH3.12 varied significantly in the apical portion of the leaf, consistent with the morphological differences between overlapping and outward curling leaves. Transcript levels of BrABF1 in the top, middle and basal segments of the leaf were significantly different between the two types. The two morphotypes contained different concentrations of IAA in the apical portion of their leaves while levels of ABA differed significantly between plant types in the top, middle, and basal leaf segments. Results from Seq-BSA, RNA-Seq and metabolite analyses all support a role for IAA and ABA in heading type formation. These findings increase our understanding of the molecular basis for pattern formation of the leafy head in Chinese cabbage and will contribute to future work developing more desirable leafy head patterns.http://journal.frontiersin.org/article/10.3389/fgene.2017.00176/fullChinese cabbageheading typeplant hormoneBrGH3.12BrABF1Seq-BSA
collection DOAJ
language English
format Article
sources DOAJ
author AiXia Gu
Chuan Meng
YueQi Chen
Lai Wei
Hui Dong
Yin Lu
YanHua Wang
XuePing Chen
JianJun Zhao
ShuXing Shen
spellingShingle AiXia Gu
Chuan Meng
YueQi Chen
Lai Wei
Hui Dong
Yin Lu
YanHua Wang
XuePing Chen
JianJun Zhao
ShuXing Shen
Coupling Seq-BSA and RNA-Seq Analyses Reveal the Molecular Pathway and Genes Associated with Heading Type in Chinese Cabbage
Frontiers in Genetics
Chinese cabbage
heading type
plant hormone
BrGH3.12
BrABF1
Seq-BSA
author_facet AiXia Gu
Chuan Meng
YueQi Chen
Lai Wei
Hui Dong
Yin Lu
YanHua Wang
XuePing Chen
JianJun Zhao
ShuXing Shen
author_sort AiXia Gu
title Coupling Seq-BSA and RNA-Seq Analyses Reveal the Molecular Pathway and Genes Associated with Heading Type in Chinese Cabbage
title_short Coupling Seq-BSA and RNA-Seq Analyses Reveal the Molecular Pathway and Genes Associated with Heading Type in Chinese Cabbage
title_full Coupling Seq-BSA and RNA-Seq Analyses Reveal the Molecular Pathway and Genes Associated with Heading Type in Chinese Cabbage
title_fullStr Coupling Seq-BSA and RNA-Seq Analyses Reveal the Molecular Pathway and Genes Associated with Heading Type in Chinese Cabbage
title_full_unstemmed Coupling Seq-BSA and RNA-Seq Analyses Reveal the Molecular Pathway and Genes Associated with Heading Type in Chinese Cabbage
title_sort coupling seq-bsa and rna-seq analyses reveal the molecular pathway and genes associated with heading type in chinese cabbage
publisher Frontiers Media S.A.
series Frontiers in Genetics
issn 1664-8021
publishDate 2017-12-01
description In Chinese cabbage, heading type is a key agricultural trait of significant economic importance. Using a natural microspore-derived doubled haploid plant, we generated self-crossed progeny with overlapping or outward curling head morphotypes. Sequencing-based bulked segregant analysis (Seq-BSA) revealed a candidate region of 0.52 Mb (A06: 1,824,886~2,347,097 bp) containing genes enriched for plant hormone signal transduction. RNA Sequencing (RNA-Seq) analysis supported the hormone pathway enrichment leading to the identification of two key candidate genes, BrGH3.12 and BrABF1. The regulated homologous genes and the relationship between genes in this pathway were also revealed. Expression of BrGH3.12 varied significantly in the apical portion of the leaf, consistent with the morphological differences between overlapping and outward curling leaves. Transcript levels of BrABF1 in the top, middle and basal segments of the leaf were significantly different between the two types. The two morphotypes contained different concentrations of IAA in the apical portion of their leaves while levels of ABA differed significantly between plant types in the top, middle, and basal leaf segments. Results from Seq-BSA, RNA-Seq and metabolite analyses all support a role for IAA and ABA in heading type formation. These findings increase our understanding of the molecular basis for pattern formation of the leafy head in Chinese cabbage and will contribute to future work developing more desirable leafy head patterns.
topic Chinese cabbage
heading type
plant hormone
BrGH3.12
BrABF1
Seq-BSA
url http://journal.frontiersin.org/article/10.3389/fgene.2017.00176/full
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