Genome resequencing and comparative variome analysis in a Brassica rapa and Brassica oleracea collection

Feng Cheng; Jian Wu; Chengcheng Cai; Lixia Fu; Jianli Liang; Theo Borm; Mu Zhuang; Yangyong Zhang; Fenglan Zhang; Guusje Bonnema; Xiaowu Wang

doi:10.1038/sdata.2016.119

Genome resequencing and comparative variome analysis in a Brassica rapa and Brassica oleracea collection

Feng Cheng, Jian Wu, Chengcheng Cai, Lixia Fu, Jianli Liang, Theo Borm, Mu Zhuang, Yangyong Zhang, Fenglan Zhang, Guusje Bonnema^*, Xiaowu Wang

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

21 Citations (Scopus)

Abstract

The closely related species Brassica rapa and B. oleracea encompass a wide range of vegetable, fodder and oil crops. The release of their reference genomes has facilitated resequencing collections of B. rapa and B. oleracea aiming to build their variome datasets. These data can be used to investigate the evolutionary relationships between and within the different species and the domestication of the crops, hereafter named morphotypes. These data can also be used in genetic studies aiming at the identification of genes that influence agronomic traits. We selected and resequenced 199 B. rapa and 119 B. oleracea accessions representing 12 and nine morphotypes, respectively. Based on these resequencing data, we obtained 2,249,473 and 3,852,169 high quality SNPs (single-nucleotide polymorphisms), as well as 303,617 and 417,004 InDels for the B. rapa and B. oleracea populations, respectively. The variome datasets of B. rapa and B. oleracea represent valuable resources to researchers working on evolution, domestication or breeding of Brassica vegetable crops.

Original language	English
Article number	160119
Journal	Scientific Data
Volume	3
DOIs	https://doi.org/10.1038/sdata.2016.119
Publication status	Published - 2016

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title = "Genome resequencing and comparative variome analysis in a Brassica rapa and Brassica oleracea collection",

abstract = "The closely related species Brassica rapa and B. oleracea encompass a wide range of vegetable, fodder and oil crops. The release of their reference genomes has facilitated resequencing collections of B. rapa and B. oleracea aiming to build their variome datasets. These data can be used to investigate the evolutionary relationships between and within the different species and the domestication of the crops, hereafter named morphotypes. These data can also be used in genetic studies aiming at the identification of genes that influence agronomic traits. We selected and resequenced 199 B. rapa and 119 B. oleracea accessions representing 12 and nine morphotypes, respectively. Based on these resequencing data, we obtained 2,249,473 and 3,852,169 high quality SNPs (single-nucleotide polymorphisms), as well as 303,617 and 417,004 InDels for the B. rapa and B. oleracea populations, respectively. The variome datasets of B. rapa and B. oleracea represent valuable resources to researchers working on evolution, domestication or breeding of Brassica vegetable crops.",

author = "Feng Cheng and Jian Wu and Chengcheng Cai and Lixia Fu and Jianli Liang and Theo Borm and Mu Zhuang and Yangyong Zhang and Fenglan Zhang and Guusje Bonnema and Xiaowu Wang",

year = "2016",

doi = "10.1038/sdata.2016.119",

language = "English",

volume = "3",

journal = "Scientific Data",

issn = "2052-4463",

publisher = "Macmillan Publishers",

}

Genome resequencing and comparative variome analysis in a Brassica rapa and Brassica oleracea collection. / Cheng, Feng; Wu, Jian; Cai, Chengcheng; Fu, Lixia; Liang, Jianli; Borm, Theo; Zhuang, Mu; Zhang, Yangyong; Zhang, Fenglan; Bonnema, Guusje; Wang, Xiaowu.

In: Scientific Data, Vol. 3, 160119, 2016.

Research output: Contribution to journal › Article › Academic › peer-review

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AU - Cheng, Feng

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AU - Cai, Chengcheng

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AU - Liang, Jianli

AU - Borm, Theo

AU - Zhuang, Mu

AU - Zhang, Yangyong

AU - Zhang, Fenglan

AU - Bonnema, Guusje

AU - Wang, Xiaowu

PY - 2016

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AB - The closely related species Brassica rapa and B. oleracea encompass a wide range of vegetable, fodder and oil crops. The release of their reference genomes has facilitated resequencing collections of B. rapa and B. oleracea aiming to build their variome datasets. These data can be used to investigate the evolutionary relationships between and within the different species and the domestication of the crops, hereafter named morphotypes. These data can also be used in genetic studies aiming at the identification of genes that influence agronomic traits. We selected and resequenced 199 B. rapa and 119 B. oleracea accessions representing 12 and nine morphotypes, respectively. Based on these resequencing data, we obtained 2,249,473 and 3,852,169 high quality SNPs (single-nucleotide polymorphisms), as well as 303,617 and 417,004 InDels for the B. rapa and B. oleracea populations, respectively. The variome datasets of B. rapa and B. oleracea represent valuable resources to researchers working on evolution, domestication or breeding of Brassica vegetable crops.

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