Construction of a high-density genetic map with whole genome sequencing in Nicotiana tabacum L

Zhijun Tong; Juhong Zhou; Zhihui Xiu; Fangchan Jiao; Yafei Hu; Fengya Zheng; Xuejun Chen; Yanli Li; Dunhuang Fang; Shiming Li; Xingfu Wu; Jianmin Zeng; Shancen Zhao; Jianbo Jian; Bingguang Xiao

doi:10.1016/j.ygeno.2019.11.015

Construction of a high-density genetic map with whole genome sequencing in Nicotiana tabacum L

Genomics. 2020 Mar;112(2):2028-2033. doi: 10.1016/j.ygeno.2019.11.015. Epub 2019 Nov 21.

Authors

Zhijun Tong¹, Juhong Zhou², Zhihui Xiu³, Fangchan Jiao⁴, Yafei Hu⁵, Fengya Zheng⁶, Xuejun Chen⁷, Yanli Li⁸, Dunhuang Fang⁹, Shiming Li¹⁰, Xingfu Wu¹¹, Jianmin Zeng¹², Shancen Zhao¹³, Jianbo Jian¹⁴, Bingguang Xiao¹⁵

Affiliations

¹ Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan 650021, People's Republic of China. Electronic address: tzj861@163.com.
² BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China. Electronic address: zhoujuhong@genomics.cn.
³ BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China. Electronic address: xiuzhihui@genomics.cn.
⁴ Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan 650021, People's Republic of China. Electronic address: jfc99002@163.com.
⁵ BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China. Electronic address: huyafei@genomics.cn.
⁶ BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China. Electronic address: zhengfengya@genomics.cn.
⁷ Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan 650021, People's Republic of China. Electronic address: cxjkm@163.com.
⁸ Joint Institute of Tobacco Molecular Breeding, People's Republic of China. Electronic address: liyanli@genomics.cn.
⁹ Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan 650021, People's Republic of China. Electronic address: fdhkm@sina.com.
¹⁰ Joint Institute of Tobacco Molecular Breeding, People's Republic of China. Electronic address: lishiming@genomics.cn.
¹¹ Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan 650021, People's Republic of China. Electronic address: ynyxwxf@sina.com.
¹² Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan 650021, People's Republic of China. Electronic address: zengjm2017@163.com.
¹³ Joint Institute of Tobacco Molecular Breeding, People's Republic of China. Electronic address: zhaoshancen@genomics.cn.
¹⁴ BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China. Electronic address: jianjianbo@genomics.cn.
¹⁵ Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan 650021, People's Republic of China. Electronic address: xiaobgsubmission@126.com.

PMID: 31760041
DOI: 10.1016/j.ygeno.2019.11.015

Abstract

Tobacco (Nicotiana tabacum L.) is an essential commercial crop and an ideal model plant for biological mechanism studies. As an allopolyploid species, tobacco harbors a massive and complex genome, which makes the application of molecular markers complicated and challenging. In our study, we performed whole-genome sequencing of an intraspecific recombinant inbred line (RIL) population, a F1 generation and their parents. With the Nicotiana tabacum (K326 cultivar) genome as reference, a total of 45,081 markers were characterized to construct the genetic map, which spanned a genetic distance of 3486.78 cM. Evaluation of a two-dimensional heat map proved the high quality of the genetic map. We utilized these markers to anchor scaffolds and analyzed the ancestral genome origin of linkage groups (LGs). Furthermore, such a high-density genetic map will be applied for quantitative trait locus (QTL) detection, gene localization, genome-wide association studies (GWAS), and marker-assisted breeding in tobacco.

Keywords: Genetic linkage map; Resequencing; SNPs; Tobacco.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Contig Mapping
Genetic Linkage*
Genome, Plant*
Nicotiana / genetics*
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Whole Genome Sequencing