High-density SNP genetic linkage map construction and quantitative trait locus mapping for resistance to cucumber mosaic virus in tobacco (Nicotiana tabacum L.)
Genetic linkage maps are essential for studies of genetics, genomic structure, and genomic evolution, and for mapping quantitative trait loci (QTL). Identification of molecular markers and construction of genetic linkage maps in tobacco (Nicotiana tabacum L.), a classical model plant and important e...
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| Published in | The Crop journal Vol. 7; no. 4; pp. 539 - 547 |
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| Main Authors | , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Elsevier B.V
01.08.2019
KeAi Communications Co., Ltd |
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| Online Access | Get full text |
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| Abstract | Genetic linkage maps are essential for studies of genetics, genomic structure, and genomic evolution, and for mapping quantitative trait loci (QTL). Identification of molecular markers and construction of genetic linkage maps in tobacco (Nicotiana tabacum L.), a classical model plant and important economic crop, have remained limited. In the present study we identified a large number of single nucleotide polymorphism (SNP) markers and constructed a high-density SNP genetic map for tobacco using restriction site-associated DNA sequencing. In 1216.30 Gb of clean sequence obtained using the Illumina HiSeq 2000 sequencing platform, 99,647,735 SNPs were identified that differed between 203 sequenced plant genomes and the tobacco reference genome. Finally, 13,273 SNP markers were mapped on 24 high-density tobacco genetic linkage groups. The entire linkage map spanned 3421.80 cM, with a mean distance of 0.26 cM between adjacent markers. Compared with genetic linkage maps published previously, this version represents a considerable improvement in the number and density of markers. Seven QTL for resistance to cucumber mosaic virus (CMV) in tobacco were mapped to groups 5 and 8. This high-density genetic map is a promising tool for elucidation of the genetic bases of QTL and for molecular breeding in tobacco. |
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| AbstractList | Genetic linkage maps are essential for studies of genetics, genomic structure, and genomic evolution, and for mapping quantitative trait loci (QTL). Identification of molecular markers and construction of genetic linkage maps in tobacco (Nicotiana tabacum L.), a classical model plant and important economic crop, have remained limited. In the present study we identified a large number of single nucleotide polymorphism (SNP) markers and constructed a high-density SNP genetic map for tobacco using restriction site-associated DNA sequencing. In 1216.30 Gb of clean sequence obtained using the Illumina HiSeq 2000 sequencing platform, 99,647,735 SNPs were identified that differed between 203 sequenced plant genomes and the tobacco reference genome. Finally, 13,273 SNP markers were mapped on 24 high-density tobacco genetic linkage groups. The entire linkage map spanned 3421.80 cM, with a mean distance of 0.26 cM between adjacent markers. Compared with genetic linkage maps published previously, this version represents a considerable improvement in the number and density of markers. Seven QTL for resistance to cucumber mosaic virus (CMV) in tobacco were mapped to groups 5 and 8. This high-density genetic map is a promising tool for elucidation of the genetic bases of QTL and for molecular breeding in tobacco. Genetic linkage maps are essential for studies of genetics, genomic structure, and genomic evolution, and for mapping quantitative trait loci (QTL). Identification of molecular markers and construction of genetic linkage maps in tobacco (Nicotiana tabacum L.), a classical model plant and important economic crop, have remained limited. In the present study we identified a large number of single nucleotide polymorphism (SNP) markers and constructed a high-density SNP genetic map for tobacco using restriction site-associated DNA sequencing. In 1216.30 Gb of clean sequence obtained using the Illumina HiSeq 2000 sequencing platform, 99,647,735 SNPs were identified that differed between 203 sequenced plant genomes and the tobacco reference genome. Finally, 13,273 SNP markers were mapped on 24 high-density tobacco genetic linkage groups. The entire linkage map spanned 3421.80 cM, with a mean distance of 0.26 cM between adjacent markers. Compared with genetic linkage maps published previously, this version represents a considerable improvement in the number and density of markers. Seven QTL for resistance to cucumber mosaic virus (CMV) in tobacco were mapped to groups 5 and 8. This high-density genetic map is a promising tool for elucidation of the genetic bases of QTL and for molecular breeding in tobacco. Keywords: Single nucleotide polymorphism, Genetic linkage map, Tobacco, Cucumber mosaic virus, Quantitative trait loci |
| Author | Cheng, Lirui Chen, Xiaocui Ren, Min Ma, Bing Geng, Ruimei Cheng, Yazeng Yang, Aiguo Jiang, Caihong Liu, Dan |
| Author_xml | – sequence: 1 givenname: Lirui surname: Cheng fullname: Cheng, Lirui email: chenglirui@caas.cn organization: Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, Shandong, China – sequence: 2 givenname: Xiaocui surname: Chen fullname: Chen, Xiaocui organization: Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, Shandong, China – sequence: 3 givenname: Caihong surname: Jiang fullname: Jiang, Caihong organization: Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, Shandong, China – sequence: 4 givenname: Bing surname: Ma fullname: Ma, Bing organization: Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, Shandong, China – sequence: 5 givenname: Min surname: Ren fullname: Ren, Min organization: Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, Shandong, China – sequence: 6 givenname: Yazeng surname: Cheng fullname: Cheng, Yazeng organization: Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, Shandong, China – sequence: 7 givenname: Dan surname: Liu fullname: Liu, Dan organization: Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, Shandong, China – sequence: 8 givenname: Ruimei surname: Geng fullname: Geng, Ruimei organization: Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, Shandong, China – sequence: 9 givenname: Aiguo surname: Yang fullname: Yang, Aiguo email: yangaiguo@caas.cn organization: Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, Shandong, China |
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| Keywords | Quantitative trait loci Tobacco Single nucleotide polymorphism Genetic linkage map Cucumber mosaic virus |
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| SubjectTerms | chromosome mapping Cucumber mosaic virus DNA shuffling evolution Genetic linkage map genetic markers genome genomics linkage groups Nicotiana tabacum Quantitative trait loci sequence analysis Single nucleotide polymorphism Tobacco |
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| Title | High-density SNP genetic linkage map construction and quantitative trait locus mapping for resistance to cucumber mosaic virus in tobacco (Nicotiana tabacum L.) |
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