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

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

doi:10.1016/j.ygeno.2019.11.015

Cited by 14 publications

(12 citation statements)

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“…In addition, marker density was associated with collinearity as more markers meant a greater probability of markers aligning to the corresponding reference genome sequences. The markers on a high-density genetic map were typically developed by reduced-representation sequencing [ 14 , 30 ] or re-sequencing [ 17 – 19 , 31 ], which could yield thousands of randomly distributed markers. But the reference genomes of plants always harbor hundreds of Mbp at least.…”

Section: Discussionmentioning

confidence: 99%

A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.)

Zhao

Xu³

et al. 2021

BMC Plant Biol

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Background Lycium Linn. (Solanaceae) is a genus of economically important plants producing fruits and leaves with high nutritional value and medicinal benefits. However, genetic analysis of this plant and molecular breeding for quality improvement are limited by the lack of sufficient molecular markers. Results In this study, two parental strains, ‘Ningqi No. 1’ (Lycium barbarum L.) and ‘Yunnan Gouqi’ (Lycium yunnanense Kuang et A.M. Lu), and 200 F1 hybrid individuals were resequenced for genetic analysis. In total, 8,507 well-selected SNPs were developed, and a high-density genetic map (NY map) was constructed with a total genetic distance of 2,122.24 cM. A consensus genetic map was established by integrating the NY map and a previously published genetic map (NC map) containing 15,240 SNPs, with a total genetic distance of 3,058.19 cM and an average map distance of 0.21 cM. The 12 pseudochromosomes of the Lycium reference genome were anchored using this consensus genetic map, with an anchoring rate of 64.3%. Moreover, weak collinearities between the consensus map and the pepper, potato, and tomato genomes were observed. Twenty-five stable QTLs were identified for leaf- and fruit-related phenotypes, including fruit weight, fruit longitude, leaf length, the fruit index, and the leaf index; these stable QTLs were mapped to four different linkage groups, with LOD scores ranging from 2.51 to 19.37 and amounts of phenotypic variance explained from 6.2% to 51.9%. Finally, 82 out of 188 predicted genes underlying stable QTLs for fruit-related traits were differentially expressed according to RNA-seq analysis. Conclusions A chromosome-level assembly can provide a foundation for further functional genomics research for wolfberry. The genomic regions of these stably expressed QTLs could be used as targets for further fine mapping and development of molecular markers for marker-assisted selection (MAS). The present study provided valuable information on saturated SNP markers and reliable QTLs for map-based cloning of functional genes related to yield and morphological traits in Lycium spp.

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Section: Discussionmentioning

confidence: 99%

A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.)

Zhao

Xu³

et al. 2021

BMC Plant Biol

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“…The genome of tobacco (4.5 Gb) is complex, with numerous repetitive sequences (Kenton et al 1993). Advances in sequencing technologies and genome assembly methods have enabled the generation of a nearly complete reference genome for allotetraploid tobacco (Thimmegowda et al 2018;Tong et al 2020). In addition, the development of molecular genetic markers is increasing (Ganal et al 2009;Thimmegowda et al 2018).…”

Section: Introductionmentioning

confidence: 99%

“…For example, both restriction site-associated DNA sequencing (RAD-seq) and whole genome resequencing approaches have been employed to identify single-nucleotide polymorphisms (SNPs) and to construct linkage maps (Xiao et al 2015;Thimmegowda et al 2018). Recently, a genetic map with 45,081 SNPs markers has been constructed by whole genome sequencing using a tobacco population including 274 accessions (Tong et al 2020). This high-density genetic map provides a foundation for tobacco quantitative trait locus (QTL) studies.…”

Section: Introductionmentioning

confidence: 99%

“…However, studies of molecular mechanisms underlying related traits are scarce, despite implications for molecular breeding. In this study, we identified QTLs associated with important agronomic traits, chemical compound contents of dry leaves, and hazardous substances in processed cigarettes using a published high-density genetic map with whole genome sequencing (Tong et al 2020). QTLs for seven agronomic traits, including plant height, leaf number, stem girth, internode length, length of the largest leaf, width of the largest leaf, and yield, were mapped to linkage group 6 (LG6).…”

Section: Introductionmentioning

confidence: 99%

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Quantitative trait locus mapping and genomic selection of tobacco (Nicotiana tabacum L.) based on high-density genetic map

Tong

Xiu

Yao

et al. 2021

Plant Biotechnol Rep

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Tobacco (Nicotiana tabacum L.) is an economic crop and a model organism for studies of plant biology and genetics. As an allotetraploid plant generated from interspecific hybridization, tobacco has a massive genome (4.5 Gb). Recently, a genetic map with 45,081 single nucleotide polymorphism (SNP) markers was constructed using whole-genome sequencing data for a tobacco population including 274 individuals. This provides a basis for quantitative trait locus (QTL) mapping and genomic selection, which have been widely applied to other crops but have not been feasible in tobacco. Based on this high-density genetic map, we identified QTLs associated with important agronomic traits, chemical compounds in dry leaves, and hazardous substances in processed cigarettes. The LOD values for major QTLs were highest for agronomic traits, followed by chemical compounds and hazardous substances. In addition to the identification of molecular markers, we evaluated genomic selection models and found that BayesB had the highest prediction accuracy for the recombinant inbred line population. Our results offer new insights into the genetic mechanism underlying important traits, such as agronomic traits and quality-related chemical compounds in tobacco, and will be able to support the application of molecular breeding to tobacco.

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“…nih.gov/bioproject). At present, only a few studies have focused on the genome-wide SNP identification and genetic map construction in tobacco (Matsuoka et al 2004;Edwards et al 2010;Xiao et al 2015;Tong et al 2020).…”

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confidence: 99%

Construction of high-density genetic map and QTL mapping in Nicotiana tabacum backcrossing BC4F3 population using whole-genome sequencing

Tong¹,

Jiang²,

He³

et al. 2021

CZECH J GENET PLANT

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Backcrossing is a powerful tool for plant breeding. The improved marker-assisted backcrossing intends to transfer targeted genes or quantitative trait loci (QTLs) of interest from a donor parent into a recurrent parent. In this study, a tobacco BC4F3 population was generated using Y3 and K326 as hybrid parents and YF1-1 as F<sub>1</sub> parents. High-throughput sequencing data of 381 pedigree populations were used to construct high-density genetic maps containing 24 142 high-quality single nucleotide polymorphism (SNP) markers with an average genetic distance of 0.59 cM. A genome module analysis was then performed for all the offspring. A total of forty-three candidate QTLs for six agronomics traits were identified. This study provides original biomarkers for tobacco breeding and offers clues for prospective backcrossing applications in other plants.

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

Cited by 14 publications

References 46 publications

A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.)

A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.)

Quantitative trait locus mapping and genomic selection of tobacco (Nicotiana tabacum L.) based on high-density genetic map

Construction of high-density genetic map and QTL mapping in Nicotiana tabacum backcrossing BC4F3 population using whole-genome sequencing

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