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

Tong Z., Jiang S., He W., Chen X., Yin L., Fang D., Hu Y., Jiao F., Zhang Ch., Zeng J., Wu X., Zhao S., Jian J., Xiao B. (2021): Construction of high-density genetic map and QTL mapping in Nicotiana tabacum backcrossing BC4F3 population using whole-genome sequencing. Czech J. Genet. Plant Breed., 57: 102112.

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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 F1 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.

Agacka-Mołdoch M., Rehman Arif M.A., Lohwasser U., Doroszewska T., Lewis R.S., Börner A. (2021): QTL analysis of seed germination traits in tobacco (Nicotiana tabacum L.). Journal of Applied Genetics, Advance Access published March 5, 2021, doi:10.1007/s13353-021-00623-6.
Amankwa G.A., Mishra S., Shearer A.D., Saude C., Van Hooren D.L., Richmond M.D. (2019): CTH144 flue-cured tobacco F1 hybrid. Canadian Journal of Plant Science, 99: 966–968.
Baldwin B.G. (1992): Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: An example from the compositae. Molecular Phylogenetics and Evolution, 1: 3–16.
Bindler G., Plieske J., Bakaher N., Gunduz I., Ivanov N., Van der Hoeven R., Ganal M., Donini P. (2011): A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development. Theoretical and Applied Genetics, 123: 219–230.
Cai C., Deng H., Feng J., Cheng L., Yu J., Wang X. (2014): Preliminary genetic analysis of relevant traits in flue-cured tobacco at growth and development period. Acta Tabacaria Sinica, 20: 70–77, 84.
Chen Y., Chen Y., Shi C., Huang Z., Zhang Y., Li S., Li Y., Ye J., Yu C., Li Z., Zhang X., Wang J., Yang H., Fang L., Chen Q. (2018): SOAPnuke: A MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. GigaScience, 7: 1–6.
Edwards K.D., Bombarely A., Story G.W., Allen F., Mueller L.A., Coates S.A., Jones L. (2010): TobEA: An atlas of tobacco gene expression from seed to senescence. BMC Genomics, 11: 142.
Edwards K.D., Fernandez-Pozo N., Drake-Stowe K., Humphry M., Evans A.D., Bombarely A., Allen F., Hurst R., White B., Kernodle S.P., Bromley J.R., Sanchez-Tamburrino J.P., Lewis R.S., Mueller L.A. (2017): A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency. BMC Genomics, 18: 448.
Gazdová B., Široký J., Fajkus J., Brzobohatý B., Kenton A., Parokonny A., Heslop-Harrison J.S., Palme K., Bezděk M. (1995): Characterization of a new family of tobacco highly repetitive DNA, GRS, specific for the Nicotiana tomentosiformis genomic component. Chromosome Research, 3: 245–254.
Hasan M.M., Rafii M.Y., Ismail M.R., Mahmood M., Alam M.A., Abdul Rahim H., Malek M.A., Latif M.A. (2016): Introgression of blast resistance genes into the elite rice variety MR263 through marker-assisted backcrossing. Journal of the Science of Food and Agriculture, 96: 1297–1305.
Julio E., Denoyes-Rothan B., Verrier J.L., Dorlhac De Borne F. (2006a): Detection of QTLs linked to leaf and smoke properties in Nicotiana tabacum based on a study of 114 recombinant inbred lines. Molecular Breeding, 18: 69–91.
Kimurto P., Oyier M., Mulwa R., Songok S., Towett B., Cheruiyot E., Varshney R.K., Gaur P.M., Mahender T., Ganga Rao N.V.P.R., Silim S., Siambi M. (2017): Performance of marker assisted backcross breeding (MABC) elite chickpea lines under drought conditions in Kenya. In: InterDrought-V, Hyderabad, Feb 21–25, 2017.
Leitch I.J., Hanson L., Lim K.Y., Kovarik A., Chase M.W., Clarkson J.J., Leitch A.R. (2008): The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae). Annals of Botany, 101: 805–814.
Li H.-L., Chen M.-X., Zhou D.-X., Chen S.-H., Tao A.-F., Li Y.-K., Ma H.-B., Qi J.-M., Guo Y.-C. (2011): QTL analysis of six important traits in tobacco (Nicotiana tabacum L.). Acta Agronomica Sinica, 37: 1577–1584.
Lin T.Y., Kao Y.Y., Lin S., Lin R.F., Chen C.M., Huang C.H., Wang C.K., Lin Y.Z., Chen C.C. (2001): A genetic linkage map of Nicotiana plumbaginifolia/Nicotiana longiflora based on RFLP and RAPD markers. Theoretical and Applied Genetics, 103: 905–911.
Ma J.K.C., Drossard J., Lewis D., Altmann F., Boyle J., Christou P., Cole T., Dale P., van Dolleweerd C.J., Isitt V., Katinger D., Lobedan M., Mertens H., Paul M.J., Rademacher T., Sack M., Hundleby P.A.C., Stiegler G., Stoger E., Twyman R.M., Vcelar B., Fischer R. (2015): Regulatory approval and a first-in-human phase I clinical trial of a monoclonal antibody produced in transgenic tobacco plants. Plant Biotechnology Journal, 13: 1106–1120.
Matsuoka K., Demura T., Galis I., Horiguchi T., Sasaki M., Tashiro G., Fukuda H. (2004): A comprehensive gene expression analysis towards the understanding of growth and differentiation of tobacco BY-2 cells. Plant & Cell Physiology, 45: 1280–1289.
McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., Kernytsky A., Garimella K., Altshuler D., Gabriel S., Daly M., DePristo M.A. (2010): The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20: 1297–1303.
Nawaz Z., Kakar K.U., Ullah R., Yu S., Zhang J., Shu Q.Y., Ren X.-L. (2019): Genome-wide identification, evolution and expression analysis of cyclic nucleotide-gated channels in tobacco (Nicotiana tabacum L.). Genomics, 111: 142–158.
Ofner I., Lashbrooke J., Pleban T., Aharoni A., Zamir D. (2016): Solanum pennellii backcross inbred lines (BILs) link small genomic bins with tomato traits. Plant Journal, 87: 151–160.
Pandey K., Dangi R., Prajapati U., Kumar S., Maurya N.K., Singh A.V., Pandey A.K., Singh J., Rajan R. (2019): Advance breeding and biotechnological approaches for crop improvement: A review. International Journal of Chemical Studies, 7: 837–841.
Priyadarshan P.M., Priyadarshan P.M. (2019): Introduction to plant breeding. In: Plant Breeding: Classical to Modern, Singapore, Springer: 3–33.
Qi J.M., Wang T., Chen Sh., Fance P.P., Tao A.F., Liang J.X., Wu W.R. (2006): Genetic diversity and genetic relatives analysis of tobacco germplasm based on inter-simple sequence repeat (ISSR). Acta Agronomica Sinica, 32: 373–378.
Rastas P. (2017): Lep-MAP3: Robust linkage mapping even for low-coverage whole genome sequencing data. Bioinformatics, 33: 3726–3732.
Ren N., Timko M.P. (2001): AFLP analysis of genetic polymorphism and evolutionary relationships among cultivated and wild Nicotiana species. Genome, 44: 559–571.
Saini A.K., Chauhan P.K., Singh V., Sharma P. (2013): Phytochemical, antioxidant and in vitro antibacterial activity of aqueous and ethanolic fruit extracts of Kigelia africana. Indian Journal of Pharmaceutical and Biological Research, 1: 46–52.
Sun M., Cheng L., Jiang C., Zhu C., Ren M., Zhang Y., Zhang Y., Liu D., Zhao Q., Geng R., Hu X., Yang A., Wang Y. (2018): Identification of a major QTL affecting resistance to brown spot in tobacco (Nicotiana tabacum L.) via linkage and association mapping methods. Euphytica, 214: 1–14.
Swanson C.P. (1956): The Genus Nicotiana. Origins, Relationships and Evolution of Its Species in the Light of Their Distribution, Morphology and Cytogenetics. Parts I-V: Distribution, Morphology, Cytology of Species, Cytology of F1 Interspecific Hybrids, Phylesis. Thomas Harper Goodspeed The Genus Nicotiana. Origins, Relationships and Evolution of Its Species in the Light of Their Distribution, Morphology and Cytogenetics. Part VI: Taxonomy. Goodspeed T.H., Wheeler H.M., Hutchinson P.C. The Quarterly Review of Biology, 31: 47–48.
Tong Z.J., Zhang Y.H., Chen X.J., Zeng J.M., Fang D.H., Xiao B.G. (2019): Mapping of quantitative trait loci conferring resistance to brown spot in cigar tobacco cultivar Beinhart1000-1. Acta Agronomica Sinica, 45: 477–482.
Tong Z., Zhou J., Xiu Z., Jiao F., Hu Y., Zheng F., Chen X., Li Y., Fang D., Li S., Wu X., Zeng J., Zhao S., Jian J., Xiao B. (2020): Construction of a high-density genetic map with whole genome sequencing in Nicotiana tabacum L. Genomics, 112: 2028–2033.
Tusé D., Tu T., McDonald K.A. (2014): Manufacturing economics of plant-made biologics: Case studies in therapeutic and industrial enzymes. BioMed Research International, 2014: 256135.
Van Ooijen J.W. (2009): MapQTL 6, Software for the Mapping of Quantitative Trait Loci in Experimental Populations of Diploid Species. Northampton,Advance Access.
Vanhercke T., El Tahchy A., Liu Q., Zhou X.R., Shrestha P., Divi U.K., Ral J.P., Mansour M.P., Nichols P.D., James C.N., Horn P.J., Chapman K.D., Beaudoin F., Riuz-Lopez N., Larkin P.J., de Feyter R.C., Singh S.P., Petrie J.R. (2014): Metabolic engineering of biomass for high energy density: Oilseed-like triacylglycerol yields from plant leaves. Plant Biotechnology Journal, 12: 231–239.
Xiao B.-G., Yang B.-C. (2007): Assessment of genetic diversity among tobacco germplasms by ISSR markers. Scientia Agricultura Sinica, 40: 2153–2161.
Xiao B., Tan Y., Long N., Chen X., Tong Z., Dong Y., Li Y. (2015): SNP-based genetic linkage map of tobacco (Nicotiana tabacum L.) using next-generation RAD sequencing. Journal of Biological Research-Thessaloniki, 22: 11.
Xu Y., Zhang X.Q., Harasymow S., Westcott S., Zhang W., Li C. (2018): Molecular marker-assisted backcrossing breeding: an example to transfer a thermostable β-amylase gene from wild barley. Molecular Breeding, 38: 1–9.
Zhao L., Li W., Wang B., Gao Y., Sui X., LiuY., Chen X., Yao X., Jiao F., Song Z. (2019): Development of a PVY resistant flue-cured tobacco line via EMS mutagenesis of eIF4E. Agronomy, 10: 36.
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