High-density SNP genetic linkage map construction and quantitative trait locus mapping for resistance to cucumber mosaic virus in tobacco (Nicotiana tabacum L.)

The Crop Journal - Tập 7 - Trang 539-547 - 2019
Lirui Cheng1, Xiaocui Chen1,2, Caihong Jiang1, Bing Ma1, Min Ren1, Yazeng Cheng1, Dan Liu1, Ruimei Geng1, Aiguo Yang1
1Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266100, Shandong, China
2Key Laboratory of Zunyi Crop Gene Resource and Germplasm Innovation, Zunyi Academy of Agricultural Sciences, Zunyi 563006, Guizhou, China

Tài liệu tham khảo

Leitch, 2008, The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae), Ann. Bot., 101, 805, 10.1093/aob/mcm326 Sierro, 2013, Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis, Genome Biol., 14, R60, 10.1186/gb-2013-14-6-r60 Sierro, 2014, The tobacco genome sequence and its comparison with those of tomato and potato, Nat. Commun., 5, 3833, 10.1038/ncomms4833 Daniell, 2001, Medical molecular farming: production of antibodies, biopharmaceuticals and edible vaccines in plants, Trends Plant Sci., 219, 10.1016/S1360-1385(01)01922-7 Fischer, 2004, Plant-based production of biopharmaceuticals, Curr. Opin. Plant Biol., 7, 152, 10.1016/j.pbi.2004.01.007 Lin, 2001, A genetic linkage map of Nicotiana plumbaginifolia/Nicotiana longiflora based on RFLP and RAPD markers, Theor. Appl. Genet., 103, 905, 10.1007/s001220100618 Nishi, 2003, Identification of DNA markers of tobacco linked to bacterial wilt resistance, Theor. Appl. Genet., 106, 765, 10.1007/s00122-002-1096-9 Bindler, 2007, A microsatellite marker based linkage map of tobacco, Theor. Appl. Genet., 114, 341, 10.1007/s00122-006-0437-5 Bindler, 2011, A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development, Theor. Appl. Genet., 123, 219, 10.1007/s00122-011-1578-8 Tong, 2012, Large-scale development of microsatellite markers in Nicotiana tabacum and construction of a genetic map of flue-cured tobacco, Plant Breed., 131, 674, 10.1111/j.1439-0523.2012.01984.x Lu, 2013, Development of DArT markers for a linkage map of flue-cured tobacco, Chin. Sci. Bull., 58, 641, 10.1007/s11434-012-5453-z Ganal, 2009, SNP identification in crop plants, Curr. Opin. Plant Biol., 12, 211, 10.1016/j.pbi.2008.12.009 Huang, 2013, Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus, BMC Genomics, 14, 717, 10.1186/1471-2164-14-717 Clevenger, 2015, Single nucleotide polymorphism identification in polyploids: a review, example, and recommendations, Mol. Plant, 8, 831, 10.1016/j.molp.2015.02.002 Singh, 2015, Single-nucleotide polymorphism identification and genotyping in Camelina sativa, Mol. Breed., 35, 35, 10.1007/s11032-015-0224-6 Ansorge, 2009, Next-generation DNA sequencing techniques, New Biotechnol., 25, 195, 10.1016/j.nbt.2008.12.009 Li, 2009, SNP detection for massively parallel whole-genome resequencing, Genome Res., 19, 1124, 10.1101/gr.088013.108 Varshney, 2009, Next-generation sequencing technologies and their implications for crop genetics and breeding, Trends Biotechnol., 27, 522, 10.1016/j.tibtech.2009.05.006 Metzker, 2010, Sequencing technologies-the next generation, Nat. Rev. Genet., 11, 31, 10.1038/nrg2626 Wei, 2013, Applications and challenges of next-generation sequencing in Brassica species, Planta, 238, 1005, 10.1007/s00425-013-1961-6 Baird, 2008, Rapid SNP discovery and genetic mapping using sequenced RAD markers, PLoS One, 3, 10.1371/journal.pone.0003376 Davey, 2010, RADSeq: next-generation population genetics, Brief. Funct. Genomics, 9, 416, 10.1093/bfgp/elq031 Kakioka, 2013, A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae), BMC Genomics, 14, 32, 10.1186/1471-2164-14-32 Barchi, 2011, Identification of SNP and SSR markers in eggplant using RAD tag sequencing, BMC Genomics, 12, 304, 10.1186/1471-2164-12-304 Barchi, 2012, A RAD tag derived marker based eggplant linkage map and the location of QTLs determining anthocyanin pigmentation, PLoS One, 7, 10.1371/journal.pone.0043740 Chutimanitsakun, 2011, Construction and application for QTL analysis of a restriction site associated DNA (RAD) linkage map in barley, BMC Genomics, 11, 4, 10.1186/1471-2164-12-4 Poland, 2012, Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach, PLoS One, 7, 10.1371/journal.pone.0032253 Wang, 2015, Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing, DNA Res., 22, 147, 10.1093/dnares/dsu047 Wang, 2015, Molecular mapping of restriction-site associated DNA markers in allotetraploid upland cotton, PLoS One, 10 Zhou, 2014, Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq), BMC Genomics, 15, 35, 10.1186/1471-2164-15-351 Gupta, 2015, Genome-wide polymorphism detection in peanut using next-generation restriction-site-associated DNA (RAD) sequencing, Mol. Breed., 35, 145, 10.1007/s11032-015-0343-0 Xiao, 2015, SNP-based genetic linkage map of tobacco (Nicotiana tabacum L.) using next-generation RAD sequencing, J. Biol. Res., 22, 11 Gong, 2016, Construction of a high-density SNP genetic map in flue-cured tobacco based on SLAF-seq, Mol. Breed., 36, 100, 10.1007/s11032-016-0514-7 Scholthof, 2011, Top 10 plant viruses in molecular plant pathology, Mol. Plant Pathol., 12, 938, 10.1111/j.1364-3703.2011.00752.x Troutman, 1958, Resistance in tobacco to CMV, Virology, 6, 303, 10.1016/0042-6822(58)90084-9 Holmes, 1960, Inheritance in tobacco of an improved resistance to infection by TMV, Virology, 12, 59, 10.1016/0042-6822(60)90149-5 Holmes, 1961, Concomitant inheritance of resistance to several viral diseases in tobacco, Virology, 13, 409, 10.1016/0042-6822(61)90271-9 Wan, 1983, Breeding tobacco resistant to cucumber mosaic virus in Taiwan, Euphytica, 33, 17, 10.1007/BF00022745 Li, 2008, SOAP: short oligonucleotide alignment program, Bioinformatics, 24, 713, 10.1093/bioinformatics/btn025 Van Ooijen, 2006 Voorrips, 2002, MapChart: software for the graphical presentation of linkage maps and QTLs, J. Hered., 93, 77, 10.1093/jhered/93.1.77 Ren, 2009, Rapid propagation technology study on variable plant of tobacco variety “Hongda”, J. Yunnan Agric. Univ., 24, 913 Li, 2007, A modified algorithm for the improvement of composite interval mapping, Genetics, 175, 361, 10.1534/genetics.106.066811 Zhang, 2008, Interactions between markers can be caused by the dominance effect of quantitative trait loci, Genetics, 180, 1177, 10.1534/genetics.108.092122 Meng, 2015, QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations, Crop J., 3, 269, 10.1016/j.cj.2015.01.001 Churchill, 1994, Empirical threshold value for quantitative trait mapping, Genetics, 138, 963, 10.1093/genetics/138.3.963 Karlin, 1997, Compositional differences within and between eukaryotic genomes, Proc. Natl. Acad. Sci. U. S. A., 94, 10227, 10.1073/pnas.94.19.10227 Zhao, 2014, Rapid SNP discovery and a RAD-based high-density linkage map in jujube (Ziziphus Mill.), PLoS One, 9 Julio, 2006, Detection of QTLs linked to leaf and smoke properties in Nicotiana tabacum based on a study of 114 recombinant inbred lines, Mol. Breed., 18, 69, 10.1007/s11032-006-9019-0 Vontimitta, 2012, Mapping of quantitative trait loci affecting resistance to Phytophthora nicotianae in tobacco (Nicotiana tabacum L.) line Beinhart1000, Mol. Breed., 29, 89, 10.1007/s11032-010-9528-8 Xiao, 2013, Location of genomic regions contributing to resistance in tobacco cultivar Florida 301, Crop Sci., 53, 473, 10.2135/cropsci2012.06.0376 Lan, 2014, Mapping of quantitative trait loci conferring resistance to bacterial wilt in tobacco (Nicotiana tabacum L.), Plant Breed., 133, 672, 10.1111/pbr.12202 Cheng, 2015, Quantitative trait loci mapping for plant height in tobacco using linkage and association mapping methods, Crop Sci., 55, 641, 10.2135/cropsci2014.05.0404 Lim, 2004, Genome evolution in allotetraploid Nicotiana, Biol. J. Linn. Soc., 82, 599, 10.1111/j.1095-8312.2004.00344.x Doyle, 2008, Evolutionary genetics of genome merger and doubling in plants, Annu. Rev. Genet., 42, 443, 10.1146/annurev.genet.42.110807.091524 Palukaitis, 1992, Cucumber mosaic virus, Adv. Virus Res., 41, 281, 10.1016/S0065-3527(08)60039-1 Chen, 2015, Assessing the genetic diversity and resistance to cucumber mosaic virus and tobacco etch virus of tobacco cultivars in China, Australas. Plant Pathol., 44, 365, 10.1007/s13313-015-0350-y Takahashi, 2001, Mapping the virus and host genes involved in the resistance response in cucumber mosaic virus-infected Arabidopsis thaliana, Plant Cell Physiol., 42, 340, 10.1093/pcp/pce039 Kang, 2010, Molecular mapping and characterization of a single dominant gene controlling CMV resistance in peppers (Capsicum annuum L.), Theor. Appl. Genet., 120, 1587, 10.1007/s00122-010-1278-9 Essafi, 2009, Dissection of the oligogenic resistance to cucumber mosaic virus in the melon accession PI 161375, Theor. Appl. Genet., 118, 275, 10.1007/s00122-008-0897-x Guo, 2017, Rapid identification of QTLs underlying resistance to cucumber mosaic virus in pepper (Capsicum frutescens), Theor. Appl. Genet., 130, 41, 10.1007/s00122-016-2790-3 Shi, 2018, Inheritance and QTL mapping of cucumber mosaic virus resistance in cucumber (Cucumis sativus L.), PLoS One, 13, 10.1371/journal.pone.0200571