Dissection of Genetic Variations for Tobacco Bacterial Wilt Resistance Based on Joint Linkage and Linkage Disequilibrium Mapping

LAI Ruiqiang; LI Ronghua; XIA Yanshi; GUO Peiguo; YUAN Qinghua; ZHAO Weicai; ZHANG Zhenchen

doi:10.13496/j.issn.1007-5119.2019.06.001

CHINESE TOBACCO SCIENCE > 2019 > 40(6): 1-10. > DOI: 10.13496/j.issn.1007-5119.2019.06.001

LAI Ruiqiang, LI Ronghua, XIA Yanshi, GUO Peiguo, YUAN Qinghua, ZHAO Weicai, ZHANG Zhenchen. Dissection of Genetic Variations for Tobacco Bacterial Wilt Resistance Based on Joint Linkage and Linkage Disequilibrium Mapping[J]. CHINESE TOBACCO SCIENCE, 2019, 40(6): 1-10. DOI: 10.13496/j.issn.1007-5119.2019.06.001

Citation:

PDF (583 KB)

Dissection of Genetic Variations for Tobacco Bacterial Wilt Resistance Based on Joint Linkage and Linkage Disequilibrium Mapping

1. School of Life Sciences, Guangzhou University, Guangzhou 510006, China;
2. Guangdong Academy of Agricultural Sciences Institute of Crops, Guangzhou 510643, China;
3. Guangdong Tobacco Nanxiong Research Institute, Nanxiong, Guangdong 512400, China

More Information

Received Date: June 24, 2019
Revised Date: October 03, 2019
Available Online: November 30, 2023

Graphical Abstract

Abstract

Abstract

A population with 133 F7 recombinant inbred lines (RIL) derived from the cross of “Yueyan 98”×“118-3” and a natural population with 94 tobacco accessions were used as materials, and joint linkage and linkage disequilibrium (LD) mapping analysis for tobacco bacterial wilt (TBW) resistance was carried out by using 253 SSR and 293 InDel markers. Four QTLs with 12%-30.10% of the explanation rate were detected by linkage analysis of the RIL population in four environments; and 8 haplotypes were found to be closely related to TBW resistance in three environments and explained 8.78%-11.42% of phenotypic variation by LD mapping with natural population. The integrated linkage-LD mapping of the RIL and natural populations was carried out and 8 haplotypes were detected to be closely associated with TBW resistance and explained 4.95%-6.93% of phenotypic variation. Four haplotypes were found to be associated with TBW resistance in at least two of the three analytical methods, two (Hap227 and Hap370) of them are with positive phenotypic effect, and the other two (Hap289, Hap368) are with negative effect. The results indicate that the strategy of joint linkage-LD mapping could accurately detect QTLs related to TBW resistance, and these haplotypes could provide reference for TBW resistance research and screening of TBW resistance materials.
- tobacco,
- bacterial wilt resistance,
- linkage analysis,
- association analysis,
- joint linkage and linkage disequilibrium mapping

FullText(HTML)

References (44)

References

[1]	LAN T, ZHENG S, YANG L, et al. Mapping of quantitative trait loci conferring resistance to bacterial wilt in tobacco (Nicotiana tabacum L.)[J]. Plant Breeding, 2015, 133(5):672-677.
[2]	NISHI T, TAJIMA T, NOGUCHI S, et al. Identification of DNA markers of tobacco linked to bacterial wilt resistance[J]. Theoretical and Applied Genetics, 2003, 106(4):765-770.
[3]	QIAN Y, WANG X, WANG D, et al. The detection of QTLs controlling bacterial wilt resistance in tobacco (N. tabacum, L.)[J]. Euphytica, 2013, 192(2):259-266.
[4]	DRAKE-STOWE K, BAKAHER N, GOEPFERT S, et al. Multiple disease resistance loci affect soilborne disease resistance in tobacco (Nicotiana tabacum)[J]. Phytopathology, 2017, 107(9):1055-1061.
[5]	袁清华,马柱文,张振臣,等. 烟草品种大叶密合抗青枯病相关QTL的检测[J]. 中国烟草学报,2018,24(3):77-81. YUAN Q H, MA Z W, ZHANG Z C, et al. Detection of QTL associated with tobacco bacterial wilt resistance in cultivar Dayemihe[J]. Acta Tabacaria Sinica, 2018, 24(3):77-81.
[6]	FLINT-GARCIA S A, THUILLET A C, YU J, et al. Maize association population:a high-resolution platform for quantitative trait locus dissection[J]. Plant Journal for Cell & Molecular Biology, 2005, 44(6):1054-1064.
[7]	SALVI S, TUBEROSA R. To clone or not to clone plant QTLs:present and future challenges[J]. Trends in Plant Science, 2005, 10(6):297-304.
[8]	ERSOZ E S, YU J, BUCKLER E S. Applications of linkage disequilibrium and association mapping in crop plants[M]//Genomics-assisted crop improvement. Dordrecht:Springer Netherlands, 2007:97-119.
[9]	吴超,夏岩石,李荣华,等. 烟草青枯病抗性与分子标记的关联分析[J]. 烟草科技,2015(10):1-12. WU C, XIA Y S, LI R H, et al. Association analysis of tobacco bacterial wilt resistance with molecular markers[J]. Tobacco Science & Technology, 2015(10):1-12.
[10]	赖瑞强,李荣华,夏岩石,等. 烟草种质的SSR标记遗传多样性及青枯病抗性的关联分析[J]. 中国烟草学报,2018,24(6):67-77. LAI R Q, LI R H, XIA Y S, et al. SSR marker-based genetic diversity analysis of tobacco germplasm and association analysis with resistance to bacterial wilt[J]. Acta Tabacaria Sinica, 2018, 24(6):67-77.
[11]	MACKAY I, POWELL W. Methods for linkage disequilibrium mapping in crops[J]. Trends in Plant Science, 2007, 12(2):57-63.
[12]	COLLARD BCY, JAHUFER MZZ, BROUWER J B, et al. An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement:the basic concepts[J]. Euphytica, 2005, 142(1-2):169-196.
[13]	MYLES S, PEIFFER J, BROWN P, et al. Author information. association mapping:critical considerations shift from genotyping to experimental design[J]. Plant Cell, 2009, 21(8):2194-2202.
[14]	DU Q, GONG C, WANG Q, et al. Genetic architecture of growth traits in populus revealed by integrated quantitative trait locus (QTL) analysis and association studies[J]. New Phytologist, 2015, 209(3):1067-1082.
[15]	LOU Q, CHEN L, MEI H, et al. Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice[J]. Journal of Experimental Botany, 2015, 66(15):4749-4757.
[16]	ZHANG C, ZHOU Z, YONG H, et al. Analysis of the genetic architecture of maize ear and grain morphological traits by combined linkage and association mapping[J]. Theoretical and Applied Genetics, 2017, 130(5):1011-1029.
[17]	刘文杰,李荣华,夏岩石,等. 利用荧光SSR和MFLP标记技术分析烟草核心种质的遗传多样性[J]. 分子植物育种,2016,14(10):2869-2881. LIU W J, LI R H, XIA Y S, et al. Analysis of genetic diversity for core tobacco germplasm by using fluorescent SSR and fluorescent MFLP marker techniques[J]. Molecular Plant Breeding, 2016, 14(10):2869-2881.
[18]	申莉莉. 烟草突变体筛选与鉴定方法篇:2.烟草抗主要病虫害突变体的筛选与鉴定[J]. 中国烟草科学,2012,33(2):102-104. SHEN L L. Screening and identification methods of tobacco mutants:2. screening and identification of tobacco resistant mutants to main pests and diseases[J]. Chinese Tobacco Science, 2012, 33(2):102-104.
[19]	高加明,王志德,张兴伟,等. 香料烟青枯病抗性基因的遗传分析[J]. 中国烟草科学,2010,31(1):1-4. GAO J M, WANG Z D, ZHANG X W, et al. Genetic analysis on resistance to bacterial wilt in oriental tobacco[J]. Chinese Tobacco Science, 2010, 31(1):1-4.
[20]	李荣华,夏岩石,刘顺枝,等. 改进的CTAB提取植物DNA方法[J]. 实验室研究与探索,2009,28(9):14-16. LI R H, XIA Y S, LIU S Z, et al. CTAB-improved method of DNA extraction in plant[J]. Research and Exploration in Laboratory, 2009, 28(9):14-16.
[21]	BINDLER G, PLIESKE J, BAKAHER, N, et al. A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development[J]. Theoretical & Applied Genetics, 2011, 123(2):219-230.
[22]	BINDLER G, VAN Der HOEVEN R, GUNDUZ I, et al. A microsatellite marker based linkage map of tobacco[J]. Theoretical & Applied Genetics, 2007, 114(2):341-349.
[23]	TONG Z, YANG Z, CHEN X, et al. Large-scale development of microsatellite markers in Nicotiana tabacum and construction of a genetic map of flue-cured tobacco[J]. Plant Breeding, 2012, 131(5):674-680.
[24]	范江,刘勇,童治军,等. 烤烟品种'Oxford207'青枯病抗性的遗传分析与分子标记初选[J]. 中国农学通报,2013,29(34):50-55. FAN J, LIU Y, TONG Z J, et al. Inheritance of resistance to Ralstonia solanacearum in flue-cured tobacco ‘Oxford07’ and molecular marker screen[J]. Chinese Agricultural Science Bulletin, 2013, 29(34):50-55.
[25]	李海洋,李荣华,夏岩石,等. 基于RAD-seq数据开发烟草多态性SSR标记[J]. 中国烟草科学,2018,39(1):1-9. LI H Y, LI R H, XIA Y S, et al. Development of polymorphic SSR markers in tobacco based on RAD sequencing[J]. Chinese Tobacco Science, 2018, 39(1):1-9.
[26]	郭培国,刘文杰,李海洋,等. 一种快速有效检测SSR标记的非变性聚丙烯酰胺凝胶的银染方法[J]. 广州大学学报(自然科学版),2016,15(4):8-12,49. GUO P G, LIU W J, LI H Y, et al. A rapid and effective method of silver staining for detecting SSR markers in nondenaturing polyacrylamide gels[J]. Journal of Guangzhou University(Natural Science Edition), 2016, 15(4):8-12, 49.
[27]	ZERR T, HENIKOFF S. Automated band mapping in electrophoretic gel image using background information[J]. Nucleic Acids Research, 2005, 33(9):2806-2812.
[28]	刘凯,邓志英,张莹,等. 小麦茎秆断裂强度相关性状QTL的连锁和关联分析[J]. 作物学报,2017,43(4):483-495. LIU K, DENG Z Y, ZHANG Y, et al. Linkage analysis and genome-wide association study of QTLs controlling stem-breaking-strength-related traits in wheat[J]. Acta Agronomica Sinica, 2017, 43(4):483-495.
[29]	CHURCHILL G A, DOERGE R W. Empirical threshold values for quantitative trait mapping[J]. Genetics, 1994, 138(3):963-971.
[30]	BARRETT J C, FRY B, MALLER J, et al. Haploview:analysis and visualization of LD and haplotype maps[J]. Bioinformatics, 2005, 21(2):263-5.
[31]	YU J, PRESSOIR G, BRIGGS W H, et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness[J]. Nature Genetics, 2006, 38(2):203-208.
[32]	BENJAMINI Y H, HOCHBERG Y. Controlling the false discovery rate-a practical and powerful approach to multiple testing[J]. Journal of the Royal Statistical Society. Series B:Methodological, 1995, 57:289-300.
[33]	LU Y, ZHANG S, SHAH T, et al. Joint linkage-linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize[J]. Proc Natl Acad Sci USA, 2010, 107(45):19585-19590.
[34]	ZHANG T, QIAN N, ZHU X, et al. Variations and transmission of QTL alleles for yield and fiber qualities in upland cotton cultivars developed in China[J]. PLoS One, 2013, 8(2):e57220.
[35]	何云刚,金力,黄薇. 单核苷酸多态性与连锁不平衡研究进展[J]. 基础医学与临床,2004,24(5):487-490. HE Y G, JIN L, HUANG W. Advance in the research of single nucleotide polymorphism and linkage disequilibrium[J]. Basic Medical Sciences and Clinics, 2004, 24(5):487-490.
[36]	李英慧,袁翠平,张辰,等. 基于大豆胞囊线虫病抗性候选基因的SNP位点遗传变异分析[J]. 遗传,2009,31(12):1259-1264. LI Y H, YUAN C P, ZHANG C, et al. Genetic variation of SNP loci based on candidate gene for resistance to soybean cyst nematode[J]. Hereditas, 2009, 31(12):1259-1264.
[37]	谭贤杰,吴子恺,程伟东,等. 关联分析及其在植物遗传学研究中的应用[J]. 植物学报,2011,46(1):108-118. TAN X J, WU Z K, CHENG W D, et al. Association analysis and its application in plant genetic research[J]. Bulletin of Botany, 2011, 46(1):108-118.
[38]	PHILLIPS M S, LAWRENCE R, SACHIDANANDAM R, et al. Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots[J]. Nature Genetics, 2003, 33(3):382-387.
[39]	王荣焕,王天宇,黎裕. 关联分析在作物种质资源分子评价中的应用[J]. 植物遗传资源学报,2007,8(3):366-372. WANG R H, WANG T Y, LI Y. Application of association analysis in molecular evaluation of crop germplasm resources[J]. Journal of Plant Genetic Resources, 2007, 8(3):366-372.
[40]	MATSUDA T, OHASHI Y. Inheritance of resistance to bacterial wilt resistant varieties in tobacco[J]. Jap. Tour. Breeding, 1973, 23(4):175-180.
[41]	MATSUDA T. Fundamental studies on the breeding of bacterial wilt resistant varieties in tobacco[J]. Bulletin of the Utsunomiya Tobacco Experiment Station, 1997, 15:1-95.
[42]	范江. 烟草种质青枯病抗性鉴定与分子标记筛选[D]. 长沙:湖南农业大学,2012. FAN J. Tobacco germplasm bacterial wilt resistance identification and molecular marker screening[D]. Changsha:Hunan Agricultural University, 2012.
[43]	冯芳君,罗利军,李荧,等. 水稻InDel和SSR标记多态性的比较分析[J]. 分子植物育种,2005,3(5):725-730. FENG F J, LUO L J, LI Y, et al. Comparative analysis of polymorphism of InDel and SSR markers in rice[J]. Molecular Plant Breeding, 2005, 3(5):725-730.
[44]	杨友才,周清明,朱列书. 烟草青枯病抗性基因的遗传分析及RAPD标记[J]. 中国烟草学报,2006,12(2):38-42. YANG Y C, ZHOU Q M, ZHU L S. Heredity and RAPD markers analysis of resistance gene to tobacco bacterial wilt[J]. Acta Tabacaria Sinica, 2006, 12(2):38-42.