全基因组关联分析在茶叶研究中的应用进展
CSTR:
作者:
作者单位:

南京农业大学园艺学院,南京 210095

作者简介:

房婉萍,E-mail:fangwp@njau.edu.cn

通讯作者:

马媛春,E-mail:myc@njau.edu.cn

中图分类号:

S571.103

基金项目:

国家自然科学基金项目(31972460);国家现代茶叶产业技术体系专项(CARS-19);江苏省一带一路创新合作项目(BZ2019012);贵州省科技计划项目(ZK[2021]154)


Application of genome-wide association analysis in studying tea
Author:
Affiliation:

College of Horticulture,Nanjing Agricultural University,Nanjing 210095,China

  • 摘要
  • | |
  • 访问统计
  • |
  • 参考文献 [60]
  • |
  • 相似文献 [20]
  • |
  • 引证文献
  • | |
  • 文章评论
    摘要:

    全基因组关联分析(genome-wide association analysis,GWAS)是以高通量测序技术为基础,结合生物信息学和统计学方法,在全基因组水平上鉴定调控复杂性状的基因变异,是研究复杂农艺性状和遗传变异最有力和最有效的研究方法,其核心是研究遗传变异和目标性状之间的关联。GWAS研究检测到的关联位点一般很少,而且关联的位点仅能解释很少一部分性状变异。本文介绍了影响GWAS的主要因素,总结了GWAS在茶叶饮料消费、茶树重要农艺性状、茶叶品质和茶树群体结构研究中取得的一系列进展,提出了茶树GWAS研究中遇到的问题和未来的发展方向。

    Abstract:

    Genome-wide association analysis(GWAS) is based on high-throughput sequencing technology,combined with bioinformatics and statistical methods,to identify genetic variants that regulate complex traits at the genome-wide level.It is the most powerful and effective method to study the genetic variation of complex agronomic traits and diseases,and its core is to study the association between genetic variation and target traits.This review briefly introduces the basic principles,processes and influencing factors of GWAS analysis.A series of progress made by GWAS in studying the tea beverage consumption,important agronomic traits of tea trees,tea quality and the population structure of tea plant were summarized.Finally,the problems encountered and the direction of development in the GWAS research of tea plant were discussed.It will provide a basis for using GWAS in further researches on the selection of tea consumers,the genetics and breeding of tea plant.

    参考文献
    [1] 叶乃兴.茶学研究法[M].北京:中国农业出版社,2011.YE N X.Research methods of tea science[M].Beijing:China Agriculture Press,2011 (in Chinese).
    [2] ZHANG X T,CHEN S,SHI L Q,et al.Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis[J/OL].Nature genetics,2021,53 (6):1250[2022-03-07].https://doi.org/10.1038/s41588-021-00895-y.
    [3] LIN X H,SUN D W.Recent developments in vibrational spectroscopic techniques for tea quality and safety analyses[J].Trends in food science & technology,2020,104:163-176.
    [4] ZHANG L,HO C T,ZHOU J,et al.Chemistry and biological activities of processed Camellia sinensis teas:a comprehensive review[J].Comprehensive reviews in food science and food safety,2019,18(5):1474-1495.
    [5] XIA E H,TONG W,WU Q,et al.Tea plant genomics:achievements,challenges and perspectives[J/OL].Horticulture research,2020,7 (1):7 [2022-03-07].https://doi.org/10.1038/s41438-019-0225-4.
    [6] XIA E H,ZHANG H B,SHENG J,et al.The tea plant genome provides insights into tea flavor and independent evolution of caffeine biosynthesis[J].Molecular plant,2017,10(6):866-877.
    [7] CHEN J D,ZHENG C M,JIAN Q J,et al.The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization event in tea plant[J].Horticulture research,2020,7 (1):63-73.
    [8] XIA E H,TONG W,HOU Y,et al.The reference genome of tea plant and resequencing of 81 diverse accessions provide insights into its genome evolution and adaptation[J].Molecular plant,2020,13(7):1013-1026.
    [9] ZHANG Q J,LI W,LI K,et al.The chromosome-level reference genome of tea tree unveils recent bursts of non-autonomous LTR retrotransposons in driving genome size evolution[J].Molecular plant,2020,13(7):935-938.
    [10] WANG X C,FENG H,CHANG Y X,et al.Population sequencing enhances understanding of tea plant evolution[J/OL].Nature communications,2020,11 (1):4447 [2022-03-07].https://doi.org/10.1038 /s41467-020-18228-8.
    [11] ZHANG W Y,ZHANG Y J,QIU H J,et al.Genome assembly of wild tea tree dasz reveals pedigree and selection history of tea varieties[J/OL].Nature communications,2020,11 (1):3719 [2022-03-07].https://doi.org/10.1038/s41467-020-17498-6.
    [12] WANG P J,YU J X,JIN S,et al.Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome[J/OL].Horticulture research,2021,8 (1):107 [2022-03-07].https://doi.org/10.1038/s41438-021-00542-x.
    [13] ERSOZ E S,YU H M,BUCKLER E S.Applications of linkage disequilibrium and association mapping in crop plants[M].Dordrecht:Springer ,2008:97-119.
    [14] 赵振卿,顾宏辉,盛小光,等.作物数量性状位点研究进展及其育种应用[J].核农学报,2014,28(9):1615-1624.ZHAO Z Q,GU H H,SHENG X G,et al.Advances and applications in crop quantitative trait locus[J].Journal of nuclear agricultural sciences,2014,28(9):1615-1624(in Chinese with English abstract).
    [15] FREEMAN J L,PERRY G H,FEUK L,et al.Copy number variation:new insights in genome diversity[J].Genome research,2006,16(8):949-961.
    [16] KORTE A,FARLOW A.The advantages and limitations of trait analysis with GWAS:a review[J].Plant methods,2013,9 (4):749-764.
    [17] ZUK O,HECHTER E,SUNYAEV S R,et al.The mystery of missing heritability:genetic interactions create phantom heritability[J].PNAS,2012,109(4):1193-1198.
    [18] WEI W H,HEMANI G,HALEY C S.Detecting epistasis in human complex traits[J].Nature reviews genetics,2014,15 (11):722-733.
    [19] WINHAM S J,BIERNACKA J M.Gene-environment interactions in genome-wide association studies:current approaches and new directions[J].Journal of child psychology and psychiatry,2013,54(10):1120-1134.
    [20] THOMAS D.Gene-environment interactions in human diseases[J].Nature reviews genetics,2005,6 (4):287-298.
    [21] MYLES S,PEIFFER J,BROWN P J,et al.Association mapping:critical considerations shift from genotyping to experimental design[J].The plant cell,2009,21(8):2194-2202.
    [22] GIBSON G.Rare and common variants:twenty arguments[J].Nature reviews genetics,2012,13 (2):135-145.
    [23] HAZELETT D J,COETZEE S G,COETZEE G A.A rare variant,which destroys a FoxA1 site at 8q24,is associated with prostate cancer risk[J].Cell cycle,2013,12(2):379-380.
    [24] GOURAB D,YIP W,IULIANA I,et al.Rare variant analysis for family-based design[J/OL].PLoS One,2017,8 (1):e48495 [2022-03-07].https://doi.org/10.1371/journal.pone.0048495.
    [25] CORTES L T,ZHANG Z W,YU J M.Status and prospects of genome-wide association studies in plants[J/OL].Plant genome,2021,14 (1):e20077 [2022-03-07].https://doi.org/10.1002/tpg2.20077.
    [26] PATERSON A H,LANDER E S,HEWITT J D,et al.Resolution of quantitative traits into mendelian factors by using a complete linkage map of restriction fragment length polymorphisms[J].Nature,1988,335 (6192):721-726.
    [27] LANDER E,KRUGLYAK L.Genetic dissection of complex traits - guidelines for interpreting and reporting linkage results[J].Nature genetics,1995,11 (3):241-247.
    [28] THORNSBERRY J M,GOODMAN M M,DOEBLEY J,et al.Dwarf8 polymorphisms associate with variation in flowering time[J].Nature genetics,2001,28 (3):286-289.
    [29] YU J M,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.
    [30] KLASEN J R,BARBEZ E,MEIER L,et al.A multi-marker association method for genome-wide association studies without the need for population structure correction[J/OL].Nature communications,2016,7:13299 [2022-03-07].https://doi.org/10.1038/ncomms13299.
    [31] KANG H M,ZAITLEN N A,WADE C M,et al.Efficient control of population structure in model organism association mapping[J].Genetics,2008,178(3):1709-1723.
    [32] TAYLOR A E,DAVEY SMITH G,MUNAFò M R.Associations of coffee genetic risk scores with consumption of coffee,tea and other beverages in the UK Biobank[J].Addiction,2018,113(1):148-157.
    [33] CORNELIS M C.Genetic determinants of beverage consumption:implications for nutrition and health[J].Advances in food and nutrition research,2019,89:1-52.
    [34] ZHONG V W,KUANG A L,DANNING R D,et al.A genome-wide association study of bitter and sweet beverage consumption[J].Human molecular genetics,2019,28(14):2449-2457.
    [35] FURUKAWA K,IGARASHI M,JIA H,et al.A genome-wide association study identifies the association between the 12q24 locus and black tea consumption in Japanese populations[J/OL].Nutrients,2020,12(10):3182 [2022-03-07].https://doi.org/10.3390/nu12103182.
    [36] MATOBA N,AKIYAMA M,ISHIGAKI K,et al.GWAS of 165,084 Japanese individuals identified nine loci associated with dietary habits[J].Nature human behaviour,2020,4 (3):308-316.
    [37] COLE J B,FLOREZ J C,HIRSCHHORN J N.Comprehensive genomic analysis of dietary habits in UK Biobank identifies hundreds of genetic associations[J/OL].Nature communications,2020,11 (1) :1467 [2022-03-07].https://doi.org/10.1038/s41467-020-15193-0.
    [38] MALIK M A,UMAR M,GUPTA U,et al.Phospholipase C Epsilon 1 (PLCE1 rs2274223A>G,rs3765524C>T and rs7922612C>T) polymorphisms and esophageal cancer risk in the Kashmir Valley[J].Asian Pacific journal of cancer prevention:APJCP,2014,15(10):4319-4323.
    [39] LU L T,CHEN H F,WANG X J,et al.genome-level diversification of eight ancient tea populations in the guizhou and yunnan regions identifies candidate genes for core agronomic traits[J/OL].Horticulture research,2021,8 (1):190 [2022-03-07].https://doi.org/10.1038/s41438-021-00617-9.
    [40] AN Y L,MI X Z,ZHAO S Q,et al.Revealing distinctions in genetic diversity and adaptive evolution between two varieties of Camellia sinensis by whole-genome resequencing[J/OL].Frontiers in plant science,2020,11:603819[2022-03-07].https://doi.org/10.3389/fpls.2020.603819.
    [41] TAN L Q,WANG L Y,XU L Y,et al.SSR-based genetic mapping and QTL analysis for timing of spring bud flush,young shoot color,and mature leaf size in tea plant (Camellia sinensis)[J].Tree genetics & genomes,2016,12(3):1-13.
    [42] ZHANG F,TIAN W L,CEN L,et al.Population structure analysis and genome-wide association study of tea (Camellia Sinensis (L.) Kuntze) germplasm in Qiannan,China,based on SLAF-Seq technology[J].Phyton-international journal of experimental botany,2022,91 (4):791-809.
    [43] 史春彦,张前东,张晓平,等.济南市长清区茶树种植适宜性农业区划[J].山东农业科学,2016,48(10):81-85.SHI C Y,ZHANG Q D,ZHANG X P,et al.Suitable agricultural regionalization for tea planting in Changqing district of Ji’nan City[J].Shandong agricultural sciences,2016,48(10):81-85(in Chinese with English abstract).
    [44] WANG R J,GAO X F,YANG J,et al.Genome-wide association study to identify favorable SNP allelic variations and candidate genes that control the timing of spring bud flush of tea (Camellia sinensis) using SLAF-seq[J].Journal of agricultural and food chemistry,2019,67(37):10380-10391.
    [45] YAMASHITA H, UCHIDA T, TANAKA Y, et al. Genomic predictions and genome-wide association studies based on RAD-seq of quality-related metabolites for the genomics-assisted breeding of tea plants[J]. Scientific reports, 2020, 10 (1): 17480 [2022-03-07].https://doi.org/10.1038/s41598-020-74623-7.
    [46] HAZRA A,KUMAR R,SENGUPTA C,et al.Genome-wide SNP discovery from Darjeeling tea cultivars - their functional impacts and application toward population structure and trait associations[J].Genomics,2021,113(1):66-78.
    [47] FANG K X,XIA Z Q,LI H J,et al.Genome-wide association analysis identified molecular markers associated with important tea flavor-related metabolites[J/OL].Horticulture research,2021,8 (1):42 [2022-03-07].https://doi.org/10.1038/s41438-021-00477-3.
    [48] HUANG R,WANG J Y,YAO M Z,et al.Qe trait loci mapping for free amino acid content using an albino population and SuantitativNP markers provides insight into the genetic improvement of tea plants[J/OL].Horticulture research,2022,9:uhab029[2022-03-07].https://doi.org/10.1093/hr/uhab029.
    [49] IWATA H,MINAMIKAWA M F,KAJIYA-KANEGAE H,et al.Genomics-assisted breeding in fruit trees[J].Breeding science,2016,66(1):100-115.
    [50] XIAO Q L,BAI X L,ZHANG C,et al.Advanced high-throughput plant phenotyping techniques for genome-wide association studies:a review[J].Journal of advanced research,2022,35:215-230.
    [51] YANG W N,FENG H,ZHANG X H,et al.Crop phenomics and high-throughput phenotyping:past decades,current challenges,and future perspectives[J].Molecular plant,2020,13(2):187-214.
    [52] JIANG L B,SUN L D,YE M X,et al.Functional mapping of N deficiency-induced response in wheat yield-component traits by implementing high-throughput phenotyping[J].The plant journal,2019,97(6):1105-1119.
    [53] RASHEED A,XIA X C,OGBONNAYA F,et al.Genome-wide association for grain morphology in synthetic hexaploid wheats using digital imaging analysis[J/OL].BMC plant biology,2014,14:128[2022-03-07].https://doi.org/10.1186/1471-2229-14-128.
    [54] SHAKOOR N,LEE S,MOCKLER T C.High throughput phenotyping to accelerate crop breeding and monitoring of diseases in the field[J].Current opinion in plant biology,2017,38:184-192.
    [55] NOH J,DO Y S,KIM G H,et al.A genome-wide association study for the detection of genes related to apple Marssonina Blotch disease resistance in apples[J/OL].Scientia horticulturae,2020,262:108986[2022-03-07].https://doi.org/10.1016/j.scienta.2019.108986.
    [56] PENG Z,BREDESON J V,WU G A,et al.A chromosome-scale reference genome of trifoliate orange (Poncirus trifoliata) provides insights into disease resistance,cold tolerance and genome evolution in Citrus[J].The plant journal,2020,104(5):1215-1232.
    [57] HUANG X,ZHAO Y,WEI X,et al.Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm[J].Nature genetics,2012,44:32-39.
    [58] CHEN W,WANG W S,PENG M,et al.Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals[J/OL].Nature communications,2016,7:12767 [2022-03-07].https://doi.org/10.1038/ncomms12767.
    [59] ZHU G T,WANG S C,HUANG Z J,et al.Rewiring of the fruit metabolome in tomato breeding[J].Cell,2018,172(1/2):249-261.
    [60] LEE T,KIM H,LEE I.Network-assisted crop systems genetics:network inference and integrative analysis[J].Current opinion in plant biology,2015,24:61-70
    引证文献
    网友评论
    网友评论
    分享到微博
    发 布
引用本文

房婉萍,雷小刚,杨彬,王亚,马媛春.全基因组关联分析在茶叶研究中的应用进展[J].华中农业大学学报,2022,41(5):33-40

复制
分享
文章指标
  • 点击次数:
  • 下载次数:
  • HTML阅读次数:
  • 引用次数:
历史
  • 收稿日期:2022-01-05
  • 在线发布日期: 2022-10-11
文章二维码