GWAS for genetics of complex quantitative traits: Genome to pangenome and SNPs to SVs and k-mers

被引：19

作者：

Gupta, Pushpendra K. ^{[1
]}

机构：

[1] Ch Charan Singh Univ Meerut, Dept Genet & Plant Breeding, Meerut 250004, Uttar Pradesh, India

来源：

BIOESSAYS | 2021年 / 43卷 / 11期

关键词：

genome; pangenome; GWAS; k-mers; MLM; MLMM; MTMM; SVs; COPY NUMBER VARIATIONS; FALSE DISCOVERY RATE; MIXED-MODEL APPROACH; WIDE ASSOCIATION; PAN-GENOME; LINKAGE DISEQUILIBRIUM; MISSING HERITABILITY; STRUCTURAL VARIATION; EMPIRICAL BAYES; BONFERRONI;

D O I：

10.1002/bies.202100109

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The development of improved methods for genome-wide association studies (GWAS) for genetics of quantitative traits has been an active area of research during the last 25 years. This activity initially started with the use of mixed linear model (MLM), which was variously modified. During the last decade, however, with the availability of high throughput next generation sequencing (NGS) technology, development and use of pangenomes and novel markers including structural variations (SVs) and k-mers for GWAS has taken over as a new thrust area of research. Pangenomes and SVs are now available in humans, livestock, and a number of plant species, so that these resources along with k-mers are being used in GWAS for exploring additional genetic variation that was hitherto not available for analysis. These developments have resulted in significant improvement in GWAS methodology for detection of marker-trait associations (MTAs) that are relevant to human healthcare and crop improvement.

引用

页数：13

共 130 条

[1] Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato [J].

Alonge, Michael ;

Wang, Xingang ;

Benoit, Matthias ;

Soyk, Sebastian ;

Pereira, Lara ;

Zhang, Lei ;

Suresh, Hamsini ;

Ramakrishnan, Srividya ;

Maumus, Florian ;

Ciren, Danielle ;

Levy, Yuval ;

Harel, Tom Hai ;

Shalev-Schlosser, Gili ;

Amsellem, Ziva ;

Razifard, Hamid ;

Caicedo, Ana L. ;

Tieman, Denise M. ;

Klee, Harry ;

Kirsche, Melanie ;

Aganezov, Sergey ;

Ranallo-Benavidez, T. Rhyker ;

Lemmon, Zachary H. ;

Kim, Jennifer ;

Robitaille, Gina ;

Kramer, Melissa ;

Goodwin, Sara ;

McCombie, W. Richard ;

Hutton, Samuel ;

Van Eck, Joyce ;

Gillis, Jesse ;

Eshed, Yuval ;

Sedlazeck, Fritz J. ;

van der Knaap, Esther ;

Schatz, Michael C. ;

Lippman, Zachary B. .

CELL, 2020, 182 (01) :145-+

[2] 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana [J].

Alonso-Blanco, Carlos ;

Andrade, Jorge ;

Becker, Claude ;

Bemm, Felix ;

Bergelson, Joy ;

Borgwardt, Karsten M. ;

Cao, Jun ;

Chae, Eunyoung ;

Dezwaan, Todd M. ;

Ding, Wei ;

Ecker, Joseph R. ;

Exposito-Alonso, Moises ;

Farlow, Ashley ;

Fitz, Joffrey ;

Gan, Xiangchao ;

Grimm, Dominik G. ;

Hancock, Angela M. ;

Henz, Stefan R. ;

Holm, Svante ;

Horton, Matthew ;

Jarsulic, Mike ;

Kerstetter, Randall A. ;

Korte, Arthur ;

Korte, Pamela ;

Lanz, Christa ;

Lee, Cheng-Ruei ;

Meng, Dazhe ;

Michael, Todd P. ;

Mott, Richard ;

Muliyati, Ni Wayan ;

Nagele, Thomas ;

Nagler, Matthias ;

Nizhynska, Viktoria ;

Nordborg, Magnus ;

Novikova, Polina Yu. ;

Pico, F. Xavier ;

Platzer, Alexander ;

Rabanal, Fernando A. ;

Rodriguez, Alex ;

Rowan, Beth A. ;

Salome, Patrice A. ;

Schmid, Karl J. ;

Schmitz, Robert J. ;

Seren, Umit ;

Sperone, Felice Gianluca ;

Sudkamp, Mitchell ;

Svardal, Hannes ;

Tanzer, Matt M. ;

Todd, Donald ;

Volchenboum, Samuel L. .

CELL, 2016, 166 (02) :481-491

[3]

Altemose N., 2021, COMPLETE GENOMIC EPI, V2021, DOI 10.1101/2021.07.12.452052

[4] Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes [J].

Aranzana, MJ ;

Kim, S ;

Zhao, KY ;

Bakker, E ;

Horton, M ;

Jakob, K ;

Lister, C ;

Molitor, J ;

Shindo, C ;

Tang, CL ;

Toomajian, C ;

Traw, B ;

Zheng, HG ;

Bergelson, J ;

Dean, C ;

Marjoram, P ;

Nordborg, M .

PLOS GENETICS, 2005, 1 (05) :531-539

[5] Resistance gene cloning from a wild crop relative by sequence capture and association genetics [J].

Arora, Sanu ;

Steuernagel, Burkhard ;

Gaurav, Kumar ;

Chandramohan, Sutha ;

Long, Yunming ;

Matny, Oadi ;

Johnson, Ryan ;

Enk, Jacob ;

Periyannan, Sambasivam ;

Singh, Narinder ;

Hatta, M. Asyraf Md ;

Athiyannan, Naveenkumar ;

Cheema, Jitender ;

Yu, Guotai ;

Kangara, Ngonidzashe ;

Ghosh, Sreya ;

Szabo, Les J. ;

Poland, Jesse ;

Bariana, Harbans ;

Jones, Jonathan D. G. ;

Bentley, Alison R. ;

Ayliffe, Mick ;

Olson, Eric ;

Xu, Steven S. ;

Steffenson, Brian J. ;

Lagudah, Evans ;

Wulff, Brande B. H. .

NATURE BIOTECHNOLOGY, 2019, 37 (02) :139-+

[6] Plant pan-genomes are the new reference [J].

Bayer, Philipp E. ;

Golicz, Agnieszka A. ;

Scheben, Armin ;

Batley, Jacqueline ;

Edwards, David .

NATURE PLANTS, 2020, 6 (08) :914-920

[7] Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize [J].

Belo, Andre ;

Zheng, Peizhong ;

Luck, Stanley ;

Shen, Bo ;

Meyer, David J. ;

Li, Bailin ;

Tingey, Scott ;

Rafalski, Antoni .

MOLECULAR GENETICS AND GENOMICS, 2008, 279 (01) :1-10

[8] CONTROLLING THE FALSE DISCOVERY RATE - A PRACTICAL AND POWERFUL APPROACH TO MULTIPLE TESTING [J].

BENJAMINI, Y ;

HOCHBERG, Y .

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1995, 57 (01) :289-300

[9] Copy number variation in livestock: A mini review [J].

Bhanuprakash, V. ;

Chhotaray, Supriya ;

Pruthviraj, D. R. ;

Rawat, Chandrakanta ;

Karthikeyan, A. ;

Panigrahi, Manjit .

VETERINARY WORLD, 2018, 11 (04) :535-541

[10] Genome-Wide Study of Structural Variants in Bovine Holstein, Montbeliarde and Normande Dairy Breeds [J].

Boussaha, Mekki ;

Esquerre, Diane ;

Barbieri, Johanna ;

Djari, Anis ;

Pinton, Alain ;

Letaief, Rabia ;

Salin, Gerald ;

Escudie, Frederic ;

Roulet, Alain ;

Fritz, Sebastien ;

Samson, Franck ;

Grohs, Cecile ;

Bernard, Maria ;

Klopp, Christophe ;

Boichard, Didier ;

Rocha, Dominique .

PLOS ONE, 2015, 10 (08)

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