Literature DB >> 35641764

A Practical Guide to Using Structural Variants for Genome-Wide Association Studies.

Marc-André Lemay1, Sidiki Malle2.   

Abstract

Structural variants (SVs) are known to have large functional impacts on phenotypes of agricultural interest, but they have yet to be routinely used for GWAS. Apart from the difficulty in obtaining high-quality SV genotype data for large populations, one of the main hurdles to using SVs for GWAS lies in formatting of genotype data for use with popular GWAS programs. This protocol describes how typical SV genotype data can be formatted for input to three GWAS programs commonly used by the plant genetics community: TASSEL, GAPIT, and mrMLM.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  GAPIT; Structural variation; TASSEL; VCF file; mrMLM

Mesh：

Year:  2022        PMID： 35641764     DOI： 10.1007/978-1-0716-2237-7_10

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  28 in total

Review 1.  Structural variation and genome complexity: is dispensable really dispensable?

Authors:  Fabio Marroni; Sara Pinosio; Michele Morgante
Journal:  Curr Opin Plant Biol       Date:  2014-02-16       Impact factor: 7.834

2.  Pan-Genome of Wild and Cultivated Soybeans.

Authors:  Yucheng Liu; Huilong Du; Pengcheng Li; Yanting Shen; Hua Peng; Shulin Liu; Guo-An Zhou; Haikuan Zhang; Zhi Liu; Miao Shi; Xuehui Huang; Yan Li; Min Zhang; Zheng Wang; Baoge Zhu; Bin Han; Chengzhi Liang; Zhixi Tian
Journal:  Cell       Date:  2020-06-17       Impact factor: 41.582

Review 3.  Mechanisms underlying structural variant formation in genomic disorders.

Authors:  Claudia M B Carvalho; James R Lupski
Journal:  Nat Rev Genet       Date:  2016-02-29       Impact factor: 53.242

4.  Identification of a functional transposon insertion in the maize domestication gene tb1.

Authors:  Anthony Studer; Qiong Zhao; Jeffrey Ross-Ibarra; John Doebley
Journal:  Nat Genet       Date:  2011-09-25       Impact factor: 38.330

5.  Copy number variation at the GL7 locus contributes to grain size diversity in rice.

Authors:  Yuexing Wang; Guosheng Xiong; Jiang Hu; Liang Jiang; Hong Yu; Jie Xu; Yunxia Fang; Longjun Zeng; Erbo Xu; Jing Xu; Weijun Ye; Xiangbing Meng; Ruifang Liu; Hongqi Chen; Yanhui Jing; Yonghong Wang; Xudong Zhu; Jiayang Li; Qian Qian
Journal:  Nat Genet       Date:  2015-07-06       Impact factor: 38.330

Review 6.  Structural variation in the sequencing era.

Authors:  Steve S Ho; Alexander E Urban; Ryan E Mills
Journal:  Nat Rev Genet       Date:  2019-11-15       Impact factor: 53.242

Review 7.  Mechanisms of change in gene copy number.

Authors:  P J Hastings; James R Lupski; Susan M Rosenberg; Grzegorz Ira
Journal:  Nat Rev Genet       Date:  2009-08       Impact factor: 53.242

8.  Large-scale copy number polymorphism in the human genome.

Authors:  Jonathan Sebat; B Lakshmi; Jennifer Troge; Joan Alexander; Janet Young; Pär Lundin; Susanne Månér; Hillary Massa; Megan Walker; Maoyen Chi; Nicholas Navin; Robert Lucito; John Healy; James Hicks; Kenny Ye; Andrew Reiner; T Conrad Gilliam; Barbara Trask; Nick Patterson; Anders Zetterberg; Michael Wigler
Journal:  Science       Date:  2004-07-23       Impact factor: 47.728

Review 9.  Genome structural variation discovery and genotyping.

Authors:  Can Alkan; Bradley P Coe; Evan E Eichler
Journal:  Nat Rev Genet       Date:  2011-03-01       Impact factor: 53.242

10.  Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.

Authors:  Michael Alonge; Xingang Wang; Matthias Benoit; Sebastian Soyk; Lara Pereira; Lei Zhang; Hamsini Suresh; Srividya Ramakrishnan; Florian Maumus; Danielle Ciren; Yuval Levy; Tom Hai Harel; Gili Shalev-Schlosser; Ziva Amsellem; Hamid Razifard; Ana L Caicedo; Denise M Tieman; Harry Klee; Melanie Kirsche; Sergey Aganezov; T Rhyker Ranallo-Benavidez; Zachary H Lemmon; Jennifer Kim; Gina Robitaille; Melissa Kramer; Sara Goodwin; W Richard McCombie; Samuel Hutton; Joyce Van Eck; Jesse Gillis; Yuval Eshed; Fritz J Sedlazeck; Esther van der Knaap; Michael C Schatz; Zachary B Lippman
Journal:  Cell       Date:  2020-06-17       Impact factor: 66.850
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