Literature DB >> 24583583

Efficient imputation of missing markers in low-coverage genotyping-by-sequencing data from multiparental crosses.

B Emma Huang1, Chitra Raghavan, Ramil Mauleon, Karl W Broman, Hei Leung.   

Abstract

We consider genomic imputation for low-coverage genotyping-by-sequencing data with high levels of missing data. We compensate for this loss of information by utilizing family relationships in multiparental experimental crosses. This nearly quadruples the number of usable markers when applied to a large rice Multiparent Advanced Generation InterCross (MAGIC) study.

Entities:  

Keywords:  GBS; HMM; MAGIC; MPRIL

Mesh：

Substances：

Year:  2014        PMID： 24583583      PMCID： PMC4012496          DOI： 10.1534/genetics.113.158014

Source DB:  PubMed          Journal:  Genetics        ISSN： 0016-6731            Impact factor:   4.562


  18 in total

1.  R/qtl: QTL mapping in experimental crosses.

Authors:  Karl W Broman; Hao Wu; Saunak Sen; Gary A Churchill
Journal:  Bioinformatics       Date:  2003-05-01       Impact factor: 6.937

2.  Imputing missing genotypes with weighted k nearest neighbors.

Authors:  Holger Schwender
Journal:  J Toxicol Environ Health A       Date:  2012

3.  R/mpMap: a computational platform for the genetic analysis of multiparent recombinant inbred lines.

Authors:  B Emma Huang; Andrew W George
Journal:  Bioinformatics       Date:  2011-01-08       Impact factor: 6.937

Review 4.  From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants.

Authors:  Colin Cavanagh; Matthew Morell; Ian Mackay; Wayne Powell
Journal:  Curr Opin Plant Biol       Date:  2008-03-04       Impact factor: 7.834

5.  Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes.

Authors:  Xun Xu; Xin Liu; Song Ge; Jeffrey D Jensen; Fengyi Hu; Xin Li; Yang Dong; Ryan N Gutenkunst; Lin Fang; Lei Huang; Jingxiang Li; Weiming He; Guojie Zhang; Xiaoming Zheng; Fumin Zhang; Yingrui Li; Chang Yu; Karsten Kristiansen; Xiuqing Zhang; Jian Wang; Mark Wright; Susan McCouch; Rasmus Nielsen; Jun Wang; Wen Wang
Journal:  Nat Biotechnol       Date:  2011-12-11       Impact factor: 54.908

6.  Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation.

Authors:  Judson A Ward; Jasbir Bhangoo; Felicidad Fernández-Fernández; Patrick Moore; J D Swanson; Roberto Viola; Riccardo Velasco; Nahla Bassil; Courtney A Weber; Daniel J Sargent
Journal:  BMC Genomics       Date:  2013-01-16       Impact factor: 3.969

7.  Discovery of genome-wide DNA polymorphisms in a landrace cultivar of Japonica rice by whole-genome sequencing.

Authors:  Yuko Arai-Kichise; Yuh Shiwa; Hideki Nagasaki; Kaworu Ebana; Hirofumi Yoshikawa; Masahiro Yano; Kyo Wakasa
Journal:  Plant Cell Physiol       Date:  2011-01-21       Impact factor: 4.927

8.  A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.

Authors:  Robert J Elshire; Jeffrey C Glaubitz; Qi Sun; Jesse A Poland; Ken Kawamoto; Edward S Buckler; Sharon E Mitchell
Journal:  PLoS One       Date:  2011-05-04       Impact factor: 3.240

9.  Imputation of unordered markers and the impact on genomic selection accuracy.

Authors:  Jessica E Rutkoski; Jesse Poland; Jean-Luc Jannink; Mark E Sorrells
Journal:  G3 (Bethesda)       Date:  2013-03-01       Impact factor: 3.154

10.  Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding.

Authors:  Nonoy Bandillo; Chitra Raghavan; Pauline Andrea Muyco; Ma Anna Lynn Sevilla; Irish T Lobina; Christine Jade Dilla-Ermita; Chih-Wei Tung; Susan McCouch; Michael Thomson; Ramil Mauleon; Rakesh Kumar Singh; Glenn Gregorio; Edilberto Redoña; Hei Leung
Journal:  Rice (N Y)       Date:  2013-05-06       Impact factor: 4.783
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  21 in total

1.  Imputing Genotypes in Biallelic Populations from Low-Coverage Sequence Data.

Authors:  Christopher A Fragoso; Christopher Heffelfinger; Hongyu Zhao; Stephen L Dellaporta
Journal:  Genetics       Date:  2015-12-29       Impact factor: 4.562

Review 2.  MAGIC populations in crops: current status and future prospects.

Authors:  B Emma Huang; Klara L Verbyla; Arunas P Verbyla; Chitra Raghavan; Vikas K Singh; Pooran Gaur; Hei Leung; Rajeev K Varshney; Colin R Cavanagh
Journal:  Theor Appl Genet       Date:  2015-04-09       Impact factor: 5.699

3.  Accurate Genotype Imputation in Multiparental Populations from Low-Coverage Sequence.

Authors:  Chaozhi Zheng; Martin P Boer; Fred A van Eeuwijk
Journal:  Genetics       Date:  2018-07-25       Impact factor: 4.562

4.  Genotyping Platforms for Genome-Wide Association Studies: Options and Practical Considerations.

Authors:  David L Hyten
Journal:  Methods Mol Biol       Date:  2022

Review 5.  Efficient genome-wide genotyping strategies and data integration in crop plants.

Authors:  Davoud Torkamaneh; Brian Boyle; François Belzile
Journal:  Theor Appl Genet       Date:  2018-01-19       Impact factor: 5.699

6.  Punctuated distribution of recombination hotspots and demarcation of pericentromeric regions in Phaseolus vulgaris L.

Authors:  Mehul S Bhakta; Valerie A Jones; C Eduardo Vallejos
Journal:  PLoS One       Date:  2015-01-28       Impact factor: 3.240

7.  Scanning and Filling: Ultra-Dense SNP Genotyping Combining Genotyping-By-Sequencing, SNP Array and Whole-Genome Resequencing Data.

Authors:  Davoud Torkamaneh; Francois Belzile
Journal:  PLoS One       Date:  2015-07-10       Impact factor: 3.240

8.  A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea.

Authors:  Alice Kujur; Deepak Bajaj; Hari D Upadhyaya; Shouvik Das; Rajeev Ranjan; Tanima Shree; Maneesha S Saxena; Saurabh Badoni; Vinod Kumar; Shailesh Tripathi; C L L Gowda; Shivali Sharma; Sube Singh; Akhilesh K Tyagi; Swarup K Parida
Journal:  Sci Rep       Date:  2015-06-10       Impact factor: 4.379

9.  Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea.

Authors:  Deepak Bajaj; Shouvik Das; Saurabh Badoni; Vinod Kumar; Mohar Singh; Kailash C Bansal; Akhilesh K Tyagi; Swarup K Parida
Journal:  Sci Rep       Date:  2015-07-24       Impact factor: 4.379

10.  High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS).

Authors:  Subodh Verma; Shefali Gupta; Nitesh Bandhiwal; Tapan Kumar; Chellapilla Bharadwaj; Sabhyata Bhatia
Journal:  Sci Rep       Date:  2015-12-03       Impact factor: 4.379
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