Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa)

PloS One
Hasina BegumSusan R McCouch

Abstract

Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering ...Continue Reading

References

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Citations

Feb 22, 2016·BMC Genomics·Aurore DesgrouxMarie-Laure Pilet-Nayel
Aug 14, 2015·Plant Biotechnology Journal·Yang Jae KangSuk-Ha Lee
Apr 3, 2016·Journal of Experimental Botany·Matthias WissuwaTerry J Rose
Sep 2, 2016·Frontiers in Plant Science·Peng ZhangHanhua Tong
Aug 9, 2016·Annual Review of Cell and Developmental Biology·Takehiko Ogura, Wolfgang Busch
Feb 23, 2017·Annual Review of Plant Biology·Abdelbagi M Ismail, Tomoaki Horie
Mar 30, 2017·Plant Cell Reports·Jitendra KumarShiv Kumar
Feb 6, 2018·Breeding Science·Kenji FujinoTakashi Sato
Jan 11, 2019·Genes·Gwen Iris Descalsota-EmpleoB P Mallikarjuna Swamy
Apr 30, 2017·G3 : Genes - Genomes - Genetics·Christopher A FragosoMathias Lorieux
Sep 19, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Moses NyineRony Swennen
Mar 6, 2018·The Plant Genome·Juan E RosasLucía Gutiérrez
Mar 13, 2020·Plant Biotechnology Journal·Wolfram WeckwerthRajeev K Varshney
Jun 9, 2020·Critical Reviews in Biotechnology·Ramaswamy ManimekalaiMallikarjuna Kandalam
Oct 19, 2017·Genetics, Selection, Evolution : GSE·Deniz AkdemirJulio Isidro-Sánchez
Nov 6, 2015·Frontiers in Plant Science·Mettu M Reddy, Kandasamy Ulaganathan
Oct 8, 2016·The New Phytologist·Jennifer E Spindel, Susan R McCouch
Aug 20, 2017·Scientific Reports·Venea Dara DaygonMelissa A Fitzgerald
Jul 26, 2019·PeerJ·Sai Mukund RamakrishnanSunish K Sehgal

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Methods Mentioned

BETA
PCA
genotyping

Software Mentioned

TASSEL
Genstat
JMP Pro
Gramene
GEMMA
PLINK
R
MAS
FastImputationBitFixedWindow
PLoS

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