Open access resources for genome-wide association mapping in rice.

Susan R Mccouch,Yuxin Shi,Namrata Singh,Sheila Mae Q Mercado,Sandra E Harrington,Francisco Agosto-Perez,Anthony J Greenberg,Masahiro Yano,Hei Leung,Kenneth L Mcnally,Paula R Kuser-Falcão,Mark H Wright,Pavel Korniliev,Darcy A Branchini,Ma Elizabeth B Naredo,Genevieve Declerck,Kowaru Ebana,Chih‐Wei Tung ,Melissa A Fitzgerald ,Anna M Mcclung ,G C Eizenga ,Lyza Maron ,Jason G Mezey

doi:10.1038/ncomms10532

Abstract

Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement.

Highlights

Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations
minor allele frequency (MAF), major allele frequency; single-nucleotide polymorphisms (SNPs), single-nucleotide polymorphism. *Accessions phenotyped for grain length. wPrivate SNPs are the SNPs segregating only in the indicated subpopulation
Of the genic SNPs, 55% are distributed within exons, 36% within introns, 3% within 50-untranslated regions (UTRs) and 6% within 30-UTRs

Summary

Introduction

Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. The unique combinations of locally adapted allele complexes in different subpopulations provide ideal characteristics for GWAS, including both universal and population-specific large effect alleles, extended linkage disequilibrium (LD) within some subpopulations that is advantageous for mapping with low marker coverage, rapid LD decay within other subpopulations offering improved mapping resolution and an abundance of well-partitioned genetic variation among subpopulations These properties, in combination with a small, tractable genome (380 Mb), and the ability to produce immortal panels comprised of thousands of inbred, homozygous individuals, make it possible to evaluate the same traits in different environments simultaneously, and to evaluate a variety of different traits on the same germplasm over time. The ability to make controlled matings and to generate large populations each generation provides a powerful system for validating loci and for harnessing their value by introgressing favourable alleles into other genetic backgrounds

Methods

Results

Conclusion