Open access resources for genome-wide association mapping in rice

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.

Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis

“…Although not functionally validated, these two nonsynonymous SNP mutations are believed to change the polarity and therefore enzymatic activity of GBSSI. All these previously observed SNPs and insertion mutations, including other previously published GBSSI alleles summarized in Supplemental Table S3, were not represented in the high density rice array (McCouch et al, 2016) and therefore were not detected in this study. Instead, a highly significant SNP was identified in the promoter region of GBSSI located at the 2769 bp of the start codon (Table II and Supplemental Fig.…”

“…Most of the accessions were composed of indica (n = 229), while the rest were admixed-indica (n = 7), tropical japonica (n = 6), and admixture (n = 2; McCouch et al, 2016). GWAS on AAC revealed a prominent peak on chromosome 6 ( Fig.…”

“…A total of 320 accessions (Table I) were selected from the 498 indica landraces identified by McCouch et al (2016) for Rice Diversity Panel 2. Paddy rice samples of five additional varieties used in a previous study to represent diversity in amylose classes were also obtained from the IRRI Genetic Resources Center.…”

“…The genomewide association study used the SNP genotype data from the High-Density Rice Array project (McCouch et al, 2016). Nonbiallelic SNP markers were removed and the remaining markers were filtered in a stepwise manner.…”

“…With the availability of 3000 sequenced rice genomes (The 3000 Rice Genomes Project, 2014) and genotype data from the High-Density Rice Array project (McCouch et al, 2016), phenotyping has become the major bottleneck in screening for rice grains with altered digestibility properties. The in vivo glycemic index estimation is low throughput and requires adherence to complex clinical and ethical requirements.…”