Genome-wide association and high-resolution phenotyping link oryza sativa panicle traits to numerous trait-specific QTL clusters

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Rice panicle architecture is a key target of selection when breeding for yield and grain quality. However, panicle phenotypes are difficult to measure and susceptible to confounding during genetic mapping due to correlation with flowering and subpopulation structure. Here we quantify 49 panicle phenotypes in 242 tropical rice accessions with the imaging platform PANorama. Using flowering as a covariate, we conduct a genome-wide association study (GWAS), detect numerous subpopulation-specific associations, and dissect multi-trait peaks using panicle phenotype covariates. Ten candidate genes in pathways known to regulate plant architecture fall under GWAS peaks, half of which overlap with quantitative trait loci identified in an experimental population. This is the first study to assess inflorescence phenotypes of field-grown material using a high-resolution phenotyping platform. Herein, we establish a panicle morphocline for domesticated rice, propose a genetic model underlying complex panicle traits, and demonstrate subtle links between panicle size and yield performance.Rice panicle architecture is a key target of selection when breeding for yield and grain quality. However, panicle phenotypes are difficult to measure and susceptible to confounding during genetic mapping due to correlation with flowering and subpopulatio710527FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)2011/03110-

Genetic architecture of cold tolerance in rice (<i>Oryza sativa</i>) determined through high resolution genome-wide analysis

<div><p>Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (<i>Oryza sativa</i> L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1) is a global collection of over 400 <i>O</i>. <i>sativa</i> accessions representing the five major subpopulations from the <i>INDICA</i> and <i>JAPONICA</i> varietal groups, with a genotypic dataset consisting of 700,000 SNP markers. The objectives of this study were to evaluate the RDP1 accessions for the complex, quantitatively inherited cold tolerance traits at the germination and reproductive stages, and to conduct genome-wide association (GWA) mapping to identify SNPs and candidate genes associated with cold stress at these stages. GWA mapping of the germination index (calculated as percent germination in cold divided by warm treatment) revealed 42 quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage, including 18 in the panel as a whole, seven in <i>temperate japonica</i>, six in <i>tropical japonica</i>, 14 in <i>JAPONICA</i>, and nine in <i>INDICA</i>, with five shared across all subpopulations. Twenty-two of these QTLs co-localized with 32 previously reported cold tolerance QTLs. GWA mapping of cold tolerance at the reproductive stage detected 29 QTLs, including seven associated with percent sterility, ten with seed weight per panicle, 14 with seed weight per plant and one region overlapping for two traits. Fifteen co-localized with previously reported QTLs for cold tolerance or yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to with lipid metabolism, response to stimuli, response to biotic stimuli (suggesting cross-talk between biotic and abiotic stresses), and oxygen binding. Overall the <i>JAPONICA</i> accessions were more tolerant to cold stress than <i>INDICA</i> accessions.</p></div

Gene Ontology (GO) term enrichment analysis of the germination index candidate genes.

<p>The GO analysis describes the gene products in terms of their associated biological processes, cellular components and molecular functions independent of species.</p

Summary statistics for cold tolerance at the germination and reproductive stages.

<p>The mean, range and standard error are given for the germination index (calculated as percent germination in cold divided by warm treatment) based on the two subspecies, <i>INDICA</i> and <i>JAPONICA</i>, and four subpopulations <i>aus</i>, <i>indica</i>, <i>temperate japonica</i> and <i>tropical japonica</i>. At the reproductive stage, 186 <i>JAPONICA</i> accessions which produced panicles were evaluate for three traits.</p

Summary of SNP positions for cold tolerance at the reproductive stage as identified by GWA mapping.

<p>Traits measured were percent sterility, seed weight per panicle and seed weight per plant. All SNPs above the threshold (p-value = 0.0001) are included. Reported QTLs and candidate genes associated with spikelet fertility and seed set which are co-located to these segments are identified.</p

Summary of SNP positions for cold tolerance at germination as identified by GWA mapping.

<p>All SNPs above the threshold (p-value = 0.0001) are included. The accessions were grouped as <i>ALL</i> RDP1 accessions, <i>INDICA</i>, <i>JAPONICA</i>, <i>temperate japonica</i> and <i>tropical japonica</i>. Reported QTLs and candidate genes associated with cold tolerance which are co-located to these segments are identified.</p

Data from: Complex disease and phenotype mapping in the domestic dog

The domestic dog is becoming an increasingly valuable model species in medical genetics, showing particular promise to advance our understanding of cancer and orthopaedic disease. Here we undertake the largest canine genome-wide association study to date, with a panel of over 4,200 dogs genotyped at 180,000 markers, to accelerate mapping efforts. For complex diseases, we identify loci significantly associated with hip dysplasia, elbow dysplasia, idiopathic epilepsy, lymphoma, mast cell tumour and granulomatous colitis; for morphological traits, we report three novel quantitative trait loci that influence body size and one that influences fur length and shedding. Using simulation studies, we show that modestly larger sample sizes and denser marker sets will be sufficient to identify most moderate- to large-effect complex disease loci. This proposed design will enable efficient mapping of canine complex diseases, most of which have human homologues, using far fewer samples than required in human studies

Open access resources for genome-wide association mapping in rice

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