14 research outputs found
Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions
<div><p>Background</p><p>In this study we carried out a genome-wide association analysis for plant and grain morphology and root architecture in a unique panel of temperate rice accessions adapted to European pedo-climatic conditions. This is the first study to assess the association of selected phenotypic traits to specific genomic regions in the narrow genetic pool of temperate japonica. A set of 391 rice accessions were GBS-genotyped yieldingâafter data editingâ57000 polymorphic and informative SNPS, among which 54% were in genic regions.</p><p>Results</p><p>In total, 42 significant genotype-phenotype associations were detected: 21 for plant morphology traits, 11 for grain quality traits, 10 for root architecture traits. The FDR of detected associations ranged from 3 · 10<sup>â7</sup> to 0.92 (median: 0.25). In most cases, the significant detected associations co-localised with QTLs and candidate genes controlling the phenotypic variation of single or multiple traits. The most significant associations were those for flag leaf width on chromosome 4 (<i>FDR</i> = 3 · 10<sup>â7</sup>) and for plant height on chromosome 6 (<i>FDR</i> = 0.011).</p><p>Conclusions</p><p>We demonstrate the effectiveness and resolution of the developed platform for high-throughput phenotyping, genotyping and GWAS in detecting major QTLs for relevant traits in rice. We identified strong associations that may be used for selection in temperate irrigated rice breeding: e.g. associations for flag leaf width, plant height, root volume and length, grain length, grain width and their ratio. Our findings pave the way to successfully exploit the narrow genetic pool of European temperate rice and to pinpoint the most relevant genetic components contributing to the adaptability and high yield of this germplasm. The generated data could be of direct use in genomic-assisted breeding strategies.</p></div
Phenotypic correlations among plant morphology, grain quality and root traits.
<p>Phenotypic correlations among plant morphology, grain quality
and root traits.</p
Manhattan and Q-Q plots of GWAS results for shoot and root dry weight.
<p>Manhattan and Q-Q plots of GWAS results for shoot and root dry weight.</p
Stacked barplot for the ancestry of the available 391 rice accessions with K = 5.
<p>Stacked barplot for the ancestry of the available 391
rice accessions with K = 5.</p
Manhattan and Q-Q plots of GWAS results for grain quality traits.
<p>Manhattan and Q-Q plots of GWAS results for grain quality traits.</p
Average LD as a function of inter-marker distance estimated in the panel of 391 accessions.
<p>Average LD as a function of inter-marker distance
estimated in the panel of 391 accessions.</p
Manhattan and Q-Q plots of GWAS results for root traits.
<p>Manhattan and Q-Q plots of GWAS results for root traits.</p
Descriptive statistics of collected phenotypes.
<p>Descriptive statistics of collected phenotypes.</p
Most significant associations between SNP genotypes and shoot, grain and root phenotypes in the analysed rice accessions.
<p>Most significant associations between SNP genotypes and shoot, grain and root phenotypes in the analysed rice accessions.</p