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. 2016 May 26;11(5):e0155425.
doi: 10.1371/journal.pone.0155425. eCollection 2016.

Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions

Filippo Biscarini  1 , Paolo Cozzi  2 , Laura Casella  1 , Paolo Riccardi  1 , Alessandra Vattari  1 , Gabriele Orasen  3 , Rosaria Perrini  3 , Gianni Tacconi  4 , Alessandro Tondelli  4 , Chiara Biselli  3 , Luigi Cattivelli  4 , Jennifer Spindel  5 , Susan McCouch  5 , Pamela Abbruscato  1 , Giampiero Valé  3   4 , Pietro Piffanelli  1 , Raffaella Greco  1
Affiliations

Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions

Filippo Biscarini et al. PLoS One. .

Abstract

Background: 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 yielding-after data editing-57000 polymorphic and informative SNPS, among which 54% were in genic regions.

Results: 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 · 10-7 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 (FDR = 3 · 10-7) and for plant height on chromosome 6 (FDR = 0.011).

Conclusions: 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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Stacked barplot for the ancestry of the available 391 rice accessions with K = 5.
Fig 2
Fig 2. Neighbour-joining trees of the 391 accessions (left) and of the 153 (centre) and 93 (right) subsets used for plant & grain and root phenotyping respectively.
Temperate japonica accessions in blue, tropical japonica in red, indica in green, aus in violet, and aromatic in black.
Fig 3
Fig 3. Phenotypic correlations among plant morphology, grain quality and root traits.
Fig 4
Fig 4. Average LD as a function of inter-marker distance estimated in the panel of 391 accessions.
Fig 5
Fig 5. Manhattan and Q-Q plots of GWAS results for plant morphology traits.
Fig 6
Fig 6. Manhattan and Q-Q plots of GWAS results for grain quality traits.
Fig 7
Fig 7. Manhattan and Q-Q plots of GWAS results for root traits.
Fig 8
Fig 8. Manhattan and Q-Q plots of GWAS results for thick root traits.
Fig 9
Fig 9. Manhattan and Q-Q plots of GWAS results for shoot and root dry weight.
Fig 10
Fig 10. Manhattan and Q-Q plots of GWAS results for shoot and root dry weight.
See this image and copyright information in PMC

References

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