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Genome-wide Association Study (GWAS) of Mesocotyl Elongation Based on Re-Sequencing Approach in Rice

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Genome-wide Association Study (GWAS) of Mesocotyl Elongation Based on Re-Sequencing Approach in Rice

Jinhong Wu et al. BMC Plant Biol.

Abstract

Background: Mechanized dry seeded rice can save both labour and water resources. Rice seedling establishment is sensitive to sowing depth while mesocotyl elongation facilitates the emergence of deeply sown seeds.

Results: A set of 270 rice accessions, including 170 from the mini-core collection of Chinese rice germplasm (C Collection) and 100 varieties used in a breeding program for drought resistance (D Collection), was screened for mesocotyl lengths of seedlings grown in water (MLw) in darkness and in 5 cm sand culture (MLs). Twenty six accessions (10.53 %) have MLw longer than 1.0 cm. Eleven accessions had the highest mesocotyl lengths, i.e. 1.4 - 5.05 cm of MLw and 3.0 - 6.4 cm in 10 cm sand culture, including 7 upland landraces or varieties. The genotypic data of 1,019,883 SNPs were developed by re-sequencing of those accessions. A whole-genome SNP array (Rice SNP50) was used to genotype 24 accessions as a validation panel, giving 98.41 % of consistent SNPs with the re-sequencing data in average. GWAS based on compressed mixed linear model was conducted using GAPIT. Based on a threshold of -log(P) ≥8.0, 13 loci were associated to MLw on rice chromosome 1, 3, 4, 5, 6 and 9, respectively. Three associated loci, on chromosome 3, 6, and 10, were detected for MLs. A set of 99 associated SNPs for MLw, based on a compromised threshold (-log(P) ≥7.0), located in intergenic regions or different positions of 36 annotated genes, including one cullin and one growth regulating factor gene.

Conclusions: Higher proportion and extension of elongated mesocotyls were observed in the mini-core collection of rice germplasm and upland rice landraces or varieties, possibly causing the correlation between mesocotyl elongation and drought resistance. GWAS found 13 loci for mesocotyl length measured in dark germination that confirmed the previously reported co-location of two QTLs across populations and experiments. Associated SNPs hit 36 annotated genes including function-matching candidates like cullin and GRF. The germplasm with elongated mesocotyl, especially upland landraces or varieties, and the associated SNPs could be useful in further studies and breeding of mechanized dry seeded rice.

Figures

Fig. 1
Fig. 1
Varied mesocotyl lengths among rice landraces or varieties, measured in seedlings from dark germination in water (MLw) or 5 cm sand culture (MLs)
Fig. 2
Fig. 2
Mesocotyl lengths of 30 rice germplasm accessions measured in sand or soil culture with two seeding depths
Fig. 3
Fig. 3
Neighbor joining tree of 270 rice accessions showed a two-subpopulation structure in consistence with the classification of indica (in red) and japonica (in blue) subspecies. Four aus accessions (in green) were grouped into two subpopulations
Fig. 4
Fig. 4
Manhattan plots of genome-wide association mapping for mesocotyl lengths measured in dark germination with water (MLw, a) and in 5 cm sand culture (MLs, b) and Quantile-Quantile plots for MLs (c) and MLs (d)

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