Abstract
BackgroundMechanized 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.ResultsA 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.ConclusionsHigher 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0608-0) contains supplementary material, which is available to authorized users.
Highlights
Mechanized dry seeded rice can save both labour and water resources
The mesocotyl lengths measured in dark germination (MLw) and in sand culture (MLs) had highly significant correlation (r = 0.784**; Additional file 1: Table S1)
If confirmed in further studies like candidate gene cloning, the results demonstrate the high power of Genome-wide association study (GWAS) based on high dense single nucleotide polymorphism (SNP)
Summary
Mechanized dry seeded rice can save both labour and water resources. TPR has several advantages like higher yield potential, Wu et al BMC Plant Biology (2015) 15:218 seeding can save water, but are labour costing. Mechanized dry seeding is probably the most efficient way of rice seedling establishment, saving 30 % labour than machine-transplanting rice (MTPR) as estimated in Korean trials [3]. A minimum of 600 mm of cumulative rainfall was required to complete field puddling and transplanting of rice in the Philippines, much higher than 150 mm cumulative rainfall required by dry seeding [4]. MDSR has been widely adopted and will expand to much larger area if effective managements are available to control weeds and to maintain uniform plant density, e.g. fine tillage, better land levelling, more appropriate seed placement, improved nutrient application, varieties with higher seedling vigor and lodge resistance [6]. The appropriate techniques are not fully available yet to ensure the perfect seedling establishments
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