Abstract
Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r2>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30-day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several co-localized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates.
Highlights
Rice (O. sativa L.) is the main staple food crop worldwide
We present here the results of an association mapping study for root depth and associated traits in a panel of japonica accessions genotyped with single nucleotide polymorphisms (SNPs) derived from Genotyping by sequencing (GBS)
The average heterozygosity, calculated from the SNP markers, was low (1.3%), as expected for DNA extracted from single plants that had been selffertilized for two generations
Summary
Rice (O. sativa L.) is the main staple food crop worldwide. In 2011, rice crops occupied 164.1 M ha (http://faostat.fao.org [accessed 28/01/2013]). Rice is grown in a variety of environments, covering a wide range of latitudes and altitudes. This crop exhibits a relatively high water demand in comparison with other cereals, and it is characterized by a broad range of adaptation in terms of the hydrological conditions tolerated. Adaptation to a given hydrological regime imposes specific requirements in terms of tolerance to abiotic constraints (submergence or drought). Rice exhibits a large variability in root traits [4] that is related to both the organization of the species into varietal groups and the adaptation of these groups to a specific ecosystem [5]. The ability of a variety to develop a deep root system is greatly affected by the physical, chemical and biological conditions of the soil, and sub-optimal conditions can substantially reduce differences between varieties through genotype x environment interactions [6]
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