Abstract
BackgroundDespite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them.ResultsThe panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed.ConclusionsSome of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0747-y) contains supplementary material, which is available to authorized users.
Highlights
Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits
Rice is grown on 82 % of the agricultural area, which corresponds to 7.75 M ha for a production of 43.6 million tons in 2012 [1]
Rice is mainly grown under irrigated conditions in the river deltas, notably the Mekong delta in South Vietnam (52 % of Vietnam rice production) and
Summary
Local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Vietnam is a tropical country in Southeast Asia with a rice-based agricultural economy. Rice is grown on 82 % of the agricultural area, which corresponds to 7.75 M ha for a production of 43.6 million tons in 2012 [1]. Vietnam is the world’s second rice exporter (6.4 million tons in 2012). Between spring and summer, all of the central areas of Vietnam are subject to periods of recurrent and severe drought that affect rice plantlets just after planting or plants during grain filling and can result in important yield losses. To improve rice drought resistance, an ideotype with a large number of deep and thick roots and a high root-to-shoot ratio was
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