Background

Rice is a global staple crop, being the main calorific component of many people living subsistence livelihoods. Rice can accumulate toxic elements such as arsenic, with the crop water management strongly affecting uptake. This study utilises the Bengal and Assam Aus Panel to conduct genome wide association (GWA) mapping for arsenic in shoots and grains of rice grown over 2 years under continually flooded (CF) and alternate wetting and drying (AWD). The aim was to assess genotype by water management interaction, identify quantitative trait loci (QTL) for arsenic accumulation, and propose candidate genes for lowering grain arsenic.

Results

AWD significantly reduced grain arsenic across all cultivars on average by 15.7 and 15.1% in year 1 and 2 respectively and shoot arsenic by 27.0% compared to the plants grown under CF. There was a weak cultivar by treatment interaction for grain for arsenic.All traits were strongly influenced by cultivar. GWA mapping identified a large number of 74 individual QTLs for arsenic, with six QTLs showing stability across years and/or water treatments. Three of the loci (one on chromosome 3, one on chromosome 4, and one on chromosome 5) were investigated in detail using an approach of clustering cultivars that had similar haplotypes for the QTL regions and then looking at the phenotypic values across the clusters. Two of the identified QTLs co-localised with known genes involved in arsenic accumulation, including Lsi2 which has not previously been reported to underlie a grain arsenic QTL.

Conclusions

This study has identified a number of novel QTLs for arsenic accumulation, as well as cultivars that consistently accumulate less arsenic over multiple field traits. The use of a haplotype clustering approach after GWA mapping has allowed for the effect, in terms of arsenic accumulation, to be determined for cultivars that share similar genomic sequence. Allocating nine high yielding Bangladeshi cultivars to these clusters has identified the potential of utilising these QTLs in breeding programmes; for example, incorporation of the QTL on chromosome 5 should decrease grain arsenic in elite high yielding Bangladeshi cultivars by 10% in all high yielding cultivars studied.

中文翻译：

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淹水或交替湿润和干燥灌溉时调节稻米中砷含量的遗传基因座。

背景

水稻是全球主要农作物，是许多维持生计的人们的主要热量成分。稻米会积聚砷等有毒元素，而农作物水分管理会严重影响其吸收。这项研究利用孟加拉和阿萨姆邦专家小组进行了全基因组关联（GWA）定位，绘制了在连续淹没（CF）和交替湿润和干燥（AWD）下种植2年以上水稻的芽和谷粒中的砷。目的是通过水管理相互作用评估基因型，确定砷积累的数量性状位点（QTL），并提出降低谷物砷含量的候选基因。

结果

与在CF条件下种植的植物相比，AWD在第1年和第2年平均显着降低了所有品种的谷物砷含量，分别降低了15.7％和15.1％，而射出砷则降低了27.0％。砷对谷物的处理相互作用弱于品种。所有性状都受到品种的强烈影响。GWA测绘确定了74个单独的砷QTL，其中六个QTL在多年和/或水处理过程中表现出稳定性。使用聚类的方法对QTL区域具有相似单倍型的聚类方法进行了详细研究，研究了三个基因座（一个位于3号染色体上，一个位于4号染色体上，一个位于5号染色体上），然后查看了整个簇的表型值。已鉴定的两个QTL与涉及砷积累的已知基因（包括Lsi2）共定位 先前尚未报道其是谷物砷QTL的基础。

结论

这项研究已经确定了许多新颖的QTL，用于砷的积累，以及在多个田间性状上持续积累较少砷的品种。在GWA作图后使用单倍型聚类方法，就砷积累而言，可以确定具有相似基因组序列的品种的效应。将9个高产孟加拉国品种分配到这些集群中，已经确定了在育种计划中利用这些QTL的潜力。例如，在所有研究的高产品种中，在5号染色体上掺入QTL可使精英高产孟加拉国品种的谷物砷含量降低10％。