Norton Gareth J, Travis Anthony J, Talukdar Partha, Hossain Mahmud, Islam Md Rafiqul, Douglas Alex, Price Adam H
School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, Scotland.
Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh.
Rice (N Y). 2019 Jul 22;12(1):54. doi: 10.1186/s12284-019-0307-9.
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.
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.
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.
水稻是全球主要粮食作物，是许多维持生计的人们的主要热量来源。水稻会积累砷等有毒元素，作物的水分管理对其吸收有很大影响。本研究利用孟加拉和阿萨姆奥氏稻品种面板，对在连续淹水（CF）和干湿交替（AWD）条件下种植两年的水稻地上部和籽粒中的砷进行全基因组关联（GWA）图谱分析。目的是评估基因型与水分管理的相互作用，确定砷积累的数量性状位点（QTL），并提出降低籽粒砷含量的候选基因。
与CF条件下生长的植株相比，AWD使所有品种的籽粒砷含量在第1年和第2年平均分别显著降低15.7%和15.1%，地上部砷含量降低27.0%。籽粒砷含量存在较弱的品种与处理相互作用。所有性状都受品种的强烈影响。GWA图谱分析确定了大量74个单独的砷QTL，其中6个QTL在年份和/或水分处理中表现出稳定性。使用对QTL区域具有相似单倍型的品种聚类方法，然后观察各聚类间的表型值，对其中3个位点（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）进行了详细研究。已鉴定出的两个QTL与参与砷积累的已知基因共定位，包括Lsi2，此前尚未报道其为籽粒砷QTL的基础基因。
本研究确定了多个新的砷积累QTL，以及在多个田间性状中砷积累始终较少的品种。GWA图谱分析后使用单倍型聚类方法，可以确定具有相似基因组序列的品种在砷积累方面的效应。将9个高产孟加拉品种分配到这些聚类中，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，将5号染色体上的QTL引入优良高产孟加拉品种中，应可使籽粒砷含量降低10%。
