Background

Arsenic (As) is an unwanted toxic mineral that threatens the major rice-growing regions in the world, especially in South Asia. Rice production in Bangladesh and India depends on As-contaminated groundwater sources for irrigating paddy fields, resulting in elevated amounts of As in the topsoil. Arsenic accumulating in rice plants has a significant negative effect on human and animal health. Here, we present a quantitative trait locus (QTL) mapping study to identify candidate genes conferring As toxicity tolerance and accumulation in rice (Oryza sativa L.) seedlings. An early backcross breeding population consisting of 194 lines derived from a cross between WTR1 (indica) and Hao-an-nong (japonica) was grown in hydroponics for 25 days, from the seventh day exposed to an environmentally relevant concentration of 10 ppm As.

Results

Arsenic toxicity leads to significantly negative plant responses, including reduced biomass, stunted plant growth, reduced leaf chlorophyll content, and increased shoot As concentration ranging from 9 to 20 mg kg^− 1. Marker-trait association was determined for seven As-related traits using 704 single nucleotide polymorphism (SNP) markers generated from a 6 K SNP-array. One QTL was mapped on chromosome 1 for relative chlorophyll content, two QTLs for As content in roots were mapped on chromosome 8, and six QTLs for As content in shoots were mapped on chromosomes 2, 5, 6, and 9. Using the whole-genome sequence of the parents, we narrowed down the number of candidate genes associated with the QTL intervals based on the existence of a non-synonymous mutation in genes between the parental lines. Also, by using publicly available gene expression profiles for As stress, we further narrowed down the number of candidate genes in the QTL intervals by comparing the expression profiles of genes under As stress and control conditions. Twenty-five genes showing transcription regulation were considered as candidate gene nominees for As toxicity-related traits.

Conclusions

Our study provides insight into the genetic basis of As tolerance and uptake in the early seedling stage of rice. Comparing our findings with the previously reported QTLs for As toxicity stress in rice, we identified some novel and co-localized QTLs associated with As stress. Also, the mapped QTLs harbor gene models of known function associated with stress responses, metal homeostasis, and transporter activity in rice. Overall, our findings will assist breeders with initial marker information to develop suitable varieties for As-contaminated ecosystems.

中文翻译：

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水稻回交育种群体中与砷毒性应激相关的基因组区域图谱（Oryza sativa L.）。

背景

砷 (As) 是一种有害的有毒矿物质，威胁着世界主要水稻种植区，尤其是南亚。孟加拉国和印度的水稻生产依赖受砷污染的地下水源来灌溉稻田，导致表土中砷含量升高。砷在水稻植株中积累对人类和动物健康具有显着的负面影响。在这里，我们提出了数量性状位点（QTL）作图研究，以确定赋予水稻（Oryza sativa L. ）幼苗砷毒性耐受性和积累的候选基因。早期回交育种群体由来自 WTR1（籼稻）和好安农（粳稻）杂交的 194 个品系组成，在水培法中生长 25 天，从第七天开始暴露于环境相关浓度 10 ppm 的砷。

结果

砷毒性会导致植物产生显着的负面反应，包括生物量减少、植物生长迟缓、叶片叶绿素含量降低以及地上部砷浓度增加（9 至 20 mg kg − 1 ^）。使用 6 K SNP 阵列生成的 704 个单核苷酸多态性 (SNP) 标记确定了 7 个 As 相关性状的标记-性状关联。1 个相对叶绿素含量 QTL 定位在 1 号染色体上，2 个根部 As 含量 QTL 定位在 8 号染色体上，6 个茎部 As 含量 QTL 定位在 2、5、6 和 9 号染色体上。根据亲本的基因组序列，我们根据亲本系之间基因中是否存在非同义突变，缩小了与 QTL 区间相关的候选基因的数量。此外，通过使用公开的 As 胁迫基因表达谱，我们通过比较 As 胁迫和对照条件下基因的表达谱，进一步缩小了 QTL 区间内候选基因的数量。二十五个显示转录调控的基因被认为是砷毒性相关性状的候选基因提名者。

结论

我们的研究深入了解了水稻幼苗期砷耐受性和吸收的遗传基础。将我们的研究结果与之前报道的水稻砷毒性胁迫的 QTL 进行比较，我们发现了一些与砷胁迫相关的新的共定位 QTL。此外，映射的 QTL 还包含与水稻应激反应、金属稳态和转运蛋白活性相关的已知功能的基因模型。总的来说，我们的研究结果将帮助育种者获得初始标记信息，以开发适合受砷污染的生态系统的品种。