Mapping of genomic regions associated with arsenic toxicity stress in a backcross breeding populations of rice (Oryza sativa L.)

Abstract

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.

Keywords: Arsenic toxicity; Candidate genes; Quantitative trait loci; Rice; Single nucleotide polymorphisms.

Fig. 1

Phenotypic trait variation in parents of mapping population under As toxicity stress for 18 days. (A) Chlorophyll content; (B) plant height; (C) root length; (D) shoot dry weight; (E) root dry weight; (F) arsenic content in shoot and root tissue. Vertical bars represent standard errors of means (n = 3). Different letters above the data points indicate significant differences between genotypes by LSD test (P < 0.05)

Fig. 2

Box plot distribution of measured As-related stress in the population; control with no As and treatment with 10 ppm As a substitution for 18 days. Control: without As substitution, Treatment: with 10 ppm As substitution

Fig. 3

Heat map is showing the correlation coefficient of As-related traits. RCC: relative chlorophyll content; RPH: relative plant height; RRL: relative root length; RSBM: relative shoot biomass; RRBM: relative root biomass; AsS: As content in shoots; AsR: As content in roots

Fig. 4

Chromosomal distribution of polymorphic single nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs) detected in this study. QTLs were located on the chromosome based on the physical position of the SNP marker

Fig. 5

Transcriptional regulation of genes contained in identified QTL regions. Only genes containing non-synonymous SNPs showing significant expression response under As^(III) stress are plotted. Gene expression data adopted from Yu et al. (2012)