Joint genetic and network analyses identify loci associated with root growth under NaCl stress in Arabidopsis thaliana.

Plants have evolved a series of tolerance mechanisms to saline stress, which perturbs physiological processes throughout the plant. To identify genetic mechanisms associated with salinity tolerance, we performed linkage analysis and genome-wide association study (GWAS) on maintenance of root growth of Arabidopsis thaliana in hydroponic culture with weak and severe NaCl toxicity. The top 200 single-nucleotide polymorphisms (SNPs) determined by GWAS could cumulatively explain approximately 70% of the variation observed at each stress level. The most significant SNPs were linked to the genes of ATP-binding cassette B10 and vacuolar proton ATPase A2. Several known salinity tolerance genes such as potassium channel KAT1 and calcium sensor SOS3 were also linked to SNPs in the top 200. In parallel, we constructed a gene co-expression network to independently verify that particular groups of genes work together to a common purpose. We identify molecular mechanisms to confer salt tolerance from both predictable and novel physiological sources and validate the utility of combined genetic and network analysis. Additionally, our study indicates that the genetic architecture of salt tolerance is responsive to the severity of stress. These gene datasets are a significant information resource for a following exploration of gene function.

Association mapping of cadmium, copper and hydrogen peroxide tolerance of roots and translocation capacities of cadmium and copper in Arabidopsis thaliana.

Association mapping analysis of Cd, Cu and H (2)O (2) tolerance, judged by relative root length (RRL: % of root length in stress condition relative to that in control condition), and Cd and Cu translocation ratios (amount of metal in the shoot to the total) were performed using 90 accessions of Arabidopsis thaliana. Using 140 SNPs that were distributed across the genome, association mapping analysis was performed with a haploid setting by the Q + K method, which minimizes detection of false associations by combining the Q-matrix of the structured association (Q) with kinship (K) to control for the population structure. Six, five and five significant (-log (10)P-value is 1.3 > or =) linkages were detected between the SNPs and Cd, Cu and H(2)O(2) resistant RRLs, respectively. In addition, six significant linkages were identified with translocation capacities of Cd and Cu. Among those detected loci, two each of Cu and Cd tolerance RRLs were collocated with those of H(2)O(2) tolerance RRL, while one locus each was detected by Cu and Cd tolerance RRLs that collocated with their translocation ratios. These results suggested that these factors might partly explain the phenotypic variation of tolerance RRLs to Cd and Cu of Arabidopsis thaliana. Finally, using a different approach to analyze interactions between individual phenotypes, namely clustering analysis, we found an expected segregation of resistant SNPs (single-nucleotide polymorphisms) of the multiple RRLs in the typical accession groups carrying multiple traits. Almost none of the loci detected by association mapping analysis were linked to the loci of previously identified critical genes regulating the traits, suggesting that this could be useful to identify complex architecture of genetic factors determining variation among multiple accessions.

Quantitative trait loci controlling resistance to cadmium rhizotoxicity in two recombinant inbred populations of Arabidopsis thaliana are partially shared by those for hydrogen peroxide resistance.

To understand mechanisms of cadmium (Cd) tolerance variation associated with root elongation in Arabidopsis thaliana, quantitative trait loci (QTLs) and epistasis were analyzed using relative root length (RRL: % of the root length in +Cd to -Cd) as a tolerant index. Using the composite interval mapping method, three major QTLs (P < 0.05) were detected on chromosomes 2, 4 and 5 in the recombinant inbred population derived from a cross between Landsberg erecta (Ler-0) and Columbia (Col-4). The highest logarithm of odds (LOD) of 5.6 was detected with the QTL on chromosome 5 (QTL5), which is linked to the genetic marker CDPK9 and explained about 26% of the Cd tolerance variation. There was no significant difference in Cd-translocation ratio from roots to shoots between tolerant and sensitive recombinant inbreed lines (RILs), while greater accumulations of reactive oxygen species were observed in the roots of sensitive RILs. This suggested that accumulation of ROS would explain Cd tolerance variation of the Ler/Col RILs, which is mainly controlled by the QTL on chromosome 5. The QTL5 in Ler/Col population was also detected as one of the major QTLs controlling tolerances to hydrogen peroxide and to copper, which is another ROS generating rhizotoxic metal. The same chromosomal position was detected as a common major QTL for Cd and hydrogen peroxide tolerances in a different recombinant inbreed (RI) population derived from a cross of Col-gl1 and Kashmir (Kas-1). These data, along with a multitraits QTL analysis in both sets of RILs, suggest that peroxide damage depends on the genotype at a major Cd-tolerant locus on the upper part of chromosome 5.