Genetic factors underlying boron toxicity tolerance in rice: genome-wide association study and transcriptomic analysis

Neto, Joao Braga de Abreu; Hurtado-Perez, María Clara; Wimmer, Monika; Frei, Michael

doi:10.1093/jxb/erw423

Cited by 17 publications

(17 citation statements)

References 72 publications

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“…Necrosis of leaves and decreased growth was previously reported in rice under excess Mn conditions in hydroponics experiments [ 5 , 13 , 18 ]. In addition, we observed significant negative correlation between LDI and all biomass traits ( Table 2 ), similar to previous experiments, in which a diverse rice population was screened for boron toxicity tolerance in rice [ 28 ]. Therefore, cell death symptoms produced by these toxicities can serve as reliable indicators of response to stress.…”

Section: Discussionsupporting

confidence: 88%

“…The 700 k SNP data used for mapping [ 29 ] provided approximately one SNP every 500 bp, covering all 12 chromosomes of rice. SNPs with minor allele frequency of less than 5% were removed [ 24 , 27 , 28 ], resulting in a total of 416741 SNPs. Maker information was retrieved for 271 rice genotypes, which were used for association mapping.…”

Section: Methodsmentioning

confidence: 99%

“…With the 700 k SNP data used in this study, linkage disequilibrium (LD) decay is rapid within short distances between the SNP markers [ 29 ]. Therefore, declaration of candidate loci based on linkage disequilibrium blocks as adopted in previous studies using 44 k SNP data [ 24 – 28 ] might lead to false exclusion of candidate genes. Therefore, we applied a 200 kb window on either side of significant SNP to search putative candidate genes [ 40 ].…”

Section: Methodsmentioning

confidence: 99%

“…Rice being a self-pollinating species, genotyping data generated for a mapping population can be reused to study the genetic architecture of different traits. Accordingly, a 44 k SNPs map for 413 rice genotypes was used to study aluminium toxicity tolerance [ 24 ], ozone tolerance [ 25 ], internal phosphorus use efficiency [ 26 ], iron toxicity tolerance [ 27 ] and boron toxicity tolerance [ 28 ]. A high density array (HDRA) of SNPs with 700 k polymorphic sites for 1536 rice genotypes was developed and verified by mapping loci associated with grain size [ 29 ].…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice

et al. 2018

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Manganese (Mn) is an essential micro-nutrient for plants, but flooded rice fields can accumulate high levels of Mn2+ leading to Mn toxicity. Here, we present a genome-wide association study (GWAS) to identify candidate loci conferring Mn toxicity tolerance in rice (Oryza sativa L.). A diversity panel of 288 genotypes was grown in hydroponic solutions in a greenhouse under optimal and toxic Mn concentrations. We applied a Mn toxicity treatment (5 ppm Mn2+, 3 weeks) at twelve days after transplanting. Mn toxicity caused moderate damage in rice in terms of biomass loss and symptom formation despite extremely high shoot Mn concentrations ranging from 2.4 to 17.4 mg g-1. The tropical japonica subpopulation was more sensitive to Mn toxicity than other subpopulations. Leaf damage symptoms were significantly correlated with Mn uptake into shoots. Association mapping was conducted for seven traits using 416741 single nucleotide polymorphism (SNP) markers using a mixed linear model, and detected six significant associations for the traits shoot manganese concentration and relative shoot length. Candidate regions contained genes coding for a heavy metal transporter, peroxidase precursor and Mn2+ ion binding proteins. The significant marker SNP-2.22465867 caused an amino acid change in a gene (LOC_Os02g37170) with unknown function. This study demonstrated significant natural variation in rice for Mn toxicity tolerance and the possibility of using GWAS to unravel genetic factors responsible for such complex traits.

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Section: Discussionsupporting

confidence: 88%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice

et al. 2018

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“…In our study, the DH lines did not differ in shoot Cd concentration ( S2 Fig), whereas in the abovementioned study, a significant phenotypic difference in the DH lines for shoot Cd concentration was reported [38]. In agreement with our results, it has been shown that boron (B) tolerance indicators such as chlorosis and necrosis were not correlated with B uptake and translocation into rice shoots, suggesting that shoot-based tolerance mechanisms played an important role in B toxicity [39]. A possible tolerance mechanism was demonstrated for tolerant cultivars of barley and wheat, in which efflux transporters pump B from the intracellular phase, into the less sensitive apoplast of the leaves [40].…”

Section: Cd-tolerance Related Qtls In Different Populations and Cellusupporting

confidence: 90%

Combined QTL mapping and RNA-Seq profiling reveals candidate genes associated with cadmium tolerance in barley

et al. 2020

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The high toxicity of cadmium (Cd) and its ready uptake by plants has become a major agricultural problem. To investigate the genetic architecture and genetic regulation of Cd tolerance in barley, we conducted quantitative trait loci (QTL) analysis in the phenotypically polymorphic Oregon Wolfe Barley (OWB) mapping population, derived from a cross between Rec and Dom parental genotypes. Through evaluating the Cd tolerance of 87 available doubled haploid lines of the OWB mapping population at the seedling stage, one minor and one major QTL were detected on chromosomes 2H and 6H, respectively. For chlorosis and necrosis traits, the major QTL explained 47.24% and 38.59% of the phenotypic variance, respectively. RNA-Seq analysis of the parental seedlings under Cd treatment revealed 542 differentially expressed genes between Cd-tolerant Rec and Cd-susceptible Dom genotypes. By analyzing sequence variations in transcribed sequences of the parental genotypes, 155,654 SNPs and 1,525 InDels were identified between the two contrasting genotypes and may contribute to Cd tolerance. Finally, by integrating the data from the identified QTLs and RNA-Seq analysis, 16 Cd tolerance-related candidate genes were detected, nine of which were metal ion transporters. These results provide promising candidate genes for further gene cloning and improving Cd tolerance in barley.

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Boric Acid Inhibition of Trichophyton rubrum Growth and Conidia Formation

Schmidt

2017

Biol Trace Elem Res

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Trichophyton rubrum is a common human dermatophyte that is the causative agent of 80-93% of fungal infections of the skin and nails. While dermatophyte infections in healthy people are easily treatable with over-the-counter medications, such infections pose a higher risk for patients with compromised immune function and impaired regenerative potential. The efficacy of boric acid (BA) for the treatment of vaginal yeast infections prompted an investigation of the effect of BA on growth and morphology of T. rubrum. This is of particular interest since BA facilitates wound healing, raising the possibility that treating athlete's foot with BA, either alone or in combination with other antifungal drugs, would combine the benefits of antimicrobial activity and tissue regeneration to accelerate healing of infected skin. The data presented here show that BA represses T. rubrum growth at a concentration reported to be beneficial for host tissue regeneration. Oxygen exposure increases BA toxicity, and mycelia growing under BA stress avoid colonizing the surface of the growth surface, which leads to a suppression of aerial mycelium growth and surface conidia formation. BA penetrates into solid agar matrices, but the relative lack of oxygen below the substrate surface limits the effectiveness of BA in suppressing growth of embedded T. rubrum cells.

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Genetic factors underlying boron toxicity tolerance in rice: genome-wide association study and transcriptomic analysis

Abstract: HighlightGenetic factors associated with boron toxicity tolerance in rice were explored through an integrated approach combining genome-wide association study and transcriptomics.

Cited by 17 publications

References 72 publications

Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice

Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice

Combined QTL mapping and RNA-Seq profiling reveals candidate genes associated with cadmium tolerance in barley

Boric Acid Inhibition of Trichophyton rubrum Growth and Conidia Formation

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