Silencing of the Rice Gene LRR1 Compromises Rice Xa21 Transcript Accumulation and XA21-Mediated Immunity

Caddell, Daniel; Park, Chang Jin; Thomas, Nicholas; Canlas, Patrick E.; Ronald, Pamela C.

doi:10.1186/s12284-017-0162-5

Cited by 14 publications

(8 citation statements)

References 32 publications

(66 reference statements)

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“…Similarly, silencing of an LRR1 gene was found to compromise resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae in rice ( Oryza sativa L.) (Caddell et al., 2017). In GWAS studies of sorghum mini core collection and SAP lines, regarding anthracnose and head smut, leucine rich repeat containing proteins were listed as top candidate genes associated with response to anthracnose (Ahn et al., 2019; Cuevas et al., 2018a; Prom et al., 2019).…”

Section: Resultsmentioning

confidence: 99%

Genome‐wide association analysis for response of Senegalese sorghum accessions to Texas isolates of anthracnose

Ahn

Prom

et al. 2021

The Plant Genome

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Anthracnose disease of sorghum is caused by Colletotrichum sublineola, a filamentous fungus. The genetic basis of resistance to anthracnose in sorghum is largely unclear, especially in Senegalese sorghum germplasm. In this study, 163 Senegalese sorghum accessions were evaluated for response to C. sublineola, and a genomewide association study (GWAS) was performed to identify genetic variation associated with response to C. sublineola using 193,727 single nucleotide polymorphisms (SNPs) throughout the genome. Germplasm diversity analysis showed low genetic diversity and slow linkage disequilibrium (LD) decay among the Senegalese accessions. Phenotypic analysis resulted in relatively low differences to C. sublineola among the tested population. Genome-wide association study did not identify any significant association based on a strict threshold for the number of SNPs available.However, individual analysis of the top eight SNPs associated with relative susceptibility and resistance identified candidate genes that have been shown to play important roles in plant stress tolerance in previous studies. This study identifies sorghum genes whose annotated properties have known roles in host defense and thus identify them as candidates for use in breeding for resistance to anthracnose.

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Section: Resultsmentioning

confidence: 99%

Genome‐wide association analysis for response of Senegalese sorghum accessions to Texas isolates of anthracnose

Ahn

Prom

et al. 2021

The Plant Genome

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“…This gene encodes an immune receptor kinase whose functions result in subsequent activation of an intracellular defence response. Additionally, a previous study found that silencing OsXA21 led to rice susceptibility to Xoo infection [82]. Recently, Ye et al [80] reported that many RLKs are involved in responses to abiotic stresses, including the salt-stress response in plants.…”

Section: Discussionmentioning

confidence: 99%

Comparative Genomic Analysis of Rice with Contrasting Photosynthesis and Grain Production under Salt Stress

Lekklar

Suriya-arunroj

Pongpanich

et al. 2019

Genes

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Unfavourable environmental conditions, including soil salinity, lead to decreased rice (Oryza sativa L.) productivity, especially at the reproductive stage. In this study, we examined 30 rice varieties, which revealed significant differences in the photosynthetic performance responses under salt stress conditions during the reproductive stage, which ultimately affected yield components after recovery. In rice with a correlation between net photosynthetic rate (PN) and intercellular CO2 concentration (Ci) under salt stress, PN was found to be negatively correlated with filled grain number after recovery. Applying stringent criteria, we identified 130,317 SNPs and 15,396 InDels between two “high-yield rice” varieties and two “low-yield rice” varieties with contrasting photosynthesis and grain yield characteristics. A total of 2,089 genes containing high- and moderate-impact SNPs or InDels were evaluated by gene ontology (GO) enrichment analysis, resulting in over-represented terms in the apoptotic process and kinase activity. Among these genes, 262 were highly expressed in reproductive tissues, and most were annotated as receptor-like protein kinases. These findings highlight the importance of variations in signaling components in the genome and these loci can serve as potential genes in rice breeding to produce a variety with salt avoidance that leads to increased yield in saline soil.

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“…Of the other six protein-types several had mutations on leucine rich repeats (LRR); LRR4, LRR9, LRR10 and LRR22, and on the NLS. The LRR repeats are previously reported to be associated with disease resistance conveyed via Xa genes (Caddell et al, 2017), and hence, a mutation in these repeats could alter the function of the gene. Therefore, further studies to verify the identified protein-types through phenotypic assays are recommended.…”

Section: Thirteen Confirmed Xa21 Haplotypes and Nine Protein-typesmentioning

confidence: 99%

Haplotype diversity analysis of bacterial leaf blight resistance gene <i>Xa21</i> in rice

2018

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Bacterial leaf blight (BLB) caused by Xanthomonasoryzaepv. oryzae (Xoo) is a devastative rice disease. Resistance gene Xa21 is known to convey a stable resistance against a broad spectrum of Xoo races. Assessment of Xa21 genetic diversity and defining haplotypes is the initial step towards identification of haplotypes that associate with desired phenotypes. In this study, an alignment of a 2,778 bp coding sequence (CDS) from 1,618 rice accessions revealed 18 single nucleotide polymorphisms and six insertion/deletions (InDel), each with ≥ 5% occurrence among the accessions. A total of 13 confirmed-haplotypes (≥ 1% occurrence) and 113 putative haplotypes (≤ 1 % occurrence) were identified. The 13 confirmed haplotypes were represented by 1,341 rice accessions that deferred at 22 sites belonging to 12 rice subpopulations from 70 countries. The Xa21 CDS has a haplotype diversity of 0.8203, and a nucleotide diversity of 0.15448. Further, the haplotype network shows a high substitution rate between the haplotype pairs of Xa21, with two distinctive clusters created as a result of a 19-bp InDel in CDS. Based on 14 non-synonymous sites identified within the CDS, nine protein-types were identified. Of these three protein-types are truncated owing to a premature stop codon at 180 th position of the polypeptide chain due to the said 19-bp InDel in the ectodomain, and represents 45% of the accessions. The ectodomain of XA21 protein is crucial for immune responses, and hence, these haplotypes with truncated proteins could be important in eliciting the function of XA21.

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Silencing of the Rice Gene LRR1 Compromises Rice Xa21 Transcript Accumulation and XA21-Mediated Immunity

Cited by 14 publications

References 32 publications

Genome‐wide association analysis for response of Senegalese sorghum accessions to Texas isolates of anthracnose

Genome‐wide association analysis for response of Senegalese sorghum accessions to Texas isolates of anthracnose

Comparative Genomic Analysis of Rice with Contrasting Photosynthesis and Grain Production under Salt Stress

Haplotype diversity analysis of bacterial leaf blight resistance gene <i>Xa21</i> in rice

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