Functional Analysis of <i>Pid3-A4</i>, an Ortholog of Rice Blast Resistance Gene <i>Pid3</i> Revealed by Allele Mining in Common Wild Rice

Lv, Qiming; Xu, Xiao; Shang, Junjun; Jiang, Guicheng; Pang, Zhe; Zhou, Zhao-Nian; Wang, Jing; Liu, Ya; Li, Ting; Li, Xiaobing; Xu, Junfeng; Cheng, Zhihui; Zhao, Xianfeng; Li, Shigui; Zhu, Lihuang

doi:10.1094/phyto-10-12-0260-r

Cited by 62 publications

(42 citation statements)

References 30 publications

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“…Up to now, at least 78 major blast resistance ( R ) genes have been identified and mapped genetically on 11 rice chromosomes in exception of chromosome 3. Among the mapped blast R genes, 24 have been cloned [2]–[5] and functionally analyzed. With these known and cloned blast R genes, rice blast resistance breeding has become much more effective than before by using molecule markers linked to the known blast R genes [6].…”

Section: Introductionmentioning

confidence: 99%

Excavation of Pid3 Orthologs with Differential Resistance Spectra to Magnaporthe oryzae in Rice Resource

Shang

et al. 2014

PLoS ONE

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Twenty-six orthologs of the rice blast resistance gene Pid3 from cultivated varieties and wild rice accessions distributed in different areas were cloned by allele mining. Sequence analysis showed that while each of the orthologous genes from indica varieties and most wild accessions encodes a complete NBS-LRR protein, each of the proteins encoded by those from japonica varieties and few wild rice accessions presents a premature termination. Eleven of the 26 orthologs were selected for blast resistance testing by transforming into the blast susceptible rice variety TP309, respectively. Inoculation of 23 M. oryzae strains collected from diverse regions of China to the respective transgenic plants revealed that 6 Pid3 orthologs showed susceptible to all the tested strains, while the other 5 orthologs showed differential resistance spectra in a gradually spectrum-widen order as Pid3-W3, Pid3-W4, Pid3-I3, Pid3-W5 and Pid3-I1. Amino acid sequences alignment of these orthologs indicated that the sequence diversities between the blast resistance orthologs were mostly located in the LRR domain such as the substitutions of Q694H,D856H,Q896R,D899E etc. However, the differences between the resistance orthologs and the susceptible ones were mostly located in the NBS domain. The present experiments provide an example of that the ortholog evaluation of plant R genes could be an efficient way to expand the rice blast resistance and some other plant disease resistance as well for breeding.

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Section: Introductionmentioning

confidence: 99%

Excavation of Pid3 Orthologs with Differential Resistance Spectra to Magnaporthe oryzae in Rice Resource

Shang

et al. 2014

PLoS ONE

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“…The wheat powdery mildew resistance gene Pm3 with 17 identified functional alleles is a remarkable example of natural variations present in GenBank accessions and can be efficiently utilized for conferring broad-spectrum disease resistance. For rice blast resistance gene, functional orthologous have been found in wild rice O. rufipogon accessions (Lv et al, 2013; Xu et al, 2014; Ashkani et al, 2015) defining their utility in widening the genetic base of cultivated rice varieties. A novel allele of PSTOL1 gene is identified in O. glaberrima (CG14) and being transferred to the NERICAs (New Rice for Africa) cultivars using allele-specific markers.…”

Section: Discussionmentioning

confidence: 99%

Novel Alleles of Phosphorus-Starvation Tolerance 1 Gene (PSTOL1) from Oryza rufipogon Confers High Phosphorus Uptake Efficiency

et al. 2017

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Limited phosphorus availability in the soil is one of the major constraints to the growth and productivity of rice across Asian, African and South American countries, where 50% of the rice is grown under rain-fed systems on poor and problematic soils. With an aim to determine novel alleles for enhanced phosphorus uptake efficiency in wild species germplasm of rice Oryza rufipogon, we investigated phosphorus uptake1 (Pup1) locus with 11 previously reported SSR markers and sequence characterized the phosphorus-starvation tolerance 1 (PSTOL1) gene. In the present study, we screened 182 accessions of O. rufipogon along with Vandana as a positive control with SSR markers. From the analysis, it was inferred that all of the O. rufipogon accessions undertaken in this study had an insertion of 90 kb region, including Pup1-K46, a diagnostic marker for PSTOL1, however, it was absent among O. sativa cv. PR114, PR121, and PR122. The complete PSTOL1 gene was also sequenced in 67 representative accessions of O. rufipogon and Vandana as a positive control. From comparative sequence analysis, 53 mutations (52 SNPs and 1 nonsense mutation) were found in the PSTOL1 coding region, of which 28 were missense mutations and 10 corresponded to changes in the amino acid polarity. These 53 mutations correspond to 17 haplotypes, of these 6 were shared and 11 were scored only once. A major shared haplotype was observed among 44 accessions of O. rufipogon along with Vandana and Kasalath. Out of 17 haplotypes, accessions representing 8 haplotypes were grown under the phosphorus-deficient conditions in hydroponics for 60 days. Significant differences were observed in the root length and weight among all the genotypes when grown under phosphorus deficiency conditions as compared to the phosphorus sufficient conditions. The O. rufipogon accession IRGC 106506 from Laos performed significantly better, with 2.5 times higher root weight and phosphorus content as compared to the positive control Vandana. In terms of phosphorus uptake efficiency, the O. rufipogon accessions IRGC 104639, 104712, and 105569 also showed nearly two times higher phosphorus content than Vandana. Thus, these O. rufipogon accessions could be used as the potential donor for improving phosphorus uptake efficiency of elite rice cultivars.

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“…Functional orthologs of the rice blast resistance gene Pid3 have been found primarily in most screened indica types and wild rice varieties (Shang et al, 2009). Lv et al, (2013) isolated an ortholog of Pid3 from a common wild rice accession A4 (O. rufipogon) using sequencingbased allele mining, called Pid3-A4, with confirmation of different amount of resistance spectra. Thereafter, Xu et al (2014) isolated 26 orthologs of Pid3 from cultivated and wild rice accessions and evaluate their respective blast resistance by gene transformation and blast inoculation.…”

Section: Allele Mining and Blast Resistance Genesmentioning

confidence: 99%

“…Blast resistance (Kiyosawa and Ando, 1990;Joshi et al, 2009) 2 Pid3 6 Blast resistance (Joshi et al, 2009;Shang et al, 2009;Sharma et al, 2009;Rai et al, 2011a;Lv et al, 2013;Xu et al, 2014) 3 Pi-ta(+) 12 Blast resistance (Yang et al, 2007) 4 Pi-2 6 Blast resistance (Hittalmani et al, 2013) 5 Pi54 11 Blast resistance (Kumari et al, 2013) 6 Pi-z(t) 6 Blast resistance (Sharma et al, 2009) 7 AC134922 11 Blast resistance 8…”

Section: Tilling and Eco-tillingmentioning

confidence: 99%

Allele Mining Strategies: Principles and Utilisation for Blast Resistance Genes in Rice (Oryza sativaL.)

Ashkani

Yusop²,

Shabanimofrad³

et al. 2015

Current Issues in Molecular Biology

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Allele mining is a promising way to dissect naturally occurring allelic variants of candidate genes with essential agronomic qualities. With the identification, isolation and characterisation of blast resistance genes in rice, it is now possible to dissect the actual allelic variants of these genes within an array of rice cultivars via allele mining. Multiple alleles from the complex locus serve as a reservoir of variation to generate functional genes. The routine sequence exchange is one of the main mechanisms of R gene evolution and development. Allele mining for resistance genes can be an important method to identify additional resistance alleles and new haplotypes along with the development of allele-specific markers for use in marker-assisted selection. Allele mining can be visualised as a vital link between effective utilisation of genetic and genomic resources in genomics-driven modern plant breeding. This review studies the actual concepts and potential of mining approaches for the discovery of alleles and their utilisation for blast resistance genes in rice. The details provided here will be important to provide the rice breeder with a worthwhile introduction to allele mining and its methodology for breakthrough discovery of fresh alleles hidden in hereditary diversity, which is vital for crop improvement.

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Functional Analysis of Pid3-A4, an Ortholog of Rice Blast Resistance Gene Pid3 Revealed by Allele Mining in Common Wild Rice

Cited by 62 publications

References 30 publications

Excavation of Pid3 Orthologs with Differential Resistance Spectra to Magnaporthe oryzae in Rice Resource

Excavation of Pid3 Orthologs with Differential Resistance Spectra to Magnaporthe oryzae in Rice Resource

Novel Alleles of Phosphorus-Starvation Tolerance 1 Gene (PSTOL1) from Oryza rufipogon Confers High Phosphorus Uptake Efficiency

Allele Mining Strategies: Principles and Utilisation for Blast Resistance Genes in Rice (Oryza sativaL.)

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