scholarly journals SNPs, InDels, and Microsatellites within and near to Rice NBS-LRR Resistance Gene Candidates

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2297
Author(s):  
Mark J. Quinton-Tulloch ◽  
Katherine A. Steele
Keyword(s):  
Indica Rice ◽  
R Gene ◽  
R Genes ◽  
Rice Varieties ◽  
Sequence Comparisons ◽  
Bioinformatic Tools ◽  
Genome Wide ◽  
Resistant Varieties ◽  
Resistance Gene Candidates ◽  
Bioinformatics Study

Plant resistance genes (R-genes) drive the immune responses of crops against specific pathotypes of disease-causing organisms. Over time, genetic diversity in R-genes and R-pseudogenes has arisen among different rice varieties. This bioinformatics study was carried out to (i) predict the full sets of candidate nucleotide-binding site leucine-rich repeat (NLR) R-genes present in six rice genomes; (ii) detect variation within candidate R-genes; (iii) identify potential selectable markers within and near to LRR genes among 75 diverse indica rice genomes. Four high quality indica genomes, plus the standard japonica and indica reference genomes, were analysed with widely available bioinformatic tools to identify candidate R-genes and R-pseudogenes. They were detected in clusters, consistent with previous studies. BLAST analysis of cloned protein sequences of 31 R-gene loci gave confidence in this approach for detection of cloned NLR R-genes. Approximately 10% of candidate R-genes were located within 1 kb of a microsatellite (SSR) marker. Sequence comparisons among indica rice genomes detected SNPs or InDels in 334 candidate rice R-genes. There were significantly more SNPs and InDels within the identified NLR R-gene candidates than in other types of gene. The genome-wide locations of candidate R-genes and their associated markers are presented here for the potential future development of improved disease-resistant varieties. Limitations of in silico approaches used for R-gene discovery are discussed.

scholarly journals Variation in seed longevity among diverse Indica rice varieties

2019 ◽  
Vol 124 (3) ◽  
pp. 447-460 ◽  
Author(s):  
Jae-Sung Lee ◽  
Marlina Velasco-Punzalan ◽  
Myrish Pacleb ◽  
Rocel Valdez ◽  
Tobias Kretzschmar ◽  
...  
Keyword(s):  
Indica Rice ◽  
A Priori ◽  
Rice Genome ◽  
Sugar Metabolism ◽  
Probit Analysis ◽  
Seed Longevity ◽  
Rice Varieties ◽  
Genome Wide ◽  
Group A ◽  
Harvest Moisture

Abstract Background and Aims Understanding variation in seed longevity, especially within closely related germplasm, will lead to better understanding of the molecular basis of this trait, which is particularly important for seed genebanks, but is also relevant to anyone handling seeds. We therefore set out to determine the relative seed longevity of diverse Indica rice accessions through storage experiments. Since antioxidants are purported to play a role in seed storability, the antioxidant activity and phenolic content of caryopses were determined. Methods Seeds of 299 Indica rice accessions harvested at 31, 38 and 45 d after heading (DAH) between March and May 2015 and differing in harvest moisture content (MC) were subsequently stored at 10.9 % MC and 45 °C. Samples were taken at regular intervals and sown for germination. Germination data were subjected to probit analysis and the resulting parameters that describe the loss of viability during storage were used for genome-wide association (GWA) analysis. Key Results The seed longevity parameters, Ki [initial viability in normal equivalent deviates (NED)], −σ−1 (σ is the time for viability to fall by 1 NED in experimental storage) and p50 [time for viability to fall to 50 % (0 NED)], varied considerably across the 299 Indica accessions. Seed longevity tended to increase as harvest MC decreased and to decrease as harvest MC increased. Eight major loci associated with seed longevity parameters were identified through GWA analysis. The favourable haplotypes on chromosomes 1, 3, 4, 9 and 11 enhanced p50 by ratios of 0.22–1.86. Conclusions This is the first study to describe the extent of variation in σ within a species’ variety group. A priori candidate genes selected based on rice genome annotation and gene network ontology databases suggested that the mechanisms conferring high seed longevity might be related to DNA repair and transcription, sugar metabolism, reactive oxygen species scavenging and embryonic/root development.

scholarly journals Dynamic Insertion of Pot3 in AvrPib Prevailing in a Field Rice Blast Population in the Philippines Led to the High Virulence Frequency Against the Resistance Gene Pib in Rice

2019 ◽  
Vol 109 (5) ◽  
pp. 870-877 ◽  
Author(s):  
Toluwase Olukayode ◽  
Berlaine Quime ◽  
Yin-Chi Shen ◽  
Mary Jeannie Yanoria ◽  
Suobing Zhang ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Rice Blast ◽  
Indica Rice ◽  
The Philippines ◽  
Avirulence Gene ◽  
Rice Varieties ◽  
Breeding Programs ◽  
Genome Wide ◽  
A Genome ◽  
Polymerase Chain

The Magnaporthe oryzae avirulence gene AvrPib is required for the resistance mediated by its cognate resistance gene Pib, which has been intensively used in indica rice breeding programs in many Asian countries. However, the sequence diversity of AvrPib among geographically distinct M. oryzae populations was recently shown to be increasing. Here, we selected a field population consisting of 248 rice blast isolates collected from a disease hotspot in Philippine for the analysis of AvrPib haplotypes and their pathogenicity against Pib. We found that all of the isolates were virulent to Pib and each of them contained an insertion of Pot3 transposon in AvrPib. Moreover, Pot3 insertion was detected in different genomic positions, resulting in three different AvrPib haplotypes, designated avrPib-H1 to H3. We further conducted a genome-wide Pot2 fingerprinting analysis by repetitive element palindromic polymerase chain reaction (PCR) and identified seven different lineages out of 47 representative isolates. The isolates belonging to the same lineage often had the same AvrPib haplotype. In contrast, the isolates having the same AvrPib haplotypes did not always belong to the same lineages. Both mating types MAT1-1 and MAT1-2 were identified in the population in Bohol and the latter appeared dominant. On the host side, we found that 32 of 52 released rice varieties in the Philippines contained Pib diagnosed by PCR gene-specific primers and DNA sequencing of gene amplicons, suggesting that it was widely incorporated in different rice varieties. Our study highlights the genetic dynamics of rice blast population at both the AvrPib locus and the genome-wide levels, providing insight into the mechanisms of the mutations in AvrPib leading to the breakdown of Pib-mediated resistance in rice.

scholarly journals Assessment of potentiality of known bacterial blight resistant genes against Xanthomonas oryzae pv. oryzae pathotypes exist in Bangladesh

2021 ◽  
Vol 6 (3) ◽  
pp. 257-267
Author(s):  
Md. Mahbubul Haque ◽  
Md. Mostafa Masud ◽  
Md. Mokarram Hossain ◽  
Md. Mamunur Rashid ◽  
Md. Zahangir Alam ◽  
...  
Keyword(s):  
Host Resistance ◽  
Bacterial Blight ◽  
Xanthomonas Oryzae ◽  
R Gene ◽  
R Genes ◽  
Near Isogenic Lines ◽  
Rice Varieties ◽  
Isogenic Lines ◽  
Resistant Genes ◽  
Resistance Reaction

Bacterial blight (BB) caused by X. oryzae pv. oryzae is a destructive disease of rice and causes 30-50% losses to rice depending on the outbreak. Development BB resistant rice varieties have long been considered as one of the most effective approach to control the disease. However, the durability of host resistance is breaking down due to the change of pathotypes of X. oryzae pv. oryzae globally. Pathotypic analyses of 239 X. oryzae pv. oryzae Bangladeshi isolates on Near Isogenic Lines (NILs) containing resistance (R) gene (s) revealed the existence of eight pathotypes of X. oryzae pv. oryzae. Among eight pathotypes, pathotypes IV and V were considered as major comprising  maximum number of isolates, (30.13% and 23.01%, respectively), whereas pathotype VIII considered as minor consisting only 2.51% of total isolates. Pathotype, I showed highest virulence or aggressiveness compatible with all NILs, whereas pathotype VIII exhibited lowest virulence to these NILs. Bacterial blight resistant genes viz. Xa1 (75.00%), Xa11 (62.50%) and Xa21 (50.00%) showed resistance to most of the pathotypes while Xa4 performed worst as compared to all others R-genes. In pyramid lines, IRBBB63 (Xa5+Xa7+Xa13) and IRBB57 (Xa5+Xa7 +Xa21) showed resistance reaction and IRBB61 (Xa4+Xa5+Xa7), IRBB60 (Xa4+Xa5+Xa13+Xa21), IRBB54 (Xa5+Xa21), and IRBB53 (Xa4+Xa21) showed susceptible reaction to X. oryzae pv. oryzae pathotypes. These results collectively indicated the deployment of Xa1, Xa11, Xa4, Xa5, Xa7, Xa13 and Xa21 either alone or in combination against BB would be a best choice for the development of BB resistant rice varieties in Bangladesh.

scholarly journals Plant resistance and strategies for breeding resistant varieties

2002 ◽  
Vol 38 (SI 1 - 6th Conf EFPP 2002) ◽  
pp. S9-S14 ◽  
Author(s):  
D.A.C. Pink ◽  
P. Hand
Keyword(s):  
Plant Transformation ◽  
Marker Assisted Selection ◽  
Specific Resistance ◽  
Durable Resistance ◽  
Resistance Breeding ◽  
R Gene ◽  
R Genes ◽  
Resistant Varieties ◽  
Plant Phenotype ◽  
The Impact

An explanation of the ‘boom-bust’ cycle of resistance breeding was provided by the gene-for-gene relationship between a pathogen and its host. Despite this understanding, most R genes continued to be deployed singly and resistance has been ephemeral. The reasons for breeding ‘single R gene’ varieties are discussed. Alternative strategies for the deployment of R genes and the use of quantitative race non-specific resistance have been advocated in order to obtain durable resistance. The feasibility of both of these approaches is discussed taking into account the impact of technologies such as plant transformation and marker-assisted selection. A change in focus from durability of the plant phenotype to that of the crop phenotype is advocated.

Genetic analysis for bacterial blight resistance in indica rice (Oryza sativa L.) cultivars

2019 ◽  
Vol 56 (3) ◽  
pp. 247-255 ◽  
Author(s):  
Manish Kumar ◽  
Ravi Pratap Singh ◽  
Onkar Nath Singh ◽  
Prakash Singh ◽  
Pandurang Arsode ◽  
...  
Keyword(s):  
Disease Severity ◽  
Bacterial Blight ◽  
Oryza Sativa L ◽  
Indica Rice ◽  
Rice Variety ◽  
R Gene ◽  
R Genes ◽  
Bacterial Blight Resistance ◽  
Disease Response ◽  
Allelic Interaction

Prior information on genetics of bacterial blight (BB) resistance (R) genes is imperative for its successful utilization in trait development and breeding for new resistant varietiesin rice. This experiment was aimed to assess the genetics of BB resistance in susceptible but popular rice variety HUR-917 and IRBB 66 (isogenic lines of IR 24) which harbors five R genes. Bioassay results in the parental lines and crosses were revealed resistance and susceptible disease response in R gene(s) positive and negative lines, respectively with varying range of Xoo (Xanthomonas oryzae pv oryzae) pathotype specificity. Phenomics of F2 and Back Cross (BC) generations showed existence of non-allelic interaction (13:3) between R genes with substantial variability in disease severity. The plants carrying mono hetero-allelic R gene has exsertedModerately susceptible (MS) disease reaction with 6.42 to 8.86 disease severities, however, lines carrying 2 R gene(s) could be able to disease severity Moderate susceptible MS to Moderate Resistant MR against all pathotypes existing in the region make it valid that the doses complementarity and presence of interaction in R genes are major determinant in R expression. It was recorded that presence of two or more R genes (Xa21+xa13; Xa21+ xa13+xa5) exerted broad spectrum BB resistance, hence found more suitable to combat this disease in HUR-917.

scholarly journals The Genetic Architecture of Disease Resistance in Maize: A Synthesis of Published Studies

2006 ◽  
Vol 96 (2) ◽  
pp. 120-129 ◽  
Author(s):  
Randall J. Wisser ◽  
Peter J. Balint-Kurti ◽  
Rebecca J. Nelson
Keyword(s):  
Disease Resistance ◽  
Genetic Architecture ◽  
Visual Inspection ◽  
Statistical Tests ◽  
R Gene ◽  
R Genes ◽  
Consensus Map ◽  
Maize Germplasm ◽  
Genome Wide ◽  
Breeding Schemes

Fifty publications on the mapping of maize disease resistance loci were synthesized. These papers reported the locations of 437 quantitative trait loci (QTL) for disease (dQTL), 17 resistance genes (R-genes), and 25 R-gene analogs. A set of rules was devised to enable the placement of these loci on a single consensus map, permitting analysis of the distribution of resistance loci identified across a variety of maize germplasm for a number of different diseases. The confidence intervals of the dQTL were distributed over all 10 chromosomes and covered 89% of the genetic map to which the data were anchored. Visual inspection indicated the presence of clusters of dQTL for multiple diseases. Clustering of dQTL was supported by statistical tests that took into account genome-wide variations in gene density. Several novel clusters of resistance loci were identified. Evidence was also found for the association of dQTL with maturity-related QTL. It was evident from the distinct dQTL distributions for the different diseases that certain breeding schemes may be more suitable for certain diseases. This review provides an up-to-date synthesis of reports on the locations of resistance loci in maize.

scholarly journals Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage

2018 ◽  
Vol 37 (3) ◽  
pp. 529-539 ◽  
Author(s):  
Mengchen Zhang ◽  
Jing Ye ◽  
Qun Xu ◽  
Yue Feng ◽  
Xiaoping Yuan ◽  
...  
Keyword(s):  
Association Study ◽  
Cold Tolerance ◽  
Genome Wide Association Study ◽  
Indica Rice ◽  
Genome Wide Association ◽  
Bud Burst ◽  
Rice Varieties ◽  
Genome Wide

scholarly journals Assessment of powdery mildew (Blumeria graminis f. sp. hordei) resistance genes in Turkish barley varieties

2009 ◽  
Vol 89 (1) ◽  
pp. 31-36 ◽  
Author(s):  
Ahmet Zeybek ◽  
Şahin Dere ◽  
Gülay Gök ◽  
Asude Çallak ◽  
Mahinur S. Akkaya
Keyword(s):  
Hordeum Vulgare ◽  
Powdery Mildew ◽  
Resistance Genes ◽  
Blumeria Graminis ◽  
Leaf Segment ◽  
R Gene ◽  
R Genes ◽  
Resistant Varieties

Thirty-four Turkish barley (Hordeum vulgare) varieties were tested for the presence of resistance genes (R-genes) to powdery mildew (Blumeria graminisf. sp.hordei) using the “leaf segment test” with nine isolates of the fungus. The most commonly found R-gene wasMla8, while a combination of R-genesMlgandMl(CP)was found in three varieties (Tokak 157/37, Beysehir 98, Konevei 98). The geneMlhwas found in four varieties (Obruk 86, Anadolu 86, Çıldır 02, Özdemir 05), while no R-gene was found in three varieties (Hamidiye 85, Yesevi 93, Bülbül 89). No clear inferences could be made for the partly-resistant varieties Gemici 7243, Yea 793.12 and Akhisar 98 using the test isolates selected, which suggests the presence of still unidentified R-genes. Overall, 10 previously characterized R-genes for powdery mildew (Mla8,Ml(La),Mlg,Ml(CP),Mlh,Mlat,Mla1,Mlh,Mla7,Mlra) were present in Turkish barley varieties, along with some other(s) still to be identified.

scholarly journals Identification and Analysis of Micro-Exon Genes in the Rice Genome

2019 ◽  
Vol 20 (11) ◽  
pp. 2685 ◽  
Author(s):  
Qi Song ◽  
Fang Lv ◽  
Muhammad Tahir ul Qamar ◽  
Feng Xing ◽  
Run Zhou ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Stop Codon ◽  
Indica Rice ◽  
Rice Genome ◽  
Protein Structures ◽  
Wide Distribution ◽  
Rna Seq ◽  
Rice Varieties ◽  
Genome Wide ◽  
Alternatively Spliced

Micro-exons are a kind of exons with lengths no more than 51 nucleotides. They are generally ignored in genome annotation due to the short length, whereas recent studies indicate that they have special splicing properties and important functions. Considering that there has been no genome-wide study of micro-exons in plants up to now, we screened and analyzed genes containing micro-exons in two indica rice varieties in this study. According to the annotation of Zhenshan 97 (ZS97) and Minghui 63 (MH63), ~23% of genes possess micro-exons. We then identified micro-exons from RNA-seq data and found that >65% micro-exons had been annotated and most of novel micro-exons were located in gene regions. About 60% micro-exons were constitutively spliced, and the others were alternatively spliced in different tissues. Besides, we observed that approximately 54% of genes harboring micro-exons tended to be ancient genes, and 13% were Oryza genus-specific. Micro-exon genes were highly conserved in Oryza genus with consistent domains. In particular, the predicted protein structures showed that alternative splicing of in-frame micro-exons led to a local structural recombination, which might affect some core structure of domains, and alternative splicing of frame-shifting micro-exons usually resulted in premature termination of translation by introducing a stop codon or missing functional domains. Overall, our study provided the genome-wide distribution, evolutionary conservation, and potential functions of micro-exons in rice.

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