Rice Blast Resistance Gene Pi-ta Research Articles

Analysis of the Relationship between Blast Resistance Genes and Disease Resistance of Rice Germplasm via Functional Molecular Markers

Rice blast disease is one of the most devastating diseases of rice (Oryza sativa L.) caused by the fungus Magnaporthe oryzae (M. oryzae), and neck blast is the most destructive phase of this illness. The underlying molecular mechanisms of rice blast resistance are not well known. Thus, we collected 150 rice varieties from different ecotypes in China and assessed the rice blast resistances under the natural conditions that favoured disease development in Jining, Shandong Province, China in 2017. Results showed that 92 (61.3%) and 58 (38.7%) rice varieties were resistant and susceptible to M. oryzae, respectively. Among the 150 rice varieties screened for the presence of 13 major blast resistance (R) genes against M. oryzae by using functional markers, 147 contained one to eight R genes. The relationship between R genes and disease response was discussed by analysing the phenotype and genotype of functional markers. The results showed that the rice blast resistance gene Pita was significantly correlated with rice blast resistance. Our results provided a basis for the further understanding of the distribution of 13 major R genes of rice blast in the germplasm resources of the tested rice varieties, and were meaningful for rice disease resistance breeding.

Statistical inference of selection and divergence of the rice blast resistance gene Pi-ta.

The resistance gene Pi-ta has been effectively used to control rice blast disease, but some populations of cultivated and wild rice have evolved resistance. Insights into the evolutionary processes that led to this resistance during crop domestication may be inferred from the population history of domesticated and wild rice strains. In this study, we applied a recently developed statistical method, time-dependent Poisson random field model, to examine the evolution of the Pi-ta gene in cultivated and weedy rice. Our study suggests that the Pi-ta gene may have more recently introgressed into cultivated rice, indica and japonica, and U.S. weedy rice from the wild species, O. rufipogon. In addition, the Pi-ta gene is under positive selection in japonica, tropical japonica, U.S. cultivars and U.S. weedy rice. We also found that sequences of two domains of the Pi-ta gene, the nucleotide binding site and leucine-rich repeat domain, are highly conserved among all rice accessions examined. Our results provide a valuable analytical tool for understanding the evolution of disease resistance genes in crop plants.

Molecular diversity in rice blast resistance gene Pi-ta makes it highly effective against dynamic population of Magnaporthe oryzae

Rice blast is one of the important diseases of rice which can be effectively managed by the deployment of resistance genes. Pi-ta is one of the major blast resistant genes effective against pathogen populations in different parts of India. We analysed allelic variants of Pi-ta from 48 rice lines selected after phenotyping of 529 rice landraces across three eco-geographical blast hot spot regions. Besides, Pi-ta orthologue sequences of 220 rice accessions belonging to wild and cultivated species of rice were also included in the study for a better evo-devo perspective of the diversity present in the gene and the selection pressures acting on this locus. We obtained high nucleotide variations (SNPs and insertion-deletions) in the intronic region. We also identified 64 haplotypes based on nucleotide polymorphism in these alleles. Pi-ta orthologues of Indian landraces were scattered in eight major haplotypes indicating its heterogenous nature. We identified a total of 47 different Pi-ta protein variants on the basis of deduced amino acid residues amongst the orthologues. Five unique and novel Pi-ta variants were identified for the first time in rice landraces exhibiting different reaction types against the Magnaporthe oryzae population. A high value of Pi(non/syn) was observed only in the leucine-rich domain of the alleles cloned from Indian landraces, indicating strong selective forces acting on this region. The detailed molecular analysis of the Pi-ta orthologues provides insights to a high degree of inter- and intraspecific relationships amongst the Oryza species. We identified rice landraces possessing the effective alleles of this resistance gene which can be used in future blast resistance breeding programmes.

Indica and japonica crosses resulting in linkage block and recombination suppression on rice chromosome 12.

Understanding linkage block size and molecular mechanisms of recombination suppression is important for plant breeding. Previously large linkage blocks ranging from 14 megabases to 27 megabases were observed around the rice blast resistance gene Pi-ta in rice cultivars and backcross progeny involving an indica and japonica cross. In the present study, the same linkage block was further examined in 456 random recombinant individuals of rice involving 5 crosses ranging from F2 to F10 generation, with and without Pi-ta containing genomic indica regions with both indica and japonica germplasm. Simple sequence repeat markers spanning the entire chromosome 12 were used to detect recombination break points and to delimit physical size of linkage blocks. Large linkage blocks ranging from 4.1 megabases to 10 megabases were predicted from recombinant individuals involving genomic regions of indica and japonica. However, a significantly reduced block from less than 800 kb to 2.1megabases was identified from crosses of indica with indica rice regardless of the existence of Pi-ta. These findings suggest that crosses of indica and japonica rice have significant recombination suppression near the centromere on chromosome 12.

Molecular Evolution of the Rice Blast Resistance Gene Pi-ta in Invasive Weedy Rice in the USA

The Pi-ta gene in rice has been effectively used to control rice blast disease caused by Magnaporthe oryzae worldwide. Despite a number of studies that reported the Pi-ta gene in domesticated rice and wild species, little is known about how the Pi-ta gene has evolved in US weedy rice, a major weed of rice. To investigate the genome organization of the Pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the US, we analyzed nucleotide sequence variation at the Pi-ta gene and its surrounding 2 Mb region in 156 weedy, domesticated and wild rice relatives. We found that the region at and around the Pi-ta gene shows very low genetic diversity in US weedy rice. The patterns of molecular diversity in weeds are more similar to cultivated rice (indica and aus), which have never been cultivated in the US, rather than the wild rice species, Oryza rufipogon. In addition, the resistant Pi-ta allele (Pi-ta) found in the majority of US weedy rice belongs to the weedy group strawhull awnless (SH), suggesting a single source of origin for Pi-ta. Weeds with Pi-ta were resistant to two M. oryzae races, IC17 and IB49, except for three accessions, suggesting that component(s) required for the Pi-ta mediated resistance may be missing in these accessions. Signatures of flanking sequences of the Pi-ta gene and SSR markers on chromosome 12 suggest that the susceptible pi-ta allele (pi-ta), not Pi-ta, has been introgressed from cultivated to weedy rice by out-crossing.

Erratum: Artificial introgression of a large chromosome fragment around the rice blast resistance gene Pi-ta in backcross progeny and several elite rice cultivars

Erratum: Artificial introgression of a large chromosome fragment around the rice blast resistance gene Pi-ta in backcross progeny and several elite rice cultivars

Artificial introgression of a large chromosome fragment around the rice blast resistance gene Pi-ta in backcross progeny and several elite rice cultivars

Studying the size of genomic introgressions should lead to a better understanding of linkage disequilibrium in crop breeding. In this study, progeny of the cross between a tropical japonica rice cultivar Katy containing the rice blast resistance gene Pi-ta and a temperate japonica cultivar M202 (pi-ta)' [corrected]. were inoculated with the race IB49 of Magnaporthe oryzae that recognizes Pi-ta. The resistant progeny were identified during backcrossing for five generations. Two progeny of each of the 22 BC(5)F(1) were genotyped using 12 simple sequence repeat markers around the Pi-ta genomic region on chromosome 12. Unlinked DNA in 43 BC(5)F(2) individuals was found primarily from the recurrent parent M202 as expected. However, unexpectedly, various sizes of genomic fragments around Pi-ta ranging from half (14 Mbp) to the entire chromosome (27 Mbp) were found from the donor. Similarly, large segments of comparable sizes of the Pi-ta genomic region originating from a landrace indica variety Tetep from Vietnam were also identified in Pi-ta containing US rice cultivars, Katy, Madison, Kaybonnet, and Drew. It was also determined that Tetep had an identical chromosome 12 to another landrace cultivar Tadukan from the Philippines. The most widely grown indica cultivar IR64 was found to contain the same 6.4 Mbp around Pi-ta. This study demonstrates that a large portion of the chromosome was maintained by artificial selection for blast resistance during crop breeding.

Cloning and analyzing of rice blast resistance gene <I>Pi-ta</I><SUP>+</SUP> allele from Jinghong erect type of common wild rice (<I>Oryza rufipogon</I> Griff) in Yunnan

A 4,672 bp DNA sequence including the whole coding region and partial non-coding region of rice blast resistance gene Pi-ta+ has been cloned from Jinghong erect type of common wild rice (Oryza rufipogon Griff) in Yunnan by polymerase chain reaction method. The coding region shares 99.86% and 98.78% identity with the corresponding regions of the reported cultivated rice Yashiro-mochi and Yuanjiang type of common wild rice respectively. There are 4 nucleotides difference in the coding region and 6 in intron of the cloned Pi-ta+ gene,compared with Pi-ta from Yashiro-mochi. Pi-ta+ gene in Jinghong erect type of common wild rice has been proved to be a rare existing Pi-ta+ allele, because there was a alanine rather than a serine at the position 918 within the predicted amino acid sequence of PITA. Pi-ta+ allele can cause disease resistance response to rice blast pathogens in plant cells. Differences in DNA sequence, deduced amino acid sequence and antibacterial spectrum may make the Pi-ta+ allele new resistant characteristics. Finding and cloning of Pi-ta+ allele from Jinghong erect type of common wild rice in Yunnan provides a basement for further utilization of the wild rice resources.

A Telomeric Avirulence Gene Determines Efficacy for the Rice Blast Resistance Gene Pi-ta

A Telomeric Avirulence Gene Determines Efficacy for the Rice Blast Resistance Gene Pi-ta

Construction of an 800-kb contig in the near-centromeric region of the rice blast resistance gene Pi-ta2 using a highly representative rice BAC library.

We constructed a rice Bacterial Artificial Chromosome (BAC) library from green leaf protoplasts of the cultivar Shimokita harboring the rice blast resistance gene Pi-ta. The average insert size of 155 kb and the library size of seven genome equivalents make it one of the most comprehensive BAC libraries available, and larger than many plant YAC libraries. The library clones were plated on seven high density membranes of microplate size, enabling efficient colony identification in colony hybridization experiments. Seven percent of clones carried chloroplast DNA. By probing with markers close to the blast resistance genes Pi-ta2(closely linked to Pi-ta) and Pi-b, respectively located in the centromeric region of chromosome 12 and near the telomeric end of chromosome 2, on average 2.2 +/- 1.3 and 8.0 +/- 2.6 BAC clones/marker were isolated. Differences in chromosomal structures may contribute to this wide variation in yield. A contig of about 800 kb, consisting of 19 clones, was constructed in the Pi-ta2 region. This region had a high frequency of repetitive sequences. To circumvent this difficulty, we devised a "two-step walking" method. The contig spanned a 300 kb region between markers located at 0 cM and 0.3 cM from Pi-ta. The ratio of physical to genetic distances (> 1,000 kb/cM) was more than three times larger than the average of rice (300 kb/cM). The low recombination rate and high frequency of repetitive sequences may also be related to the near centromeric character of this region. Fluorescent in situ hybridization (FISH) with a BAC clone from the Pi-b region yielded very clear signals on the long arm of chromosome 2, while a clone from the Pi-ta2 region showed various cross-hybridizing signals near the centromeric regions of all chromosomes.