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Identification of a new rice blast resistance gene, Pid3, by genomewide comparison of paired nucleotide-binding site--leucine-rich repeat genes and their pseudogene alleles between the two sequenced rice genomes.
Genetics. 2009 Aug; 182(4):1303-11.G

Abstract

Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases. The two major subspecies of Asian cultivated rice (Oryza sativa L.), indica and japonica, have shown obvious differences in rice blast resistance, but the genomic basis that underlies the difference is not clear. We performed a genomewide comparison of the major class of resistant gene family, the nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family, between 93-11 (indica) and Nipponbare (japonica) with a focus on their pseudogene members. We found great differences in either constitution or distribution of pseudogenes between the two genomes. According to this comparison, we designed the PCR-based molecular markers specific to the Nipponbare NBS-LRR pseudogene alleles and used them as cosegregation markers for blast susceptibility in a segregation population from a cross between a rice blast-resistant indica variety and a susceptible japonica variety. Through this approach, we identified a new blast resistance gene, Pid3, in the indica variety, Digu. The allelic Pid3 loci in most of the tested japonica varieties were identified as pseudogenes due to a nonsense mutation at the nucleotide position 2208 starting from the translation initiation site. However, this mutation was not found in any of the tested indica varieties, African cultivated rice varieties, or AA genome-containing wild rice species. These results suggest that the pseudogenization of Pid3 in japonica occurred after the divergence of indica and japonica.

Authors+Show Affiliations

State Key Laboratory of Plant Genomics and National Plant Gene Research Centre, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

19506306

Citation

Shang, Junjun, et al. "Identification of a New Rice Blast Resistance Gene, Pid3, By Genomewide Comparison of Paired Nucleotide-binding Site--leucine-rich Repeat Genes and Their Pseudogene Alleles Between the Two Sequenced Rice Genomes." Genetics, vol. 182, no. 4, 2009, pp. 1303-11.
Shang J, Tao Y, Chen X, et al. Identification of a new rice blast resistance gene, Pid3, by genomewide comparison of paired nucleotide-binding site--leucine-rich repeat genes and their pseudogene alleles between the two sequenced rice genomes. Genetics. 2009;182(4):1303-11.
Shang, J., Tao, Y., Chen, X., Zou, Y., Lei, C., Wang, J., Li, X., Zhao, X., Zhang, M., Lu, Z., Xu, J., Cheng, Z., Wan, J., & Zhu, L. (2009). Identification of a new rice blast resistance gene, Pid3, by genomewide comparison of paired nucleotide-binding site--leucine-rich repeat genes and their pseudogene alleles between the two sequenced rice genomes. Genetics, 182(4), 1303-11. https://doi.org/10.1534/genetics.109.102871
Shang J, et al. Identification of a New Rice Blast Resistance Gene, Pid3, By Genomewide Comparison of Paired Nucleotide-binding Site--leucine-rich Repeat Genes and Their Pseudogene Alleles Between the Two Sequenced Rice Genomes. Genetics. 2009;182(4):1303-11. PubMed PMID: 19506306.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Identification of a new rice blast resistance gene, Pid3, by genomewide comparison of paired nucleotide-binding site--leucine-rich repeat genes and their pseudogene alleles between the two sequenced rice genomes. AU - Shang,Junjun, AU - Tao,Yong, AU - Chen,Xuewei, AU - Zou,Yan, AU - Lei,Cailin, AU - Wang,Jing, AU - Li,Xiaobing, AU - Zhao,Xianfeng, AU - Zhang,Meijun, AU - Lu,Zhike, AU - Xu,Jichen, AU - Cheng,Zhukuan, AU - Wan,Jianmin, AU - Zhu,Lihuang, Y1 - 2009/06/08/ PY - 2009/6/10/entrez PY - 2009/6/10/pubmed PY - 2010/2/2/medline SP - 1303 EP - 11 JF - Genetics JO - Genetics VL - 182 IS - 4 N2 - Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases. The two major subspecies of Asian cultivated rice (Oryza sativa L.), indica and japonica, have shown obvious differences in rice blast resistance, but the genomic basis that underlies the difference is not clear. We performed a genomewide comparison of the major class of resistant gene family, the nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family, between 93-11 (indica) and Nipponbare (japonica) with a focus on their pseudogene members. We found great differences in either constitution or distribution of pseudogenes between the two genomes. According to this comparison, we designed the PCR-based molecular markers specific to the Nipponbare NBS-LRR pseudogene alleles and used them as cosegregation markers for blast susceptibility in a segregation population from a cross between a rice blast-resistant indica variety and a susceptible japonica variety. Through this approach, we identified a new blast resistance gene, Pid3, in the indica variety, Digu. The allelic Pid3 loci in most of the tested japonica varieties were identified as pseudogenes due to a nonsense mutation at the nucleotide position 2208 starting from the translation initiation site. However, this mutation was not found in any of the tested indica varieties, African cultivated rice varieties, or AA genome-containing wild rice species. These results suggest that the pseudogenization of Pid3 in japonica occurred after the divergence of indica and japonica. SN - 1943-2631 UR - https://www.unboundmedicine.com/medline/citation/19506306/Identification_of_a_new_rice_blast_resistance_gene_Pid3_by_genomewide_comparison_of_paired_nucleotide_binding_site__leucine_rich_repeat_genes_and_their_pseudogene_alleles_between_the_two_sequenced_rice_genomes_ L2 - http://www.genetics.org/cgi/pmidlookup?view=long&pmid=19506306 DB - PRIME DP - Unbound Medicine ER -