Synteny analysis of gene clusters for pizh and pigm as blast disease resistance in 11 Oryza and three related species

Document Type : Original Article

Authors

1 Department of Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran

2 Department of Chemistry, Academic Center for Education, Culture & Research (ACECR), Kermanshah, Iran

Abstract

Introduction: Rice, a key agricultural crop globally, is vital for feeding millions of people. Blast is one of the important diseases of rice and it causes severe damage to many rice fields every year. This disease is caused by the fungus Magnaporthe oryzae, which infects plant tissues and significantly reduces performance.The genus Oryza belongs to the Poaceae family and comprises 24 different species. Species within this genus are divided into two categories in terms of genome: diploid and tetraploid. The existence of synteny between genes specially those that cause resistance to plant diseases is considered a very suitable way to identify genes from other species. The pizh and pigm gene clusters play a role in rice blast disease resistance in rice. Synteny in pizh and pigm clusters was investigated in 11 species of Oryzaand three related species.
Materials and methods: The pizh and pigm gene clusters were identified in 13 other species using the BLASTN tool.  Subsequently, the genome sequences of these 13 species were obtained from the NCBI database then, all genes for all species were compared together by BLASN tool to construct the homology file (BLAST file). After, the genes were mapped to the respective species by Gmap software. Finally, gene blocks exhibiting synteny were identified through the utilization of the MCScanX software.
Results: The results of synteny analysis of blast resistance genes in 14 studied species showed synteny only in five species: O. meridionalis, O. sativa indica, O. glumipatula, O. barthii, and O. glaberrima. Synteny was not observed in other species, including O. sativa japonica, regarding these gene clusters for blast resistance. According to the results, it could be concluded that the gene cluster involved in blast disease resistance, has not been spread and preserved between different chromosomes of studied Oryza species during evolution. In fact, they are located mainly on chromosomes Number 6 and 9. Micro synteny for the species including O. meridionalis, O.sativa indica, O. glumipatula, O. barthii and O. glaberrima were observed, but no synteny was observed for other five Oryza species and three wild relatives. It is necessary to mention that these genes are clustered on chromosome Number 6 for O. sativa japonica, however, they have no synteny with other species.
Conclusion: Species including O. meridionalis, O.sativa indica, O. glumipatula, O. barthii and O. glaberrima may be used as a promising source of blast resistance for blast resistance breeding programs.

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References

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