Identification and validation of novel alleles of rice blast resistant gene Pi54, and analysis of their nucleotide diversity in landraces and wild Oryza species
- 373 Downloads
Rice blast is a devastating fungal disease, which limits rice production severely. To identify novel alleles of blast resistant gene, Pi54, and to understand its diversity exist among wild Oryza species and landraces sequence-based allele mining strategy was employed. In this study, sixteen Pi54 alleles were sequenced from landraces and wild Oryza species which have genome ranging from AA to EE. Overall analysis confirmed that the alleles derived from wild species had more divergence than the landraces. Among all wild Oryza alleles, Pi54 aus derived from O. australiensis, showed the highest diversity. Comparison of protein domains revealed that LRR region had more variations than NBS region. Haplo-groups among the ecotypes were analyzed based on their Pi54 sequence. Interestingly, four different haplo-groups were identified, that were supported by phylogeny analysis. Among 16 analyzed alleles, two alleles, Pi54 ab, Pi54 btj derived from landraces-Amana Bavo and Boha Thulasi Joha showed superior phenotypic reaction than the reference allele (Pi54 Tetep), and these alleles were validated by allelism test. These alleles have potential application in blast resistance breeding programs and identified SNPs and Indel among the alleles can be useful in development of allele specific markers. The present study helped to gain insights into the evolutionary adaptation of the resistant gene and its allelic distribution and diversity among the Oryza species.
KeywordsPi54 Allele mining Rice blast NBS-LRR Land races Oryza sativa
The Authors thank the Department of Biotechnology, Government of India for providing funds for carrying out the research work.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
- Fukuoka S, Yamamoto S, Mizobuchi R, Yamanouchi U, Ono K, Kitazawa N, Yasuda N, Fujita Y, Nguyen TTT, Koizumi S, Sugimoto K, Matsumoto T, Yano M (2014) Multiple functional polymorphisms in a single disease resistance gene in rice enhance durable resistance to blast. Sci Rep 4:4550. doi: 10.1038/srep04550 CrossRefGoogle Scholar
- Kaur N, Street K, Mackay M, Yahiaoui N, Keller B (2008) Allele mining and sequence diversity at the wheat powdery mildew resistance locus Pm3, Proceedings of the 11th International wheat genetics symposium, Sydney. 1–3Google Scholar
- Khush GS, Jena KK (2009) Current status and future prospects for research on blast resistance in rice (Oryza sativa L.). In: Advances in genetics, genomics and control of rice blast disease. Springer, New York. p. 1–10Google Scholar
- Madhav MS, Laha GS, Padmakumari AP, Somasekhar N, Mangrauthia SK, Viraktamath BC (2013) Phenotyping rice for molecular plant breeding. In: Panguluri SK, Kumar AA (Eds) Phenotyping for plant breeding: Applications of phenotyping methods for crop improvement, Springer pub ISBN: 978-1-4614-8319-9 (Print) 978-1-4614-8320-5 (Online), 1–40 ppGoogle Scholar
- McCouch SR, Sweeney M, Li J, Jiang H, Thomson M, Septiningsih E, Edwards J, Moncada P, Xiao J, Garris A, Tai T, Martinez C, Tohme J, Sugiono M, McClung A, Yuan LP, Ahn SN (2007) Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa. Euphytica 154:317–339CrossRefGoogle Scholar
- Nunziata A, Ruggieri V, Frusciante L, Barone A (2007) Allele mining at the locus Gro 1 in Solanum wild species. VIth International solanaceae conference, Acta Hort 745, ISHS 449–456Google Scholar
- Ramkumar G, Srinivasarao K, Mohan KM, Sudharshan I, Sivaranjani AKP, Gopalakrishna K, Neeraja CN, Balachandran SM, Sundaram RM, Prasad MS, Rani NS, Prasad AMP, Viraktamath BC, Madhav MS (2011) Development and validation of functional marker targeting an InDel in the major rice blast disease resistance gene Pi54 (Pikh). Mol Breed 27:129–135CrossRefGoogle Scholar
- Ramkumar G, Madhav MS, Devi SJSR, Manimaran P, Mohan KM, Prasad MS, Balachandran SM, Neeraja CN, Sundaram RM, Viraktamath BC (2014) Nucleotide diversity of Pita, a major blast resistance gene and identification of its minimal promoter. Gene 546:250–256. doi: 10.1016/j.gene.2014.06.001 CrossRefPubMedGoogle Scholar
- Sharma TR, Madhav MS, Singh BK, Shanker P, Jana TK, Dalal V, Pandit A, Singh A, Gaikwad K, Upreti HC, Singh NK (2005) High-resolution mapping, cloning and molecular characterization of the Pi-kh gene of rice, which confers resistance to Magnaporthe grisea. Mol Genet Gen 274:569–578CrossRefGoogle Scholar
- Thakur S, Singh PK, Das A, Rathour R, Variar M, Prashanthi SK, Singh AK, Singh UD, Chand D, Singh NK, Sharma TR (2015) Extensive sequence variation in rice blast resistance gene Pi54 makes it broad spectrum in nature. Front Plant Sci 6:345. doi: 10.3389/fpls.2015.00345 CrossRefPubMedPubMedCentralGoogle Scholar
- Xu X, Lv Q, Shang J, Pang Z, Zhou Z, Wang J, Jiang G, Tao Y, Xu Q, Li X, Zhao X, Li S, Xu J, Zhu L (2014) Excavation of Pid3 orthologs with differential resistance spectra to Magnaporthe oryzae in rice resource. PLoS ONE 9:e93275. doi: 10.1371/journal.pone.0093275 CrossRefPubMedPubMedCentralGoogle Scholar