Abstract
The genetic diversity of 45 farmers’ varieties collected from agro-climatic zones of central India were characterized using 26 simple sequence repeats (SSRs) and ten blast-linked markers. A total of 58 alleles representing 26 SSR loci were detected with frequency ranging from 2 to 4 (mean 2.23) alleles per locus. The polymorphism information content values for SSR markers varied from 0.50 to 0.88 for the primers RM449 and RM279, respectively. Further, the average marker index and effective multiplex ratio of 3.31 and 4.48 per primer, respectively could be observed. A dendrogram based on UPGMA exhibited clear-cut discrimination of the farmers’ varieties into two major clusters representing their geographical origin. Out of ten blast resistance genes screened, only Pik-h was widely distributed with 97.8% frequency and farmers’ variety Dihula Safed showed amplification for maximum of seven blast resistance genes. Inclusively, all the 45, indigenous farmers’ varieties represented a wide range of genetic variability and SSR markers proved to be a powerful tool in revealing genetic diversity and relationships. The presence of different blast resistance genes in farmers’ varieties with diverse traits can be utilized further in the future breeding programme.
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Abbreviations
- SSR:
-
Simple sequence repeats
- PCR:
-
Polymerase chain reaction
References
Anupam A, Jahangir I, Syed Mohammad Q, Anantha S, Das SP, Mukund V, Mandal NP (2017) Genetic diversity analysis of rice germplasm in Tripura State of Northeast India using drought and blast linked markers. Rice Sci 24(1):10–20. https://doi.org/10.1016/j.rsci.2016.07.003
Babu BK, Meena V, Agarwal V, Agrawal PK (2014) Population structure and genetic diversity analysis of Indian and exotic rice (Oryza sativa L.) accessions using SSR markers. Mol Biol Rep 41(7):4328–4339. https://doi.org/10.1007/s11033-014-3304-5
Chen X, Shang J, Chen D, Lei C, Zou Y, Zhai W, Liu G, Xu J, Ling Z, Cao G, Ma B, Wang Y, Zhao X, Li S, Zhu LA (2006) A B-lectin receptor kinase gene conferring rice blast resistance. Plant J 46:794–804. https://doi.org/10.1111/j.1365-313X.2006.02739.x.
Choudhury B, Khan ML, Dayanandan S (2013) Genetic structure and diversity of indigenous rice varieties (Oryza sativa L.) in eastern Himalayan region of northeast India. Springer plus 2:228–323. https://doi.org/10.1186/2193-1801-2-228
DeWoody JA, Honeycutt RL, Skow LC (1995) Microsatellite markers in white-tailed deer. J Hered 86(4):317–319. https://doi.org/10.1093/oxfordjournals.jhered.a111593
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
Ferreira ME, Grattapaglia D (1998) Introduction to the Use of molecular markers in genetic analysis. 2nd edn. Embrapa- Cenargen, Brasilia: 220.
Fuentes JL, Correa-Victoria FJ, Escobar F, Prado G, Aricapa G, Duque MC et al (2008) Identification of microsatellite markers linked to the blast resistance gene Pi-1 (t) in rice. Euphytica 160(3):295–304. https://doi.org/10.1007/s10681-007-9497-0
Hayashi K, Yoshida H, Ashikawa I (2006) Development of PCR based allele specific and InDel marker sets for nine rice blast resistance genes. Theor Appl Genet 113(2):251–260. https://doi.org/10.1007/s00122-006-0290-6
Imam J, Alam S, Mandal NP, Variar M, Shukla P (2014) Molecular screening for identification of blast resistance genes in northeast and eastern Indian rice germplasm (Oryza sativa L.) with PCR based markers. Euphytica 196(2):199–211. https://doi.org/10.1007/s10681-013-1024-x
Jia YL, Wang ZH, Singh P (2002) Development of dominant rice blast Pi-ta resistance gene markers. Crop Sci 42(6):2145–2149. https://doi.org/10.2135/cropsci2002.2145
Jia YL, Redus M, Wang ZH, Rutger JN (2004) Development of a SNLP marker from the Pi-ta blast resistance gene by Tri-primer PCR. Euphytica 138(1):97–105. https://doi.org/10.1023/b:euph.0000047079.42768.4d
** L, Lu Y, **. Theor Appl Genet 121(3):475–487
Kuroda Y, Sato YI, Bounphanousay C, Kono Y, Tanaka K (2007) Genetic structure of three Oryza AA genome species (O. rufipogon, O nivara and O sativa) as assessed by SSR analysis on the Vientiane Plain of Laos. Conserv Genet 8(1):149–158. https://doi.org/10.1007/s10592-006-9156-3
Liu G, Lu G, Zeng L, Wang GL (2002) Two broad spectrum resistance genes, Pi9(t) and Pi2(t), are physically linked on rice chromosome. Mol Genet Genom 267:472–480. https://doi.org/10.1007/s00438-002-0677-2
Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Islam KN, Mohammad AL (2013) A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance. Int J Mol Sci 14(11):22499–22528. https://doi.org/10.3390/ijms141122499
Musibau A, Azeez AO, Adubi, Felicia, Durodola A (2018) Landraces and crop genetic improvement, rediscovery of landraces as a resource for the future, Oscar Grillo, Intech Open, DOI: https://doi.org/10.5772/intechopen.75944. Available from: https://www.intechopen.com/books/rediscovery-of-landraces-as-a-resource-for-thefuture/landraces-and-crop-genetic-improvement
Pusadee T, Jamjod S, Chiang YC, Rerkasem B, Schaal BA (2009) Genetic structure and isolation by distance in a landrace of Thai rice. Proc Natl Acad Sci USA 106:13880–13885. https://doi.org/10.1073/pnas.0906720106
Qu SH, Liu GF, Zhou B, Bellizzi M, Zeng LR, Dai LY, Han B, Wang GL (2006) The broad spectrum blast resistance gene Pi9 encodes a nucleotide-binding site leucine-rich repeat protein and is a member of a multigene family in rice. Genetics 172(3):1901–1914. https://doi.org/10.1534/genetics.105.044891
Ram SG, Thiruvengadam V, Vinod KK (2007) Genetic diversity among cultivars, landraces and wild relatives of rice as revealed by microsatellite markers. J Appl Genet 48(4):337–345. https://doi.org/10.1007/s12041-019-1131-0
Rohlf FJ (1997) NTSYS-PC: numerical taxonomy and multivariate analysis system. Exeter Software, New York, USA
Roy S, Marndi BC, Mawkhlieng B, Banerjee A, Yadav RM, Mishra AK, Bansal KC (2016) Genetic diversity and structure in hill rice (Oryza sativa L.) landraces from the North-Eastern Himalayas of India. BMC Genet 17:107. https://doi.org/10.1186/s12863-016-0414-1
RoyChowdhury M, Jia Y, Jackson A, Jia MH, Fjellstrom R, Cartwright RD (2012) Analysis of rice blast resistance gene Pi–z in rice germplasm using pathogenicity assays and DNA markers. Euphytica 184:35–46. https://doi.org/10.1007/s10681-011-0481-3
Sharma TR, Madhav MS, Singh BK, Shanker P, Jana TK, Dalal V et al (2005) High-resolution map**, cloning and molecular characterization of the Pi-kh gene of rice, which confers resistance to Magnaporthe grisea. Mol Genet Genomics 274(6):569–578. https://doi.org/10.1007/s00438-005-0035-2 (PMID: 16228246)
Sharma TR, Rai AK, Gupta SK, Vijayan J, Devanna BN, Ray S (2012) Rice blast management through host plant resistance: retrospect and prospects. Agric Res 1:37–52. https://doi.org/10.1007/s40003-011-0003-5
Sharma R, Joshi A, Maloo SR, Rajamani G (2012) Assessment of genetic finger printing using molecular marker in plants: a review. Sci Res Impact 1:29–36
Sharma R, Maloo SR, Choudhary S, Jain D (2015) Microsatellite markers: an important DNA fingerprinting tool for characterization of crop plants. J Plant Sci Res 31(1):83–89. https://doi.org/10.5897/AJBx10.021
Singh N, Choudhury DR, Tiwari G, Singh AK, Kumar S, Srinivasan K, Tyagi RK, Sharma AD, Singh NK, Singh R (2016) Genetic diversity trend in Indian rice varieties: an analysis using SSR markers. BMC Genet 17(1):127. https://doi.org/10.1186/s12863-016-0437-7
Sinha AK (2014) Threatened traditional rice (Oryza sativa L.) varieties of lateritic region of West Bengal-status, distribution and conservation. Int J Appl Biosci 2(2):111–116
Sneath PHA, Sokal RR (1973) Numerical taxonomy: the principles and practice of numerical classification. Freeman, San Francisco, p 573
Tanksley SD, Mc Couch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066. https://doi.org/10.1126/science.277.5329.1063
Thomson M, Septiningsih E, Suwardjo F, Santoso T, Silitonga T, McCouch S (2007) Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theor Appl Genet 114:559–568. https://doi.org/10.1007/s00122-006-0457-1
Tu M, Lu BR, Zhu YY, Wang YY (2007) Abundant within varietal genetic diversity in rice germplasm from Yunnan Province of China revealed by SSR fingerprints. Biochem Genet 45(11):789–801. https://doi.org/10.1007/s10528-007-9118-6
Yadav S, Singh A, Singh MR, Goel N, Vinod KK, Mohapatra T, Singh AK (2013) Assessment of genetic diversity in Indian rice germplasm (Oryza sativa L.): use of random versus trait-linked microsatellite markers. J Genet 92(3):545–557. https://doi.org/10.1007/s12041-013-0312-5
Yadav MK, Aravindan S, Ngangkham U, Raghu S, Prabhukarthikeyan SR, Keerthana U, Mandi BC, Totan A, Munda S, Deshmukh R, Pramesh D, Samantaray S, Rath PC (2019) Blast resistance in Indian rice landraces: genetic dissection by gene specific markers. PLoS ONE 14(1):0211061. https://doi.org/10.1371/journal.pone.0211061
Zhang F, Chen SM, Chen FD, Fang WM, Li FT (2010) A prelim-inary genetic linkage map of chrysanthemum (Chrysanthemum morifolium) cultivars using RAPD, ISSR and AFLP markers. Sci Hortic 125:422–428. https://doi.org/10.1016/j.scienta.2010.03.028
Zhang P, Li J, Li X, Liu X, Zhao X, Lu Y (2011) Population structure and genetic diversity in a rice core collection (Oryza sativa L.) investigated with SSR markers. PLoS ONE 6(12):e27565
Zhu D, Kang H, Li Z, Liu M, Zhu X, Wang Y et al (2016) A genome–wide association study of field resistance to Magnaporthe oryzae in rice. Rice 9(1):44. https://doi.org/10.1186/s12284-016-0116-3
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The authors are gratefully acknowledge Director, Biotechnology Centre and staff members for the support and suggestions for the improvement of the manuscript.
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The research work was carried out with no external funding or financial support. The work was conducted by the M.Sc. student to fulfil his thesis work for his degree programme.
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SM and RS Conceived and designed the and performed the experiments, RS, SM and AK Analyzed the data, RS, SM and SRK, Contributed reagents/materials/analysis tools, RS, AK, GKK, LG and SRK Contributed to the writing of the manuscript. All authors have read and approved the final manuscript.
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Meena, S., Sharma, R., Kumar Singh, S. et al. Genetic diversity of farmers’ varieties of rice of central India using microsatellite and blast linked markers. J. Plant Biochem. Biotechnol. 32, 225–238 (2023). https://doi.org/10.1007/s13562-022-00798-x
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DOI: https://doi.org/10.1007/s13562-022-00798-x