Hostname: page-component-78c5997874-lj6df Total loading time: 0 Render date: 2024-11-20T02:39:10.907Z Has data issue: false hasContentIssue false
  • English
  • Français

Chakhao (delicious) rice landraces (Oryza sativa L.) of North-east India: collection, conservation and characterization of genetic diversity

Published online by Cambridge University Press:  02 January 2014

Somnath Roy ,
A. Banerjee ,
A. Pattanayak ,
S. S. Roy ,
R. S. Rathi ,
A. K. Misra ,
S. V. Ngachan  and
K. C. Bansal
Somnath Roy*
Affiliation:
National Bureau of Plant Genetic Resources (NBPGR), Regional Station, Umiam, Meghalaya793 103, India
A. Banerjee
Affiliation:
ICAR Research Complex for NEH Region, Umiam, Meghalaya793 103, India
A. Pattanayak
Affiliation:
ICAR Research Complex for NEH Region, Umiam, Meghalaya793 103, India
S. S. Roy
Affiliation:
ICAR Research Complex for NEH Region, Manipur Centre, Imphal795 004, India
R. S. Rathi
Affiliation:
National Bureau of Plant Genetic Resources (NBPGR), Regional Station, Umiam, Meghalaya793 103, India
A. K. Misra
Affiliation:
National Bureau of Plant Genetic Resources (NBPGR), Regional Station, Umiam, Meghalaya793 103, India
S. V. Ngachan
Affiliation:
ICAR Research Complex for NEH Region, Umiam, Meghalaya793 103, India
K. C. Bansal
Affiliation:
NBPGR, Pusa Campus, New Delhi110 012, India
*
* Corresponding author. E-mail: sroypbr@gmail.com
Get access Rights & Permissions [Opens in a new window]

Abstract

Rice landraces have been developed through artificial selection imposed by farmers during the long-term domestication process. Although the global rice diversity is well characterized, few studies have conducted an in-depth analysis of genetic diversity on a local scale. In India, there are many locally adapted non-Basmati aromatic rice landraces in which the pace of improvement is slow, despite their high economic values. The aromatic and quality rice landraces of Manipur, locally called Chakhao (delicious), are important, considering their high economic and cultural values. To conserve and encourage improvement of these landraces, we collected Chakhao accessions from eight districts of Manipur. The aim of the current study was to investigate the level of genetic diversity and structure of 37 Chakhao landraces based on genotyping with 47 microsatellite markers. The genetic diversity analysis revealed high gene diversity (0.673) within the Chakhao population, with values ranging from 0.303 (Poireiton) to 0.471 (mixed Chakhao). The Chakhao rice accessions could be divided into six subgroups based on genetic structure analyses. The population structure derived from the STRUCTURE analysis largely correlated with the farmers' classification of Chakhao landraces. The results of genetic diversity analyses and the indigenous knowledge of the names and use of Chakhao landraces would facilitate the conservation and utilization of this unique genetic resource.

Keywords

aromatic riceChakhaoconservationgenetic diversitySSR
Type
Research Article
Information
Plant Genetic Resources , Volume 12 , Issue 3 , December 2014 , pp. 264 - 272
Copyright
Copyright © NIAB 2014 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Borba, TCDO, Brondani, RPV, Rangei, PHN and Brondani, C (2009) Microsatellite marker-mediated analysis of the EMBRAPA rice core collection genetic diversity. Genetics 137: 293–304.Google Scholar
Caicedo, AL, Williamson, SH, Hernandez, RD, Boyko, A, Fledel-Alon, A, York, TL, Polato, NR, Olsen, KM, Nielsen, R, McCouch, SR, Bustamante, CD and Purugganan, MD (2007) Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genetics 3: e163.Google Scholar
Cavalli-Sforza, LL and Edwards, AWF (1967) Phylogenetic analysis. Models and estimation procedures. American Journal of Human Genetics 19: 233–257.Google Scholar
Choudhury, B, Khan, ML and Dayanandan, S (2013) Genetic structure and diversity of indigenous rice (Oryza sativa) varieties in the Eastern Himalayan region of Northeast India. SpringerPlus 2: 228.Google Scholar
Cruz, DN and Khush, GS (2000) Rice grain quality evaluation procedures. In: Singh, RK, Singh, US and Khush, GS (eds) Aromatic Rices. New Delhi: Oxford & IBH Co. Pvt. Ltd, pp. 15–28.Google Scholar
Das, B, Sengupta, S, Parida, SK, Roy, B, Ghosh, M, Prasad, M and Ghosh, TK (2013) Genetic diversity and population structure of rice landraces from Eastern and North Eastern states of India. BMC Genetics 14: 71.Google Scholar
Earl, DA and von Holdt, BM (2011) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Available at http://taylor0.biology.ucla.edu/structureHarvester/.Google Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620.Google Scholar
Gao, Li-Zhi, Zhang, Chi-Hong, Chang, Li-Ping, Jia, Ji-Zeng, Qiu, Zong-En and Dong, Yu-Shen (2005) Microsatellite diversity within Oryza sativa with emphasis on indica–japonica divergence. Genetics Research 85: 1–14.Google Scholar
Garris, AJ, Tai, TH, Coburn, J, Kresovich, S and McCouch, S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169: 1631–1638.Google Scholar
Hamrick, JL and Godt, MJ (1996) Conservation genetics of endangered plant species. In: Avise, JC and Hamrick, JL (eds) Conservation Genetics: Case Histories from Nature. New York: Chapman & Hall, pp. 281–304.Google Scholar
Jain, S, Jain, KR and McCouch, SR (2004) Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. Theoretical and Applied Genetics 109: 965–977.Google Scholar
Nagaraju, M, Mohanty, KK, Chaudhary, D and Gangadharan, CA (1991) Simple technique to detect scent in rice. Oryza 28: 109–110.Google Scholar
Pavel, AB and Vasile, CI (2012) PyElph – a software tool for gel images analysis and phylogenetics. BMC Bioinformatics 13: 9.Google Scholar
Peakall, R and Smouse, PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics 28: 2537–2539.Google Scholar
Prashanth, SR, Parani, M, Mohanty, BP, Talame, V, Tuberosa, R and Parida, A (2002) Genetic diversity in cultivars and landraces of Oryza sativa subsp. indica as revealed by AFLP markers. Genome 45: 451–459.Google Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.Google Scholar
Rohlf, FJ (2000) NTSYSpc 2.1, Numerical Taxonomy and Multivariate Analysis System. Setauket, NY: Exeter Software.Google Scholar
Roy, S, Rathi, RS, Misra, AK, Bhatt, BP and Bhandari, DC (2013) Phenotypic characterization of indigenous rice (Oryza sativa L.) germplasm collected from the state of Nagaland, India. Plant Genetic Resources: Characterization and utilization. DOI 10.1017/S1479262113000282.Google Scholar
Thomson, MJ, Septiningsih, EM, Suwardjo, F, Santoso, TJ, Silitonga, TS and McCouch, SR (2007) Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theoretical and Applied Genetics 14: 559–568.Google Scholar
Thomson, MJ, Polato, NR, Prasetiyono, J, Trijatmiko, KR, Silitonga, TS and McCouch, SR (2009) Genetic diversity of isolated populations of Indonesian landraces of rice (Oryza sativa L.) collected in East Kalimantan on the Island of Borneo. Rice 2: 80–92.Google Scholar
Tu, M, Lu, BR, Zhu, Y and Wang, Y (2007) Abundant within-varietal genetic diversity in rice germplasm from Yunnan province of China revealed by SSR fingerprints. Biochemical Genetics 45: 789–801.Google Scholar
Xu, YB, Beachell, H and McCouch, SR (2004) A marker-based approach to broadening the genetic base of rice in the USA. Crop Science 44: 1947–1959.Google Scholar
Yeh, FC, Yang, R and Boyle, T (1999) POPGENE. Version 1.31. Microsoft Window-based Freeware for Population Genetic Analysis. Edmonton, AB: University of Alberta.Google Scholar
Yu, SB, Xu, WJ, Vijayakumar, CHM, Ali, J, Fu, BY, Xu, JL, Jiang, YZ, Marghirang, R, Domingo, J, Aquino, C, Virmani, SS and Li, ZK (2003) Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program. Theoretical and Applied Genetics 108: 131–140.Google Scholar
Supplementary material: File

Roy et al. Supplementary Material

Tables and Figure

Download Roy et al. Supplementary Material(File)
File 2.2 MB