Genetic survey of 10 Indian coconut landraces by simple sequence repeats (SSRs)

Abstract A rich genetic diversity of coconut exists in farmer's fields, which represent valuable genetic resource for breeding. The study was conducted to assess the pattern of diversity in 102 coconut palms representing 10 landraces from 3 coconut-growing communities of India using 14 simple sequence repeat (SSR) markers. A total of 90 alleles were detected with an average of 6.42 alleles per locus and an average polymorphism information content of 0.61. Expected heterozygosity ( H e ) was highest for the two tall landraces from Pallikkara community, while the least heterozygosity was observed for the dwarf coconut landraces from Vayalar community. Mean fixation index ( F ST ) of 0.42 indicates a high level of population differentiation. A low gene flow ( N m ) of 0.37 was observed. Based on molecular data, genetic similarities were calculated. The unweighted pair group method with arithmetic averages (UPGMA) cluster analysis grouped the landraces according to their geographical locations and breeding behaviour. The practical implications of this study in farmer participatory evaluation and conservation of coconut genetic resources are highlighted.

[1]  R. von Bothmer,et al.  Assessing the allozyme variation in cultivars and Swedish landraces of rye (Secale cereale L.). , 2004, Hereditas.

[2]  B. Weir,et al.  Allozyme diversity in plant species. , 1990 .

[3]  W. Powell,et al.  Evaluating genetic relationships between indigenous coconut (Cocos nucifera L.) accessions from Sri Lanka by means of AFLP profiling , 1998, Theoretical and Applied Genetics.

[4]  G. R. Ashburner,et al.  Fruit component analysis of south Pacific coconut palm populations , 1997, Genetic Resources and Crop Evolution.

[5]  W. Powell,et al.  Use of microsatellite DNA markers to investigate the level of genetic diversity and population genetic structure of coconut (Cocos nucifera L.). , 2000, Genome.

[6]  G. R. Ashburner,et al.  RAPD analysis of South Pacific coconut palm populations , 1997 .

[7]  W. Powell,et al.  Identification and characterization of microsatellite loci in coconut (Cocos nucifera L.) and the analysis of coconut populations in Sri Lanka. , 1999, Molecular ecology.

[8]  Y. Sugimura,et al.  Biometric analysis on diversity of coconut palm: cultivar classification by botanical and agronomical traits , 1997, Euphytica.

[9]  L. Baudouin,et al.  The development of a microsatellite kit and dedicated software for use with coconuts , 2002 .

[10]  S. Brush.  A Farmer-based approach to conserving crop germplasm , 1991, Economic Botany.

[11]  S WRIGHT,et al.  Genetical structure of populations. , 1950, Nature.

[12]  O. H. Frankel,et al.  Conservation and Evolution , 1983 .

[13]  H. Harries.  The evolution, dissemination and classification ofCocos nucifera L. , 1978, The Botanical Review.

[14]  P. Hall,et al.  Genetic diversity and mating system in a tropical tree, Carapa guianensis (Meliaceae) , 1994 .

[15]  M. Ruiz-Rodríguez,et al.  Population genetics, lethal yellowing disease, and relationships among mexican and imported coconut ecotypes , 2006 .

[16]  R. Varshney,et al.  Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.) , 2003, Theoretical and Applied Genetics.

[17]  J. T. Oliver,et al.  Poverty reduction in coconut growing communities Volume I: the framework and project plan , 2003 .

[18]  K. Edwards,et al.  Isolation and characterization of polymorphic microsatellites in Cocos nucifera L. , 1999, Genome.

[19]  Rong‐Cai Yang,et al.  PopGene, the user-friendly shareware for population genetic analysis, molecular biology and biotechnology center , 1997 .

[20]  W. Powell,et al.  Levels and distribution of genetic diversity of coconut (Cocos nucifera L., var. Typica form typica) from Sri Lanka assessed by microsatellite markers , 2001, Euphytica.

[21]  R. Manimekalai,et al.  Genetic relationship and diversity in Indian coconut accessions based on RAPD markers , 2004 .

[22]  M. Nei.  Analysis of gene diversity in subdivided populations. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[23]  B. Weir,et al.  Plant Population Genetics, Breeding, and Genetic Resources , 1989 .

[24]  Luc Baudouin,et al.  Evaluation de quelques écotypes de cocotier par une approche biométrique. 1. Etude des populations de Grands , 1993 .

[25]  The Conservation of Plant Biodiversity , 1995 .

[26]  D. Piñero,et al.  Diversity and phylogenetic analysis in Cocos nucifera L. in Mexico , 2002, Genetic Resources and Crop Evolution.

[27]  L. Baudouin,et al.  Genetic diversity in coconut (Cocos nucifera L.) revealed by restriction fragment length polymorphism (RFLP) markers , 1998, Euphytica.

[28]  Steven J. Brown,et al.  Analysis of genetic diversity and population structure within Florida coconut (Cocos nucifera L.) germplasm using microsatellite DNA, with special emphasis on the Fiji Dwarf cultivar , 2003, Theoretical and Applied Genetics.

[29]  O. Panaud,et al.  Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.) , 1996, Molecular and General Genetics MGG.

[30]  B. A. Jerard,et al.  Phenotypic Diversity of Foliar Traits in Coconut Germplasm* , 2005, Genetic Resources and Crop Evolution.