Analisis Struktur Populasi Kelapa Dalam dan Genjah

4.4 Simpulan

Sebanyak 16 marka SNAP yang digunakan, terdapat dua belas primer yang termasuk kategori cukup informatif membedakan gen dari tiap individu dalam 41 populasi yang diuji. Sedangkan empat primer lainnya WRKY61, SUS117, SACPD1, dan SUS111 dikategorikan tidak informatif. Aksesi kelapa Dalam dan Genjah dengan marka SNAP dapat dipisahkan ke dalam tiga kelompok yang berbeda dengan piranti lunak DARwin menggunakan metode Neighbour Joining. Struktur genetik populasi dengan piranti lunak STRUCTURE dapat membagi kelapa Dalam dan Genjah atas dua subgrup populasi, dari perhitungan ad hoc maksimum ΔK diperoleh pada K=2. Subgrup pertama adalah kelapa Dalam dan subgrup kedua adalah kelapa Genjah. Daftar Pustaka Buchert G, Rajora O, Hood J, Dancik B. 1997. Effects of harvesting on genetic diversity in old-growth eastern white pine Pinus strobes L. in Ontario, Canada. Consv Biol. 113:747-758. Buckeridge M, Santos H, Tine M. 2000. Mobilisation of storage cell wall polysaccharides in seeds. Plant Physiol Biochem. 38:141-156. Ching A, Caldwell KS, Jung M, Dolan M, Smith OSH, Tingey S, Morgante M, Rafalski AJ. 2002. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics. 193:1-14. Devakumar K, Niral V, Jerard BA, Jayabose C, Chandramohanan R, Jacob PM. 2010. Microsatellite analysis of distinct coconut accessions from Agati and Kavaratti islands, Lakshadweep, India. Sci Hortic. 125:309-315. Drenkard E, Richter BG, Rozen S, Stutius LM, Angell NA, Mindrinos M, Cho RJ, Oefner PJ, Davis RW, Ausubel FM. 2000. A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis. Plant Physiol. 124:1483-1492. Earl DA, vonHoldt BM. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Res. 42:359-361. Eulgem T, Rushton PJ, Robatzek S, Somssich IE. 2000. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 5:199-206. Evanno GS, Regnaut J, Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 14:2611-2620. Geromel C, Ferreira LP, Guerreiro SMC, Cavalari AA, Pot D, Pereira LFP, Leroy T, Vieira LGE, Mazzafera P, Marraccini P. 2006. Biochemical and genomic analysis of sucrose metabolism during coffee Coffea arabica fruit development. J Exp Bot. 57:3243-3258. Govindaraj M, Vetriventham M, Srinivasan M. 2015. Importance of genetic diversity assesment in crop plants and its recent advances: an overview of its analytical perspectives. Genet Res Intl. 2015:1-14. doi: 10.11552015431487. Gregorius HR. 1978. The concept of genetic diversity and its formal relationship to heterozygosity and genetic distance. Mathematical Biosciences. 413- 4:253-271. Gupta PK, Roy JK, Prasad M. 2001. Single nucleotide polymorphism: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plant. Curr Sci. 804:524-535. Herrera M, Alan W, James W, David N, Raymond J. 2007. Usefulness of WRKY gene-derived markers for assessing genetic population structure: an example with Florida coconut cultivars. Sci Hortic. 115:19-26. Johnson CS, Kolevski B, Smyth DR. 2002. Transparent Testa Glabra2, a trichome and seed coat development gene of Arabidopsis, encodes a WRKY transcription factor. Plant Cell. 14:1359-1375. Kachroo A, Fu D-Q, Havens W, Navarre DR, Kachroo P, Ghabrial SA. 2008. An oleic acid –mediated pathway induces constitutive defense signaling and enhanced resistance to multiple pathogens in soybean. MPMI. 21:564-575. Kimura M. 1983. Rare variant alleles in the light of the neutral theory. Mol Biol Evol. 1:84-93. Lebrun P, N’cho YP, Seguin M, Grivet L, Baudouin L. 1998. Genetic diversity in coconut Cocos nucifera L. revealed by restriction fragment length polymorphism RFLP markers. Euphytica 101:103-108. Liu K, Muse SV. 2005. Power Marker: an integrated analysis environment for genetic marker analysis. Bioinformatics. 21:2128-2137. Luo M, Dennis ES, Berger F, Peacock W, Chaudhury A. 2005. MINISEED3 MINI3, a WRKY family gene, and HAIKU2 IKU2, a leucine rich repeat LRR KINASE gene, are regulators of seed size in Arabidopsis. PNAS. 102:17531-17536. Manimekalai R, Nagarajan P. 2006. Assesing genetic relationships among coconut Cocos nucifera L. accessions using inter simple sequence repeat markers. Sci Hortic. 108:49-54. Marshall D, Brown A. 1975. Optimum sampling strategies in genetic conservation. A basic sampling strategy: theory and practice Diakses tanggal: April 01, 2014, Tersedia pada: http:cropgenebank.sgrp.cgiar.orgimagesfileprocedurescollecting1995 Chapter5.pdf . Mateescu RG, Zhang Z, Tsai K, Phavaphutanon J, Burton WNI, Lust G, Quaas R, Murphy K, Acland GM, Todhunter RJ. 2005. Analysis of allele fidelity, polymorphic information content, and density of microsatellites in a genome-wide screening for hip dysplasia in a crossbreed pedigree. J Hered. 967:847-853. Meerow AW, Wisser RJ, Brown JS, Kuhn DN, Schnell RJ, Broschat TK. 2003. 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. Theor Appl Genet. 106:715- 726. Nei M. 1987. Molecular Evolutionary Genetics. New York US: Columbia University Press. Peakall R, Smouse PE. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics. 28:2537-2539. doi: 10.1093bioinformaticsbts460. Perera L, Russel J, Provan J, Powell W. 2000. Studying genetic relationship among coconut varietiespopulations using microsatellite markers. Euphytica. 132:121-128. Perera L, Russel JR, Provan J, Mc Nicol JW, Powell W. 1998. Evaluating genetic relationships between indigenous coconut Cocos nucifera L accessions from Sri Lanka by means of AFLP profilling. Theor Appl Genet 96:545- 550. Perrier X, Flori A, Bonnot F. 2003. Data analysis methods. Montpellier FR: Enfield Science Publishers. Potomati A, Buckeridge MS. 2002. Effect of abcisic acid on the mobilisation of galactomannan and embryo development of Sesbania virgata Cav. Pers. Leguminose-Faboideae. Revista Brasil Bot. 25:303-310. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics. 155:945-959. Rajesh MK, Arunachalam V, Nagarajan P, Lebrun P, Samsudeen K, Thamban C. 2008. Genetic survey of 10 Indian coconut landraces by simple sequence repeats SSRs. Sci Hortic. 118:282-287. Rivera R. 1999. Isolation and characterization of polymorphic microsatellites in Cocos nucifera L. Genom. 42:668-675. Rizhsky L, Liang H, Mittler R. 2002. The combined effect of drought stress and heat shock on gene expression in tobacco. Plant Physiol. 130:1143-1151. Robatzek S, Somssich IE. 2001. A new member of the Arabidopsis WRKY transcription family, AtWRKY6, is associated with both senescence- and defense related processes. Plant J. 28:123-133. Ryu HS, Han M, Lee SK, Cho JI, Ryoo N, Heu S, Lee YH, Bhoo SH, Wang GL, Hahn TR, et al. 2006. A comprehensive expression analysis of the WRKY gene superfamily in rice plants during defense response. Plant Cell Rep. 25:836-847. Sajib AM, Hossain M, Mosnaz ATMJ, Hossain H, Islam M, Ali S, Prodhan SH. 2012. SSR marker-based molecular characterization and genetic diversity analysis of aromatic landraces of rice Oryza sativa L .. BioSci Biotech. 1:107-116. Tang N, Shahin A, Bijman P, Liu J, Tuyl V, Arens P. 2013. Genetic diversity and structure in a collection of tulip cultivars assessed by SNPmarkers. Sci Hortic. 2013161:286-292. Teulat B, Aldam C, Trehin R, Lebrun R, Barker JHA, Arnold GM, Karp A, Baudouin L, Rognon F. 2000. An analysis of genetic diversity in coconut Cocos nucifera L. populations from across the geographic range using sequence-tagged microsatellites SSRs and AFLPs. Theor Appl Genet. 100:764-771. Ulker B, Somssich IE. 2004. WRKY transcription factors: from DNA binding towards biological function. Curr Opin Plant Biol. 7:491-498. Upadhyay A, Jayadev K, Manimekalai R, Parthasarathy VA. 2004. Genetic relationship and diversity in Indian coconut accessions based on RAPD markers. Sci Hortic. 99:353-362. Xiao Y, Yi L, Yaodong Y, Haikuo F, Wei X, Annaliese M, Songlin Z, Ross S, Fei Q. 2013. Development of microsatellite markers in Cocos nucifera and their application in evaluating the level of genetic diversity of Cocos nucifera. Plant Omics J. 6:193-200. Yu D, Chen C, Chen Z. 2001. Evidence for an important role of WRKY DNA binding proteins in the regulation of NPR1 gene expression. Plant Cell. 13:1527-1539.