Molecular characterization and genetic diversity analysis of Jatropha curcas L. in India using RAPD and AFLP analysis (original) (raw)
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High genetic diversity of Jatropha curcas assessed by ISSR
Genetics and Molecular Research
Jatropha curcas L. is a highly promising oilseed for sustainable production of biofuels and bio-kerosene due to its high oil content and excellent quality. However, it is a perennial and incipiently domesticated species with none stable cultivar created until now despite genetic breeding programs in progress in several countries. Knowledge of the genetic structure and diversity of the species is a necessary step for breeding programs. The molecular marker can be used as a tool for speed up the process. This study was carried out to assess genetic diversity of a germplasm bank represented by J. curcas accessions from different provenance beside interspecific hybrid and backcrosses generated by IAC breeding programs using inter-simple sequence repeat markers. The molecular study revealed 271 bands of which 98.9% were polymorphic with an average of 22.7 polymorphic bands per primer. Genetic diversity of the germplasm evaluated was slightly higher than other germplasm around the world and ranged from 0.55 to 0.86 with an average of 0.59 (Jaccard index). Cluster analysis (UPGMA) revealed no clear grouping as to the geographical origin of accessions, consistent with genetic structure analysis using the Structure software. For diversity analysis between groups, accessions were divided into eight groups by origin. Nei's genetic distance between groups was 0.14. The results showed the importance of Mexican accessions, congeneric wild species, and interspecific hybrids for conservation and development of new genotypes in breeding programs.
State of the art of genetic diversity research in Jatropha curcas
2011
Jatropha curcas (Euphorbiaceae) is a mesoamerican plant. However, till date, it is extensively grown in tropical and subtropical regions of the world. The seeds have high oil content, which can be transformed into biodiesel. In the present review, the geographical origin of J. curcas is discussed, then, advances of research in the genetic diversity are summarized and contrasted. Proposed future research in this species include: (a) the collection and characterization of germplasm around the world, including the center of origin, (b) the study of the genetic variation within the context of population genetics, using morphological, chemical and molecular markers, (c) the use of genome information from other Euphorbiaceae, and subsequently (d) crop breeding to increase oil productivity. Key words: Jatropha, Mexico, molecular markers, population genetics.
Molecular Biology Reports, 2012
Jatropha curcas L. (Euphorbiaceae) has acquired a great importance as a renewable source of energy with a number of environmental benefits. Very few attempts were made to understand the extent of genetic diversity of J. curcas germplasm. In the present study, efforts were made to analyze the genetic diversity among the elite germplasms of J. curcas, selected on the basis of their performance in field using random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSR). The plants were selected on the basis of height, canopy circumference, number of seeds per fruit, weight of 100 seeds, seed yield in grams per plant and oil content. Out of 250 RAPD (with 26 primers), 822 AFLP (with 17 primers) and 19 SSR band classes, 141, 346 and 7 were found to be polymorphic, respectively. The percentage polymorphism among the selected germplasms using RAPD, AFLP and SSR was found to be 56.43, 57.9, and 36.84, respectively. The Jaccard's similarity coefficient was found 0.91, 0.90 and 0.91 through RAPD, AFLP and SSR marker systems, respectively. Principle component analysis (PCA) and dendrogarm analysis of genetic relationship among the germplasm using RAPD, AFLP and SSR data showed a good correlation for individual markers. The germplasm JCC-11, 12, 13, 14 and 15 whose yield found to be high were clustered together in dendrogram and PCA analysis though JCC11 is geographically distinct from others. In overall analysis JCC6 (in RAPD), JCC8 (in AFLP) and JCC 6 and JCC10 (in SSR) were found genetically diverse. Characterization of geographically distinct and genetically diverse germplasms with varied yield characters is an important step in marker assisted selection (MAS) and it can be useful for breeding programs and QTL mapping.
Genetic diversity and structure of Jatropha curcas L. in its centre of origin
Plant Genetic Resources, 2014
To investigate the genetic diversity and structure ofJatropha curcasL. oilseed plant, in this study, native populations from Chiapas, Mexico, were evaluated, using microsatellite DNA markers. A total of 93 representative samples were selected from seven sites in two regions in the state of Chiapas grouped by geographical proximity, where leaf samples were collected to isolate the genomic DNA. Individual polymerase chain reactions were carried out with ten pairs of specific oligonucleotides for the microsatellites ofJ. curcas, separating the products of amplification by acrylamide electrophoresis. Twenty-seven fragments were detected (77% polymorphic) with which heterozygous individuals were distinguished. The most informative microsatellite wasJcps20(nine alleles, polymorphic index content 0.354). The average polymorphism per population was 58%. The Hardy–Weinberg tests revealed a reproductive pattern of non-random mating. The diversity descriptors and the analysis of molecular vari...
Molecular Characterization of Genetic Diversity in Jatropha curcas L
Jatropha curcas L. (Euphorbiaceae) is a small tree with valuable attributes, including that as a commercially important non-edible oilseed that grows naturally in the equatorial Americas and has spread to other tropical countries. J. curcas has been found to be the most suitable tree species for production of biodiesel as it can be grown as a quick yielding plant even in problem soils and adverse climatic conditions. J. curcas has been neglected in the past and little systematic work has been done on productivity aspects. It is highly cross-pollinated and is known for continued seedling propagation, it is anticipated for the existence of wide genetic variability offering significant scope for selecting superior genotypes, which will help to improve productivity and provide sound scientific base to this crop. Few attempts have been directed to improve it as a crop plant and characterize it at molecular level. However, understanding the genetic relationship and variation is important for efficient parental selection and different techniques are being used in the study of variations in J. curcas. Application of molecular markers in J. curcas studies would be the right tool to differentiate plant varieties, for choosing right parents for cross pollination and for marker assisted breeding. In the present paper, we have reviewed the studies conducted at the molecular level to characterize the genetic diversity in J. curcas.
Genetic diversity assessment of Jatropha curcas L. germplasm from Northeast India
Biomass & Bioenergy, 2011
Genetic variability in the wild genotypes of Jatropha curcas L., collected from different parts of Northeast India, was analyzed using two different single primer amplification reactions (SPAR) methods, viz., inter-simple sequence repeats (ISSR) and directed amplification of minisatellite DNA (DAMD). A total of 36 genotypes were used to investigate the existing natural genetic variation at intra-specific level. One hundred forty nine (149) amplification products were scored by ISSR and DAMD, both of which collectively showed 75.83% polymorphism with a mean intra-population genetic diversity (HS) of 0.1309. However, their level of diversity at inter- and intra-population levels was significant, with the percentage of polymorphic loci (P) ranging from 22.82% to 44.30%, Shannon’s information index (Hpop) from 0.1302 to 0.2541 and Nei’s gene diversity (HE) from 0.0831 to 0.1723 with mean Nei’s gene diversity (HT) 0.2202 and the overall estimate of gene flow being (Nm) 0.8085. Analysis of molecular variance (AMOVA) showed that 68.88% of variation at intra-population level, whereas 31.12% variation was recorded at inter-population level. Cluster analysis also supported the existence of genetic diversity in the genotypes of J. curcas collected from Assam and Meghalaya provinces of Northeast India. Present investigation suggests the efficiency of SPAR methods to estimate the genetic diversity precisely which can define genetic relationship and population genetics of J. curcas.► ISSR and DAMD markers were used to analyze genetic diversity in J. curcas from Northeast India. ► High variation at intra-population level was recorded with moderate gene flow values. ► Clustering pattern did not reveal any geographical isolation and/or ecological differentiation. ► Data shows that geographical differentiation of J. curcas in Northeast India is not pronounced. ► Efficacy of SPAR methods to estimate the genetic diversity is emphasized.
The phylogenetic relationships of 13 Jatropha genotypes from different parts of the India were analysed using 34 polymerase chain reaction (PCR) markers (20 random amplified polymorphic DNAs (RAPDs) and 14 inter simple sequence repeats (ISSRs)). Amplification of genomic DNA of the 13 genotypes, using RAPD analysis, yielded 107 fragments that could be scored, of which 91 were polymorphic, with an average of 4.55 polymorphic fragments per primer. Number of amplified fragments ranged from one (OPA20, OPB19, OPD13) to nine (OPA18) and which varied in size from 200 to 2,500 bp. Percentage of polymorphism ranged from 40% (OPB18) to a maximum of 100% (14 primers). Resolution power ranged from a minimum of 0.153 (OPA20, OPB19) to a maximum of 11.23 (OPB15). Out of 25 ISSR primers used, 14 were able to amplify. These primers produced 81 bands across 13 genotypes, of which 62 were polymorphic. The number of amplified fragment ranging from two (ISSR 7, ISSR 8, ISSR 16) to nine (ISSR 12) and which varied in size from 200 to 2,500 bp. Of the 81 fragments amplified bands, 62 were polymorphic, with an average of 4.42 polymorphic fragments per primer. Percentage of polymorphism ranged from 37.5% (ISSR 2, ISSR10) to a maximum of 100% (seven primers). The primers based on poly (GA) produced maximum number of bands (nine) while, poly (AT) and many other motifs gave no amplification at all with any of these thirteen genotypes. RAPD markers were more efficient than the ISSR assay with regards to polymorphism detection, as they detected 84.26% as compared to 76.54% for ISSR markers. But, resolving power (Rp), average bands per primer, Nei's genetic diversity (h), Shannon's Information Index (I), total genotype diversity among population (Ht), within population diversity (Hs) and gene flow (Nm) estimates were more for ISSR as compared to RAPD markers . The regression test between the two Nei's genetic diversity indexes gave r 2 = 0.3318, showing low regression between RAPD and ISSR based similarities. Regression value for ISSR and ISSR + RAPD combined data is moderate (0.6027), while it is maximum for RAPD and ISSR+RAPD based similarities (0.9125). Thus both the markers are equally important for genetic diversity analysis in Jatropha curcas. Clustering of genotypes within groups was not similar when RAPD and ISSR derived dendrogram were compared, whereas the pattern of clustering of the genotypes remained more or less the same in RAPD and combined data of RAPD + ISSR. Principal Coordinates Analysis (PCA) analysis was also employed to evaluate the resolving power of the markers to differentiate between the genotypes. These analyses, carried out for both (ISSR and RAPD) markers, allowed us to identify four main groups partially corresponding to the four J. curcas collection sites. The results of the present study can be seen as a starting point for future researches on the population and evolutionary genetics of these genotypes.
Characterization of genetic diversity in Jatropha curcas L. germplasm using RAPD and ISSR markers
2012
Jatropha curcas L. is a rapidly emerging biofuel crop attracting a lot of interest, triggering large investments and rapid expansion of cultivation areas. In the present investigation, the genetic relationships of 29 J. curcas accessions were assessed based on randomly amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) analyses. A total of 72 polymorphic primers (47 RAPD and 25 ISSR) were used. Amplification of genomic DNA of the 29 genotypes, using RAPD analysis, yielded 552 fragments that could be scored, of which 334 were polymorphic with an average of 7.1 polymorphic fragments per primer. Number of amplified fragments varied from 2 to 23 and ranged in size from 100-3,500 bp. The 25 polymorphic ISSR primers used in the study produced 336 bands across 29 genotypes, of which 201 were polymorphic. The number of amplified bands varied from 7 to 20 with a size range of 100-3,500 bp. Molecular polymorphism was 60.5 and 59.8% with RAPD and ISSR markers, respectively. Mantel test between the two Jaccard's similarity matrices gave r=0.8623, showing good fit correlation between RAPD and ISSR based similarities. Clustering of genotypes within groups remained more or less similar in ISSR and combined data of RAPD and ISSR.