Modelling wildlife distributions: Logistic Multiple Regression vs Overlap Analysis

We compare the results, benefits and disadvantages of two techniques for modelling wildlife species distribution: Logistic Regression and Overlap Analysis. While Logistic Regression uses mathematic equations to correlate variables with presence/absence of the species. Overlap Analysis simply combine variables with the presence points, eliminating the non-explanatory variables and recombining the others. Both techniques were performed in a Geographic Information System and we attempted to minimise the spatial autocorrelation of data. The species used was the Schreiber's green lizard Lacerta schreiberi and the study area was Portugal, using 10 X 10 km UTM squares. Both techniques identified the same group of variables as the most important for explaining the distribution of the species. Both techniques gave high average correct classification rates for the squares with presence of the species (79% for Logistic Regression and 92% for Overlap Analysis). Correct absence classification was higher with Logistic Regression (73%) than with Overlap Analysis (32%), Overlap Analysis tends to maximise the potential area of occurrence of the species, which induces a reduced correct classification of absences, since many absences will fall in the potential area. This is because a single presence in a given class of a variable makes all the area of that class to be considered as potential. The technique does not consider that the species may occasionally occupy an unfavourable region. Although, in Logistic Regression, modelling procedures are more complex and time-consuming, the results are more statistically robust. Moreover. Logistic Regression has the capability of associating probability of occurrence to the potential area. Overlap Analysis is very simple in building procedures and swift in obtaining reliable potential areas. It is a valid technique especially in exploratory analysis of species distributions or in the initial stages of research when data may be scarce.     

Genetic relationship among wild,landraces and cultivars of hazelnut (Corylus avellana) from Portugal revealed through ISSR and AFLP markers

The genus Corylus, a member of the birch family Betulaceae, includes several species that are widely distributed throughout temperate regions of the Northern Hemisphere. This study assesses the genetic diversity in 26 international cultivars and 32 accessions of Corylus avellana L. from Portugal: 13 wild genotypes and 19 landraces. The genetic relationships among the 58 hazelnuts (Corylus avellana L.) were analyzed using inter simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP) markers. Eighteen ISSR primers and seven AFLP primer pairs generated a total of 570 unambiguous and repeatable bands, respectively, from which 541 (95.03 %) were polymorphic for both markers. Genetic similarity index values ranged from 0.239 for wild types and cultivars to 0.143 for landraces and wild types. The genetic relationships were presented as a Neighbor-Joining method dendrogram and a two-dimensional principal coordinate analysis (PCoA) plot. The Neighbor-Joining dendrogram showed three main clusters, and the PCoA analysis has shown to be congruent with the hierarchical analysis. Bayesian analysis clustered all individuals into three groups showing a good separation among wild genotypes, landraces and cultivars. The genetic diversity found on wild genotypes and Portuguese landraces may provide relevant information for the diversity conservation and it will be useful in breeding programs and to identify local selections for preservation.     

Comparison of ISSR,IRAP and REMAP markers for assessing genetic diversity in different species of <Emphasis Type="Italic">Brassica</Emphasis> sp.

Molecular markers provide facilities in order to study genetic diversity and relationship among genotypes. In this study, genetic diversity among 35 genotype of Brassica sp. (belonging B. napus, B. juncea, B. rapa, B. nigra) were determined using 13 ISSR, 3 IRAP markers and 18 REMAP (primer combinations of ISSR and retrotransposon primer). The percentage of polymorphism for ISSR, IRAP and REMAP was 96.38, 94 and 96%, respectively. By comparison between markers, ISSRs indicated the highest expected heterozygosity (He) and Shannon’s information index (I) with value of 0.34 and 0.51, respectively, while REMAP marker had by far the highest number of polymorphic bands (340) and marker index (7.1) among all fragments scored over all markers. In pattern of clustering based on Bayesian methods, K = 8 was resulted for combined data clustering that was more organized clustering for genotypes compared to others. This research suggests the combined data of ISSR, IRAP and REMAP markers are most reliable than each solely marker whilst have been clustered genotypes in their taxonomic classification of Brassica without any mixture. Principle coordinate analysis (PCoA) separated 35 genotypes in four groups which all of genotypes were clustered correctly based on their taxonomic classification. The findings of this study provide the valuable insight into the Brassica species relationships in terms of similarity among genotypes which can be helpful in breeding programs, and also demonstrate that retrotransposon markers are legible for genetic diversity and next genetic analysis in Brassica genus.     

Structured diversity using EST-PCR and EST-SSR markers in a set of wild blueberry clones and cultivars

Blueberries are perennial, vegetatively propagated out-crossing shrubs with great potential of health benefits. In tetraploid blueberry (Vaccinium spp.), genetic analyses have focused more on diversity, whereas genetic structure has been studied less extensively. This study investigated the genetic structure and diversity in 28 wild clones, six cultivars and two selections of lowbush, half-high and highbush blueberries. Summary statistics, structure estimation and clustering by neighbour-joining (NJ), principal coordinate analysis (PCoA) and by the analysis of molecular variance (AMOVA), using 10 expressed sequence tag-polymerase chain reaction (EST-PCR) and two EST-simple sequence repeat (SSR) primer pairs, were performed to characterize and discriminate the genotypes. A total of 213 markers were detected. Wide genetic diversity was evident from high values of expected heterozygosities, Shannon's index and polymorphism information content, and from AMOVA. Structure analysis subdivided the lowbush blueberries into three distinct groups leaving the half-high and highbush blueberries into one cluster which was in agreement with the NJ clustering and PCoA. Twelve EST-primer pairs efficiently differentiated wild and cultivated blueberries, making this technology valuable for genome mapping and for long-term conservation of blueberry resources for the benefit of germplasm conservation and breeding purposes.     

Genetic variability and population structure of Bergenia ciliata (Saxifragaceae) in the Western Himalaya inferred from DAMD and ISSR markers

Genetic variability and population structure of Bergenia ciliata (Haw.) Sternb., commonly known as “Pashanbheda” (Stone-breaker), collected from the Western Himalayan region of India were estimated using two DNA fingerprinting methods viz., directed amplification of minisatellite DNA (DAMD) and inter simple sequence repeats (ISSR). The cumulative data analysis of DAMD and ISSR markers for 74 accessions from eight populations showed 86.1% polymorphism. Analysis of molecular variance (AMOVA) showed highest percentage of variation within individuals of populations (73.6%) and 21.7% among populations. STRUCTURE and PCoA analyses on the hierarchical partitioning of genetic diversity showed strong admixture of individuals among the eight assumed geographical populations of B. ciliata. The data suggests that high genetic flow is one of the major factors responsible for low genetic differentiation. Preservation of genetic diversity of B. ciliata is important, both to promote adaptability of the populations to changing environment as well as to preserve a large gene pool for future prospection. The present study using DAMD and ISSR markers, therefore, provide the means of rapid characterization of accessions within the populations, and thus enable the selection of appropriate accessions for further utilization in conservation and prospection programmes.     

Genetic diversity and variance of Stentor coeruleus (Ciliophora: Heterotrichea) inferred from inter-simple sequence repeat (ISSR) fingerprinting

We used inter-simple sequence repeat fingerprinting to analyze the genetic structure of 16 populations of Stentor coeruleus from three lakes and three ponds in China. Using 14 polymorphic primers, a total of 99 discernible DNA fragments were detected, among which 76 (76.77%) were polymorphic, indicating median genetic diversity in these populations. Further, both Nei's gene diversity (h) and Shannon's information index (I) between the different populations revealed a median genetic diversity. At the same time, gene flow was interpreted to be low. The main factors responsible for the median level of diversity and low gene flow within populations are probably due to a low frequency of sexual recombinations. Analysis of molecular variance showed that there was high genetic differentiation among the five water bodies. Both cluster analysis and a nonmetric multidimensional scaling analysis suggested that genotypes isolated from the same locations displayed a higher genetic similarity than those from different ones, separating populations into subgroups according to their geographical locations. However, there is a weak positive correlation between the genetic distance and geographical distance.     

The genetic diversity of planktic foraminifera and the global distribution of ribosomal RNA genotypes

Fossil planktic foraminifers in the ocean sediments play an unparalleled role in our understanding of the oceanographic environment in the past. An in depth knowledge of their diversity, ecology and biogeography in the modern ocean lies central to the interpretation of the fossil assemblages. In comparison with their benthic counterparts, planktic foraminifera have a very limited diversity of around fifty extant morphospecies. Their morphospecies diversity peaks in the sub-tropics and decreases steeply towards the poles. Traditional species concepts have partitioned morphological types into distinct species (morphospecies) based on test shape, but genetic studies show that individual morphospecies are actually complexes of several discrete genetic types (genotypes). Many of these genotypes have distinct ecologies and novel adaptations that are consistent with species-level classification, indicating that the true diversity of planktic foraminifers has been greatly underestimated. Although planktic foraminifera are clearly capable of long-distance dispersal, they may be constrained by both physical and ecological barriers that vary according to the evolutionary history and ecology of the individual genotypes within a morphospecies. These differences lead to diverse biogeographies. Here, we provide an overview of the genetic and biogeographic data available to date for the planktic foraminifera and present global biogeographies highlighting the distribution of genetic types in the eight planktic foraminiferal morphospecies for which detailed molecular evidence is available.     

Application of EST-derived microsatellite markers for analysis of genetic variation in tall fescue and its comparison with morphological markers

Analysis of genetic diversity in germplasm collections is an important component of crop improvement programs. This study was conducted to analyze genetic variation and to classify tall fescue genotypes based on phenotypic evaluation and EST-SSR molecular markers. Twenty-five genotypes were assessed based on phenotypic and 42 EST-SSR molecular markers according to a completely randomized block design with three replications during eight years (2007–2014). Results indicated that the effect of year, genotype and their interaction were significant for all of the measured traits. Both morphological and molecular assessments showed considerable genetic variation among genotypes. The estimates of broad-sense heritability (h²_b) were moderate to high (h²_b = 42.1–78.4) for the traits studied. Based on EST-SRR analysis, a total number of 229 alleles were detected with an average of 4.58 alleles per marker. Average PIC value was 0.49 with a range of 0.014 for NFA140 to 0.95 for NFA047. Phenotypic evaluations and EST-SSR molecular marker classified genotypes into 3 and 7 clusters, respectively which mainly supported geographical origins. The general correspondence was observed between morphological and molecular classification. Therefore, combining the molecular markers with morphological responses could be more beneficial to describe genetic variation and distinguish superior genotypes for future breeding programs.     

Molecular characterization of the wild relatives of wheat using CAAT-box derived polymorphism

A molecular assessment of genetic diversity was performed on a set of 228 selected accessions belonging to the different Aegilops and Triticum species using CAAT-box derived polymorphism (CBDP) markers. Fifteen CBDP primers generated 141 polymorphic fragments with an average of 9.40 per primer. The average of polymorphic information content and resolving power revealed a high efficiency of CBDP markers in analyzing genetic diversity among different wheat genotypes. The diversity indexes including polymorphic loci percent, number of observed and effective alleles, Shannon’s index and gene diversity among different populations were 76.24%, 1.67, 1.49, 0.42 and 0.28, respectively. These essentially coincided with the analysis of molecular variance results, indicating that 86, 68, and 59.46% of genetic variation were found within two Aegilops and Triticum genera and their populations, respectively. Genetic relationships inferred from cluster analysis was matched with STRUCTURE analysis, disclosing the accessions were grouped based on their genomic constitution. Furthermore, these results were confirmed by principal coordinate analysis (PCoA). Taken together, our results suggest that CBDP markers will be useful for genetic diversity assessment in the domesticated and wild relatives of wheat.     

A method for combining molecular markers and phenotypic attributes for classifying plant genotypes

Classifying genotypes into clusters based on DNA fingerprinting, and/or agronomic attributes, for studying genetic and phenotypic diversity is a common practice. Researchers are interested in knowing the minimum number of fragments (and markers) needed for finding the underlying structural patterns of diversity in a population of interest, and using this information in conjunction with the phenotypic attributes to obtain more precise clusters of genotypes. The objectives of this study are to present: (1) a retrospective method of analysis for selecting a minimum number of fragments (and markers) from a study needed to produce the same classification of genotypes as that obtained using all the fragments (and markers), and (2) a classification strategy for genotypes that allows the combination of the minimum set of fragments with available phenotypic attributes. Results obtained on seven experimental data sets made up of different plant species, number of individuals per species’ and number of markers, showed that the retrospective analysis did indeed find few relevant fragments (and markers) that best discriminated the genotypes. In two data sets, the classification strategy of combining the information on the relevant minimum fragments with the available morpho-agronomic attributes produced compact and well-differentiated groups of genotypes.     

Molecular Genetic Diversity of Major Indian Rice Cultivars over Decadal Periods

Genetic diversity in representative sets of high yielding varieties of rice released in India between 1970 and 2010 was studied at molecular level employing hypervariable microsatellite markers. Of 64 rice SSR primer pairs studied, 52 showed polymorphism, when screened in 100 rice genotypes. A total of 184 alleles was identified averaging 3.63 alleles per locus. Cluster analysis clearly grouped the 100 genotypes into their respective decadal periods i.e., 1970s, 1980s, 1990s and 2000s. The trend of diversity over the decadal periods estimated based on the number of alleles (Na), allelic richness (Rs), Nei’s genetic diversity index (He), observed heterozygosity (Ho) and polymorphism information content (PIC) revealed increase of diversity over the periods in year of releasewise and longevitywise classification of rice varieties. Analysis of molecular variance (AMOVA) suggested more variation in within the decadal periods than among the decades. Pairwise comparison of population differentiation (Fst) among decadal periods showed significant difference between all the pairs except a few. Analysis of trends of appearing and disappearing alleles over decadal periods showed an increase in the appearance of alleles and decrease in disappearance in both the categories of varieties. It was obvious from the present findings, that genetic diversity was progressively on the rise in the varieties released during the decadal periods, between 1970s and 2000s.     

Population structure and genetic analysis of different utility types of mango (Mangifera indica L.) germplasm of Andhra Pradesh state of India using microsatellite markers

Genetic analysis of 90 mango genotypes including juicy, table, dual and pickle types from different parts of Andhra Pradesh of India was carried out employing 143 mango-specific microsatellite markers. Of the 143, 34 were new mango-specific microsatellite loci isolated in the course of the present investigation by constructing an (CA) _n and (TG) _n -enriched genomic library. Characterization of the 90 genotypes resulted in the detection of 301 alleles from 106 polymorphic loci with an average of 2.87 alleles per locus and polymorphism information content of 0.67. UPGMA cluster analysis grouped all the genotypes into two major groups with a genetic similarity range of 47–88 %. Grouping of the genotypes based on the utility type was observed only at sub-cluster level. Study of population structure by a model-based STRUCTURE analysis revealed the germplasm to exist in four gene pools. Overall F _st of 0.11 indicated genetic differentiation between the populations to be low. Analysis of molecular variance revealed that major proportion of the variation was within the individuals (62.25 %). The molecular marker-based study of genetic diversity suggests that the germplasm studied representing the kind of variability would be a valuable genetic resource for future breeding and association mapping in search for new and novel alleles.     

Genetic diversity in cultivated carioca common beans based on molecular marker analysis

A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.     

Comparative analysis of genetic diversity in pea assessed by RFLP- and PCR-based methods

DNA-based molecular-marker techniques have been proven powerful in genetic diversity estimations. Among them, RFLP was the first and is still the most commonly used in the estimation of genetic diversity of eukaryotic species. The recently developed PCR-based multiple-loci marker techniques, which include RAPD, AFLP, Microsatellite-AFLP and inter-SSR PCR, are playing increasingly important roles in this type of research. Despite the wide application of these techniques, no direct comparison of these methods in the estimation of genetic diversity has been carried out. Here we report a direct comparison of DNA-based RFLP with various PCR-based techniques regarding their informativeness and applicability for genetic diversity analysis. Among ten pea genotypes studied, all the PCR-based methods were much more informative than cDNA-RFLP. Genetic diversity trees were derived from each marker technique, and compared using Mantel's test. By this criterion, all trees derived from the various molecular marker techniques, except for the tree derived from inter-SSR PCR, were significantly correlated, suggesting that these PCR-based techniques could replace RFLP in the estimation of genetic diversity. On the basis of this result, AFLP analysis was applied to assess the genetic diversity of a sample of accessions representing the various species and subspecies within the genus Pisum.     

The genetic structure of populations of the vulnerable aquatic macrophyte <Emphasis Type="Italic">Ranunculus nipponicus</Emphasis> (Ranunculaceae)

Ranunculus nipponicus (Makino) Nakai is a vulnerable aquatic macrophyte in the Kinki district, which is the southernmost distribution of this species in Japan. The genetic diversity and structure within and among eleven extant populations were assessed using the inter-simple sequence repeats (ISSR) polymerase chain reaction in association with combinations of propagation pattern (clonal and/or seeds) and genotypic geographical structure. In total, 53 bands were amplified, of which 18 (34%) were polymorphic. Analysis of the ISSR bands identified 46 genotypes among 81 individuals from one stream population and 72 distinct genotypes among 147 individuals in the Kinki district. An unweighted pair group method with arithmetic mean (UPGMA) dendrogram showed some unity among upstream and downstream subpopulations within one stream and eleven populations. The Shannon index of genetic diversity was 0.109 for one stream population and 0.313 for total genetic diversity, suggesting relatively high genetic diversity. Analysis of molecular variance (AMOVA) revealed that 84.1% of the total genetic diversity occurred among populations and the remaining diversity (15.9%) occurred within populations. Significant genetic differentiation occurred among populations in the Kinki district. These results suggest that conservation of each population is important for maintaining genetic diversity of R. nipponicus in this district. An erratum to this article can be found at     

Genetic Variation and Clonal Diversity of Psammochloa villosa(Poaceae) Detected by ISSR Markers

Genetic variation and clonal diversity of seven Psammochloavillosa(Poaceae) populations from northwest China were investigatedusing inter simple sequence repeat (ISSR) markers. Of the 84primers screened, 12 produced highly reproducible ISSR bands.Using these primers, 173 discernible DNA fragments were generatedwith 122 (70.5%) being polymorphic, indicating considerablegenetic variation at the species level. In contrast, there wererelatively low levels of polymorphism at the population levelwith the percentage of polymorphic bands (PPB) ranging from6.1 to 26.8. Analysis of molecular variance (AMOVA) showed thata large proportion of genetic variation (87.46%) resided amongpopulations, while only 12.54% resided among individuals withinpopulations. Clonal diversity was also high with 98 genets beingdetected from among 157 individuals using 12 ISSR primers. Theevenness of distribution of genotypes in P. villosa populationsvaried greatly, with all of the genotypes being local ones.No significant differences in genetic or clonal diversity werefound between populations in mobile or fixed dunes. The mainfactor responsible for the high level of differentiation amongpopulations and the low level of diversity within populationsis probably the clonal nature of this species, although selfingmay also affect the population genetic structure to some extent.The efficiency of ISSRs in identifying genetic individuals wasmuch higher than that of allozymes. An approximately asymptoticcorrelation was found between the number of genets detectedand the number of polymorphic loci used, suggesting that useof a high number of polymorphic bands is critical in genet identification.Copyright 2001 Annals of Botany Company Psammochloa villosa, ISSRs, genetic variation, clonal diversity     

SPAR methods revealed high genetic diversity within populations and high gene flow of Vanda coerulea Griff ex Lindl (Blue Vanda), an endangered orchid species

Molecular genetic fingerprints of seven populations of Vanda coerulea comprising of thirty-two genotypes from Northeast India were developed using PCR based markers. Genetic variability in the wild genotypes of V. coerulea was analyzed using two different single primer amplification reactions (SPAR) methods, viz., random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR). A total of 32 genotypes were used to investigate the existing natural genetic diversity at intra-specific level. Two hundred and twenty six (226) amplification products were scored by RAPD and ISSR, both of which collectively showed 58.88% polymorphism with a mean intra-population genetic diversity (Hpop) of 0.119. However, their level of diversity at inter- and intra-population levels was significant, with the percentage of polymorphic loci (Pp) ranging from 17.70% to 45.13%, Shannon's information index (I) from 0.105 to 0.268 and Nei's gene diversity (h) from 0.072 to 0.185 with mean Nei's gene diversity 0.174 and the overall estimate of gene flow being (Nm) 1.165. Analysis of molecular variance (AMOVA) showed 96.07% of variation at intra-population level, whereas 3.93% variation was recorded at inter-population level. Only one major cluster was detected by cluster analysis using the unweighted pair-group method with arithmetic average (UPGMA). Present investigation suggests the efficiency of SPAR methods to estimate the genetic diversity of V. coerulea and can be seen as a starting point for future research on the population and evolutionary genetics of this species.     

Genetic variability of introduced and local Spanish peach cultivars determined by SSR markers

A set of 94 peach cultivars including Spanish native peach and foreign commercial cultivars were analyzed using 15 SSR markers, selected for their high level of polymorphism. The number of alleles obtained varied from two to 11 with an average of 6.73 giving 185 different genotypes. All the cultivars showed a unique genetic profile, each one using different genotypic combination of all loci. BPPCT001 was the most informative locus showing also the highest discrimination power. Only six loci allowed the unambiguous separation of all the Spanish native cultivars studied, and the genotypic combination of only eight loci permitted the total differentiation of the 94 peach cultivars analyzed. The six selected loci (BPPCT001, BPPCT006, BPPCT008, PS9f8, UDP98-022, and UDP98-412) seem to be very useful for future Spanish peach identification works, and they will help to establish a molecular data base for native peach cultivars. UPGMA analysis was performed from the genetic distance matrix, and allowed the arrangement of all genotypes according to their genetic diversity. The genetic diversity among cultivars, observed in this work, led to their separation according to their regional origin, their morphological characteristics, and especially according to their fruit traits. Analysis of molecular variance was performed for seven populations from different regions of Spain and USA to examine the distribution of genetic variation of the studied accessions, showing that the major variation occurred within populations in each geographic site. The results reveal the existence of two diversity regions in Spain for peach germplasm.     

Population genetic structure of Carchesium polypinum (Ciliophora: Peritrichia) in four Chinese lakes inferred from ISSR fingerprinting: high diversity but low differentiation

Although the peritrichous ciliate Carchesium polypinum is common in freshwater, its population genetic structure is largely unknown. We used inter-simple sequence repeat (ISSR) fingerprinting to analyze the genetic structure of 48 different isolates of the species from four lakes in Wuhan, central China. Using eight polymorphic primers, 81 discernible DNA fragments were detected, among which 76 (93.83%) were polymorphic, indicating high genetic diversity at the isolate level. Further, Nei's gene diversity (h) and Shannon's Information index (I) between the different isolates both revealed a remarkable genetic diversity, higher than previously indicated by their morphology. At the same time, substantial gene flow was found. So the main factors responsible for the high level of diversity within populations are probably due to conjugation (sexual reproduction) and wide distribution of swarmers. Analysis of molecular variance (AMOVA) showed that there was low genetic differentiation among the four populations probably due to common ancestry and flooding events. The cluster analysis and principal component analysis (PCA) suggested that genotypes isolated from the same lake displayed a higher genetic similarity than those from different lakes. Both analyses separated C. polypinum isolates into subgroups according to the geographical locations. However, there is only a weak positive correlation between the genetic distance and geographical distance, suggesting a minor effect of geographical distance on the distribution of genetic diversity between populations of C. polypinum at the local level. In conclusion, our studies clearly demonstrated that a single morphospecies may harbor high levels of genetic diversity, and that the degree of resolution offered by morphology as a marker for measuring distribution patterns of genetically distinct entities is too low.     

Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties

Simple sequence repeat (SSR) and Single Nucleotide Polymorphic (SNP), the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR) and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC) values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA) indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA) with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD) derived Δk was plotted against the K to determine the number of populations. In case of SSR maximum Δk was at K=5 whereas, in case of SNP maximum Δk was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis.