Microsatellite marker-based identification and genetic relationships of olive cultivars from the Extremadura region of Spain

Seventy-seven olive accessions corresponding to 25 cultivars from the Extremadura region of Spain were studied using four microsatellite or SSR markers in order to fingerprint them, and evaluate genetic similarity and relationships between local and introduced olive cultivars. The number of alleles per locus ranged from 4 to 8, with a mean of 6.25 alleles per primer pair (a total of 25 alleles). The observed heterozygosity ranged from 0.58 to 0.95, while the expected heterozygosity varied between 0.68 and 0.83. The polymorphism information content values ranged from 0.63 to 0.79. The mean polymorphism information content value of 0.70 for the SSR loci provided sufficient discriminating ability to evaluate the genetic diversity among the cultivars. The SSR data allowed unequivocal identification of all the cultivars; a combination of three SSR markers was sufficient to discriminate all 25 olive cultivars. A dendrogram was prepared, using the unweighted pair-group method with arithmetic mean clustering algorithm; it depicted the pattern of relationships between the cultivars. Most of the local cultivars grouped according to their geographic origin. No clear clustering trends were observed when the morphological traits of fruit endocarps or fruit use of cultivars were employed as analysis criteria. We conclude that there is a high level of variability among local olive cultivars from the Extremadura region at both the morphological and molecular levels; these data should be useful for identifying and distinguishing local germplasm.     

Genetic diversity among cultivars, landraces and wild relatives of rice as revealed by microsatellite markers

Genetic diversity among 35 rice accessions, which included 19 landraces, 9 cultivars and 7 wild relatives, was investigated by using microsatellite (SSR) markers distributed across the rice genome. The mean number of alleles per locus was 4.86, showing 95.2% polymorphism and an average polymorphism information content of 0.707. Cluster analysis based on microsatellite allelic diversity clearly demarcated the landraces, cultivars and wild relatives into different groups. The allelic richness computed for the clusters indicated that genetic diversity was the highest among wild relatives (0.436), followed by landraces (0.356), and the lowest for cultivars. Allelic variability among the SSR markers was high enough to categorize cultivars, landraces and wild relatives of the rice germplasm, and to catalogue the genetic variability observed for future use. The results also suggested the necessity to introgress genes from landraces and wild relatives into cultivars, for cultivar improvement.     

Molecular characterization and genetic diversity analysis of soybean (Glycine max (L.) Merr.) germplasm accessions in India

Molecular characterization and genetic diversity among 82 soybean accessions was carried out by using 44 simple sequence repeat (SSR) markers. Of the 44 SSR markers used, 40 markers were found polymorphic among 82 soybean accessions. These 40 polymorphic markers produced a total of 119 alleles, of which five were unique alleles and four alleles were rare. The allele number for each SSR locus varied between two to four with an average of 2.97 alleles per marker. Polymorphic information content values of SSRs ranged from 0.101 to 0.742 with an average of 0.477. Jaccard’s similarity coefficient was employed to study the molecular diversity of 82 soybean accessions. The pairwise genetic similarity among 82 soybean accessions varied from 0.28 to 0.90. The dendrogram constructed based on genetic similarities among 82 soybean accessions identified three major clusters. The majority of genotypes including four improved cultivars were grouped in a single subcluster IIIa of cluster III, indicating high genetic resemblance among soybean germplasm collection in India.

Electronic supplementary material

The online version of this article (doi:10.1007/s12298-014-0266-y) contains supplementary material, which is available to authorized users.     

Assessment of genetic diversity and relationship among a collection of US sweet sorghum germplasm by SSR markers

Sweet sorghum (Sorghum bicolor L.) is a type of cultivated sorghums and has been recognized widely as potential alternative source of bio-fuel because of its high fermentable sugar content in the stalk. A substantial variation of sugar content and related traits is known to exist in US sweet sorghum. The objectives of the study were to assess the genetic diversity and relationship among the US sweet sorghum cultivars and lines using SSR markers and to examine the genetic variability within sweet sorghum accessions for sugar content. Sixty-eight sweet sorghum and four grain sorghum cultivars and lines were genotyped with 41 SSR markers that generated 132 alleles with an average of 3.22 alleles per locus. Polymorphism information content (PIC) value, a measure of gene diversity, was 0.40 with a range of 0.03–0.87. The genetic similarity co-efficient was estimated based on the segregation of the 132 SSR alleles. Clustering analysis based on the genetic similarity (GS) grouped the 72 sorghum accessions into 10 distinct clusters. Grouping based on clustering analysis was in good agreement with available pedigree and genetic background information. The study has revealed the genetic relationship of cultivars with unknown parentage to those with known parentage. A number of diverse pairs of sweet sorghum accessions were identified which were polymorphic at many SSR loci and significantly different for sugar content as well. Information generated from this study can be used to select parents for hybrid development to maximize the sugar content and total biomass, and development of segregating populations to map genes controlling sugar content in sweet sorghum.     

Mapping quantitative trait loci for important agronomic traits in finger millet (<Emphasis Type="Italic">Eleusine coracana</Emphasis>) mini core collection with genomic and genic SSR markers

Allele identification for agro-morphological traits and stress resistance is a major concern across the globe for improving productivity of finger millet. Here, we used 46 genomic and 58 genic simple sequence repeats (SSRs) markers in a set of 66 accessions used to constitute a global mini-core collection for analysing their genetic structure as a population and establishing association among markers and twenty morphological traits including resistance to finger blast. Phenotypic data revealed a wide range of variation for all traits except flag leaf width and flag leaf sheath width. We got amplification of 81 alleles by the 31 genomic SSRs at an average of 2.61 alleles per locus. Polymorphism information content (PIC) values varied from 0.21 to 0.75 and average gene diversity was 0.49. Structure analysis of the population using the genomic SSR data divided the accessions into two clusters where Indian and exotic accessions were grouped in separate clusters. Genic SSRs which were associated with blast resistance genes, amplified 36 alleles at an average of 2 alleles per locus. PIC values ranged from 0.32 to 0.37 and average gene diversity was 0.45. Population structure analysis using data from these SSRs grouped the accessions into three clusters, which broadly correspond to their reaction to blast disease. Twenty-two significant associations were found using the GLM approach for 20 agro-morphological traits both in 2012 and 2014, while, 7 and 5 significant marker-trait associations were identified using MLM in 2012 and 2014 respectively. The SSR markers FMBLEST35 and FMBLEST36 designed from the Pi21 gene sequence of rice were found to be associated with blast disease resistance in finger millet indicating that the gene homologues play a significant role in an important role for neck blast resistance.     

Automated sizing of fluorescent-labeled simple sequence repeat (SSR) markers to assay genetic variation in soybean

 Simple Sequence Repeat (SSR) allele sizing provides a useful tool for genotype identification, pedigree analysis, and for estimating genetic distance between organisms. Soybean [Glycine max (L.) Merr.] cultivars are identified for Plant Variety Protection (PVP) purposes by standard pigmentation and morphological traits. However, many commercial soybeans arise from a limited number of elite lines and are often indistinguishable based on these traits. A system based on SSR markers would provide unique DNA profiles of cultivars. Fluorescent labeling of alleles combined with automated sizing with internal size standards in each gel lane was used as an alternative to standard [³²P] labeling to assess genetic variability in soybean. Allelic frequencies at 20 SSR loci were determined in 35 soybean genotypes that account for greater than 95% of the alleles in North American soybean cultivars based upon pedigree analysis. An average of 10.1 alleles per locus (range: 5–17), with a mean gene diversity of 0.80 (range: 0.50 to 0.87) were observed at the 20 SSR loci. The 20 loci successfully distinguished modern soybean cultivars that are identical for morphological and pigmentation traits, as well as 7 soybean genotypes reported to be indistinguishable using 17 RFLP probes. Pedigrees of 7 cultivars were studied to estimate stability of SSRs in soybean across generations. Of the 7 pedigrees 6 had one locus in the progeny with an allele(s) that was not present in either parent. These new alleles are most likely the result of mutation. The mutation rate of SSR alleles in soybean was similar to that reported in humans. To avoid difficulty associated with mutation, DNA fingerprint data should be determined from the bulk of 30-50 plants of a cultivar. Received: 24 March 1997 / Accepted: 4 April 1997     

Development and characterization of microsatellite markers in Indian sesame (Sesamum indicum L.)

The genetic characterization of Indian sesame cultivars and related wild species was analysed using 102 simple sequence repeat (SSR; microsatellite) markers. Of these, 62 were novel sesame-specific microsatellites isolated in the course of the present investigation by constructing genomic libraries. Characterization of the 68 sesame accessions and three related wild species using 72 polymorphic SSR primers resulted in the detection of 170 alleles. The number of alleles ranged from two to four with an average of 2.5 alleles per locus. Polymorphic information content of the markers ranged from 0.43 to 0.88 with an average of 0.66. UPGMA cluster analysis grouped all the accessions into two major clusters with a genetic similarity ranging from 0.40 to 0.91. A moderate to high level of genetic variability was observed. The three wild accessions used in the study formed separate clades and distant genetic relationships were observed between the cultivar lines and wild species. Differentiation of genotypes according to geographical region was not observed. Analysis of molecular variance (AMOVA) analysis revealed that a high percentage of variation was within populations (87.1 %). An overall F _st of 0.11 among the populations indicated low population differentiation. The SSR markers developed will be useful for further genetic analysis, linkage mapping and selection of parents in future breeding programmes.     

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.     

Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.]

SSR markers are desirable markers in analysis of genetic diversity, quantitative trait loci mapping and gene locating. In this study, SSR markers were developed from two genomic libraries enriched for (GA)n and (CA)n of foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China. A total of 100 SSR markers among the 193 primer pairs detected polymorphism between two mapping parents of an F₂ population, i.e. “B100” of cultivated S. italica and “A10” of wild S. viridis. Excluding 14 markers with unclear amplifications, and five markers unlinked with any linkage group, a foxtail millet SSR linkage map was constructed by integrating 81 new developed SSR markers with 20 RFLP anchored markers. The 81 SSRs covered nine chromosomes of foxtail millet. The length of the map was 1,654 cM, with an average interval distance between markers of 16.4 cM. The 81 SSR markers were not evenly distributed throughout the nine chromosomes, with Ch.8 harbouring the least (3 markers) and Ch.9 harbouring the most (18 markers). To verify the usefulness of the SSR markers developed, 37 SSR markers were randomly chosen to analyze genetic diversity of 40 foxtail millet accessions. Totally 228 alleles were detected, with an average 6.16 alleles per locus. Polymorphism information content (PIC) value for each locus ranged from 0.413 to 0.847, with an average of 0.697. A positive correlation between PIC and number of alleles and between PIC and number of repeat unit were found [0.802 and 0.429, respectively (P < 0.01)]. UPGMA analysis revealed that the 40 foxtail millet cultivars could be grouped into five clusters in which the landraces’ grouping was largely consistent with ecotypes while the breeding varieties from different provinces in China tended to be grouped together. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Simple Sequence Repeat Analysis of Genetic Diversity in Primary Core Collection of Peach （Prunus persica）

In this study, the genetic diversity of 51 cultivars in the primary core collection of peach （Prunus persica （L.） Batsch） was evaluated by using simple sequence repeats （SSRs）. The phylogenetic relationships and the evolutionary history among different cultivars were determined on the basis of SSR data. Twenty-two polymorphic SSR primer pairs were selected, and a total of 111 alleles were identified in the 51 cultivars, with an average of 5 alleles per locus. According to traditional Chinese classification of peach cultivars, the 51 cultivars in the peach primary core collection belong to six variety groups. The SSR analysis revealed that the levels of the genetic diversity within each variety group were ranked as Sweet peach 〉 Crisp peach 〉 Flat peach 〉 Nectarine 〉 Honey Peach 〉 Yellow fleshed peach. The genetic diversity among the Chinese cultivars was higher than that among the introduced cultivars. Cluster analysis by the unweighted pair group method with arithmetic averaging （UPGMA） placed the 51 cultivars into five linkage clusters. Cultivar members from the same variety group were distributed in different UPGMA clusters and some members from different variety groups were placed under the same cluster. Different variety groups could not be differentiated in accordance with SSR markers. The SSR analysis revealed rich genetic diversity in the peach primary core collection, representative of genetic resources of peach.     

Study of genetic diversity and relationships among accessions of foxtail millet [Setaria italica (L.) P. Beauv.] in Korea, China, and Pakistan using SSR markers

In this study, 28 simple sequence repeat (SSR) primer sets were used to analyze the genetic diversity, population structure, and genetic relationships among 37 accessions of foxtail millet from Korea, China and Pakistan. A total of 298 alleles were detected with an average allele number of 10.6 per locus among 37 foxtail millet accessions. The number of alleles per locus ranged from 2 (b226) to 20 (b236). Of the 298 alleles, 138 alleles (46.3%) were rare (frequency < 0.05), 152 alleles (51.0%) were detected at an intermediate frequency (range, 0.05?C0.50), and eight alleles (2.7%) were abundant (frequency > 0.50), respectively. The average gene diversity values were 0.652, 0.692, and 0.491 and polymorphic information content values were 0.621, 0.653, and 0.438, for accessions from Korea, China, and Pakistan, respectively. The accessions from China showed higher SSR diversity than those from Korea and Pakistan. A phylogenetic tree constructed using the un-weighted pair group methods with arithmetic mean algorithm revealed three major groups of accessions that were not congruent with geographical distribution patterns with a few exceptions. The lack of correlation between the accession clusters and their geographic location indicates that the diffusion of foxtail millet from China to Korea might have occurred through multiple routes. Our results provide support for the origin and diffusion route of foxtail millet in East Asia. This SSR-based assessment of genetic diversity, genetic relationships, and population structure among genetic resources of foxtail millet landraces will be valuable to foxtail millet breeding and genetic conservation programs in Korea.     

Analysis of genetic diversity among persimmon cultivars using microsatellite markers

In the Mediterranean area, the production of persimmon (Diospyros kaki Thumb) [2n = 6x = 90] has increased recently as an alternative to the major fruit crops. In Spain, production relies almost exclusively on the cultivar “Rojo Brillante” which accounts for 83% of the crop. A crop based on a monovarietal culture implies several commercial risks that can compromise the future of the crop. Although the species was introduced in Europe very recently, it is well adapted to the climate of southern Europe. However, the recent introduction from Japan, the mistakes on the identity of varieties in the collections due to a bad translation of variety names from Japanese, and the lack of genetic characterization of many varieties have caused difficulties for effective management of the available genetic resources. The present paper was aimed at exploring the genetic diversity among different persimmon cultivars, including those collected in the European survey as well as Japanese cultivars. Seventy-one persimmon cultivars coming from two European collections that included accessions from Japan, Italy, and Spain were analyzed using 19 polymorphic microsatellite markers. A total of 206 alleles were obtained, with a mean value of 10.8 alleles per locus. A neighbor joining dendrogram and a principal coordinate analysis arranged the cultivars according to their genetic relationships. Analysis of molecular variance revealed significant genetic variability between and within groups, 73.3% and 85.2% for astringent-type and country origin, respectively. The simple sequence repeat markers classified the persimmon cultivars according to their genetic relationship.     

Use of simple sequence repeat markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp) cultivars resistant and susceptible to red rot

Red rod is an economically important disease of sugarcane caused by the fungus Colletotrichum falcatum. We used a simple sequence repeat (SSR)-based marker system to identify and analyze genetic relationships of red rot resistant and susceptible sugarcane cultivars grown in Pakistan. Twenty-one highly polymorphic SSR markers were used for DNA fingerprinting and genetic diversity analysis of 20 sugarcane cultivars. These SSR markers were found to be highly robust; we identified 144 alleles, with 3-11 alleles per marker and a mean of 6.8. Three SSR markers were able to identify all 20 cultivars. DNAMAN(?)-generated homology tree was used to analyze genetic diversity among these cultivars; all cultivars shared 58% or more similarity. We correlated polymorphism information content and resolving power values with marker effectiveness in the process of sugarcane cultivar identification. We concluded that a small number of SSR-derived DNA markers will allow breeders to identify red rot resistant and susceptible cultivars.     

Genetic diversity among alfalfa (Medicago sativa) cultivars coming from a breeding program, using SSR markers

Alfalfa (Medicago sativa) is an autotetraploid, allogamous and heterozygous species whose cultivars are synthetic populations. The breeders apply selection pressure for some agronomic traits within a breeding pool to increase the frequency of favorable individuals. The objective of this study was to investigate the differentiation level among seven cultivars originating from one breeding program, and between these cultivars and the breeding pool, with eight SSR markers. These highly polymorphic and codominant markers, together with recent population genetic statistics extended to autotetraploids, offer tools to analyse genetic diversity in alfalfa. The number of alleles per locus varied between 3 and 24. All loci were at a panmictic equilibrium in the cultivars, except one, probably because of null alleles. With seven SSR loci, each cultivar was at panmictic equilibrium. The mean gene diversity was high, ranging from 0.665 to 0.717 in the cultivars. The parameter F _ST indicated a low but significant diversity among cultivars. Among 21 pairs of cultivars, 15 were significantly different. The breeding pool also had a high diversity, and was significantly different from each cultivar except the most recent one. Considering the characteristics of the breeding program and the mode of cultivar elaboration, we found that they were unable to generate a large variety differentiation. Estimation of population genetics parameters at SSR loci can be applied for assessing the differences between cultivars or populations, either for variety distinction or the management of genetic resources.     

Molecular characterization of oilseed rape accessions collected from multi continents for exploitation of potential heterotic group through SSR markers

Evaluation of the genetic diversity in conventional and modern rapeseed cultivars is essential for conservation, management and utilization of these genetic resources for high yielding hybrid production. The objective of this research was to evaluate a collection of 86 oilseed rape cultivars with 188 simple sequence repeat (SSR) markers to assess the genetic variability, heterotic group identity and relationships within and between the groups identified among the genotypes. A total of 631 alleles at 188 SSR markers were detected including 53 and 84 unique and private alleles respectively, which indicated great richness and uniqueness of genetic variation in these selected cultivars. The mean number of alleles per locus was 3.3 and the average polymorphic information content was 0.35 for all microsatellite loci. Unweighted Pair Group Method with Arithmetic Mean clustering and principal component analysis consistently divided all the cultivars into four distinct groups (I, II, III and IV) which largely coincided with their geographical distributions. The Chinese origin cultivars are predominantly assembled in Group II and showed wide genetic base because of its high allelic abundance at SSR loci while most of the exotic cultivars grouped into Group I and were highly distinct owing to the abundant private and unique alleles. The highest genetic distance was found between Group I and IV, which mainly comprised of exotic and newly synthesized yellow seeded (1728-1 and G1087) breeding lines, respectively. Our study provides important insights into further utilization of exotic Brassica napus accessions in Chinese rapeseed breeding and vice versa.     

Diversification of indigenous gene- pool by using exotic germplasm in lentil (Lens culinaris Medikus subsp. culinaris)

Genetic diversity was studied among 21 accessions of lentil using SSR markers and morphological traits in order to assess the diversification of Indian gene-pool of lentil through introgression of exotic genes and introduction of germplasm. Among these , 16 genotypes either had ‘Precoz’ gene, an Argentine line in their pedigree or genes from introduced lines from ICARDA. Sixty five SSR markers and eight phenotypic traits were used to analyse the level of genetic diversity in these genotypes. Forty three SSR markers (66 %) were polymorphic and generated a total of 177 alleles with an average of 4.1 alleles per SSR marker. Alleles per marker ranged from 2 to 6. The polymorphic information content ranged 0.33 to 0.80 with an average of 0.57, suggesting that SSR markers are highly polymorphic among the studied genotypes. Genetic dissimilarity based a dendrogram grouped these accessions into two main clusters (cluster I and cluster II) and it ranged 33 % to 71 %, suggesting high level of genetic diversity among the genotypes. First three components of PCA based morphological traits explained higher variance (95.6 %) compared to PCA components based on SSR markers (42.7 %) of total genetic variance. Thus, more diversity was observed for morphological traits and genotypes in each cluster and sub-cluster showed a range of variability for seed size, earliness, pods/plant and plant height. Molecular and phenotypic diversity analysis thus suggested that use of germplasm of exotic lines have diversified the genetic base of lentil germplasm in India. This diversified gene-pool will be very useful in the development of improved varieties of lentil in order to address the effect of climate change, to adapt in new cropping systems niches such as mixed cropping, relay cropping, etc. and to meet consumers’ preference.     

The southwestern origin and eastward dispersal of pear (<Emphasis Type="Italic">Pyrus pyrifolia</Emphasis>) in East Asia revealed by comprehensive genetic structure analysis with SSR markers

Pyrus pyrifolia is considered one of the most important cultivated Pyrus species. Hundreds of landraces and bred cultivars have been developed through the natural and artificial hybridizations necessary due to self-incompatibility. In this study, the genetic diversity of 478 Pyrus accessions, including Chinese landraces, bred cultivars, and wild samples, as well as introduced pear cultivars from Japan and Korea, was investigated with a set of 17 simple sequence repeat (SSR) markers distributed across all 17 linkage groups of the pear genome. A total of 121 alleles were detected, including 4 rare alleles with a frequency lower than 5%. Diversity statistics indicated a high level of genetic variation as quantified by the average values of the observed heterozygosity, the expected heterozygosity, and Wright’s fixation index, at 0.76, 0.78, and 0.02, respectively. Population structure and discriminant analysis of principal component analysis implied extensive genetic communication between sand pears in China and revealed four contiguous geographical clusters with overlapping geographical regions. The diversity of the four clusters and approximate Bayesian computation (ABC) indicated that sand pear spread from west to east along the Pearl River and Yangtze River valleys. High diversity and polyphyletic genetic components of cultivars in southwestern China further support southwestern China as the probable center of divergence for Pyrus species. A core collection of 80 out of 470 cultivars was selected, accounting for about 17% of accessions, and capturing 91% of all alleles, including all rare alleles. Our research provides a comprehensive understanding of sand pear germplasm in East Asia and constructs a preliminary core collection, which will be useful for association genetics studies, germplasm conservation, and breeding programs.     

Microsatellite based analysis of genetic diversity of popular black pepper genotypes in South India

The genotypes of black pepper are morphologically and genotypically highly diverse and carry all the cumulative variations inherited and maintained through generations. The present study describes the Simple Sequence Repeat (SSR) or microsatellite based assessment of genetic diversity among forty popular genotypes and four different species of black pepper in Southern region of India. For isolation of SSR primers, our earlier attempts with enrichment strategies like ‘Triplex affinity capture’ did not extract a single SSR primer due to close proximity of restriction sites to the SSR motif. Hence we developed a ‘Sequential Reverse Genome Walking (SRGW)’ strategy with better enrichment efficiency of 72% that generated seven new SSR primers. Genotyping precisely discriminated majority of genotypes which indicated that the SSR primers are very informative. A total of 62 alleles with an average of 15.5 alleles over 4 loci were identified. All the SSR primers showed an average Polymorphism Information Content (PIC) value of 0.85. The estimated average Shared Allele Frequency ranged between 1.57 and 20.12%. The PCA plot revealed four closely related individual groups and identified Karimunda, Wild pepper and a local landrace ‘local b’ as the most divergent genotypes. Cluster analysis exposed the genetic relatedness between hybrids and selections with other known cultivars. The introduction of black pepper from South India to Malaysia was emphasized from the observation of genetic similarity of Malaysian cultivar ‘Kuching’ with other indigenous popular cultivars. The study was first to portray the precise genetic relatedness among the major indigenous genotypes of black pepper.     

Assessing temporal changes in genetic diversity of maize varieties using microsatellite markers

To quantify genetic diversity among modern and earlier maize cultivars, 133 varieties, representative of the maize grown in France during the last five decades, were fingerprinted using 51 SSR. The varieties were grouped into four periods. For each period, allelic richness, genetic diversity and genetic differentiation among periods were computed. A total of 239 alleles were generated. Allelic richness, in terms of number of alleles per locus, for each period was 4.5, 3.6, 3.9 and 3.6 respectively. Genetic diversity corresponding to Neis unbiased heterozygosity was calculated, based on allelic frequencies. Values ranged from 0.56 to 0.61. Period I presented the highest genetic diversity, whereas the three other periods all presented a similar value. A great proportion of the total genetic diversity (H_T=0.59) was conserved within all periods (H_S=0.57), rather than among periods (G_ST=0.04). The analysis of molecular variance showed that the variation among periods represented only 10% of the total molecular variation. However, the differentiation among periods, although low, was significant, except for the last two periods. Our results showed that the genetic diversity has been reduced by about 10% in the maize cultivars bred before 1976 compared to those bred after 1985. The very low differentiation (G_ST=0.21%) observed among cultivars of the last two decades should alert French maize breeders to enlarge genetic basis in their variety breeding programmes.     

Genetic Similarity Among Tunisian Olive Cultivars and Two Unknown Feral Olive Trees Estimated Through SSR Markers

We used eight informative microsatellite markers for fingerprinting and evaluation of genetic similarity among 15 Tunisian olive (Olea europaea L.) cultivars and two feral unknown trees named Soulela 1 and Soulela 2. Thirty-one alleles were revealed, and the number of alleles per SSR varied from 2 (UDO12) to 6 (GAPU71A). Cluster analysis grouped cultivars into three main clusters. The two unknown varieties could not be reliably classified into any of these cultivar groups. SSR analysis indicated the presence of three erroneous denominations of cultivars. We resolved two synonymy cases (Zalmati and Chemlali; Rkhami and Chetoui) and one case of homonymy (Chemlali Tataouine). Genetic analyses of DNA extracted from leaves, oils, and embryos of the two unknown cultivars and the two major Tunisian olive cultivars (Chemlali and Chetoui) were also studied. We conclude that the reliable identification of these two feral cultivars needs to be addressed by a larger set of markers.