Maximum Number Of Alleles Research Articles

Exploring the Genetic Diversity and Population Structure of Daphnia cucullata Sars, 1862 in Boreal Lakes (Latvian Lakeland) Based on Microsatellites

We have used Daphnia cucullata (Crustacea: Cladocera) as a model organism for the first time in the four deepest Latvian lakes from the Boreal biogeographical region in order to find the genetic diversity of these populations. During the research, we detected the most appropriate microsatellite markers for future genetic studies of Daphnia cucullata populations of lakes Svente, Riča, Dridzis and Geraņimovas-Ilzas in the Boreal biogeographical region. Based on these microsatellite markers, we determined the genetic diversity of these populations. The loci Dgm105 and Dgm101 had the maximum number of alleles and the maximum number of private alleles. The specific locus Dgm105 had five private alleles (62% of all detected alleles), and locus Dgm101 had four private alleles (57% of all detected alleles) in these loci. We determined the observed heterozygosity (Hobs) and the expected heterozygosity (Hexp) level (via Hardy–Weinberg equilibrium), the number of polymorphic loci, the number of detected alleles in each analyzed microsatellite locus, the average number of alleles at the locus (Na), the average effective number of alleles at the locus (Ne), the FST of the population’s genetic differentiation, the genetic distance (D) (following Nei) and the significance (χ2-test) of differences between the levels of observed and expected heterozygosity. It was shown that Daphnia cucullata populations from lakes with a low number of zooplankton taxa (Riča and Geraņimovas-Ilzas) have a higher genetic diversity compared to lakes with a high number of zooplankton taxa (Dridzis and Svente). It was found that Daphnia cucullata populations from lakes Dridzis and Svente have the least genetic distance, and these populations form a single genetic group, as confirmed via clustering.

Genetic Diversity and Relationship of Shanlan Upland Rice Were Revealed Based on 214 Upland Rice SSR Markers.

Shanlan upland rice (Oryza sativa L.) is a unique upland rice variety cultivated by the Li nationality for a long time, which has good drought resistance and high utilization value in drought resistance breeding. To explore the origin of Shanlan upland rice and its genetic relationship with upland rice from other geographical sources, 214 upland rice cultivars from Southeast Asia and five provinces (regions) in southern China were used to study genetic diversity by using SSR markers. Twelve SSR primers were screened and 164 alleles (Na) were detected, with the minimum number of alleles being 8 and the maximum number of alleles being 23, with an average of 13.667. The analysis of genetic diversity and analysis of molecular variance (AMOVA) showed that the differences among the materials mainly came from the individuals of upland rice. The results of gene flow and genetic differentiation revealed the relationship between the upland rice populations, and Hainan Shanlan upland rice presumably originated from upland rice in Guangdong province, and some of them were genetically differentiated from Hunan upland rice. It can be indirectly proved that the Li nationality in Hainan is a descendant of the ancient Baiyue ethnic group, which provides circumstantial evidence for the migration history of the Li nationality in Hainan, and also provides basic data for the advanced protection of Shanlan upland rice, and the innovative utilization of germplasm resources.

Evaluation of physicochemical characteristics and genetic diversity of widely consumed rice varieties in Kyaukse area, Myanmar

Consumer preferences are greatly influenced by eating and cooking qualities of rice grains, along with the economic value of a specific rice variety. This study was to evaluate ten rice varieties including the check variety IR64 on their physicochemical, cooking and eating qualities as well as to identify their genetic diversity using SSR markers. Most rice varieties are medium-grain types based on length-breadth ratio, whereas the famous Myanmar rice variety, Paw San Bay Kyar, (PSBK) is bold. PSBK showed the best cooking and eating quality traits with intermediate amylose content (AC), intermediate gelatinization temperature (GT), soft gel consistency (GC), and the highest elongation ratio among the studied rice varieties. Seventeen SSR markers linked with cooking and eating traits were used to assess the extent of polymorphism and genetic variation among ten rice varieties. There were 49 alleles in total, with an average of 2.88 alleles per locus. RM592 had the maximum number of alleles. The average PIC value ranged from 0.22 (RM540) to 0.77 (RM592). Cluster analysis with UPGMA method based on Jaccard’s similarity coefficient divided ten rice varieties into two main groups and four sub-clusters. In multiple regression analysis, RM190 and Wx primers were discovered to be significantly associated with AC, GC and GT of cooking and eating quality traits. This study could contribute to the choice of rice varieties with superior cooking and eating qualities for rice breeding programs by implementing physicochemical characteristics and molecular analysis.

Evaluation of Agronomic Performance and Genetic Diversity Analysis Using Simple Sequence Repeats Markers in Selected Wheat Lines

Crop improvement is the fundamental goal of plant biologists, and genetic diversity is the base for the survival of plants in nature. In this study, we evaluated 20 wheat lines for morphological and genetic diversity using eight simple sequence repeats markers from Wheat Microsatellite Consortium (WMC). Morphologically, variations were observed among all of the different wheat lines for the studied trait except for single spike weight. The highest values for different agronomic traits were recorded for the different wheat lines. The maximum days to heading were recorded for Borlaug-16 (128.3 ± 2.52 days). Similarly, days to maturity were recorded and were highest in Markaz-19 (182.3 ± 5.13 days), followed by Borlaug-16 (182.0 ± 4.58 days). The highest plant height was observed for Zincol-16 (122.3 ± 2.51 cm), followed by Markaz-19 (120.0 ± 14.79 cm) and Borlaug-16 (119.7 ± 6.8 cm). The productivity measured by 100-grain weight was highest in the case of Zincol-16 (84.0 ± 7.5 g). In contrast, wheat lines Shahkar, Sehar, and Farid-6 showed the lowest values for the traits tested. The results of genetic diversity revealed a total number of 16 alleles at eight SSR markers with an average of 2.00 ± 0.534 alleles per locus. Out of eight SSR markers, one marker (WMC105) was monomorphic, and six were dimorphic, showing two alleles at each locus. The maximum number of alleles (3) was observed for marker WMC78, in which genotypes AC and AA were predominantly found in high-yielding lines Borlaug-2016 and Zincol-2016 that were distantly related to other varieties. Zincol-2016 was also agronomically distinct from the rest of the 19 wheat lines. The results obtained from this study may be of importance for the scientific community to further explore the underlying genetic polymorphism associated high yielding varieties using marker-assisted selection for sustainable agriculture.

Development of genomic SSR markers in Gymnema sylvestre (Retz.) R.Br. ex Sm. using next generation DNA sequencing and their application in genetic diversity analysis

Gymnema sylvestre (Retz.) R.Br. ex Sm. is one of the important medicinal plants widely used in traditional medicine due to its anti-diabetic properties. Due to its medicinal properties, huge pressure on its natural resources of G. sylvestre is under severe threat of diversity loss. Further, the lack of molecular markers in G. sylvestre is the limiting factor for the adoption of modern genomic studies. In the present study, DNA was isolated from G. sylvestre leaves which were used for NGS sequencing (Illumina HiSeq 2500 NGS platform). After de-novo assembly of raw reads, 77679 contigs were identified with the sum of contigs length 1, 246, 048, 78 bp. Among all the assembled contigs, 55859 contigs with SSR motifs were identified. Based on repeat sequences, we designed SSR markers using the MISA tool. The hexanucleotide SSR was the most prominent among other SSR types. Among various SSR motifs identified, AT/TA, AG/CT, and AC/GT repeats were most frequently found in dinucleotide repeats. A total of 100 SSR primer pairs were synthesized through the flanking sequences of SSR motifs using Primer3 in which 58 primers were amplified and 42 were not amplified. Novel genomic SSR markers were used for the genetic diversity analysis of 26 genotypes of G. sylvestre. Fifty-eight primer pairs produced alleles ranging from 1 to 6. The maximum number of alleles (6) were generated by Xdagsm10 which showed the highest polymorphic information content (0.602) and allelic diversity (0.662) followed by Xdagsm96 recorded maximum PIC (0.607) and allelic diversity (0.671). According to the UPGMA dendrogram, the genotypes are clustered into three major groups, and they are not formed according to geographical origin. Among all the genotypes, DGS10, DGS22, DGS16, DGS5, and DGS23 were found to be distinctly divergent which can be used in the future breeding programme. Primers Xdagsm10 and Xdagsm96 are highly efficient polymorphic markers that can be used to distinguish the genotypes of G. sylvestre, and are highly useful in the molecular breeding programme.

Evaluation of agro-morphological traits, seed characterization and genetic diversity of local rice (Oryza sativa L.) varieties of Pakistan

Broad base genetic diversity is essential for a sustainable crop yield to provide tolerance against biotic and abiotic stresses. In Pakistan, rice is ranked second as a staple food and cultivated under different climatic zones. However, very little is known in terms of rice genetic diversity. The present research was performed to evaluate the genetic diversity among 12 local rice varieties by using 5 Simple sequence repeats (SSR) markers. Furthermore, agro-morphological parameters and seed quality of these varieties were studied. The maximum plant height (204.3 cm) and panicle length (40.1 cm) were observed for Hans-raj. The highest numbers of primary and secondary panicle branches were observed in Ratua-81 (51) and super basmati (62), respectively. Super basmati showed highest number of filled grains (264.3) and total number of grains (315) per panicle. The minimum days to maturity (140) was recorded for ratua-81 and highest 1000 grains weight (27 g) was recorded for Ksk-133. The highest concentration of elements, e.g. zinc (Zn) was observed in Ks-282 (44 µg/g), Iron (Fe) in hansraj (190.3 µg/g), manganese in bamla sufaid (111.3 µg/g), copper (Cu) in hansraj (856.3 µg/g), lead (Pb) in super basmati (3883.3 µg/g), and nickel (Ni) was found in basmati-385 (314.6 ug/g). For the genetic diversity analysis, five SSR markers were used and a total of 60 alleles were amplified with 20% polymorphism where RM28130 showed the highest Polymorphic information content (PIC) value (0.60). The maximum number of alleles (3) were produced by RM28089. Based on secondary panicle branches and total number of filled grains, Super basmati showed best panicle architecture and grain yield, which can be used in breeding program to develop high yielding aromatic rice genotypes. The highest number of filled grains and total number of grains per panicle were observed in super basmati, which indicated the potential adaptation. Basmati-2000, Hansraj, Ks-282, Super basmati and Basmati surkh-161 were found to be highly rich in micronutrients (iron, zinc, copper, lead and manganese). The maximum genetic distance was observed in basmati-2000 and basmati surkh 161 genotypes.

Simple Sequence Repeats-Based Genetic Characterization and Varietal Identification of Potato Varieties Grown in Pakistan

The potato (Solanum tuberosum L.) is an important cash crop with a complex genome and with features of aneuploidy with a high level of heterozygosity. It is a prerequisite for potato breeding to have knowledge of genetic diversity and population structure. To understand the genetic characteristics of potato cultivars in Pakistan, 25 potato varieties were characterized with simple sequence repeat (SSR) markers to distinguish closely related varieties. In total, 214 alleles were amplified with 35 SSR markers exhibiting 89.2% polymorphism. The maximum number of alleles and polymorphic alleles per locus were 20 and 14 for the markers S25 and S174, respectively. The polymorphic information content (PIC) extended from 0.00–0.87. The size of the amplified PCR product ranged between (30–1000 bp). A cluster analysis divided the 25 varieties into three clusters: cluster I revealed the most diversity, followed by cluster II with 11 varieties and cluster III with 13 varieties. Nei’s genetic diversity and minimum spanning network (MSN) depicted the Mozika variety as the most diverse compared to the rest of the varieties. Nei’s coefficient was found to vary from 0.53 to 0.95. Out of the 25 studied varieties, 16 were uniquely identified by 29 polymorphic SSR bands of different sizes with a maximum size amplified by S4026/4027 (800bp) and a minimum by S170 (90bp). The genetic diversity and varietal identification determined in the present study has molecular and breeding-related significance with respect to the utilization and protection of intellectual property rights of potato cultivars for sustainable potato production in Pakistan.

Distribution of clones among hosts for the lizard malaria parasite Plasmodium mexicanum.

BackgroundMalaria parasites reproduce asexually, leading to the production of large numbers of genetically identical parasites, here termed a clonal line or clone. Infected hosts may harbor one or more clones, and the number of clones in a host is termed multiplicity of infection (MOI). Understanding the distribution of parasite clones among hosts can shed light on the processes shaping this distribution and is important for modeling MOI. Here, I determine whether the distribution of clones of the lizard malaria parasite Plasmodium mexicanum differ significantly from statistical distributions commonly used to model MOI and logical extensions of these models.MethodsThe number of clones per infection was assessed using four microsatellite loci with the maximum number of alleles at any one locus used as a simple estimate of MOI for each infection. I fit statistical models (Poisson, negative binomial, zero-inflated models) to data from four individual sites to determine a best fit model. I also simulated the number of alleles per locus using an unbiased estimate of MOI to determine whether the simple (but potentially biased) method I used to estimate MOI influenced model fit.ResultsThe distribution of clones among hosts at individual sites differed significantly from traditional Poisson and negative binomial distributions, but not from zero-inflated modifications of these distributions. A consistent excess of two-clone infections and shortage of one-clone infections relative to all fit distributions was also observed. Any bias introduced by the simple method for estimating of MOI did not appear to qualitatively alter the results.ConclusionsThe statistical distributions used to model MOI are typically zero-truncated; truncating the Poisson or zero-inflated Poisson yield the same distribution, so the reasonable fit of the zero-inflated Poisson to the data suggests that the use of the zero-truncated Poisson in modeling is adequate. The improved fit of zero-inflated distributions relative to standard distributions may suggest that only a portion of the host population is located in areas suitable for transmission even at small sites (<1 ha). Collective transmission of clones and premunition may also contribute to deviations from standard distributions.

Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers

BackgroundDate palm tree (Phoenix dactylifera L.) is a perennial monocotyledonous plant belonging to the Arecaceae family, a special plant with extraordinary nature that gives eminent contributions in agricultural sustainability and huge socio-economic value in many countries of the world including Ethiopia. Evaluation of genetic diversity across date palms at DNA level is very important for breeding and conservation. The result of this study could help to design for genetic improvement and develop germplasm introduction programmes of date palms mainly in Ethiopia. ResultsIn this study, 124 date palm genotypes were collected, and 10 polymorphic microsatellite markers were used. Among 10 microsatellites, MPdCIR085 and MPdCIR093 loci showed the highest value of observed and expected heterozygosity, maximum number of alleles, and highest polymorphic information content values. A total of 112 number of alleles were found, and the mean number of major allele frequency was 0.26, with numbers ranging from 0.155 (MPdCIR085) to 0.374 (MPdCIR016); effective number of alleles with a mean value of 6.61, private alleles ranged from 0.0 to 0.65; observed heterozygosity ranged from 0.355 to 0.726; expected heterozygosity varied from 0.669 to 0.906, polymorphic information content with a mean value of 0.809; fixation index individuals relative to subpopulations ranged from 0.028 for locus MPdCIR032 to 0.548 for locus MPdCIR025, while subpopulations relative to total population value ranged from − 0.007 (MPdCIR070) to 0.891 (MPdCIR015). All nine accesstions, neighbour-joining clustering analysis, based on dissimilarity coefficient values were grouped into five major categories; in population STRUCTURE analysis at highest K value, three groups were formed, whereas DAPC separated date palm genotypes into eight clusters using the first two linear discriminants. Principal coordinate analysis was explained, with a 17.33% total of variation in all populations. Generally, the result of this study revealed the presence of allele variations and high heterozygosity (> 0.7) in date palm genotypes. ConclusionsMicrosatellites (SSR) are one of the most preferable molecular markers for the study of genetic diversity and population structure of plants. In this study, we found the presence of genetic variations of date palm genotypes in Ethiopia; therefore, these genetic variations of date palms is important for crop improvement and conservation programmes; also, it will be used as sources of information to national and international genbanks.

Polymorphism in spring and winter rapeseed varieties (Brassica napus L.) identified by ssr markers

Purpose. To assess the genetic diversity of rapeseed varieties using SSR markers in order to create breeding material and use that material in complex in vitro selection for drought and salt tolerance. Methods. PCR analysis, cluster analysis. Results. The results of analysis of rapeseed varieties polymorphism based on molecular-genetic markers is presented.As a result of the analysis of rapeseed varieties, 41 alleles were detected using the studied markers, that is, an average of 10.3 alleles per marker. The number of polymorphic loci identified by four microsatellite markers (Ra3-H09, Na12-A02, FITO-063 and Na10-B07) was 24. The polymorphism level of the studied varieties was 51% on average and varied between 33% (identified by FITO-063) and 87% (identified by Na12-A02). According to the frequency distribution of the obtained alleles, the highest frequency by SSR marker Ra3-H09 had a 117 bp allele identified in three varieties: ‘Senator Liuks’, ‘Danhal’ and ‘Chornyi Veleten’. It was found that the unique alleles identified by Ra3-H09 were the alleles at a frequency of 0.06 and size of 135 bp (variety ‘Aliot’) and 156 bp (variety ‘Kliff’). FITO-063 marker identified the smallest number of alleles (5) at a frequency distribution ranging from 0.11 to 0.33. The unique alleles identified by FITO-063 marker were the ones at a frequency of 0.1 and size of 258 bp (variety ‘Geros’) and 273 bp (variety ‘Chornyi Veleten’). The maximum number of alleles was obtained using Na12-A02 marker. The distribution showed the highest frequency (0.11) for the 158 bp and 192 bp alleles. Using Na10-B07 marker, three alleles were identified at a frequency of 0.04. These 144, 156 and 194-bp alleles were found in varieties ‘Kliff’, ‘Geros’ and ‘Nelson’. Cluster analysis revealed four variety clusters: ‘Senator Liuks’ and ‘Danhal’, ‘NK Technik’ and ‘NK Petrol’, ‘Geros’ and ‘Aliot’, ‘Kliff’ and ‘Nelson’. ‘Chornyi Veleten’ variety did not enter any cluster. The most distant varieties are ‘Kliff’ and ‘Nelson’ with a genetic distance value of 3.32. Foreign varieties ‘NK Technik’ and ‘NEC Petrol’ with the value of genetic distances between them equal 1.41 appeared to be the most similar by the four studied SSR markers. Other varieties differed by at least one marker. Conclusions. Consequently, using the set of four microsatellite markers provides an assessment of rapeseed varietal diversity that can be used in complex in vitro selection for drought and salt tolerance.

Microsatellite Loci Polymorphism of Apple (Malus domestica Borkh.) Genotypes with Different Ploidy Level

In this paper, the microsatellite (SSR) loci analysis was used to study apple genotypes with different levels of ploidy. A total of 47 samples were studied (9 diploids, 21 triploids, and 17 tetraploids) for seven microsatellite loci (GD147, Hi02C07, CH02c11, CH04c07, CH03d07, CH02c09, and GD12). It was possible to refine the pedigrees for some forms. It was established that the tetraploidss 20-9-30 and 20-9-27, selected in a hybrid family from the crossing of Wealthy 4x and Antonovka Obyknovennaya, were probably obtained from the self-pollination of the maternal form, since in the most loci they did not inherit alleles from the paternal form. As a result of the alleles distribution analysis, the spontaneous triploid cultivars Nizkorosloe and Sinap Orlovsky were revealed to be formed from the merge of an unreduced ovum and haploid pollen, since in the heterozygous loci both alleles are inherited from the maternal form and only one from the paternal form. According to the obtained data, studied tetraploids may be divided into two groups, which also reflect the features of tetraploids origin. The first group includes tetraploids inherited alleles from one initial diploid form (including spontaneous and induced tetraploids, as well as forms from self-pollination of the tetraploid maternal form). These teraploids, like diploids, amplify 1–2 alleles per locus (on average, for all 7 loci, one genotype amplifies 13 alleles). The second group includes tetraploids carrying alleles from several initial diploid forms. Tetraploids of this group are highly heterozygous and amplify 3–4 alleles at most loci (the maximum number of alleles at all loci, 24 alleles, was identified in the form 30-47-88). Tetraploids of the second group have a greater potential for the genetic diversity of its offspring. Analysis of polymorphism of microsatellite loci can be used (1) as an alternative or additional method for identifying the triploid hybrids from heteroploid crosses of orthoploid forms, which is based on the analysis of the loci most polymorphic in parental forms, and (2) for the analysis of true hybridity (verification of pedigrees), including tetraploid forms. Moreover, we identified the most polymorphic loci suitable for the above purposes. The aspects of qualitative and quantitative interpretation of the fragment analysis of microsatellite loci results are considered. The possibilities and limitations of the SSR analysis for detection of apple ploidy level are discussed.

Polymorphism in the major histocompatibility complex (MHC class II B) genes of the Rufous-backed Bunting (Emberiza jankowskii).

Genetic diversity is one of the pillars of conservation biology research. High genetic diversity and abundant genetic variation in an organism may be suggestive of capacity to adapt to various environmental changes. The major histocompatibility complex (MHC) is known to be highly polymorphic and plays an important role in immune function. It is also considered an ideal model system to investigate genetic diversity in wildlife populations. The Rufous-backed Bunting (Emberiza jankowskii) is an endangered species that has experienced a sharp decline in both population and habitat size. Many historically significant populations are no longer present in previously populated regions, with only three breeding populations present in Inner Mongolia (i.e., the Aolunhua, Gahaitu and Lubei557 populations). Efforts focused on facilitating the conservation of the Rufous-backed Bunting (Emberiza jankowskii) are becoming increasingly important. However, the genetic diversity of E. jankowskii has not been investigated. In the present study, polymorphism in exon 2 of the MHCIIB of E. jankowskii was investigated. This polymorphism was subsequently compared with a related species, the Meadow Bunting (Emberiza cioides). A total of 1.59 alleles/individual were detected in E. jankowskii and 1.73 alleles/individual were identified in E. cioides. The maximum number of alleles per individual from the three E. jankowskii populations suggest the existence of at least three functional loci, while the maximum number of alleles per individual from the three E. cioides populations suggest the presence of at least four functional loci. Two of the alleles were shared between the E. jankowskii and E. cioides. Among the 12 unique alleles identified in E. jankowskii, 10.17 segregating sites per allele were detected, and the nucleotide diversity was 0.1865. Among the 17 unique alleles identified in E. cioides, eight segregating sites per allele were detected, and the nucleotide diversity was 0.1667. Overall, compared to other passerine birds, a relatively low level of MHC polymorphism was revealed in E. jankowskii, which was similar to that in E. cioides. Positive selection was detected by PAML/SLAC/FEL analyses in the region encoding the peptide-binding region in both species, and no recombination was detected. Phylogenetic analysis showed that the alleles from E. jankowskii and E. cioides belong to the same clade and the two species shared similar alleles, suggesting the occurrence of a trans-species polymorphism between the two Emberiza species.

Cost-effective development of highly polymorphic microsatellite in Japanese quail facilitated by next-generation sequencing.

Next-generation sequencing technologies permit rapid and cost-effective identification of numerous putative microsatellite loci. Here, from the genome sequences of Japanese quail, we developed microsatellite markers containing dinucleotide repeats and employed these for characterisation of genetic diversity and population structure. A total of 385 individuals from 12 experimental and one wild-derived Japanese quail lines were genotyped with newly developed autosomal markers. The maximum number of alleles, expected heterozygosity and polymorphic information content (PIC) per locus were 10, 0.80 and 0.77 respectively. Approximately half of the markers were highly informative (PIC ≥ 0.50). The mean number of alleles per locus and observed heterozygosity within a line were in the range of 1.3-4.1 and 0.11-0.53 respectively. Compared with the wild-derived line, genetic diversity levels were low in the experimental lines. Genetic differentiation (FST ) between all pairs of the lines ranged from 0.13 to 0.83. Genetic clustering analyses based on multilocus genotypes of individuals showed that most individuals formed clearly defined clusters corresponding to the origins of the lines. These results suggest that Japanese quail experimental lines are highly structured. Microsatellite markers developed in this study may be effective for future genetic studies of Japanese quail.

Ploidy in the alpine sedgeKobresia pygmaea(Cyperaceae) and related species: combined application of chromosome counts, new microsatellite markers and flow cytometry

Polyploidy is a fundamental mechanism in evolution, but is hard to detect in taxa with agmatoploidy or aneuploidy. We tested whether a combination of chromosome counting, microsatellite analyses and flow cytometric measurements represents a suitable approach for the detection of basic chromosome numbers and ploidy in Kobresia (Cyperaceae). Chromosome counting resulted in 2n = 64 for Kobresia pygmaea and K. cercostachys, 2n = 58 and 64 for K. myosuroides, and 2n = 72 for K. simpliciuscula. We characterized eight microsatellite loci for K. pygmaea, which gave a maximum of four alleles per individual. Cross-species amplification was tested in 26 congeneric species and, on average, six of eight loci amplified successfully. Using flow cytometry, we confirmed tetraploidy in K. pygmaea. Basic chromosome numbers and ploidy were inferred from chromosome counts and the maximum number of alleles per locus. We consider the basic numbers as x = 16 and 18, with irregularities derived from agmatoploidy and aneuploidy. Across all Kobresia taxa, ploidy ranged from diploid up to heptaploid. The combination of chromosome counts and microsatellite analyses is an ideal method for the determination of basic chromosome numbers and for inferring ploidy, and flow cytometry is a suitable tool for the identification of deviating cytotypes. (C) 2014 The Linnean Society of London

Z-chromosome linked dinucleotide strs: association with reproduction traits in chicken

The study was conducted on 96 unrelated chickens belonging to three strains, namely, White Leghorn (PL2), Punjab Broiler (PB2) and Punjab Red (PR). Five pairs of Z-chromosome linked microsatellite loci (Ase50, MCW154, HUR0404, HUR0411 and HUR0412) were studied in the selected strains with an aim to genetically characterize the divergent stocks and to associate the polymorphism with growth and production traits. The microsatellite band patterns were resolved using 3.5% metaphore agarose gel at 80-100 volts. The number of alleles in the microsatellite loci varied from 8 to 10 among the different germplasms, indicating high degree of polymorphism across the three breeds. Locus HUR0412 had the maximum number of alleles (10), thus it is the most polymorphic among all the loci under study. The allele ‘I’ of the locus HUR0412 is the candidate private allele that could be used to characterize PL2 breed. Except for the HUR0412 locus no other loci could be characterised for harbouring strain specific private allele. The PIC value was the highest in loci as: Ase50 in PL2 (0.715), MCW154 in PR (0.739) and PB2 (0.827). The HUR0412 locus exhibited significant difference among different genotypes of layer (PL2 and PR) females for the traits like, body weight at 40 weeks of age (BWT40), egg no. at 40 weeks (ENO40), age of sexual maturity (ASM) and rate of lay. The performance trait, egg mass (EMASS) was significantly different (P£0.05) among the genotypes of layers for the locus MCW154. The Chi-square test for various loci and breeds were significant i.e. the population were not in Hardy-Weinberg equilibrium.

Trait linked microsatellite marker based diversity analysis for yield attributing traits in some bengal landraces of rice (Oryza sativaL.)

Forty one diverse rice genotypes collected from West Bengal have been studied to assess genetic diversity using five SSR markers linked with QTL of yield attributing traits. Genotypes were grown at the Gayeshpur Regional Research Station (New Alluvial Zone), Bidhan Chandra Krishi Viswavidyalaya, West Bengal, India. Results shown that Polymorphic pattern were generated by all five SSR primers which altogether produced 14 reproducible alleles. Most of the markers generated two reproducible alleles whereas RM-3 and RM-16 generated three and four alleles respectively. The percentage of highest frequency alleles among the markers ranging from 70.73 % (RM-16) to 95.12 % (RM-5) where as PIC values varied from 0.1488 (RM-3) to 0.314 (RM-130). RM-16 generated maximum number of alleles although PIC value was maximum in case of RM-130. These two markers could be used for diversity analysis related to yield attributes in rice. The dendogram revealed 7 clusters at a cut-off similarity coefficient level of 0.64. At the similarity coefficient level of 0.35 and 0.62 Kumargore and Oradhan respectively were distinct where as rest of the genotypes grouped into 5 major clusters. On the basis of yield performance as well as presence of rare alleles of the used markers, Tulaipanji, Kumargore, Butadhan, Oradhan can be considered further as parental material for development of high yielding varieties of rice.

Cytogenetics and characterization of microsatellite loci for a South American pioneer tree species, Croton floribundus

Despite the recent advances in plant population genetic studies, the lack of information regarding pedigree, ploidy level, or mode of inheritance for many polyploids can compromise the analysis of the molecular data produced. The aim of this study was to examine both microsatellite and cytogenetic characteristics of the pioneer tree Croton floribundus Spreng. (Euphorbiaceae) to test for the occurrence of polyploidy in the species and to evaluate its implications for the appropriate use of SSR markers. Seven microsatellite markers were developed and screened for 62 individuals from a semi-deciduous tropical forest in Brazil. Chromosome number, meiotic behavior, and pollen viability were evaluated from male flower buds. All SSR loci were highly polymorphic. The number of bivalents observed in meiosis n = 56 (2n = 8× = 112) and the maximum number of alleles per individual (Ni = 8) demonstrated the occurrence of polyploidy in C. floribundus. The normal meiotic pairing and the high pollen viability suggested that C. floribundus is a regular and stable polyploid, most likely an allopolyploid. The combined SSR and cytogenetic data provided new evidence on the origin and evolution of the species as well as assured the accurate use of SSR loci for population genetic studies of the polyploid pioneer species.

Panmixia in the endangered slipper lobster Scyllarides latus from the northeastern Atlantic and western Mediterranean

In the marine realm, it is important to understand the connectivity and population dynamics of commercially exploited species; this information promotes sustainable fishing practices. The large slipper lobster, Scyllarides latus (Latreille, 1803), is a commercially valuable crustacean that has been over-exploited in many areas throughout its distribution range in the northeastern (hereafter NE) Atlantic and the Mediterranean. Here, we report the first molecular population genetic study of S. latus based on 9 nuclear microsatellite loci. A total of 128 specimens of S. latus were collected in the Western Mediterranean (2 locations) and four regions (13 locations) in the NE Atlantic, including Southern Portugal and the Macaronesian archipelagos of Azores, Canary Islands and Cape Verde. Maximum number of alleles per locus ranged from 4 to 14, and observed heterozygosity per locus ranged from 0.143 to 0.795 (0.539 ± 0.087, mean ± SE). Pairwise region estimates of FST, RST and Dest were very low (<0.040) and not significant in all comparisons. Bayesian clustering analysis also suggested homogeneity in S. latus across all regions. The Almeria-Oran front, an important biogeographic boundary between the Atlantic and Mediterranean basins, was not found to have a significant impact on the genetic structuring of S. latus. Overall, all of our analyses of genetic differentiation and migration suggested panmixia in S. latus across its distributional range. Such pattern is likely to result from its high fecundity and long-lived pelagic larva, which can promote high levels of connectivity between geographically distant populations. Future conservation strategies should manage all S. latus populations jointly (one stock).

Development and Characterization of Microsatellite Markers (SSR) in Sesamum (Sesamum indicum L.) Species

Microsatellites, also known as simple sequence repeats (SSRs), are the class of repetitive DNA sequences present throughout the genome of many plant and animal species. Recent advances in molecular genetics had been the introduction of microsatellite markers to investigate the genetic structuring of natural plant populations. We have employed an enrichment strategy for microsatellite isolation by using multi-enzymes digestion, microsatellite oligoprobes, and streptavidin magnetic beads in Sesamum (Sesamum indicum L.). More than 200 SSR motifs were detected (SSR motifs ≥2 repeat units or 6 bp); 80 % of the clones contained SSR motifs. When regarding SSRs with four or more repeat units and a minimum length of 10 bp, 132 of them showed repeats. Eighteen SSR markers were initially characterized for optimum annealing temperature using a gradient PCR technique. Among the 18 SSR markers characterized, five were found to be polymorphic and used to analyze 60 Sesamum germplasm accessions. The maximum number of alleles detected was four with a single primer and the least number of two alleles with three primers with an average PIC value of 0.77. SSRs are a valuable tool for estimating genetic diversity and analyzing the evolutionary and historical development of cultivars at the genomic level in sesame breeding programs.

Molecular characterisation and similarity relationships among iranian basil (Ocimum basilicum L.) accessions using inter simple sequence repeat markers

The study of genetic relationships is a prerequisite for plant breeding activities as well as for conservation of genetic resources. In the present study, genetic diversity among 50 Iranian basil (Ocimum basilicum L.) accessions was determined using inter simple sequence repeat (ISSR) markers. Thirty-eight alleles were generated at 12 ISSR loci. The number of alleles per locus ranged from 1 to 5 with an average of 3.17. The maximum number of alleles was observed at the A7, 818, 825 and 849 loci, and their size ranged from 300 to 2500 bp. A similarity matrix based on Jaccard's coefficient for all 50 basil accessions gave values from 1.00-0.60. The maximum similarity (1.00) was observed between the "Urmia" and "Shahr-e-Rey II" accessions as well as between the "Urmia" and "Qazvin II" accessions. The lowest similarity (0.60) was observed between the "Tuyserkan I" and "Gom II" accessions. The unweighted pair- group method using arithmetique average UPGMA clustering algorithm classified the studied accessions into three distinct groups. All of the basil accessions, with the exception of "Babol III", "Ahvaz II", "Yazd II" and "Ardebil I", were placed in groups I and II. Leaf colour was a specific characteristic that influenced the clustering of Iranian basil accessions. Because of this relationship, the results of the principal coordinate analysis (PCoA) approximately corresponded to those obtained through cluster analysis. Our results revealed that the geographical distribution of genotypes could not be used as a basis for crossing parents to obtain high heterosis, and therefore, it must be carried out by genetic studies.