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Simple Summary: It is generally accepted that the process of insect mass-rearing, used to apply the sterile insect technique, promotes adaptation to the captive environment and a reduction in the genetic diversity of the population. Here, we compare the genetic diversity of two mass-reared strains of the Mexican fruit fly (Anastrepha ludens) and a wild population, using nuclear DNA. In this study, we found similar values of heterozygosity, allelic richness, and level of inbreeding among strains. These results indicate that mass-rearing conditions do not always reduce genetic diversity. Our findings contribute to understanding the genetic make-up resulting from adaptation to mass-rearing conditions. The application of the sterile insect technique (SIT) requires the adaptation of insects to mass-rearing conditions. It is generally accepted that this adaptation may include a reduction in genetic diversity and an associated loss of desirable characteristics for the effective performance of sterile insects in the field. Here, we compare the genetic diversity of two mass-reared strains of the Mexican fruit fly, Anastrepha ludens, and a wild (WIL) population collected near Tapachula, Mexico, using seven DNA microsatellites as molecular genetic markers. The mass-reared strains were a bisexual laboratory strain (LAB) with approximately 130 generations under mass-rearing and a genetic sexing strain, Tapachula-7 (TA7), also under mass-rearing for 100 generations. Our results revealed an overall low level of genetic differentiation (approximately 15%) among the three strains, with the LAB and WIL populations being genetically most similar and TA7 most genetically differentiated. Although there were some differences in allele frequencies between strains, our results show that overall, the adaptation to mass-rearing conditions did not reduce genetic variability compared to the wild sample in terms of heterozygosity or allelic richness, nor did it appear to alter the level of inbreeding with respect to the wild populations. These results are contrary to the general idea that mass-rearing always results in a reduction in genetic diversity. Overall, our findings can contribute to a better understanding of the impact that adaptation to mass-rearing conditions may have on the genetic make-up of strains. [ABSTRACT FROM AUTHOR]

The application of the sterile insect technique (SIT) requires the adaptation of insects to mass-rearing conditions. It is generally accepted that this adaptation may include a reduction in genetic diversity and an associated loss of desirable characteristics for the effective performance of sterile insects in the field. Here, we compare the genetic diversity of two mass-reared strains of the Mexican fruit fly, Anastrepha ludens, and a wild (WIL) population collected near Tapachula, Mexico, using seven DNA microsatellites as molecular genetic markers. The mass-reared strains were a bisexual laboratory strain (LAB) with approximately 130 generations under mass-rearing and a genetic sexing strain, Tapachula-7 (TA7), also under mass-rearing for 100 generations. Our results revealed an overall low level of genetic differentiation (approximately 15%) among the three strains, with the LAB and WIL populations being genetically most similar and TA7 most genetically differentiated. Although there were some differences in allele frequencies between strains, our results show that overall, the adaptation to mass-rearing conditions did not reduce genetic variability compared to the wild sample in terms of heterozygosity or allelic richness, nor did it appear to alter the level of inbreeding with respect to the wild populations. These results are contrary to the general idea that mass-rearing always results in a reduction in genetic diversity. Overall, our findings can contribute to a better understanding of the impact that adaptation to mass-rearing conditions may have on the genetic make-up of strains.

Nineteen microsatellite loci, obtained by the whole genome sequencing approach, were developed and validated for the 'smooth cauliflower' coral Stylophora pistillata, a widespread Indo Pacific branching coral species. A sample size of 40 colonies collected at five reef sites along the northern Gulf of Eilat, the Red Sea, were genotyped, revealing loci reproducibly and suitable outcomes for wide applications, including population genetic studies. The 19 new microsatellite loci in this sample were composed of 4–20 alleles/locus, of which 10 microsatellites are highly polymorphic (≥10 alleles/locus). The observed and expected heterozygosity ranged between 0.289 and 0.957 (mean 0.597) and 0.101 and 0.911 (mean 0.726), respectively, and the Fixation Index (F), which also indicates the inbreeding coefficient, ranges between −0.174 and 0.569 (mean 0.207). The polymorphic information content (PIC) ranges between 0.100 and 0.904 (mean 0.699). This new set of microsatellite loci will be employed for population genetics studies as for identifying the distribution of various genotypes within S. pistillata chimeras. [ABSTRACT FROM AUTHOR]

Nineteen microsatellite loci, obtained by the whole genome sequencing approach, were developed and validated for the ‘smooth cauliflower’ coral Stylophora pistillata, a widespread Indo Pacific branching coral species. A sample size of 40 colonies collected at five reef sites along the northern Gulf of Eilat, the Red Sea, were genotyped, revealing loci reproducibly and suitable outcomes for wide applications, including population genetic studies. The 19 new microsatellite loci in this sample were composed of 4–20 alleles/locus, of which 10 microsatellites are highly polymorphic (≥10 alleles/locus). The observed and expected heterozygosity ranged between 0.289 and 0.957 (mean 0.597) and 0.101 and 0.911 (mean 0.726), respectively, and the Fixation Index (F), which also indicates the inbreeding coefficient, ranges between −0.174 and 0.569 (mean 0.207). The polymorphic information content (PIC) ranges between 0.100 and 0.904 (mean 0.699). This new set of microsatellite loci will be employed for population genetics studies as for identifying the distribution of various genotypes within S. pistillata chimeras.

Cowpea (Vigna unguiculata (L.)) is an important crop for food security in Senegal; therefore, understanding the genetic diversity of local germplasm is relevant for crop improvement and genetic maintenance in the era of climate change. For this purpose, 15 microsatellite markers were used to estimate the genetic diversity of Senegalese cowpea germplasm, including 671 accessions grown in eight regions and 66 wild relatives and intermediate forms (weedy). For the cultivated, the main expected heterozygosity (mHe) ranged between 0.317 (Fatick) and 0.439 (South). A narrow genetic variation between accessions from the different regions was observed with genetic similarity ranging from 0.861 to 0.965 and genetic differentiation indices (Fst) between 0.018 and 0.100. The accessions from southern Senegal (Kédougou, Sédhiou, and Kolda regions) are more diverse than the others. However, the accessions from the North (Saint-Louis) are genetically different from other regions. The diversity analysis in wild relatives from Senegal, which had never been performed before, revealed that the wild/weedy forms remain more diverse than the cultivated with genetic diversity values (He) of 0.389 and 0.480, respectively. STRUCTURE software divided the Senegalese germplasm into five subpopulations. Three of them (i, ii, and iii) included only cultivated accessions from several regions, one (v) mainly from Saint-Louis, and one (iv) the wild/weedy with some cultivated accessions. Our results support the hypothesis that Vigna unguiculata var. spontanea is the wild progenitor of cowpea. The accessions from the South, the northern recession accessions, and the wild/weedy could serve as sources of new genes for the genetic improvement of cowpea in Senegal. [ABSTRACT FROM AUTHOR]

Malnutrition leads to high mortality especially in developing countries. Present study comprised 11 high yielding wheat (Triticum aestivum L.) genotypes sown during rabi 2014-15 and 2015-16 and crosses attempted during 2014-15 and sown at Research Field of CCS Haryana Agricultural University, Hisar, Haryana. Forty nine microsatellite markers linked with identified QTLs for micronutrient were used for the genetic diversity assessment among bread wheat parents their F1s. Out of 49, 38 SSRs were found polymorphic which amplified a total of 76 alleles with an average of 2.00 alleles per locus. The range of amplified PCR products ranged from 100 to 480 bp. Estimates of similarity coefficient among parents and F1s suggest enough divergence and averaged to 0.71. Enough genetic variability was observed for all the 14 agronomic traits in all genotypes. Selection of genotypes from different clusters helps in making proper choice of breeding programme. In the present study, the information generated about genetic diversity will be useful for selection of parents for breeding including gene mapping and ultimately for marker assisted selection (MAS) for micronutrient content improvement worldwide.

The aim of this study was to assess genetic diversity within the set of 55 Tunisian castor genotypes using 20 SSR primers. PCR amplification of DNA using 20 primers for SSR analysis produced 141 DNA fragments that could be scored in all 55 genotypes of castor. The number of amplified fragments varied from 4 (Rco 15) to 10 (Rco 29 and Rco 33). Of the 141 amplified bands, all 141 were polymorphic, with an average of 7.05 polymorphic bands per primer. The polymorphism information content (PIC) value varied from 0.719 (Rco 15) to 0.879 (Rco 29), with an average of 0.825 and index diversity (DI) value varied from 0.745 (Rco 15) to 0.881 (Rco 29) with an average of 0.832. 100% of used SSR markers had PIC and DI values higher than 0.7 that means high polymorphism of chosen markers used for analysis. Probability of identity (PI) was low ranged from 0.002 (Rco 29 and Rco 41) to 0.018 (Rco 15) with an average of 0.007. A dendrogram based on UPGMA analysis separated 55 Tunisian castor genotypes into 4 clusters (1, 2, 3, 4). Knowledge on the genetic diversity of castor can be used for future breeding programs for increased oil production to meet the ever increasing demand of castor oil for industrial uses as well as for biodiesel production. [ABSTRACT FROM AUTHOR]

Pathogen diseases are increasingly threatening forest trees under the current climate change, causing a remarkable decrease in the stability of forest ecosystems. Ash (Fraxinus excelsior L.) dieback due to Hymenoscyphus fraxineus has been noted in Poland since 1992 and has spread over many European countries. The aim of this study was to test the hypothesis that ash trees affected by dieback could exhibit a reduced vessel size and density along the trunk, as well as a lowered width of annual wood rings, leading to the weakening of water transport towards the crown. Dead and dying ash trees were sampled in a forest district severely affected by ash decline in southern Poland. Wood samples were collected at different height along the trunk and several wood anatomical characteristics of annual tree rings over the period 2002-2011 were examined. Dead trees showed a stronger reduction in radial growth than dying trees over the period considered. Moreover, the diameter of vessels increased from the crown to the base in both dead and dying trees, while the density decreased. Significant differences between dead and dying trees were detected in size and density of vessels in the period analyzed, as well as in the width of annual rings. DNA extracted from wood samples was analyzed using SSR markers and the main genetic parameters of dead and dying trees were estimated, finding similar levels of polymorphism and only slight non-significant differences between the two health groups. Our results are consistent with the hypothesis that pathogens could disrupt the hormonal control of wood formation by interfering with the polar auxin transport, progressively leading to the death of ash trees.

Dipterocarpus dyeri is an endangered species in lowland tropical forests of Vietnam because of habitat fragmentation and over-exploitation of this species. It plays an important economic and ecological role in Vietnam. Due to the importance and lack of information on its genetic diversity and mating system, we investigated genetic parameters in adults and juveniles of this species in two natural populations about 10 km apart. Eight polymorphic microsatellite loci were analysed and showed high genetic diversity in adults (HO = 0.475-0.563, HE = 0.551-0.649) and juveniles (HO = 0.47-0.513, HE = 0.576-0.685) in both populations. Results revealed differences of genetic diversity between two adult (FST = 0.123) and two juvenile populations (FST = 0.188). However, the differences were negligible and indicated that the fragmented habitat had negligible effect on genetic diversity. Gene flow or gene migration between two populations in adults or juveniles remained (Nm > 1), although this value reduced slightly in the latter. Analysis of the mating system indicated high outcrossing rate of D. dyeri (tm = 0.8). Biparental mating (tm - ts) was relatively high (0.19-0.25) and suggested high tendency of mating system between relatives. Genetic conservation should derive from correlated outcrossing. [ABSTRACT FROM AUTHOR]

The largest population of goats (62%) in Ecuador is in the dry forest region in the south of the country. A Creole goat, named “Chusca Lojana”, has adapted to the dry forest region where environmental conditions are warm-dry, with sparse vegetation. Knowledge of the genetic information of the Creole goat is important to determine intra-racial diversity, the degree of genetic distance among other breeds of goats, and the possible substructure of the population, which is valuable for the conservation of such a species’ genetic resources. A total of 145 samples of the Creole goat was taken from the four biotypes previously identified. Genetic analyses were performed using 38 microsatellites recommended for studies of goat genetic diversity (FAO-ISAG). The results of within-breed genetic diversity showed a mean number of alleles per locus (MNA) of 8, an effective number of alleles (Ae) of 4.3, an expected heterozygosity (He) of 0.71, an observed heterozygosity (Ho) of 0.63, polymorphic information content (PIC) of 0.67, and an FIS value of 0.11. Between-breed genetic diversity among 43 goat populations (native of Spain, American Creole, Europeans, and Africans) showed the following values: FIS = 0.087, FIT = 0.176, and FST = 0.098. Regarding the analysis of the population structure, the results showed that the Creole Chusca Lojana goat population is homogeneous and no genetic separation was observed between the different biotypes (FST = 0.0073). In conclusion, the Chusca Lojana goat has a high genetic diversity, without exhibiting a genetic substructure. Therefore, it should be considered as a distinct population because crossbreeding with other breeds was not detected.

The current study aims at the molecular characterization of Pistacia atlantica Desf. Subsp atlantica in Northwestern Algeria. The genome size estimation was performed for the first time for the species using flow cytometry on 97 samples. The flow cytometry analysis led to estimate a very small genome (2C = 1.21 ± 0.02 pg). Meristematic somatic cells of male floral buds showed the best prometaphase which on (2 n = 2x = 30) chromosome complement was observed. Two chromosomes bearing satellites showed evident and large secondary constrictions. sixty-one genotypes were characterized using 6 SSR microsatellites. A total of 26 alleles were amplified. Allele frequencies ranged from 0.008 to 0.68. Eight rare alleles (30.8%) were observed. The observed heterozygosity (Ho) ranged from 0.35 to 0.67, while the expected heterozygosity (He) ranged from 0.48 to 0.77. The loci Pislen 526 and Pislen 114 were the most polymorphic with 7 and 6 observed alleles respectively. Pislen 526 and PKATG014 were the most informative markers. Cluster analysis based on the euclidean distance using (UPGMA) led to observe divergences between genotypes within site and between sites. The current study is the first molecular characterization of the subspecies; it indicated an evident diversity due to a genetic flow between populations. More genetic diversity studies are required to learn about the structure and the evolution of natural P. atlantica subsp. atlantica using more SSR markers and more accessions from other areas. [ABSTRACT FROM AUTHOR]

Latin American Creole chickens are generally not characterized; this is the case in Ecuador, where the lack of scientific information is contributing to their extinction. Here, we developed a characterization of the genetic resources of Ecuadorian chickens located in three continental agroecosystems (Pacific coastal, Andean, and Amazonian). Blood samples of 234 unrelated animals were collected in six provinces across Ecuador: Bolívar, Chimborazo, Cotopaxi, Guayas, Morona Santiago, and Tungurahua, in order to perform a genetic characterization and population structure assessment using the AVIANDIV project microsatellites panel (30 loci) and D-loop sequences of mitochondrial DNA and comparing with reference data from other breeds or genetic lines. The results indicate that Ecuadorian Creole chickens are the result of the admixture of different genetic groups that occurred during the last five centuries. While the influence of South Spanish breeds is demonstrated in the colonial age, genetic relationships with other breeds (Leghorn, Spanish fighter cock) cannot be discarded. The geographical configuration of the country and extreme climate variability have influenced the genetic isolation of groups constituting a homogeneous genetic status into the whole population. This is not only a source of genetic variation, but also a critical point because genetic drift produces a loss of genetic variants.

The effects of temperature pre-treatment, thidiazuron, naphthaleneacetic acid, and 6-benzylaminopurine on in vitro gynogenic plant production from un-pollinated melon (Cucumis melo L.) ovaries were investigated. Simple sequence repeat (SSR) marker analysis was conducted to identify the homozygous diploid individuals. The temperature pre-treatment (4°C) for 4 days increased embryo formation frequency (63.3%) significantly. Addition of thidiazuron (0.04 and 0.02 mg/l) in the induction medium significantly increased the number of responding ovaries (46.6%, 65.83%), respectively. The maximum number of plantlet regeneration (22.5%) was achieved by culturing the ovary derived embryos on Murashigue and Skoog medium (MS medium) supplement with 0.6 mg/l 6-benzylaminopurine. Spontaneous doubled haploids originated directly through embryogenesis were subjected to genetic analysis using SSR molecular marker with 23 primers pair for homozygosity. SSR markers with microsatellite CMGA172, confirmed that the alleles in the parental material were also present in the gynogenic plantlets, but amplified only two alleles as compared to four alleles of the heterozygous parent material at same locus. Therefore these regenerated plantlets were consider homozygous and produced through a process of gametophytic embryogenesis.

Chinese cherry ( Prunus pseudocerasus Lindl.) is an ancient fruit crop with highly economic and ornamental values. It originated in China and the cultivation history can be traced back to 3,000 - 4,000 years ago. Over such a long-term domestication process, a large number of genetic variations have been accumulated in different landraces. However, their utilization for cultivar improvement is limited by the scarcity of information involving genetic diversity and population structure. Here, 17 populations comprised of 140 individuals were collected from four geographic areas: Sichuan Basin (SC), Qinglin Mountain (QL), Yungui Plateau (YG) and North of China (NC), and analyzed using a set of 20 microsatellite markers. In total, 126 polymorphic loci were generated, with 6.3 loci per primer. The global expected heterozygosity ( He = 0.63) and Shannon information index ( I = 1.23) implied a moderately high level of genetic variation. Two major clusters (cluster 1 and cluster 2) were demonstrated based on population structure analysis, which implied the presence of two potential domestication sites of Chinese cherry landraces. Individuals from SC were assigned to cluster 1 and those from QL, YG and NC were grouped into cluster 2. Samples from QL region contained the most plentiful admixture genetic components, implied the possibility of being one transition region of genetic variation. Moreover, botanical characteristics, such as long lifespan, inbreeding preference as well as vegetative propagation, might lead to a relatively low level but significant genetic divergence among populations. Finally, conservation strategies were proposed to protect these valuable natural germplasm based on these results. [ABSTRACT FROM AUTHOR]

Tuber species are ectomycorrhizal ascomycetes establishing relationships with different host trees and forming hypogeous fruiting bodies known as truffles. Among Tuber species, Tuber aestivum Vittad. has a wide distributional range being found naturally all over Europe. Here, we performed large-scale population genetic analyses in T. aestivum to (i) investigate its genetic diversity at the European scale, (ii) characterize its genetic structure and test for the presence of ecotypes and (iii) shed light into its demographic history. To reach these goals, 230 ascocarps from different populations were genotyped using 15 polymorphic simple sequence repeat markers. We identified 181 multilocus genotypes and four genetic groups which did not show a clear geographical separation; although, one of them was present exclusively in Southeast France, Italy and Spain. Fixation index values between pairs of genetic groups were generally high and ranged from 0.29 to 0.45. A significant deficit of heterozygosity indicated a population expansion instead of a recent population bottleneck, suggesting that T. aestivum is not endangered in Europe, not even in Mediterranean regions. Our study based on a large-scale population genetic analysis suggests that genetically distinct populations and likely ecotypes within T. aestivum are present. In turn, this study paves the way to future investigations aimed at addressing the biological and/or ecological factors that have concurred in shaping the population genetic structure of this species. Present results should also have implications for the truffle market since defining genetic markers are now possible at least for some specific T. aestivum genetic groups. [ABSTRACT FROM AUTHOR]

The intra-specific diversity and genetic structure within the Alexandrium pacificum Litaker ( A. catenella – Group IV) populations along the Temperate Asian coasts, were studied among individuals isolated from Japan to China. The UPGMA dendrogram and FCA revealed the existence of 3 clusters. Assignment analysis suggested the occurrence of gene flows between the Japanese Pacific coast (cluster-1) and the Chinese Zhejiang coast (cluster-2). Human transportations are suspected to explain the lack of genetic difference between several pairs of distant Japanese samples, hardly explained by a natural dispersal mechanism. The genetic isolation of the population established in the Sea of Japan (cluster-3) suggested the existence of a strong ecological and geographical barrier. Along the Pacific coasts, the South–North current allows limited exchanges between Chinese and Japanese populations. The relationships between Temperate Asian and Mediterranean individuals suggested different scenario of large-scale dispersal mechanisms. [ABSTRACT FROM AUTHOR]

The popularity of pomegranate ( Punica granatum L.) is increasing among growers and consumers due to its nutritional value, nutraceutical properties and adaptability to different soils and climate conditions. Pomegranate is characterized by a large variability in terms of domestic, wild and ornamental genotypes, and for seed-hardness, juiciness, rind and aril color, sugar/acid ratio, antioxidant activity, fatty acids, phenols and arils anthocyanins content. Evaluation of pomegranate germplasm has usually been performed using fruit morphological and chemical traits, whereas genetic studies received less attention. The aim of the present work was: (a) to carry on a morphological and biochemical characterization of a set of pomegranate genotypes collected in Puglia region, Southeastern Italy and (b) to investigate genetic diversity by microsatellite markers. A two-year study was carried out for the evaluation of 13 pomegranate genotypes, sweet and sour, of Italian and Israeli origin. Significant differences were observed for many of the parameters investigated, in particular fruit and aril size and maturity index of fruits, titratable acidity, total polyphenol content and antioxidant activity of juices and oil content of seeds. Genetic analysis on the pomegranate collection identified 53 SSR loci able to distinguish the different genotypes and to estimate genetic distances. In the dendrogram, pomegranate genotypes clustered according to both geographical origin and morphological–chemical traits (skin color, size, taste and polyphenolic content), suggesting that SSR markers could be effective to detect the genetic diversity of pomegranate, thus facilitating the exploitation of this fruit species germplasm. In general, morphological, chemical and genetic parameters allowed to clearly distinguish the Italian genotypes from the Israeli ones. [ABSTRACT FROM AUTHOR]

Highlights: [•] Diverse grape cultivars display distinct phenolic profiles. [•] Analysis of non-coding DNA fragments (SSR markers) of Vitis vinifera L. [•] Significant correlation between SSR-based data of grapes and wine phenolics. [ABSTRACT FROM AUTHOR]

Gene based microsatellite markers are becoming more popular as compared to traditional random genomic microsatellite markers due to rapid and inexpensive method of isolation and their cross species portability. The present study documents occurrence of microsatellites in the transcriptome of seabuckthorn, a plant with immense medicinal, nutritional and ecological value. De novo assembly of over 80 million high quality short reads generated by high throughput next generation sequencing yielded 88297 putative unigenes. Of these, 7.69 % unigenes harbored microsatellite repeats with an average of one microsatellite per 6.704 Kb transcriptome. Dinucleotide repeats were most abundant followed by trinucleotide repeats. Microsatellites were densely populated in coding regions followed by 3′ and 5′ untranslated regions. AG and AAG type repeats were most frequently represented. Of the microsatellite positive unigenes, 48.81 % could be assigned gene ontology (GO) terms in order to assess associations between microsatellite containing unigenes and biological role of known genes. Utility of unigene specific microsatellites was assessed on the basis of polymorphism(s) detected in 18 seabuckthorn collections from Leh (India) using a set of randomly selected 25 unigene specific microsatellites. The findings presented here are likely to find immense use in future breeding and molecular biology research projects in seabuckthorn aiming at its overall development as a crop. [ABSTRACT FROM AUTHOR]

Abstract: We have identified a large number of microsatellites from Pseudosciaena crocea, an economically important fish species in China, by taking advantage of the Roche 454 sequencing technology. A total of 2535 simple sequence repeats (SSR) motifs were identified among which dinucleotides were the most frequent (59.61%), followed by tetra- (29.94%) and trinucleotides (7.06%). Among dinucleotide repeats, the most frequent repeats were AC motifs, accounting for 79.15% of the total. AAT (36.31%) and TCTA (39.66%) motifs were the most frequent of the tri- and tetranucleotide motifs, respectively. A total of 1068 microsatellite loci had flanking sequences suitable for setting primers for polymerase chain reactions (PCR). To verify the identified SSRs, 40 primer pairs were randomly selected for PCR. In total, 32 primer sets (80.00%) produced strong PCR products matching their expected sizes, and 27 (67.50%) were polymorphic. In an analysis of 34 wild individuals from the Zhangzhou Sea area (Fujian Province, China) with the 27 primer sets, the number of alleles per locus ranged from 5 to 11 and the mean allelic richness was 6.74. Linkage disequilibrium was not observed between any pair of loci, indicating that the markers were independent. A Hardy–Weinberg equilibrium test revealed significant deviation in 6 of the 27 microsatellite loci after sequential Bonferroni corrections. This microsatellite isolation method is cost- and time-effective in comparison to traditional approaches. [Copyright &y& Elsevier]

In Vanuatu, an oceanic archipelago located in south-west Pacific, taro ( Colocasia esculenta (L.) Schott) is one of the staple crops. An eco-geographical survey of its genetic resources was conducted in ten villages, each located on a different island. A sample of 344 landraces referred as the National Sample (NS) was collected. Its genetic diversity was assessed using nine microsatellites markers and then was compared with an International Core Sample (ICS) that was previously distributed in the ten villages of the study in order to test the geographical distribution of allelic diversity as an effective mean for the on-farm conservation of root crops. The ICS was composed of 41 accessions, including 23 originating from South-East Asia. The molecular dataset revealed in the NS (1) 324 distinct multilocus genotypes, (2) six genetic clusters mainly differentiated by rare alleles, (3) a geographical structure of the genetic resources of taro based, within each village, on the dominance of one or two of these clusters rather that their exclusivity, and (4) an analogy between the patterns of dominant clusters between villages and the past and present social networks. In addition, accessions from the ICS revealed 52 new alleles. Based on these findings, we formulate hypotheses regarding the processes involved in the genetic diversification of taro in Vanuatu. We also discuss the use of this set of microsatellite markers along with the molecular dataset obtained from this study as effective tools to monitor the diversity and evolution of taro in the future. [ABSTRACT FROM AUTHOR]

In this study, twelve polymorphic microsatellite markers were developed for Coilia ectenes (synonym C. nasus). In a sample of 30 C. ectenes individuals in a Wuhan population from Yangtze River, a total of 78 alleles were detected, and the number of alleles per locus ranged from 3 to 12. The observed and expected heterozygosities ranged from 0.100 to 1.000 and from 0.098 to 0.899, respectively. Six loci significantly deviated from the Hardy-Weinberg equilibrium after Bonferroni correction ( P < 0.004), and no significant linkage disequilibrium between pairs of loci was found. The applicability of these markers in a closely related species, C. mystus, was evaluated by cross-species amplification. These microsatellite markers will be useful in studies on population genetics, conservation genetics, and fishery management and in the construction of genetic linkage maps of C. ectenes and C. mystus. [ABSTRACT FROM AUTHOR]

The significance of the taxonomic distinction of two species of Blackbutt was studied by analysing patterns of genetic (microsatellite markers; n = 13) and phenetic (capsule morphology) differentiation. Analysis of genetic structure using a Bayesian modelling approach on range-wide samples of both taxa (n = 457) showed the major division was within the more widely distributed species, Eucalyptus pilularis, and not aligned with taxonomy. Comparisons of intra- and inter-taxon genetic differentiation in paired-samples of taxa from each of four locations spanning the distribution of the more restricted E. pyrocarpa, showed that around twice as much variation was found among locations within taxa, than between taxa. Despite the lack of differentiation at effectively neutral microsatellite markers, significant phenetic differences (including capsule size) were evident between taxa at most sites. A landscape mosaic of taxa, coincident with changes in elevation, vegetation and soil types, suggested some phenetic differences were probably adaptive and spatial differentiation was stabilised by environmental factors. An absence of morphological intermediates and a lack of correlation in the rankings of locus inter-taxon differentiation (Phi) across locations, was consistent with parapatric origins for E. pyrocarpa. We conclude the taxa are at the lower end of the speciation spectrum and might best be viewed as ecotypes, divergent in evolutionary potential, but with genomes broadly permeable to inter-taxa gene flow. Gene exchange between plantings of E. pilularis and nearby E. pyrocarpa forest is likely as the two taxa appear to have few barriers to reproduction. [ABSTRACT FROM AUTHOR]

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Here we report development and characterization of 14 polymorphic microsatellite loci from Sebastes schlegel. Polymorphism at these loci revealed from 3 to 23 alleles. The observed heterozygosity ranged from 0.34 to 1.00, and the expected heterozygosity ranged from 0.31 to 0.95. No linkage disequibrium was found. Two loci were significantly deviated from HWE (P<0.01). The 14 loci were also surveyed in four other Sebastes species and 12 loci successfully amplified, where allelic diversity ranged from highly polymorphic to monomorphic. These results demonstrate these microsatellite markers can be used for the study of intra- and inter-specific genetic diversity. [ABSTRACT FROM AUTHOR]

The population of grape (Vitis vinifera L), commonly cultivated in India, shows a wide range of ripening periods and fruit quality and is an unexploited resource for breeding programs. The main purpose of this study was to fingerprint these accessions and to construct a molecular database including the cultivars commonly grown in India. A total of 42 genotypes were analyzed using seven microsatellite simple sequence repeat (SSR) markers and their main morphological and agronomic characteristics were compared. A total of 45 alleles in all 42 genotypes were obtained with 7 primers with an average number of 6.4 alleles per locus. The dissimilarity matrix showed that a maximum of 110 units was obtained between the genotypes “Convent Large Black” and “Arka Hans,” while a minimum dissimilarity if 37 units were obtained between the genotypes “Anab-e-Shahi” and “Dilkhush.” In the dendrogram the microsatellite segregated the genotypes into two clusters (A and B) at 476 units with two subclusters each. The subclusters grouped genotypes predominantly as A1 with seeded fruits, A2 with seedless fruits, B1 with pigmented and seedless fruits, and B2 with colorless and seeded fruits. The use of seven polymorphic microsatellite markers and the level of genetic variability detected within Indian grapevine germplasm suggested that this is a reliable, efficient, and effective marker system that can be used for diversity analysis and subsequently in crop improvement programs. [ABSTRACT FROM AUTHOR]

Abstract: Genetic parameters for somatic growth rate in sea bass were estimated in two experiments where 27 (year-class 1997) to 30 (year-class 1998) families of sea bass (3 dams mated with 9–10 sires according to a full factorial design) were raised mixed in the same tanks starting shortly before hatching (48 h post fertilization). Trials were performed under two temperature (experiment 1, 1997: group high temperature (HT) and group low temperature (LT)) and two density regimes (experiment 2, 1998: group high density (HD) and group low density (LD)) with a subset of the mating design (18 families) being reproduced in the two experiments. All the fish were genotyped at 3–6 microsatellite loci which allowed them to be assigned to the individual breeders used in the mating design. Heritability of (log-transformed) body weight was estimated from the sire component of variance at a mean size of 20.0–21.6 cm (standard length (SL)) using a simple additive model and a restricted maximum likelihood algorithm. Estimates were 0.31±0.12 (group HT and group HD), 0.50±0.19 (group low temperature (LT)) and 0.60±0.22 (group low density (LD)), while an overall estimate using data from both year-classes was 0.29±0.13 indicating an important additive genetic component in growth rate of the sea bass in all conditions. Correlations of the estimated breeding values (EBV) of the sires between treatments and years were moderate (range=0.01–0.51), suggesting the occurrence of genotype×environment effects. Growth was followed from the age of 341 days post fertilization (dpf) (mean SL±S.D.=16.0±1.9 cm) to the age of 818 dpf (mean SL=32.6±3.1 cm) in the HT group. h 2 estimates tended to increase with the age of the fish (0.21±0.10 at 341 dpf to 0.56±0.20 at 818 dpf, r values=0.90, P =0.04). Genetic correlations among log weights recorded at various ages were high (range=0.61–0.85, average=0.70), indicating stability of the genetic values throughout the growth phase sampled and that growth as estimated at the earliest stage examined (341 dpf, 90 g) can be used as a predictor of later progeny growth (until 818 dpf, 737 g). [Copyright &y& Elsevier]

The effects of rearing density and size grading on sex ratios in 30 families of sea bass reared in the same tank from the fertilization stage onwards were investigated. Two extreme density treatments (high versus low) were applied in quadruplicates throughout the labile period for sex determination. An excess of males (88%) was found in all groups. Growth was faster under low density from 49 to 191 days post fertilization (p.f.) (27–10% relative difference in length) and was then equivalent between the two groups until the end of the treatments (414 days p.f.). Density had no effect on sex ratio, suggesting that the high densities usually applied in aquaculture are not involved in the systematic excess of males reported in farmed populations. The fish were genotyped at three to six microsatellite loci. This allowed them to be assigned to the individual breeders used in the mating design. The percentage of females was significantly influenced by both the dam and the sire, highlighting the existence of genetic variation of sex ratio.Repeated size grading performed from 84 to 199 days p.f. had no effect on the sex ratio of the overall population studied showing that sex determination had not been affected by the treatment. However, the highest percentages of females were found in the lead classes from 84 days p.f. Most of the fish in this lead group were descended from one dam and the percentage of females found in the individual families were higher in this class than in the non-graded group. These results show that females start growing faster than males long before morphological sexual differentiation occurs. [Copyright &y& Elsevier]

Poecilia vivipara is a small fish found throughout the coastal lowlands of South America. We report the isolation and characterization of 25 microsatellite loci in this tropical fish. In 24 individuals from two populations, 18 loci were polymorphic. The loci had 2-12 alleles, expected heterozygosities of 0.194-0.836, observed heterozygosities of 0.208-0.792, and discriminatory powers of 0.202-0.872. Four loci showed significant deviations from Hardy-Weinberg equilibrium. The microsatellite loci will be useful for investigating genetic diversity and population genetic structure, which will contribute to the development of efficient conservation programs for coastal lowlands where P. vivipara occurs. [ABSTRACT FROM AUTHOR]

The cattle egret ( Bubulcus ibis) is an invasive species across American continent. Understanding the population genetics of this species is necessary for population monitoring and the development of effective management strategies. Here we present 11 microsatellite loci isolated from B. ibis sampled in the southeastern Brazil. Of the 32 primer pairs that were tested on samples from 35 individuals, 11 (34 %) were polymorphic for population-level analyses. The number of alleles per locus ranged from 2 to 4. The expected heterozygosity ranged from 0.083 to 0.561. All loci conformed to Hardy-Weinberg and linkage equilibrium. Cross-amplification was successful for 7 of the 11 B. ibis microsatellite loci that were tested in samples from eight Ardeidae species. These markers are the first published microsatellites for B. ibis and they will be useful to understand the population structure and colonization of the American continent by this species. [ABSTRACT FROM AUTHOR]

The present study reports isolation and characterization of 11 polymorphic microsatellite markers for Nycticorax nycticorax. A total of 82 alleles were detected with an average of 7.5 alleles per locus. The observed heterozygosity (HO) ranged from 0.25 to 1.00, and the expected heterozygosity (HE) ranged from 0.51 to 0.88. Analyses revealed no evidence for Linkage disequilibrium between any two loci, and only one locus was significantly deviated from HWE with the estimation of exact P values by the Markov chain method (P<0.001). The 11 loci were successfully amplified in 11 other Ardeidae species. These results demonstrate these markers can be used for the study of intra- and inter-specific genetic diversity. [ABSTRACT FROM AUTHOR]

This work reports the characterization of 11 polymorphic microsatellite loci in section Caulorrhizae. The primer pairs were designed from Arachis pintoi and showed full transferability to Arachis repens species . These new markers were used to evaluate the genetic diversity in germplasm (accessions and cultivars) of section Caulorrhizae. This new set of markers detected greater gene diversity than morphological and molecular markers such as AFLP (amplified fragment length polymorphism) and RAPD (rapid analysis of polymorphic DNA) previously used in this germplasm. [ABSTRACT FROM AUTHOR]

The largest population of goats (62%) in Ecuador is in the dry forest region in the south of the country. A Creole goat, named "Chusca Lojana", has adapted to the dry forest region where environmental conditions are warm-dry, with sparse vegetation. Knowledge of the genetic information of the Creole goat is important to determine intra-racial diversity, the degree of genetic distance among other breeds of goats, and the possible substructure of the population, which is valuable for the conservation of such a species' genetic resources. A total of 145 samples of the Creole goat was taken from the four biotypes previously identified. Genetic analyses were performed using 38 microsatellites recommended for studies of goat genetic diversity (FAO-ISAG). The results of within-breed genetic diversity showed a mean number of alleles per locus (MNA) of 8, an effective number of alleles (Ae) of 4.3, an expected heterozygosity (He) of 0.71, an observed heterozygosity (Ho) of 0.63, polymorphic information content (PIC) of 0.67, and an F IS value of 0.11. Between-breed genetic diversity among 43 goat populations (native of Spain, American Creole, Europeans, and Africans) showed the following values: F IS = 0.087, F IT = 0.176, and F ST = 0.098. Regarding the analysis of the population structure, the results showed that the Creole Chusca Lojana goat population is homogeneous and no genetic separation was observed between the different biotypes (F ST = 0.0073). In conclusion, the Chusca Lojana goat has a high genetic diversity, without exhibiting a genetic substructure. Therefore, it should be considered as a distinct population because crossbreeding with other breeds was not detected., Competing Interests: The authors declare no conflict of interest.

Simple Summary: In Ecuador, the production of Ecuadorian Creole chicken is of crucial importance in the economy and for the nutrition of families. These chickens represent a focal point in scientific research for three main reasons: (1) they are an unknown genetic resource derived from 500 years of environmental and human selection and represent an important reservoir of genetic variability and adaptability; (2) Ecuadorian Creole chicken production is normally familiar, in a marginal dimension, and it is an important source of economic input for medium–low income communities; and (3) being a local genetic resource, it is available to local communities without intermediary international enterprises and represents the starting point for food sovereignty. We aimed to measure the level of genetic diversity and its phylogenetic position compared with other outgroup breeds using information from microsatellite and mitochondrial markers. Our results showed that these chicken populations represent a great reservoir of genetic variability; however, the genetic fragmentation owing to the high geographical diversity of the country could compromise the conservation status and, therefore, the establishment of an official breeding program is needed for the conservation and valuation of these avian populations, with this genetic characterization being a first step. Latin American Creole chickens are generally not characterized; this is the case in Ecuador, where the lack of scientific information is contributing to their extinction. Here, we developed a characterization of the genetic resources of Ecuadorian chickens located in three continental agroecosystems (Pacific coastal, Andean, and Amazonian). Blood samples of 234 unrelated animals were collected in six provinces across Ecuador: Bolívar, Chimborazo, Cotopaxi, Guayas, Morona Santiago, and Tungurahua, in order to perform a genetic characterization and population structure assessment using the AVIANDIV project microsatellites panel (30 loci) and D-loop sequences of mitochondrial DNA and comparing with reference data from other breeds or genetic lines. The results indicate that Ecuadorian Creole chickens are the result of the admixture of different genetic groups that occurred during the last five centuries. While the influence of South Spanish breeds is demonstrated in the colonial age, genetic relationships with other breeds (Leghorn, Spanish fighter cock) cannot be discarded. The geographical configuration of the country and extreme climate variability have influenced the genetic isolation of groups constituting a homogeneous genetic status into the whole population. This is not only a source of genetic variation, but also a critical point because genetic drift produces a loss of genetic variants. [ABSTRACT FROM AUTHOR]