Analysis of Endangered Andalusian Black Cattle (Negra Andaluza) Reveals Genetic Reservoir for Bovine Black Trunk.

This comprehensive study on the Andalusian Black cattle breed reveals a substantial population decline, with the average herd size decreasing significantly from 305.54 to 88.28 animals per herd. This decline is primarily attributed to agricultural changes and the introduction of foreign meat-focused breeds. The male-to-female ratio shift is noteworthy, with more cows than bulls, impacting selection intensity for both genders. Inbreeding levels, though relatively low historically (5.94%) and currently (7.23%), raise concerns as 37.08% historically and 48.82% currently of the animals exhibit inbreeding. Positive assortative mating is evident, reflected by the increasing non-random mating coefficient (α). Key ancestors play a crucial role in shaping genetic diversity, with one ancestor significantly influencing the current genetic pool and the top 10 ancestors contributing substantially. Breed maintains a conservation index of 2.75, indicating relatively high genetic diversity. Recent conservation efforts have led to an increase in registered animals. The Cañadas Reales, historical transhumance routes, may have contributed to genetic connections among provinces. Challenges include the historical bottleneck, demographic changes, and potential impacts from reproductive practices. The Andalusian Black breed's conservation necessitates ongoing efforts in genealogical registration, targeted breeding programs, and collaborative initiatives to address the observed demographic shifts and ensure sustainable genetic diversity.

Assembly and analysis of the chloroplast genome of Amorphophallus kachinensis Engler & Gehrmann (Araceae) from Southwestern China: implications for conservation and utilization.

Konjac glucomannan consists of D-mannose and D-glucose units and is a hydrocolloid obtained from the corm of Amorphophallus species. Due to its bioactive properties, biodegradability, and hydrophilic ability, glucomannan is widely used in the fields of food, medicine, and industry. Amorphophallus species have been cultivated as cash crops in many Asian countries. Amorphophallus kachinensis Engler & Gehrmann 1911 is naturally distributed in southwestern China, Laos, and northern Thailand. To help the genetic assessment and conservation of this species, the first chloroplast genome of A. kachinensis was sequenced on the Illumina sequencing platform. We assembled the chloroplast genome using the software GetOrganelle and annotated the genome by Geseq and Cpgavas 2. The assembled chloroplast genome was 173,330 bp long, and the average GC content was 35% (GenBank accession number: PP072244). The chloroplast genome of A. kachinensis contained one large single copy, one small single copy, and two inverted repeats, with lengths of 92,030 bp, 15,118 bp, 33,091 bp, and 33,091 bp, respectively. We successfully annotated 132 genes across the genome, which was consistent with other Amorphophallus species. The phylogenetic tree indicates a sub-divergence in the Amorphophallus genus with two main genetic groups detected among eight species. The two genetic groups should be treated as distinct evolutionarily significant units when making conservation strategies. Our study enriched the chloroplast genome resources of the Amorphophallus genus and could help future phylogeographic studies, protection, and utilization of wild resources.

Genetic impact of external Targhee sires at the U.S. Sheep Experiment Station: a case study of introgression.

Sheep breeders requested that the U.S. Sheep Experiment Station (USSES) to participate in national genetic evaluation through the National Sheep Improvement Program (NSIP). The reasons included the need for (1) a comparison of the productivity of industry and United States Department of Agriculture (USDA) lines, (2) transparency of USDA flocks, (3) genetic ties for NSIP by sampling of industry flocks, and (4) development of premium genetic lines for public release. In response, USSES began to incorporate external sires from NSIP participating flocks into the USSES Targhee flock. Our objective, based on a pedigree analysis, was to test if introgression of external genetics into the flock was achieved. The pedigree included 13,189 animals with mean maximum generations, mean complete generations, and mean equivalent complete generations of 4.2, 1.8, and 2.6, respectively. The mean generation interval was 3.1 yr. The reference population was defined as lambs born from 2021 to 2023 (n = 792). Two additional populations were defined as the current mature ewe flock (n = 123) and the current mature rams (n = 14). The Genetic Conservation Index averaged 7.7 for the full population and 25.7 for the reference population. Overall inbreeding was 0.003 for the full population and 0.006 for the reference population. The rate of inbreeding was 0.0003 per generation. Average relatedness was 0.015 for the full population and 0.018 for the reference population. The effective number of founders, effective number of ancestors, and founder genome equivalents contributing to the reference population were 60, 39, and 19.1, respectively. The ratio of the effective number of founders to the effective number of ancestors was 1.5, indicating the presence of genetic bottlenecks. Measures of effective population size ranged from 102 to 547. Of the 704 offspring produced by external sires, 17 ram lambs and 132 ewe lambs were retained for breeding. The USSES sires produced 299 offspring with 2 ram lambs and 51 ewe lambs retained. Incorporating external sires resulted in a cumulative percentage of genetic variance of 48.8, 49.1, and 44.2 of external genetics for the reference population, current mature ewe flock, and current mature rams, respectively. Stakeholder needs were addressed by introgression of external sires and participation in NSIP, but future selection practices need to be modified to maintain a minimum of 50% USSES core genetics in the flock.

Estimates of heterozygosity from single nucleotide polymorphism markers are context-dependent and often wrong.

Genetic diversity is frequently described using heterozygosity, particularly in a conservation context. Often, it is estimated using single nucleotide polymorphisms (SNPs); however, it has been shown that heterozygosity values calculated from SNPs can be biased by both study design and filtering parameters. Though solutions have been proposed to address these issues, our own work has found them to be inadequate in some circumstances. Here, we aimed to improve the reliability and comparability of heterozygosity estimates, specifically by investigating how sample size and missing data thresholds influenced the calculation of autosomal heterozygosity (heterozygosity calculated from across the genome, i.e. fixed and variable sites). We also explored how the standard practice of tri- and tetra-allelic site exclusion could bias heterozygosity estimates and influence eventual conclusions relating to genetic diversity. Across three distinct taxa (a frog, Litoria rubella; a tree, Eucalyptus microcarpa; and a grasshopper, Keyacris scurra), we found heterozygosity estimates to be meaningfully affected by sample size and missing data thresholds, partly due to the exclusion of tri- and tetra-allelic sites. These biases were inconsistent both between species and populations, with more diverse populations tending to have their estimates more severely affected, thus having potential to dramatically alter interpretations of genetic diversity. We propose a modified framework for calculating heterozygosity that reduces bias and improves the utility of heterozygosity as a measure of genetic diversity, whilst also highlighting the need for existing population genetic pipelines to be adjusted such that tri- and tetra-allelic sites be included in calculations.

Population Structure and Genetic Diversity of the Toona ciliata (Meliaceae) Complex Assayed with Chloroplast DNA Markers.

Toona ciliata is a deciduous or semi-deciduous tree species and belongs to the Toona genus of the Meliaceae family. Owing to low natural regeneration and over-exploitation, the species is listed as an endangered species at level II in China and its conservation has received increasing concern. Here, we sampled 447 individuals from 29 populations across the range-wide distribution of the T. ciliata complex in China and assessed their genetic variation using two chloroplast DNA markers. The results showed that the overall haplotype diversity and nucleotide diversity per site were high at h = 0.9767 and π = 0.0303 for the psbA-trnH fragment and h= 0.8999 and π = 0.0189 for the trnL-trnL fragment. Phylogenetic analysis supported the division of the natural distribution of T. ciliata complex into western and eastern regions. The genetic diversity was higher in the western region than in the eastern region, showing significant phylogeographic structure. Genetic differentiation among populations was moderate (Φst=42.87%), and the effects of isolation by distance (IBD) were significant. A neutrality test and mismatch distribution analysis indicated that the distribution of the T. ciliata complex generally did not expand, although a few local populations could likely expand after bottleneck effects. The overall results were complementary to and consolidated previous studies using mitochondrial and nuclear DNA markers. We finally discussed strategies for the genetic conservation of the T. ciliata complex.

Assessing the phylogenetic relationship among varieties of Toona ciliata (Meliaceae) in sympatry with chloroplast genomes.

Toona ciliata is an endangered species due to over-cutting and low natural regeneration in China. Its genetic conservation is of an increasing concern. However, several varieties are recognized according to the leaf and flower traits, which complicates genetic conservation of T. ciliata. Here, we sequenced the whole chloroplast genome sequences of three samples for each of four varieties (T. ciliata var. ciliata, T. ciliata var. yunnanensis, T. ciliata var. pubescens, and T. ciliata var. henryi) in sympatry and assessed their phylogenetic relationship at a fine spatial scale. The four varieties had genome sizes ranged from 159,546 to 159,617 bp and had small variations in genome structure. Phylogenomic analysis indicated that the four varieties were genetically well-mixed in branch groups. Genetic diversity from the whole chloroplast genome sequences of 12 samples was low among varieties (average π = 0.0003). Besides, we investigated genetic variation of 58 samples of the four varieties in sympatry using two markers (psaA and trnL-trnF) and showed that genetic differentiation was generally insignificant among varieties (Ф st = 0%-5%). Purifying selection occurred in all protein-coding genes except for the ycf2 gene that was under weak positive selection. Most amino acid sites in all protein-coding genes were under purifying selection except for a few sites that were under positive selection. The chloroplast genome-based phylogeny did not support the morphology-based classification. The overall results implicated that a conservation strategy based on the T. ciliata complex rather than on intraspecific taxon was more appropriate.

Comparative transcriptome analysis reveals deep molecular landscapes in stony coral Montipora clade.

Introduction: Coral reefs, among the most invaluable ecosystems in the world, face escalating threats from climate change and anthropogenic activities. To decipher the genetic underpinnings of coral adaptation and resilience, we undertook comprehensive transcriptome profiling of two emblematic coral species, Montipora foliosa and Montipora capricornis, leveraging PacBio Iso-Seq technology. These species were strategically selected for their ecological significance and their taxonomic proximity within the Anthozoa class. Methods: Our study encompassed the generation of pristine transcriptomes, followed by thorough functional annotation via diverse databases. Subsequently, we quantified transcript abundance and scrutinized gene expression patterns, revealing notable distinctions between the two species. Results: Intriguingly, shared orthologous genes were identified across a spectrum of coral species, highlighting a substantial genetic conservation within scleractinian corals. Importantly, a subset of genes, integral to biomineralization processes, emerged as exclusive to scleractinian corals, shedding light on their intricate evolutionary history. Furthermore, we discerned pronounced upregulation of genes linked to immunity, stress response, and oxidative-reduction processes in M. foliosa relative to M. capricornis. These findings hint at the presence of more robust mechanisms in M. foliosa for maintaining internal equilibrium and effectively navigating external challenges, underpinning its potential ecological advantage. Beyond elucidating genetic adaptation in corals, our research underscores the urgency of preserving genetic diversity within coral populations. Discussion: These insights hold promise for informed conservation strategies aimed at safeguarding these imperiled ecosystems, bearing ecological and economic significance. In synthesis, our study seamlessly integrates genomic inquiry with ecological relevance, bridging the gap between molecular insights and the imperative to conserve coral reefs in the face of mounting threats.

A gene bank's collection of genetic diversity among minor chicken breeds.

Genetic differences among heritage or fancier breeds of chickens have not been quantified in the United States. Gene banks collecting germplasm for conserving these breeds need this information as do breeders and companies raising them. Our goal was to evaluate genetic diversity of 10 heritage/fancier chicken breeds that are a component of the national collection and to use this information to establish a baseline of their genetic diversity and future conservation efforts. Breeds could be broadly classified as European, Asian, Mediterranean, and United States (US) in origin. The US breeds were composite breeds developed between the 1849 and 1935. Animals (n = 24-31 per breed) were sampled for DNA analysis from 2 or 3 hatcheries per breed and a total of 8 hatcheries. The hatcheries were assumed to maintain and breed their own populations of the studied breeds. Effective population sizes ranged from 47 to 145 and used to estimate probabilities of extinction for a 50-generation timeline. It was determined that Crevecoeur and Aseel had a probability of extinction that exceeded 40%, the remaining 8 breeds had probabilities of <28%. ADMIXTURE analysis indicated the minimal CV corresponded to 9 populations. In that analysis New Hampshire and Rhode Island Red were classified as the same population, which was not unusual given that New Hampshire was developed as a subpopulation of Rhode Island Red. Crevecoeur and Buttercup were the 2 most genetically divergent breeds based on pairwise Fst among the breeds and principal component analysis, which was supported by the ADMIXTURE results. Inbreeding coefficients computed from genomic information was lowest for Crevecoeur, Rhode Island Red, Buttercup, and Andalusian (0.8-2.6%), while New Hampshire, Buckeye, and Aseel were highest (12.8-14.3%). Within breed Fst among hatcheries supplying animals for sampling generally indicated a genetic structure was present on a breed-by-breed basis. Genetic relationships within hatchery were also computed for each breed. Several of the hatcheries had sent samples that suggested genetic relationships as high as half-sibs while several others had genetic relationships closer to first cousins. We conclude that the chicken breeds evaluated have substantial genetic variability within the in situ populations and the gene bank has captured this diversity for future use.

Preserving Porcine Genetics: A Simple and Effective Method for On-Site Cryopreservation of Ear Tissue Using Direct Cover Vitrification.

Cell cryopreservation is widely used for porcine genetic conservation; however, isolating and freezing primary cells in farms without adequate experimental equipment and environment poses a significant challenge. Therefore, it is necessary to establish a quick and simple method to freeze tissues on-site, which can be used for deriving primary fibroblasts when needed to achieve porcine genetic conservation. In this study, we explored a suitable approach for porcine ear tissue cryopreservation. The porcine ear tissues were cut into strips and frozen by direct cover vitrification (DCV) in the cryoprotectant solution with 15% EG, 15% DMSO and 0.1 M trehalose. Histological analysis and ultrastructural evaluation revealed that thawed tissues had normal tissue structure. More importantly, viable fibroblasts could be derived from these tissues frozen in liquid nitrogen for up to 6 months. Cells derived from thawed tissues did not show any cell apoptosis, had normal karyotypes and could be used for nuclear transfer. These results suggest that this quick and simple ear tissue cryopreservation method can be applied for porcine genetic conservation, especially in the face of a deadly emerging disease in pigs.

Conservation of vaccine antigen sequences encoded by sequenced strains of Streptococcus equi subsp. equi.

BACKGROUND: Streptococcus equi subspecies equi (S equi) is the cause of Strangles, one of the most prevalent diseases of horses worldwide. Variation within the immunodominant SeM protein has been documented, but a new eight-component fusion protein vaccine, Strangvac, does not contain live S equi or SeM and conservation of the antigens it contains have not been reported. OBJECTIVE: To define the diversity of the eight Strangvac antigens across a diverse S equi population. STUDY DESIGN: Genomic description. METHODS: Antigen sequences from the genomes of 759 S equi isolates from 19 countries, recovered between 1955 and 2018, were analysed. Predicted amino acid sequences in the antigen fragments of SEQ0256(Eq5), SEQ0402(Eq8), SEQ0721(EAG), SEQ0855(SclF), SEQ0935(CNE), SEQ0999(IdeE), SEQ1817(SclI) and SEQ2101(SclC) in Strangvac and SeM were extracted from the 759 assembled genomes and compared. RESULTS: The predicted amino acid sequences of SclC, SclI and IdeE were identical across all 759 genomes. CNE was truncated in the genome of five (0.7%) isolates. SclF was absent from one genome and another encoded a single amino acid substitution. EAG was truncated in two genomes. Eq5 was truncated in four genomes and 123 genomes encoded a single amino acid substitution. Eq8 was truncated in three genomes, one genome encoded four amino acid substitutions and 398 genomes encoded a single amino acid substitution at the final amino acid of the Eq8 antigen fragment. Therefore, at least 1579 (99.9%) of 1580 amino acids in Strangvac were identical in 743 (97.9%) genomes, and all genomes encoded identical amino acid sequences for at least six of the eight Strangvac antigens. MAIN LIMITATIONS: Three hundred and seven (40.4%) isolates in this study were recovered from horses in the UK. CONCLUSIONS: The predicted amino acid sequences of antigens in Strangvac were highly conserved across this collection of S equi.

Phylogeography of Amygdalus mongolica in relation to Quaternary climatic aridification and oscillations in northwestern China.

Quaternary period geological events and climatic oscillations significantly affect the geographic structure and genetic diversity of species distribution in arid northwestern China. Amygdalus mongolica is a relict and endangered shrub that occurs primarily in arid areas of northwestern China. Based on variation patterns present at three cpDNA regions (psbK-psbI, trnL-trnF and trnV) and in one nDNA sequence (ITS1-ITS4) in 174 individuals representing 15 populations, the spatial genetic structure and demographic history of A. mongolica was examined across its entire geographic range. The 17 different haplotypes and 10 ribotypes showed two lineages, distributed across the Western (Mazong Mountains, Hexi Corridor, and Alxa Left Banner) and Eastern regions (Urad Houqi, Yinshan Mountains, Urad Zhongqi, and Daqing Mountains) according to the median-joining network and the BI (Bayesian inference) and ML (Maximum likelihood) trees. AMOVA analysis demonstrated that over 65% of the observed genetic variation was related to this lineage split. The expansions of the Ulanbuhe and Tengger deserts and the eastward extension of the Yinshan Mountains since the Quaternary period likely interrupted gene flow and triggered the observed divergence in the two allopatric regions; arid landscape fragmentation accompanied by local environmental heterogeneity further increased local adaptive differentiation between the Western and Eastern groups. Based on the evidence from phylogeographical patterns and the distribution of genetic variation, A. mongolica distributed in the eastern and western regions are speculated to have experienced eastward migration along the southern slopes of the Lang Mountains and westward migration along the margins of the Ulanbuhe and Tengger deserts to the Hexi Corridor, respectively. For setting a conservation management plan, it is recommended that the south slopes of the Lang Mountains and northern Helan Mountains be identified as the two primary conservation areas, as they have high genetic variation and habitats that are more suitable.

Process of Introduction of Australian Braford Cattle to South America: Configuration of Population Structure and Genetic Diversity Evolution.

This study analyzes the evolution of the population structure and genetic diversity of Braford cattle in South America from 1949 to 2019 to suggest effective strategies for breeding in the future. The percentage of bulls historically increased. The average generational interval decreased to 11.78 years for the current population. Average inbreeding (F) and coancestry (C) are low and show a historically increasing trend (0.001% to 0.002%, respectively). The degree of nonrandom mating (α) increased from -0.0001 to 0.0001 denoting a change in the trend to mate similar individuals. The average relatedness coefficient (ΔR) increased in the current period from 0.002% to 0.004%. A single ancestor explained 4.55% to 7.22% of the population's gene pool. While the effective population size based on the individual inbreeding rate (NeFi) was 462.963, when based on the individual coancestry rate (NeCi), it was 420.168. Genetic diversity loss is small and mainly ascribed to bottlenecks (0.12%) and to unequal contributions of the founders (0.02%). Even if adequate levels of diversity can be found, practices that consider the overuse of individual bulls (conditioned by nature or not), could lead to a long-term reduction in diversity. The present results permit tailoring genetic management strategies that are perfectly adapted to the needs that the population demands internationally.

Developmental potential of cryopreserved gonadal germ cells from 7-day-old chick embryos recovered using the PBS(-) method.

1. A series of experiments were conducted to examine the developmental potential of cryopreserved gonadal germ cells (GGCs) recovered from both males and females on embryo day 7 (7 d-GGCs) using the PBS(-) method. Germline chimeras were produced by transferring 200 frozen/unfrozen 7 d-GGCs recovered from female/male Rhode Island Red (RIR) embryos into the dorsal aorta of 2-day-old female and male white leghorn (WL) embryos.2. Germ-cell recipient embryos were hatched and raised to sexual maturity and progeny testing was conducted by mating with RIR of the opposite sex. Brown-feathered progeny chicks were hatched in all eight possible progeny testing combinations, except for male GGC recipients produced by transferring female GGCs. Furthermore, brown-feathered progeny chicks were hatched when frozen-thawed sperm from male germline chimeras, produced by transferring unfrozen 7d-GGCs, were inseminated in normal female RIR and female WL germline chimeras.3. The results indicated that cryopreserved female/male GGCs from 7-day-old chick embryos, recovered using the PBS(-) method, were fully capable of developing into normal spermatozoa and ova in the gonad of recipient embryos under appropriate GGC donor/recipient combinations.

Evaluation of a panel of microsatellite markers to study their applications in Serrapinnus notomelas and to reveal the genetic diversity in Hyphessobrycon eques.

Jewel tetra (Hyphessobrycon eques) is a freshwater fish found in several rivers and basins in South America. The present study is the first study to create a panel of microsatellite markers for detecting genetic diversity in H. eques and evaluating the application of these markers in Serrapinnus notomelas. In total, 44 individuals were genotyped from the natural (WIL, n = 20) and stock in captivity (CAP, n = 24) population. Moreover, 19 microsatellite markers were obtained, of which only 8 loci presented a high degree polymorphism. In total, 45 alleles were detected, ranging from 126 bp (Hype2G2) to 420 bp (Hype2E2). The Hardy-Weinberg equilibrium (p < 0.05) revealed significant difference in one locus in WIL (Hype1G4) and three loci in CAP (Hype1F4, Hype2C3, and Hype2G2). Null alleles (p < 0.05) were present in only one locus (Hype1G4). The WIL and CAP populations revealed high genetic diversity during FST analysis. The cross-amplification test for S. notomelas revealed that only two loci (Hype2C3 and Hype2G2B) presented satisfactory transferability results. The developed microsatellite primers will be useful in studying the genetic diversity and population structure of H. eques in wild populations and fish farms in the Brazilian and other South American basins.

Evaluation of genetic diversity and population structure in four indigenous duck breeds in Vietnam.

This study characterized genetic diversity and population structure of four indigenous Vietnamese duck breeds and an exotic breed for setting the conservation priority. A total of 200 samples from four duck breeds (Sincheng, Minhhuong, Muongchieng and Bauben) and an exotic breed (Supermeat) were genotyped for fifteen microsatellite markers. The average number of alleles per locus was 14.07. A moderate genetic diversity was observed for indigenous breeds as mean of observed and expected heterozygosity as Ho = 0.50 and He = 0.57, respectively. The Bauben had the lowest values of Ho (0.41) and He (0.48) while Sincheng had the highest values of Ho (0.6) and He (0.69), respectively. The inbreeding coefficients (FIS) ranged from 0.12 to 0.16, and all breeds were significantly under heterozygote deficit. Nei's genetic distance was the shortest between Minhhuong and Muongkhieng. The discriminant analysis of principal components of studied breeds resulted in four genetic clusters. The Minhhuong and Muongkhieng breeds joined the same genetic cluster while other breeds had their own clusters. These results indicated that the possibility to combine Minhhuong and Muongkhieng for reducing the cost of conservation and suggested that conservation of the Bauben should be prioritized to avoid inbreeding depression and genetic drift.

Derivation and characterization of putative embryonic stem cells isolated from blastoderms of Taiwan Country chicken for the production of chimeric chickens.

The conservation of Taiwan Country chicken (TCC) is important due to concerns for the local breed's adaptability to the area and disease resistance. Furthermore, the genetic resource base of native chickens can be used to improve egg and meat production efficiency in commercial TCC. As the embryonic stem cells (ESCs) hold great potential for regenerative medicine and species conservation, the aims of this study were to isolate and characterize ESCs of TCC. The blastodermal cells (BCs) were isolated from the zona pellucida of stage X chicken embryos and cultured in conditioned medium for the proliferation and maintenance of BCs in vitro. The quantitative real-time polymerase chain reaction (qPCR) results showed that POUV, SOX2 and NANOG were expressed in the putative ESCs. In addition, the expression of pluripotent markers, SSEA-1 and SSEA-4, was detected. The DiI-stained ESCs were injected into the dorsal aorta of the E3.5 recipient fetuses soon after staining and the injected embryos were continuously incubated and checked on day 7 of incubation. It was shown that some DiI-positive cells were found in the 7-d-old chimeric embryos. The results demonstrated that some pluripotent cells existed in the cultured BCs for the production of germline chimeric embryos from TCC.

Phylogeography of Toona ciliata (Meliaceae) Complex in China Inferred from Cytonuclear Markers.

Toona ciliata is an important timber species but is recognized as an endangered species at level II in China. Its genetic conservation is of increasing concern. Provenance trials and other breeding programs were conducted to develop seed transfer rules and multiplications. Here, we investigated twenty-nine populations sampled across the natural distribution of the T. ciliata complex using mtDNA and nrDNA ITS (ribosomal internal transcribed spacer) markers. Haplotype diversity was h = 0.190 ± 0.202 and nucleotide diversity was π = 0.000383 ± 0.000536 for mtDNA marker. Nucleotide diversity for ITS sequences was 0.00837 ± 0.000783. Haplotypes exhibited phylogeographic structure in spatial distribution. The extent of genetic differentiation was significant (Fst = 0.6994 ± 0.0079 for ITS and 0.8870 ± 0.0077 for mtDNA marker). Isolation by distance (IBD) and by elevation (IBE) occurred among populations. Phylogenetic relationships from mtDNA marker indicated three genetically distinct regions, each without IBD effects. Compared with pollen flow, seed flow was strongly impeded in the western region, but extensive in the central region, and less impeded in the eastern region. Most populations did not exhibit expansion, with only a few populations showing expansion after bottleneck effects. We discussed a strategy of region-based genetic conservation and proposed to conserve multiple populations in the western and eastern regions and a few populations in the central region.

Genetic relationships and diversity analysis in Turkish laurel (Laurus nobilis L.) germplasm using ISSR and SCoT markers.

Laurel (Laurus nobilis L.) has been used in the Mediterranean basin since ancient ages. Nowadays, Turkey, Mexico, Portugal, Italy, Spain, France, Algeria, and Morocco use aromatic leaves for commercial purposes, and Turkey is the largest exporter in the world. In this study, molecular characterization, and genetic relationships of 94 Turkish laurel genotypes were determined by ISSR and SCoT markers. The experiment was conducted with 16 ISSR and 10 SCoT markers. While 348 of 373 bands were polymorphic with a 93.3% polymorphism rate, Nei's genetic distances ranged between 0.17 and 0.70 with 0.39 mean in ISSR. In SCoT, 175 of 227 bands were polymorphic with 77.1% polymorphism rate, and Nei's genetic distances varied between 0.12 and 0.51. Sufficient genetic diversity determined with diversity parameters consisting of the average Shannon's information index (ISSR: 0.46, SCoT:0.35), the overall gene diversity (ISSR:0.19, SCoT:0.18), and the effective number of alleles (ISSR:1.52, SCoT:1.38). AMOVA (Analysis of molecular variance) revealed most of the variation was within genotypes (96%). Neighbor-joining algorithms, principal coordinate analysis (PCoA), and model-based structure resulted in harmony and clustered according to the geographical regions and provinces they collected. Genotypes were divided into two groups in ISSR and SCoT with UPGMA clustering resulting in a similar polymorphism distribution. The correlation coefficient (r) determined by marker systems' Nei's genetic distances was 0.25. The results of the study put forward resources for advanced breeding techniques, contribute to the preservation of genetic diversity, and management of genetic resources for the breeders.

Genetic diversity and population structure of Jamunapari goat in India using pedigree analysis.

Pedigree records of 6821 Jamunapari goats of India were collected from 1980 to 2011 and used to evaluate the population structure and genetic diversity in this flock. Animals born between 2009 and 2011 represented the current reference population. The average pedigree completeness index (PCI) and numbers of equivalent complete generations (EqG) were estimated for the entire (PCI = 0.18, EqG = 2.24) and reference (PCI = 0.31, EqG = 3.45) populations. The average generation interval was 3.33 years. The average inbreeding coefficient and the average relatedness were 0.46 and 1.06%, respectively, for the entire population and 0.77 and 3.87% for the reference population. The rate of inbreeding was 0.06% per generation. The effective population size (Ne), estimated from increases in inbreeding coefficients between the first and third equivalent complete generations, was 52.65, but periodic introductions of unrelated breeding males resulted in average inbreeding levels in the reference population that were lower than those predicted from the estimate of Ne. Effective numbers of founders (fe), ancestors (fa), founder genomes equivalents (fg), and non-founder genomes (fng) were 51, 39, 25.8, and 48.2, respectively. The fe/fa ratio in the reference population was 1.31 and indicated that occasional bottlenecks had occurred in the population. The 14 most influential ancestors contributed 50% of the genetic variability in the reference population, with a maximum individual contribution of 9.25%. Approximately 1.9% of the initial heterozygosity had been lost from the population, indicating that substantial genetic diversity still exists in this flock.

Cross species amplification and characterization of microsatellite markers in Leporinus friderici (Characiformes, Anostomidae) / Amplificação cruzada e caracterização de marcadores microssatélites em Leporinus friderici (Characiformes, Anostomidae)

ABSTRACT: Leporinus friderici is a migratory neotropical fish with elevated ecological and economic importance in Brazil. Microsatellite markers are highly important in population genetic studies, management, and conservation programs; however, no markers are available for this species. In this study, seven microsatellite loci, previously developed for Megaleporinus obtusidens, were successfully cross-amplified in L. friderici. Among these loci, five presented moderate to high genetic variability levels, with four to seven alleles per loci and expected heterozygosities varying from ≥ 0.574 to 1.000. These markers represent a valuable tool for the future management and ecological studies involving this species and group of neotropical fishes.

RESUMO: Leporinus friderici é um peixe neotropical migratório com elevada importância ecológica e econômica no Brasil. Os marcadores microssatélites são conhecidos por sua importância em estudos genéticos populacionais, programas de manejo e conservação, no entanto, não existem marcadores disponíveis para esta espécie. Neste estudo, sete locos microssatélites, previamente desenvolvidos para Megaleporinus obtusidens foram amplificados com sucesso em L. friderici. Dentre esses loci, cinco apresentaram variabilidade genética moderada a alta, com quatro a sete alelos por loci e heterozigosidades esperadas variando de ≥ 0,574 a 1.000. Esses marcadores representam uma ferramenta valiosa para futuros manejos e estudos ecológicos envolvendo esta espécie e este grupo de peixes neotropicais.