High Levels Of Heterozygosity Research Articles

A haplotype-resolved draft genome of the European sardine (Sardina pilchardus).

BackgroundThe European sardine (Sardina pilchardus Walbaum, 1792) is culturally and economically important throughout its distribution. Monitoring studies of sardine populations report an alarming decrease in stocks due to overfishing and environmental change, which has resulted in historically low captures along the Iberian Atlantic coast. Important biological and ecological features such as population diversity, structure, and migratory patterns can be addressed with the development and use of genomics resources.FindingsThe genome of a single female individual was sequenced using Illumina HiSeq X Ten 10x Genomics linked reads, generating 113.8 gigabase pairs of data. Three draft genomes were assembled: 2 haploid genomes with a total size of 935 megabase pairs (N50 103 kilobase pairs) each, and a consensus genome of total size 950 megabase pairs (N50 97 kilobase pairs). The genome completeness assessment captured 84% of Actinopterygii Benchmarking Universal Single-Copy Orthologs. To obtain a more complete analysis, the transcriptomes of 11 tissues were sequenced to aid the functional annotation of the genome, resulting in 40,777 genes predicted. Variant calling on nearly half of the haplotype genome resulted in the identification of >2.3 million phased single-nucleotide polymorphisms with heterozygous loci.ConclusionsA draft genome was obtained, despite a high level of sequence repeats and heterozygosity, which are expected genome characteristics of a wild sardine. The reference sardine genome and respective variant data will be a cornerstone resource of ongoing population genomics studies to be integrated into future sardine stock assessment modelling to better manage this valuable resource.

Whole-Genome Sequencing of the Opportunistic Yeast Pathogen Candida inconspicua Uncovers Its Hybrid Origin.

Fungal infections such as those caused by Candida species are increasingly common complications in immunocompromised patients. The list of causative agents of candidiasis is growing and comprises a set of emerging species whose relative global incidence is rare but recurrent. This is the case of Candida inconspicua, which prevalence has increased 10-fold over the last years. To gain novel insights into the emergence of this opportunistic pathogen and its genetic diversity, we performed whole genome sequencing of the type strain (CBS180), and of 10 other clinical isolates. Our results revealed high levels of genetic heterozygosity structured in non-homogeneous patterns, which are indicative of a hybrid genome shaped by events of loss of heterozygosity (LOH). All analyzed strains were hybrids and could be clustered into two distinct clades. We found large variability across strains in terms of ploidy, patterns of LOH, and mitochondrial genome heterogeneity that suggest potential admixture between hybrids. Altogether, our results identify a new hybrid species with virulence potential toward humans and underscore the potential role of hybridization in the emergence of novel pathogenic lineages.

Extended regions of suspected mis-assembly in the rat reference genome

We performed whole-genome sequencing for eight inbred rat strains commonly used in genetic mapping studies. They are the founders of the NIH heterogeneous stock (HS) outbred colony. We provide their sequences and variant calls to the rat genomics community. When analyzing the variant calls we identified regions with unusually high levels of heterozygosity. These regions are consistent across the eight inbred strains, including Brown Norway, which is the basis of the rat reference genome. These regions show higher read depths than other regions in the genome and contain higher rates of apparent tri-allelic variant sites. The evidence suggests that these regions may correspond to duplicated segments that were incorrectly overlaid as a single segment in the reference genome. We provide masks for these regions of suspected mis-assembly as a resource for the community to flag potentially false interpretations of mapping or functional results.

Extra‐pair offspring are less heterozygous than within‐pair offspring in American redstarts Setophaga ruticilla

The vast majority of bird species are socially monogamous; however, extra‐pair paternity is nearly ubiquitous and a number of theories have been proposed to explain the prevalence of this mixed mating strategy. Here, we test the genetic compatibility hypothesis – the idea that females seek extra‐pair copulations with males whose genes are more compatible with her own. For this study, we examined eight years of paternity data (2004–2011) from a Nearctic‐Neotropical migratory bird, the American redstart Setophaga ruticilla, breeding in southeastern Ontario, Canada. We predicted that females paired with genetically similar males (higher relatedness) would be more likely to produce extra‐pair offspring and that extra‐pair offspring would have higher levels of heterozygosity than within‐pair offspring. Alternatively, because this population experiences high levels of immigration, females may produce extra‐pair offspring with more genetically similar males because of the potential for outbreeding depression. Using five highly variable microsatellite markers, we examined patterns of relatedness among social pairs as well as measures of offspring heterozygosity. In contrast to our predictions, we found no difference in relatedness between social pairs where the females produced extra‐pair offspring and social pairs where the females produced only within‐pair offspring. However, extra‐pair offspring were significantly less heterozygous than within‐pair offspring. Together, these findings suggest that females a) are not engaging in extra‐pair fertilizations based on relatedness to their social mate and b) appear to be mating with extra‐pair males that are more genetically similar to themselves. We suggest there may be benefits for females to mate with genetically similar extra‐pair males in highly outbred populations with high rates of immigration, such as for maintaining co‐adapted gene complexes or genes coding for local adaptations.

Estimation of genetic diversity and relatedness in a mango germplasm collection using SNP markers and a simplified visual analysis method

Mango is a globally important tropical fruit but lacks genomic tools to support cultivar identification and to enable breeding efforts. Assessing the genetic diversity and relatedness of mango germplasm is essential for identifying genetically distant parents with favorable agronomic traits to produce hybrid populations enabling selection of improved cultivars. We thus genotyped 1915 mango accessions from the United States, Senegal, Thailand, and Australia with 272 single nucleotide polymorphism (SNP) markers identifying over 520,000 genotypes. These accessions represent the available diversity from both public and private germplasm collections in these countries, as well as accessions from smaller international collections. The study included Mangifera indica, other Mangifera species, and accessions from half sibling populations. Genotype data were analyzed using an affinity propagation method to define 258 groups. Using a simple visual method, no more than 30 SNPs are needed to distinguish a single cultivar of interest from all other cultivars in the dataset enabling the accurate identification of important commercial cultivars. As these SNP markers provided accurate genotype data for accessions from different genera as well as half siblings, the majority of the genetic diversity of the mango germplasm and related species that were genotyped has been captured. The dataset contains a large collection of open-pollinated half siblings from known maternal parents. A simple visual method can also be used to identify self-pollinated individuals among the half siblings of known maternal parents and, in some cases, to infer likely candidates for the paternal parent. Identification of self-pollinated individuals is particularly important in terms of selection of improved cultivars, as due to high levels of heterozygosity, self-pollinated progeny are likely to uncover deleterious recessive alleles. Genotyping of progeny at the seedling stage and removal of self-pollinated progeny can increase the efficiency and decrease the costs of selection of improved cultivars from open-pollinated populations.

Microsatellite-based Genetic Diversity and Mutation-Drift Equilibrium in Dharwadi Buffalo (Bubalus bubalis) of India

Genetic diversity was assessed in a buffalo population (Dharwadi) of Karnataka by utilizing 25 heterologous bovine microsatellite markers. Genotypic status of individuals at each locus was identified by automated DNA sequencer, and allelic data were analyzed for genetic diversity parameters. Observed number of alleles varied between 5 and 19 with 13.12 ± 0.80 alleles per locus. High level of heterozygosity (0.63) indicated plenty of existing genetic diversity in this buffalo population. Within-population inbreeding estimate (FIS) was significantly positive (0.186) and 88% of the investigated loci contributed toward the homozygote excess. Accordingly, significant deviation from Hardy–Weinberg equilibrium was observed at 24 of 25 analyzed loci. The population did not suffer reduction in effective population size in the last few generations. Assessment of Dharwadi buffalo population for mutation-drift equilibrium did not reveal significant heterozygosity excess under all the models of microsatellite evolution as per Sign test. No shift was recorded in the frequency distribution of alleles, and a normal L-shaped curve indicated absence of any recent genetic bottleneck. The study highlighted sufficient genetic variability within Dharwadi buffalo population that can be utilized in combination with phenotype and production information for registration as a distinct breed of Indian buffalo.

Genetic outcomes of translocation of bighorn sheep in Arizona

ABSTRACTTranslocation is an important management tool that has been used for >50 years in Arizona, USA, to increase bighorn sheep (Ovis canadensis) population densities and to restore herds to suitable habitat throughout their historical range. Yet, translocation can also alter the underlying genetic diversity and spatial structure of managed wildlife species in beneficial or detrimental ways. To evaluate the long‐term effect of translocation actions on bighorn sheep, we characterized statewide genetic structure and diversity using microsatellite and mitochondrial DNA data in 16 indigenous and translocated (supplemented or reintroduced) Arizona populations sampled between 2005 and 2012. Populations that were recipients of translocated animals showed no reduction in genetic diversity with allelic richness and heterozygosity estimates equivalent to, and in some cases greater than, indigenous source populations. The indigenous population occupying the Silver Bell Mountains population displayed the lowest indices of genetic diversity but shared mitochondrial DNA haplotypes with the Mohawk Mountains, Sierra Pinta, and Cabeza Prieta populations, indicating past connectivity and potential opportunities for genetic management if warranted. Bayesian clustering on genetic similarity and genetic divergence estimates corroborated previous work differentiating Rocky Mountain bighorn sheep (O. c. canadensis) and 2 desert lineages corresponding with Nelson's (O. c. nelsoni) and Mexican desert bighorn sheep (O. c. mexicana). In northern Arizona, assignment tests confirmed the presence of 2 indigenous metapopulations of Nelson's desert bighorn sheep in the Black Mountains and Grand Canyon and indicated that gene flow from the Grand Canyon population has likely played a role in maintaining genetic diversity and mitigating founder effects among multiple translocated populations in the area. In southern Arizona, we detected genetic structure consistent with 2 metapopulations of Mexican desert bighorn sheep representing a departure from current management practices that consider this lineage to be a single genetic unit. Several lines of genetic evidence presented in this study suggest that the Bill Williams River area is the contemporary contact zone for the 2 desert lineages; however, the degree to which translocation has enhanced introgression is unknown. Despite relative isolation from other herds, the translocated Rocky Mountain bighorn sheep population in eastern Arizona had high levels of allelic richness and heterozygosity and a negative inbreeding coefficient, conceivably as a result of multiple translocation events from sources in Colorado and New Mexico, USA. Although translocation management has successfully contributed to the reestablishment of bighorn sheep populations in Arizona without diminishing genetic diversity, future translocation should proceed with caution to preserve the genetic integrity and potential local adaptation within the Nelson's and Mexican desert bighorn sheep metapopulations identified in this study. © 2019 The Wildlife Society.

High-resolution characterization of allelic and haplotypic HLA frequency distribution in a Spanish population using high-throughput next-generation sequencing

Next-generation sequencing (NGS) at the HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1 and -DRB3/4/5 loci was performed on 282 healthy unrelated individuals from different major regions of Spain. High-resolution HLA genotypes defined by full sequencing of class I loci and extended coverage of class II loci were obtained to determine allele frequencies and also to estimate extended haplotype frequencies. HLA alleles were typed at the highest resolution level (4-field level, 4FL); with exception of a minor deviation in HLA-DPA1, no statistically significant deviations from expected Hardy Weinberg Equilibrium (HWE) proportions were observed for all other HLA loci. This study provides new 4FL-allele and -haplotype frequencies estimated for the first time in the Spanish population. Furthermore, our results describe extended haplotypes (including the less frequently typed HLA-DPA1 and HLA-DQA1 loci) and show distinctive haplotype associations found at 4FL-allele definition in this Spanish population study. The distinctive allelic and haplotypic diversity found at the 4FL reveals the high level of heterozygosity and specific haplotypic associations displayed that were not apparent at 2-field level (2FL). Overall, these results may contribute as a useful reference source for future population studies, for HLA-disease association studies as a healthy control group dataset and for improving donor recruitment strategies of bone marrow registries. HLA genotyping data of this Spanish population cohort was also included in the 17th International Histocompatibility and Immunogenetics Workshop (IHIW) as part of the study of HLA diversity in unrelated worldwide populations using NGS.

Evaluation of genetic diversity within sweet cherry accessions of Czech genetic resources by molecular SSR markers

Sweet cherry is a vegetatively propagated, perennial plant with high level of heterozygosity and ancient breeding history. Therefore, it is necessary to keep, conserve and evaluate known genetic resources for future breeding programs and fruit production stability. In present, the utilization of DNA molecular genetic methods is the best suitable method for evaluation of individual accessions, so that we eliminated duplications and characterized genetic relationships. Recently, there are many different molecular methods but the most reliable are SSR markers. In our work, we used PCR primer combinations for 20 SSR and 2 EST-SSR markers for analyses of 82 current, old and local sweet cherry cultivars from Czech genetic resources of the Research and Breeding Institute of Pomology in Holovousy. In total, 113 polymorphic markers were amplified which we used for hierarchical cluster analysis of genetic variability. The resulting dendrogram corresponded with genealogical and geobotanical characteristics of individual accessions which were divided into five clusters. The breeding history of several known accessions was also proved.

Micropropagation of Morus cathayana through in vitro culture from local Bogor, West Java, Indonesia

Wulandari YRE, Harjosudirjo MA. 2019. Micropropagation of Morus cathayana through in vitro culture from local Bogor, West Java, Indonesia. Nusantara Bioscience 11: 18-22. Mulberry (Morus spp.) is a dicotyledonous plant known for its medicinal benefits as well as silkworm breeding (Bombyx mori L.) to produce silk. Morus cathayana mainly cultivated due to its high content of 1-deoxynojirimycin, widely utilized as an anti-diabetic agent. However, common practice in planting and maintenance of mulberry generate less profit, contributed to its long juvenile period and high heterozygosity level. Hence the development and cultivation through plant tissue culture techniques are necessary. The purpose of this research was to obtain the best combination of thidiazuron as a plant growth regulator. M. cathayana branches with nodal segments were used as explants. Research stages were explants initiation into Murashige and Skoog media, shoot induction in MS media as control and MS+BAP 1 mg/L+NAA 0.25 mg/L+TDZ 0.1, 0.5, 1 mg/L as treatment media, and statistical data analysis. Greater increase in shoot growth was observed in MS+BAP 1 mg/L+NAA 0.25 mg/L+TDZ 0.5 mg/L media, while the formation of shoots and calluses on the explants grown in control and treatment media showed no significant growth.

Genetic variation in Hydrangea macrophylla (Thunb.) Ser. in Russia based on simple sequence repeat markers

Genetic diversity and genetic relationships among 39 accessions of Hydrangea macrophylla (Thunb.) Ser. were analyzed using 38 previously developed simple sequence repeat markers (SSRs). A total of 38 polymorphic primers representing 166 bands with an average of 4.53 polymorphic bands per primer were selected. The number of alleles detected per locus ranged from two to eight with a total of 163 alleles amplified. The size of the amplified fragments ranged from 70 to180 base pairs. The effective multiallelic markers with high level of heterozygosity (more than 0.7) and effective number of alleles (more than 3.5) were identified. In this study nine SSR markers showed clear polymorphisms. The dendrogram grouped all hybrids in three major clusters, and two of these clusters included only mophead cultivars. The lacecap cultivars clustered more closely to each other. The results of this research could be used in breeding programs of H. macrophylla.

Strikingly high levels of heterozygosity despite 20 years of inbreeding in a clonal honey bee.

Inbreeding (the mating between closely related individuals) often has detrimental effects that are associated with loss of heterozygosity at overdominant loci, and the expression of deleterious recessive alleles. However, determining which loci are detrimental when homozygous, and the extent of their phenotypic effects, remains poorly understood. Here, we utilize a unique inbred population of clonal (thelytokous) honey bees, Apis mellifera capensis, to determine which loci reduce individual fitness when homozygous. This asexual population arose from a single worker ancestor approximately 20years ago and has persisted for at least 100 generations. Thelytokous parthenogenesis results in a 1/3 of loss of heterozygosity with each generation. Yet, this population retains heterozygosity throughout its genome due to selection against homozygotes. Deep sequencing of one bee from each of the three known sub-lineages of the population revealed that 3,766 of 10,884 genes (34%) have retained heterozygosity across all sub-lineages, suggesting that these genes have heterozygote advantage. The maintenance of heterozygosity in the same genes and genomic regions in all three sub-lineages suggests that nearly every chromosome carries genes that show sufficient heterozygote advantage to be selectively detrimental when homozygous.

Ecological and genetic features of the Ukrainian Antoninsko- Zozulinetsky species of scaly carp (Cyprinus carpio L.) population

The main ecological and genetic features of growing in the internal reservoirs of Ukraine of promising populations of the Antonino-Zozulentskyi sparse carp are presented. A morphometric evaluation of the breeding material was conducted. The studied herd is homogeneous, the coefficients of variability are stable and correspond to the normative indexes of Ukrainian flint breed. According to the results of the analysis, the pedigrees were divided into classes, elite groups were isolated, from which the material material was formed for performing carp reproduction. Species-specific features of the genetic structure were revealed by distribution of allelic frequencies by albumin loci, esterase, transferrin. The analysis of the genetic structure showed the specificity of the distribution of allelic frequencies and genotypic composition of the protein loci. An analysis of the variety of genotypes of the studied populations in the context of the farms gave an opportunity to detect specific genotypes according to the transferrin locus, and the lack of some theoretically expected ones, namely TF АВ, ВВ snd DD. Specific in Medzhybizh fishpond, the genotypes of TF С1С1 were genotypes for scapular carps, the specifics of the TF С1С2 genotype, Antoninus — AC1 and AC2, were specific for carps from the Staraya Sinyava fishpond. The differences in terms of average heterozygosity are obtained, which makes it possible to control the level of variability in the genetic structure of the studied populations. A statistically significant excess of heterozygotes was found in most loci except TF and EST in the study group. The highest level of heterozygosity in the studied groups of carp is marked by loci ALB (78.8–82.8%) snd ME (72.7–82.8 %). The obtained data indicate that the optimal level of genetic heterogeneity (60–71%) in the carps of the «Medzhybizh» and «Antonina» sites is observed in comparison with the «Stara Synyava» section, where it is the lowest (57%). Data were obtained for the use of individual genetic-biochemical systems for differentiation and the conduct of permanent genetic monitoring of the populations of scaly carp. Promising and ecological safety of carp growing in Ukraine is proved.

Comprehensively Characterizing the Cytological Features of Saccharum spontaneum by the Development of a Complete Set of Chromosome-Specific Oligo Probes.

Chromosome-specific identification is a powerful technique in the study of genome structure and evolution. However, there is no reliable cytogenetic marker to unambiguously identify each of the chromosomes in sugarcane (Saccharum spp., Poaceae), which has a complex genome with a high level of ploidy and heterozygosity. In this study, we developed a set of oligonucleotide (oligo)-based probes through bioinformatic design and massive synthetization. These probes produced a clear and bright single signal in each of the chromosomes and their eight homologous chromosomes in the ancient species Saccharum spontaneum (2n = 8x = 64). Thus, they can be used as reliable markers to robustly label each of the chromosomes in S. spontaneum. We then obtained the karyotype data and established a nomenclature based on chromosomal sizes for the eight chromosomes of the octoploid S. spontaneum. In addition, we also found that the 45S and 5S rDNAs demonstrated high copy number variations among different homologous chromosomes, indicating a rapid evolution of the highly repeated sequence after polyploidization. Our fluorescence in situ hybridization (FISH) assay also demonstrated that these probes could be used as cross-species markers between or within the genera of Sorghum and Saccharum. By comparing FISH analyses, we discovered that several chromosome rearrangement events occurred in S. spontaneum, which might have contributed to the basic chromosome number reduction from 10 in sorghum to 8 in sugarcane. Consistent identification of individual chromosomes makes molecular cytogenetic study possible in sugarcane and will facilitate fine chromosomal structure and karyotype evolution of the genus Saccharum.

Preferential Homologous Chromosome Pairing in a Tetraploid Intergeneric Somatic Hybrid (Citrus reticulata + Poncirus trifoliata) Revealed by Molecular Marker Inheritance.

The creation of intergeneric somatic hybrids between Citrus and Poncirus is an efficient approach for citrus rootstock breeding, offering the possibility of combining beneficial traits from both genera into novel rootstock lineages. These somatic hybrids are also used as parents for further tetraploid sexual breeding. In order to optimize these latter breeding schemes, it is essential to develop knowledge on the mode of inheritance in the intergeneric tetraploid hybrids. We assessed the meiotic behavior of an intergeneric tetraploid somatic hybrid resulting from symmetric protoplast fusion of diploid Citrus reticulata and diploid Poncirus trifoliata. The analysis was based on the segregation patterns of 16 SSR markers and 9 newly developed centromeric/pericentromeric SNP markers, representing all nine linkage groups of the Citrus genetic map. We found strong but incomplete preferential pairing between homologues of the same ancestral genome. The proportion of gametes that can be explained by random meiotic chromosome associations (τ) varied significantly between chromosomes, from 0.09 ± 0.02 to 0.47 ± 0.09, respectively, in chromosome 2 and 1. This intermediate inheritance between strict disomy and tetrasomy, with global preferential disomic tendency, resulted in a high level of intergeneric heterozygosity of the diploid gametes. Although limited, intergeneric recombinations occurred, whose observed rates, ranging from 0.09 to 0.29, respectively, in chromosome 2 and 1, were significantly correlated with τ. Such inheritance is of particular interest for rootstock breeding because a large part of the multi-trait value selected at the teraploid parent level is transmitted to the progeny, while the potential for some intergeneric recombination offers opportunities for generating plants with novel allelic combinations that can be targeted by selection.

Construction of a high-density genetic linkage map and QTL analysis for hazelnut breeding

Hazelnut breeding is a slow activity due to the long lifecycle of the plant, the long time between pollination and reliable phenotype observation in the progeny, the presence of self-incompatibility and the high level of heterozygosity. Improved knowledge on the hazelnut genome and the development of marker-assisted selection would greatly facilitate breeding programs. Objective of this study was the construction of high-density genetic maps and the detection of QTL (quantitative trait loci) related to phenological, vegetative and productive traits, by using an F1 progeny obtained by crossing ‘Tonda Gentile delle Langhe’ (female parent, hereafter TGdL) with ‘Merveille de Bollwiller’ (syn. ‘Hall’s Giant’ male parent, MB). Genotyping-by-sequencing (GBS), followed by SNP mining using a Samtools-based pipeline, yielded 7,980 SNP markers. Independent linkage maps were constructed for each parent on the basis of the double pseudo-testcross mapping strategy. The linkage map for TGdL consisted of 1,236 markers covering a total genetic length of 900.4 cM, with a mean inter-marker distance of 0.83 cM. A reciprocal translocation was detected in TGdL between two non-homologous chromosomes. The linkage map for MB was based on segregation at 1,211 markers covering a total genetic length of 899.1 cM, with a mean inter-marker distance of 0.82 cM. Plant and nut traits were recorded during five years and statistically analyzed with molecular data to identify marker/QTL associations for flowering and bud burst time, sucker habit and nut traits, such as nut and seed size, roundness index, percent kernel and ease of pellicle removal.

Population history provides foundational knowledge for utilizing and developing native plant restoration materials.

A species’ population structure and history are critical pieces of information that can help guide the use of available native plant materials in restoration treatments and decide what new native plant materials should be developed to meet future restoration needs. In the western United States, Pseudoroegneria spicata (bluebunch wheatgrass; Poaceae) is an important component of grassland and shrubland plant communities and commonly used for restoration due to its drought resistance and competitiveness with exotic weeds. We used next‐generation sequencing data to investigate the processes that shaped P. spicata's geographic pattern of genetic variation across the Intermountain West. Pseudoroegneria spicata's genetic diversity is partitioned into populations that likely differentiated since the Last Glacial Maximum. Adjacent populations display varying magnitudes of historical gene flow, with migration rates ranging from multiple migrants per generation to multiple generations per migrant. When considering the commercial germplasm sources available for restoration, genetic identities remain representative of the wildland localities from which germplasm sources were originally developed, and they maintain high levels of heterozygosity and nucleotide diversity. However, the commercial germplasm sources represent a small fraction of the overall genetic diversity of P. spicata in the Intermountain West. Given the low migration rates and long divergence times between some pairs of P. spicata populations, using commercial germplasm sources could facilitate undesirable restoration outcomes when used in certain geographic areas, even if the environment in which the commercial materials thrive is similar to that of the restoration site. As such, population structure and history can be used to provide guidance on what geographic areas may need additional native plant materials so that restoration efforts support species and community resilience and improve outcomes.

OR24 HLA allele and haplotype frequencies characterized using next-generation sequencing methods in unrelated world-wide populations: Summary from the 17th international HLA and immunogenetics workshop

Aim The primary goal of the 17th IHIWS was to advance the field of Histocompatibility and Immunogenetics research as well as clinical practices through the application of NGS technologies. Analyses of very-high resolution NGS HLA profiles sampled from different populations will be useful for reconstructing human history and may improve match predictions for unrelated donor selection algorithms. Methods In the unrelated population HLA diversity project, 15 laboratories from 10 different countries contributed HLA genotype data generated by various NGS methods. HLA population data included well-defined large datasets from the USA and East Asia and smaller samples from Europe, Australia, and Western Asia. Participants uploaded data in HML/XML format into the 17th IHIW database, data was systematically reviewed, and statistical analysis was performed using the genetic software PyPop v.0.7.0 to estimate; (i) allele frequencies, (ii) heterozygosity, (iii) conformity to HWE, (iv) selective neutrality, (v) 2-locus haplotypes and (vi) LD. The software BIGDAWG was used to estimate extended haplotype frequencies by an EM algorithm. Inter-population variance was determined using Nei’s genetic distances which were then used to construct phylogenetic dendrograms. Results Amongst each population, test of selective neutrality often revealed an excess of heterozygous compared with neutral expectations. A comparison of the HLA genetic diversity estimated at the 4 and 2 fields revealed that diversity at the majority of loci, particularly for populations of European descent, was lower at the 2-field resolution. African descent populations had a lower number of distinct HLA alleles at class I and II loci compared to other groups but exhibited higher levels of heterozygosity. Two-locus haplotype analyses revealed distinct HLA associations at the 4 − field. Analyses of extended haplotype frequencies, estimated both in the presence and absence of DP loci, showed unique haplotypes that were common to each ethnic group although some haplotypes were shared amongst different ethnic groups. Conclusions This workshop project provided a vast amount of new information about HLA genetic diversity at the intronic level and will be a useful resource for anthropological studies, disease association studies and transplantation.

Population genetics of benzimidazole-resistant Haemonchus contortus and Haemonchus placei from buffalo and cattle: implications for the emergence and spread of resistance mutations

The population genetics of nematode parasites are poorly understood with practical reference to the selection and spread of anthelmintic resistance mutations. Haemonchus species are important to study the nematode population genetics due to their clinical importance in ruminant livestock, and the availability of genomic resources. In the present study, it has been examined that Haemonchus contortus and Haemonchus placei populations from three buffalo and nine cattle hosts. Seventy-three individual adult worms of H. contortus and 148 of H. placei were analysed using a panel of seven microsatellite markers. The number of alleles per locus in H. contortus and H. placei indicated that all populations were polymorphic for the microsatellites used in the present study. Genetic diversity parameters included high levels of allelic richness and heterozygosity, indicating effective population sizes, high mutation rates and high transmission frequencies in the area. Genetic structure parameters revealed low genetic differentiation between and high levels of genetic variation within H. contortus and H. placei populations. Population dynamic analyses showed an absence of heterozygosity excess in both species, suggesting that there was no deviation from genetic drift equilibrium. Our results provide a proof of concept for better understanding of the consequences of specific control strategies, climatic change or management strategies on the population genetics of anthelmintic resistance alleles in Haemonchus spp. infecting co-managed buffalo and cattle.

Speciation Success of Polyploid Plants Closely Relates to the Regulation of Meiotic Recombination.

Polyploidization is a widespread phenomenon, especially in flowering plants that have all undergone at least one event of whole genome duplication during their evolutionary history. Consequently, a large range of plants, including many of the world’s crops, combines more than two sets of chromosomes originating from the same (autopolyploids) or related species (allopolyploids). Depending on the polyploid formation pathway, different patterns of recombination will be promoted, conditioning the level of heterozygosity. A polyploid population harboring a high level of heterozygosity will produce more genetically diverse progenies. Some of these individuals may show a better adaptability to different ecological niches, increasing their chance for successful establishment through natural selection. Another condition for young polyploids to survive corresponds to the formation of well-balanced gametes, assuring a sufficient level of fertility. In this review, we discuss the consequences of polyploid formation pathways, meiotic behavior and recombination regulation on the speciation success and maintenance of polyploid species.