Heterozygosity In Populations Research Articles

An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster.

Maintaining genetic diversity in cultured shellfish can be challenging due to high variance in individual reproductive success, founder effects, and rapid genetic drift, but is important to retain adaptive potential and avoid inbreeding depression. To support broodstock management and selective breeding in cultured Pacific oysters (Crassostrea (Magallana) gigas), we developed an amplicon panel targeting 592 genomic regions and SNP variants with an average of 50 amplicons per chromosome. Target SNPs were selected based on elevated observed heterozygosity or differentiation in Pacific oyster populations in British Columbia, Canada. The use of the panel for parentage applications was evaluated using multiple generations of oysters from a breeding program on Vancouver Island, Canada (n = 181) and families selected for Ostreid herpesvirus-1 resistance from the Molluscan Broodstock Program in Oregon, USA (n = 136). Population characterization was evaluated using wild, naturalized, farmed, or hatchery oysters sampled throughout the Northern Hemisphere (n = 190). Technical replicates showed high genotype concordance (97.5%; n = 68 replicates). Parentage analysis found suspected pedigree and sample handling errors, demonstrating the panel's value for quality control in breeding programs. Suspected null alleles were identified and found to be largely population dependent, suggesting population-specific variation impacting target amplification. Null alleles were identified using existing data without the need for pedigree information, and once they were removed, assignment rates increased to 93.0% and 86.0% of possible assignments in the two breeding program datasets. A pipeline for analyzing the amplicon sequence data from sequencer output, amplitools, is also provided.

Meta-analyses of reproductive changes in angiosperm populations in response to elevation reveal a lack of global patterns.

Elevation is a major factor shaping plant populations on a global scale. At the same time, reproductive traits play a major role in plant fitness. With increasing altitude and increasingly harsh conditions, decreases in pollinator visitation rates, sexual investment, seed set, and heterozygosity (due to increased selfing) are expected. In response, selection and/or phenotypic plasticity could lead to an increase in plants' floral displays to increase their attractiveness to pollinators and compensates for the negative fitness impacts of reduced pollinator activity. A large body of literature tests these hypotheses at the among-species level, but empirical evidence at the population level (i.e., wihin-species), where adaptive change may occur, is still limited to species-specific studies. Unravelling the global patterns of change in the reproductive traits, flower visitation rates and heterozygosity of plant populations across variable environmental conditions, especially climate can help us to understand how species are able to cope with shifting conditions associated with global change, particularly in mountains. Here, we used meta-analytic approaches to assess the reproductive changes of plant populations in response to elevation on a global scale. We used a data set with 243 paired populations of plants at 'lower' and 'higher' elevations, spanning an elevation range of 0-4380 m asl and taken from 121 angiosperm species and 115 published studies. We analyzed changes in flower number, size and longevity, pollen production, flower visitation rate, seed set and expected heterozygosity.We then tested whether the observed patterns for each trait were dependent upon plant phylogeny and various ecogeographical factors and species traits. We found no evidence of elevation having a global effect on the reproductive traits of angiosperm populations. This null global pattern was not affected by geograph or phylogenetics. Our results suggest that changes in reproductive traits, flower visitation rates, and heterozygosity in plant populations across elevations are specific to each species and ecosystem. Hence, macroevolutionary (across species) and macroecological patterns of elevation of plant reproduction reported previously are apparently not simply the outcome of microevolutionary changes (within species). This apparent specificity of response across plant species poses difficulties in predicting the effects of global changes and, specifically, climatic changes, on the fate of plant species, populations, and communities.

Genetic Structure and Diversity of Hatchery and Wild Populations of Yellow Catfish Tachysurus fulvidraco (Siluriformes: Bagridae) from Korea.

Yellow catfish Tachysurus fulvidraco is an important commercial fish species in South Korea. However, due to their current declines in its distribution area and population size, it is being released from hatchery populations into wild populations. Hatchery populations also produced from wild broodstocks are used for its captive breeding. We reported 15 new microsatellite DNA markers of T. fulvidraco to identify the genetic diversity and structure of its hatchery and wild populations, providing baseline data for useful resource development strategies. The observed heterozygosity of the hatchery populations ranged from 0.816 to 0.873, and that of the wild populations ranged from 0.771 to 0.840. Their inbreeding coefficient ranged from -0.078 to 0.024. All populations experienced a bottleneck (p < 0.05), with effective population sizes ranging from 21 to infinity. Their gene structure was divided into two groups with STRUCTURE results of K = 2. It was confirmed that each hatchery population originated from a different wild population. This study provides genetic information necessary for the future development and conservation of fishery resources for T. fulvidraco.

A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography.

The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.

Genetic evaluation of F2 and F3 interspecific hybrids of mung bean (Vigna radiata L. Wilczek) using retrotransposon‐based insertion polymorphism and sequence‐related amplified polymorphism markers

Mung bean (Vigna radiata L. Wilczek) is a self‐pollinating and indispensable pulse crop in Indonesia. While low yield productivity is a major concern, genetic improvement is possible through interspecific hybridization. However, interspecific hybridization is relatively infrequent and produces low recombination exchanges, significantly limiting crop breeding efficiency. Thus, a comprehensive study is needed of the selection and genetic diversity evaluation of progenies in advanced generations derived from interspecific hybridization using a specific molecular marker. This study aims to confirm the heterozygosity in the F2 population and assess the genetic diversity in F3 mung bean populations resulting from interspecific hybridization between the mung bean and common bean. We designed the retrotransposon‐based insertion polymorphism (RBIP) marker by identifying the syntenic regions in the flanking sequences of retrotransposon insertion in common bean and mung bean. The RBIP marker can be applied to distinguish the heterozygote progenies from the homozygote progenies. Six combinations of sequence‐related amplified polymorphism (SRAP) primers were used in the genotyping of F3 mung bean progenies. The SRAP marker showed a high degree of polymorphism of up to 100%, while high genetic variation was observed within the population (71%) of mung bean progenies. The F3.4 population had the greatest number of genotypes and displayed the highest number of effective alleles, private alleles, and percentage of polymorphic loci, suggesting the existence of high genetic diversity within this population. These genetic diversity data are exceptionally critical for future genetic research since it has potentially high yield production. The genomic and marker‐assisted selection studies will support the major goals of the mung bean breeding program.

Population mixing mediates the intestinal flora composition and facilitates invasiveness in a globally invasive fruit fly

BackgroundChanges in population heterozygosity and genetic diversity play important roles in mediating life history traits of organisms; these changes often lead to phenotypic evolution in offspring, which become superior to their parents. In the present study, we examined phenotypic differentiation, the intestinal microbiome composition, and metabolism shift in the oriental fruit fly (Bactrocera dorsalis) by comparing an inbred (monophyletic) original population and an outbred (mixed) invasive population.ResultsThe results showed that the outbred population of B. dorsalis had significantly higher biomass, adult longevity, and fecundity than the inbred population. Additionally, intestinal microflora analysis revealed that both Diutina rugosa and Komagataeibacter saccharivorans were significantly enriched in the outbred population with higher genetic heterozygosity. D. rugosa enrichment altered amino acid metabolism in the intestinal tract, and supplementing essential amino acids (e.g. histidine and glutamine) in the diet led to an increase in pupal weight of the outbred population. Additionally, transcriptome analysis revealed that the HSPA1S gene was significantly downregulated in the outbred population. HSPA1S was involved in activation of the JNK-MAPK pathway through negative regulation, caused the upregulation of juvenile hormone (JH), and led to an increase in biomass in the outbred flies.ConclusionIn conclusion, the outbred population had an altered intestinal microbe composition, mediating metabolism and transcriptional regulation, leading to phenotypic differentiation; this may be a potential mechanism driving the global invasion of B. dorsalis. Thus, multiple introductions could lead to invasiveness enhancement in B. dorsalis through population mixing, providing preliminary evidence that changes in the intestinal microbiome can promote biological invasion.1rGLpfiTdGk3QvEMFY5kHbVideo

Genome-wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds.

Analysis of genomic data is becoming more and more common for the effective management of livestock breeding programmes, even in the case of local populations. In this work, the genome-wide data of Nero Siciliano pig breed were compared to that of wild boar, Italian local and cosmopolitan breeds to investigate its genetic structure, and runs of homozygosity (ROH) and heterozygosity patterns. The Nero Siciliano has been reported to have the highest rate of genetic diversity among the Italian breeds, and a genetic variability comparable to that of the cosmopolitan breeds. Analyses of genomic structure and relationships underlined its proximity to wild boar, and an internal substructure probably linked to different family lines. The breed showed a low value of inbreeding estimated from ROH, and the highest diversity index among the Italian breeds, even if lower than that of the cosmopolitans. Four ROH islands in three chromosomes (SSC8, SSC11, and SSC14) and one heterozygosity-rich region (SSC1) were identified in Nero Siciliano, highlighting genomic regions related to productive QTL. Across breeds, SSC8 and SSC14 were the chromosomes with most ROH islands, with Mora Romagnola and wild boar showing the highest level of autozygosity. Chromosomes SSC2, SSC6, SSC8 and SSC13 showed the majority of runs of heterozygosity regions, mainly found in the cosmopolitan pig breeds, which reported several genes associated with health-related QTL. The outlined results can help to better identify the genomic profile of this local breed in order to plan matings, maintain adequate internal diversity and exploit the production system.

Development of SSR molecular markers and genetic diversity analysis of Clematis acerifolia from Taihang Mountains.

Investigating the genetic diversity and population structure is important in conserving narrowly distributed plants. In this study, 90 Clematis acerifolia (C. acerifolia) plants belonging to nine populations were collected from the Taihang Mountains in Beijing, Hebei, and Henan. Twenty-nine simple sequence repeats (SSR) markers developed based on RAD-seq data were used to analyze the genetic diversity and population structure of C. acerifolia. The mean PIC value for all markers was 0.2910, indicating all SSR markers showed a moderate degree of polymorphism. The expected heterozygosity of the whole populations was 0.3483, indicating the genetic diversity of both C. acerifolia var. elobata and C. acerifolia were low. The expected heterozygosity of C. acerifolia var. elobata (He = 0.2800) was higher than that of C. acerifolia (He = 0.2614). Genetic structure analysis and principal coordinate analysis demonstrated that C. acerifolia and C. acerifolia var. elobata showed great genetic differences. Molecular variance analysis (AMOVA) demonstrated that within-population genetic variation (68.31%) was the main contributor to the variation of the C. acerifolia populations. Conclusively, C. acerifolia var. elobata had higher genetic diversity than C. acerifolia, and there are significant genetic differences between C. acerifolia and C. acerifolia var. elobata, and small genetic variations within the C. acerifolia populations. Our results provide a scientific and rational basis for the conservation of C. acerifolia and provide a reference for the conservation of other cliff plants.

Genetic diversity analysis of Wamena Arabica Coffee (Coffea arabica L.) based on SSR markers

Wamena is notable for producing and exporting high-quality coffee. However, a molecular method based on its polymorphism and not affected by external factors is required since morphological observations alone are frequently insufficient for identifying the coffee. The objective of this study is to identify Wamena Arabica coffee in the Jayawijaya District using simple sequence repeats (SSRs) molecular markers. This research involved several stages, including DNA isolation and purification, PCR SSR amplification with 5 primers, polymorphism, and heterozygosity level analysis. The results analysis proved that 30 alleles of 32 coffee genotypes were successfully amplified, with fragment sizes ranging from 176 to 553bp. The Car M052 locus (0.29%) had the least polymorphism with only two alleles, while the CarM101 locus (0.82%) had the most with 12 alleles, that high and low polymorphism indicated a measure of PIC scores. Heterozygosity analysis showed that the coffee samples were highly heterozygous. And based on the results of the bootstrap analysis, the phenogram shows that the coffee samples are divided into six clusters, with a cophenetic correlation coefficient (r) of 0.948 (excellent fit). This study proved that all SSR loci succeeded in amplifying 30 alleles and could be identified molecularly based on the genetic variation of the Wamena Arabica coffee genotypes in Papua. It seems highly possible that there is a mix of traits through gene flow and exchange between coffee genotypes, and the heterozygosity in the Arabica population on plantations. As a result, it is very important further analysis to confirm the findings.

Microsatellite marker assisted molecular diversity and population structure analysis of Kaempferia galanga Linn. germplasm collected from different parts of India

Kaempferia galanga Linn. is an endangered medicinal and aromatic crop with a wide range of importance in the field of pharmaceutical industries. The current study is sought to examine the molecular variance and population diversity for the first time within the core collection of K. galanga germplasm. For this study, a total of 132 accessions of K. galanga were collected from various states of India and all the germplasm has been maintained ex-situ at the experimental farm of CSIR-NEIST, Jorhat. Initially, 58 simple sequence repeats (SSR) markers were tested among them 48 markers that were the most efficient, sensitive, with positive predictive and polymorphism were used in the study. The population structure analysis of K. galanga showed nine clusters based on the Bayesian model. The estimated population heterozygosity ranged from 0.117 to 0.250. According to the Analysis of molecular variance study (AMOVA), the variation within the population (68%) was more than among the population (32%). The genetic diversity among the population (Fst) was in the range of 0.28–0.60. The accessions under study demonstrated a high amount of polymorphism with a 99.4% polymorphism observed in molecular investigation. The outcome of the study would help in the identification of the genetic variance for unique germplasm which would be of great aid in the breeding program of K. galanga.

Modeling genetic benefits and financial costs of integrating biobanking into the conservation breeding of managed marsupials.

Managed breeding programs are an important tool in marsupial conservation efforts but may be costly and have adverse genetic effects in unavoidably small captive colonies. Biobanking and assisted reproductive technologies (ARTs) could help overcome these challenges, but further demonstration of their potential is required to improve uptake. We used genetic and economic models to examine whether supplementing hypothetical captive populations of dibblers (Parantechinus apicalis) and numbats (Myrmecobius fasciatus) with biobanked founder sperm through ARTs could reduce inbreeding, lower required colony sizes, and reduce program costs. We also asked practitioners of the black-footed ferret (Mustela nigripes) captive recovery program to complete a questionnaire to examine the resources and model species research pathways required to develop an optimized biobanking protocol in the black-footed ferret. We used data from this questionnaire to devise similar costed research pathways for Australian marsupials. With biobanking and assisted reproduction, inbreeding was reduced on average by between 80% and 98%, colony sizes were on average 99% smaller, and program costs were 69- to 83-fold lower. Integrating biobanking made long-standing captive genetic retention targets possible in marsupials (90% source population heterozygosity for a minimum of 100 years) within realistic cost frameworks. Lessons from the use of biobanking technology that contributed to the recovery of the black-footed ferret include the importance of adequate research funding (US$4.2 million), extensive partnerships that provide access to facilities and equipment, colony animals, appropriate research model species, and professional and technical staff required to address knowledge gaps to deliver an optimized biobanking protocol. Applied research investment of A$133 million across marsupial research pathways could deliver biobanking protocols for 15 of Australia's most at-risk marsupial species and 7 model species. The technical expertise and ex situ facilities exist to emulate the success of the black-footed ferret recovery program in threatened marsupials using these research pathways. All that is needed now for significant and cost-effective conservation gains is greater investment by policy makers in marsupial ARTs.

Reproductive characteristics, population genetics, and pairwise kinship inform strategic recovery of a plant species in a fragmented landscape

AbstractPopulation genetics and understanding of mating systems provide fundamental information for conservation planning. Pairing these methods is a powerful tool in the study of threatened species, however, they are rarely applied in concert. We examined the mating system and used molecular genetics to measure pairwise kinship and the potential for inbreeding inHibbertia spanantha, a critically endangered long‐lived shrub endemic to the Sydney Basin, Australia, as a model for conservation planning of species in highly fragmented populations. In situ hand pollination experiments demonstrated that the species is preferentially outcrossing, with limited ability to self‐pollinate (either autogamously or geitonogamously). Although population genetics confirmed high levels of kinship and clonality, there is currently enough population heterozygosity for successful open pollination, primarily through buzz pollination by Sweat Bees (Lasioglossum [Chilalictus]). High levels of clonality and population kinship in one population may be the cause of reduced fitness, identified because our outcrossing pollination treatment produced significantly more seeds with greater viability and seed mass than the open treatments. Differences in weight of filled (viable) seeds were identified between populations, although not treatments, where clonal dominance may be swamping pollinator foraging activities. Identification of species mating system, population reproductive capacity, and impacts of fragmentation on population genetic health provides a robust basis for strategic planning and conservation of this critically endangered species, including establishment of an ex situ population and genetic rescue through population augmentation. These methods are easily applicable and particularly relevant to other plant species with small populations or those occurring in fragmented systems.

Traits of the pollination process in Gladiolus imbricatus and Iris sibirica (Iridaceae)

Results of a study of self-pollination in two of Ukrainian flora's threatened species, Gladiolus imbricatus and Iris sibirica (Iridaceae), are presented. To confirm or refute the occurrence of self-pollination in G. imbricatus and I. sibirica, an experiment was conducted on pollen germination on their stigmas. It has been found that in G. imbricatus pollination with autogenous pollen grains on the last day of flowering leads to the growth of pollen tubes in the cases of both hand and natural pollination. However, pollen grains on the stigma of an isolated I. sibirica flower were not detected on the first or last day of flowering, which means the absence of a mechanism of autonomous pollen transfer within the meranthium. Ungerminated pollen grains were also found on the stigma after autogenous hand pollination. It has been experimentally confirmed that in the absence of pollinators at the end of the flowering phase in G. imbricatus, as well as in some other members of the genus, self-pollination and self-fertilization are possible, which contribute to the wellbeing of populations and species. With regard to I. sibirica, it has been found that the autogamous self-incompatibility inherent in this species prevents inbreeding, maintaining heterozygosity in plant populations, allowing plants' better adaptation to different environmental conditions.

Myostatin (MSTN) Gene Polymorphism Using PCR-RFLP Method In Kerinci Ducks

This study aims to determine body weight, body weight gain, and body measurements of male and female Kerinci ducks, as well as to determine the diversity of MSTN genes and the association of the MSTN gene on body weight, body weight gain, and body sizes in Kerinci ducks. The materials used were 96 Kerinci ducks and 96 Kerinci duck blood samples. Data analysis included: T-test, T2-hotelling, Principal Component Analysis (PCA), genotype frequency, allele, Hardy-Weinberg equilibrium, Heterozygosity, and PIC. The results showed that body weights at 2 and 3 months of age, body weight gain of 2-3 months and body sizes of 3 months old male Kerinci ducks were significantly different (P &lt;0.05) higher than female Kerinci ducks. Body size markers of male and female Kerinci ducks were the length of the sternum, the length of the shank, and the circumference of the shank, while the shape identifier was the length of the wings. The MSTN|MboI gene in Kerinci ducks was polymorphic. The population of Kerinci ducks was in Hardy-Weinberg equilibrium (P&lt;0.05). Kerinci duck population heterozygosity showed H0&lt;He. The MSTN|MboI gene was associated with BB, PBB, and body measurements of male and female Kerinci ducks, and the best genotype was (-/-).

Changes of Barley Stripe Rust Populations in the United States from 1993 to 2017.

Barley stripe rust is a relatively new disease in the United States. The pathogen, Puccinia striiformis f. sp. hordei (Psh), was first observed in Texas in 1991 and has spread north and westwards and mainly caused epidemics in the western United States. A total of 447 isolates collected from 1993 to 2017 were identified as 382 multilocus genotypes (MLGs) using 14 simple sequence repeat markers. The MLGs were clustered into six molecular groups (MGs) using the discriminant analysis of principal components and the hierarchical cluster analysis, and the MGs had significant differences in frequency in different years. MG1 was present in the population prior to the year 2000. MG2, MG3, and MG4 became predominate after 2000. MG5 was detected in all 24 years but more frequent from 2010 to 2017. MG6 was the most recent group detected mainly from 2011 to 2017 and had the highest correlation coefficient with the virulence phenotypes among the MGs. The heterozygosity and genotypic diversity of the Psh populations increased from 2000 to 2017, even more from 2010 to 2017. The results indicate rapid genetic changes from year to year, with major molecular group changes around 2000 and 2010. The possible mechanisms underlying the population changes are discussed.

Genetics of randomly bred cats support the cradle of cat domestication being in the Near East

Cat domestication likely initiated as a symbiotic relationship between wildcats (Felis silvestris subspecies) and the peoples of developing agrarian societies in the Fertile Crescent. As humans transitioned from hunter-gatherers to farmers ~12,000 years ago, bold wildcats likely capitalized on increased prey density (i.e., rodents). Humans benefited from the cats’ predation on these vermin. To refine the site(s) of cat domestication, over 1000 random-bred cats of primarily Eurasian descent were genotyped for single-nucleotide variants and short tandem repeats. The overall cat population structure suggested a single worldwide population with significant isolation by the distance of peripheral subpopulations. The cat population heterozygosity decreased as genetic distance from the proposed cat progenitor’s (F.s. lybica) natural habitat increased. Domestic cat origins are focused in the eastern Mediterranean Basin, spreading to nearby islands, and southernly via the Levantine coast into the Nile Valley. Cat population diversity supports the migration patterns of humans and other symbiotic species.

Development and validation of a low-density SNP panel for paternity and kinship analysis and evaluation of genetic variability and structure of commercial Pacific white shrimp (Litopenaeus vannamei) populations from Brazil

Genetic improvement programs of the Pacific white shrimp (Litopenaeus vannamei) have been implemented worldwide aiming to enhance growth, survival and disease resistance traits. The use of low-density SNP panels for performing high-throughput, low-cost paternity assignments, kinship determination and evaluating genetic variability parameters and structure in L. vannamei broodstock lines will help increase observed genetic gains. Samples from four selection lines from a breeding nucleus (N = 167), from seven retail stores in Brazil (N = 191), and from families (offspring, known dams and putative sires) from a commercial breeding nucleus (N = 257) were used in the study. All samples were genotyped with a set of 96 SNP markers mined from a dataset developed locally. Observed minor allele frequencies for 88 quality-controlled SNPs ranged between 0.11 and 0.5 with an average of 0.38. Mean observed population heterozygosity varied from 0.319 to 0.471. Mean estimated population Fis was 0.022 and ranged from −0.075 to 0.109. STRUCTURE and PCA analysis revealed retail store samples to have a mean composition of 85% from a common population, suggesting a common post larvae producer supplied the different grow out farms and/or wholesale merchants from different sampled areas. Overall average estimated probabilities of non-exclusion considering one known parent and one putative parent was 1.1 × 10–6, 7.0 × 10–4 considering no known parents, and 2.6 × 10–10 considering a putative pair of sire and dam. Parentage analysis using CERVUS resulted in correct dam assignments of all tested offspring. Sire assignments with >95% confidence were obtained in all cases. Obtained results indicate the developed SNP panel provides a viable tool for performing large-scale high-throughput kinship and paternity assignments, and population structure and assignment of commercial Pacific white shrimp broodstock. The developed tool can provide pedigree information and improve genetic gains in breeding programs that seek to increase grow-out survival rates and overall productivity in biologically and non-biologically challenging production environments.

Assessment of genetic diversity and relationship of the two Sanga type cattle of Botswana based on microsatellite markers.

The study was performed to evaluate genetic variation on two Sanga type cattle found in Botswana: Tswana and Tuli using twelve microsatellite markers. All amplified loci were polymorphic with 75 and 77 alleles genotyped in the Tswana and Tuli populations, respectively. The total number of alleles per locus ranged from 2 (BM1818) to 10 (TGLA227) with total mean of 6.25 for Tswana and 6.43 for Tuli population. Almost all the markers showed high polymorphic information content (PIC) apart from BM1818 (0.375) and INRA23 (0.393) which were moderately informative in Tswana population. Most of the markers were in Hardy-Weinberg equilibrium except for CSSRM60 and CSSM66 loci in Tswana population and ETH10, ETH225 and CSSM66 loci in Tuli population. A total of 103 unique alleles were genotyped across the two breeds with 49-shared, and 26 and 28 were unique to Tswana and Tuli populations, respectively. The expected heterozygosity (He) values were higher than the observed heterozygosity (Ho) in both populations: Tswana (He = 0.7895 ± 0.033 vs Ho = 0.631 ± 0.091) and Tuli (He = 0.8123 ± 0.033 vs Ho = 0.556 ± 0.021). The inbreeding coefficient was 0.200 ± 0.002 and 0.332 ± 0.001 in Tswana and Tuli populations, respectively. Analysis of molecular variance revealed 6.8% of the total genetic variation corresponding to differences between the two breeds and 93.2% within populations. The genetic identity between the two breeds was 56% and there were similar levels of multilocus heterozygosity and allelic diversity in the two breeds. The use of Tswana and Tuli breeds in a crossbreeding programme is likely to result in minimal heterosis and therefore not recommended.

Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.

Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity.

Selection Balancing at Innate Immune Genes: Adaptive Polymorphism Maintenance in Toll-Like Receptors

Balancing selection is a classic mechanism for maintaining variability in immune genes involved in host–pathogen interactions. However, it remains unclear how widespread the mechanism is across immune genes other than the major histocompatibility complex (MHC). Although occasional reports suggest that balancing selection (heterozygote advantage, negative frequency-dependent selection, and fluctuating selection) may act on other immune genes, the current understanding of the phenomenon in non-MHC immune genes is far from solid. In this review, we focus on Toll-like receptors (TLRs), innate immune genes directly involved in pathogen recognition and immune response activation, as there is a growing body of research testing the assumptions of balancing selection in these genes. After reviewing infection- and fitness-based evidence, along with evidence based on population allelic frequencies and heterozygosity levels, we conclude that balancing selection maintains variation in TLRs, though it tends to occur under specific conditions in certain evolutionary lineages rather than being universal and ubiquitous. Our review also identifies key gaps in current knowledge and proposes promising areas for future research. Improving our understanding of host–pathogen interactions and balancing selection in innate immune genes are increasingly important, particularly regarding threats from emerging zoonotic diseases.