Inbreeding Values Research Articles

Unravelling genetic diversity and genetic structure of Senna italica Mill. in Rabigh region, Saudi Arabia

Senna italica is a perennial plant distributed in desert and subtropical regions of the world. In Rabigh Province, western Saudi Arabia, the few persisting populations of this species are exposed to many threats, including overcutting and, recently, human habitation. These threats are predicted to be exacerbated with the advancement of aridification caused by climate change. The conservation and revival of the diminished populations of S. italica requires an assessment of their genetic diversity and genetic differentiation. To accomplish this objective, we applied 10 simple sequence repeat (SSR) primer pairs, with which 10 polymorphic loci were confirmed. These polymorphic loci were used to determine the population genetics of 60 plant accessions sampled from 5 populations of S. italica located in five sites in Rabigh Province: Wadi EL Khaneg, Wadi Al Johfa, Wadi Al Hakak and Wadi Khurieba and Wadi Wadi Albaidaa . Low to moderate levels of genetic diversity were found in all populations (the values of the PPL% ranged between 51.5% and 21.5%) along with a decreased value of HT (0.451) and a considerable inbreeding value (F= 0.4552), which verified an obvious shortage of heterozygotes. High genetic differentiation among the populations and a low level of gene flow suggest isolation among the S. italica populations, which caused a severe deficiency in gene migration. The data obtained herein will inspire several recommendations for conservation the existing populations, including seed preservation, and management of human activities. All of these actions are urgently needed to prevent imminent extinction.

Genome-wide analyses of genomic diversity, population structure and selection signatures in Italian turkey populations

Italian local turkey populations are an important source of genetic diversity that should be preserved through an in vivo approach. Whole genome sequencing (WGS) and genotyping datasets were used to assess genetic variability within and across populations, to perform a genome-wide comparative analysis among populations and to identify selection signatures in Italian turkey populations. We used new data from 73 WGS samples (12X) representing five turkey populations, together with previous data from 107 birds genotyped with the Affymetrix 600K single nucleotide polymorphism (SNP) turkey array from 11 populations. The PCA and Admixture show a relatively strong isolation effect between the populations. Moreover, the values of genomic inbreeding based on ROH (FROH) showed marked differences among populations and ranged from 0.096 to 0.643. Selective sweeps were identified using the integrated haplotype score (iHS) within the local group, the commercial line, and the Narragansett breed, resulting in the identification of 20, 19, and 27 regions with a total of 73, 48, and 90 candidate genes, respectively. Some of these genes such as FAM107B, MSTN, PDZRN4, HSF2 and GJA1 are associated with heat stress, growth, and carcass traits. We conclude that our results improve our understanding of the genomic architecture of the Italian turkey populations. The findings of iHS suggest that selection can play a significant role in shaping selection signatures in local turkey populations and could provide a basis for identifying gene mutations that may be beneficial in adaptation to climate change. Our results will be useful in developing and implementing conservation and selection plans for Italian turkey populations.

Взаимосвязь геномного и расчетного инбридинга в популяции крупного рогатого скота голштинской породы Свердловской области

Abstract. The purpose of this paper is to study the inbreeding change of Holstein cattle in Sverdlovsk region and to show the correlation between genomic and estimated inbreeding. Methods. The study was conducted in six farms of the Sverdlovsk region and included 512 cows and heifers with date of birth from 2007 to 2022 and 12 breeding bulls. Chips GGP Bovine 150K (Neogen, USA) and Bovine 50K (Illumina, USA) were used for genotyping. Genome inbreeding estimates F were conducted with --het function in PLINK v1.9. Homozygosity inbreeding coefficient FROH was calculated with “sliding window” package of detectRUNS; FPED was taken from SELEX database, where it was calculated by pedigrees with Wright-Kislovsky formula. Scientific novelty. The comparison of genomic inbreeding for different age groups and estimation of correlations with pedigree inbreeding was conducted in Sverdlovsk region for the first time. Results. Our studies show that inbreeding coefficients increase radically from younger to older age groups. Holstein breed bulls show the highest value of inbreeding. At the same time heterozygosity level, estimated with sMLH tends to decrease with age. In addition, a strong correlation between estimated by pedegree inbreeding FPED and date of birth, as well as weak correlations between FPED and genomic coefficients (which have strong correlations with each other) were established.

Ultraviolet signaling in a butterfly is preferred by females and conveys male genetic quality.

Indicator models of sexual selection posit that females choose males on the basis of traits that reveal male genetic quality and thereby enjoy increased offspring production. Here, we report that females of the butterfly Eurema hecabe receive indirect benefits from choosing males based on their ultraviolet (UV) wing coloration, a heritable and condition-dependent trait in this species. We first used a large laboratory-bred pedigree to demonstrate a per-family association between inbreeding and male UV trait value. Females exerted choice for UV-bright males within this protocol, and the average male UV trait value increased over six consecutive generations, presumably due to such selection and despite an increasing rate of pedigree-wide inbreeding. We then experimentally imposed a standard strength of inbreeding upon lines of divergent male UV trait values. Inbreeding depressed the siring performance of low UV treatment males more severely and resulted in a marginal reduction of their UV brightness, which rebounded sharply following subsequent outcrossing. These findings are consistent with the ornament-based signaling of genetic quality as a function of underlying individual-level mutational load.

Genealogical structure and genetic variability: A step towards conservation of white Morada Nova sheep in semi-arid region

Morada Nova breed has a low effective herd, and its white variety is in risk of extinction in Brazilian semi-arid region. This study aimed to evaluate white Morada Nova sheep’s genetic variability and population structure in four flocks. These are the only flocks in the world. The assessed parameters of pedigree integrity and a genealogy record of 219 animals. 44.74 % did not have pedigree information on their mother or father, and 50.47 % did not have available information on their grandparents. 52.97 % had a pedigree in their first ancestry (obtained through the average of known parents), 23.74 % in the second, 13.58 % in the third, and 5.33 % in the fourth. The effective size was 10.7, considering the complete equivalent generation. The effective number of founding animals (fe) and ancestors (fa) was 10, indicating the effective participation of all founding animals in the population over the generations, reducing losses of genetic variability. Out of all the ancestors, only 3 explained 50 % of the population’s genetic variability, reflecting the low values of fa and fe. The population’s average inbreeding and kinship coefficients were 2.61 and 4.54. The F statistics of Wright, Fis, Fst, and Fit, were −0.012, 0.016, and 0.003. The genetic conservation index (GCI) had an average of 2.01 ± 1.29, with minimum and maximum values of 1.0 and 6.38, respectively. Approximately, 71 % of the population had GCI below 2.0, while only 5.9 % of sheep had an GCI bigger than 5.0. This indicates the absence of sub-structures inf the population. There is no population subdivision, considering the genealogical structure of the evaluated flocks. The inbreeding and kinship coefficient values are controlled and serve as a starting point for establishing a future management plan for the genetic variability of the flock. It is recommended to use strategies to increase the effective population size, to meet the minimum number recommended by FAO and to promote the conservation and genetic improvement of the breed.

Population genetics and phylogeographic history of the insular lizard Podarcis lilfordi (Gunther, 1874) from the Balearic Islands based on genome-wide polymorphic data.

Islands provide a great system to explore the processes that maintain genetic diversity and promote local adaptation. We explored the genomic diversity of the Balearic lizard Podarcis lilfordi, an endemic species characterized by numerous small insular populations with large phenotypic diversity. Using the newly available genome for this species, we characterized more than 300,000 SNPs, merging genotyping-by-sequencing (GBS) data with previously published restriction site-associated DNA sequencing (RAD-Seq) data, providing a dataset of 16 island populations (191 individuals) across the range of species distribution (Menorca, Mallorca, and Cabrera). Results indicate that each islet hosts a well-differentiated population (F ST = 0.247 ± 0.09), with no recent immigration/translocation events. Contrary to expectations, most populations harbor a considerable genetic diversity (mean nucleotide diversity, P i = 0.144 ± 0.021), characterized by overall low inbreeding values (F IS < 0.1). While the genetic diversity significantly decreased with decreasing islet surface, maintenance of substantial genetic diversity even in tiny islets suggests variable selection or other mechanisms that buffer genetic drift. Maximum-likelihood tree based on concatenated SNP data confirmed the existence of the two major independent lineages of Menorca and Mallorca/Cabrera. Multiple lines of evidence, including admixture and root testing, robustly placed the origin of the species in the Mallorca Island, rather than in Menorca. Outlier analysis mainly retrieved a strong signature of genome differentiation between the two major archipelagos, especially in the sexual chromosome Z. A set of proteins were target of multiple outliers and primarily associated with binding and catalytic activity, providing interesting candidates for future selection studies. This study provides the framework to explore crucial aspects of the genetic basis of phenotypic divergence and insular adaptation.

Comprehensive analysis of runs of homozygosity and heterozygosity in Holstein cattle on the basis of medium and high density SNP panels and large population sample

Abstract This study reports runs of homozygosity (ROH) and heterozygosity (ROHet) distributed in a large population of Holstein cattle on the basis of two microarrays of medium (50k; 2163 animals; 54 609 SNPs) and high single nucleotide polymorphism (SNP) density (HD; 600 animals; 777 692 SNPs). To assess the inbreeding values of Holstein cattle, the ROH-based genomic inbreeding coefficient (FROH) was calculated. The comparison of SNP panels suggested that FROH values above 4 Mb should be considered for panels of medium densities as a relatively reliable measure of inbreeding. Moreover, ROH hotspots and coldspots were identified and compared between the HD and 50k SNP panels and were carefully examined for association with production and functional traits. The obtained results pinpointed genomic regions presumably under selection pressure in Holstein cattle. The regions overlapped with a large number of genes, including GHR, GBF1, SUMF1, CCL28, NIM1K, U6, BTRC and FABP1, many of which are involved in important Holstein cattle characteristics. We also found that some ROH hotspots and coldspots identified with the HD panel were not detected with the 50k panel, mainly because of insufficient SNP density in certain genomic regions. This suggests that using medium-density panels might not be the best choice when precise identification of ROH patterns is the main goal. In summary, in this work, we confirmed that a high-density SNP panel compared to a medium-density SNP panel allows for more precise identification of ROH patterns, especially in the case of short ROH that could be associated with ancestral inbreeding.

Analysis of the level of inbreeding and relatedness of Bull Terrier dogs – the popular stud dog effect

The aim of the study was to analyze the level of homozygosity of a bull terrier dog population due to its small size, forcing mating in kinship and, possibly, overuse of popular stud dogs. The pedigrees of 107 bull terrier dogs (35 males and 72 females), born in 2008-2016 were used to obtain the inbreeding coefficients for all animals and relatedness coefficients between dogs, between bitches and between bitches and dogs. Pedigrees of bull terriers were also analyzed for occurrence the most common stud dogs. The frequency of occurrence of a popular sire was found according to its position in the pedigree. For the most common stud dog, a list of his sons and their progeny was created. In total about 75% of individuals from the studied population were inbred and their average inbreeding was over 0.04. Almost 95% of bull terriers were related with the average relatedness amounting to over 0.07. The highest value of an individual's inbreeding was almost 0.18, and the highest relationship coefficient was between bitches (over 0.61). There was a popular stud dog in the analyzed population that appeared 113 times in the pedigrees of 107 tested animals and his genes were passed on by his 10 sons as well. It should be noticed that the studied population requires constant monitoring of genetic variability and limiting the overuse of popular stud dogs, which should lead to maintain the variability.

Genome-Wide Analysis of Milk Production Traits and Selection Signatures in Serbian Holstein-Friesian Cattle.

To improve the genomic evaluation of milk-related traits in Holstein-Friesian (HF) cattle it is essential to identify the associated candidate genes. Novel SNP-based analyses, such as the genetic mapping of inherited diseases, GWAS, and genomic selection, have led to a new era of research. The aim of this study was to analyze the association of each individual SNP in Serbian HF cattle with milk production traits and inbreeding levels. The SNP 60 K chip Axiom Bovine BovMDv3 was deployed for the genotyping of 334 HF cows. The obtained genomic results, together with the collected phenotypic data, were used for a GWAS. Moreover, the identification of ROH segments was performed and served for inbreeding coefficient evaluation and ROH island detection. Using a GWAS, a polymorphism, rs110619097 (located in the intron of the CTNNA3 gene), was detected to be significantly (p < 0.01) associated with the milk protein concentration in the first lactation (adjusted to 305 days). The average genomic inbreeding value (FROH) was 0.079. ROH islands were discovered in proximity to genes associated with milk production traits and genomic regions under selection pressure for other economically important traits of dairy cattle. The findings of this pilot study provide useful information for a better understanding of the genetic architecture of milk production traits in Serbian HF dairy cows and can be used to improve lactation performances in Serbian HF cattle breeding programs.

Pedigree analysis in the mhorr gazelle (Nanger dama mhorr): Genetic variability evolution of the captive population.

Breeding programs have an essential role in the recovery of threatened populations through optimal genetic management and mating strategies. The dama gazelle (Nanger dama) is a North African ungulate listed as critically endangered. The mhorr subspecies is extinct in the wild and currently survives thanks to the creation in 1971 of an ex situ breeding program. The aim of the present study was to assess the evolution of genetic variability in this mhorr gazelle captive population, as well as the mating strategy used in two reference populations studied (Almeria and Europe). The entire pedigree, with 2739 animals, was analyzed to measure demographic characters, pedigree completeness level, probability of gene origin, level of relatedness and genetic structure of the population. The population size has been progressively increasing, with up to 264 individuals alive in Europe at the time of the study. The average number of equivalent complete generations was 5.55. The effective number of founders and ancestors was both 3, and the founder genome equivalent was 1.99. The genetic contributions of the four main ancestors were unbalanced. The average values of inbreeding and average relatedness for the whole pedigree were, respectively, 28.34% and 50.14%. The effective population size was 8.7 by individual increase in inbreeding and 9.8 by individual increase in coancestry. F-statistics evidenced a very small level of population subdivision (F ST = 0.033370). The mating strategy used, based on the minimum coancestry of the individuals, has minimized the losses of genetic variability and helped to balance the genetic contributions between ancestors. The strategy also avoided large subdivisions within the population and the appearance of new bottlenecks. This study shows how pedigree analysis can both be used to determine the genetic variability of the population and to assess the influence of the mating strategy used in the breeding program on such variability.

Genetic characteristics of Atlantic salmon (Salmo salar) stocking material released into Polish rivers

Abstract In Poland, stocking rivers with Atlantic salmon (Salmo salar L.) began in the nineteenth century, and become intensive in the 1990s. Currently, it is performed by the Polish Angling Association, and institutions involved in the program “Stocking Polish Marine Areas.” The aim of this study was to evaluate the genetic variation of the salmon stocked in recent years in Poland. For this purpose, salmon stocks from three broodstocks and two river populations (Słupia and Parsęta) were investigated. Eleven microsatellite loci were amplified. The total number of alleles detected across all loci ranged from 46 to 81 in the stocks. The average observed heterozygosity across all investigated loci was 0.59; and the expected heterozygosity was 0.58. The populations remained in Hardy–Weinberg equilibrium. The average Garza-Williamson M index value for all populations was low suggesting a reduction in genetic variation because of the founder effect. Genetic distance among populations was high between the Lithuanian stock (Rutki and Parsęta) and the group of Latvian origin (Aquamar–Żelkówko–Słupia). Several admixture traces were recorded in all stocks with the smallest evidence of this in the Rutki stock. Inbreeding values per generation were typical of those observed in breeding stocks (0–3%). The effective population size values were low or very low for all the stocks (Ne 15-37).

Genomic analysis of geographical structure and diversity in the capercaillie (Tetrao urogallus)

The capercaillie is widespread throughout the boreal forests of northern Eurasia, but faces serious conservation challenges in the southernmost mountain ranges, where the populations are fragmented and some are critically endangered. To develop effective conservation strategies for these populations, it is essential to have information on both their genetic diversity and the genetic structure of the species. In this work, we used a reduced representation (ddRAD) genomic sequencing technique to analyze the genetic structure of the capercaillie across its European range and to assess the inbreeding levels in some of the most threatened populations. Our population structure analysis suggested the existence of two evolutionarily significant units, one formed by the two populations from the Iberian Peninsula and the other by the populations from the rest of Europe. Genetic diversity showed a significant decrease in the Iberian populations with respect to the other European populations. An isolation-with-migration model supported these results and allowed us to estimate the parameters of the population tree. The inbreeding coefficients estimated for the Iberian capercaillies showed relatively low levels in the Pyrenees. However, some individuals with very high inbreeding values were detected in the Cantabrian Mountains, suggesting that some of its subpopulations are substantially isolated. The population structure results and the genomic monitoring method we used to assess inbreeding levels may be crucial for the conservation and recovery of the most endangered capercaillie populations.

Genome-wide scan for runs of homozygosity in South American Camelids

BackgroundAlpaca (Vicugna pacos), llama (Lama glama), vicugna (Vicugna vicugna) and guanaco (Lama guanicoe), are the camelid species distributed over the Andean high-altitude grasslands, the Altiplano, and the Patagonian arid steppes. Despite the wide interest on these animals, most of the loci under selection are still unknown. Using whole-genome sequencing (WGS) data we investigated the occurrence and the distribution of Runs Of Homozygosity (ROHs) across the South American Camelids (SACs) genome to identify the genetic relationship between the four species and the potential signatures of selection.ResultsA total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500 kb) and genomic inbreeding values. Longer ROHs (> 500 kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively.ConclusionsThe signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to harsh environment. Alpaca and llama hint a selection driven by environment as well as by farming purpose while vicugna and guanaco showed selection signals for adaptation to harsh environment. Interesting, signatures of selection on KAT6B gene were identified for both vicugna and guanaco, suggesting a positive effect on wild populations fitness. Such information may be of interest to further ecological and animal production studies.

Inbreeding depression and its effect on sperm quality traits in Pietrain pigs.

In most cases, inbreeding is expected to have unfavourable effects on traits in livestock. The consequences of inbreeding depression could be substantial, primarily in reproductive and sperm quality traits, and thus lead to decreased fertility. Therefore, the objectives of this study were (i) to compute inbreeding coefficients using pedigree (FPED ) and genomic data based on runs of homozygosity (ROH) in the genome (FROH ) of Austrian Pietrain pigs, and (ii) to assess inbreeding depression on four sperm quality traits. In total, 74,734 ejaculate records from 1034 Pietrain boars were used for inbreeding depression analyses. Traits were regressed on inbreeding coefficients using repeatability animal models. Pedigree-based inbreeding coefficients were lower than ROH-based inbreeding values. The correlations between pedigree and ROH-based inbreeding coefficients ranged from 0.186 to 0.357. Pedigree-based inbreeding affected only sperm motility while ROH-based inbreeding affected semen volume, number of spermatozoa, and motility. For example, a 1% increase in pedigree inbreeding considering 10 ancestor generations (FPED10 ) was significantly (p < 0.05) associated with a 0.231% decrease in sperm motility. Almost all estimated effects of inbreeding on the traits studied were unfavourable. It is advisable to properly manage the level of inbreeding to avoid high inbreeding depression in the future. Further, analysis of effects of inbreeding depression for other traits, including growth and litter size for the Austrian Pietrain population is strongly advised.

Population Genetics, Genetic Structure, and Inbreeding of Commiphora gileadensis (L.) C. Chr Inferred from SSR Markers in Some Mountainous Sites of Makkah Province.

Commiphora gileadensis (L.) C. Chr is a perennial plant existing mainly in the southern and western mountains of the Arabian Peninsula. In the Makkah province, the remaining populations are threatened by many factors such as overcutting, overgrazing, and urban developments. These dangers are expected to be aggravated by the progression of aridification factors arising from climate change. To overcome the decline in remaining populations of this valuable species, a timely evaluation of the population's genetic variables and genetic structure is vital for the conservation of existing C. gileadensis populations. In this study, we used 61 SSR primers to achieve this objective. Only 50 loci showed polymorphisms, which led to further analysis of the population genetics for 600 genotypes that were collected from 50 populations of C. gileadensis found in 10 different sites in the Makkah region: Gebel Al Muliesaa, Wadi Albathna, Wadi Houra, Wadi Albaidaa, Wadi Elebiedia, Gebel Kniethl, Wadi Sayaa, Wadi Elbarasa, Wadi Alfawara, and Wadi Alkharar. The results showed an obvious decrease in genetic diversity variables in all studied populations. The range of PPL was between 8 and 40; additionally, the low HT value of 0.804 and the high value of inbreeding, Fis = 0.238, reflected a severe lack of heterozygotes. High levels of FST and GST and low gene flow indicate considerable segregation among the C. gileadensis populations, which creates a barrier to gene migration. Our data suggest the need for conservation planning for C. gileadensis in order to avoid the species' forthcoming extinction. Efforts should be largely oriented around managing water consumption, prohibiting overcutting and overgrazing, and establishing appropriate seed banks.

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.

Genetic diversity analysis of Indonesian indigenous goat breeds based on microsatellite markers

Goats are important livestock in Indonesia as a source of animal protein and income. Indonesia has several indigenous goat breeds with distinct characteristics. 379 unrelated goats were randomly selected from seven indigenous Indonesian goat breeds and collected from individual farmers in various Indonesian provinces. Microsatellite characterization of indigenous Indonesian goats was carried out using 12 specific microsatellite markers. The total number of alleles obtained from the 12 microsatellite loci was 97, with an average score of 8.08, and the number of effective alleles ranged from 1.413 (ILSTS005) to 4168 (INRA23), with an average value of 2.608. A total of 11 private alleles was found in some goat breeds, but the frequencies were very low, 0.71 – 8.86%. The average of polymorphic information content ranged from 0.239 (ETH10) to 0.726 (INRA23). The mean rate of inbreeding value between populations (Fis) was 0.050, and within the population (Fit) was 0.151. The mean expected heterozygosity was 0.54, and the mean observed heterozygosity was 0.52. Except for the Gembrong goat (GEM), the observed number of alleles, polymorphic information content, and expected heterozygosity were all moderate. This study will support the management of livestock genetic resources and conserving endangered Indonesian goat breeds, such as the Gembrong goat.

Uncovering inbreeding, small populations, and strong genetic isolation in an Australian threatened frog, Litoria littlejohni

AbstractThe status of many amphibian populations remains unclear due to undetected declines driven by disease and difficulties in obtaining accurate population estimates. Here, we used genome complexity reduction-based sequencing technology to study the poorly understood Littlejohn’s treefrog, Litoria littlejohni across its fragmented distribution in eastern Australia. We detected five identifiable genetic clusters, with moderate to strong genetic isolation. At a regional scale, population isolation was likely driven by population crashes, resulting in small populations impacted by founder effects. Moderate genetic isolation was detected among populations on the Woronora Plateau despite short distances between population clusters. Evidence of recent declines was apparent in three populations that had very small effective population size, reduced genetic diversity and high inbreeding values. The rates of inbreeding detected in these populations combined with their small size leave these populations at elevated risk of extinction. The Cordeaux Cluster was identified as the most robust population as it was the largest and most genetically diverse. This study exemplifies the value of employing genetic methods to study rare, cryptic species. Despite low recapture rates using traditional capture-recapture demographic methods, we were able to derive population estimates, describe patterns of gene flow, and demonstrate the need for urgent conservation management.

The Relationship between Inbreeding and Fitness Is Different between Two Genetic Lines of European Bison

The pedigree data for European bison are published in the European Bison Pedigree Book, established one hundred years ago. The species passed a serious bottleneck and was kept in captivity for more than 30 years. After reintroduction, some individuals were captured and moved to enclosures, which caused gaps in pedigree data. To prevent the underestimation of inbreeding value, only animals with a fully known pedigree were used in the analysis. European bison were divided into two genetic lines, Lowland-Caucasian (LC) and Lowland (LB), with different numbers of founders (all 12 vs. 7 of them). The relation between inbreeding and survival up to one month of age, calculated using logistic regression, gave different results for every genetic line. In the LC line (N = 5441), the average inbreeding level was equal to 0.253 and the influence into survival was negative (exp(B) = 0.190), but in the LB line (N = 1227), the inbreeding level was much higher (0.410) but the influence into survival was positive (exp(B) = 6.596). It could be assumed that the difference between lines is a result of purging in the first period of species restitution.

Genetic relationships of the Yucatan black hairless pig with Iberian breeds using single nucleotide polymorfisms

To conduct ex-situ creole pig conservation programs, it is essential to determine which breeding animals will be used, preferentially those with a more significant Iberian genetic component to preserve their origin. This study used a Yucatan black hairless pigs (YBHP) subpopulation to estimate its genetic diversity and population structure. One hundred four adult pigs were selected for the absence of hair, black skin (without spots), black hoof, and straight snout. The porcine-GGP-50K chip was used for SNP genotyping in YBHP, and information on Iberian and Yucatán hairless pigs from the United States (USYU) was taken from databases. All analysis was performed using PLINK v1.9 and v2.1 software. Inbreeding and fixation index values were lower in YBHP, with high observed heterozygosity and allogamy index values, which agree with those obtained in the populations of Canarias and Chato Murciano. According to the clusters generated by the “Genome-Wide Identity by State” analysis, four groups were identified, one of which included pigs from Guadyerbas, USYU, and YBHP. Between populations, YBHP was closely related to the hairless pigs from Guadyerbas, USYU, and Canarias. Principal component analysis showed the same result. According to the results obtained from the runs of homozygosity investigation, aimed to get pools consensus of regions of overlapping, 119 SNPs associated with genes and biological processes were identified. The BMP7 and NSUN2 genes were associated with epithelial cell differentiation, morphogenesis, and epithelial development. For nutrient metabolism: energy, the HADHA, PPARA, ADD1/SREBF1, and FAT1genes were identified.