Inbreeding Coefficient Research Articles

Analysis of Inter-Primer Binding Site Retrotransposon Length Polymorphism in Selected Group of Vaccinium corymbosum

Abstract The genetic variability in 13 selected genotypes of Vaccinium corymbosum using re-trotransposon-based iPBS markers system was characterized in this study. The four selected iPBS primers amplified 232 fragments, average 58 fragments per primer, approximately 53.16% of which were polymorphic. The polymorphism information content of iPBS marker was 0.238. The hierarchical cluster using unweighted pair group method with arithmetic mean analysis divided selected genotypes into two main groups and several subgroups. The values of the Jaccard coefficient of genetic relatedness were between 0.036–0.243. The similarity between two sample sets was 3.6%–24.3%. This study confirmed inter-PBS amplification technique as a reproducible and trustable marker system, but has proved to be an effective DNA fingerprinting technology to generate polymorphism in Vaccinium corymbosum.

Population Structure and Selection Signatures in Chinese Indigenous Zhaotong Pigs Revealed by Whole-Genome Resequencing

Zhaotong pig (ZTP) is a Chinese indigenous pig breed in Yunnan Province, known for its unique body shape and appearance, good meat quality, strong foraging ability, and adaptability. However, there is still a lack of research on its genome. In order to investigate the genetic diversity, population structure, and selection signatures of the breed, we conducted a comprehensive analysis by resequencing on 30 ZTPs and comparing them with genomic data from 10 Asian wild boars (AWBs). A total of 45,514,452 autosomal SNPs were detected in the 40 pigs, and 23,649,650 SNPs were retained for further analysis after filtering. The HE, HO, PN, MAF, π, and Fis values were calculated to evaluate the genetic diversity, and the results showed that ZTPs had higher genetic diversity and lower inbreeding coefficient compared with AWBs. Population structure was analyzed using NJ tree, PCA, ADMIXTURE, and LD methods. It was found that ZTPs were population independent of AWBs and had a lower LD decay compared to AWBs. Moreover, the results of the IBS genetic distance and G matrix showed that most of the individuals had large genetic distances and distant genetic relationships in ZTPs. Selection signatures were detected between ZTPs and AWBs by using two methods, FST and π ratio. Totals of 1104 selected regions and 275 candidate genes were identified. Finally, functional enrichment analysis identified some annotated genes that might affect fat deposition (NPY1R, NPY5R, and NMU), reproduction (COL3A1, COL5A2, GLRB, TAC3, and MAP3K12), growth (STAT6 and SQOR), tooth development (AMBN, ENAM, and ODAM), and immune response (MBL2, IL1A, and DNAJA3). Our results will provide a valuable basis for the future effective protection, breeding, and utilization of ZTPs.

Genetic Diversity and Association Analysis of Traits Related to Water-Use Efficiency and Nitrogen-Use Efficiency of Populus deltoides Based on SSR Markers

Populus deltoides is one of the primary tree species for bioenergy production in temperate regions. In arid/semi-arid northern China, the scarcity of water and nitrogen significantly limits the productivity of poplar plantations. The identification of relevant molecular markers can promote the breeding of resource-efficient varieties. In this study, 188 genotypes of P. deltoides from six provenances served as experimental material. Genetic differentiation analysis, analysis of molecular variance (AMOVA), principal coordinate analysis (PCoA), unweighted pair group method with arithmetic mean (UPGMA) clustering, and genetic structure analysis were performed using selected simple sequence repeat (SSR) markers. Based on these analyses, the association analysis of water-use efficiency (WUE) and nitrogen-use efficiency (NUE) were conducted using general linear model (GLM) and mixed linear model (MLM) approaches. The results showed that 15 pairs of SSR primers successfully amplified across all 188 individuals, with an average of 7.33 alleles (Na) observed per primer pair. The polymorphism information content (PIC) ranged from 0.060 to 0.897, with an average of 0.544, indicating high genetic diversity in the selected markers. The average inbreeding coefficient intra-population (Fis), inbreeding coefficient inter-population (Fit), and inter-population genetic fraction coefficient (Fst) values were 0.005, 0.135, and 0.132, respectively, indicating high heterozygosity, substantial inbreeding within populations, and moderate genetic differentiation, with an average gene flow (Nm) of 1.964, suggesting substantial gene flow between populations. Additionally, molecular variance was primarily within individuals (84.12%). Genetic structure analysis revealed four subgroups, with some degree of genetic admixture among the provenances. In the GLM model, 11 markers were significantly associated with five traits (p < 0.05), with an average contribution rate of 15.82%. Notably, SSR132 and SSR143 were significantly associated with multiple traits (p < 0.05). The MLM model identified two markers (SSR47 and SSR85) significantly associated with ground diameter (p < 0.05) and one marker (SSR80) significantly associated with NUE (p < 0.05). This study identifies loci associated with WUE and NUE, laying a foundation for future genetic improvement and marker-assisted breeding strategies in poplar.

Genetic consequences of the dramatic decline in the north-west pre-caspian saiga (Saiga tatarica tatarica) population: a comparison of modern and museum samples on mtDNA and microsatellite loci

The North-West Pre-Caspian saiga (Saiga tatarica tatarica) population numbers was about 800 thousand individuals in the middle of the last century. There was a dramatic decline at the end of the 20th century, and by 2015 this saiga population numbers and was about five thousand animals. Our paper presents the results of microsatellite loci and of the mtDNA control region analysis obtained for the museum saiga samples from the North-West Pre-Caspian population, collected at the peak of their numbers in the 1950s. We compared these data with our previous results for the samples collected during the population depression in1999–2016. There were no noticeable differences of mtDNA control region diversity between the museum and modern saiga samples. The most vivid genetic consequence of the severe decline in population numbers was a significant increase of the inbreeding coefficient (Fis) calculated from the microsatellite loci.

Genetic Adaptations of the Tibetan Pig to High-Altitude Hypoxia on the Qinghai-Tibet Plateau.

The Tibetan Plateau's distinctive high-altitude environment, marked by extreme cold and reduced oxygen levels, presents considerable survival challenges for both humans and mammals. Natural selection has led to the accumulation of adaptive mutations in Tibetan pigs, enabling them to develop distinctive adaptive phenotypes. Here, we aim to uncover the genetic mechanisms underlying the adaptation of Tibetan pigs to high-altitude hypoxia. Therefore, we conducted a systematic analysis of 140 whole-genome sequencing (WGS) data points from different representing pig populations. Our analysis identified a total of 27,614,561 mutations, including 22,386,319 single-nucleotide variants (SNVs) and 5,228,242 insertions/deletions (INDELs, size < 50 bp). A total of 11% (2,678,569) of the SNVs were newly identified in our project, significantly expanding the dataset of genetic variants in Tibetan pigs. Compared to other pig breeds, Tibetan pigs are uniquely adapted to high-altitude environments, exhibiting the highest genetic diversity and the lowest inbreeding coefficient. Employing the composite of multiple signals (CMS) method, we scanned the genome-wide Darwinian positive selection signals and identified 32,499 Tibetan pig positively selected SNVs (TBPSSs) and 129 selected genes (TBPSGs), including 213 newly discovered genes. Notably, we identified eight genes (PHACTR1, SFI1, EPM2A, SLC30A7, NKAIN2, TNNI3K, and PLIN2) with strong nature selection signals. They are likely to improve cardiorespiratory function and fat metabolism to help Tibetan pigs become adapted to the high-altitude environment. These findings provide new insights into the genetic mechanisms of high-altitude adaptation and the adaptive phenotypes of Tibetan pigs.

Genomic Exploration of Essential Hypertension in African-Brazilian Quilombo Populations: A Comprehensive Approach with Pedigree Analysis and Family-Based Association Studies.

Essential Hypertension (EH) is a global health issue. Despite extensive research, much of EH heritability remains unexplained. We investigated the genetic basis of EH in African-derived individuals from partially isolated quilombo populations in Vale do Ribeira (SP-Brazil). Samples from 431 individuals (167 affected, 261 unaffected, 3 unknown) were genotyped using a 650k SNP array. Estimated global ancestry proportions were 47% African, 36% European, and 16% Native American. We constructed six pedigrees using additional data from 673 individuals and created three non-overlapping SNP subpanels. We phased haplotypes and performed local ancestry analysis to account for admixture. Genome-wide linkage analysis (GWLA) and fine-mapping via family-based association studies (FBAS) were conducted, prioritizing EH-associated genes through systematic approach involving databases like PubMed, ClinVar, and GWAS Catalog. Linkage analysis identified 22 regions of interest (ROIs) with LOD scores ranging 1.45-3.03, encompassing 2363 genes. Fine-mapping (FBAS) identified 60 EH-related candidate genes and 117 suggestive/significant variants. Among these, 14 genes, including PHGDH , S100A10 , MFN2 , and RYR2 , were strongly related to hypertension harboring 29 suggestive/significant SNPs. Through a complementary approach - combining admixture-adjusted GWLA based on Markov chain Monte Carlo methods, FBAS on known and imputed data, and gene prioritizing - new loci, variants, and candidate genes were identified. These findings provide targets for future research, replication in other populations, facilitate personalized treatments, and improve public health towards African-derived underrepresented populations. Limitations include restricted SNP coverage, self-reported pedigree data, and lack of available EH genomic studies on admixed populations for independent validation, despite the performed genetic correlation analyses using summary statistics.

Inbreeding Effect on Maternal Mortality and Fertility in the Habsburg Dynasty.

We investigated inbreeding effects on longevity and fertility in the House of Habsburg, one of the principal royal dynasties of Europe. A total number of 124 Habsburg marriages, involving 107 men and 124 women, in the period of approximately 1450-1800 were considered for the analysis. Kinship and inbreeding coefficients were computed from genealogical information, which included more than 8000 individuals. We found a significant negative association between age of death and inbreeding coefficient (F) in those women who had children (regression coefficient b = -1.06, p = 0.0008). This result led us to investigate possible inbreeding effects on maternal mortality in the period of 4 weeks after the childbirth. A strong inbreeding depression on maternal survival was detected through the Kaplan-Meier curve for groups of women with different level of inbreeding (log-rank test p = 0.0001) and the Cox proportional hazards regression analysis (hazard ratio = 2.36, p = 0.0008). Effect on fertility was also found as more inbred women had longer interbirth intervals (b = 154.66, p = 0.022). Effects of male or female inbreeding on the number of children per woman were not detected through zero-inflated regression models suggesting that reproductive compensation might be occurring among the more inbred and less-fecund women. The effect of inbreeding in adulthood in the Habsburg lineage was at least as important as that previously reported on prereproductive survival. To our knowledge, our results are the first evidence of an inbreeding effect on maternal mortality in humans.

Genetic Diversity Losses in Mantis Shrimp Oratosquilla oratoria Offspring Created for Supportive Releases Using an Ecological Breeding in Earthen Pond Method

ABSTRACTArtificial breeding of mantis shrimp Oratosquilla oratoria, using the ecological breeding in earthen pond (EBEP) method, has been carrying out from 2019, and the produced larvae have always been used for supportive breeding programs in Bohai Bay. To assess the degree of fidelity of enhancement programs used an EBEP method to native genetic pools, genetic diversity at 10 microsatellite loci was analyzed in three hatchery offspring populations, their wild parent stocks, and their wild contemporaneous offspring. Significant decrease in the almost genetic diversity parameters and highly significant differences in shannon's information index (decreasing by 22.54%–40.97%) and allelic richness (33.80%–46.87%) were observed between in hatchery populations. This further created relatively more genetic differentiation between the hatchery and wild population, as the pairwise Fst values and genetic distances showed. The mean pairwise relatedness coefficients showed higher values within hatchery populations and lower values within wild populations. Hatchery populations contained the fewest full‐sib families and offspring were extremely distributed in 10–11 full‐sib groups in each hatchery population. The relatively small number of actual spawning females and large variance in parental contribution to the next generation possibly causes allele reduction in the hatchery population, which in turn leads to a decrease in allelic diversity and an increase in genetic similarities among individuals. Promoting synchrony of ovarian development in females, providing good conditions for incubation and larvae culture and balancing the contributions of parents will be important in future breeding propagation.

Assessment of inbreeding coefficients and inbreeding depression on complex traits from genomic and pedigree data in Nelore cattle.

Nelore cattle play a key role in tropical production systems due to their resilience to harsh conditions, such as heat stress and seasonally poor nutrition. Monitoring their genetic diversity is essential to manage the negative impacts of inbreeding. Traditionally, inbreeding and inbreeding depression are assessed by pedigree-based coefficients (F), but recently, genetic markers have been preferred for their precision in capturing the inbreeding level and identifying animals at risk of reduced productive and reproductive performance. Hence, we compared the inbreeding and inbreeding depression for productive and reproductive performance traits in Nelore cattle using different inbreeding coefficient estimation methods from pedigree information (FPed), the genomic relationship matrix (FGRM), runs of homozygosity (FROH) of different lengths (> 1Mb (genome), between 1 and 2Mb - FROH 1-2; 2-4 Mb FROH 2-4 or > 8 Mb FROH >8) and excess homozygosity (FSNP). The correlation between FPed and FROH was lower when the latter was based on shorter segments (r = 0.15 with FROH 1-2, r = 0.20 with FROH 2-4 and r = 0.28 with FROH 4-8). Meanwhile, the FPed had a moderate correlation withFSNP (r = 0.47) and high correlation withFROH >8 (r = 0.58)and FROH-genome (r = 0.60). The FROH-genome was highly correlated with inbreeding based on FROH>8 (r = 0.93) and FSNP (r = 0.88). The FGRM exhibited a high correlation with FROH-genome (r = 0.55)and FROH >8 (r = 0.51) and a lower correlation with other inbreeding estimators varying from 0.30 for FROH 2-4 to 0.37 for FROH 1-2. Increased levels of inbreeding had a negative impact on the productive and reproductive performance of Nelore cattle. The unfavorable inbreeding effect on productive and reproductive traitsranged from 0.12 to 0.51 for FPed, 0.19-0.59 for FGRM, 0.21-0.58 for FROH-genome, and 0.19-0.54 for FSNP per 1% of inbreeding scaled on the percentage of the mean. When scaling the linear regression coefficients on the standard deviation, the unfavorable inbreeding effect varied from 0.43 to 1.56% for FPed, 0.49-1.97% for FGRM, 0.34-2.2% for FROH-genome, and 0.50-1.62% for FSNP per 1% of inbreeding.The impact of the homozygous segments on reproductive and performance traits varied based on the chromosomes. This shows that specific homozygous chromosome segments can be signs of positive selection due to their beneficial effects on the traits. The low correlation observed between FPed and genomic-based inbreeding estimates suggests that the presence of animals with one unknown parent (sire or dam) in the pedigree does not account for ancient inbreeding. The ROH hotspots surround genes related to reproduction, growth, meat quality, and adaptation to environmental stress. Inbreeding depression has adverse effects on productive and reproductive traits in Nelore cattle, particularly on age at puberty in young bulls and heifer calving at 30 months, as well as on scrotal circumference and body weight when scaled on the standard deviation of the trait.

Identifiable Information Value of Standard Autosomal STR in Indigenous Populations of Russia for Determination of First-Degree Relatedness

The effects of the demographic history of mankind have led to the fact that the indigenous peoples of Dagestan and Siberia are inferior in terms of genetic diversity to the populations of Europe, which affects the level of identification informativeness of standard forensic autosomal markers in these populations. In our study, we evaluated the effectiveness of two standard sets of autosomal STRs (13 CODIS, 20 CODIS, Combined DNA Index System) for the genetic testing of parent-child relatedness in four highly inbred populations of the Russian Federation and the Russian population, using two types of reference frequencies. The results of the study confirmed the assumption that the level of identification informativity of standard autosomal markers in highly inbred populations of Siberia and Dagestan is lower than in the Russian population. The total information content of markers of the new CODIS standard exceeds the threshold values required in the order of the Ministry of Health and Social Development of the Russian Federation (No. 346n). At the same time, the probability of a false positive result increases with an increase in the inbreeding coefficient in the population.

Runs of Homozygosity Decipher Genetic Diversity in Cattle Breed Dwelling in the Colder Regions of the World

Background: Our study focuses on Yakutian cattle, a Siberian native breed, examining its inbreeding and diversity through genome-wide analysis of runs of homozygosity (ROHs). Yakutian cattle are adapted to Siberia’s harsh sub-arctic conditions, enduring temperatures below −70°C. However, the population genetics studies on this breed are scanty, to document the genetic uniqueness in these cattle. Results: We analyzed 40 Yakutian cattle with strict quality control for ROH detection yielding 683 homozygous segments, averaging 17 per individual with an average length of 9 Mb. ROH regions were found to be involved in important pathways pertaining to cold adaptation. Autozygosity ranged from 1% to 12% of the genome, with a relatively low average inbreeding coefficient (FROH) of 0.057, as compared to other breeds. Also, the different diversity indicators, namely, principal component analysis, heterozygosity, and effective population size analysis, revealed the prevalence of genetic diversity within the breed. Conclusion: Our findings on ROH are the first of its kind in Yakutian cattle that support their adaptability to colder environments, as evidenced by low inbreeding and high genetic diversity.

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.

Analyses of whole-genome sequences from 185 North American Thoroughbred horses, spanning 5 generations

Whole genome sequences (WGS) of 185 North American Thoroughbred horses were compared to quantify the number and frequency of variants, diversity of mitotypes, and autosomal runs of homozygosity (ROH). Of the samples, 82 horses were born between 1965 and 1986 (Group 1); the remaining 103, selected to maximize pedigree diversity, were born between 2000 and 2020 (Group 2). Over 14.3 million autosomal variants were identified with 4.5–5.0 million found per horse. Mitochondrial sequences associated the North American Thoroughbreds with 9 of 17 clades previously identified among diverse breeds. Individual coefficients of inbreeding, estimated from ROH, averaged 0.266 (Group 1) and 0.283 (Group 2). When SNP arrays were simulated using subsets of WGS markers, the arrays over-estimated lengths of ROH. WGS-based estimates of inbreeding were highly correlated (r > 0.98) with SNP array-based estimates, but only moderately correlated (r = 0.40) with inbreeding based on 5-generation pedigrees. On average, Group 1 horses had more heterozygous variants (P < 0.001), more total variants (P < 0.001), and lower individual inbreeding (FROH; P < 0.001) than horses in Group 2. However, the distribution of numbers of variants, allele frequency, and extent of ROH overlapped among all horses such that it was not possible to identify the group of origin of any single horse using these measures. Consequently, the Thoroughbred population would be better monitored by investigating changes in specific variants, rather than relying on broad measures of diversity. The WGS for these 185 horses is publicly available for comparison to other populations and as a foundation for modeling changes in population structure, breeding practices, or the appearance of deleterious variants.

Breeding work with kazakh horses Zhabe type

Background and Aim. Kazakh horses of Zhabе type differ from local horses in their higher live weight and larger body measurements. Breeding work with Kazakh horses of the Zhabе type is carried out at Tailak farm in Zharminsky district of East Kazakhstan through targeted reproduction, cultivation, and widespread use of the best individuals based on their origin, exterior, productivity, adaptation to year-round grazing, and quality of offspring from stallions and mares. Individuals that are not up to these standards are strictly culled. The aim of the research is to determine meat productivity and study genetic characteristics of a sample of modern population of Kazakh horses of Zhabe type using DNA markers.Materials and Methods. The material for the study was DNA genotyping data from 20 horses of the Kazakh breed type Zhabe. The horses were genotyped according to 17 STR lоci rеcommended by the Internаtional Sоciety for Animаl Gеnetics (ISАG). The international alphabetical code was used to identify alleles. Genetic and population analyses were performed using the GenAIEx software 6.5. The follоwing indicаtors wеre calculаted: the averаge numbеr of allеles per lоcus (Na), the effеctive numbеr of allеles (Ne), levеls of expеcted (He) and obsеrved heterozygоsity (Ho), and inbreеding cоefficient (FIS) .Results. A study on 17 STR loci of DNA in Kazakh horses Zhabе type has shown that they have a unique allele pool with a significant number of identified alleles and high genetic variability. The average inbreeding coefficient (FIS) is negative (-0.059), indicating that the genetic diversity of this breed is preserved within this group.Conclusion. The improvement of these horses is achieved through breeding and cultivation of animals with high genetic potential for productivity, which is passed down through generations of descendants. This is done by carefully selecting horses with desirable traits for breeding.

Genetic Diversity and Selection Signal Analysis of Hu Sheep Based on SNP50K BeadChip.

This research is designed to examine the genetic diversity and kinship among Hu sheep, as well as to discover genes associated with crucial economic traits. A selection of 50 unrelated adult male Hu sheep underwent genotyping with the SNP50K BeadChip. Seven indicators of genetic diversity were assessed based on high-quality SNP data: effective population size (Ne), polymorphic information content (PIC), polymorphic marker ratio (PN), expected heterozygosity (He), observed heterozygosity (Ho), effective number of alleles, and minor allele frequency (MAF). Plink software was employed to compute the IBS genetic distance matrix and detect runs of homozygosity (ROHs), while the G matrix and principal component analysis were performed using GCTA software. Selective sweep analysis was carried out using ROH, Pi, and Tajima's D methodologies. This study identified a total of 64,734 SNPs, of which 56,522 SNPs remained for downstream analysis after quality control. The population displayed relatively high genetic diversity. The 50 Hu sheep were ultimately grouped into 12 distinct families, with families 6, 8, and 10 having the highest numbers of individuals, each consisting of 6 sheep. Furthermore, a total of 294 ROHs were detected, with the majority having lengths between 1 and 5 Mb, and the inbreeding coefficient FROH was 0.01. In addition, 41, 440, and 994 candidate genes were identified by ROH, Pi, and Tajima's D methods, respectively, with 3 genes overlapping (BMPR1B, KCNIP4, and FAM13A). These results offer valuable insights for future Hu sheep breeding, genetic assessment, and population management.

Population genetic analysis of the Lviv region based on surname data

Aim. The study aimed to determine indicators characterizing the population structure of the Lviv region. Methods. The study employed the method of describing the genetic structure of the population using surnames, as proposed by I. Barrai. Results. Indicators of population structure in district populations of the Lviv region exhibited a wide range of values. The basic index, the isonymy index (I), varied between 2.3 and 26.5 (×10-4). The inbreeding coefficient (FST) ranged from 11.2 to 66.1 (×10-5), the migration index (v) from 70.8 to 212.9 (10-4), the diversity index (a) from 3.8 to 22.9 (×102), the entropy index (H) from 10.0 to 13.0, and the redundancy of surnames (R) from 26.1 to 36.2. In some settlements, there is an accumulation of bearers of the same surname, which can be explained by the founder effect. Conclusions. The rates of isonymy, inbreeding, and migration in district populations were several times higher than those observed in the regional population. The level of isonymy was lowest in areas with high tourist and transit activity.

Pedigree-based analysis of population structure and genetic diversity in high-milch Vrindavani crossbred cattle of India.

The present study aimed to elucidate the population structure and genetic diversity along with the estimation of genealogical parameters in Vrindavani cattle using pedigree data. The study was based on pedigree data on 12,718 animals, spread across multiple generations during a 52-year period (between 1971 and 2023). The pedigree data was used to estimate different population genealogical parameters including the generation interval; pedigree completeness; rate and level of inbreeding; effective population size; and parameters characterizing the probabilities of gene origin. The ENDOG program was used for estimation of different parameters while using population after 2010as reference cohort. The results revealed the maximum number of generations (MG) to be 13, while the numbers of completed (CG) and equivalent generations (EqG) were 3.23 and 1.95, respectively. The mean generation interval for the population was 6.9years. The average inbreeding coefficient of animals in the whole and reference population was 1.11 and 3.44%, respectively; with 0.68% rate of inbreeding per generation. The average additive relationship among all the animals and those in the reference population was 1.16 and 5.49%, respectively. The average effective population sizes for the maximum, equivalent, and complete generations were 115.56, 56.42, and 46.02, respectively. The effective population size on the basis of regression and log-regression on birth date was 77.40 and 71.24, respectively. The probabilities of gene origin were estimated by the effective number of founders (fe) and ancestors (fa), which was 115 and 78, respectively. The fe/fa ratio in the reference population was 1.20, indicating that occasional bottlenecks may have occurred in the population. The analysis revealed a loss of 5.3% of total heterozygosity as compared to base population, though significant variability exists in the latest generations. The results revealed that considerable genetic variability exists within the population that may be exploited through appropriate breed improvement programs targeting various economic traits.

Study of extended homozygous chromosome regions in Italian partridge breed of chickens

Selection and accompanying inbreeding are the basis for breeding chicken breeds. With the advent of modern molecular methods for assessing inbreeding, it has become possible to identify genes and their functions in the homozygous regions (ROH) of chicken chromosomes. In this study, a genome-wide analysis of homozygous regions of chromosomes in Italian partridge chickens was carried out using an SNP chip Illumina Chicken 60KSNPiSelectBeadChipchip. An average of 177 ± 5 ROH-sequences per chicken were identified in the chicken chromosomes, and the average inbreeding coefficient was 0.30 ± 0.01. It was determined that the chicken genome is dominated by short ROH-sequences of 0.25–2 Mbp. ROH-sequences longer than 8 Mbp indicating recent inbreeding account for no more than 2.2%. It was found that, in general, ROH-sequences are more densely distributed in chicken microchromosomes, with the exception of chromosome 16, which does not have ROH-sequences. This fact is due to the heterozygosity of the alleles of the genes responsible for immunity, located in microchromosome 16. ROH-islands were found in the chicken chromosomes 1, 5, and 14. The genes in ROH-islands are responsible for feather pecking in chickens (DMD gene), immune status (TAB3, EIF2S3 genes), body weight (IL1RAPL1 gene), pH of meat (EIF2S3, APOO, KLHL15 genes), egg production (APOO gene), feed uptake (SAT1 gene), aggressiveness of roosters (SLITRK6 gene), transport of intracellular components in developing neurons and protection of heterochromatin in the cell nuclei of neurons (NDE1 gene), adaptation of chickens to tropical living conditions (CDIN1 gene). Thus, ROH analysis allowed us to identify genes potentially selectable as a result of breeding Italian partridge breed chickens.

Pedigree-Based Description of Danubia Alba Rabbit Breed Lines.

The diversity of livestock animal breeds is an integral part of global biodiversity and requires careful management for sustainability and future availability. Avoiding inbreeding is a crucial aspect of mating of breeding animals. Our aims were to describe the quality of the pedigree, generation interval, gene origin, inbreeding, and effective population size of Danubia Alba rabbit lines. Line "D" is the maternal, whereas lines "C" and "X" are used as the paternal lines. The pedigree information was followed back from the actual breeding rabbits up to the founder animals. The rabbits having offspring in 2023 were chosen as reference populations for each line. The complete generation equivalent (GenCom) was 17.68 for line "C", 18.32 for line "D", and 17.49 for line "X", respectively. The maximum number of generations (GenMax) was above 30 for each line. The estimated bottleneck effect is mostly the result of selection and not a real genetic loss. The Wright inbreeding coefficient (F_Wright) was the highest for the "X" line rabbits, whereas it was the lowest for the line "D". Kalinowski's decomposition of inbreeding showed that it originated mostly from the past; the current fixation of alleles was quite similar for the line "C" and "D". Based on the predicted effective population sizes, it seems that there is no problem in maintaining of Danubia Alba lines.

Unraveling the genomic diversity and admixture history of captive tigers in the United States

Genomic studies of endangered species have primarily focused on describing diversity patterns and resolving phylogenetic relationships, with the overarching goal of informing conservation efforts. However, few studies have investigated genomic diversity housed in captive populations. For tigers (Panthera tigris), captive individuals vastly outnumber those in the wild, but their diversity remains largely unexplored. Privately owned captive tiger populations have remained an enigma in the conservation community, with some believing that these individuals are severely inbred, while others believe they may be a source of now-extinct diversity. Here, we present a large-scale genetic study of the private (non-zoo) captive tiger population in the United States, also known as "Generic" tigers. We find that the Generic tiger population has an admixture fingerprint comprising all six extant wild tiger subspecies. Of the 138 Generic individuals sequenced for the purpose of this study, no individual had ancestry from only one subspecies. We show that the Generic tiger population has a comparable amount of genetic diversity relative to most wild subspecies, few private variants, and fewer deleterious mutations. We observe inbreeding coefficients similar to wild populations, although there are some individuals within both the Generic and wild populations that are substantially inbred. Additionally, we develop a reference panel for tigers that can be used with imputation to accurately distinguish individuals and assign ancestry with ultralow coverage (0.25×) data. By providing a cost-effective alternative to whole-genome sequencing (WGS), the reference panel provides a resource to assist in tiger conservation efforts for both ex- and in situ populations.