Inbreeding Coefficient Research Articles

Genomic characterisation and diversity assessment of eight endangered Belgian sheep breeds

Assessing the genetic diversity of local breeds is essential for conserving these unique breeds, which may possess unique traits. This study provides the genomic characterisation of eight indigenous sheep breeds in Belgium based on pedigree and single nucleotide polymorphism (SNP) analysis. A total of 687 sheep were genotyped and were subjected to a rigorous quality control, resulting in a set of 45 978 autosomal SNPs. Pedigree analysis showed breed-average inbreeding estimates between 3.3% and 11.3%. The genomic analysis included an assessment of runs of homozygosity (ROH) to examine the genomic inbreeding coefficient, with breed-average inbreeding coefficients estimated between 4.1% and 8.5%. Runs of homozygosity islands were identified in six of the eight breeds studied, with some exhibiting an incidence of up to 58%. Interestingly, several ROH islands overlapped with other breeds included in this study, as well as with international sheep breeds. Pedigree-based effective population sizes were estimated below 100 for all breeds, whereas genomic-based effective population sizes were below 24, indicating that these eight local sheep breeds are endangered. Principal component analysis, admixture analyses, and Fst computations were used to study the population structure and genetic differences. A neighbour−joining tree using 95 international sheep breeds positioned the eight local breeds in the group of milksheep, Texel sheep and the Scandinavian breeds. Additionally, the investigation of paternal oY1 genotypes revealed diverse lineage origins within the Belgian sheep population. This study refines and deepens our knowledge about the local sheep breeds in Belgium, thereby improving their management and conservation. Moreover, as these breeds are linked to other international breeds, these insights are significant for the global scientific community.

Genetic Structure and Genome-Wide Association Analysis of Growth and Reproductive Traits in Fengjing Pigs.

The Fengjing pig is one of the local pig breed resources in China and has many excellent germplasm characteristics. However, research on its genome is lacking. To explore the degree of genetic diversity of the Fengjing pig and to deeply explore its excellent traits, this study took Fengjing pigs as the research object and used the Beadchip Array Infinium iSelect-96|XT KPS_PorcineBreedingChipV2 for genotyping. We analyzed the genetic diversity, relatedness, inbreeding coefficient, and population structure within the Fengjing pig population. Our findings revealed that the proportion of polymorphic markers (PN) was 0.469, and the effective population size was 6.8. The observed and expected heterozygosity were 0.301 and 0.287, respectively. The G-matrix results indicated moderate relatedness within the population, with certain individuals exhibiting closer genetic relationships. The NJ evolutionary tree classified Fengjing boars into five family lines. The average inbreeding coefficient based on ROH was 0.318, indicating a high level of inbreeding. GWAS identified twenty SNPs significantly associated with growth traits (WW, 2W, and 4W) and reproductive traits (TNB and AWB). Notably, WNT8B, RAD21, and HAO1 emerged as candidate genes influencing 2W, 4W, and TNB, respectively. Genes such as WNT8B were verified by querying the PigBiobank database. In conclusion, this study provides a foundational reference for the conservation and utilization of Fengjing pig germplasm resources and offers insights for future molecular breeding efforts in Fengjing pigs.

Does a coexisting congener of a mixed mating species affect the genetic structure and selfing rate via reproductive interference?

Reproductive interference is defined as an interspecific interaction that reduces fitness via mating processes. Although its ecological and evolutionary consequences have attracted much attention, how reproductive interference affects the population genetic structures of interacting species is still unclear. In flowering plants, recent studies found that self-pollination can mitigate the negative effects of reproductive interference. Selfing-biased seed production is expected to increase population-level inbreeding and the selfing rate, and limits gene flow via pollinator outcrossing among populations. We examined the population genetics of the mixed-mating annual herb Commelina communis f. ciliata, focusing on reproductive interference by the sympatric competing congener C. communis using microsatellite markers. First, we found that almost all C. c. f. ciliata populations had relatively high inbreeding coefficients. Then, comparing sympatric and allopatric populations, we found evidence that reproductive interference from a competing congener increased the inbreeding coefficient and selfing rate. Allopatric populations exhibit varied selfing rates while almost all sympatric populations exhibit extremely high selfing rates, suggesting that population selfing rates were also influenced by unexamined factors, such as pollinator limitation. Besides, our findings revealed that reproductive interference from a competing congener did not limit gene flow among populations. We present the first report on how reproductive interference affects the genetic aspects of populations. Our results suggested that the high selfing rate of C. c. f. ciliata promotes its sympatric distribution with C. communis, even in the presence of reproductive interference, although it is not clear whether reproductive interference directly causes the high selfing rate.

GENETIC DIVERSITY OF AWASSI SHEEP REARED IN FERTILE CRESCENT BASED ON MICROSATELLITES: A REVIEW

In general, many domestic breeds of livestock evolved to different geographical regions, Awassi sheep in particular, adapted to Fertile Crescent region where cradle of domestication took place. Awassi sheep has tremendous genetic diversity compared to other domestic sheep breeds of the world. Nowadays, Awassi sheep is in danger of losing their unique and ancient genetic diversity as a result mainly of unwarranted crossing with high-yielding exotic breeds. Another reason for losing diversity is reduction in the population size of Awassi sheep in their origin region of the Fertile Crescent. Unveiling genetic diversity marks the inaugural phase in the execution of breeding and conservation initiatives. Previous literature revealed that microsatellite markers were widely used and accepted until nowadays as useful molecular markers for evaluating genetic diversity of sheep populations along with other markers such as Single Nucleotide Polymorphisms (SNP). Most studies based on microsatellite markers provided information on genetic diversity parameters (e.g. observed and expected heterozygosity, PIC, alleles number, inbreeding coefficient, effective population size, genetic distances values and cluster analyses) within and among Awassi populations. These markers enabled phylogenetic relationships among populations by tree building approach based on genetic distance values. On the other hand, crossbreeding practices are thought to contribute to the genetic erosion of the original Awassi sheep breed, while a reduction in population size is anticipated to have adverse effects on genetic diversity. In this work, we reviewed the microsatellite-based studies which have been published for detecting genetic diversity of Awassi sheep breed in various countries of Fertile Crescent. Key words: Genetic diversity, Awassi Sheep, Fertile Crescent, Genetic Markers.

Comparative growth, survival, and feed conversion factor of the F1 generation of two new strains of tilapia Oreochromis niloticus produced by mass selection

Growth, survival, and use of feed of the F1 generation of two new strains of tilapia Oreochromis niloticus (GenBank Strain Y = OK078792 to OK078796 and Strain A = OK078797 to OK078807) produced by mass selection was compared with a known fast-growing commercial strain in Mexico (GenBank Strain Q = OR744820 to OR744838), during a grow-out phase of 165 days. Genetic variability including observed (Ho) and expected (He) heterozygosity, inbreeding coefficient (Fis), and paired comparisons of strain fixation index (Fst) of the three strains were also compared, and an additional analysis of molecular variance (AMOVA) was performed. Twelve hapas of 8.2 m3 (four for each strain) were stocked at a density of 25 org m−3 of 4.58 ± 0.67 g, which were fed with 45 to 25% crude protein feed under a dynamic feeding scheme of 8 to 3% live weight. Growth was estimated by growth rates in weight and length, and by the weight-specific growth rate (SGR). The use of feed was estimated by the total feed consumption rate and the feed conversion factor (FCF). Results indicate no significant differences (P > 0.05) in growth parameters of the three strains, except in SGR which was significantly higher in the control strain (Q) (2.75% day−1) as compared with strains Y and A (2.51 and 2.59% day−1 respectively). The average final weight and size of the fish were 314.6 ± 11.8 g and 25.5 ± 0.4 cm respectively. No significant differences (P > 0.05) were found in survival and feed utilisation among strains, with average values of 96.4% survival, feed consumption of 3.91 g day−1, and FCF of 2.08. Results of genetic diversity indicate that there were no significant differences (P > 0.05) in Ho and He of the three strains, with average values of 0.310 and 0.280 respectively. Fis values were negative and similar for the three strains, with a mean value of −0.109 which indicates no consanguinity in their populations. Finally, the paired comparisons of Fst were significantly different (P < 0.001), showing relatively low values but different from 0 (Y vs. A = 0.025, A vs. Q = 0.041 and Y vs. Q = 0.055), indicating slight but significant population differentiation between strains. In conclusion, the performance and genetic variability of the F1 generation of the two new strains suggest that valuable broodstock is now available for mass production of fry, with similar performance as to one of the best strains of tilapia in Mexico.

The population genomics of Conyza spp. in soybean macroregions suggest the spread of herbicide resistance through intraspecific and interspecific gene flow

Herbicide-resistant Conyza spp. are a threat to many crops. These widespread weeds are closely related species and often cooccur. To characterize the origins of their resistance and the mechanisms underlying their spread, we assessed the genomic variation in glyphosate-resistant Conyza spp. in Brazil. Twenty populations were sampled from soybean fields across four macroregions (MRSs). A genotyping-by-sequencing study resulted in 2,998 single-nucleotide polymorphisms (SNPs) obtained for C. bonariensis (L.) and the closely related C. sumatrensis (Retz) E. Walker. Higher genomic diversity (π) and heterozygosity (HO/HE) and lower inbreeding coefficient (FIS) values were detected in populations of Conyza spp. from MRS 1 (southern) than in those from other MRSs. Strong genomic structure clustered individuals into three groups (FST = 0.22; p value = 0.000) associated with the MRSs. Thus, resistance to glyphosate originated from independent selection in different MRSs across Brazil. Our dataset supports the occurrence of intraspecific gene flow in Brazil and identified individuals of C. bonariensis that did not group within species. These findings suggest that allelic introgressions within and among species have impacted the evolution and spread of resistance to glyphosate in Conyza spp. We discuss how to mitigate new resistance cases, particularly for the released stacked traits herbicide tolerance in soybeans.

Genome-wide assessment of runs of homozygosity to estimate inbreeding in a closed Nellore herd

The objective of this study was to compare the inbreeding coefficients estimated from pedigree data (FPED), traditionally used for internal monitoring by herds and breeding programs, with genomic estimates through the genomic relationship matrix (FGRM) and runs of homozygosity (FROH). Besides, we used the genotype data to obtain the linkage disequilibrium (LD), population effective size (Ne), runs of homozygosity (ROH) islands and functional analysis of the genes presented in ROH islands. Male calves and sires from a closed Nellore herd (Lemgruber line) were genotyped with the Z-chip v2 (Neogen, Lincoln, Nebraska, USA) that contains approximately 30 thousand SNP markers. After quality control, 1088 animals and 21,351 SNPs remained for analysis. Runs of homozygosity (ROH) segments were identified in all analyzed animals, with an average number of 57.93 and average length of 2.95 Mb. We observed a higher occurrence of ROH up to 9 Mb, suggesting a proper mating scheme, which corroborate with LD and Ne analysis results. Estimates of FPED, FGRM and FROH ranged from 0 to 0.2856, from 0.0705 to 0.3686 and from 0.0229 to 0.2762, respectively. Low to moderate correlations were observed between FPED and FGRM (0.17, P < 0.001); FPED and FROH (0.20, P < 0.001) and FGRM and FROH (0.92, P < 0.001). Nevertheless, considering our results we were successful in use runs of homozygosity for estimating autozygosity in a closed Nellore herd. Besides, from ROH islands, we were able to identify a candidate gene (HTR1A) for docility in this Nellore herd.

Analyzing Runs of Homozygosity Reveals Patterns of Selection in German Brown Cattle.

An increasing trend in ancestral and classical inbreeding coefficients as well as inbreeding depression for longevity were found in the German Brown population. In addition, the proportion of US Brown Swiss genes is steadily increasing in German Browns. Therefore, the aim of the present study was to analyze the presence and genomic localization of runs of homozygosity (ROH) in order to evaluate their associations with the proportion of US Brown Swiss genes and survival rates of cows to higher lactations. Genotype data were sampled in 2364 German Browns from 258 herds. The final data set included 49,693 autosomal SNPs. We identified on average 35.996 ± 7.498 ROH per individual with a mean length of 8.323 ± 1.181 Mb. The genomic inbreeding coefficient FROH was 0.122 ± 0.032 and it decreased to 0.074, 0.031 and 0.006, when genomic homozygous segments > 8 Mb (FROH>8), >16 Mb (FROH>16) and >32 Mb (FROH>32) were considered. New inbreeding showed the highest correlation with FROH>32, whereas ancestral inbreeding coefficients had the lowest correlations with FROH>32. The correlation between the classical inbreeding coefficient and FROH was 0.572. We found significantly lower FROH, FROH>4, FROH>8 and FIS for US Brown Swiss proportions <60% compared to >80%. Cows surviving to the 2nd, 4th, 6th, 8th, and 10th lactation had lower genomic inbreeding for FROH and up to FROH>32, which was due to a lower number of ROH and a shorter average length of ROH. The strongest ROH island and consensus ROH shared by 50% of the animals was found on BTA 6 at 85-88 Mb. The genes located in this genomic region were associated with longevity (NPFFR2 and ADAMTS3), udder health and morphology (SLC4A4, NPFFR2, GC and RASSF6), milk production, milk protein percentage, coagulation properties of milk and milking speed (CSN3). On BTA 2, a ROH island was detected only in animals with <60% US Brown Swiss genes. Genes within this region are predominantly important for dual-purpose cattle breeds including Original Browns. For cows reaching more than 9 lactations, an exclusive ROH island was identified on BTA 7 with genes assumed to be associated with longevity. The analysis indicated that genomic homozygous regions important for Original Browns are still present and also ROH containing genes affecting longevity may have been identified. The breeding of German Browns should prevent any further increase in genomic inbreeding and run a breeding program with balanced weights on production, robustness and longevity.

Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies

BackgroundThe Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressures on these breeds differ substantially. The aim of this study was to assess genetic diversity in both breeds through expected (HE) and observed heterozygosity (HO) and effective population size (Ne). Furthermore, we aimed to identify runs of homozygosity (ROH) to estimate and compare genomic inbreeding and signatures of selection in the breeds.ResultsHO was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with HE of 0.34 for both breeds. Based on genomic data, the Ne for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies. Genomic inbreeding coefficient (FROH) ranged from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony, with the majority of inbreeding attributed to short ROHs in both breeds. Several ROH islands associated with performance were identified in the Icelandic horse, featuring target genes such as DMRT3, DOCK8, EDNRB, SLAIN1, and NEURL1. Shared ROH islands between both breeds were linked to metabolic processes (FOXO1), body size, and the immune system (CYRIB), while private ROH islands in Exmoor ponies were associated with coat colours (ASIP, TBX3, OCA2), immune system (LYG1, LYG2), and fertility (TEX14, SPO11, ADAM20).ConclusionsEvaluations of genetic diversity and inbreeding reveal insights into the evolutionary trajectories of both breeds, highlighting the consequences of population bottlenecks. While the genetic diversity in the Icelandic horse is acceptable, a critically low genetic diversity was estimated for the Exmoor pony, which requires further validation. Identified signatures of selection highlight the differences in the use of the two breeds as well as their adaptive trait similarities. The results provide insight into genomic regions under selection pressure in a gaited performance horse breed and various adaptive traits in small-sized native horse breeds. This understanding contributes to preserving genetic diversity and population health in these equine populations.

Secure discovery of genetic relatives across large-scale and distributed genomic data sets.

Finding relatives within a study cohort is a necessary step in many genomic studies. However, when the cohort is distributed across multiple entities subject to data-sharing restrictions, performing this step often becomes infeasible. Developing a privacy-preserving solution for this task is challenging owing to the burden of estimating kinship between all the pairs of individuals across data sets. We introduce SF-Relate, a practical and secure federated algorithm for identifying genetic relatives across data silos. SF-Relate vastly reduces the number of individual pairs to compare while maintaining accurate detection through a novel locality-sensitive hashing (LSH) approach. We assign individuals who are likely to be related together into buckets and then test relationships only between individuals in matching buckets across parties. To this end, we construct an effective hash function that captures identity-by-descent (IBD) segments in genetic sequences, which, along with a new bucketing strategy, enable accurate and practical private relative detection. To guarantee privacy, we introduce an efficient algorithm based on multiparty homomorphic encryption (MHE) to allow data holders to cooperatively compute the relatedness coefficients between individuals and to further classify their degrees of relatedness, all without sharing any private data. We demonstrate the accuracy and practical runtimes of SF-Relate on the UK Biobank and All of Us data sets. On a data set of 200,000 individuals split between two parties, SF-Relate detects 97% of third-degree or closer relatives within 15 h of runtime. Our work enables secure identification of relatives across large-scale genomic data sets.

Local versus regional patterns in zoospore dispersal of the kelp Eisenia bicyclis (Laminariales, Phaeophyceae)

SummaryIt is generally accepted that kelp populations have a metapopulation structure. Most zoospores settle near to their parent individual, and infrequent but long‐distance dispersal of zoospores contributes to gene flow between local populations. Population genetic analysis of single nucleotide polymorphism genotyping by MIG‐seq (i.e. multiplexed inter‐simple sequence repeats genotyping by sequencing) was performed on the dominant kelp, Eisenia bicyclis, in two areas: Kitsunezaki (a sheltered area) and Shimoda (an exposed site). Regional scale analysis of genetic structure was conducted at six sites in Kitsunezaki and three sites in Shimoda. When viewed on a regional scale based on the inbreeding coefficient within the local population, the inbreeding ratio was higher in Shimoda than in Kitsunezaki, probably as a result of the limited vertical zonal distribution in the exposed environment. Vertically wide distribution in the sheltered environment apparently enabled frequent crossing among individuals in Kitsunezaki. By contrast, when viewed on a local scale based on the pairwise kinship coefficient (FST) between populations, gene flow among local populations in Shimoda occurred over a wide area, but was limited in Kitsunezaki. In Shimoda, genetic exchange between local populations, even if inbreeding is locally active, is likely to support metapopulation maintenance and rapid recovery of local populations. In Kitsunezaki, however, genetic exchange among local populations is limited within few 100 m, and the metapopulation structure will decline in the long term because of inbreeding depression. Local dispersal distance of zoospores was investigated based on parent–offspring analysis in the Kitsunezaki population, which revealed that zoospores mainly settled within 5 m of their parent. However, some zoospores traveled over 27 m within the 4 × 30 m study area. The present study shows the importance of examination at different spatial scales when investigating zoospore dispersal of laminarialean kelps.

The Prevalence and Patterns of Consanguineous Marriages and Associated Factors in Southeast of Iran

Background: Consanguineous union is a common practice and the culturally preferred form of marriage in developing countries, including Iran, with several health-related and social adverse outcomes. Objectives: This study aimed to identify the prevalence of consanguineous marriages and their sociodemographic correlates among marrying couples living in Zahedan, southeast of Iran. Methods: This cross-sectional study included 738 couples attending the Pre-Marriage Counselling Center in Zahedan, southeast Iran. All information was gathered during face-to-face interviews. Multivariate logistic regression models were fitted using the forward likelihood ratio method to identify the correlates of consanguineous marriages. Results: The prevalence of consanguineous unions was 46.7% of the total marriages. First-cousin unions were the most frequent type, comprising 30.2% of total marital unions. The average inbreeding coefficient (F) in consanguineous couples was calculated as 0.0516 (95% CI: 0.0481-0.0551). Consanguinity was found to be associated with ages younger than 20 years, lower levels of education, rural residence, Balouch and Sistani ethnicity, lower income, parental consanguinity, and marriages arranged by parents. Conclusions: The results of this study showed that the tradition of consanguineous unions is still a preferred practice among people living in southeast Iran, especially among socioeconomically disadvantaged individuals. There is a need for health education programs to improve the knowledge of marrying couples about consanguineous marriages to reduce the potential risk of genetic disorders in offspring.

Genetic Variation among Rare Florida Endemic Hymenocallis henryae Populations and the Implication for Conservation and Management

Hymenocallis henryae is a rare, charismatic spider lily endemic to the Florida panhandle. Currently under review to determine if listing under the Endangered Species Act is warranted, this species has undescribed genetic diversity, information crucial to the listing process. We conducted field observations of 21 historic populations across the species’ geographical range and performed genomic analyses of 279 individuals from 19 extant populations. Most populations had fewer than 40 individuals, while populations with &gt;100 individuals were found exclusively on managed lands. Genetic diversity was uniformly low within populations (HE: 0.074–0.093), with low to moderate inbreeding coefficients (FIS: 0.068–0.431). Genetic differentiation was relatively low among most populations (FST: 0–0.098), although there was statistical support for isolation by distance. In addition, we found high genetic similarity and lack of population structure across the species range. Clonal propagation through fused bulbs is a common reproductive strategy. We confirmed current threats (habitat change, residential development, fire suppression) and identified several coastal populations threatened by sea level rise. It is recommended to continue with in situ protection and management as well as the establishment of ex situ living collections to preserve populations most at risk of extirpation from habitat loss and degradation.

Runs of homozygosity analysis and genomic inbreeding estimation in Sumba Ongole cattle (Bos indicus) using a BovineSNP50K BeadChip.

Runs of homozygosity (ROH) is a biocomputational technique for identifying homozygous regions in the genomics of livestock. This study aimed to determine the ROH in Sumba Ongole (SO) bulls (n = 48) using the BovineSNP50K BeadChip. GenomeStudio 2.0 software was used to generate the BovineSNP50K BeadChip output. The ROH and ROH-based inbreeding coefficients (FROH) were determined using the detect RUNS R v4.1.0 package. Using the following filtering criteria, PLINK v1.90 software was used to perform genotype quality control: (1) Individuals and single-nucleotide polymorphism (SNPs) had call rates >0.95; (2) more than 0.05 was the minor allele frequency; (3) the list contained only SNPs linked to autosomes; and (4) SNPs that strongly deviated (p < 1e-6) from Hardy-Weinberg equilibrium were removed. Subsequently, 25,252 autosomal SNP markers were included in the ROH and FROH analyses. In general, the number and length of ROH segments in pool animals were 149.77 ± 16.02 Mb and 486.13 ± 156.11 Mb, respectively. Furthermore, the ROH segments in the animals under study can be discriminated into two classes of 1-4 Mb (83.33%) and 4-8 Mb (16.67%). Subsequently, Bos taurus autosomes (BTA) 1, BTA6, and BTA14 had significant homozygous segments comprising 13 genes. Despite this, the average FROH in pool animals was 0.20 ± 0.06. These findings indicate that a recent inbreeding event in SO cattle occurred many generations ago. Furthermore, the candidate genes identified from the ROH analysis indicate phenotypic attributes associated with environmental adaptation and economic traits.

Whole-genome resequencing identifies candidate genes associated with heat adaptation in chickens

The wide distribution and diverse varieties of chickens make them important models for studying genetic adaptation. The aim of this study was to identify genes that alter heat adaptation in commercial chicken breeds by comparing genetic differences between tropical and cold-resistant chickens. We analyzed whole-genome resequencing data of 186 chickens across various regions in Asia, including the following breeds: Bian chickens (B), Dagu chickens (DG), Beijing-You chickens (BY), and Gallus gallus jabouillei from China; Gallus gallus murghi from India; Vietnam native chickens (VN); Thailand native chickens (TN) and Gallus gallus spadiceus from Thailand; and Indonesia native chickens (IN), Gallus gallus gallus, and Gallus gallus bankiva from Indonesia. In total, 5,454,765 SNPs were identified for further analyses. Population genetic structure analysis revealed that each local chicken breed had undergone independent evolution. Additionally, when K = 5, B, BY, and DG chickens shared a common ancestor and exhibited high levels of inbreeding, suggesting that northern cold-resistant chickens are likely the result of artificial selection. In contrast, the runs of homozygosity (ROH) and the ROH-based genomic inbreeding coefficient (FROH) results for IN, TN, and VN chickens showed low levels of inbreeding. Low population differentiation index values indicated low differentiation levels, suggesting low genetic diversity in tropical chickens, implying increased vulnerability to environmental changes, decreased adaptability, and disease resistance. Whole-genome selection sweep analysis revealed 69 candidate genes, including LGR4, G6PC, and NBR1, between tropical and cold-resistant chickens. The genes were further subjected to GO and KEGG enrichment analyses, revealing that most of the genes were primarily enriched in biological synthesis processes, metabolic processes, central nervous system development, ion transmembrane transport, and the Wnt signaling pathway. Our study identified heat adaptation genes and their functions in chickens that primarily affect chickens in high-temperature environments through metabolic pathways. These heat-resistance genes provide a theoretical basis for improving the heat-adaptation capacity of commercial chicken breeds.

Ignoring within‐flower self‐fertilization and inbreeding depression biases estimates of selection on floral traits in a perennial alpine herb

Abstract Within‐flower self‐pollination should be the major source of self‐fertilization in mixed‐mating species that present single or few flowers simultaneously. It is also an often unmeasured source of selfing in species with many flowers open simultaneously. In self‐compatible species in which pistil and stamen numbers vary, the rate of within‐flower selfing should depend on the number of pistils and stamens, the timing of flowering and the morphology of subsidiary floral traits. The intensity and direction of selection on these traits should thus also depend on the level of inbreeding depression. Here, we measured the dependence of the within‐flower selfing rate on floral sex allocation, phenology, petal length and floral stalk height in a population of the perennial herb Pulsatilla alpina (Ranunculaceae) in which most individuals had single flowers. We estimated inbreeding depression in the population by comparing inbreeding coefficients between parents and seed progeny using microsatellite markers. We then estimated selection on the measured traits via female reproductive success at the flower level and compared our estimates with a hypothetical scenario in which inbreeding depression was assumed to be absent. Inbreeding depression was estimated to be severe (0.95). The within‐flower selfing rate varied widely among flowers and depended positively on stamen number and negatively on pistil number and flowering date, supporting the predictions of a mass‐action model. The dependence of the selfing rate on the measured floral traits consistently predicted (non‐linear) patterns of selection under high inbreeding depression that were distinct from those under a hypothetical scenario of no inbreeding depression. Synthesis. While previous research has emphasized the importance of mass‐action mating on selfing among flowers of plants with large floral displays, our results demonstrate its importance for selfing within individual flowers. They also demonstrate the importance of accounting for both the selfing rate and inbreeding depression when inferring selection on floral and other traits via female fitness.

Assessing different metrics of pedigree and genomic inbreeding and inbreeding effect on growth, fertility, and feed efficiency traits in a closed-herd Nellore cattle population

BackgroundThe selection of individuals based on their predicted breeding values and mating of related individuals can increase the proportion of identical-by-descent alleles. In this context, the objectives of this study were to estimate inbreeding coefficients based on alternative metrics and data sources such as pedigree (FPED), hybrid genomic relationship matrix H (FH), and ROH of different length (FROH); and calculate Pearson correlations between the different metrics in a closed Nellore cattle population selected for body weight adjusted to 378 days of age (W378). In addition to total FROH (all classes) coefficients were also estimated based on the size class of the ROH segments: FROH1 (1–2 Mb), FROH2 (2–4 Mb), FROH3 (4–8 Mb), FROH4 (8–16 Mb), and FROH5 (> 16 Mb), and for each chromosome (FROH_CHR). Furthermore, we assessed the effect of each inbreeding metric on birth weight (BW), body weights adjusted to 210 (W210) and W378, scrotal circumference (SC), and residual feed intake (RFI). We also evaluated the chromosome-specific effects of inbreeding on growth traits.ResultsThe correlation between FPED and FROH was 0.60 while between FH and FROH and FH and FPED were 0.69 and 0.61, respectively. The annual rate of inbreeding was 0.16% for FPED, 0.02% for FH, and 0.16% for FROH. A 1% increase in FROH5 resulted in a reduction of up to -1.327 ± 0.495 kg in W210 and W378. Four inbreeding coefficients (FPED, FH, FROH2, and FROH5) had a significant effect on W378, with reductions of up to -3.810 ± 1.753 kg per 1% increase in FROH2. There was an unfavorable effect of FPED on RFI (0.01 ± 0.0002 kg dry matter/day) and of FROH on SC (-0.056 ± 0.022 cm). The FROH_CHR coefficients calculated for BTA3, BTA5, and BTA8 significantly affected the growth traits.ConclusionsInbreeding depression was observed for all traits evaluated. However, these effects were greater for the criterion used for selection of the animals (i.e., W378). The increase in the genomic inbreeding was associated with a higher inbreeding depression on the traits evaluated when compared to pedigree-based inbreeding. Genomic information should be used as a tool during mating to optimize control of inbreeding and, consequently, minimize inbreeding depression in Nellore cattle.

Assessment of the genetic similarity between the novoaltayskaya horse breed and the original breeds by microsatellite DNA loci

The research was carried out for the purpose of a comparative assessment of the allele pool of the Novoaltayskaya horse breed and the breeds that participated in its creation. The experimental sample included 5736 horses, including: Novoaltayskaya breed – 363, Altai – 39, Lithuanian Heavy Draft – 159, Russian Heavy Draft – 617, Soviet d Heavy Draft – 288, Orlov trotter – 4,177, Budenny – 93. Population genetic analysis was performed using generally accepted methods. The following indicators were determined: the total number of alleles at 17 loci, the average number of alleles per locus, the level of polymorphism, observed and expected heterozygosity, coefficients of intrapopulation inbreeding, genetic similarity and genetic distances. It was established that horses of the Novo-Altai breed had the highest level of genetic diversity (154 alleles) and polymorphism (Ae = 4,909). Analysis of genetic differentiation showed the absence of intrapopulation inbreeding in the groups of Altai, Lithuanian Heavy Draft and Budenny breeds. Groups of horses of the Novoaltayskaya, Orlov trotter, Russian Heavy Draft and Soviet Heavy Draft breeds were distinguished by a slight deficiency of heterozygotes. It has been established that horses of the Novoaltayskaya and Heavy Draft breeds are characterized by a high frequency of occurrence of the HTG6 O allele, and the Altai breed is characterized by a high frequency of occurrence of the HTG4 M allele. A number of loci of alleles identical in spectrum to those of the Altai, Russian Heavy Draft and Soviet Heavy Draft breeds were identified in the Novoaltayskaya horse. Cluster analysis demonstrated a high level of genetic similarity of horses of the Novoaltayskaya breed with the Russian Heavy Draft (0,903) and Altai (0,899) breeds. As part of the study, using molecular genetic markers, new data was obtained on horses of seven breeds, with the help of which it is possible to improve breeding programs in horse breeding, allowing to control the biodiversity and genetic similarity of populations, preserving the originality and heterogeneity of the allele pool of horses of different breeds.

Presence of the knockdown resistance (kdr) mutations in the head lice (Pediculus humanus capitis) population in the North of Iran.

Head lice infestation continues to be a major health problem worldwide. In order to solve this problem, frequent use of pediculocides has caused growing resistance among head lice population. This study aims to investigate the presence of the knockdown resistance (kdr) mutation in the head lice population in northern Iran. Adult head lice were collected from 115 infested individuals referring to the health centers in different parts of Mazandaran province, northern Iran. 38 samples were randomly selected, and Polymerase chain reaction (PCR) was used to amplify a 332-bp and ⁓ 900-bp fragment of the α-subunit of the voltage-sensitive sodium channel (VSSC) gene. According to the analysis of a 332-bp fragment of the VSSC gene, the frequency of kdr T917I mutation including homozygous susceptible (SS), heterozygous resistant (RS), and homozygous resistant (RR) were 45.83%, 12.5%, and 41.66%, respectively. The total frequency of the resistance allele was 54.16%. The results of the 900-bp fragment of the VSSC gene showed two new mutations in the IIS1-2 extracellular loop (H813P) and IIS2 (S825R) and old well-known kdr mutations (M815I-T917I-L920F). The results of Hardy-Weinberg's exact equilibrium test showed that the frequency of genotypes in the studied areas is different from expectations. Moreover, a positive inbreeding coefficient value (F is >0) was found in studied areas which indicated an excess of homozygotes. Overall, the results showed a high frequency of resistant alleles in the northern region of the country. Therefore, it is necessary to develop appropriate control programs for the treatment of pediculosis.

An evaluation of potential inbreeding depression in wild Mexican wolves

AbstractEstimates of the influence of inbreeding on the fitness of wild animals can guide genetic conservation in rare species. Conservation genetics is important in Mexican wolves (Canis lupus baileyi) because the current population descended from 7 founders and mean inbreeding is relatively high. As an endangered subspecies, Mexican wolves are actively managed using select conflict avoidance measures and by placing captive‐born foster pups into wild litters. We obtained data on inbreeding coefficients of wolf pups and adults based on a pedigree dating to 1957 and data on reproduction for wild wolf packs during 1998–2022. We estimated trends in inbreeding coefficients and the associations between dam, sire, and pup inbreeding coefficients and pup recruitment to age 9 months, and assessed 3 components of recruitment: probability of producing a litter, number of pups produced, and recruitment conditional on successful reproduction. We generated estimates using generalized linear mixed models and bootstrapped estimates of confidence intervals. Mean inbreeding coefficients were high (0.227, SD = 0.047) in the wild population, but we detected no significant evidence of an increase during 2010–2022. Overall, the net associations of dam, sire, and pup inbreeding coefficients with our primary fitness metric, pup recruitment to age 9 months, did not differ from zero. While high inbreeding coefficients are a concern for the long‐term recovery of the subspecies, the stable level of inbreeding, lack of evidence for inbreeding depression, high pup production (5.1 pups/litter, SD = 1.64), and rapid population growth (384% increase from 2010–2022) indicate that inbreeding has not prevented rapid progress towards recovery goals under current management practices.