PSXVI-17 Estimation of inbreeding in local sheep breeds of west Asian and central Asian origin based on high-density SNP-genotypes

Maintaining high levels of genetic diversity is a key factor of successful breeding of resilient, resistant to diseases and productive sheep. Prevention of inbreeding is of special importance in the mountainous hard-to-get habitats where gene flow is limited or absent. An assessment of inbreeding coefficients based only on pedigree information is not always correct. In addition, pedigree information is often missing for flocks of native sheep. In this regard, we performed a genomic assessment of inbreeding in 15 local sheep breeds inhabiting severe environments of Russia and neighboring Asian countries based on estimations of standardized multilocus heterozygosity (sMLH) and runs of homozygosity [F(ROH)]. For this study, we used SNP genotypes of twelve Russian local breeds (n = 316) and three Kyrgyz local breeds (n = 68), which were generated using Ovine Infinium® HD SNP BeadChip (Illumina, CA, USA). The sMLH values were calculated using R package inbreedR and visualized in R package ggplot2. The F(ROH) values were calculated using the R package detectRUNS by applying the consecutive runs method. Mean sMLH values were varied from 0.962 ± 0.006 in the Andean breed to 1.031 ± 0.002 in the Buryat breed and averaged to 1.001± 0.004. The least mean F(ROH) value was detected in the Mongolian breed (0.0043 ± 0.0009) while the greatest ones were observed in the Alai and Andean breeds (0.0364 ± 0.0049 and 0.0357 ± 0.0061, respectively). The strong negative correlations between sMLH and F(ROH) were detected for all of studied breeds (r2 = –0.8496, CI = –0.8752… –0.8192). The obtained data is relevant for control of inbreeding level in the populations and for future sustainable management of native fat-tailed sheep breeds. The study was funded by RSF No. 19-16-00070.

A simulation study of a honeybee breeding scheme accounting for polyandry, direct and maternal effects on colony performance

Background Efficient breeding programs are difficult to implement in honeybees due to their biological specificities (polyandry and haplo-diploidy) and complexity of the traits of interest, with performances being measured at the colony scale and resulting from the joint effects of tens of thousands of workers (called direct effects) and of the queen (called maternal effects). We implemented a Monte Carlo simulation program of a breeding plan designed specifically for Apis mellifera’s populations to assess the impact of polyandry versus monoandry on colony performance, inbreeding level and genetic gain depending on the individual selection strategy considered, i.e. complete mass selection or within-family (maternal lines) selection. We simulated several scenarios with different parameter setups by varying initial genetic variances and correlations between direct and maternal effects, the selection strategy and the polyandry level. Selection was performed on colony phenotypes. Results All scenarios showed strong increases in direct breeding values of queens after 20 years of selection. Monoandry led to significantly higher direct than maternal genetic gains, especially when a negative correlation between direct and maternal effects was simulated. However, the relative increase in these genetic gains depended also on their initial genetic variability and on the selection strategy. When polyandry was simulated, the results were very similar with either 8 or 16 drones mated to each queen. Across scenarios, polyandrous mating resulted in equivalent or higher gains in performance than monoandrous mating, but with considerably lower inbreeding rates. Mass selection conferred a ~ 20% increase in performance compared to within-family selection, but was also accompanied by a strong increase in inbreeding levels (25 to 50% higher). Conclusions Our study is the first to compare the long-term effects of polyandrous versus monoandrous mating in honeybee breeding. The latter is an emergent strategy to improve specific traits, such as resistance to varroa, which can be difficult or expensive to phenotype. However, if used during several generations in a closed population, monoandrous mating increases the inbreeding level of queens much more than polyandrous mating, which is a strong limitation of this strategy.

Some Genetic and Environmental Effects on Equine Asthma in Polish Konik Horses

Current knowledge of the genetic and environmental backgrounds of equine asthma seems to be insufficient, especially for primitive horse breeds. The main objectives of this study were to estimate the effects of sex, birth period, stud, parentage line and inbreeding on asthma morbidity in Polish Konik horses. Records of 274 horses (housed in two studs) were analysed. These animals were allocated to maternal and paternal lines. Individual inbreeding coefficients were extracted from the additive relationship matrix. Horses underwent diagnosis based on observation of the basic symptoms (high frequency of coughing and excessive nasal discharge). Subsequently, some horses (28 individuals) were clinically examined to confirm the earlier observations. Generally, no significant effects of parentage line on heaves morbidity were identified by the use of logistic regression, although the Pearson’s chi-squared test had shown that individuals of some maternal and paternal lines had a predisposition to severe equine asthma. It was concluded that the individual inbreeding level is not associated with the incidence of EA, but a significant effect of the maternal inbreeding coefficient may be observed. It was also found that there is some variability in the incidence of this disease between studs.

Genetic Diversity and Population Genetic Structure of a Guzerá (Bos indicus) Meta-Population

The Brazilian Guzerá population originated from a few founders introduced from India. These animals adapted well to the harsh environments in Brazil, were selected for beef, milk, or dual-purpose (beef and milk), and were extensively used to produce crossbred animals. Here, the impact of these historical events with regard to the population structure and genetic diversity in a Guzerá meta-population was evaluated. DNA samples of 744 animals (one dairy, nine dual-purpose, and five beef herds) were genotyped for 21 microsatellite loci. Ho, He, PIC, Fis, Fit, and Fst estimates were obtained considering either farms or lineages as subpopulations. Mean Ho (0.73) and PIC (0.75) suggest that genetic diversity was efficiently conserved. Fit, Fis and Fst values (95% CI) pointed to a low fixation index, and large genetic diversity: Fit (Farms = 0.021–0.100; lineages = 0.021–0.100), Fis (Farms = –0.007–0.076; lineages = −0.014–0.070), and Fst (Farms = 0.0237–0.032; lineages = 0.029–0.038). The dual-purpose herds/selection lines are the most uniform subpopulation, while the beef one preserved larger amounts of genetic diversity among herds. In addition, the dairy herd showed to be genetically distant from other herds. Taken together, these results suggest that this Guzerá meta-population has high genetic diversity, a low degree of population subdivision, and a low inbreeding level.

Towards deciphering the structure of long homozygous stretches in cattle genome

p-to-day there is no as universally accepted software tool and threshold parameters to identify runs of homozygosity ( ROH ). The relative position of POH segments in the cattle genome has not been studied extensively. Specific objective of this study was to evaluate the effect of allowed missing and heterozygous SNPs in ROH on their number, on the estimate of inbreeding level, and on structure of ROH segments in the cattle genome. In this study 371 Holsteinized cows from six herds were genotyped with BovineSNP50 array. To identify ROH, the consecutive and sliding runs were carried out with detectRUNS and Plink tools. Neither effect was shown for missing SNPs genotype calls. Allowing even one heterozygous SNP resulted in significant bias of ROH data. Furthermore, the sliding runs identified less ROH than consecutive runs. The mean coefficient of inbreeding across herds was 0.111 ± 0.003 and 0.104 ± 0.003 based on consecutive and sliding runs respectively. It was shown how, using the heterozygous SNPs in ROH, may be possible to derive a distribution of ROH segments in the cow genome. We suggested it was similar to normal distribution. Furthermore, frequency of ROH in the chromosomes did not depend on their length. Of 29 chromosomes, the most abundant with ROH were BTA 14, BTA 7, and BTA 18. The result of this study confirmed more accurately identification of ROH with consecutive runs, uneven their distribution in the cattle genome, significant bias of the data due to allowing heterozygous SNPs in ROH.

THE EFFECT OF INBREEDING ON PREWEANING GROWTH OF YANKASA SHEEP

The accumulated and annual levels of inbreeding and their effects on growth traits of lambs were investigated using data collected over 11 years at the National Animal Production Research Institute Zaria. Inbreeding level averaged 1.313% per year, cumulating to 14.45% over the years. Average individuals inbreeding coefficients of offspring from sires used for more than one breeding period was 0.103% across the inbred individuals and 0.004% over all lambs. Regression coefficients of growth traits (everage values per year) on inbreeding levels by year were – 0.185kg ± 1.820g and -0.391kg for birth weight, preweaning average daily gain and weaning weight, respectively. All regression coefficients indicated that birth weight and weaning weight declined by 0.185kg and 0.391kg, respectively while preweaning average daily gain increased by 1.820g. Conscious efforts to reduce inbreeding level and its effects on growth traits will greatly lead to improved productivity

Exploration of the Exogenous Male Yak Introduction Breeding Model and its Effects on Tibetan Small-Sized Family Farms

A total of three family farms including Village No. 9 in Nima township, Nerong Naqu County (NQA); Village No. 11 in Nima township, Nerong Naqu County (NQB); and Yare township, Gegi County, Ali District (GJ) from three ecology yak populations (EYP) were selected for this study to identify the most optimized mode of exogenous male adult yak introduction (EMI) within EYP for solving the inbreeding problem caused by the small-scale yak husbandry system. Exogenous adult male yaks from the same EYP with different proportions (100% to NQA, 50% to NQB, and 0% to GJ) were introduced, and 10 microsatellites were used to detect the genetic diversity of these populations before (in 2017) and after (in 2019) the introduction of exogenous adult male yaks (EMI). Results showed that the divergence between the observed and the expected heterozygosity of the NQA and NQB populations was reduced in 2019, while the number of markers significantly deviating from Hardy–Weinberg equilibrium (P<0.05) and FIS (inbreeding coefficient) within populations decreased compared with that in 2017. In contrast, the FIS of GJ population without EMI continued to increase (from 0.011 to 0.033) over the years 2017 to 2019. Moreover, genetic differences between the populations (Pairwise Fixation index, FST) showed that EMI increased the genetic divergence between populations. Overall, this study shows that the introduction of exogenous male adult yaks not only effectively reduces the degree of population deviation from equilibrium but also decreases the inbreeding level within the population within a few generations. This study also provides a valuable management model for stable yak production on small sized family farms

Different molecular changes underlie the same phenotypic transition: origins and consequences of independent shifts to homostyly within species

The molecular basis of phenotypic convergence, a key topic in evolutionary biology and ecology, has been investigated especially between species. However, it remains unclear whether mutations in the same or different positions of the same gene, or in different genes underlie phenotypic convergence within species. A classic example of convergence is the transition from outcrossing to selfing in plants, illustrated by the repeated shift from heterostyly to homostyly. Heterostyly is characterized by the reciprocal position of male and female sexual organs in two (or three) distinct, incompatible floral morphs, while homostyly is characterized by a single, self-compatible floral morph. Primula has long served as the prime model for studies of heterostyly and homostyly. Here, we elucidate the phenotypic and molecular origins of homostyly in P. vulgaris and its microevolutionary consequences by integrating microsatellite analyses of both progeny arrays and natural populations characterized by varying frequencies of homostyles with DNA sequence analyses of the gene controlling the position of female sexual organs (CYPᵀ). We found that: homostyles evolved repeatedly from short-styled individuals in association with different types of loss-of-function mutations in CYPᵀ and, consequently, short-styled individuals occur at lower frequencies than long-styled individuals across populations with all three morphs; the shift to homostyly promotes a shift to selfing; and intra-population frequency of homostyles is positively correlated with selfing rate and inbreeding level, increasing genetic differentiation among populations. These results elucidate the connections between the genotypic and phenotypic levels of convergence and the effects of contrasting floral morphologies on reproductive strategies.

100 The evolution and premature hyperactivation of kinetic sperm subpopulations are affected by inbreeding level in Retinta cattle

Computer-assisted sperm analysis (CASA) has become a powerful tool to study sperm heterogeneity because it allows to cluster individual sperm in subpopulations (Sp) according to their kinetic parameters, which are associated with fertility and sperm quality. In cattle, inbreeding (mating between close relatives) affects sperm quality. Inbreeding estimation has become more accurate with the increasing availability of genomic methodologies, such as the detection of runs of homozygosity (ROH). Additionally, genomic inbreeding values (FROH) allow us to determine which metabolic pathways are differentially affected by this genetic trait. The aim of this study was to assess the effect of inbreeding on evolution of sperm Sp over time in cattle. Sperm samples (n=100) from 50 Retinta bulls (two replicates) were analysed in a sperm longevity experiment at time 0 (T0, after thawing), 1 (T1) and 2 (T2) h. At each time point, eight parameters were measured using a CASA system (Sperm Class Analyzer 5.4), including curvilinear velocity (VCL, μm/s), straight-line velocity (VSL, μm/s); average path velocity (VAP, μm/s), percentage of linearity (LIN,%: VSL/VCL), percentage of straightness (STR,%: VSL/VAP), wobble coefficient (WOB,%: VAP/VCL), mean amplitude of lateral head displacement (ALH, μm) and beat-cross frequency (BCF, Hz). The presence of Sp was determined by a two-step multivariate analysis including non-hierarchical followed by hierarchical analysis in 80,154 motile sperm. Four sperm Sp were identified: Sp1 (rapid and highly progressive sperm); Sp2 (progressive sperm with intermediate speed); Sp3 (slow and non-progressive sperm); and Sp4 (fastest, hyperactive-like, non-progressive sperm). To determine the effect of inbreeding, individuals were clustered into lowly (FROH &lt; 0.125, n=27) and highly (FROH &gt; 0.125, n=23) inbred individuals. After thawing (T0), the percentage of sperm Sp4 was higher and showed premature hyperactivation in highly inbred animals, which was previously associated with reduced fertility (Table 1). However, highly inbred individuals showed an increased percentage of rapid (Sp1) and intermediate (Sp2) progressive sperm after T1 and T2 incubation, respectively, compared with lowly inbred bulls (P&lt;0.001). These results suggest that sperm velocity and progression persist for longer in highly inbred bulls, at least after a short incubation. In conclusion, our results demonstrate that inbreeding affects sperm motility pattern and premature hyperactivation in cattle. Table 1. Percentage of subpopulations (Sp) by inbreeding group and time Time Sp1 Sp2 Sp3 Sp4 Highly inbred Lowly inbred Highly inbred Lowly inbred Highly inbred Lowly inbred Highly inbred Lowly inbred 0 33.17a 34a 32.39a 32.56a 28.07a 27.93a 6.37b 5.51a 1 31.73b 26.13a 36.75a 41.65b 23.80a 24.37a 7.72a 7.85a 2 11.73b 7.67a 53.75b 48.78a 29.68a 39.27b 4.83a 4.28a a,bDifferent superscripts by subpopulation in the same row denote significant difference (P&lt;0.05).

Genetic Diversity Analysis among 27 Indian Goat Populations using Microsatellite Markers

Background: Livestock genetic diversity studies focus on their within and diversity, breed history, adaptive variations, ancestral information, site of domestication and parentage testing and assess the genetic uniformity, admixture or subdivision, inbreeding, or introgression in the population which is helpful in breed formation and their sustainable utilization.Methods: The present research work was conducted during the year 2016-17 at National Bureau of Animal Genetics Resources, Karnal-132001. STR data of 25 markers on 1237 random samples of 27 goat populations was used for analysis. The genetic diversity analysis of new population viz: Narayanpatna, Raighar, Kalahandi, Malkangiri of Odisha state and Rohilkhandi (UK) and their association studies with other Indian goat breeds was performed.Result: It was found that used markers are highly polymorphic- and the studied breeds/population showed great diversity and distributed mostly on the basis of physio-geographical condition and type of production but among new populations diversity was least which might be due to exchange of animal for breeding purposes. The studied new goat populations were well differentiated from other goat breeds which might be due to physio-geographical condition and breeding practices, so these may be considered as separate breeds/populations. In conclusion, the results showed high level of conserved genetic diversity in the Indian goat breeds. The smaller and isolated new population showed less diversity and a higher inbreeding level as compared to registered breeds.