skater: an R package for SNP-based kinship analysis, testing, and evaluation

Motivation: SNP-based kinship analysis with genome-wide relationship estimation and IBD segment analysis methods produces results that often require further downstream process- ing and manipulation. A dedicated software package that consistently and intuitively imple- ments this analysis functionality is needed. Results: Here we present the skater R package for SNP-based kinship analysis, testing, and evaluation with R. The skater package contains a suite of well-documented tools for importing, parsing, and analyzing pedigree data, performing relationship degree inference, benchmarking relationship degree classification, and summarizing IBD segment data. Availability: The skater package is implemented as an R package and is released under the MIT license at https://github.com/signaturescience/skater. Documentation is available at https://signaturescience.github.io/skater.

Genealogical analyses in open population of Silla Argentino horses belonging to the national police of Colombia

This study aimed to evaluate population parameters, genetic diversity and identify the ancestors with the highest genetic contribution of an open population of Silla Argentino horses in Colombia using pedigree data. 508 horses born between 1998 and 2018 were evaluated, called reference population (RP). The ancestors of the RP were added, defining the total population (TP) whit 1,861 horses born since 1905. Population parameters were estimated, including inbreeding coefficient (F), effective population size (Ne), effective number of founders (fe), ancestors (fa), and founder genomes (fg) and generation interval (GIN). The GIN was 10.1 (TP) and 7.7 (RP) years. The estimate of F for the RP was 0.3%, indicating control in mattings. The Ne was 317 (RP) and 179 (TP). The probability of genes origin indicated values for fe, fa and fg of 386, 187 and 351 (TP), and 161, 64 and 56 (RP), respectively, evidencing a reduction of genetic variability in the RP. Half of the genetic variation in the equine population studied was explained by 40 ancestors. The results show loss of genetic diversity in the RP and the genetic contribution of the ancestors suggests the need to increase the number of stallions for breeding and guide mating to increase genetic diversity in the new generations of Silla Argentino horses of the Colombian National Police

Genetic diversity, viability and conservation value of the global captive population of the Moroccan Royal lions

This study evaluates the diversity of the so-called ‘Moroccan Royal lions’ using genealogical information. Lions are no longer extant in North Africa, but the previous wild population was an important element of the now-recognised northern subspecies (Panthera leo leo) that ranged across West Africa, North Africa and the Middle East into India. The remaining captive population of ‘Moroccan Royal lions’ seems to be significantly endangered by the loss of diversity due to the effective population size decrease. The pedigree file of this captive lion population consisted of 454 individuals, while the reference population included 98 animals (47 males and 51 females). The completeness of the pedigree data significantly decreased with an increasing number of generations. The highest percentage of pedigree completeness (over 70%) was achieved in the first generation of the reference population. Pedigree-based parameters derived from the common ancestor and gene origin were used to estimate the state of diversity. In the reference population, the average inbreeding coefficient was 2.14%, while the individual increase in inbreeding over generations was 2.31%. Overall, the reference population showed lower average inbreeding and average relatedness compared with the pedigree file. The number of founders (47), the effective number of founders (24) and the effective number of ancestors (22) were estimated in the reference population. The effective population size of 14.02 individuals confirms the critically endangered status of the population and rapid loss of diversity in the future. Thus, continuous monitoring of the genetic diversity of the ‘Moroccan Royal lion’ group is required, especially for long-term conservation management purposes, as it would be an important captive group should further DNA studies establish an affinity to P. leo leo.

Reverse Genetic Screen for Deleterious Recessive Variants in the Local Simmental Cattle Population of Switzerland

We herein report the result of a large-scale reverse genetic screen in the Swiss Simmental population, a local dual-purpose cattle breed. We aimed to detect possible recessively inherited variants affecting protein-coding genes, as such deleterious variants can impair fertility and rearing success significantly. We used 115,000 phased SNP data of almost 10 thousand cattle with pedigree data. This revealed evidence for 11 genomic regions of 1.17 Mb on average, with haplotypes (SH1 to SH11) showing a significant depletion in homozygosity and an allele frequency between 3.2 and 10.6%. For the proposed haplotypes, it was unfortunately not possible to evaluate associations with fertility traits as no corresponding data were available. For each haplotype region, possible candidate genes were listed based on their known function in development and disease. Subsequent mining of single-nucleotide variants and short indels in the genomes of 23 sequenced haplotype carriers allowed us to identify three perfectly linked candidate causative protein-changing variants: a SH5-related DIS3:p.Ile678fs loss-of-function variant, a SH8-related CYP2B6:p.Ile313Asn missense variant, and a SH9-related NUBPL:p.Ser143Tyr missense variant. None of these variants occurred in homozygous state in any of more than 5200 sequenced cattle of various breeds. Selection against these alleles in order to reduce reproductive failure and animal loss is recommended.

What is the best fitness measure in wild populations? A case study on the power of short-term fitness proxies to predict reproductive value

Fitness is at the core of evolutionary theory, but it is difficult to measure accurately. One way to measure long-term fitness is by calculating the individual’s reproductive value, which represents the expected number of allele copies an individual passes on to distant future generations. However, this metric of fitness is scarcely used because the estimation of individual’s reproductive value requires long-term pedigree data, which is rarely available in wild populations where following individuals from birth to death is often impossible. Wild study systems therefore use short-term fitness metrics as proxies, such as the number of offspring produced. This study obtained three frequently used short-term proxies for fitness obtained at different offspring life stages (eggs, hatchlings, fledglings and recruits), and compared their ability to predict reproductive values derived from the genetic pedigree of a wild passerine bird population. We used twenty years of precise field observations and a near-complete genetic pedigree to calculate reproductive success, individual growth rate and de-lifed fitness as lifetime fitness measures, and as annual de-lifed fitness. We compared the power of these metrics to predict reproductive values and lineage survival to the end of the study period. The three short-term fitness proxies predict the reproductive values and lineage survival only when measured at the recruit stage. There were no significant differences between the different fitness proxies at the same offspring stages in predicting the reproductive values and lineage survival. Annual fitness at one year old predicted reproductive values equally well as lifetime de-lifed fitness. However, none of the short-term fitness proxies was strongly associated with the reproductive values. In summary, the commonly short-term fitness proxies capture long-term fitness with intermediate accuracy at best, if measured at recruitment stage. As lifetime fitness measured at recruit stage and annual fitness in the first year of life were the best proxies of long-term fitness, we encourage their future use.

Estimation of Pool Construction and Technical Error

Pooling animals with extreme phenotypes can improve the accuracy of genetic evaluation or provide genetic evaluation for novel traits at relatively low cost by exploiting large amounts of low-cost phenotypic data from animals in the commercial sector without pedigree (data from commercial ranches, feedlots, stocker grazing or processing plants). The average contribution of each animal to a pool is inversely proportional to the number of animals in the pool or pool size. We constructed pools with variable planned contributions from each animal to approximate errors with different numbers of animals per pool. We estimate pool construction error based on combining liver tissue, from pulverized frozen tissue mass from multiple animals, into eight sub-pools containing four animals with planned proportionality (1:2:3:4) by mass. Sub-pools were then extracted for DNA and genotyped using a commercial array. The extracted DNA from the sub-pools was used to form super pools based on DNA concentration as measured by spectrophotometry with planned contribution of sub-pools of 1:2:3:4. We estimate technical error by comparing estimated animal contribution using sub-samples of single nucleotide polymorphism (SNP). Overall, pool construction error increased with planned contribution of individual animals. Technical error in estimating animal contributions decreased with the number of SNP used.

PSIX-1 Canadian Vytelle technology for determining residual feed intake in raising Qazaq Aqbas bull calves

Selection for residual feed intake (RFI) allows you to reduce feed costs and increase productivity of beef cattle. An increase in feed productivity by 10% can lead to an increase in profits by 43%, raising livestock with a low RFI can reduce feed intake by 12%, reduce methane emissions by 30%, and manure reduction by 17%. To obtain reliable trial results when determining the RFI, it is necessary to ensure the following conditions: 1) the same age of animals 2) the exchange of pedigree data between users of the system, which makes it possible to compare the EPDs within Vytelle Systems. Objects of research:QazaqAqbas bull calves (n = 46) at the age of 10–12 months in ZhanaBerekeLLP in Akmola region of Kazakhstan. Trial results confirm that residual feed intake in group 1 varied from -0.81 to 1.11, in group 2 - from -0.80 to 1.09. The RFI Rank was higher in group 1 (12.5). RADG in group 1 was at the level of -0.57 ... 0.58, in group 2 - -0.58 ... 1.13. According to the numerical rating of the animal (RADG Rank), the average value in group 1 was 12.5, in group 2 - 11.5. The average live weight at the beginning (START WT.) and end (END WT.) in the first group was 254.16 and 287.62 kg, in the second group 239.99 and 273.09 kg. The ADG in two groups was at the same level - 0.70 and 0.69 kg. The average Dry Matter Intake per day by animals during the trial was higher in the first group - 4.15, in the second group it was 3.65. For the first time in Kazakhstan national QazaqAqbas breed is tested for RFI, RADG, ADG, DMI, Raw F:G, Adj F:G.

54 Genetics Reloaded: Large-scale Collection of Novel Phenotypes in Turkey

Effective application of genomic selection methodologies require genomic information, population-based pedigree data, and high-quality phenotypes. The implementation of such selection programs can increase the accuracy of breeding values, therefore improving the ability to estimate the genetic merit of livestock. In particular, traits with low heritability are amenable to genomic selection. The objective of this presentation is to outline improvement of traits such as livability, disease resistance, fertility, and other health and welfare traits in turkeys, which could considerably advance breeding programs. The aim of this study was to apply different methodologies (ssGBLUP, random regression approaches, etc.) to novel and conventional traits collected in commercial turkey lines (15,000 turkeys genotyped at 65K). This reference population was used to assess the increase in accuracy of selection using genomic information, which ranged from 0 to +0.3, depending on the trait. A further goal of the study was to monitor inbreeding within the different lines. A large number of high-quality phenotypes related to fertility, growth, production, and carcass composition were collected, as well as additional health and behaviour phenotypes related to livability. These traits are being developed for use in performance testing. Furthermore, meat quality (e.g. white striation, water holding capacity, pH, sheer force and colour, etc.) and total carcass composition phenotypes were analysed. With improved methodology, more detailed phenotypic information, and comprehensive data collection and integration, we present more accurate selection of parent stock for application in applied poultry breeding programs.

Major Depressive Disorder and Lifestyle: Correlated Genetic Effects in Extended Twin Pedigrees

In recent years, evidence has accumulated with regard to the ubiquity of pleiotropy across the genome, and shared genetic etiology is thought to play a large role in the widespread comorbidity among psychiatric disorders and risk factors. Recent methods investigate pleiotropy by estimating genetic correlation from genome-wide association summary statistics. More comprehensive estimates can be derived from the known relatedness between genetic relatives. Analysis of extended twin pedigree data allows for the estimation of genetic correlation for additive and non-additive genetic effects, as well as a shared household effect. Here we conduct a series of bivariate genetic analyses in extended twin pedigree data on lifetime major depressive disorder (MDD) and three indicators of lifestyle, namely smoking behavior, physical inactivity, and obesity, decomposing phenotypic variance and covariance into genetic and environmental components. We analyze lifetime MDD and lifestyle data in a large multigenerational dataset of 19,496 individuals by variance component analysis in the ‘Mendel’ software. We find genetic correlations for MDD and smoking behavior (rG = 0.249), physical inactivity (rG = 0.161), body-mass index (rG = 0.081), and obesity (rG = 0.155), which were primarily driven by additive genetic effects. These outcomes provide evidence in favor of a shared genetic etiology between MDD and the lifestyle factors.

Comparison of breeding strategies for the creation of a synthetic pig line

Creating a new synthetic line by crossbreeding means complementary traits from pure breeds can be combined in the new population. Although diversity is generated during the crossbreeding stage, in this study, we analyze diversity management before selection starts. Using genomic and phenotypic data from animals belonging to the first generation (G0) of a new line, different simulations were run to evaluate diversity management during the first generations of a new line and to test the effects of starting selection at two alternative times, G3 and G4. Genetic diversity was characterized by allele frequency, inbreeding coefficients based on genomic and pedigree data, and expected heterozygosity. Breeding values were extracted at each generation to evaluate differences in starting selection at G3 or G4. All simulations were run for ten generations. A scenario with genomic data to manage diversity during the first generations of a new line was compared with a random and a selection scenario. As expected, loss of diversity was higher in the selection scenario, while the scenario with diversity control preserved diversity. We also combined the diversity management strategy with different selection scenarios involving different degrees of diversity control. Our simulation results show that a diversity management strategy combining genomic data with selection starting at G4 and a moderate degree of diversity control generates genetic progress and preserves diversity.