Pedigree analysis of a highly fragmented population, the Lidia cattle breed

A novel missense variant in endothelin-2 (EDN2) causes a growth and respiratory lethal syndrome in bovine

The high level of fragmentation of the Spanish Lidia cattle breed, divided into lineages called ‘castas’ and into herds within lineages based on reproductive isolation, increases the risk of homozygosity and the outbreak of recessive genetic defects. Since 2004, an increasing number of calves have been identified in a Lidia herd with signs of severe growth retardation, respiratory alterations and juvenile lethality, which constitutes a novel inherited syndrome in cattle and was subsequently termed growth and respiratory lethal syndrome. We performed a genome‐wide association study on a cohort of 13 affected calves and 24 putative non‐carrier parents, mapping the disease to a wide 6 cM region on bovine chromosome 3 (p < 10⁻⁷). Whole genome re‐sequencing of three affected calves and three putative non‐carrier parents identified a novel missense variant (c.149G>A|p.Cys50Tyr) in exon 2 of the endothelin 2 (EDN2) gene. Bioinformatic analyses of p.Cys50Tyr effects predicted them to be damaging for both the structure and the function of the edn2 protein, and to create a new site of splicing that may also affect the pattern of pre‐mRNA splicing and exon definition. Sanger sequencing of this variant on the rest of the sample set confirmed the segregation pattern obtained with whole genome re‐sequencing. The identification of the causative variant and the development of a diagnostic genetic test enable the efficient design of matings to keep the effective population size as high as possible, as well as providing insights into the first EDN2‐associated hereditary disease in cattle or other species.

Process of Introduction of Australian Braford Cattle to South America: Configuration of Population Structure and Genetic Diversity Evolution

Simple Summary

The Braford breed originated in the USA and Australia from a cross between the Brahman and Hereford breeds to obtain animals suitable for the subtropical climate and resistant to hoof diseases, eye cancer, and ectoparasites, mainly ticks. This resistance to ticks was what attracted the attention of South American breeders, who acquired animals from Australia. The first breeder to do so was Uruguay around 1970. From then on, the breed was distributed across Argentina, Paraguay, and Brazil. Each country has its own association of breeders, and each one keeps the herdbook of the breed where the animals are registered. Selective breeding was conducted, thereby shaping genetic diversity over the years. The analysis of the pedigree database allowed us to evaluate these changes and the evolution of diversity over time. The objective of the present work was to analyze the population structure of the Braford breed in four countries, the repercussions of founders and ancestors, and the parameters of genetic diversity to suggest effective strategies for Braford breeders.

Abstract

This study analyzes the evolution of the population structure and genetic diversity of Braford cattle in South America from 1949 to 2019 to suggest effective strategies for breeding in the future. The percentage of bulls historically increased. The average generational interval decreased to 11.78 years for the current population. Average inbreeding (F) and coancestry (C) are low and show a historically increasing trend (0.001% to 0.002%, respectively). The degree of nonrandom mating (α) increased from −0.0001 to 0.0001 denoting a change in the trend to mate similar individuals. The average relatedness coefficient (ΔR) increased in the current period from 0.002% to 0.004%. A single ancestor explained 4.55% to 7.22% of the population’s gene pool. While the effective population size based on the individual inbreeding rate (NeFi) was 462.963, when based on the individual coancestry rate (NeCi), it was 420.168. Genetic diversity loss is small and mainly ascribed to bottlenecks (0.12%) and to unequal contributions of the founders (0.02%). Even if adequate levels of diversity can be found, practices that consider the overuse of individual bulls (conditioned by nature or not), could lead to a long-term reduction in diversity. The present results permit tailoring genetic management strategies that are perfectly adapted to the needs that the population demands internationally.

Analyses of Genetic Diversity in the Endangered “Berrenda” Spanish Cattle Breeds Using Pedigree Data

Simple Summary

The two “berrenda” cattle breeds are important for the conservation of livestock genetic diversity in Spain. They have a great phenotypic and genotypic uniqueness and both of them are important from the cultural and the tourist perspectives. They also contribute to the conservation of the traditional “Dehesa” ecosystem. Both breeds are considered as endangered ones, but their genealogies have never been used for quantifying the risk status of their populations. The aim of this work was to monitor the structure of the “Berrenda en Negro” and the “Berrenda en Colorado” populations, their inbreeding rate and some other parameters that could be useful to prevent losses in their genetic diversity and to conduct and analyze the effect of the conservation programs developed by ANABE Breeders Association and finally, as a tool to implement some selective measures. We found that both “berrenda” cattle breeds retain a huge genetic variability from their founders’ populations, although they have been affected by a shallow depth in their pedigrees; as a consequence, we suggest increasing exchanges of breeding animals among herds, more specifically in the case of the “Berrenda en Negro” breed.

Abstract

Pedigree analyses of two endangered cattle breeds were performed in order to study the structure and the genetic variability in their populations. Pedigree data were analyzed from 12,057 individuals belonging to the “Berrenda en Negro” cattle breed (BN) and 20,389 individuals belonging to the “Berrenda en Colorado” cattle breed (BC) that were born between 1983 and 2020. BN and BC reference populations (RP) were set up by 2300 and 3988 animals, respectively. The generation interval in BN and BC reference populations was equal to 6.50 and 6.92 years, respectively. The pedigree completeness level was 82.76% in BN and 79.57% in BC. The inbreeding rates were 4.5% in BN and 3.4% in BC, respectively. The relationship among animals when they were born in different herds was 1.8% in BN and 5% in BC; these values increased to 8.5% and 7.7%, respectively when comparing animals that were born in the same herd. The effective number of founding herds was 23.9 in BN and 60.9 in BC. Number of ancestors needed to explain 50% of genes pool in the whole population was 50 and 101, in BN and in BC, respectively. The effective population size based on co-ancestries was 92.28 in BN and 169.92 in BC. The genetic variability has been maintained in both populations over time and the results of this study suggest that measures to promote the conservation of the genetic variability in these two breeds would go through for the exchange of breeding animals among farms and for monitoring the genetic contributions before implementing any selective action.

Distributional characterizations and testing for differences of relatedness and inbreeding of a subpopulation of American Hereford bulls

Beta distributions are characterized by two determining parameters and a parameter space from 0 to 1, and may be useful for examining population genetic parameters such as the relationship or inbreeding coefficients. Often subpopulations exist within breeds that are congregated around particular lineages of cattle or ancestors that breeders value. These subpopulations are more related to each other than to the majority of other animals; they may have higher inbreeding as well. Value may be added to these subpopulations because of their relatedness with important or renowned ancestors. The objectives of this work were to compare the relatedness and inbreeding of a group of 26 modern bulls from a subpopulation of the American Hereford breed relative to 1) 30 males with the most descendants present in the pedigree, 2) 15 renowned American Hereford bulls considered important individuals in the breed's history, and 3) 19 prominent subpopulation male ancestors. Conformance of the mean relationship coefficients of the bulls with the three groups and the mean inbreeding coefficient with all pedigree animals to beta distributions was assessed by 1) visually determining the parameters of the beta distributions based on the entire pedigree, 2) testing the mean relationship coefficient or inbreeding coefficient of the group of subpopulation bulls for its positional inclusion in those distributions, and 3) bootstrap sampling methodology. The mean relationship coefficients of the 26 Trask bulls with the 30 bulls with the most descendants, the 15 renowned ancestors, and the 19 Trask male ancestors were 0.15, 0.132, and 0.208, respectively. Testing of these means in beta distributions indicated that the group of 26 Trask bulls were no more related to the three groups of bulls than all of the animals in the pedigree (0.06 < P < 0.25). Bootstrap sampling indicated that the 26 bulls were more related to the three groups of male ancestors than the remainder of the animals in the pedigree (P < 0.0001). The mean inbreeding coefficient of the 26 bulls (0.13) did not differ from the overall inbreeding coefficient (0.056) when tested using a beta distribution; however, bootstrap sampling indicated otherwise (P < 0.0001). Results may indicate the inadequacy of visually parameterizing a beta distribution. Quantification of pedigree relatedness of a group of animals to key ancestors, especially with no DNA available, may add value to that group and individuals.

Genetic Diversity in the Portuguese Mertolenga Cattle Breed Assessed by Pedigree Analysis

Simple Summary

The conservation and maintenance of genetic diversity is one of the priorities of the Convention of Biological Diversity and is included in the United Nations (UN’s) Sustainable Development Goals. The evaluation of the genetic variability of a breed is fundamental for its future use in a sustainable way, being indispensable to outline a successful conservation or improvement strategy. Preserving genetic diversity in a population is one of the main objectives for a breed conservation program. Nevertheless, the correct management of genetic diversity is also essential for the adaptation of a population to a new environment, production system or genetic improvement. For the purpose of population monitoring, assessing changes in genetic variability and genetic erosion in animal populations, many methodologies based on pedigree analyses of inbreeding and relationships, and on the probability of genetic origin from different herds, founders and ancestors, have been used. This study presents several genetic diversity indicators in a Portuguese native cattle breed, Mertolenga, assessed by pedigree analysis, and demonstrates the usefulness of these indicators and how they can be used in the genetic management of a breed.

Abstract

The Mertolenga beef cattle, currently with 27,000 breeding females in Portugal, is the largest Portuguese native breed, despite some variation in the breeding stock over the last years. The purpose of this study was to estimate parameters related to the population structure and genetic diversity and to investigate the major factors affecting genetic erosion in the breed, based on the pedigree herdbook information collected since the 1950s, including records on 221,567 animals from 425 herds. The mean generation intervals were 6.4 years for sires and 7.1 years for dams, respectively. The rate of inbreeding per year was 0.183% ± 0.020% and the correspondent effective population size was 38.83. In the reference population (35,017 calves born between 2015 and 2019), the average inbreeding and relatedness were 8.82% ± 10% and 2.05% ± 1.26%, respectively. The mean relationship among animals from the same and from different herds was 29.25% ± 9.36% and 1.87% ± 1.53%, respectively. The estimates for the effective number of founders, ancestors, founding herds and herds supplying sires were 87.9, 59.4, 21.4 and 73.5, respectively. Although the situation of the Mertolenga breed is not alarming, these results indicate the need to adopt measures to maintain the genetic variability of the population.

Refining the genetic structure and relationships of European cattle breeds through meta-analysis of worldwide genomic SNP data, focusing on Italian cattle

The availability of genotyping assays has allowed the detailed evaluation of cattle genetic diversity worldwide. However, these comprehensive studies did not include some local European populations, including autochthonous Italian cattle. In this study, we assembled a large-scale, genome-wide dataset of single nucleotide polymorphisms scored in 3,283 individuals from 205 cattle populations worldwide to assess genome-wide autozygosity and understand better the genetic relationships among these populations. We prioritized European cattle, with a special focus on Italian breeds. Moderate differences in estimates of molecular inbreeding calculated from runs of homozygosity (FROH) were observed among domesticated bovid populations from different geographic areas, except for Bali cattle. Our findings indicated that some Italian breeds show the highest estimates of levels of molecular inbreeding among the cattle populations assessed in this study. Patterns of genetic differentiation, shared ancestry, and phylogenetic analysis all suggested the occurrence of gene flow, particularly among populations originating from the same geographical area. For European cattle, we observed a distribution along three main directions, reflecting the known history and formation of the analyzed breeds. The Italian breeds are split into two main groups, based on their historical origin and degree of conservation of ancestral genomic components. The results pinpointed that also Sicilian breeds, much alike Podolian derived-breeds, in the past experienced a similar non-European influence, with African and indicine introgression.

Detection of selection signatures for agonistic behaviour in cattle

The identification of genomic regions including signatures of selection produced by domestication and its subsequent artificial selection processes allows the understanding of the evolution of bovine breeds. Although several studies describe the genomic variability among meat or milk production cattle breeds, there are limited studies orientated towards bovine behavioural features. This study is focused on mapping genomic signatures of selection which may provide insights of differentiation between neutral and selected polymorphisms. Their effects are studied in the Lidia cattle traditionally selected for agonistic behaviour compared with Spanish breeds showing tamed behaviour. Two different approaches, BayeScan and SelEstim, were applied using genotypic 50K SNP BeadChip data. Both procedures detected two genomic regions bearing genes previously related to behavioural traits. The frequencies of the selected allele in these two regions in Lidia breed were opposite to those found in the tamed breeds. In these genomic regions, several putative genes associated with enriched metabolic pathways related to the behavioural development were identified, as neurochondrin gene (NCDN) or glutamate ionotropic receptor kainate type subunit 3 (GRIK3) both located at BTA3 or leucine-rich repeat and Ig domain containing 2 (LINGO2) and phospholipase A2-activating protein (PLAA) at BTA8.

Genomic diversity and population structure of Mexican and Spanish bovine Lidia breed

The Lidia bovine breed is distinguished for its low genetic exchangeability given its selection on aggressive behavior, its management uniqueness and its subdivided structure. In this study, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture of 468 animals from Mexican and Spanish Lidia breed populations and 64 samples belonging to 10 Spanish native and American-creole breeds using 37 148 single nucleotide polymorphisms. We found similar average inbreeding values in the Lidia breed, with different distributions within groups; variability of inbreeding values among Spanish lineages was significant and no differences were found among the Mexican sub-populations. Together, the high F_IS of the lineages and the behavior of the runs of homozygosity are consequences of the lineage's small effective population sizes, contributing to their inbreeding increase. Population admixture analysis discarded any influence on the genetic structure of the Lidia populations from the Spanish native and American-creole breeds. In addition, both Lidia populations depicted different genetic origins, with the exception of some Mexican individuals whose origins traced back to recent Spanish importations.