What can livestock breeders learn from conservation genetics and vice versa?

Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America

The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (FROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (Ne), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, FROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred Ne trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of Ne than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources.

Reproductive output and other adult life-history traits of black soldier flies grown on different organic waste and by-products

The interest in mass-rearing black soldier fly (Hermetia illucens) larvae for food and feed is rapidly increasing. This is partly sparked by the ability of the larvae to efficiently valorise a wide range of organic waste and by-products. Primarily, research has focused on the larval stage, hence underprioritizing aspects of the adult biology, and knowledge on reproduction-related traits such as egg production is needed. We investigated the impact of different organic waste and by-products as larval diets on various life-history traits of adult black soldier flies in a large-scale experimental setup. We reared larvae on four different diets: spent Brewer's grain, ground carrots, Gainesville diet, and ground oranges. Traits assessed were development time to pupa and adult life-stages, adult body mass, female lifespan, egg production, and egg hatch. Larval diet significantly impacted development time to pupa and adult, lifespan, body size, and egg production. In general, flies reared on Brewer's grain developed up to 4.7 d faster, lived up to 2.3 d longer, and produced up to 57% more eggs compared to flies reared on oranges on which they performed worst for these traits. There was no effect of diet type on egg hatch, suggesting that low-nutritious diets, i.e. carrots and oranges, do not reduce the quality but merely the quantity of eggs. Our results demonstrate the importance of larval diet on reproductive output and other adult traits, all important for an efficient valorisation of organic waste and by-products, which is important for a sustainable insect-based food and feed production.

A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle

Intramuscular fat (IMF) deposition profoundly influences meat quality and economic value in beef cattle production. Meanwhile, contemporary developments in epigenetics have opened new outlooks for understanding the molecular basics of IMF regulation, and it has become a key area of research for world scholars. Therefore, the aim of this paper was to provide insight and synthesis into the intricate relationship between epigenetic mechanisms and IMF deposition in beef cattle. The methodology involves a thorough analysis of existing literature, including pertinent books, academic journals, and online resources, to provide a comprehensive overview of the role of epigenetic studies in IMF deposition in beef cattle. This review summarizes the contemporary studies in epigenetic mechanisms in IMF regulation, high-resolution epigenomic mapping, single-cell epigenomics, multi-omics integration, epigenome editing approaches, longitudinal studies in cattle growth, environmental epigenetics, machine learning in epigenetics, ethical and regulatory considerations, and translation to industry practices from perspectives of IMF deposition in beef cattle. Moreover, this paper highlights DNA methylation, histone modifications, acetylation, phosphorylation, ubiquitylation, non-coding RNAs, DNA hydroxymethylation, epigenetic readers, writers, and erasers, chromatin immunoprecipitation followed by sequencing, whole genome bisulfite sequencing, epigenome-wide association studies, and their profound impact on the expression of crucial genes governing adipogenesis and lipid metabolism. Nutrition and stress also have significant influences on epigenetic modifications and IMF deposition. The key findings underscore the pivotal role of epigenetic studies in understanding and enhancing IMF deposition in beef cattle, with implications for precision livestock farming and ethical livestock management. In conclusion, this review highlights the crucial significance of epigenetic pathways and environmental factors in affecting IMF deposition in beef cattle, providing insightful information for improving the economics and meat quality of cattle production.

Rapid Evolutionary Adaptation to Diet Composition in the Black Soldier Fly (Hermetia illucens)

Genetic adaptation of Hermetia illucens (BSF) to suboptimal single sourced waste streams can open new perspectives for insect production. Here, four BSF lines were maintained on a single sourced, low-quality wheat bran diet (WB) or on a high-quality chicken feed diet (CF) for 13 generations. We continuously evaluated presumed evolutionary responses in several performance traits to rearing on the two diets. Subsequently, we tested responses to interchanged diets, i.e., of larvae that had been reared on low-quality feed and tested on high-quality feed and vice versa to evaluate costs associated with adaptation to different diets. BSF were found to experience rapid adaptation to the diet composition. While performances on the WB diet were always inferior to the CF diet, the adaptive responses were stronger to the former diet. This stronger response was likely due to stronger selection pressure experienced by BSF fed on the low-quality single sourced diet. The interchanged diet experiment found no costs associated with diet adaptation, but revealed cross generational gain associated with the parental CF diet treatment. Our results revealed that BSF can rapidly respond adaptively to diet, although the mechanisms are yet to be determined. This has potential to be utilized in commercial insect breeding to produce lines tailored to specific diets.

Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array

Chinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region. However, the population structure and the genetic basis of prominent characteristics of CRS are still unknown. In this study, we systematically describe their population structure, genetic diversity, and selection signature based on genotyping data from 61 CRS individuals with GGP Bovine 100 K chip. The results showed that CRS cattle had low inbreeding levels and had formed a unique genetic structure feature. Using two complementary methods (including comprehensive haplotype score and complex likelihood ratio), we identified 1291 and 1285 potentially selected genes, respectively. There were 141 genes annotated in common 106 overlapping genomic regions covered 5.62 Mb, including PLAG1, PRKG2, DGAT1, PARP10, TONSL, ADCK5, and BMP3, most of which were enriched in pathways related to muscle growth and differentiation, milk production, and lipid metabolism. This study will contribute to understanding the genetic mechanism behind artificial selection and give an extensive reference for subsequent breeding.

Genetic polymorphism in European and African sheep breeds reared in Hungary based on 48 SNPs associated with resistance to gastrointestinal parasite infection using KASP-PCR technique

This pilot study used an alternative and economically efficient technique, the Kompetitive Allele-Specific Polymerase Chain Reaction (KASP-PCR) to examine 48 SNPs from 11 parasite-resistance genes found on 8 chromosomes in 110 animals from five sheep breeds reared in Hungary; Hungarian Tsigai, White Dorper, Dorper, Ile de France, and Hungarian Merino. Allele and genotype frequencies, fixation index, observed heterozygosity, expected heterozygosity, F statistic, and their relationship with the Hardy-Weinberg equilibrium (WHE) and the polymorphic information content (PIC) were determined, followed by principal component analysis (PCA). As much as 32 SNPs out of the 48 initially studied were successfully genotyped. A total of 9 SNPs, 4 SNPs in TLR5, 1 SNP in TLR8, and 4 SNPs in TLR2 genes, were polymorphic. The variable genotype and allele frequency of the TLRs gene indicated genetic variability among the studied sheep breeds, with the Hungarian Merino exhibiting the most polymorphisms, while Dorper was the population with the most SNPs departing from the HWE. According to the PIC value, the rs430457884-TLR2, rs55631273-TLR2, and rs416833129-TLR5 were found to be informative in detecting polymorphisms among individuals within the populations, whereas the rs429546187-TLR5 and rs424975389-TLR5 were found to have a significant influence in clustering the population studied. This study reported a moderate level of genetic variability and that a low to moderate within-breed diversity was maintained in the studied populations.

Population Genetics of Manila Clam (Ruditapes philippinarum) in China Inferred from Microsatellite Markers

The Manila clam (Ruditapes philippinarum) is one of the most commercially important bivalves along the coast of China. With the continuous expansion of clam farming scale, it may lead to some serious problems, including loss of genetic variation, inbreeding depression, and reduced effective population size (N_e). In the present study, eleven microsatellite markers were used to investigate the genetic diversity and differentiation among 13 clam populations along the coast of China. As a result, 150 alleles were detected according to the genotyping results of eleven microsatellite loci. The observed heterozygosity (H_o) was estimated to be ranging from 0.437 to 0.678, while the expected heterozygosity (H_e) was calculated to be varying from 0.587 to 0.700. F_st values between populations ranged from 0.0046-0.1983. In particular, the Laizhou population had the highest genetic variability, which was significantly different from the others (all F_st values > 0.1). For all the clam populations, there was no significant linear regression between genetic and geographic distance, indicating that these populations do not follow a pattern of isolation by distance (IBD). Genetic structure was estimated according to NJ, principal coordinates (PCoA), and structure-based clustering. Estimates of effective population size range from dozens to thousands among different populations, based on linkage-disequilibrium and molecular coancestry methods. The results reveal the genetic diversity of clams and verify the hypothesis that clam population differentiation may be influenced by the mode of southern breeding and northern culture, providing guiding information for natural resource conservation and genetic breeding of clams.

Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing

German Black Pied cattle (Deutsches Schwarzbuntes Niederungsrind, DSN) are an endangered dual-purpose cattle breed originating from the North Sea region. The population comprises about 2,500 cattle and is considered one of the ancestral populations of the modern Holstein breed. The current study aimed at defining the breeds closest related to DSN cattle, characterizing their genomic diversity and inbreeding. In addition, the detection of selection signatures between DSN and Holstein was a goal. Relationship analyses using fixation index (F_ST), phylogenetic, and admixture analyses were performed between DSN and 68 other breeds from the 1000 Bull Genomes Project. Nucleotide diversity, observed heterozygosity, and expected heterozygosity were calculated as metrics for genomic diversity. Inbreeding was measured as excess of homozygosity (F_Hom) and genomic inbreeding (F_RoH) through runs of homozygosity (RoHs). Region-wide F_ST and cross-population-extended haplotype homozygosity (XP-EHH) between DSN and Holstein were used to detect selection signatures between the two breeds, and RoH islands were used to detect selection signatures within DSN and Holstein. DSN showed a close genetic relationship with breeds from the Netherlands, Belgium, Northern Germany, and Scandinavia, such as Dutch Friesian Red, Dutch Improved Red, Belgian Red White Campine, Red White Dual Purpose, Modern Angler, Modern Danish Red, and Holstein. The nucleotide diversity in DSN (0.151%) was higher than in Holstein (0.147%) and other breeds, e.g., Norwegian Red (0.149%), Red White Dual Purpose (0.149%), Swedish Red (0.149%), Hereford (0.145%), Angus (0.143%), and Jersey (0.136%). The F_Hom and F_RoH values in DSN were among the lowest. Regions with high F_ST between DSN and Holstein, significant XP-EHH regions, and RoH islands detected in both breeds harbor candidate genes that were previously reported for milk, meat, fertility, production, and health traits, including one QTL detected in DSN for endoparasite infection resistance. The selection signatures between DSN and Holstein provide evidence of regions responsible for the dual-purpose properties of DSN and the milk type of Holstein. Despite the small population size, DSN has a high level of diversity and low inbreeding. F_ST supports its relatedness to breeds from the same geographic origin and provides information on potential gene pools that could be used to maintain diversity in DSN.

Evaluation of Genetic Diversity in Dog Breeds Using Pedigree and Molecular Analysis: A Review

Domestic dogs are important for many economic and social reasons, and they have become a well-known model species for human disease. According to research, dog breeds exhibit significant levels of inbreeding and genetic diversity loss, decreasing the population’s ability to adapt in certain conditions, and indicating the need of conservation strategies. Before the development of molecular markers, pedigree information was used for genetic diversity management. In recent years, genomic tools are frequently applied for accurate estimation of genetic diversity and improved genetic conservation due to incomplete pedigrees and pedigree errors. The most frequently used molecular markers include PCR-based microsatellite markers (STRs) and DNA sequencing-based single-nucleotide polymorphism markers (SNP). The aim of this review was to highlight genetic diversity studies on dog breeds conducted using pedigree and molecular markers, as well as the importance of genetic diversity conservation in increasing the adaptability and survival of dog breed populations.

Runs of Homozygosity Analysis Reveals Genomic Diversity and Population Structure of an Indigenous Cattle Breed in Southwest China

In aiming to achieve sustainable development goals in the livestock industry, it is becoming increasingly necessary and important for the effective conservation of genetic resources. There are some indigenous cattle breeds in Sichuan, southwest China, for which, however, the genetic diversity and population structures still remain unknown because of the unavailability of systematic breeding programs and pedigree information. Xieka cattle are an indigenous breed locally distributed in southeastern Sichuan and have a long-term evolutionary adaptation to local environments and climates. In this study, we obtained 796,828 single nucleotide polymorphisms (SNPs) through sequencing the genomes of 30 Xieka cattle and used them for analyzing the genetic diversity and runs of homozygosity (ROH). The mean nucleotide diversity was 0.28 and 72% of SNPs were found to be in the heterozygous states. A total of 4377 ROH were detected with even distribution among all autosomes, and 74% of them were lower than 1 Mb in length. Meanwhile, only five ROH were found longer than 5 Mb. We further determined 19 significant genomic regions that were obviously enriched by ROH, in which 35 positional candidate genes were found. Some of these genes have been previously reported to be significantly associated with various production traits in cattle, such as meat quality, carcass performances, and diseases. In conclusion, the relatively high degree of genetic diversity of Xieka cattle was revealed using the genomic information, and the proposed candidate genes will help us optimize the breeding programs regarding this indigenous breed.

Genetic architecture of a composite beef cattle population

Composite breeds are widely used in the beef industry. Composites allow producers to combine desirable traits from the progenitor breeds and simplify herd management, without repeated crossbreeding and maintenance of purebreds. In this study, genomic information was used to evaluate the genetic composition and characteristics of a three-breed beef cattle composite. This composite population referred to as Composite Gene Combination (CGC) consisted of 50% Red Angus, 25% Charolais, 25% Tarentaise. A total of 248 animals were used in this study CGC (n=79), Red Angus (n=61), Charolais (n=79) and Tarentaise (n=29). All animals were genotyped with 777k HD panel. Principal component and ADMIXTURE analyses were carried out to evaluate the genetic structure of CGC animals. The ADMIXTURE revealed the proportion of Tarentaise increased to approximately 57% while Charolais decreased to approximately 5%, and Red Angus decreased to 38% across generations. To evaluate these changes in the genomic composition across different breeds and in CGC across generations runs of homozygosity (ROH) were conducted. This analysis showed Red Angus to have the highest total length of ROH segments per animal with a mean of 349.92 Mb and lowest in CGC with a mean of 141.10 Mb. Furthermore, it showed the formation of new haplotypes in CGC around the sixth generation. Selection signatures were evaluated through Fst and HapFlk analyses. Several selection sweeps in CGC were identified especially in chromosomes 5 and 14 which have previously been reported to be associated with coat color and growth traits. The study supports our previous findings that progenitor combinations are not stable over generations and that either direct or natural selection plays a role in modifying the progenitor proportions. Furthermore, the results showed that Tarentaise contributed useful attributes to the composite in a cool semi-arid environment and suggests a re-exploration of this breed's role may be warranted.

Strategies of preserving genetic diversity while maximizing genetic response from implementing genomic selection in pulse breeding programs

Genomic selection maximizes genetic gain by recycling parents to germplasm pool earlier and preserves genetic diversity by restricting the number of fixed alleles and the relationship in pulse breeding programs. Using a stochastic computer simulation, we investigated the benefit of optimization strategies in the context of genomic selection (GS) for pulse breeding programs. We simulated GS for moderately complex to highly complex traits such as disease resistance, grain weight and grain yield in multiple environments with a high level of genotype-by-environment interaction for grain yield. GS led to higher genetic gain per unit of time and higher genetic diversity loss than phenotypic selection by shortening the breeding cycle time. The genetic gain obtained from selecting the segregating parents early in the breeding cycle (at F₁ or F₂ stages) was substantially higher than selecting at later stages even though prediction accuracy was moderate. Increasing the number of F₁ intercross (F_1i) families and keeping the total number of progeny of F_1i families constant, we observed a decrease in genetic gain and increase in genetic diversity, whereas increasing the number of progeny per F_1i family while keeping a constant number of F_1i families increased the rate of genetic gain and had higher genetic diversity loss per unit of time. Adding 50 F₂ family phenotypes to the training population increased the accuracy of genomic breeding values (GEBVs) and genetic gain per year and decreased the rate of genetic diversity loss. Genetic diversity could be preserved by applying a strategy that restricted both the percentage of alleles fixed and the average relationship of the group of selected parents to preserve long-term genetic improvement in the pulse breeding program.

Assessment the effect of genomic selection and detection of selective signature in broilers

Due to high selection advances and shortened generation interval, genomic selection (GS) is now an effective animal breeding scheme. In broilers, many studies have compared the accuracy of different GS prediction methods, but few reports have demonstrated phenotypic or genetic changes using GS. In this study, the paternal chicken line B underwent continuous selection for 3 generations. The chicken 55 k SNP chip was used to estimate the genetic parameters and detect genomic response regions by selective sweep analysis. The heritability for body weight (BW), meat production, and abdominal fat traits were ranged from 0.12 to 0.38. A high genetic correlation was found between BW and meat production traits, while a low genetic correlation (<0.1) was found between meat production and abdominal fat traits. Selection resulted in an increase of about 516 g in BW and 140 g in breast muscle weight. Percentage of breast muscle and whole thigh were increased 0.8 to 1.5%. No change was observed in abdominal fat percentage. The genomic estimated breeding value advances was positive for BW and meat production (except whole thigh percentage), while negative for abdominal fat percentage. By selective sweep analysis, 39 common chromosomal regions and 102 protein coding genes were found to be influenced, including MYH1A, MYH1B, and MYH1D of the MYH gene family. Tight junction pathway as well as myosin complex related terms were enriched. This study demonstrates the effective use of GS for improvements in BW and meat production in chicken line B. Further, genomic regions, responsive to intensive genetic selection, were identified to contain genes of the MYH family.

Large-Scale Whole Genome Sequencing Study Reveals Genetic Architecture and Key Variants for Breast Muscle Weight in Native Chickens

Breast muscle weight (BrW) is one of the most important economic traits in chicken, and directional breeding for that results in both phenotypic and genetic changes. The Jingxing yellow chicken, including an original (without human-driven selection) line and a selected line (based on selection for increased intramuscular fat content), were used to dissect the genetic architecture and key variants associated with BrW. We detected 1069 high-impact single nucleotide polymorphisms (SNPs) with high conserved score and significant frequency difference between two lines. Based on the annotation result, the ECM-receptor interaction and fatty acid biosynthesis were enriched, and muscle-related genes, including MYOD1, were detected. By performing genome-wide association study for the BrW trait, we defined a major haplotype and two conserved SNPs that affected BrW. By integrated genomic and transcriptomic analysis, IGF2BP1 was identified as the crucial gene associated with BrW. In conclusion, these results offer a new insight into chicken directional selection and provide target genetic markers by which to improve chicken BrW.

Whole-Genome SNP Characterisation Provides Insight for Sustainable Use of Local South African Livestock Populations

Local cattle and sheep populations are important for animal production and food security in South Africa. These genetic resources are well adapted to the diverse climatic conditions and hold potential to be utilized in production systems subjected to climate change. The local beef breeds are well integrated into commercial livestock production systems with access to performance recording and genetic evaluations, while local sheep breeds are mainly utilised in smallholder and communal systems. The GeneSeek^® Genomic Profiler™ Bovine 150 K SNP genotyping array was used to evaluate the diversity and inbreeding status of four indigenous (Boran, Drakensberger, Nguni, Tuli), two composite (Bonsmara and Beefmaster) and two exotic (SA Hereford and Charolais) beef breeds. The Illumina^® Ovine 50 K SNP BeadChip was used to investigate five indigenous (Black Head Persian, Damara, Fat tail, Namaqua Afrikaner, Pedi) and three commercial (Dorper, Dohne Merino and SA Merino) populations. Although ascertainment bias was indicated by the low MAF (the autosome-wide proportion of SNPs with MAF< 0.05 ranged from 6.18 to 9.97% for cattle, and 7.59–13.81% for sheep), moderate genomic diversity was observed (mean H_o ranged from 0.296 to 0.403 for cattle, and 0.327 to 0.367 for sheep). Slightly higher levels of ROH-based inbreeding were calculated for cattle (F_ROH range: 0.018–0.104), than for sheep populations (F_ROH range: 0.002–0.031). The abundance of short ROH fragments (mean proportion of <4 Mb fragments: 0.405 for cattle, and 0.794 for sheep) indicated ancient inbreeding in both species. The eight cattle populations were categorized into indicine, taurine or Sanga subspecies based on principal component, model-based clustering and phylogenetic analyses, with high levels of admixture observed within the Drakensberger, Nguni and Tuli breeds. Within the sheep populations, a clear distinction could be seen between the dual-purpose breeds, the meat breed and the indigenous breeds. Despite directional selection practiced in the cattle breeds, genomic diversity was moderate with low inbreeding. The non-commercialized, indigenous sheep populations are more vulnerable with small effective populations. These results emphasise the value of genomic information for effective management to exploit the potential contribution of local genetic cattle and sheep resources in a changing environment.

New developments in the field of genomic technologies and their relevance to conservation management

Recent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.

Hybridization with mountain hares increases the functional allelic repertoire in brown hares

Brown hares (Lepus europaeus Pallas) are able to hybridize with mountain hares (L. timidus Linnaeus) and produce fertile offspring, which results in cross-species gene flow. However, not much is known about the functional significance of this genetic introgression. Using targeted sequencing of candidate loci combined with mtDNA genotyping, we found the ancestral genetic diversity in the Finnish brown hare to be small, likely due to founder effect and range expansion, while gene flow from mountain hares constitutes an important source of functional genetic variability. Some of this variability, such as the alleles of the mountain hare thermogenin (uncoupling protein 1, UCP1), might have adaptive advantage for brown hares, whereas immunity-related MHC alleles are reciprocally exchanged and maintained via balancing selection. Our study offers a rare example where an expanding species can increase its allelic variability through hybridization with a congeneric native species, offering a route to shortcut evolutionary adaptation to the local environmental conditions.

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.

Evolvability and evolutionary rescue

The survival prospects of threatened species or populations can sometimes be improved by adaptive change. Such evolutionary rescue is particularly relevant when the threat comes from changing environments, or when long-term population persistence requires range expansion into new habitats. Conservation biologists are therefore often interested in whether or not populations or lineages show a disposition for adaptive evolution, that is, if they are evolvable. Here, we discuss four alternative perspectives that target different causes of evolvability and outline some of the key challenges those perspectives are designed to address. Standing genetic variation provides one familiar estimate of evolvability. Yet, the mere presence of genetic variation is often insufficient to predict if a population will adapt, or how it will adapt. The reason is that adaptive change not only depends on genetic variation, but also on the extent to which this genetic variation can be realized as adaptive phenotypic variation. This requires attention to developmental systems and how plasticity influences evolutionary potential. Finally, we discuss how a better understanding of the different factors that contribute to evolvability can be exploited in conservation practice.

Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions

Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.

Breed Ancestry, Divergence, Admixture, and Selection Patterns of the Simbra Crossbreed

In this study, we evaluated an admixed South African Simbra crossbred population, as well as the Brahman (Indicine) and Simmental (Taurine) ancestor populations to understand their genetic architecture and detect genomic regions showing signatures of selection. Animals were genotyped using the Illumina BovineLD v2 BeadChip (7K). Genomic structure analysis confirmed that the South African Simbra cattle have an admixed genome, composed of 5/8 Taurine and 3/8 Indicine, ensuring that the Simbra genome maintains favorable traits from both breeds. Genomic regions that have been targeted by selection were detected using the linkage disequilibrium-based methods iHS and Rsb. These analyses identified 10 candidate regions that are potentially under strong positive selection, containing genes implicated in cattle health and production (e.g., TRIM63, KCNA10, NCAM1, SMIM5, MIER3, and SLC24A4). These adaptive alleles likely contribute to the biological and cellular functions determining phenotype in the Simbra hybrid cattle breed. Our data suggested that these alleles were introgressed from the breed's original indicine and taurine ancestors. The Simbra breed thus possesses derived parental alleles that combine the superior traits of the founder Brahman and Simmental breeds. These regions and genes might represent good targets for ad-hoc physiological studies, selection of breeding material and eventually even gene editing, for improved traits in modern cattle breeds. This study represents an important step toward developing and improving strategies for selection and population breeding to ultimately contribute meaningfully to the beef production industry.

Genetic characterisation of non-descript cattle populations in communal areas of South Africa

Context Indigenous cattle breeds represent an important genetic resource for livelihood of communal-area inhabitants. Indigenous breeds have the ability to withstand harsh climatic conditions, can adapt genetically to poor-quality forages and are resistant to parasites and diseases. These unique traits possessed by indigenous breeds are under threat because of unrestrained crossing with exotic commercial breeds, and this can lead to total loss of a breed. Aims The study was conducted to assess the genetic diversity and population structure of South African non-descript communal beef cattle populations by using 25 microsatellite markers. Methods Unrelated and non-descript animals (n = 150) were sampled from communal areas from five (5) provinces of South Africa, namely, Eastern Cape, KwaZulu–Natal, Limpopo, Mpumalanga and the North West, with 30 samples per breed taken. Six (6) known cattle breeds (n = 180) were used as a reference population. This included Angus, Afrikaner, Bonsmara, Brahman, Drakensberger and the Nguni, with 30 samples per breed. Key results High level of genetic diversity was found across the five non-descript populations, with an average heterozygosity of 75%. The Limpopo population was found to be the most diverse population, with the highest average number of alleles (8.5) and heterozygosity (ranging between observed heterozygosity of 70% and expected heterozygosity of 79%). STRUCTURE software assigned populations (2 ≤ K ≤ 20), with the most probable cluster being at K = 7. The Eastern Cape, KwaZulu–Natal and Limpopo populations had genetic material similar to those possessed by the Nguni and Bonsmara reference populations. Conclusions Results from the study showed that most genetic differentiation occurred within populations rather than among populations, and this might be due to the fact that there is no selection for or against any specific production trait expressed in the populations. Implications The obtained information will serve as a baseline for the development and implementation of sound breeding programs that will assist in controlling the gene flow, so as to lower the possible genetic dilution of the currently available genetic material.

Genome-wide assessment of genetic diversity, linkage disequilibrium and haplotype block structure in Tharparkar cattle breed of India

Knowledge about genetic diversity is very essential for the management and sustainable utilization of livestock genetic resources. In this study, we presented a comprehensive genome-wide analysis of genetic diversity, ROH, inbreeding, linkage disequilibrium, effective population size and haplotype block structure in Tharparkar cattle of India. A total of 24 Tharparkar animals used in this study were genotyped with Illumina BovineSNP50 array. After quality control, 22,825 biallelic SNPs were retained, which were in HWE, MAF > 0.05 and genotyping rate >90%. The overall mean observed (H_O) and expected heterozygosity (H_E) were 0.339 ± 0.156 and 0.325 ± 0.129, respectively. The average minor allele frequency was 0.234 with a standard deviation of ± 0.131. We identified a total of 1832 ROH segments and the highest autosomal coverage of 13.87% was observed on chromosome 23. The genomic inbreeding coefficients estimates by F_ROH, F_HOM, F_GRM and F_UNI were 0.0589, 0.0215, 0.0532 and 0.0160 respectively. The overall mean linkage disequilibrium (LD) for a total of 133,532 pairwise SNPs measured by D' and r² was 0.6452 and 0.1339, respectively. In addition, we observed a gradual decline in effective population size over the past generations.

Variation in breeding practices and geographic isolation drive subpopulation differentiation, contributing to the loss of genetic diversity within dog breed lineages

Background

Discrete breed ideals are not restricted to delimiting dog breeds from another, but also are key drivers of subpopulation differentiation. As genetic differentiation due to population fragmentation results in increased rates of inbreeding and loss of genetic diversity, detecting and alleviating the reasons of population fragmentation can provide effective tools for the maintenance of healthy dog breeds.

Results

Using a genome-wide SNP array, we detected genetic differentiation to subpopulations in six breeds, Belgian Shepherd, English Greyhound, Finnish Lapphund, Italian Greyhound, Labrador Retriever and Shetland Sheepdog, either due to geographical isolation or as a result of differential breeding strategies. The subpopulation differentiation was strongest in show dog lineages.

Conclusions

Besides geographical differentiation caused by founder effect and lack of gene flow, selection on champion looks or restricted pedigrees is a strong driver of population fragmentation. Artificial barriers for gene flow between the different subpopulations should be recognized, their necessity evaluated critically and perhaps abolished in order to maintain genetic diversity within a breed. Subpopulation differentiation might also result in false positive signals in genome-wide association studies of different traits.

Lay summary

Purebred dogs are, by definition, reproductively isolated from other breeds. However, similar isolation can also occur within a breed due to conflicting breeder ideals and geographic distances between the dog populations. We show here that both of these examples can contribute to breed division, with subsequent loss of genetic variation in the resulting breed lineages. Breeders should avoid creating unnecessary boundaries between breed lineages and facilitate the exchange of dogs between countries.

Dynamics of genomic architecture during composite breed development in cattle

Some livestock breeds face the challenge of reduced genetic variation, increased inbreeding depression owing to genetic drift and selection. Hybridization can reverse these processes and increase levels of productivity and adaptation to various environmental stressors. Samples from American Brangus were used to evaluate the indicine/taurine composition through nine generations (~45 years) after the hybridization process was completed. The purpose was to determine how hybridization alters allelic combinations of a breed over time when genetic factors such as selection and drift are operating. Furthermore, we explored genomic regions with deviations from the expected composition from the progenitor breeds and related these regions to traits under selection. The Brangus composition deviated from the theoretical expectation, defined by the breed association, of 62.5% taurine, showing taurine composition to be 70.4 ± 0.6%. Taurine and indicine proportion were not consistent across chromosomes. Furthermore, these non‐uniform areas were found to be associated with traits that were probably under selection such as intermuscular fat and average daily gain. Interestingly, the sex chromosomes were predominantly taurine, which could be due to the composite being formed particularly in the final cross that resulted in progeny designated as purebred Brangus. This work demonstrated the process of new breed formation on a genomic level. It suggests that factors like genetic drift, selection and complementarity shift the genetic architecture into a uniquely different population. These findings are important to better understand how hybridization and crossbreeding systems shape the genetic architecture of composite populations.

The Local South American Chicken Populations Are a Melting-Pot of Genomic Diversity

Chicken have a considerable impact in South American rural household economy as a source of animal protein (eggs and meat) and a major role in cultural traditions (e.g., cockfighting, religious ceremonies, folklore). A large number of phenotypes and its heterogeneity are due to the multitude of environments (from arid to tropical rain forest and high altitude) and agricultural systems (highly industrialized to subsistence agriculture). This heterogeneity also represents the successive introduction of domestic chicken into this continent, which some consider predating Columbus’ arrival to South America. In this study, we have used next-generation restriction site-associated DNA sequencing to scan for genome-wide variation across 145 South American chickens representing local populations from six countries of South America (Colombia, Brazil, Ecuador, Peru, Bolivia, and Chile). After quality control, the genotypes of 122,801 single nucleotide polymorphisms (SNPs) were used to assess the genomic diversity and interpopulation genetic relationship between those populations and their potential sources. The estimated population genetic diversity displayed that the gamefowl has the least diverse population (θπ = 0.86; θS = 0.70). This population is also the most divergent (F_ST = 0.11) among the South American populations. The allele-sharing analysis and the admixture analysis revealed that the current diversity displayed by these populations resulted from multiple admixture events with a strong influence of the modern commercial egg-layer chicken (ranging between 44% and 79%). It also revealed an unknown genetic component that is mostly present in the Easter Island population that is also present in local chicken populations from the South American Pacific fringe.

Morphological divergence in the West African shorthorn Lagune cattle populations from Benin

This study explored the potential role of agro-ecology in shaping the morphology of Lagune cattle population of Benin. A total of 708 adult Lagune cattle were sampled randomly from nine provenances in two agro-ecological zones (AEZs) and were assessed for eight qualitative and twelve linear body measurements. Data were analyzed using generalized linear model procedures (PROC GLM) followed by the multiple comparison of least square means (LSMEAN) according to the Tukey-Kramer method and multivariate analytical methods, including canonical discrimination analysis (CDA) and hierarchical ascendant classification. Irrespective of AEZ and sex, the body length (102.3 ± 9.31 cm) was greater than the wither height (93.1 ± 7.39 cm) and the body index smaller than 0.85. However, there were significant differences between the two AEZs for most of the measured morphometric and qualitative traits. Moreover, a male-biased sexual size dimorphism was recorded. The CDA based on only four basic body measurements (rump height, body length, heart girth, and ear length) and the calculated Mahalanobis distances suggest that the populations from the two AEZs are distinct and could be further considered ecotypes. Nevertheless, the overall moderate classification rate (70%) of the individual animals into their group of origin indicates interbreeding between the two populations. The pairwise Mahalanobis distances between provenances in the same AEZ were also significant. Together, these results provide supporting evidence for the existence of subdivisions in the Lagune cattle populations from South Benin. The high morphological diversity in the Lagune cattle recorded in the present study could serve as a starting point for the development of efficient selection and sound subpopulation management strategies but also for further phenotypic and genetic characterizations.

Genetic variability and relationships in nine South African cattle breeds using microsatellite markers

Genetic variability within and between breeds allows adaptation to a changing environment and consequently prepares producers for the future. Eleven bovine-specific microsatellite markers were used to genotype animals from each of nine South African cattle breeds: Afrikaner (N = 550), Angus (N = 550), Bonsmara (N = 550), Boran (N = 321), Brahman (N = 550), Drakensberger (N = 550), Nguni (N = 550), Simmental (N = 550), and Tuli (N = 311). These breeds were drawn from Bos taurus africanus, Bos taurus, and Bos indicus. Genetic variability estimates included unbiased heterozygosity, effective number of alleles, and inbreeding. Ranges of these parameters were 0.569-0.741, 8.818-11.455, and - 0.001-0.050, respectively. Breed private allele and breed pairwise comparison was also used to characterize the breeds. The analysis of population structure with K = 2 revealed clusters comprised of Sanga-indicine and taurine, while K = 3 included separate clusters of Sanga, indicine, and taurine, and with K = 9 showed the breeds arising from unique progenitor populations. This study broke new ground in molecular cattle genetic diversity by genotyping a large sample size per breed and using a larger number of breeds compared with similar studies that have been conducted in the recent past which have either used a smaller number of breeds or smaller sample sizes but with a larger number of marker loci. Thus, opportunities that arise to explore genetic diversity and relationships in both the livestock and wildlife industries in Southern Africa may capitalize on microsatellite marker databases which remain cost-effective and accessible due to their extensive use for parentage verification.

Genomic analyses suggest adaptive differentiation of northern European native cattle breeds

Native domestic breeds represent important cultural heritage and genetic diversity relevant for production traits, environmental adaptation and food security. However, risks associated with low effective population size, such as inbreeding and genetic drift, have elevated concerns over whether unique within-breed lineages should be kept separate or managed as one population. As a conservation genomic case study of the genetic diversity represented by native breeds, we examined native and commercial cattle (Bos taurus) breeds including the threatened Danish Jutland cattle. We examined population structure and genetic diversity within breeds and lineages genotyped across 770K single nucleotide polymorphism loci to determine (a) the amount and distribution of genetic diversity in native breeds, and (b) the role of genetic drift versus selection. We further investigated the presence of outlier loci to detect (c) signatures of environmental selection in native versus commercial breeds, and (d) native breed adaptation to various landscapes. Moreover, we included older cryopreserved samples to determine (e) whether cryopreservation allows (re)introduction of original genetic diversity. We investigated a final set of 195 individuals and 677K autosomal loci for genetic diversity within and among breeds, examined population structure with principal component analyses and a maximum-likelihood approach and searched for outlier loci suggesting artificial or natural selection. Our findings demonstrate the potential of genomics for identifying the uniqueness of native domestic breeds, and for maintaining their genetic diversity and long-term evolutionary potential through conservation plans balancing inbreeding with carefully designed outcrossing. One promising opportunity is the use of cryopreserved samples, which can provide important genetic diversity for populations with few individuals, while helping to preserve their traditional genetic characteristics. Outlier tests for native versus commercial breeds identified genes associated with climate adaptation, immunity and metabolism, and native breeds may carry genetic variation important for animal health and robustness in a changing climate.

The role of molecular genetics in livestock production

Genetic variations that lead to easy-to-identify phenotypic changes have always been of interest to livestock breeders since domestication. Molecular genetics has opened up possibilities for identifying these variations and understanding their biological and population effects. Moreover, molecular genetics is part of the most diverse approaches and applications in animal production nowadays, including paternity testing, selection based on genetic variants, diagnostic of genetic diseases, reproductive biotechniques, fraud identification, differentiation of hybrids, parasite identification, genetic evaluation, diversity studies, and genome editing, among others. Therefore, the objective of this review was to describe the different applications of molecular genetics in livestock production, contextualising them with examples and highlighting the importance of the study of these topics and their applications.

Heterozygosity testing and multiplex DNA panel screening as a potential tool to monitor health and inbreeding in a small, closed dog population

Background

Selective breeding in populations with a limited effective population size may result in a loss of genetic diversity, which can cause an increased concentration of specific disease liability genes. The Dutch Shepherd Dog (DSD) in the Netherlands is an example of such a breed with a small effective population.

Objective

To evaluate the measurement of genetic diversity and multiplex DNA panel screening for implementation in a breeding strategy for the Dutch Shepherd Dog (DSD) and to investigate the clinical relevance of potentially identified mutations in the multiplex DNA panel screening.

Results

Genome-wide SNP testing showed genetic isolation and reduced genetic diversity within coat variety subgroups of the DSD. Panel screening identified a Von Willebrand's Disease type I mutation. Although decreased Von Willebrand's Factor proteins were significantly lower in DSDs carrying the VWD-I allele compared to the wildtype, clinical follow-up did not show a significant association between the clinical phenotype and VWD-I genotype.

Conclusions

Genetic relationship measurement within a breed population may be a useful tool to enable breeding strategies to conserve genetic diversity. Results from a disease panel screening need to be evaluated for clinical relevance before breed selection restrictions can be considered.

Assessing genetic diversity of various Canadian sheep breeds through pedigree analyses

The loss of genetic variability in a population will drastically affect the success of a breeding program by reducing selection response and fitness and, consequently, affecting reproduction, resilience, and production efficiency. The objective of this study was to perform an in-depth analysis of the pedigree of the Canadian sheep breeds to assess the levels of inbreeding, effective population size, and other metrics of genetic diversity, which included the five most important sheep breeds in Canada: Dorset, Polypay (PO), Rideau-Arcott, Romanov (RV), and Suffolk, using a large dataset (1 336 926 animals). As measures of genetic diversity, effective population size, inbreeding coefficient, effective number of founders, effective number of founder genomes, effective number of nonfounders, and effective number of ancestors were estimated. The completeness and depth of the Canadian sheep pedigree datasets were reasonably high, with <20% parental information missing. More attention should be given to PO breed, which was found to have the smallest effective population size (55), and RV breed, which had the highest average level of inbreeding (4.8%). Techniques such as optimum contribution selection and minimum coancestry mating could be used to minimize the inbreeding of future generations, while maintaining genetic progress at a desirable level.

Genetic selection against intrauterine growth retardation in piglets: a problem at the piglet level with a solution at the sow level

Background

In polytocous livestock species, litter size and offspring weight act antagonistically; in modern pig breeds, selection for increased litter size has resulted in lower mean birth weights, an increased number of small piglets and an increased number of those affected by varying degrees of intrauterine growth retardation (IUGR). IUGR poses life-long challenges, both mental, with morphological brain changes and altered cognition, and physical, such as immaturity of organs, reduced colostrum intake and weight gain. In pigs, head morphology of newborn piglets is a good phenotypic marker for identifying such compromised piglets. Growth retardation could be considered as a property of the dam, in part due to either uterine capacity or insufficiency. A novel approach to this issue is to consider the proportion of IUGR-affected piglets in a litter as an indirect measure of uterine capacity. However, uterine capacity or sufficiency cannot be equated solely to litter size and thus is a trait difficult to measure on farm.

Results

A total of 21,159 Landrace × Large White or Landrace × White Duroc piglets (born over 52 weeks) with recorded head morphology and birth weights were followed from birth until death or weaning. At the piglet level, the estimated heritability for IUGR (as defined by head morphology) was low at 0.01 ± 0.01. Piglet direct genetic effects of birth weight (h² = 0.07 ± 0.02) were strongly negatively correlated with head morphology (− 0.93), in that IUGR-affected piglets tended to have lower birth weights. At the sow level, analysis of the proportion of IUGR-affected piglets in a litter gave a heritability of 0.20 ± 0.06, with high and negative genetic correlations of the proportion of IUGR-affected piglets with average offspring birth weight (− 0.90) and with the proportion of piglets surviving until 24 h (− 0.80).

Conclusions

This suggests that the proportion of IUGR-affected piglets in a litter is a suitable indirect measure of uterine capacity for inclusion in breeding programmes that aim at reducing IUGR in piglets and improving piglet survival.

Molecular Genetics Unveiled Unknown Family Relationships and Hybrids in an Ex-Situ Colony of African Penguins (Spheniscus demersus)

Genealogical relationships among colony members, inbreeding status, and presence of hybrids are crucial data that can assist zoo curators in captive colony management and decision-making on relocation for reproduction. This study employed molecular markers to study a large colony (n = 56) of African Penguin hosted in an Italian biopark. A panel of 15 STRs (single tandem repeats) was selected, and genotype data were analyzed using COLONY software to determine parentage relationships and compare the existing studbook information to a pedigree built from genetic analyses. The existence of extra-pair mating and the presence of hybrids were investigated: discrepancies in kinship relationships emerged following molecular parentage analysis and 10 unknown genetic relationships were revealed. Infidelity of one member of the pair was observed in 6 cases and extra-pair copulation was assessed by genetic analysis in 2 episodes. One member of the colony was found to be a hybrid (S. demersus × S. humboldti); his progeny, derived by extra-pair copulation, was traced. Three other hidden hybrids were discovered and assessed using the identified candidate private alleles. Overall, our results demonstrate that molecular methods to confirm parentage and analyze relatedness among colony members are a valuable tool to complement studbook-based genetic management of African penguin captive populations. Because a variety of behavioral dynamics (e.g., extra-pair mating) can make observations ineffective in some species and because molecular markers outperform studbook in identifying the presence of hybrids, reliance on studbook information alone is not recommended.

Assessment of genetic diversity in Coho salmon (Oncorhynchus kisutch) populations with no family records using ddRAD-seq

OBJECTIVE

Selective breeding for desirable traits is becoming popular in aquaculture. In Miyagi prefecture, Japan, a selectively bred population of Coho salmon (Oncorhynchus kisutch) has been established with the original, randomly breeding population maintained separately. Since they have been bred without family records, the genetic diversity within these populations remains unknown. In this study, we estimated the genetic diversity and key quantitative genetic parameters such as heritability and genomic breeding value for body size traits by means of genomic best linear unbiased prediction to assess the genetic health of these populations.

RESULTS

Ninety-nine and 83 females from the selective and random groups, respectively, were genotyped at 2350 putative SNPs by means of double digest restriction associated DNA sequencing. The genetic diversity in the selectively bred group was low, as were the estimated heritability and prediction accuracy for length and weight (h² = 0.26-0.28; accuracy = 0.34), compared to the randomly bred group (h² = 0.50-0.60; accuracy = 0.51-0.54). Although the tested sample size was small, these results suggest that further selection is difficult for the selectively bred population, while there is some potential for the randomly bred group, especially with the aid of genomic information.

Genetic characterization of 11 microsatellite loci in Egyptian pigeons (Columba livia domestica) and their cross-species amplification in other Columbidae populations

Aim

This study aimed to analyze the genetic diversity and relationships of 10 Egyptian pigeon populations belonging to Columba livia domestica speciesusing 11 microsatellite markers and to investigate the success of these markers amplification across another eight pigeon species.

Methods

Genomic DNA was isolated from feather samples of179 pigeon samples from 10 Egyptian breeds: Asfer Weraq (n=14), Austoraly (n=20), Reehani (n=21), Messawed (n=17), Nemssawy (n=27), Otatti (n=12), Morasla (n=17), Tumbler (n=22), Halaby Asfer (n=10), and Karakandy (n=19) in addition to Japanese feral pigeons (n=30). Genotyping was done using 11 specific polymorphic microsatellite makers. Moreover, 37 samples not belonging to C. livia domestica but belonging to another eight pigeon species were genotyped. The polymerase chain reaction (PCR) products were electrophoresed on an ABI 3130xl DNA Sequencer. The basic measures of genetic diversity and phylogenetic trees were computed using bioinformatics software.

Results

Across the 10 studied Egyptian populations, the number of alleles per locus ranged from 3 to 19 and the average number of alleles observed was 9.091. The lowest value of expected heterozygosity (0.373) was obtained for the Reehani breed, and the highest value (0.706) was found for Morasla breed. The overall expected heterozygosity of Egyptian pigeons was 0.548. The F_ST coefficient which indicates fixation coefficients of subpopulations within the total population for the 11 loci varied from 0.318 to 0.114 with a relatively high mean (0.226). In our study, the F_IS showed a relatively high average(0.037). The pairwise Reynolds's genetic distance between the11 studied pigeon populations recorded lower values between Otatti and Austoraly (0.025) and between Morasla and Japanese feral pigeons (0.054). These results are supported by clustering pattern either by the neighbor-joining phylogenetic tree or by a Bayesian clustering of STRUCTURE with the admixture method.

Conclusions

We confirm the applicability of the CliµD17, CliµT17, CliµD16, CliµD32, CliµT13, CliµD01, PG1, PG2, PG4, PG6, and PG7 microsatellite markers among Egyptian domestic pigeons and across other pigeon species using cross-species amplification method. The information from this study should be useful for genetic characterization and for developing conservation programs of this important species.

Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed

One of the major limitation for the application of QTL results in pig breeding and QTN identification has been the limited number of QTL effects validated in different animal material. The aim of the current work was to validate QTL regions through joint and specific genome wide association and haplotype analyses for growth, fatness and premier cut weights in three different genetic backgrounds, backcrosses based on Iberian pigs, which has a major role in the analysis due to its high productive relevance. The results revealed nine common QTL regions, three segregating in all three backcrosses on SSC1, 0–3 Mb, for body weight, on SSC2, 3–9 Mb, for loin bone-in weight, and on SSC7, 3 Mb, for shoulder weight, and six segregating in two of the three backcrosses, on SSC2, SSC4, SSC6 and SSC10 for backfat thickness, shoulder and ham weights. Besides, 18 QTL regions were specifically identified in one of the three backcrosses, five identified only in BC_LD, seven in BC_DU and six in BC_PI. Beyond identifying and validating QTL, candidate genes and gene variants within the most interesting regions have been explored using functional annotation, gene expression data and SNP identification from RNA-Seq data. The results allowed us to propose a promising list of candidate mutations, those identified in PDE10A, DHCR7, MFN2 and CCNY genes located within the common QTL regions and those identified near ssc-mir-103-1 considered PANK3 regulators to be further analysed.

Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed

Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP array data to evaluate genomic diversity within the Kerry population and between Kerry cattle and other European breeds. Patterns of genetic differentiation and gene flow among breeds using phylogenetic trees with ancestry graphs highlighted historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (N_e) revealed a demographic trend of diminishing N_e over time and that recent estimated N_e values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (F_ROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland.

Population genetic structure of Santa Inês sheep in Brazil

This study aimed to describe the population genetic structure and evaluate the state of conservation of the genetic variability of Santa Inês sheep in Brazil. We used pedigree data of the Santa Inês breed available in electronic processing of the Brazilian Association of Sheep Breeders. A file with 20,206 records, which enabled the calculation of the genetic conservation index (GCI), individual inbreeding coefficient (F), change in inbreeding (ΔF), effective population size (Ne), effective number of founders (ƒ_e), effective number of ancestors (ƒ_ɑ), generation interval (L), average relatedness coefficient of each individual (AR), and Wright's F-statistics (F _IT, F _IS, and F _ST). For pedigree analysis and calculation of population parameters, the program ENDOG was used. The average inbreeding coefficient ([Formula: see text]) was 0.97% and the mean average relatedness ([Formula: see text]) 0.49%. The effective numbers of founders and ancestors were, respectively, 199 and 161. The average values of F and AR increased significantly over the years. The effective population size fluctuated over the years concurrently to oscillations in inbreeding rates, wherein N _e reached just 68 in the year 2012. The mean average generation interval was 5.3 years. The Santa Inês breed in Brazil is under genetic drift process, with loss of genetic variation. It requires the implementation of a genetic management plan in the herd, for conservation and improvement of the breed.

Genetic rescue of an endangered domestic animal through outcrossing with closely related breeds: A case study of the Norwegian Lundehund

Genetic rescue, outcrossing with individuals from a related population, is used to augment genetic diversity in populations threatened by severe inbreeding and extinction. The endangered Norwegian Lundehund dog underwent at least two severe bottlenecks in the 1940s and 1960s that each left only five inbred dogs, and the approximately 1500 dogs remaining world-wide today appear to descend from only two individuals. The Lundehund has a high prevalence of a gastrointestinal disease, to which all remaining dogs may be predisposed. Outcrossing is currently performed with three Nordic Spitz breeds: Norwegian Buhund, Icelandic Sheepdog, and Norrbottenspets. Examination of single nucleotide polymorphism (SNP) genotypes based on 165K loci in 48 dogs from the four breeds revealed substantially lower genetic diversity for the Lundehund (H_E 0.035) than for other breeds (H_E 0.209–0.284). Analyses of genetic structure with > 15K linkage disequilibrium-pruned SNPs showed four distinct genetic clusters. Pairwise F_ST values between Lundehund and the candidate breeds were highest for Icelandic Sheepdog, followed by Buhund and Norrbottenspets. We assessed the presence of outlier loci among candidate breeds and examined flanking genome regions (1 megabase) for genes under possible selection to identify potential adaptive differences among breeds; outliers were observed in flanking regions of genes associated with key functions including the immune system, metabolism, cognition and physical development. We suggest crossbreeding with multiple breeds as the best strategy to increase genetic diversity for the Lundehund and to reduce the incidence of health problems. For this project, the three candidate breeds were first selected based on phenotypes and then subjected to genetic investigation. Because phenotypes are often paramount for domestic breed owners, such a strategy could provide a helpful approach for genetic rescue and restoration of other domestic populations at risk, by ensuring the involvement of owners, breeders and managers at the start of the project.

Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds

Runs of homozygosity (ROH), uninterrupted stretches of homozygous genotypes resulting from parents transmitting identical haplotypes to their offspring, have emerged as informative genome-wide estimates of autozygosity (inbreeding). We used genomic profiles based on 698 K single nucleotide polymorphisms (SNPs) from nine breeds of domestic cattle (Bos taurus) and the European bison (Bison bonasus) to investigate how ROH distributions can be compared within and among species. We focused on two length classes: 0.5-15 Mb to investigate ancient events and >15 Mb to address recent events (approximately three generations). For each length class, we chose a few chromosomes with a high number of ROH, calculated the percentage of times a SNP appeared in a ROH, and plotted the results. We selected areas with distinct patterns including regions where (1) all groups revealed an increase or decrease of ROH, (2) bison differed from cattle, (3) one cattle breed or groups of breeds differed (e.g., dairy versus meat cattle). Examination of these regions in the cattle genome showed genes potentially important for natural and human-induced selection, concerning, for example, meat and milk quality, metabolism, growth, and immune function. The comparative methodology presented here permits visual identification of regions of interest for selection, breeding programs, and conservation.

Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances

Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.

Fertility preservation through gonadal cryopreservation

Fertility preservation is an area of immense interest in today's society. The most effective and established means of fertility preservation is cryopreservation of gametes (sperm and oocytes) and embryos. Gonadal cryopreservation is yet another means for fertility preservation, especially if the gonadal function is threatened by premature menopause, gonadotoxic cancer treatment, surgical castration, or diseases. It can also aid in the preservation of germplasm of animals that die before attaining sexual maturity. This is especially of significance for valuable, rare, and endangered animals whose population is affected by high neonatal/juvenile mortality because of diseases, poor management practices, or inbreeding depression. Establishing genome resource banks to conserve the genetic status of wild animals will provide a critical interface between ex-situ and in-situ conservation strategies. Cryopreservation of gonads effectively lengthens the genetic lifespan of individuals in a breeding program even after their death and contributes towards germplasm conservation of prized animals. Although the studies on domestic animals are quite promising, there are limitations for developing cryopreservation strategies in wild animals. In this review, we discuss different options for gonadal tissue cryopreservation with respect to humans and to laboratory, domestic, and wild animals. This review also covers recent developments in gonadal tissue cryopreservation and transplantation, providing a systematic view and the advances in the field with the possibility for its application in fertility preservation and for the conservation of germplasm in domestic and wild species.

Response to selection while maximizing genetic variance in small populations

Background

Rare breeds represent a valuable resource for future market demands. These populations are usually well-adapted, but their low census compromises the genetic diversity and future of these breeds. Since improvement of a breed for commercial traits may also confer higher probabilities of survival for the breed, it is important to achieve good responses to artificial selection. Therefore, efficient genetic management of these populations is essential to ensure that they respond adequately to genetic selection in possible future artificial selection scenarios. Scenarios that maximize the maximum genetic variance in a unique population could be a valuable option. The aim of this work was to study the effect of the maximization of genetic variance to increase selection response and improve the capacity of a population to adapt to a new environment/production system.

Results

We simulated a random scenario (A), a full-sib scenario (B), a scenario applying the maximum variance total (MVT) method (C), a MVT scenario with a restriction on increases in average inbreeding (D), a MVT scenario with a restriction on average individual increases in inbreeding (E), and a minimum coancestry scenario (F). Twenty replicates of each scenario were simulated for 100 generations, followed by 10 generations of selection. Effective population size was used to monitor the outcomes of these scenarios. Although the best response to selection was achieved in scenarios B and C, they were discarded because they are unpractical. Scenario A was also discarded because of its low response to selection. Scenario D yielded less response to selection and a smaller effective population size than scenario E, for which response to selection was higher during early generations because of the moderately structured population. In scenario F, response to selection was slightly higher than in Scenario E in the last generations.

Conclusions

Application of MVT with a restriction on individual increases in inbreeding resulted in the largest response to selection during early generations, but if inbreeding depression is a concern, a minimum coancestry scenario is then a valuable alternative, in particular for a long-term response to selection.

Inference of population structure of purebred dairy and beef cattle using high-density genotype data

Information on the genetic diversity and population structure of cattle breeds is useful when deciding the most optimal, for example, crossbreeding strategies to improve phenotypic performance by exploiting heterosis. The present study investigated the genetic diversity and population structure of the most prominent dairy and beef breeds used in Ireland. Illumina high-density genotypes (777 962 single nucleotide polymorphisms; SNPs) were available on 4623 purebred bulls from nine breeds; Angus (n=430), Belgian Blue (n=298), Charolais (n=893), Hereford (n=327), Holstein-Friesian (n=1261), Jersey (n=75), Limousin (n=943), Montbéliarde (n=33) and Simmental (n=363). Principal component analysis revealed that Angus, Hereford, and Jersey formed non-overlapping clusters, representing distinct populations. In contrast, overlapping clusters suggested geographical proximity of origin and genetic similarity between Limousin, Simmental and Montbéliarde and to a lesser extent between Holstein, Friesian and Belgian Blue. The observed SNP heterozygosity averaged across all loci was 0.379. The Belgian Blue had the greatest mean observed heterozygosity (HO=0.389) among individuals within breed while the Holstein-Friesian and Jersey populations had the lowest mean heterozygosity (HO=0.370 and 0.376, respectively). The correlation between the genomic-based and pedigree-based inbreeding coefficients was weak (r=0.171; P<0.001). Mean genomic inbreeding estimates were greatest for Jersey (0.173) and least for Hereford (0.051). The pair-wise breed fixation index (F st) ranged from 0.049 (Limousin and Charolais) to 0.165 (Hereford and Jersey). In conclusion, substantial genetic variation exists among breeds commercially used in Ireland. Thus custom-mating strategies would be successful in maximising the exploitation of heterosis in crossbreeding strategies.