Nuclear sequences of mitochondrial origin in domestic yak.

Mitochondrial DNA sequences are frequently transferred into the nuclear genome, generating nuclear mitochondrial DNA sequences (NUMTs). Here, we analysed, for the first time, NUMTs in the domestic yak genome. We obtained 499 alignment matches covering 340.2 kbp of the yak nuclear genome. After a merging step, we identified 167 NUMT regions with a total length of ~ 503 kbp, representing 0.02% of the nuclear genome. We discovered copies of all mitochondrial regions and found that most NUMT regions are intergenic or intronic and mostly untranscribed. 98 different NUMT regions from domestic yak showed high homology with cow and/or wild yak genomes, suggesting selection or hybridization between domestic/wild yak and cow. To rule out the possibility that the identified NUMTs could be artifacts of the domestic yak genome assembly, we validated experimentally five NUMT regions by PCR amplification. As NUMT regions show high similarity to the mitochondrial genome can potentially pose a risk to domestic yak DNA mitochondrial studies, special care is therefore needed to select primers for PCR amplification of mitochondrial DNA sequences.

Exploring the origin of a unique mutant allele in twin-tail goldfish using CRISPR/Cas9 mutants.

Artificial selection has been widely applied to genetically fix rare phenotypic features in ornamental domesticated animals. For many of these animals, the mutated loci and alleles underlying rare phenotypes are known. However, few studies have explored whether these rare genetic mutations might have been fixed due to competition among related mutated alleles or if the fixation occurred due to contingent stochastic events. Here, we performed genetic crossing with twin-tail ornamental goldfish and CRISPR/Cas9-mutated goldfish to investigate why only a single mutated allele-chdS with a E127X stop codon (also called chdAE127X)-gives rise to the twin-tail phenotype in the modern domesticated goldfish population. Two closely related chdS mutants were generated with CRISPR/Cas9 and compared with the E127X allele in F2 and F3 generations. Both of the CRISPR/Cas9-generated alleles were equivalent to the E127X allele in terms of penetrance/expressivity of the twin-tail phenotype and viability of carriers. These findings indicate that multiple truncating mutations could have produced viable twin-tail goldfish. Therefore, the absence of polymorphic alleles for the twin-tail phenotype in modern goldfish likely stems from stochastic elimination or a lack of competing alleles in the common ancestor. Our study is the first experimental comparison of a singular domestication-derived allele with CRISPR/Cas9-generated alleles to understand how genetic fixation of a unique genotype and phenotype may have occurred. Thus, our work may provide a conceptual framework for future investigations of rare evolutionary events in domesticated animals.

Missing history of a modern domesticate: Historical demographics and genetic diversity in farm-bred red fox populations.

The first record of captive-bred red foxes (Vulpes vulpes) dates to 1896 when a breeding enterprise emerged in the provinces of Atlantic Canada. Because its domestication happened during recent history, the red fox offers a unique opportunity to examine the genetic diversity of an emerging domesticated species in the context of documented historical and economic influences. In particular, the historical record suggests that North American and Eurasian farm-bred populations likely experienced different demographic trajectories. Here, we focus on the likely impacts of founder effects and genetic drift given historical trends in fox farming on North American and Eurasian farms. A total of 15 mitochondrial haplotypes were identified in 369 foxes from 10 farm populations that we genotyped (n = 161) or that were previously published. All haplotypes are endemic to North America. Although most haplotypes were consistent with eastern Canadian ancestry, a small number of foxes carried haplotypes typically found in Alaska and other regions of western North America. The presence of these haplotypes supports historical reports of wild foxes outside of Atlantic Canada being introduced into the breeding stock. These putative Alaskan and Western haplotypes were more frequently identified in Eurasian farms compared to North American farms, consistent with historical documentation suggesting that Eurasian economic and breeding practices were likely to maintain low-frequency haplotypes more effectively than in North America. Contextualizing inter- vs. intra-farm genetic diversity alongside the historical record is critical to understanding the origins of this emerging domesticate and the relationships between wild and farm-bred fox populations.

Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs.

Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g. Europe, the Middle East, and East Asia). Ancient DNA provides a powerful resource for the study of mammalian evolution and has been widely used to understand the genetic history of domestic animals. To understand the maternal genetic history of East Asian dogs, we have made a complete mitogenome dataset of 120 East Asian canids from 38 archaeological sites, including 102 newly sequenced from 12.9 to 1 ka BP (1,000 years before present). The majority (112/119, 94.12%) belonged to haplogroup A, and half of these (55/112, 49.11%) belonged to sub-haplogroup A1b. Most existing mitochondrial haplogroups were present in ancient East Asian dogs. However, mitochondrial lineages in ancient northern dogs (northeastern Eurasia and northern East Asia) were deeper and older than those in southern East Asian dogs. Results suggests that East Asian dogs originated from northeastern Eurasian populations after the LGM, dispersing in two possible directions after domestication. Western Eurasian (Europe and the Middle East) dog maternal ancestries genetically influenced East Asian dogs from approximately 4 ka BP, dramatically increasing after 3 ka BP, and afterwards largely replaced most primary maternal lineages in northern East Asia. Additionally, at least three major mitogenome sub-haplogroups of haplogroup A (A1a, A1b, and A3) reveal at least two major dispersal waves onto the Qinghai-Tibet Plateau in ancient times, indicating eastern (A1b and A3) and western (A1a) Eurasian origins.

Association of tameness and sociability but no sign of domestication syndrome in mice selectively bred for active tameness.

Domesticated animals have been developed by selecting desirable traits following the initial unconscious selection stage, and now exhibit phenotypes desired by humans. Tameness is a common behavioural trait found in all domesticated animals. At the same time, these domesticated animals exhibit a variety of morphological, behavioural, and physiological traits that differ from their wild counterparts of their ancestral species. These traits are collectively referred to as domestication syndrome. However, whether this phenomenon exists is debatable. Previously, selective breeding has been used to enhance active tameness, a motivation to interact with humans, in wild heterogeneous stock mice derived from eight wild inbred strains. In the current study, we used tame mice to study how selective breeding for active tameness affects behavioural and morphological traits. A series of behavioural and morphological analyses on mice showed an increased preference for social stimuli and a longer duration of engagement in non-aggressive behaviour. However, no differences were observed in exploratory or anxiety-related behaviours. Similarly, selection for tameness did not affect ultrasonic vocalisations in mice, and no changes were observed in known morphological traits associated with domestication syndrome. These results suggest that there may be a link between active tameness and sociability and provide insights into the relationship between tameness and other behaviours in the context of domestication.

Naturally occurring genetic diseases caused by de novo variants in domestic animals.

With the advent of next-generation sequencing, an increasing number of cases of de novo variants in domestic animals have been reported in scientific literature primarily associated with clinically severe phenotypes. The emergence of new variants at each generation is a crucial aspect in understanding the pathology of early-onset diseases in animals and can provide valuable insights into similar diseases in humans. With the aim of collecting deleterious de novo variants in domestic animals, we searched the scientific literature and compiled reports on 42 de novo variants in 31 genes in domestic animals. No clear disease-associated phenotype has been established in humans for three of these genes (NUMB, ANKRD28 and KCNG1). For the remaining 28 genes, a strong similarity between animal and human phenotypes was recognized from available information in OMIM and OMIA, revealing the importance of comparative studies and supporting the use of domestic animals as natural models for human diseases, in line with the One Health approach.

Transferability of Nikita and Sukkula retrotransposons in domestic goose (Anser anser domesticus) genome.

This article aimed to detect the existence of barley-specific Nikita and Sukkula retrotransposons in domestic geese samples and to evaluate the evolutionary relationships between these and other transposons belonging to the family Anatidae. Inter-retrotransposonamplified polymorphism-polymerase chain reaction (IRAP-PCR) method was performed for these retrotransposons movements in three diverse domestic goose populations (Chinese x Embden crossbred, Turkish White, and Turkish Multicolor). Polymorphism ratios were between 0 and 33% in all samples for Nikita and 0-73% in all samples for Sukkula. In addition, intrapopulation genetic polymorphism rates were also 0-15% in Chinese x Embden crossbred, 0-25% in Turkish White, 0-25% in Turkish Multicolor for Nikita; while 0-27% in Chinese x Embden, and 0-50% in Turkish Multicolor for Sukkula. There was no polymorphism for Sukkula among Turkish White samples. Moreover, the neighbour-joining method was used for phylogenetic tree construction using 38 sequences of different ducks, geese, and swans. In silico analyses supported the transitions of retrotransposons in the family Anatidae. It is concluded that transposon mobility among the phylogenetically distant species may lead to understanding evolutionary relationships. This report is one of the first studies investigating retrotransposon movements in domestic geese, revealing a new perspective on the goose genome regarding mobile genetic elements.

Phenotype transition from wild mouflon to domestic sheep.

The domestication of animals started around 12,000 years ago in the Near East region. This "endless process" is characterized by the gradual accumulation of changes that progressively marked the genetic, phenotypic and physiological differences between wild and domesticated species. The main distinctive phenotypic characteristics are not all directly attributable to the human-mediated selection of more productive traits. In the last decades, two main hypotheses have been proposed to clarify the emergence of such a set of phenotypic traits across a variety of domestic species. The first hypothesis relates the phenotype of the domesticated species to an altered thyroid hormone-based signaling, whereas the second one relates it to changes in the neural crest cells induced by selection of animals for tameness. These two hypotheses are not necessarily mutually exclusive since they may have contributed differently to the process over time and space. The adaptation model induced by domestication can be adopted to clarify some aspects (that are still controversial and debated) of the long-term evolutionary process leading from the wild Neolithic mouflon to the current domestic sheep. Indeed, sheep are among the earliest animals to have been domesticated by humans, around 12,000 years ago, and since then, they have represented a crucial resource in human history. The aim of this review is to shed light on the molecular mechanisms and the specific genomic variants that underlie the phenotypic variability between sheep and mouflon. In this regard, we carried out a critical review of the most recent studies on the molecular mechanisms that are most accredited to be responsible for coat color and phenotype, tail size and presence of horns. We also highlight that, in such a complicate context, sheep/mouflon hybrids represent a powerful and innovative model for studying the mechanism by which the phenotypic traits related to the phenotypic responses to domestication are inherited. Knowledge of these mechanisms could have a significant impact on the selection of more productive breeds. In fact, as in a journey back in time of animal domestication, the genetic traits of today's domestic species are being progressively and deliberately shaped according to human needs, in a direction opposite to that followed during domestication.

Asymmetric and parallel subgenome selection co-shape common carp domestication.

BACKGROUND: The common carp (Cyprinus carpio) might best represent the domesticated allopolyploid animals. Although subgenome divergence which is well-known to be a key to allopolyploid domestication has been comprehensively characterized in common carps, the link between genetic architecture underlying agronomic traits and subgenome divergence is unknown in the selective breeding of common carps globally. RESULTS: We utilized a comprehensive SNP dataset in 13 representative common carp strains worldwide to detect genome-wide genetic variations associated with scale reduction, vibrant skin color, and high growth rate in common carp domestication. We identified numerous novel candidate genes underlie the three agronomically most desirable traits in domesticated common carps, providing potential molecular targets for future genetic improvement in the selective breeding of common carps. We found that independently selective breeding of the same agronomic trait (e.g., fast growing) in common carp domestication could result from completely different genetic variations, indicating the potential advantage of allopolyploid in domestication. We observed that candidate genes associated with scale reduction, vibrant skin color, and/or high growth rate are repeatedly enriched in the immune system, suggesting that domestication of common carps was often accompanied by the disease resistance improvement. CONCLUSIONS: In common carp domestication, asymmetric subgenome selection is prevalent, while parallel subgenome selection occurs in selective breeding of common carps. This observation is not due to asymmetric gene retention/loss between subgenomes but might be better explained by reduced pleiotropy through transposable element-mediated expression divergence between ohnologs. Our results demonstrate that domestication benefits from polyploidy not only in plants but also in animals.

Asignación de individuos a poblaciones caprinas nativas brasileñas / No disponible

A utilização de métodos mais sofisticados que possam assignar corretamente indivíduos a populações, torna-se importante em estudos de conservação, pois permitem detectar migrantes. O presente trabalho teve como objetivo assignar indivíduos a populações caprinas nativas, tendo como animais referências quatro raças exóticas, SRD (sem padrão racial definido) e três raças espanholas, utilizando o programa Structure. Considerando k=7 cluster foi possível detectar a proporção de indivíduos assignado de cada população (AU)

No disponible

Comparative analysis of morphological and behavioral characters in the domestic dog and their importance in the reconstruction of phylogenetic relationships in canids

Relationships among 25 dog breeds, classified a priori by their respective ancestral trunks, were studied using data from 29 morphological and 13 behavioral characteristics. Although a certain correlation was found between both types of traits (r = 0.13; P < 0.05), this relationship was not manifested, regarding the level of racial classification, in the obtained dendrograms. The relationships between breeds obtained from morphological data were more congruent than those obtained from behavioral data when compared with phylogenies from other sources of information (mainly electrophoretic analysis). This indicates that the morphological characters could give more and better complementary information than the behavioral ones in the reconstruction of the phylogenetic relationships of canids. The mean character difference (MCD), used as a measure of taxonomic resemblance between breeds, had a value of 0.53 (+ or - 0.12 STD), and was of a magnitude very similar to that obtained in other domestic animal species (cattle, horse, sheep and goats), indicating that a similar degree of morphological differences between breeds of these species exists.

Hacia un proyecto nacional e investigación en genomas de animales domésticos / Towards a national research genomic project on domestic animals

La investigación científica orientada a identificar, estudiar y aprovechar genes, así como a entender la organización y evolución del genoma, ha llevado a proyectos genómicos de gran escala como el Proyecto del Genoma Humano y de otros organismos de interés científico y económico para el hombre. En México es posible conformar este tipo de proyectos de forma original, con base en la extensa diversidad genética presente en poblaciones biológicas nativas que componen el patrimonio genómico nacional y utilizando diversos recursos disponibles en el dominio público. Los animales domésticos nativos en México contituyen un recurso genético valioso y único para identificar genes importantes para la industria pecuaria y la biotecnología. Sin embargo, estas variedades están amenazadas debido a las políticas de absorción y reemplazo por variedades comerciales mejoradas provenientes de países más desarrollados. La investigación genómica en animales domésticos puede ser importante para desarrollar y mantener una ganadería competitiva en una economía de mercado mundial. Por ello, se propone un proyecto genómico en animales domésticos en México cuyas metas serían: la preservación, estudio y la explotación de recursos genéticos autóctonos; la identificación, clonación y estudio de genes importantes desde el punto de vista comercial y médico, y la transferencia de tecnología a la industria animal local. Este proyecto puede ser el fundamento para estimular el desarrollo de una industria pecuaria nacional más moderna, competitiva e independiente, más adecuada a condiciones propias tanto ecológicas y económicas, como culturales y de mercado

Utilizaçäo de marcadores de DNA para o diagnóstico genômico de animais domésticos: 1. Detecçäo da mutaçäo pontual causadora da deficiência de adesäo de leucócitos bovinos (BLAD) em gado Holandês no Brasil / Use of DNA markers for genomic diagnosis of domestic animals: 1. Detection of point mutation causing bovine leukocyte adhesion deficiency (BLAD) in Brazilian Holstein cattle

Analisaram-se 10 bovinos da raça Holandesa, descendentes da linhagem Ivanhoe. Submeteram-se os DNAs, purificados a partir de leucócitos destes animais, à técnica de Polymerase Chain Reaction (PCR) e posterior digestäo com as enzimas de restriçäo Hae III e Taq I. Estabeleceu-se, desta maneira, o diagnóstico genômico da Deficiência de Adesäo de Leucócitos Bovinos (BLAD). Os exames revelaram que 2 animais eram portadores e 8, normais. A partir do desenvolvimento da metodologia de PCR, tornou-se disponível um método rápido, prático e eficiente para a seleçäo de touros em Centrais de Inseminaçäo Artificial, por meio da detecçäo de animais portadores e normais

Utilizaçäo de marcadores de DNA para o diagnóstico genômico de animais domésticos: 2. Detecçäo da mutaçäo pontual causadora da Paralisia Hipercalêmica Periódica (HYPP) em equinos da raça Quarto de Milha / Use of DNA markers for genomic diagnosis of domestic animals: 2. Detection of point mutation causing Hyperkalemic Periodic Paralysis (HYPP) in Quarter horses

Analisaram-se 12 equinos da raça Quarto de Milha, descendentes da linhagem Impressive. Submeteram-se os DNAs purificados a partir de leucócitos destes animais, à técnica de Polymerase Chain Reaction (PCR) e posterior digestäo com a enzima de restriçäo Taq I. Estabeleceu-se, dessa maneira, o diagnóstico genômico da Paralisia Hipercalcêmica Periódica (HYPP). Os exames revelaram que 9 animais eram portadores heterozigotos (N/H) e 3, normais homozigotos (N/N). A partir do desenvolvimento da metodologia de PCR tornou-se possível diagnosticar o problema e propor maneiras de controle do alastramento desse gene defectivo na populaçäo por meio da detecçäo de animais portadores e normais

Animal breeding

Animal Breeding examines in detail the various techniques that can be used in breeding animals, such as selection, cross-breeding and inbreeding. Examples of the various techniques are given, including their advantages and disadvantages in tropical and sub-tropical environments, and how they can be used to improve the core traits of animals. The book also deals with basic genetics and examines factors such as the effect of climate on animals and the importance of preserving the gene pool in native tropical breeds. This book will be an invaluable guide for anyone involved with animal breeding and livestock improvement in the tropics

Simulación genética de un hato de cerdos / Genetic simulation in swine

Se presenta un modelo aleatorio y dinámico para simular la productividad de un hato de cerdos. El modelo completo incluye dos modelos parciales, uno que representa el comportamiento genético de las características cuantitativas y otro que simula el desarrollo del hato en el tiempo. los valores fenotípicos se simulan con el modelo genético. Cada valor resulta de la suma de: 1) la media, 2) el efecto aleatorio del genotipo individual, 3) la influencia delgenotipo de los padres, 4) el efecto aleatorio del medio ambiente general y 5) el efecto aleatorio de los factores de medio ambiente comunes a los hermanos de camada. El modelo que simula el comportamiento del hato en el tiempo emplea estimadores de los parámetros de producción obtenidos en granjas porcinas de México. Para la validación del modelo se usó el método de la verificación histórica. El modelo arrojó resultados congruentes con los parámetros iniciales y con la variabilidad esperada para cada tamaño de muestra, tanto en apareamiento aleatorio como al aplicar selección, incluso en la respuesta correlacionada para características no seleccionadas. Se considera que el modelo es una representación válida de un hato de cerdos, en especial del componente genético.