Population structure and breed identification of Chinese indigenous sheep breeds using whole genome SNPs and InDels.

BACKGROUND: Accurate breed identification is essential for the conservation and sustainable use of indigenous farm animal genetic resources. In this study, we evaluated the phylogenetic relationships and genomic breed compositions of 13 sheep breeds using SNP and InDel data from whole genome sequencing. The breeds included 11 Chinese indigenous and 2 foreign commercial breeds. We compared different strategies for breed identification with respect to different marker types, i.e. SNPs, InDels, and a combination of SNPs and InDels (named SIs), different breed-informative marker detection methods, and different machine learning classification methods. RESULTS: Using WGS-based SNPs and InDels, we revealed the phylogenetic relationships between 11 Chinese indigenous and two foreign sheep breeds and quantified their purities through estimated genomic breed compositions. We found that the optimal strategy for identifying these breeds was the combination of DFI_union for breed-informative marker detection, which integrated the methods of Delta, Pairwise Wright's FST, and Informativeness for Assignment (namely DFI) by merging the breed-informative markers derived from the three methods, and KSR for breed assignment, which integrated the methods of K-Nearest Neighbor, Support Vector Machine, and Random Forest (namely KSR) by intersecting their results. Using SI markers improved the identification accuracy compared to using SNPs or InDels alone. We achieved accuracies over 97.5% when using at least the 1000 most breed-informative (MBI) SI markers and even 100% when using 5000 SI markers. CONCLUSIONS: Our results provide not only an important foundation for conservation of these Chinese local sheep breeds, but also general approaches for breed identification of indigenous farm animal breeds.

Coordination of parental performance is breeding phase-dependent in the Dovekie (Alle alle), a pelagic Arctic seabird.

Currently, parental care is becoming increasingly perceived as male and female cooperation, instead of being primarily shaped by sexual conflict. Most studies examining cooperating performance consider coordination of parental activities, and doing so focuses on a short time-window including only one stage of breeding (i.e., incubation or chick rearing period). Here, we considered the cooperation of breeding partners, investigating the coordination of parental care in a long-lived seabird species with long and extensive biparental care, the Dovekie (or Little Auk), Alle alle, and looked at the issue throughout the breeding season. Previous studies on this species revealed coordinated chick provisioning, but parental coordination during incubation remains unstudied. Using video recordings collected over the course of two breeding seasons, we tested whether coordination was subject to small-scale changes within each stage and whether there was a relationship between coordination levels across the two stages. We found that the level of parental coordination is overall high and increases during the incubation period but decreases through the chick rearing phases. There were some inter-annual differences in the coordination level both at the incubation and chick rearing stages. We also found some dependency between the coordination during the incubation and chick rearing periods. All these results suggest that coordination is not a fixed behavior but breeding-phase dependent. The present study thus provides insights into how parental care and parents' cooperation is shaped by brood needs and conditions. It also highlights a relationship between coordination levels during chick rearing and incubation periods, suggesting some extent of temporal dependence in coordination of parental performance within the breeding season.

A comprehensive study of CYP2E1 and its role in carcass characteristics and chemical lamb meat quality in different Indonesian sheep breeds.

The role of CYP2E1 in oxidation is essential for its effects on meat quality. This study used 200 Indonesian sheep (Ovis aries) to determine the SNP g allele frequencies. g. 50658168 T>C of CYP2E1 gene located in 3´-UTR region and their genetic association with lamb quality traits, including carcass characteristics, retail cut carcass, physicochemical lamb, fatty acid, cholesterol, flavor and odor, and mineral content. Further, the level of CYP2E1 mRNA and CYP2E1 protein expression in muscle were determined and correlated with lamb quality traits. CYP2E1 gene polymorphisms were identified using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis. The CYP2E1 mRNA expression levels in phenotypically divergent sheep populations were analyzed using Quantitative Real Time-PCR (qRT-PCR). Immunohistochemistry (IHC) and hematoxylin-eosin (HE) staining analysis used three samples each in the high and low lamb quality groups based on pH value and tenderness. An association study of CYP2E1 gene polymorphisms was performed using General Linear Model (GLM) analysis. The genetic association between the CC, CT, and TT genotypes at the SNP g. 50658168 T>C CYP2E1 gene and lamb quality traits were significant (P<0.05), including carcass characteristics, retail cut carcass, fatty acid, cholesterol, flavor, and odor. Lambs with the CT genotype had a higher mRNA and protein expression in high lamb quality traits. The highest CYP2E1 protein expression was localized in the longissimus dorsi. The group sample with high lamb quality had a higher area and perimeter of muscle cells. CYP2E1 can be used as a genetic marker for selecting sheep with high meat quality.

Genome-wide discovery of selection signatures in four Anatolian sheep breeds revealed by ddRADseq.

High-density genomic data analyzed by accurate statistical methods are of potential to enlighten past breeding practices such as selection by unraveling fixed regions. In this study, four native Turkish sheep breeds (80 samples) were genotyped via 296.097 single nucleotide polymorphisms (SNPs) detected by double-digest restriction site-associated DNA (ddRADseq) library preparation combined with the Illumina HiSeq X Ten instrument in order to identify genes under selection pressure. A total of 32, 136, 133, and 119 protein-coding genes were detected under selection pressure by runs of homozygosity (ROH), integrated haplotype score (iHS), the ratio of extended haplotype homozygosity (Rsb), and fixation index (FST) approaches, respectively. Of these, a total of 129 genes were identified by at least two statistical models which overlapped with a total of 52 quantitative trait loci (QTL)-associated SNPs, known to be related to fiber diameter, milk content, body weight, carcass traits, some blood parameters, and entropion. A total of six genes under selection pressure were validated by three statistical approaches five of which are of potential to be integrated into animal breeding since they were associated with wool fiber diameter (ZNF208B), behaviors related to neurocognitive development (CBX1 and NFE2L1), adaptation to high-altitude (SDK1), and anxiety causing internal stress (GSG1L). The sixth gene (COPZ1) turned out to play an important role in coping with different types of cancer in mammals. In particular, ROH analysis uncovered significant findings that the Güney Karaman (GKR) had experienced different selection practices than the Akkaraman (AKR) breed. Moreover, some genes specifically under selection in the GKR breed turned out to be associated with olfaction (OR6K6, OR6N1, OR6N2, and OR4C16), survival during the gestation period (PRR15L), and heat stress (CDK5RAP9). The results of this study imply that GKR may become genetically different from the AKR breed at the genome level due to most probably experiencing different adaptation processes occurring in raised climatic conditions. These differences should be conserved to face future challenges, while other native Turkish sheep breeds could be monitored via genome-wide high-density SNP data to obtain deeper knowledge about the effects of natural selection.

Evaluation of bioavailable 137Cs transfer from forest litter to Scarabaeidae beetle (Protaetia orientalis) through a breeding experiment in Fukuhshima.

Following the Fukushima Daiichi Nuclear Power Plant accident in 2011, most of the released 137Cs remained in the litter and surface soil of the adjacent forest floor. However, 137Cs absorption by large soil invertebrates near this site has not been estimated. The aim of this study was to understand the role of soil macroinvertebrates in 137Cs uptake from forest litter into forest ecosystems. Breeding experiments were conducted using scarab beetle larvae (Protaetia orientalis). Dissection experiments revealed that 85% of the total 137Cs was concentrated in the digestive tract of larvae, while a low proportion was absorbed into the skin and muscle tissues. The 137Cs absorption rate, indicating the transfer of 137Cs from consumed litter to larval tissue, was low (0.39%). 137Cs concentrations decreased to one-fourth from larva to imago, possibly due to excretion from the digestive tract and during eclosion. In the elimination experiment, biological half-lives were 0.26-0.64 and 0.11-0.47 days and 3.35-48.30 and 4.01-17.70 days for the digestive tract and muscle/skin tissues in the fast and slow components, respectively, corresponding to 137Cs discharge from the gastrointestinal tract and physiological clearance. In the sequential extraction experiment, litter digestion by flower chafer larvae significantly reduced the bioavailable fraction of 137Cs including water-soluble, exchangeable, oxidized, and organic forms, from 23.2% in litter to 17.7% in feces. Residual 137Cs was not reduced by digestion, probably because it was fixed in soil clay. Our study on breeding experiments of the Scarabaeidae beetle confirmed the low bioavailability of 137Cs in the litter in Fukushima. However, litter feeders may play an important role in transferring 137Cs to higher trophic levels in the forest ecosystem by extracting the bioavailable fraction of the vast stock of 137Cs on the forest floor.

Comparative study of the reproductive and growth performance of the Hamra and Rumbi ovine breeds.

Growth and reproductive performance traits are important economic indicators for analyzing the overall performance of breeding systems. This study aims to evaluate the comparative performance of two Algerian sheep (Rumbi and Hamra) in terms of growth and reproductive performance, and the effect of factors such as breed, season of birth, mode of birth and age of the mother on this performance in a semi-intensive breeding system. The reproductive performance of 577 Rumbi ewes and 1328 Hamra ewes bred at the Tiaret and Saïda experimental stations respectively, was analyzed using performance monitoring data. Fertility rates for the Rumbi and Hamra breeds of 87.14% and 78.8% respectively were practically similar (p > 0,05). Litter size at birth and weaning was significantly higher in the Hamra breed than in the Rumbi breed (p < 0,05). Weaning mortality was significantly higher in the Hamra breed than in the Rumbi breed, with an average of 22.60% versus 14.94% (p < 0,05). The effect of factors showed that there was a highly significant effect of the mother's age and season of birth on the reproductive performance of the Hamra and Rumbi breeds with a p < 0.0001 on fertility, litter size at birth, litter size at weaning and fertility. There was a significant effect of the year factor on reproductive performance with p = 0,013 for the Hamra breed and p = 0,031 for the Rumbi breed. The results of this study showed that Rumbi lambs were heavier at birth than Hamra lambs. The values observed were 4,86 kg versus 3,10 kg for the Hamra breed, with a highly significant difference (p < 0,0001), so that the average daily pre-weaning weight gains of Rumbi lambs were higher than those of Hamra lambs, at 0,195 kg/day versus 0,113 kg/day for Hamra lambs, with a high significance (p < 0,0001). The effect of factors showed that there was a significant effect of the mother's age on the ADGs (0-30), (30-70) and (70-90) of the Hamra and Rumbi breeds with a p = 0,034 and p = 0,02 respectively. There was also a highly significant effect of the birth mode effect on ADGs (0-30), (30-70) and (70-90) only for the Hamra breed with a p = 0,004. The effect of the birth weight on ADGs was not significant for both Hamra and Rumbi breeds with a p > 0,05. According to the findings of this study, the Hamra breed had superior reproductive potential and the Rumbi breed had superior growth. The Hamra breed showed better maternal skills in terms of fertility and prolificacy, while the Rumbi breed showed better lamb growth performance. Consequently, these results could be used for selective sheep breeding, taking into account the random effects of the environment and the potential of each breed.

A review of commercial captive breeding of parrots as a supply-side intervention to address unsustainable trade.

The volume and scale of commercial captive breeding of parrots have grown dramatically in recent decades. Although it has been proposed, and is often assumed, that captive breeding can reduce pressure on wild populations, there has been little scrutiny of the scale, viability, or impacts of captive breeding to prevent overexploitation among parrots, compared with similar approaches in other threatened taxa, such as pangolins or tigers. We reviewed the primary and gray literature to quantitatively and qualitatively evaluate evidence concerning 5 criteria, established a priori, for commercial captive breeding of parrots as an effective supply-side intervention. We focused on a sample of 16 threatened parrot species that are heavily traded or for which unsustainable trade has been a factor in the decline of wild populations, representing a range of taxonomic groups, life histories, and native regions. We identified multiple major gaps in knowledge of the extent to which these criteria are met, including a lack of quantitative data on breeding productivity under current commercial breeding practices, the scale and scope of commercial breeding practices in growing parrot markets, particularly in the Middle East and Asia, and the lack of financial viability of captive breeding under effective regulation to prevent laundering or use of wild-sourced specimens as breeding stock. The capacity for captive breeding to displace demand for wild-sourced parrots varied between species, and complex interactions between trade in different species and contexts sometimes made consequences of commercial production difficult to predict. Decision makers and regulatory authorities should approach commercial captive breeding of parrots with caution and take into account knowledge gaps and cross-linkages between trade in different species to avoid unanticipated consequences from stimulating and facilitating unsustainable trade in wild-sourced parrots.

Una revisión de la cría comercial de loros en cautiverio como una intervención en la oferta para abordar el comercio no sustentable Resumen El volumen y la escala de la cría comercial de loros en cautiverio ha crecido de gran manera en las últimas décadas. Aunque se ha propuesto, y a menudo se asume, que la cría en cautiverio puede reducir la presión sobre las poblaciones silvestres, apenas se ha analizado la escala, viabilidad o impacto de este método para evitar la sobreexplotación de los loros, en comparación con enfoques similares en otros taxones amenazados, como pangolines o tigres. Revisamos la bibliografía primaria y gris para evaluar cuantitativa y cualitativamente las pruebas relativas a cinco criterios, establecidos a priori, para la cría comercial de loros en cautiverio como una intervención eficaz del lado de la oferta. Usamos una muestra de 16 especies amenazadas de loros que son objeto de intenso comercio o para las que el comercio no sustentable ha sido un factor en el declive de las poblaciones silvestre para representar una gama de grupos taxonómicos, historias de vida y regiones nativas. Identificamos múltiples vacíos importantes en el conocimiento de la medida en que se cumplen estos criterios, incluida la falta de datos cuantitativos sobre la productividad de la cría en las actuales prácticas de cría comercial, la escala y el alcance de las prácticas de cría comercial en los mercados de loros en crecimiento, especialmente en Medio Oriente y Asia, y la falta de viabilidad financiera de la cría en cautiverio bajo una regulación eficaz para evitar el lavado o el uso de especímenes de origen silvestre como plantel reproductor. La capacidad de la cría en cautiverio para desplazar la demanda de loros de origen silvestre varió según las especies y las complejas interacciones entre el comercio de diferentes especies y contextos dificultaron a veces la predicción de las consecuencias de la producción comercial. Los responsables de la toma de decisiones y las autoridades reguladoras deben abordar la cría comercial de loros en cautiverio con cautela y tener en cuenta los vacíos de conocimiento y los nexos cruzados entre el comercio de diferentes especies para evitar consecuencias imprevistas derivadas de estimular y facilitar el comercio no sustentable de loros de origen silvestre.

Extended lactations in dairy cows and the effects on fertility and production.

Extending lactation length reduces the frequency of critical calving events for the cow and herewith reduces the frequency of periods with increased risk for health problems. Moreover, breeding is postponed until a moment later in lactation, which is associated with better conception rates and less days open after start of the breeding period in most studies. Potential risks of an extended lactation are that milk yield of cows at the end of the lactation may be too low which may lead to cows being overconditioned at the end of the extended lactation. Therefore, extending lactation length might not fit every cow. Individual cow characteristics like parity, milk yield level, or body condition determine the response of the cow to an extended lactation. These individual cow characteristics can be used in customized management strategies to optimize lactation length for individual cows. Customized lactation length for individual cows could limit the impact at herd level of disadvantages concerning milk losses and overconditioning and maintain benefits for improved cow health and fertility, reduced number of surplus calves and increased work satisfaction for the farmer. In conclusion, extending lactation length has interesting perspectives for health and fertility of high-producing dairy cows, although questions remain concerning management approaches to support lactation persistency of cows with an extended lactation, and consequences for calf health and development. Moreover, ongoing studies aim to develop decision support tools to select individual cows for a specific lactation length.

Trends and challenges in liquid-preserved boar semen production: From boar to product.

Boar semen production plays a pivotal role in modern swine breeding programmes, influencing the genetic progress and overall efficiency of the pork industry. This review explores the current challenges and emerging trends in liquid-preserved boar semen production, addressing key issues that impact the quality and quantity of boar semen. Advances in new reproductive technologies, boar selection, housing, semen processing, storage and transport, and the need for sustainable practices including the use of artificial intelligence are discussed to provide a comprehensive overview of the field.

ASReml-based estimation of early genetic parameters in hybrid mutton sheep populations.

The aim of this study was to analyze the effects of non-genetic factors on the estimation of genetic parameters of early growth traits in hybrid mutton sheep using ASReml software, in order to provide theoretical basis for screening the optimal hybriding combinations and accelerating the breeding process of new breeds of specialized housed-feeding mutton sheep. We selected the wellgrown hybrid Southhu (Southdown × Hu sheep) and Dorhu (Dorset × Hu sheep) sheep as the research objects, constructed weight correction formulae for SH and DH sheep at 60 and 180 days; and used ASReml software to investigate the effects of non-genetic factors on the estimation of genetic parameters of early growth traits in hybrid sheep. The results showed that the birth month and birth type were found significant for all traits (p < 0.001); the heritability of maternal effects ranged from 0.0709 to 0.1859. It was found that both SH and DH sheep emerged the potential for rapid early growth and development, early growth traits are significantly affected by maternal genetic effects, thereby the maternal effect should be taken into consideration for the purpose of improving accuracy in parameter estimations and therefore increasing the success of breeding programs.

Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies.

BACKGROUND: The Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressures on these breeds differ substantially. The aim of this study was to assess genetic diversity in both breeds through expected (HE) and observed heterozygosity (HO) and effective population size (Ne). Furthermore, we aimed to identify runs of homozygosity (ROH) to estimate and compare genomic inbreeding and signatures of selection in the breeds. RESULTS: HO was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with HE of 0.34 for both breeds. Based on genomic data, the Ne for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies. Genomic inbreeding coefficient (FROH) ranged from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony, with the majority of inbreeding attributed to short ROHs in both breeds. Several ROH islands associated with performance were identified in the Icelandic horse, featuring target genes such as DMRT3, DOCK8, EDNRB, SLAIN1, and NEURL1. Shared ROH islands between both breeds were linked to metabolic processes (FOXO1), body size, and the immune system (CYRIB), while private ROH islands in Exmoor ponies were associated with coat colours (ASIP, TBX3, OCA2), immune system (LYG1, LYG2), and fertility (TEX14, SPO11, ADAM20). CONCLUSIONS: Evaluations of genetic diversity and inbreeding reveal insights into the evolutionary trajectories of both breeds, highlighting the consequences of population bottlenecks. While the genetic diversity in the Icelandic horse is acceptable, a critically low genetic diversity was estimated for the Exmoor pony, which requires further validation. Identified signatures of selection highlight the differences in the use of the two breeds as well as their adaptive trait similarities. The results provide insight into genomic regions under selection pressure in a gaited performance horse breed and various adaptive traits in small-sized native horse breeds. This understanding contributes to preserving genetic diversity and population health in these equine populations.

Proper micro-environment alleviates mortality in laboratory mouse breeding induced by litter overlap and older dams.

The ongoing worldwide effort to reduce animal numbers in research often omits the issue of pre-weaning mortality in mouse breeding. A conservative estimate of 20% mortality would mean approximately 1.1 M mice die annually in the EU before scientific use. We hypothesize that pre-weaning mortality in laboratory mouse breeding is associated with cage social and macro/micro-environment conditions. Here we count pups from 509 C57BL/6J litters daily for accurate detection of mortality, and monitor cage micro-environment for 172 C57BL/6J litters. Probability of pups to die increases with the increase in dam age, number and age of older pups in the cage (of overlapped/cohabitating litters), and in small (<6 pups) and large (>11 pups) focal litters. Higher temperatures (>23.6 °C) and nest scores (>3.75) compensate for some of the socially-associated risks for pup death. These findings can be implemented in strategies for reducing pre-weaning mouse mortality, a more welfare-friendly and sustainable approach for science.

Impact of truncating historical data on prediction ability of dairy sheep selection candidates.

Along the last decades, the genetic evaluation methodology has evolved, improving breeding value estimates. Many breeding programmes have historical phenotypic records and large number of generations, but to make use of them could result in more inconveniences than benefits. In this study, the prediction ability of genotyped young animals was assessed by simultaneously evaluating the removal of historical data, two pedigree deepness and two methodologies (traditional BLUP and single-step genomic BLUP or ssGBLUP), using milk yield records of 40 years of three Latxa dairy sheep populations. The linear regression method was used to compare predictions of young rams before and after progeny testing, with six cut-off points, by intervals of 4 years (from 1992 to 2012), and statistics of ratio of accuracies, bias, and dispersion were calculated. The prediction accuracy of selection candidates, when genomic information was included, was the highest in all Latxa populations (between 0.54 and 0.69 with full data set). Nevertheless, the deletion of historical phenotypic data resulted on moderate accuracy gain in the bigger data size populations (mean gain 2.5%), and the smaller population took advantage of a moderate data deletion (2.7% gain by removing data until 2004), reducing accuracy when more records were removed. The bias of validation individuals was lower when the breeding value was predicted based on genomic information (between 2.1 and 13.9), being lower when the biggest amount of data was deleted in the bigger data size populations (5.2% reduction), and the smaller population was benefited from data deletion between 1996 and 2008 (3.8% bias reduction). Meanwhile, the slope of estimated genetic trend was lower when less data were included, and an overestimation of the unknown parent group estimates was observed. The results indicated that ssGBLUP evaluations were outstanding, compared with traditional BLUP evaluations, while the depth of pedigree had a very small influence, and deletion of historical phenotypic data was beneficial. Thus, Latxa routine genetic evaluations would benefit from truncating phenotypic records between 2000 and 2004, the use of two pedigree generations and the implementation of ssGBLUP methodology.

Whole-genome scan for selection signature associated with temperature adaptation in Iranian sheep breeds.

The present study aimed to identify the selection signature associated with temperature adaptation in Iranian sheep breeds raised in cold and hot environments. The Illumina HD ovine SNP600K BeadChip genomic arrays were utilized to analyze 114 animals from eight Iranian sheep breeds, namely Ghezel, Afshari, Shall, Sanjabi, Lori-Bakhtiari, Karakul, Kermani, and Balochi. All animals were classified into two groups: cold-weather breeds and hot-weather breeds, based on the environments to which they are adapted and the regions where they have been raised for many years. The unbiased FST (Theta) and hapFLK tests were used to identify the selection signatures. The results revealed five genomic regions on chromosomes 2, 10, 11, 13, and 14 using the FST test, and three genomic regions on chromosomes 10, 14, and 15 using the hapFLK test to be under selection in cold and hot groups. Further exploration of these genomic regions revealed that most of these regions overlapped with genes previously identified to affect cold and heat stress, nervous system function, cell division and gene expression, skin growth and development, embryo and skeletal development, adaptation to hypoxia conditions, and the immune system. These regions overlapped with QTLs that had previously been identified as being associated with various important economic traits, such as body weight, skin color, and horn characteristics. The gene ontology and gene network analyses revealed significant pathways and networks that distinguished Iranian cold and hot climates sheep breeds from each other. We identified positively selected genomic regions in Iranian sheep associated with pathways related to cell division, biological processes, cellular responses to calcium ions, metal ions and inorganic substances. This study represents the initial effort to identify selective sweeps linked to temperature adaptation in Iranian indigenous sheep breeds. It may provide valuable insights into the genomic regions involved in climate adaptation in sheep.

Detection of benzotriazole-type ultraviolet stabilizers in sea turtles breeding in the Northwest Pacific Ocean.

Benzotriazole-type ultraviolet stabilizers (BUVSs) are emerging contaminants whose exposure to wildlife is of concern. In this study, we investigated the contamination status of BUVSs in green turtles (Chelonia mydas) breeding at Ogasawara Islands, Japan, through chemical analysis of 10 BUVSs and 26 congeners of polychlorinated biphenyls (PCBs) in adipose tissue (n = 21) and blood plasma (n = 9). BUVSs were detected significant levels in adipose tissue (19 of 21 turtles), and UV-327 (not detected - 14.8 ng/g-lipid, detection frequency: 76 %), UV-326 (not detected - 24.1 ng/g-lipid, 29 %), and UV-328 (not detected - 5.8 ng/g-lipid, 24 %) were frequently detected. Turtles exhibiting sporadically high concentrations of BUVSs (>10 ng/g-lipid) did not necessarily correspond to individuals with high total PCB concentrations (1.03-70.2 ng/g-lipid). The sporadic occurrence pattern of BUVSs suggested that these contaminants in sea turtles cannot be explained solely by diet but are likely derived from plastic debris.

Analysis of the genetic variance of fibre diameter measured along the wool staple for use as a potential indicator of resilience in sheep.

BACKGROUND: The effects of environmental disturbances on livestock are often observed indirectly through the variability patterns of repeated performance records over time. Sheep are frequently exposed to diverse extensive environments but currently lack appropriate measures of resilience (or sensitivity) towards environmental disturbance. In this study, random regression models were used to analyse repeated records of the fibre diameter of wool taken along the wool staple (bundle of wool fibres) to investigate how the genetic and environmental variance of fibre diameter changes with different growing environments. RESULTS: A model containing a fifth, fourth and second-order Legendre polynomial applied to the fixed, additive and permanent environmental effects, respectively, was optimal for modelling fibre diameter along the wool staple. The additive genetic and permanent environmental variance both showed variability across the staple length trajectory. The ranking of sire estimated breeding values (EBV) for fibre diameter was shown to change along the staple and the genetic correlations decreased as the distance between measurements along the staple increased. This result suggests that some genotypes were potentially more resilient towards the changes in the growing environment compared to others. In addition, the eigenfunctions of the random regression model implied the ability to change the fibre diameter trajectory to reduce its variability along the wool staple. CONCLUSIONS: These results show that genetic variation in fibre diameter measured along the wool staple exists and this could be used to provide greater insight into the ability to select for resilience in extensively raised sheep populations.

An analysis of fertility and fecundity in the Australian sheep flock between 2006 and 2019.

After decades of decline, the Australian sheep flock aspires to rebuild its population of breeding ewes. A successful, rebuild will rely on high pregnancy rates and number of lambs born and reared. To examine this potential, a cross-sectional study of historical ultrasound pregnancy scanning records was undertaken using records collated from two experienced sheep pregnancy scanning businesses (years 2006 to 2019) from 15,397 mobs of ewes, totalling 7,443,314 ewes. Client details were de-identified and excluded from analyses, but details describing the mobs were retained when available, such as season of mating, production zone, ewe age, and breed. The key finding was a mean pregnancy rate (ewes pregnant per ewe scanned) of 0.76 ± 0.24, with a median of 0.83. Mobs scanned to identify fetal number had a higher mean (0.84 ± 0.15) and median (0.89) pregnancy rate. The mean reproduction rate (fetuses per ewe scanned) was 1.21 ± 0.27 and the median was 1.25. Differences were observed between the factors including age, breed, season, year or production zone but all results were lower than anticipated. The unexpected findings imply a problem exists with the fertility of many Australian sheep flocks.

Cytogenetic study of Meriz goat breeds in Iraqi Kurdistan region.

Goats are considered the leading farm animal that has a substantial role in the agricultural sector in the Kurdistan Region of Iraq. No cytological examination has been carried out on them. This experiment aims to identify the Karyotype of the local breeds of domestic goats. This experiment was conducted on the Karyotype and prepared the ideogram of Meriz goats. The determination of the relative length and centromeric index arm ratio of the chromosomes in the breed was achieved by the production of karyotypes. A total of (30)Meriz goats, consisting of (10) males and (20) females, were selected to collect blood samples for a short-term lymphocyte culture. The diploid chromosome count was observed to be (60), consisting of (29) pairs of acrocentric autosomes and one pair of allosomes, specifically the X and Y chromosomes. The acrocentric nature of the X-chromosome and the sub-metacentric nature of the Y-chromosome were identified through scientific investigation. The study observed a variation in the relative length of autosomal chromosomes in Meriz goats, with females ranging from 4.49% to 1.89% and males ranging from (4.53%) to (1.75%). The X-chromosome had a relative length of 3.96 in females, while the Y-chromosome displayed a relative length of (5.05). The findings of this karyological investigation suggest that the chromosomal composition seen in the Meriz goats under examination was within the expected range of normalcy. It is recommended that more cytogenetic analyses be conducted at the population level in order to identify individuals within the Meriz breed population who possesses numerical and/or structural chromosome abnormalities. This research is crucial for enhancing the efficiency of production and reproduction in this breed.

Application effectiveness of "Youxin-1" in genetic diversity and structure analysis of local chickens.

China's local chicken breeds are rich in resources, and have formed different germplasm characteristics in the process of long-term selection and evolution. Scientific assessment of population genetic diversity and identification of inter-breed genetic structure are of great value to the protection and innovative utilization of local chicken breed resource. In order to evaluate the application effectiveness of 23K SNP chip "Youxin-1" in the analysis of genetic diversity and genetic structure of local chickens, we used RADseq to identify genomic genetic variation of 21 local chicken breeds and developed 23K chip "Youxin-1". The genetic statistics of each variety were calculated based on two sets of SNP data, and correlation, fitting and phylogenetic analysis were carried out to evaluate the application effectiveness of the chip. The results showed that the observed heterozygosity (Ho), polymorphism information content (PIC), inbred coefficient (FROH) and genetic differentiation coefficient (Fst) calculated based on the two SNP data sets were basically consistent in the 21 local chicken breeds. The genetic diversity of Langya chicken (LA), Piao chicken (PJ) and Wenchang chicken (WC) was relatively rich. The genetic diversity of Bian chickens (BJ), Langshan chickens (LS), Gushi chickens (GS), Dongxiang blue-eggshell chickens (DX) and Beijing fatty chickens (BY) was relatively poor, and the correlation coefficients of Ho, PIC, FROH and average Fst in the two groups were 0.794, 0.901, 0.926 and 0.984, respectively, all reaching extremely significant levels (P<0.01) with a high degree of fit (P<0.001) and R2 were 0.644, 0.827, 0.916 and 0.927. For the two sets of SNP data, the evolutionary tree constructed by neighbor-joining (NJ) method and maximum likelihood (ML) method was reasonable, and the 21 local chicken breeds were generally divided into six categories, which was consistent with the formation history and geographical distribution of the varieties. The 23K chip also realized reasonable clustering of the five new varieties without individual deviation. There are some differences in the estimation of genetic statistics using SNP with different densities, and data standardization is needed. 23K chip has good efficacy in the analysis of genetic diversity and structure of local chickens.

Heterosis formation mechanism, prediction methods, and their application and prospect in pig production.

Heterosis is the phenomenon that the hybrid offspring outperform two-parent population. Hybridisation has been widely used in plant and animal production as it effectively improves the growth and developmental performance, reproductive performance and disease resistance of the offspring. Hybridization can effectively improve the growth and development performance, reproductive performance and disease resistance of offspring, so it is widely used in animal and plant production. Researchers have used cross-breeding techniques to cultivate excellent new agricultural and animal husbandry strains and supporting lines such as super-excellent Chaoyou 1000 hybrid rice, Xiaoyan No.6 hybrid wheat, Dumeng sheep, and Shanxia black pigs. However, there are still some urgent problems in the current hybrid dominance research: the existing hybrid dominance theory can only partially explain the phenomenon of plant and animal hybrid dominance, and the theory of animal hybrid dominance is less researched, and the accuracy of the existing hybrid dominance prediction methods is limited. China is the world's largest pork production and consumption country. Heterosis can effectively improve the production performance of pigs, and its application in the pig industry has important economic and research value. However, the existing research on pig hybrid production is in its infancy and needs to be further studied. In this review, we summarize the existing heterosis theory, heterosis prediction methods, and their application in pig production, to provide a reference for the application of heterosis in pig breeding.