Weighted single-step genome-wide association study for direct and maternal genetic effects associated with birth and weaning weights in sheep.

Body weight is an important economic trait for sheep meat production, and its genetic improvement is considered one of the main goals in the sheep breeding program. Identifying genomic regions that are associated with growth-related traits accelerates the process of animal breeding through marker-assisted selection, which leads to increased response to selection. In this study, we conducted a weighted single-step genome-wide association study (WssGWAS) to identify potential candidate genes for direct and maternal genetic effects associated with birth weight (BW) and weaning weight (WW) in Baluchi sheep. The data used in this research included 13,408 birth and 13,170 weaning records collected at Abbas-Abad Baluchi Sheep Breeding Station, Mashhad-Iran. Genotypic data of 94 lambs genotyped by Illumina 50K SNP BeadChip for 54,241 markers were used. The proportion of variance explained by genomic windows was calculated by summing the variance of SNPs within 1 megabase (Mb). The top 10 window genomic regions explaining the highest percentages of additive and maternal genetic variances were selected as candidate window genomic regions associated with body weights. Our findings showed that for BW, the top-ranked genomic regions (1 Mb windows) explained 4.30 and 4.92% of the direct additive and maternal genetic variances, respectively. The direct additive genetic variance explained by the genomic window regions varied from 0.31 on chromosome 1 to 0.59 on chromosome 8. The highest (0.84%) and lowest (0.32%) maternal genetic variances were explained by genomic windows on chromosome 10 and 17, respectively. For WW, the top 10 genomic regions explained 6.38 and 5.76% of the direct additive and maternal genetic variances, respectively. The highest and lowest contribution of direct additive genetic variances were 1.37% and 0.42%, respectively, both explained by genomic regions on chromosome 2. For maternal effects on WW, the highest (1.38%) and lowest (0.41%) genetic variances were explained by genomic windows on chromosome 2. Further investigation of these regions identified several possible candidate genes associated with body weight. Gene ontology analysis using the DAVID database identified several functional terms, such as translation repressor activity, nucleic acid binding, dehydroascorbic acid transporter activity, growth factor activity and SH2 domain binding.

Whole genome sequences of 70 indigenous Ethiopian cattle.

Indigenous animal genetic resources play a crucial role in preserving global genetic diversity and supporting the livelihoods of millions of people. In Ethiopia, the majority of the cattle population consists of indigenous breeds. Understanding the genetic architecture of these cattle breeds is essential for effective management and conservation efforts. In this study, we sequenced DNA samples from 70 animals from seven indigenous cattle breeds, generating about two terabytes of pair-end reads with an average coverage of 14X. The sequencing data were pre-processed and mapped to the cattle reference genome (ARS-UCD1.2) with an alignment rate of 99.2%. Finally, the variant calling process produced approximately 35 million high-quality SNPs. These data provide a deeper understanding of the genetic landscape, facilitate the identification of causal mutations, and enable the exploration of evolutionary patterns to assist cattle improvement and sustainable utilization, particularly in the face of unpredictable climate changes.

Whole-genome sequencing reveals genomic diversity and selection signatures in Xia'nan cattle.

BACKGROUND: The crossbreeding of specialized beef cattle breeds with Chinese indigenous cattle is a common method of genetic improvement. Xia'nan cattle, a crossbreed of Charolais and Nanyang cattle, is China's first specialized beef cattle breed with independent intellectual property rights. After more than two decades of selective breeding, Xia'nan cattle exhibit a robust physique, good environmental adaptability, good tolerance to coarse feed, and high meat production rates. This study analyzed the population genetic structure, genetic diversity, and genomic variations of Xia'nan cattle using whole-genome sequencing data from 30 Xia'nan cattle and 178 published cattle genomic data. RESULT: The ancestry estimating composition analysis showed that the ancestry proportions for Xia'nan cattle were mainly Charolais with a small amount of Nanyang cattle. Through the genetic diversity studies (nucleotide diversity and linkage disequilibrium decay), we found that the genomic diversity of Xia'nan cattle is higher than that of specialized beef cattle breeds in Europe but lower than that of Chinese native cattle. Then, we used four methods to detect genome candidate regions influencing the excellent traits of Xia'nan cattle. Among the detected results, 42 genes (θπ and CLR) and 131 genes (FST and XP-EHH) were detected by two different detection strategies. In addition, we found a region in BTA8 with strong selection signals. Finally, we conducted functional annotation on the detected genes and found that these genes may influence body development (NR6A1), meat quality traits (MCCC1), growth traits (WSCD1, TMEM68, MFN1, NCKAP5), and immunity (IL11RA, CNTFR, CCL27, SLAMF1, SLAMF7, NAA35, and GOLM1). CONCLUSION: We elucidated the genomic features and population structure of Xia'nan cattle and detected some selection signals in genomic regions potentially associated with crucial economic traits in Xia'nan cattle. This research provided a basis for further breeding improvements in Xia'nan cattle and served as a reference for genetic enhancements in other crossbreed cattle.

Genome-wide analysis reveals genomic diversity and signatures of selection in Qinchuan beef cattle.

BACKGROUND: Indigenous Chinese cattle have abundant genetic diversity and a long history of artificial selection, giving local breeds advantages in adaptability, forage tolerance and resistance. The detection of selective sweeps and comparative genome analysis of selected breeds and ancestral populations provide a basis for understanding differences among breeds and for the identification and utilization of candidate genes. We investigated genetic diversity, population structure, and signatures of selection using genome-wide sequencing data for a new breed of Qinchuan cattle (QNC, n = 21), ancestral Qinchuan cattle (QCC, n = 20), and Zaosheng cattle (ZSC, n = 19). RESULTS: A population structure analysis showed that the ancestry components of QNC and ZSC were similar. In addition, the QNC and ZSC groups showed higher proportions of European taurine ancestry than that of QCC, and this may explain the larger body size of QNC, approaching that of European cattle under long-term domestication and selection. A neighbor-joining tree revealed that QCC individuals were closely related, whereas QNC formed a distinct group. To search for signatures of selection in the QNC genome, we evaluated nucleotide diversity (θπ), the fixation index (FST) and Tajima's D. Overlapping selective sweeps were enriched for one KEGG pathway, the apelin signaling pathway, and included five candidate genes (MEF2A, SMAD2, CAMK4, RPS6, and PIK3CG). We performed a comprehensive review of genomic variants in QNC, QCC, and ZSC using whole-genome sequencing data. QCC was rich in novel genetic diversity, while diversity in QNC and ZSC cattle was reduced due to strong artificial selection, with divergence from the original cattle. CONCLUSIONS: We identified candidate genes associated with production traits. These results support the success of selective breeding and can guide further breeding and resource conservation of Qinchuan cattle.

Definition of metafounders based on population structure analysis.

BACKGROUND: Limitations of the concept of identity by descent in the presence of stratification within a breeding population may lead to an incomplete formulation of the conventional numerator relationship matrix ( A ). Combining A with the genomic relationship matrix ( G ) in a single-step approach for genetic evaluation may cause inconsistencies that can be a source of bias in the resulting predictions. The objective of this study was to identify stratification using genomic data and to transfer this information to matrix A , to improve the compatibility of A and G . METHODS: Using software to detect population stratification (ADMIXTURE), we developed an iterative approach. First, we identified 2 to 40 strata ( k ) with ADMIXTURE, which we then introduced in a stepwise manner into matrix A , to generate matrix A Γ using the metafounder methodology. Improvements in consistency between matrix G and A Γ were evaluated by regression analysis and through the comparison of the overall mean and mean diagonal values of both matrices. The approach was tested on genotype and pedigree information of European and North American Brown Swiss animals (85,249). Analyses with ADMIXTURE were initially performed on the full set of genotypes (S1). In addition, we used an alternative dataset where we avoided sampling of closely related animals (S2). RESULTS: Results of the regression analyses of standard A on G were - 0.489, 0.780 and 0.647 for intercept, slope and fit of the regression. When analysing S1 data results of the regression for A Γ on G corresponding values were - 0.028, 1.087 and 0.807 for k =7, while there was no clear optimum k . Analyses of S2 gave a clear optimal k =24, with - 0.020, 0.998 and 0.817 as results of the regression. For this k differences in mean and mean diagonal values between both matrices were negligible. CONCLUSIONS: The derivation of hidden stratification information based on genotyped animals and its integration into A improved compatibility of the resulting A Γ and G considerably compared to the initial situation. In dairy breeding populations with large half-sib families as sub-structures it is necessary to balance the data when applying population structure analysis to obtain meaningful results.

Weighted gene co-expression network analysis reveals genes related to growth performance in Hu sheep.

Hu sheep are a unique breed in our country with great reproductive potential, the extent of whose breeding has been steadily rising in recent years. The study subjects in this experiment were 8-month-old Hu sheep (n = 112). First of all, the growth performance, slaughter performance and meat quality of their eye muscle quality were assessed, meanwhile their live weight, carcass weight, body length, body height, chest circumference, chest depth and tube circumference were respectively 33.81 ± 5.47 kg, 17.43 ± 3.21 kg, 60.36 ± 4.41 cm, 63.25 ± 3.88 cm, 72.03 ± 5.02 cm, 30.70 ± 2.32 cm and 7.36 ± 0.56 cm, with a significant difference between rams and ewes (P < 0.01). Following that, transcriptome sequencing was done, and candidate genes related to growth performance were identified using the weighted co-expression network analysis (WGCNA) approach, which was used to identified 15 modules, with the turquoise and blue modules having the strongest association with growth and slaughter performance, respectively. We discovered hub genes such as ARHGAP31, EPS8, AKT3, EPN1, PACS2, KIF1C, C12H1orf115, FSTL1, PTGFRN and IFIH1 in the gene modules connected with growth and slaughter performance. Our research identifies the hub genes associated with the growth and slaughter performance of Hu sheep, which play an important role in their muscle growth, organ and cartilage development, blood vessel development and energy metabolic pathways. Our findings might lead to the development of potentially-useful biomarkers for the selection of growth and slaughterer performance-related attributes of sheep and other livestock.

Winter GPS tagging reveals home ranges during the breeding season for a boreal-nesting migrant songbird, the Golden-crowned Sparrow.

Determining space use for species is fundamental to understanding their ecology, and tracking animals can reveal insights into their spatial ecology on home ranges and territories. Recent technological advances have led to GPS-tracking devices light enough for birds as small as ~30 g, creating novel opportunities to remotely monitor fine-scale movements and space use for these smaller species. We tested whether miniaturized GPS tags can allow us to understand space use of migratory birds away from their capture sites and sought to understand both pre-breeding space use as well as territory and habitat use on the breeding grounds. We used GPS tags to characterize home ranges on the breeding grounds for a migratory songbird with limited available breeding information, the Golden-crowned Sparrow (Zonotrichia atricapilla). Using GPS points from 23 individuals across 26 tags (three birds tagged twice), we found home ranges in Alaska and British Columbia were on average 44.1 ha (95% kernel density estimate). In addition, estimates of territory sizes based on field observations (mean 2.1 ha, 95% minimum convex polygon [MCP]) were three times smaller than 95% MCPs created using GPS tags (mean 6.5 ha). Home ranges included a variety of land cover classes, with shrubland particularly dominant (64-100% of home range cover for all but one bird). Three birds tracked twice returned to the same breeding area each year, supporting high breeding site fidelity for this species. We found reverse spring migration for five birds that flew up to 154 km past breeding destinations before returning. GPS-tracking technology allowed for critical ecological insights into this migratory species that breeds in very remote locations.

Unraveling the genetic basis of methane emission in dairy cattle: a comprehensive exploration and breeding approach to lower methane emissions.

Ruminant animals, such as dairy cattle, produce CH4, which contributes to global warming emissions and reduces dietary energy for the cows. While the carbon foot print of milk production varies based on production systems, milk yield and farm management practices, enteric fermentation, and manure management are major contributors togreenhouse gas emissions from dairy cattle. Recent emerging evidence has revealed the existence of genetic variation for CH4 emission traits among dairy cattle, suggests their potential inclusion in breeding goals and genetic selection programs. Advancements in high-throughput sequencing technologies and analytical techniques have enabled the identification of potential metabolic biomarkers, candidate genes, and SNPs linked to methane emissions. Indeed, this review critically examines our current understanding of carbon foot print in milk production, major emission sources, rumen microbial community and enteric fermentation, and the genetic architecture of methane emission traits in dairy cattle. It also emphasizes important implications for breeding strategies aimed at halting methane emissions through selective breeding, microbiome driven breeding, breeding for feed efficiency, and breeding by gene editing.

Genetic parameters for novel climatic resilience indicators derived from automatically-recorded vaginal temperature in lactating sows under heat stress conditions.

BACKGROUND: Longitudinal records of automatically-recorded vaginal temperature (TV) could be a key source of data for deriving novel indicators of climatic resilience (CR) for breeding more resilient pigs, especially during lactation when sows are at an increased risk of suffering from heat stress (HS). Therefore, we derived 15 CR indicators based on the variability in TV in lactating sows and estimated their genetic parameters. We also investigated their genetic relationship with sows' key reproductive traits. RESULTS: The heritability estimates of the CR traits ranged from 0.000 ± 0.000 for slope for decreased rate of TV (SlopeDe) to 0.291 ± 0.047 for sum of TV values below the HS threshold (HSUB). Moderate to high genetic correlations (from 0.508 ± 0.056 to 0.998 ± 0.137) and Spearman rank correlations (from 0.431 to 1.000) between genomic estimated breeding values (GEBV) were observed for five CR indicators, i.e. HS duration (HSD), the normalized median multiplied by normalized variance (Nor_medvar), the highest TV value of each measurement day for each individual (MaxTv), and the sum of the TV values above (HSUA) and below (HSUB) the HS threshold. These five CR indicators were lowly to moderately genetically correlated with shoulder skin surface temperature (from 0.139 ± 0.008 to 0.478 ± 0.048) and respiration rate (from 0.079 ± 0.011 to 0.502 ± 0.098). The genetic correlations between these five selected CR indicators and sow reproductive performance traits ranged from - 0.733 to - 0.175 for total number of piglets born alive, from - 0.733 to - 0.175 for total number of piglets born, and from - 0.434 to - 0.169 for number of pigs weaned. The individuals with the highest GEBV (most climate-sensitive) had higher mean skin surface temperature, respiration rate (RR), panting score (PS), and hair density, but had lower mean body condition scores compared to those with the lowest GEBV (most climate-resilient). CONCLUSIONS: Most of the CR indicators evaluated are heritable with substantial additive genetic variance. Five of them, i.e. HSD, MaxTv, HSUA, HSUB, and Nor_medvar share similar underlying genetic mechanisms. In addition, individuals with higher CR indicators are more likely to exhibit better HS-related physiological responses, higher body condition scores, and improved reproductive performance under hot conditions. These findings highlight the potential benefits of genetically selecting more heat-tolerant individuals based on CR indicators.

Genetic assessment and candidate genes identification for breed-specific characteristics of Qingyuan partridge chicken based on runs of homozygosity.

BACKGROUND: Several core breeding and supporting lines of the Qingyuan partridge chicken, a representative local chicken breed in China, have been developed over 20 years. Consequently, its economic traits related to growth and reproduction have been significantly improved by breeding selection and commercial utilization, but some characteristic traits, such as partridge feathers, high meat quality and sufficient flavor, have always been retained. However, effective methods for genetic assessment and functional gene exploration of similar trait groups are lacking. The presence of identical haplotype fragments transmitted from parent to offspring results in runs of homozygosity (ROH), which offer an efficient solution. In this study, genomes of 134 Qingyuan partridge chickens representing two breeding populations and one preserved population were re-sequenced to evaluate the genetic diversity and explore functional genes by analyzing the diversity, distribution, and frequency of ROH. RESULTS: The results showed a low level of genomic linkage and degree of inbreeding within both the bred and preserved populations, suggesting abundant genetic diversity and an adequate genetic potential of the Qingyuan partridge chicken. Throughout the long-term selection process, 21 genes, including GLI3, ANO5, BLVRA, EFNB2, SLC5A12, and SVIP, associated with breed-specific characteristics were accumulated within three ROH islands, whereas another 21 genes associated with growth traits including IRX1, IRX2, EGFR, TPK1, NOVA1, BDNF and so on were accumulated within five ROH islands. CONCLUSIONS: These findings provide new insights into the genetic assessment and identification of genes with breed-specific and selective characteristics, offering a solid genetic basis for breeding and protection of Qingyuan partridge chickens.

Genetic parameters for milk yield and reproductive traits in Honduran Holstein cattle.

The aim of this study was to estimate the (co)variance components and genetic parameters for milk yield adjusted to 305d (MY305), calving-to-conception interval (CCI), number of services per conception (NSC) and calving interval (CI) of Honduran Holstein cows, by fitting a bivariate animal model using Maximum Restricted Likelihood procedures. Model included the fixed effects of calving number, the contemporary calving group (farm-season-year of calving and the cow age as covariate). The estimated means and standard deviations for MY, CCI, NSC and CI were, 5098.60 ± 1564.32 kg, 168.27 ± 104.71 days, 2.46 ± 1.69 services, and 448.73 ± 109.16 days, respectively; and their estimated heritabilities were 0.21 ± 0.05, 0.03 ± 0.028, 0.02 ± 0.024 and 0.06 ± 0.04, respectively. The genetic correlations between MY305 and CCI, NSC and CI were positive and antagonist, with values of 0.64 ± 0.52, 0.99 ± 0.56, and 0.32 ± 0.24 respectively. Even though moderate to low heritability was estimated for MY305, systematic selection for milk yield, with a reduction in reproductive efficiency, if considered as the only selection criterion is important to be considered. By including reproductive traits and considering permanent environment effects into the breeding program, might yield a slow, but constant and permanent improvement over time.

Unraveling inbreeding patterns and selection signals in Alpine Grey cattle.

Inbreeding plays a crucial role in livestock breeding, influencing genetic diversity and phenotypic traits. Genomic data have helped address limitations posed by incomplete pedigrees, providing deeper insights into breed genetic diversity. This study assesses inbreeding levels via pedigree and genomic approaches and analyzes old and recent inbreeding using runs of homozygosity (ROH), and selection signals in Alpine Grey cattle. Pedigree data from 165 575 individuals, analyzed with INBUPGF90 software, computed inbreeding coefficients. Genomic-based coefficients derived from PLINK v1.9. or DetectRUNS R package analyses of 1 180 individuals' genotypes. Common single nucleotide polymorphisms within ROH pinpointed genomic regions, aggregating into "ROH islands" indicative of selection pressure. Overlaps with USCS Genome Browser unveiled gene presence. Moderate correlations (0.20-0.54) existed between pedigree and genomic coefficients, with most genomic estimators having higher (>0.8) correlation values. Inbreeding averaged 0.04 in < 8 Mb ROH segments, and 0.03 in > 16 Mb segments; > 90% of ROHs were < 8 Mb, indicating ancient inbreeding prevalence. Recent inbreeding proved less detrimental than in cosmopolitan breeds. Two major ROH islands on chromosomes 6 and 7 harbored genes linked to immune response, disease resistance (PYURF, HERC3), and fertility (EIF4EBP3, SRA1). This study underscores the need for detailed inbreeding analyses to understand genetic characteristics and historical changes in local breeds like Alpine Grey cattle. Genomic insights, especially from ROH, facilitated overcoming pedigree limitations, illuminating breed genetic diversity. Our findings reveal ancient inbreeding's enduring genetic impact and ROH islands potential for selective sweeps, elucidating traits in Alpine Grey cattle.

Genetic parameters for reproductive traits and somatic cell score in U.S. dairy goats.

There are no studies regarding the estimation of genetic parameters and genetic trends for reproductive traits and somatic cells in goats. Their knowledge allows optimization of selection schemes. The objective of this study was to estimate genetic parameters and genetic and phenotypic trends for age at first kidding (AFK), kidding interval (KIN) and somatic cell score (SCS). Analyses were conducted within and across seven US goat breeds, namely, Nubian (NU), Alpine (AL), LaMancha (LM), Toggenburg (TO), Saanen (SA), Nigerian Dwarf (ND) and Oberhasli (OB), and a set of all of these breeds (AB). The restricted maximum likelihood methodology and trivariate animal models were used. Genetic and phenotypic trends were estimated using regression models. The average and standard deviation of AFK, KIN and SCS for AB were 573.6 ± 178.5 days, 418.8 ± 125.5 days and 4.67 ± 2.23 Log2, respectively. The heritabilities (h2) and standard errors of AFK, KIN and SCS for AB were 0.28 ± 0.02, 0.04 ± 0.02 and 0.22 ± 0.01, respectively. The h2 ranged from 0.15 (SA) to 0.37 (NU) for AFK, from 0.04 (AB) to 0.10 (AL) for KIN, and from 0.11 (TO) to 0.26 (LM and ND) for SCS. Genetic correlations between AFK and KIN and between AFK and SCS for AB were positive and weak (0.07 and 0.12, respectively) but significant (P < 0.01). Genetic correlations between SCS and KIN were significant (P < 0.01) for all the breeds and ranged from -0.15 (NU) to 0.44 (AL). Genetic correlations between AFK and SCS in the NU and AL breeds were similar (approximately 0.21). A positive genetic trend was found for KIN in the SA breed, which caused an increase in the number of days between consecutive kiddings. The genetic trend of SCS for the NU, AL and ND breeds was negative and decreased annually, which is beneficial for producers. These first results show the intensity and direction of some favorable/unfavorable relationships between AFK or KIN and SCS Log2 in some U.S. goat genetic groups.

Light pollution affects activity differentially across breeding stages in an urban exploiter: An experiment in the house sparrow (Passer domesticus).

Artificial Light At Night (ALAN) is a major urban perturbation, which can have detrimental effects on wildlife. Recent urban planning has led to an increased use of white light emission diodes (LEDs) in cities. However, little is known about the effects of this type of ALAN on wild vertebrates, especially during reproduction. We designed an experiment to test the impact of ALAN on the activity rhythms (daily time of first activity (TFA) and time of last activity (TLA)) of captive House sparrows (Passer domesticus) during several reproductive stages (from pre-breeding to post-breeding). We also tested the impact of ALAN on reproductive performance (laying date, clutch size, hatching and fledging success). Experimental birds were active earlier in the morning (earlier TFA) relative to controls although experimental and control birds did not differ in their TLA. The effect of ALAN on TFA was apparent during specific stages only (pre-breeding and chick-rearing stages), suggesting that sparrows actively adjust their activity in response to ALAN only during specific periods. This impact of ALAN on activity did not persist through the whole breeding season, suggesting that sparrows may habituate to ALAN. Alternatively, they may not be able to sustain a long-term increased activity in response to ALAN because of sleep deprivation and related physiological costs. Finally, we did not find any impact of ALAN on the reproductive performance of captive house sparrows held under optimal conditions. This suggests that ALAN may not be dramatically detrimental to the reproduction of this urban exploiter, at least when food availability is not constraining.

Protocol for the controlled reproduction of the edible frog Aubria subsigillata in aquaculture hatcheries in the Republic of Benin.

Context Aubria subsigillata is such a highly valued, edible species for the citizens of Benin that over exploitation has led to a rarefaction of wild populations. Aims The aim of captive breeding is to develop breeding protocols and farming practices for the species which will reduce hunting pressure on wild populations. Methods The methodology consisted of determining the concentration of ovulatory hormone and its method of injection into the breeding stock, followed by in vitro fertilisation of the unfertilised eggs of the females by the spermic urine of the males to determine the optimum injection method, hormone concentration for ovulation and sperm collections, and the development of in vitro fertilisation protocols using gametes obtained via the aforementioned methodologies. Key results Results indicated that 0.2IU/g concentration of gonadotropin-releasing hormone agonist administered intrafemorally enabled spontaneous release of spermic urine and ova in the breeding animals. The latency time between injection and collection of gametes was 13h in males and 27h in females at a temperature of 28.5°C. Females laid an average of 172 eggs weighing 1mg mass. Conclusions Aubria subsigillata is a frog that reproduces using stimuli (hormone), and in vitro fertilisation resulted in a high rate of fertilised eggs. Implications Artifical reproduction in A. subsigillata is carried out in five phases: (1) selection of mature broodstock; (2) hormonal injection; (3) gamete collection; (4) in vitro fertilisation; and (5) incubation. However, work should continue on improving the egg hatching rate.

Remote sensing of emperor penguin abundance and breeding success.

Emperor penguins (Aptenodytes forsteri) are under increasing environmental pressure. Monitoring colony size and population trends of this Antarctic seabird relies primarily on satellite imagery recorded near the end of the breeding season, when light conditions levels are sufficient to capture images, but colony occupancy is highly variable. To correct population estimates for this variability, we develop a phenological model that can predict the number of breeding pairs and fledging chicks, as well as key phenological events such as arrival, hatching and foraging times, from as few as six data points from a single season. The ability to extrapolate occupancy from sparse data makes the model particularly useful for monitoring remotely sensed animal colonies where ground-based population estimates are rare or unavailable.

Local chicken breeds exhibit abundant TCR-V segments but similar repertoire diversity.

The thymus-derived lymphocytes of jawed vertebrates have four T-cell receptor (TCR) chains that play a significant role in immunity. As chickens have commercial value, their immune systems require a great deal of attention. Local chicken breeds are an essential part of poultry genetic resources in China. Here, we used high-throughput sequencing to analyze the TCRα and TCRß repertoires and their relative expression levels in the native chicken breeds Baier Buff, Longyou Partridge, Xiaoshan, and Xianju. We found that TCR Vα and TCR Vß were expressed and included 17, 19, 17, and six segments of the Vα2, Vα3, Vß1, and Vß2 subgroups, respectively. V-J pairing was biased; Jα11 was utilized by nearly all Vα segments and was the most commonly used. Breed-specific V segments and V-J pairings were detected as well. The results of the principal coordinate analysis (PCoA) as well as the V-J pairing and CDR3 diversity analyses suggested that the four local chicken breeds did not significantly differ in terms of TCR diversity. Hence, they expressed not significant differentiation, and they are rich genetic resources for the development and utilization of immune-related poultry breeding.

Whole-genome selection signature differences between Chaohu and Ji'an red ducks.

Assessing the genetic structure of local varieties and understanding their genetic data are crucial for effective management and preservation. However, the genetic differences among local breeds require further explanation. To enhance our understanding of their population structure and genetic diversity, we conducted a genome-wide comparative study of Chaohu and Ji'an Red ducks using genome sequence and restriction site-associated DNA sequencing technology. Our analysis revealed a distinct genetic distinction between the two breeds, leading to divided groups. The phylogenetic tree for Chaohu duck displayed two branches, potentially indicating minimal impact from artificial selection. Additionally, our ROH (runs of homozygosity) analysis revealed that Chaohu ducks had a lower average inbreeding coefficient than Ji'an Red ducks. We identified several genomic regions with high genetic similarity in these indigenous duck breeds. By conducting a selective sweep analysis, we identified 574 candidate genes associated with muscle growth (BMP2, ITGA8, MYLK, and PTCH1), fat deposits (ELOVL1 and HACD2), and pigmentation (ASIP and LOC101797494). These results offer valuable insights for the further enhancement and conservation of Chinese indigenous duck breeds.

Physico-chemical characterization of Anopheles gambiae s.l. breeding sites and kdr mutations in urban areas of Cotonou and Natitingou, Benin.

BACKGROUND: This study aimed to investigate the relationship between the physicochemical characteristics of An. gambiae s.s. and An. coluzzii breeding sites, the susceptibility profiles to commonly used insecticides in public health, and the underlying insecticide resistance mechanisms. METHODS: Anopheles breeding sites surveys were conducted in Cotonou and Natitingou in September 2020, January and August 2021. Physicochemical properties and bacterial loads were determined in individual breeding sites. The WHO susceptibility assays were carried out using the female of the emerging adult mosquitoes. Anopheles species were identified through PCR techniques. Kdr L1014F/S, N1575Y and G119S mutations were investigated using TaqMan genotyping assays. RESULTS: Molecular analysis showed that all mosquitoes analyzed in Cotonou were Anopheles coluzzii, while those of Natitingou were Anopheles gambiae s.s. Fecal coliforms were identified as playing a role in this distribution through their significant influence on the presence of An. coluzzii larvae. WHO susceptibility assay indicated a high level of resistance to deltamethrin in the two cities. The resistance levels to deltamethrin were higher in Cotonou (X2 = 31.689; DF = 1; P < 0.0001). There was a suspected resistance to bendiocarb in Cotonou, whereas the mosquito population in Natitingou was resistant. The kdr L1014F mutation was highly observed in both mosquito populations (frequence: 86-91%), while the Ace-1 mutation was found in a small proportion of mosquitoes. In Cotonou, salinity was the only recorded physicochemical parameter that significantly correlated with the resistance of Anopheles mosquitoes to deltamethrin (P < 0.05). In Natitingou, significant correlations were observed between the allelic frequencies of the kdr L1014F mutation and pH, conductivity, and TDS. CONCLUSION: These results indicate a high level of pyrethroid resistance in the anopheles populations of both Cotonou and Natitingou. Moreover, this study report the involvement of abiotic factors influencing Anopheles susceptibility profile.