Search Results (1,232)

Days open (DO) is a critical economic and reproductive trait that is commonly employed in genetic selection. Making improvements using conventional genetic techniques is exceedingly challenging. Therefore, new techniques are required to improve the accuracy of genetic selection using genomic data. This study examined the genetic approaches of traditional AIREML and single-step genomic AIREML (ssGAIREML) to assess genetic parameters and the accuracy of estimated breeding values while also investigating SNP regions associated with DO and identifying candidate genes through a genome-wide association study (GWAS). The dataset included 59415 DO records from 36368 Thai–Holstein crossbred cows and 882 genotyped animals. The cows were classified according to their Holstein genetic proportion (breed group, BG) as follows: BG1 (>93.7% Holstein genetics), BG2 (87.5% to 93.6% Holstein genetics), and BG3 (<87.5% Holstein genetics). AIREML was utilized to estimate genetic parameters and variance components. The results of this study reveal that the average DO values for BG1, BG2, and BG3 were 97.64, 97.25, and 96.23 days, respectively. The heritability values were estimated to be 0.02 and 0.03 for the traditional AIREML and ssGAIREML approaches, respectively. Depending on the dataset, the ssGAIREML method produced more accurate estimated breeding values than the traditional AIREML method, ranging from 40.5 to 45.6%. The highest values were found in the top 20% of the dam dataset. For the GWAS, we found 12 potential candidate genes (DYRK1A, CALCR, MIR489, MIR653, SLC36A1, GNA14, GNAQ, TRNAC-GCA, XYLB, ACVR2B, SLC22A14, and EXOC2) that are believed to have a significant influence on days open. In summary, the ssGAIREML method has the potential to enhance the accuracy and heritability of reproductive values compared to those obtained using conventional AIREML. Consequently, it is a viable alternative for transitioning from conventional methodologies to the ssGAIREML method in the breeding program for dairy cattle in Thailand. Moreover, the 12 identified potential candidate genes can be utilized in future studies to select markers for days open in regard to dairy cattle. Full article

Lüliang black goat (LBG) is a unique livestock genetic resource of great significance for the local agriculture and economic development of Shanxi, China. However, the kidding rate of LBG is relatively low, which limits efforts to improve the reproductive performance and economic benefits of this breed. Therefore, improving the kidding characteristics of LBG is crucial for increasing its economic benefits. In this study, 20 LBG does were selected for whole-genome resequencing and divided into two groups: 10 in the T group (does with three consecutive kiddings of twin kids) and 10 in the S group (does with three consecutive kiddings of single kids). Based on whole-genome resequencing data, this study comprehensively assessed the population structure and genetic diversity of LBG and explored the related genes that affect reproductive performance. Three selection signal analysis methods—Fst (Fixation Index), π (nucleotide diversity), and XP-CLR (Cross Population Composite Likelihood Ratio)—were applied to screen a total of 838 genes, and enrichment analysis was performed to identify genes closely related to the reproductive performance of LBG, including ENPP3, APC, and GLI2. A generalized linear model was used to conduct a correlation analysis between non-synonymous mutations in the three genes and the number of kids produced. Two loci that were significantly correlated with kidding number were identified (p < 0.05): GLI2 g.63400363 C>T and GLI2 g.63417538 C>T. In general, the LBG population has high genetic diversity and good prospects for genetic improvement. The findings revealed that mining high-fecundity selection characteristics provides a basis for research on goat reproductive mechanisms. Full article

Semen quality and persistence are critical for evaluating the usability of individual boars in AI, a standard practice in pig breeding. We conducted GWASs on various semen traits of Duroc boars, including MOT, DEN, ABN, MMP, AIR, and ROS levels. These traits were assessed using FCM and CASA. A total of 1183 Duroc boars were genotyped using the GeneSeek GGP Porcine 50 K SNP BeadChip. The GWAS was performed using three different models: GLM, MLM, and FarmCPU. Additionally, trait heritability was estimated using single- and multiple-trait PBLUP models, yielding 0.19, 0.29, 0.13, 0.18, 0.11, and 0.14 heritability for MOT, DEN, ABN, MMP, AIR, and ROS, respectively. All semen traits exhibited low heritability except ABN, which demonstrated medium heritability. Nine candidate genes (GPX5, AWN, PSP-II, CCDC62, TMEM65, SLC8B1, TRPV4, UBE3B, and SIRT5) were potentially associated with semen traits. These genes are associated with antioxidant and mitochondrial functions in porcine sperm. Our findings provide insight into the genetic architecture of semen traits in Duroc boars, and the identified SNPs and candidate genes may enhance economic outcomes in the pig breeding industry while improving sperm quality through targeted breeding strategies. Full article

This study aimed to examine the age at first calving (AFC) in Hungarian Angus herds. This study was conducted on the basis of data from 2955 registered cows, classified into five groups (based on different Angus types), and 200 breeding bulls, which were the sires of the cows. The data were made available by the Hungarian Hereford, Angus, and Galloway Breeders’ Association. The variance and covariance components, heritability, breeding value (BV), and genetic trends of AFC between 1998 and 2021 were evaluated. A general linear model (univariate analysis of variance) was used to examine the various effects, while best linear unbiased prediction was used to estimate the population genetic parameters and BV, and linear regression analysis was used for the trend analysis. The average AFC obtained was 28.1 ± 0.1 months (SD = 5.3 months), showing a relatively large variance (CV = 18.9%). The environmental factors that influenced the development of the phenotype were the cow’s birth season (28.99%, p < 0.01), cow’s birth year (28.7%, p < 0.01), the cow’s sire (18.32%, p < 0.01), and the herd (11.77, p < 0.05). The cow’s color variant (8.10%, p > 0.05) was not significant and did not influence the AFC in this study. The direct heritability of AFC (h² = 0.51 ± 0.06) was higher than data in the literature (0.38 ± 0.05); however, the maternal heritability was low (h²_m = 0.00 ± 0.03). The correlation between direct and maternal genetic effects was zero (r_dm = −0.97 ± 1.00). The phenotypic trend of AFC increased by +0.03 months per year, which was not statistically significant. The genetic trend calculation showed no significant changes. Based on the h² and BV results, it seems that selecting a suitable sire can effectively reduce the AFC of daughters. Since AFC is also an important trait in economic terms, it would be appropriate to include AFC BV in the bull catalog. Full article

The yellowfin seabream (Acanthopagrus latus) is an economically important commercial mariculture fish in China and Southeast Asia. Only a few simple sequence repeats (SSRs) of A. latus have been isolated and reported, which has hindered breeding progress. A total of 318,862 SSRs were isolated and characterized from the A. latus genome in this study. All SSRs were 9,069,670 bp in length, accounting for 1.32% of the genome. The density and frequency of SSRs were 468.40 loci/Mb and 13,323.19 bp/Mb, respectively. The major SSRs were dinucleotides (accounting for 76.92%), followed by trinucleotides (15.75%). The most abundant SSR motif was (AC)n (168,390, accounting for 53%), with the highest frequency (245.78 loci/Mb) and density (7304.18 bp/Mb). Most SSRs were located in non-coding regions, such as intergenic regions (34.54%) and introns (56.91%). SSR-containing exons were distributed into 51 gene ontology (GO) terms and significantly enriched in immunity- and growth-related pathways. A total of 217,791 SSR markers were successfully designed. Nine SSR markers were amplified in 29 A. latus individuals, and eight of them possess high polymorphism. The cross-species transferability of 33 out of the 37 tested loci were successfully amplified in Acanthopagrus schlegelii. These results lay the foundation for the molecular marker-assisted breeding and genetic information assessment of A. latus. Full article

The Spanish Merino is the most significant sheep breed globally due to its economic and cultural importance in human history. It has also had a substantial influence on the development of other Merino and Merino-derived breeds. Historical sources indicate that crossbreeding to produce finer, higher-quality wool was already taking place in the south of the Iberian Peninsula during the Roman era. This evidence suggests that individuals with a racial pattern very similar to that of the modern Merino may have already existed on the peninsula. The presence of the skeletal remains of these animals at various human settlements dated to the late fourth and third millennia BC could provide insights into the genomics of these ancestral sheep. This study analyses ancient DNA extracted from nine skeletal remains from three archaeological sites in Southern Iberia, dated to the third millennium BC. The samples were sequenced and aligned with the ovine genome. The genetic distances observed among the samples indicate a closer relationship between several animals from the Marinaleda (Seville) and Grañena Baja (Jaén) sites. The study of the slaughter/death age profiles identified at La Minilla (La Rambla, Córdoba) suggests an approach centred on meat exploitation, while the data from Marinaleda (Seville) and Grañena Baja (Jaén) indicate the potential exploitation of secondary resources. A review of the composition of these small ruminant herds could provide insights into the type of secondary resource exploitation that may have been prioritised. Our aim is to investigate the presence of distinct production systems, differentiating between those aimed primarily at meat use and those focused on secondary products. This is the first approach to exploring the genetic evidence for sheep livestock related to its productive use during this period and in this geographical area. Full article

This study aimed to characterize microsatellites in the rabbit genome using an in silico approach and to develop and validate microsatellite markers. Blood samples were collected from 15 Baladi rabbits and 18 New Zealand White (NZW rabbits). The GMATA software was used to define SSRs in the extracted sequences. Twelve primer pairs were used to validate the loci identified and the primers developed. The total number of the detected microsatellite loci overall chromosomes was 1,136,253. The di-nucleotide microsatellite repeats dominated and exceeded 88% of the detected microsatellites in all chromosomes. There were no microsatellites detected in mitochondrial DNA. The highest relative microsatellite abundance was obtained for chromosome 19, followed by 13 and 6. The highest estimated SSR density was obtained for chromosome 14, and the lowest was for mitochondrial DNA, followed by chromosome 13. The polymorphism was 81.63% and 75.51% for Baladi and NZW rabbits, respectively. The number of detected alleles ranged between two and seven alleles/loci, and polymorphic information content was from 35% to 71%. The AMOVA analysis showed that the total variance of all levels of population structure was 15.734. The results definitely confirmed higher genetic diversity in Baladi compared with NZW rabbits. Full article

In Italy, the number of farmed dairy buffaloes rose up to approximately 436,000 heads in 2023 (+22% in the last 15 years), a fourfold increase compared to the 1980s, due to the growing market interest in mozzarella cheese. The increased demand for mozzarella cheese, in turn, requires higher production, which can result in increased methane emission from the sector. Therefore, it is necessary to establish mitigation and selection schemes for low-emission strategies. The current study aimed to highlight sources of variation in methane emission from lactating Italian Mediterranean buffaloes measured using a laser methane detector in order to identify practical and methodological aspects to consider when designing experiments focused on methane emission evaluation. Methane (CH₄), exhaled from 60 cows, was recorded twice a day during milking, over two weeks per month for at least three months throughout a whole lactation cycle. The animal (individual), days in milk, parity, month, operator, milking entry order, and milking session effects were significant for methane emission (p < 0.0001). Our results showed that laser methane detector may be used as a rapid tool for methane emission studies and highlighted which factors can account for individual measures. This instrument is easy to use, fast, versatile, and not too expensive. These characteristics make it suitable for large-scale herd screening and monitoring. Full article

Tail fat is essential for sheep survival in extreme environments, yet its significance is often overlooked, leading to the decline of fat-tailed breeds. This study identified a novel lncRNA, lncRSFD1 (TCONS_00054953), through transcriptome sequencing, showing differential expression in the tail adipose tissues of Lanzhou Fat-Tailed (LFT) sheep and Tibetan (TS) sheep. Highly expressed in adipose tissues, lncRSFD1 inhibits preadipocyte proliferation and promotes 3T3-L1 differentiation, suggesting its role in regulating fat deposition. Located in both the cytoplasm and nucleus, lncRSFD1 targets the neighboring gene PDE4DIP and may function as a molecular sponge for conserved miRNAs, including oar-miR-30a-3p, oar-miR-329b-5p, and oar-miR-431, which are known to influence fat and muscle-related physiological processes. Moreover, the core promoter of lncRSFD1 (−2607 bp to −1776 bp) harbors four SNPs (g.-2429G>A, g.-2030T>C, g.-2016C>T, g.-2015G>A) significantly associated with growth traits such as body height in Guiqian Semi-Fine Wool (GSFW) sheep. These findings suggest lncRSFD1 plays a key role in fat deposition and growth regulation, offering new insights into the molecular mechanisms of lncRNAs in sheep. It provides a potential target for genetic improvement and molecular breeding to enhance fat deposition and adaptability in sheep breeds. Full article

Crossbreeding is a traditional breeding technique and has been performed successfully in many fish species. However, distant hybridization between different genera is hard to be successful because of reproductive isolation. In this study, diploid hybrids (PL) were successfully derived from the hybridization of Ussuri catfish (Pseudobagrus ussuriensis, PU, ♀, 2n = 52) and longsnout catfish (Leiocassis longirostris, LL, ♂, 2n = 52). And the morphological data, external frame parameters, chromosomal karyotypes, DNA content measurement, mitochondrial DNA control region, and species-specific marker identification were applied to investigate the traits and genetic characterization of the PL hybrid offspring and their parents. Both quantifiable traits and shape frame parameters of the PL hybrid offspring were revealed to be intermediate between those of their parents; however, cluster analysis showed that their external morphology was more in favor of the maternal PU. The growth comparisons showed that the hybrids had significant growth advantages over maternal PU. Based on karyotype patterns, DNA contents and mitochondrial DNA, the hybrid origin and maternal inheritance of hybrid offspring were further confirmed. According to the sequence variations identified from the genome sequences of the two catfish species, one species-specific marker was developed to distinguish the PL hybrid offspring and their parents. Therefore, this study provides a successful case for intergeneric hybridization and hybrid superiority, and the PL hybrid shows promise for commercial application, pending further studies into its husbandry, health, and welfare with larger populations of fish. Full article

Natural selection and artificial breeding are crucial methods for developing new animal groups. The Baiyu black goats and Chuanzhong black goats are indigenous goat breeds from distinct ecological regions in Sichuan Province, with dramatically different growth and reproductivity. This study aimed to systematically elucidate the differences in production performance and genetic traits between Baiyu black goats and Chuanzhong black goats. We quantified growth and reproductive attributes for both breeds. Furthermore, we conducted a comprehensive analysis of genetic diversity, population structure, and selection signatures using whole-genome resequencing data. This dataset included 30 individuals from the Baiyu black goat breed, 41 from the Chuanzhong black goat breed, and an additional 59 individuals representing Chengdu grey goats, Tibetan cashmere goats, and Jianchang black goats, totaling 130 individuals across five goat breeds. The comparative analysis of production performance revealed that the weight and body size of Chuanzhong black goats were significantly higher than those of Baiyu black goats (p < 0.01). At the same time, the average kidding rate and kid-weaning survival rate of Chuanzhong black goats were also notably superior to those of Baiyu black goats (p < 0.01). The Baiyu black goats exhibited a more abundant genetic diversity and distinct genetic differences compared to the Chuanzhong black goat, according to an analysis grounded on genomic variation. The Baiyu black goats are more closely related to Tibetan cashmere goats, whereas Chuanzhong black goats share a closer genetic relationship with Chengdu grey goats. Additionally, we employed the π, Fst, and XP-EHH methodologies to identify genes related to immunity (TRIM10, TRIM15, TRIM26, and TRIM5), neurodevelopment (FOXD4L1, PCDHB14, PCDHB4, PCDHB5, PCDHB6, and PCDHB7), reproduction (BTNL2 and GABBR1), body size (NCAPG, IBSP, and MKNK1), and meat quality traits (SUCLG2 and PGM5). These results provide a theoretical basis for further resource conservation and breeding improvement of the Baiyu black goat and Chuanzhong black goat. Full article

Reproductive efficiency is a key element of profitability in dairy herds. However, the genetic evaluation of fertility traits is often challenged by the presence of high censorship rates due to various reasons. An easy approach to address this challenge is to remove the censored data from the dataset. However, removing data might bias the genetic evaluation. Therefore, addressing this issue is crucial, particularly for small populations and populations with limited size. This study uses a Moroccan Holstein dataset to compare two Gaussian linear models and a threshold linear model to handle censored records of days open (DO). Data contained 8646 records of days open across the first three parities of 6337 Holstein cows. The pedigree file comprised 11,555 animals and 14.51% of the dataset was censored. The genetic parameters and breeding values of DO were computed using three different methods: a linear model where all censored records were omitted (LM), a penalty method in which a constant equal to one estrus cycle in cattle was added to the maximum value of DO in each contemporary group to impute the censored records (PLM), and a bivariate threshold model with a penalty (PTM). The heritability estimates were equal to 0.021 ± 0.01 (PLM), 0.029 ± 0.01 (LM), and 0.033 ± 0.01 (PTM). The penalty method and the threshold linear model with a penalty showed better prediction accuracy calculated using the LR method (0.21, and 0.20, respectively). PLM and PTM had a high Spearman correlation (0.99) between the estimated breeding values of the validation dataset, which explains the high percentage of common animals in the top 20% of selected animals. The lack of changes in the ranking of animals between PLM and PTM suggests that both methods can be used to address censored data in this population. Full article

(1) Background: Cashmere goats, as one of the characteristic species, are rich in genetic resources. Protecting and rationally utilizing these genetic resources is of great significance for the genetic improvement of cashmere goats. (2) Methods: In this study, tissue samples were collected from Inner Mongolia white cashmere goats, which included the Arbas type (ARBS); Erlangshan type (ELS); Alashan type (ALS), Hanshan white cashmere goats (HS), and Ujimqin white cashmere goats (WZMQ). Genomic DNA was extracted and subjected to high-depth genome resequencing. GenoBait technology was used for probe design and site optimization, followed by the synthesis of a low-density liquid phase chip. Finally, a total of 281 individuals from five cashmere goat populations in the Inner Mongolia Autonomous Region were randomly selected to verify the chip. (3) Results: The results showed that a total of 5002 SNP sites were finally screened and retained for the synthesis of the low-density liquid chip for identifying cashmere goats in Inner Mongolia Autonomous Region. Principal component analysis and phylogenetic tree construction indicated that the ARBS, ELS, and ALS populations were clustered into one category. (4) Conclusions: This chip can accurately identify the three breeds: Inner Mongolia white cashmere goats, Hanshan white cashmere goats, and Ujimqin white cashmere goats. Full article

Livestock expresses complex traits influenced by several factors. The response of animals to variations in climatic factors, such as increases in temperature, may induce heat stress conditions. In this study, animals living at different temperatures were compared using the genome-wide Wright fixation index (F_ST). A total of 825 genotypes of Sarda breed ewes were divided into two groups based on the flocks’ average temperature over a 20-year period to compute the F_ST: 395 and 430 sheep were represented in colder and hotter groups, respectively. After LOWESS regression and CONTROL CHART application, 623 significant markers and 97 selection signatures were found. A total of 280 positional candidate genes were retrieved from a public database. Among these genomic regions, we found 51 annotated genes previously associated with heat stress/tolerance in ruminants (FCGR1A, MDH1, UGP2, MYO1G, and HSPB3), as well as immune response and cellular mechanisms related to how animals cope with thermal stress (RIPK1, SERPINB1, SERPINB9, and PELI1). Moreover, other genes were associated with milk fat (SCD, HERC3, SCFD2, and CHUK), body weight, body fat, and intramuscular fat composition (AGPAT2, ABCD2, MFAP32, YTHDC1, SIRT3, SCD, and RNF121), which might suggest the influence of environmental conditions on the genome of Sarda sheep. Full article

The ACOX1 gene is vital for fatty acid metabolism and is linked to environmental stress and physical exertion adaptation. The p.Asp237Ser variant (rs782885985) in ACOX1 is associated with increased enzyme activity and reactive oxygen species (ROS) levels. This study examined the ACOX1 polymorphism across six horse breeds in Iran: Arabian, Thoroughbred, KWPN, Caspian, Kurdish, and Turkmen. The goal was to identify differences in ACOX1 genotype distribution, potentially serving as genetic markers under selection pressure related to breed-specific traits. In a sample of 324 horses, genomic DNA was analyzed using PCR-RFLP, revealing three genotypes (TT, TG, GG). The GG genotype was most common in Kurdish and Arabian horses (86% and 70%, respectively), while the TT genotype was prevalent in Turkmen (24%) and Thoroughbred horses (23%). The T allele’s frequency in Thoroughbred and Turkmen horses suggests that ACOX1 may be under selection pressure for phenotypic traits. Differences in genotype distribution were confirmed among breeds, with no sex-based association. The study concludes that ACOX1 is a potential genetic marker for horse performance and adaptability, emphasizing the importance of genetic diversity in breeding programs. Full article