Genomic prediction has become a central paradigm in biology, enabling quantitative inference of genetic contributions to complex traits across humans, animals, and plants. Although genomic research in human genetics and animal breeding shares a highly homologous methodological foundation, significant barriers persist in their analytical paradigms and application scenarios. This study aims to promote cross-disciplinary integration by introducing human-derived polygenic scores (PGS) algorithms into animal genomic selection (GS) and proposing a PGS-GS framework with a preliminary weighting-based implementation. We systematically benchmarked the predictive performance and computational efficiency of 20 algorithms, including classical linear models, machine learning, PGS, and PGS-GS using both array and whole-genome sequencing (WGS) data across four major agricultural species: beef cattle, sheep, pigs, and chickens. Our results demonstrate that PGS and PGS-GS algorithms achieve predictive accuracy competitive with genomic best linear unbiased prediction (GBLUP) while offering markedly higher computational efficiency. Moreover, incorporating PGS-derived prior information into weighted linear and non-linear models outperformed conventional weighted GBLUP. The results provide empirical evidence to inform algorithm selection and highlight the potential of integrating human-derived PGS methodologies into animal genomic prediction frameworks.

BACKGROUND:Various methods have been widely utilized to estimate the genomic breeding values (GEBVs) for genomic prediction. Traditional approaches often relied on the assumption of linear regression models, which struggle to effectively capture the nonlinear relationships between limited phenotypic data and high-dimensional genotypic data. Deep learning (DL) provided a powerful solution for addressing nonlinear problems. Herein, we proposed a novel deep learning method, named residual attention genomic prediction (ReaGP), which was characterized by two main features. It employed residual units to mitigate gradient instability and network degradation issues, while leveraging attention mechanisms to enhance the mining of critical feature information. Moreover, genomic data processed with frequency encoding was integrated into ReaGP to achieve a richer feature representation. RESULTS:When assessing the predictive accuracy across three animal datasets and two plant datasets covering 15 traits with varying heritabilities, ReaGP improved predictive performance by 14.41% and 7.78% over linear models specifically genomic best linear unbiased prediction (GBLUP) and BayesB, and by 34.41% and 10.09% over kernel methods namely support vector regression (SVR) and reproducing kernel Hilbert space (RKHS), respectively. ReaGP achieved a 4.35% enhancement on average compared to deep neural network genomic prediction (DNNGP). Furthermore, while ReaGP has more trainable parameters than DNNGP, it requires only half the number of floating-point operations. CONCLUSIONS:We introduced a novel deep learning method for genomic prediction, which integrates residual units, attention mechanisms and frequency-encoded genomic data. Comprehensive evaluation on pig, dairy cow, Huaxi cattle, wheat and rice datasets demonstrated that ReaGP was a promising tool for most traits. Thus, ReaGP could be considered as an efficient deep learning method for genomic prediction in farm animals and crops. The source code in this study is available at https://github.com/LiJing5467/ReaGP .

BACKGROUND:Cattle have undergone complex evolutionary trajectories shaped by domestication, migration, and selection. Although runs of homozygosity (ROH) are a ubiquitous genomic feature, their full potential to decipher the evolutionary history and functional consequences in global cattle populations remains underexplored. We analyzed whole-genome sequences from 102 breeds across 17 geographic regions to conduct a global investigation of ROH landscapes, population structure, genomic inbreeding, and functional variants. RESULTS:ROH patterns revealed elevated homozygosity burdens in intensively selected European breeds, whereas South Chinese indicine showed a high short ROH burden, suggestive of a unique ancient demography. ROH-based principal component analysis (PCA) and admixture delineated taurine-indicine lineages, region-specific ancestries, inbreeding, and breeding effects. ROH-based inbreeding coefficient (FROH) exhibited greater stability for cross-population inbreeding assessment, showing a high correlation with excess of homozygosity-based inbreeding coefficient (FHOM) and a negative association with heterozygosity. Region-specific ROH hotspots, identified via permutation test, reflected a combination of local adaptation and demographic legacies. Trait-focused analyses, cross-validated with multiple selection scans, identified genes underlying growth, milk, and climate adaptation. Notably, we found missense mutations in CHEK2, SPG7, FANCA, and MSRB3, whose frequencies were significantly correlated with temperature and humidity. CONCLUSION:This study establishes ROH as a pivotal genomic marker for illuminating the dynamics of domestication, migration, inbreeding, and selection. Our findings offer valuable resources and insights for advancing genetic conservation and precision breeding in cattle under the pressures of climate change.

Genomic research is currently undergoing a paradigm shift from reliance on a single reference sequence to the use of breed-specific genomes. Chinese indicine cattle (Bos taurus indicus), characterized by their notable tick resistance and heat tolerance, display extensively genetic diversity than taurine. Here, we generated a chromosome level genome assembly of Chinese indicine cattle, achieving a contiguity N50 of 90.92 Mb and an overall size of 2.91 Gb, utilizing PacBio high-fidelity (HiFi) sequencing complemented by Hi-C sequencing technology. The assembly is characterized by near-complete chromosomes, telomeres, and less gaps. Utilizing this highly quality assembly, we explored the phylogenetic relationship and speciation time. The gene family and selection signatures analyses indicated that candidate genes and biosynthetic pathways potentially contributing to disease immunity and thermotolerance of indicine cattle. Altogether, this study enriches the bovine pangenome repository and advances our understanding of the complex evolutionary patterns and distinctive adaptation traits of Chinese indicine cattle.

The genetic dissection of complex traits in livestock continues to pose a significant challenge in the field of animal genetics and breeding. Although traditional genome-wide association studies (GWAS) are capable of localizing genetic variants associated with specific traits, they are insufficient to elucidate the underlying physiological mechanisms. An integrated analysis of multi-trait GWAS and multi-transcriptomic data systematically identifies key tissues and cell types influencing complex traits in beef cattle and elucidates their genetic regulatory basis. We systematically mapped tissue- and cell-type-specific regulatory architectures underlying 20 economically important traits in beef cattle. Tissue-level analyses revealed distinct trait-tissue associations: fatty acid traits, including C16:0 and C20:4, were enriched in liver; carcass traits, including marbling score and carcass weight, in renal cortex/medulla and longissimus dorsi muscle; meat-quality traits such as pH in cartilaginous tissues; and total fat content in bone marrow. At cellular resolution, analysis of eight trait-associated tissues identified 38 discrete cell types. Myofibers were significantly associated with most carcass traits, including rib-eye area and backfat thickness, whereas hepatocytes emerged as key regulators of fatty acid and meat-quality traits, such as C16:0 and crude protein content. Transcription factor analysis identified cell-type-specific regulators: TBX15, SOX6, and TCF12 in myofibers; FOXA2 and NR1H4 in hepatocytes; and IRF8 and IKZF1 in microglia. Notably, hepatocytes and microglia showed complementary, trait-specific association patterns: hepatocytes were enriched for C16:0 associated saturated fatty-acid metabolic pathways, while microglia were enriched for C16:1 and unsaturated fatty-acid–related pathways, suggesting potential cross-tissue coordination in lipid regulation. Our study links specific tissues and cell types to phenotypic variation in beef cattle and identifies core transcriptional regulators and pathways driving trait variation. These cell-resolved maps provide mechanistic insight into how genetic variation shapes economically important traits, offering a valuable resource for functional studies, cell-informed precision breeding strategies, and the design of large-scale molecular phenotyping.

Genome-wide association study (GWAS) analyses have identified numerous loci associated with economic traits in cattle. Many of these loci reside in noncoding regions, and the regulatory mechanisms through which they influence complex traits remain poorly understood. Here, we integrated 657 RNA-seq libraries from 275 Huaxi cattle across three tissues (longissimus dorsi muscle, liver, and subcutaneous backfat) with ∼ 10 million imputed SNP genotypes to systematically map cis-molecular quantitative trait loci (cis-molQTLs) across four transcriptomic regulatory layers: gene expression (eQTLs), splicing (sQTLs), alternative polyadenylation (aQTLs), and RNA editing (edQTLs). These cis-molQTL classes display distinct genomic distributions and functional enrichments, yet operate in a coordinated manner within complex trait regulatory networks and are significantly enriched near GWAS- and QTLdb-reported loci for growth, carcass, and meat quality traits. Using 1788 genotyped and phenotyped Huaxi cattle, a GREML framework showed that these multi-layer cis-molQTL SNPs collectively explain 61.9% of total SNP-based heritability across 19 complex traits. Incorporating cis-molQTL annotations into genomic prediction models, including MultiBLUP, BayesRC, and molGBLUP, improved prediction accuracy for most traits relative to the baseline GBLUP model (mean increase of 0.05), highlighting the value of multi-layer regulatory variation for functionally informed genomic prediction and precision breeding.

Salt stress constrains poplar growth. The mitogen-activated protein kinase (MAPK) cascade and phytohormones are key regulators of plant salt tolerance. However, the mechanisms by which MAPK cascades orchestrate hormone homeostasis under salt stress in poplar are still poorly understood. This study shows that overexpressing PeMPK7 improved poplar salt tolerance. After 12 h of NaCl treatment, salicylic acid and abscisic acid (ABA) contents in PeMPK7-overexpressing poplars were significantly higher than in wild-type plants (P < 0.05). Transcriptomic profiling revealed that PeMPK7 reprogrammed phytohormone metabolism and signaling pathways, notably up-regulating ethylene (ET) biosynthesis genes (ACS1, ACO1) together with genes associated with indole-3-acetic acid, cytokinin, ABA, gibberellic acid, and jasmonic acid. Weighted gene co-expression network analysis suggested that PeMPK7 may act upstream of NAC072, NAC002, and TGA7, which are associated with ABA metabolism and signaling under salt stress. Among differentially expressed transcription factor genes, PagERF114 expression was induced by salt in PeMPK7-overexpressing plants and could be boosted by exogenous ET. Transgenic poplars overexpressing PagERF114 displayed enhanced salt tolerance, lower MDA content, and higher SOD/POD activities, demonstrating that PagERF114 enhances salt tolerance. Taken together, our findings suggest that PeMPK7 fine-tunes phytohormone homeostasis and partially enhances salt tolerance through an ethylene-associated pathway involving PagERF114.

Integrative use of multi-omics data can enhance genomic prediction, yet its application remains challenged by the high cost, temporal specificity, and instability of transcriptomic signals across developmental stages. To address these limitations, it is crucial to utilize small, high-quality multi-omics datasets to efficiently identify stable, major-effect SNPs that can be applied to larger populations with genomic data alone. We propose AbGP (Attention-based Genomic Prediction), a framework designed to extract these robust genomic features. Using a discovery population of Huaxi cattle (HX_A, n = 218) with matched genotype and transcriptome data, AbGP employed a self-attention mechanism to identify a compact, high-value subset of SNPs (top 1.25

The functions of noncoding variants associated with complex traits in livestock remain poorly understood. In this study, we investigated two candidate noncoding variants within the XKR4-CHCHD7 locus identified from our previous analysis. Dual-luciferase reporter assays demonstrated allele-specific regulatory activity of these two regions in bovine muscle satellite cells (BMSCs), 293T cells, and C2C12 cells. Endogenous deletion of the candidate regions using a clustered regularly interspaced short palindromic repeats (CRISPR)-based high-fidelity Cas12Max (hfCas12Max) system revealed that the region containing chr14:22840845 (SNP-0845) exerted broader effects on BMSC function including reduced proliferation and migration, altered cell-cycle progression, and enhanced myogenic differentiation. Expression screening of candidate effector genes further identified PENK and TMEM68 as downstream candidate genes for SNP-0845. Rescue experiments further showed that PENK exerted stronger recovery effects than TMEM68 on the proliferation and migration defects caused by deletion of this region, supporting PENK as a major candidate effector downstream of the SNP-0845. Functional assays showed that PENK knockdown impaired BMSC proliferation and migration while promoting myogenic differentiation, whereas PENK overexpression partially reversed these effects. In vivo Penk knockdown reduced quadriceps femoris weight and altered muscle fiber composition in mice. Collectively, our findings suggest that a noncoding regulatory region modulates BMSC fate and muscle growth-related processes through PENK.

Spermatogenesis is a highly orchestrated germ cell differentiation process involving the dynamic regulation of cell fate transitions. Dissecting the molecular landscapes of spermatogenic cell types is crucial for identifying fertility-related problems and improving the reproductive performance of farm animals. Here, we conducted transcriptomic and chromosome spreading across meiotic stages of testicular cells from taurine cattle (Bos taurus), yak (Bos grunniens), and their hybrid progenies to describe the transcriptional landscape of normal spermatogenesis and identify potential regulators that are involved in hybrid sterility. The results revealed seven types of spermatogonia, ten spermatocytes and ten types of spermatids in the cattle or yak testes. In sharp contrast, the testes of the cattle-yak hybrids contained only seven spermatogonial subtypes and six types of spermatocytes. Notably, the arrest of spermatocytes at the diplotene-to-diakinesis transition was accompanied by defects in double-strand break repair. In the testes of backcrossed offspring, spermatogenic arrest was partially rescued, and round spermatozoa were produced. By performing joint analysis, we identified 115 genes that exhibited differential protein abundance in spermatocytes of cattle-yak. Among them, 24 genes carrying genomic structural variations were differentially expressed in spermatocytes of cattle-yak but recovered in those of backcrossed offspring. This work provides important insights into spermatogenesis in large animals and serves as a valuable resource for identifying the factors determining reproductive isolation.

ABSTRACTFungal pathogens secrete effectors that suppress the hypersensitive response (HR) of the host, characterised by programmed cell death, facilitating colonisation. However, how effectors manipulate host cell death remains poorly understood. In this study, we discovered that the Puccinia striiformis effector PNPi (Puccinia NPR1 interactor) suppressed BAX‐induced cell death in Nicotiana benthamiana. This virulence was mediated by the FtsN domain of PNPi, and an enhanced suppression effect was observed when Ser129 was mutated into arginine. Further RNA‐sequencing analysis revealed that auxin signalling was disturbed, with the auxin‐responsive protein IAA29‐like (NbIAA29) being downregulated during cell death suppression by PNPi. Exogenous application of auxins alleviated cell death suppression in N. benthamiana. Silencing NbIAA29 enhanced the PNPi‐induced suppression; however, this effect was reduced in NbIAA29‐silenced plants pretreated with auxins. Additionally, we confirmed the in vivo interaction between PNPi and TaIAA14, which is the homologous gene of NbIAA29 in wheat. Knocking down TaIAA14 through virus‐induced gene silencing significantly increased the fungal development and reduced wheat cell death response. Overall, these results indicate that the P. striiformis effector PNPi suppresses the cell death response by targeting TaIAA14 to facilitate infection, advancing our understanding of how P. striiformis effectors manipulate host immunity and providing a theoretical basis for new strategies of sustainable disease control.

Hybrids between closely related but genetically incompatible species are often inviable or sterile. Cattle-yak, an interspecific hybrid of yak and cattle, exhibits male-specific sterility, which limits the fixation of its desired traits and prevents genetic improvement in yak through crossbreeding. Transcriptome profiles of testicular tissues have been generated in cattle, yak, and cattle-yak; however, the genetic variations underlying differential gene expression associated with hybrid sterility have yet to be elucidated. We detected differences in the cellular composition and gene expression of testes from yak and cattle-yak at 3 mo of age, 10 mo of age, and adulthood. Histological analysis revealed that the most advanced germ cells were gonocytes (prospermatogonia) at 3 mo and spermatocytes at 10 mo. Complete spermatogenesis occurred in the seminiferous tubules of adult yak, whereas only spermatogonia and a limited number of spermatocytes were detected in the testis of adult cattle-yak. Transcriptome analysis revealed 180, 6,310, and 6,112 differentially expressed genes (DEG) in yak and cattle-yak at each stage, respectively. Next, we examined the spermatogenic cell types in the backcross generation (BC1) and detected the appearance of round spermatids, indicating the partial recovery of spermatogenesis in these animals. Compared with those in cattle-yak, 272 DEG were identified in the testes of BC1 animals. Notably, we discovered that the expression of X chromosome-linked genes was upregulated in the testis of cattle-yak compared with yak, suggesting a possible abnormality in the process of meiotic sex chromosome inactivation in hybrid animals. We next screened DEG harboring structural variations (SV) and identified a list of SV genes associated with spermatogonial development, meiotic recombination, and double-strand break repair. Furthermore, we found that the SV genes ESCO2 (establishment of sister chromatid cohesion N-acetyltransferase 2) and BRDT (bromodomain testis associated) may be involved in meiotic arrest of cattle-yak spermatocytes. Overall, our research provides a valuable database for identifying structural variant loci that contribute to hybrid sterility.

Genetic variants, many of which are in mitochondrial DNA (mtDNA), contribute to hearing loss. Screening for these variants facilitates the identification of potential carriers, as many people with these mutations do not show hearing loss at birth but show late-onset hearing loss. We conducted a population-based cohort study involving 180,458 neonates born in Beijing, China. Hearing screening was performed through detailed counseling and systematic health assessment. The patient's peripheral blood was collected, and the variants was screened by next generation sequencing. An investigation of 142 probands and their matrilineal family members indicated a homoplasmic or heteroplasmic mtDNA mutation (adenine-to-guanine mutation at position 1555 in mtDNA 12S rRNA [A1555G] or cytosine-to-thymine mutation at position 1494 in mtDNA 12S rRNA) incidence of 0.227% (409 individuals). In total, 71.8% of the probands carried the homoplasmic A1555G mutation, 21.1% had the heteroplasmic A1555G mutation, and the remaining 7.1% had the homoplasmic cytosine-to-thymine mutation at position 1494 in mtDNA 12S rRNA mutation. A mtDNA haplotype analysis showed that 50.8% of the cases belonged to haplogroup D, the predominant haplotype in this Chinese population. Individuals with haplogroups B and M, which accounted for 10.7% and 9.0% of all cases, respectively, tended to have lower hearing thresholds at higher frequencies. We found no significant difference in the rate of hearing loss between vaccinated and unvaccinated individuals with mtDNA mutations, suggesting that the amounts of aminoglycoside antibiotics contained in vaccines were insufficient to induce hearing loss. This study reveals the incidence of mtDNA variants in the largest population studied to date and establishes that carriers of mtDNA variants can safely receive vaccines with no or low aminoglycoside antibiotic levels. This study provides a paradigm for studying the impact of these mtDNA variants on disease pathogenesis and the effects of mediation strategies.

The combination of random mutagenesis and high-throughput screening is an effective strategy for optimizing protein secretion in Bacillus subtilis. However, this strategy is often limited by reliance on activity-dependent screening. Here, we developed a CATCHFIRE (chemically assisted tethering of chimera by fluorogenic-induced recognition) system-based screening method for the quantification of secreted protein, in which the small peptide FIREtag (11 amino acids) was fused to the C-terminus of a target protein, and the secretion of this protein could be detected via fluorescence after addition of the FIREmate (114 amino acids) and the fluorogenic inducer compound match540. The feasibility of this method was demonstrated by monitoring the secretion of five proteins and optimizing the secretion of a nanobody via screening of a signal peptide library and a random mutagenesis library. Together, this study offers a versatile and high-throughput screening method for optimizing target protein secretion in B. subtilis.

The F-box only protein (FBXO) family plays a critical role in protein ubiquitination, but the absence of research on the FBXO family in cattle (Bos taurus) persists. In this study, 38 FBXO family members in cattle were identified and analyzed for the first time. Phylogenetic analysis demonstrated evolutionary conservation of FBXO members across Bovinae and model species, suggesting conserved biological functions. Using transcriptomic data, three muscle-specific FBXO genes (FBXO31, FBXO32, FBXO40) were identified. Importantly, silencing these genes in bovine skeletal muscle satellite cells affected the expression of genes involved in cell proliferation and differentiation. Furthermore, EdU staining and CCK8 assays revealed that silencing FBXO32 and FBXO40 accelerated cell proliferation. These findings indicate that these FBXO genes may influence myogenesis. Collectively, the present study identified and analyzed the FBXO family members in cattle and revealed their potential effects on cattle muscle development, offering new insights for improving beef yield and quality.

[This corrects the article DOI: 10.1371/journal.pone.0322026.].

Bacillus licheniformis is a spore-forming bacterium with probiotic, environmental, and industrial applications. Many wild strains with diverse functions have been described in recent years. Nevertheless, the lack of efficient and universal genetic manipulation tools hinders the study and engineering of these strains. Here, a versatile and simple genetic manipulation toolkit is established for B. licheniformis. The cornerstone of this toolkit is a conjugative DNA transfer system. This system could effectively transfer temperature-sensitive plasmid pTSMK into all ten tested B. licheniformis strains, with efficiencies ranging from 10-5 to 10-3. Based on this DNA transfer system, the tools for maker-free knockout and knock-in, CRISPRi, as well as transposon mutagenesis, were built. A transposition frequency of 7.68 × 10-3 was observed. The toolkit developed in this study fulfills most tasks in the engineering of this species and will promote the basic and applied research of B. licheniformis.

BACKGROUND: Fatty acid composition is a complex trait governed by a polygenic architecture. Although numerous genetic variants associated with fatty acids have been identified through genome-wide association studies (GWAS), the underlying regulatory mechanisms remain incompletely understood. In this study, we employed a multi-omics approach to deeply dissect the genetic regulation of fatty acids in cattle. RESULTS: Our integrated multi-strategy GWAS framework identifies 118,697 candidate variants spanning 4,234 distinct genes associated with fatty acid compositions. Parallel expression quantitative trait locus analyses across 227 muscle and 116 adipose tissue samples reveal 673,478 significant variant-gene pairs. By integrating multi-omics datasets, including DNA methylation, histone modifications, and chromatin accessibility, we systematically annotate the regulatory landscape of fatty acid associated variants. This comprehensive analysis identifies genes, such as SCD and ACAA2, as key regulators of fatty acid synthesis and metabolism. We further characterize a regulatory variant, chr26:21,274,156, located within the same topologically associating domain as the SCD promoter and enhancer elements, potentially facilitating a 3D chromatin-mediated cis-regulation within the locus. Functional validation through dual-luciferase reporter assays and CRISPR/Cas9-mediated perturbation confirm that this variant enhances transcriptional activity and directly modulates fatty acid profiles. CONCLUSIONS: By integrating multi-omics profiles, this study provides new insights into the genetic regulation of fatty acid synthesis and metabolism. Our findings highlight target genes, regulatory elements, and functional variants that influence fatty acids, offering valuable targets for the genetic improvement of meat quality in livestock.

Cattle carcass traits are economically important in the beef industry. In the present study, we identified 184 significant genes and 822 alternative genes for 7 carcass traits using genome-wide association studies(GWAS) in 1,566 Huaxi beef cattle. We then identified 5,860 unique cis-genes and 734 trans-genes in 227 longissimus dorsi muscle(LDM) samples to better understand the genetic regulation of gene expression. Our integration study of the GWAS and cis-eQTL analysis detected 13 variants regulating 12 identical genes, in which one variant was also detected in fine-mapping analysis. Moreover, using a transcriptome-wide association study(TWAS), we identified 4 genes(TTC30B, HMGA1, PRKD3 and FXN) that were significantly related to carcass chest depth(CCD), carcass length(CL), carcass weight(CW) and dressing percentage(DP). This study identified variants and genes that may be useful for understanding the molecular mechanism of carcass traits in beef cattle.

The genetic improvement of beef cattle breeds is crucial for the advancement of the beef cattle industry. Whole-genome resequencing technology has been widely applied in genetic breeding as well as research on selection signatures in beef cattle. In this study, 20× whole-genome resequencing was performed on 282 Angus cattle from the Ningxia region, and a high-quality dataset encompassing extensive genomic variations across the entire genome was constructed. The iHS test identified 495 selection signal regions, which included pregnancy-associated glycoprotein (PAG) family genes and immune-related genes such as UL16-binding protein 21 (ULBP21), CD1b molecule (CD1B), and tumor necrosis factor ligand superfamily member 11 (TNFSF11). A quantitative trait locus (QTL) enrichment analysis revealed that several economic traits, including longissimus muscle area, marbling score, carcass weight, average daily gain, and milk yield, were significantly enriched in cattle with these selection signatures. Although the enrichment of QTLs for health traits was low, immune-related genes may indirectly contribute to improvements in production performance. These findings show the genetic basis of economic and adaptive traits in Ningxia Angus cattle, providing a theoretical foundation and guidance for further genetic improvement and breeding strategies.