Genome-wide association study reveals that the IBSP locus affects ear size in cattle.

Ear size is a classical model for hot climate adaptation following the evolution, but the genetic basis of the traits associated with ear size remains to be elucidated. Here, we performed a genome-wide association study on 158 cattle to explain the genetic mechanism of ear size. One region on BTA6 between 36.79 and 38.80 Mb included 50 suggestive SNPs and 4 significant SNPs that were significantly associated with ear size. The most significant locus (P = 1.30 × 10-8) was a missense mutation (T250I) on the seventh exon of integrin-binding sialoprotein (IBSP), which had an allele substitution effect of 23.46 cm2 for ear size. Furthermore, this mutation will cause changes in the three-dimensional structure of the protein. To further identify genes underlying this typical feature, we performed a genome scan among nine cattle breeds with different ear sizes by using SweeD. Results suggested that IBSP was under positive selection among four breeds with relatively large ear sizes. The expression levels of IBSP in ear tissues of large- and small-ear cattle were significantly different. A haplotype diversity survey of this missense mutation in worldwide cattle breeds strongly implied that the origin of this missense mutation event was Bos taurus. These findings have important theoretical importance for the exploration of major genes associated with ear size and provide important molecular markers for the identification of cattle germplasm resources.

Whole genome analyses revealed genomic difference between European taurine and East Asian taurine.

European taurine and East Asian taurine are two main clades in Bos taurus, but their genomic differences are not clearly elucidated. Here, we sequenced 16 Mongolian cattle genomes and compared them to the 92 genomes of 10 representative breeds worldwide. We found the highest LD level in Mishima cattle and the fastest LD decay in European taurine. Phylogenetic analysis revealed that Mongolian, Hanwoo and Mishima cattle were clustered into East Asian taurine. From selective sweep, gene annotation, functional enrichment and differential expression analysis, we identified selective signals including genes and/or pathways related to rapid growth and large body size in European taurine, and superior meat quality in East Asian taurine. Our findings will help us understand the evolutionary history and formation process of the breeds and provide theoretical materials regarding the genetic mechanism underlying breed characteristics and molecular breeding programmes of the taurine clades in the future.

Whole-genome resequencing reveals diversity, global and local ancestry proportions in Yunling cattle.

Yunling cattle, a three-breed cross consisting of 1/2 Brahman cattle, 1/4 Murray Grey cattle and 1/4 Yunnan Yellow cattle, has advantage of rapid growth, good meat quality, enhanced tolerance towards a hot and humid climate, tick resistance and crude feed forbearance. Here, we investigated the genetic diversity, global and local ancestry proportions by sequencing the genomes of 131 Yungling cattle and 31 Brahman cattle (for control). Furthermore, we used 35 published genomes of ancestry breeds (including Angus cattle [ancestry of Murray Grey], Wannan cattle [ancestry of Yunnan Yellow cattle: Wenshan and Dianzhong], Wenshan and Dianzhong cattle) to characterize the formation process of Yunling cattle. The highest nucleotide diversity was found in the Wannan cattle, followed by Wenshan, Dianzhong, Brahman, Yunling and Angus cattle. The results of LD decay in each breed was largely consistent with the results of nucleotide diversity, except for the faster decay in Angus cattle out of a smaller effective population size and a strong bottleneck during the breed formation. The population-structure analysis revealed that the cross-breed Yunling cattle harboured the ancestry with Angus (0.44), Brahman (0.48) and Wannan cattle (0.08). Subsequently, we used RFmix to infer local ancestry in Yunling cattle and then performed chi-squared test to obtain the segments whose proportions of a certain ancestry were excessive compared with the whole-genome level, leading to 391 Angus, 49 Brahman and 2,312 Wannan segments. Gene annotation and KEGG enrichment analysis revealed that the excessive Angus, Brahman and Wannan segments might contribute to the rapid growth, immune resistance and indigenous adaptation, respectively, in Yunling cattle. Our results help understand ancestry components and formation process in Yunling cattle and will provide an opportunity for selective breeding by molecular approaches in future.

Genome-wide association study identifies genomic loci associated with flight reaction in cattle.

Lower flight reaction is closely related to higher production in cattle, but the genetic basis of lower flight reaction is not clearly understood. Here, we sampled a total of 45 Brahman cattles and 166 Yunling cattles with flight distance (FD), and 73 Brahman cattles and 288 Yunling cattles with crush score (CS) and flight speed (FS), whereas there were 45 Brahman cattles and 161 Yunling cattles with all three traits. The FD, CS and FS in Brahman cattle were significantly lower than those in Yunling cattle. The flight reaction traits had negative correlation with conformational traits (e.g., body weight, withers height and body length). Based on SNPs derived from a subset of 162 whole genomes (25 Brahman genomes and 100 Yunling genomes with FD, 30 Brahman and 131 Yunling genomes with CS and FS), genome-wide association study with mixed linear model was performed to test potential associations between flight reaction traits and genomic variants. We identified five, two and two genomic loci suggestively associated with FD, CS and FS, respectively. Five out of five candidate genes for FD (LOC789753, LRP6, CTIF, SLC9A9 and ZEB1) were reported to be related to Alzheimer's disease representing cognitive impairment in human, which was consistent with the finding that cognitive-behavioural intervention decreased the FD of cows to human. In CS, a very strong association locus was assigned to CDH8, a cadherin involved in synaptic adhesion, axon outgrowth and guidance, whose deletion was associated with autism spectrum disorder. In FS, a very strong association locus was assigned to GABRG2, a gamma-aminobutyric acid (a major inhibitory neurotransmitter in brain) receptor, whose polymorphisms were associated with suicidal behaviour in schizophrenia patients. Our findings will provide targets for molecular-marker selection and genetic manipulation of cattle improvement to meeting the growing demand for lower flight reaction to human.

Wolbachia Infection Dynamics in Tribolium confusum (Coleoptera: Tenebrionidae) and Their Effects on Host Mating Behavior and Reproduction.

Wolbachia interact with their hosts in a broad variety of relationships that range from parasitism to mutualism. To improve the understanding of complex relationships between Wolbachia and host, we performed not only mating and crossing experiments to investigate effects of Wolbachia on mate choice, mating performance, and reproduction in the confused flour beetles Tribolium confusum (Jacquelin du Val), but also quantitative PCR to determine Wolbachia spatiotemporal infection density dynamics within beetles. Wolbachia induced strong cytoplasmic incompatibility, but had no effects on male mate choice and mating performance. Compared with Wolbachia-uninfected females, infected females had very high fecundity irrespective of male's infection status. Wolbachia infection densities in beetles were higher in eggs and adults and in the reproductive tissues and abdomens, whereas Wolbachia density in adults did not differ between sexes and among different ages. These results suggest that Wolbachia have evolved mutualistic interactions with T. confusum, which provides the first evidence of Wolbachia mutualisms in this beetle species. We discussed these findings and their evolutionary implications in light of Wolbachia-host interactions.

FZ-AD005, A Novel DLL3-Targeted Antibody-drug Conjugate with Topoisomerase I Inhibitor, Shows Potent Antitumor Activity in Preclinical Models.

Delta-like ligand 3 (DLL3) is overexpressed in small-cell lung cancer (SCLC) and has been considered an attractive target for SCLC therapy. Rovalpituzumab tesirine (Rova-T) was the first DLL3-targeted antibody-drug conjugate (ADC) to enter clinical studies. However, serious adverse events limited progress in the treatment of SCLC with Rova-T. In this study, we developed a novel DLL-3-targeted ADC, FZ-AD005, by using DXd with potent cytotoxicity and a relatively better safety profile to maximize the therapeutic index. FZ-AD005 was generated by a novel anti-DLL3 antibody FZ-A038 and a valine-alanine (Val-Ala) dipeptide linker to conjugate DXd. Moreover, Fc-silencing technology was introduced in FZ-AD005 to avoid off-target toxicity mediated by FcγRs and showed negligible Fc-mediated effector functions in vitro. In preclinical evaluation, FZ-AD005 exhibited DLL3-specific binding and demonstrated efficient internalization, bystander killing, and excellent in vivo antitumor activities in cell line-derived xenografts (CDX) and patient-derived xenograft (PDX) models. FZ-AD005 was stable in circulation with acceptable pharmacokinetic profiles in cynomolgus monkeys. FZ-AD005 was well tolerated in rats and monkeys. The safety profile of FZ-AD005 was favorable and the highest non-severely toxic dose was 30 mg/kg in cynomolgus monkeys. In conclusion, FZ-AD005 has the potential to be a superior DLL3-targeted ADC with a wide therapeutic window and is expected to provide clinical benefits for the treatment of SCLC patients.

Prognosis and influencing factors of follicular thyroid cancer.

OBJECTIVES: Follicular thyroid cancer (FTC) is prone to distant metastasis, and patients with distant metastasis often have poor prognosis. In this study, the impact of metastasis and other relevant factors on the prognosis of follicular thyroid carcinoma was examined. METHODS: This was a retrospective study. Data were obtained from Zhejiang Cancer Hospital, Sun Yat-sen University Cancer Center and Hangzhou First People's Hospital affiliated with Zhejiang University School of Medicine, from January 2009 to June 2021 for 153 FTC patients. The patients were assigned into three groups according to their distant metastasis: distant metastasis at initial diagnosis (M1), distant metastasis during follow-up (M2), and no evidence of distant metastasis over the course of the study (M0). Data were collected and summarized on clinical data, laboratory parameters, imaging features, postoperative pathologic subtypes, and metastases. The Cox proportional hazard model was used to perform the univariate and multivariate analysis. Kaplan-Meier curves were used to evaluate cancer-specific survival (CSS). RESULTS: Based on metastasis, the patients were assigned into three groups, including 31 in the M1 group, 15 in the M2 group, and 107 in the M0 group. These individuals were followed up for an average of 5.9 years, and the group included 46 patients with distant metastasis (31 confirmed at diagnosis and 15 found during follow-up). Univariate Cox regression analysis showed that age, Hashimoto's thyroiditis (HT), surgery method, postoperative adjuvant therapy, histologic subtype, nodule size, calcification, TSH, and distant metastasis all impacted prognosis. Multivariate Cox regression analysis suggested that histologic subtype (widely invasive; HR: 7.440; 95% CI: 3.083, 17.954; p < 0.001), nodule size (≥40 mm; HR: 8.622; 95% CI: 3.181, 23.369; p < 0.001) and distant metastasis (positive; HR: 6.727; 95% CI: 2.488, 18.186; p < 0.001) were independent risk factors affecting the prognosis of follicular thyroid cancer. CONCLUSIONS: Histologic subtype, nodule size, and distant metastasis are important risk factors for the prognosis of follicular thyroid cancer. Patients with metastatic follicular thyroid cancer have a poor prognosis, especially with metastasis at the time of initial diagnosis. As a result, this group of patients requires individualized treatment and closer follow-up.

AI diagnosis of Bethesda category IV thyroid nodules.

Thyroid nodules are a common disease, and fine needle aspiration cytology (FNAC) is the primary method to assess their malignancy. For the diagnosis of follicular thyroid nodules, however, FNAC has limitations. FNAC can classify them only as Bethesda IV nodules, leaving their exact malignant status and pathological type undetermined. This imprecise diagnosis creates difficulties in selecting the follow-up treatment. In this retrospective study, we collected ultrasound (US) image data of Bethesda IV thyroid nodules from 2006 to 2022 from five hospitals. Then, US image-based artificial intelligence (AI) models were trained to identify the specific category of Bethesda IV thyroid nodules. We tested the models using two independent datasets, and the best AI model achieved an area under the curve (AUC) between 0.90 and 0.95, demonstrating its potential value for clinical application. Our research findings indicate that AI could change the diagnosis and management process of Bethesda IV thyroid nodules.

Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity.

Unlike PIWI-interacting RNA (piRNA) in other species that mostly target transposable elements (TEs), >80% of piRNAs in adult mammalian testes lack obvious targets. However, mammalian piRNA sequences and piRNA-producing loci evolve more rapidly than the rest of the genome for unknown reasons. Here, through comparative studies of chickens, ducks, mice, and humans, as well as long-read nanopore sequencing on diverse chicken breeds, we find that piRNA loci across amniotes experience: (1) a high local mutation rate of structural variations (SVs, mutations ≥ 50 bp in size); (2) positive selection to suppress young and actively mobilizing TEs commencing at the pachytene stage of meiosis during germ cell development; and (3) negative selection to purge deleterious SV hotspots. Our results indicate that genetic instability at pachytene piRNA loci, while producing certain pathogenic SVs, also protects genome integrity against TE mobilization by driving the formation of rapid-evolving piRNA sequences.

Value of deep learning models based on ultrasonic dynamic videos for distinguishing thyroid nodules.

Objective: This study was designed to distinguish benign and malignant thyroid nodules by using deep learning(DL) models based on ultrasound dynamic videos. Methods: Ultrasound dynamic videos of 1018 thyroid nodules were retrospectively collected from 657 patients in Zhejiang Cancer Hospital from January 2020 to December 2020 for the tests with 5 DL models. Results: In the internal test set, the area under the receiver operating characteristic curve (AUROC) was 0.929(95% CI: 0.888,0.970) for the best-performing model LSTM Two radiologists interpreted the dynamic video with AUROC values of 0.760 (95% CI: 0.653, 0.867) and 0.815 (95% CI: 0.778, 0.853). In the external test set, the best-performing DL model had AUROC values of 0.896(95% CI: 0.847,0.945), and two ultrasound radiologist had AUROC values of 0.754 (95% CI: 0.649,0.850) and 0.833 (95% CI: 0.797,0.869). Conclusion: This study demonstrates that the DL model based on ultrasound dynamic videos performs better than the ultrasound radiologists in distinguishing thyroid nodules.

Comparisons of Hematological and Biochemical Profiles in Brahman and Yunling Cattle.

Brahman cattle are tolerant to parasite challenges and heat stress. Yunling cattle are three-way hybrids that are half Brahman cattle, a fourth Murray Grey cattle and a fourth Yunnan Yellow cattle, with good beef performance. The hematological and biochemical parameters can reflect the physiology and metabolic conditions of cattle, and there are valuable indicators of production performance and adaptability that can be found by studying the cattle. To assess the health status and differences, we compared 55 hematological and biochemical parameters of 28 Brahman cattle and 65 Yunling cattle using an automatic biochemical analyzer. Our results showed that 27 hematological and biochemical indices of Brahman cattle were lower than those of Yunling cattle, whereas the other parameters were higher. There are 20 indices with significant differences that were detected between Brahman and Yunling cattle (with p ≤ 0.01 or 0.01 ≤ p ≤ 0.05, respectively), and no significant differences were found for other indices (p > 0.05). Based on these results, Yunling cattle may have a better physical condition than Brahman cattle, may be better at adapting to local environments, and can maintain a good production and reproduction performance. As a new breed that is half Brahman, the abilities of Yunling cattle, including adaptability, stress resistance and tolerance to crude feed, were better than Brahman cattle under the same management conditions.

Genome-wide association study identifies quantitative trait loci affecting cattle temperament.

Cattle temperament is an interesting trait due to its correlation with production efficiency, labor safety, and animal welfare. To date, however, its genetic basis is not clearly understood. Here, we performed a genome-wide association study for a series of temperament traits in cattle, assessed with via open field and novel object tests, using autosomal single nucleotide polymorphisms (SNPs) derived from the whole-genome sequence. We identified 37 and 29 genome-wide significant loci in the open field and novel object tests, respectively. Gene set analysis revealed the most significant pathway was the neuroactive ligand-receptor interaction pathway, which may be essential for emotional control in cattle. Analysis of the expression levels of 18 tissue-specific genes based on transcriptomic data showed enrichment in the brain, with some candidate genes involved in psychiatric and neurodegenerative diseases in humans. Based on principal component analysis, the first principal component explained the largest variance in the open field and novel object test data, and the most significant loci were assigned to SORCS3 and SESTD1, respectively. Our findings should help facilitate cattle breeding for sound temperament by pyramiding favorable alleles to further improve cattle production.

Food to politics: Representations of genetically modified organisms in cartoons on the Internet in China.

Controversies around genetically modified (GM) food have become particularly prevalent in China. To understand the situation, 257 GM cartoons were collected from various Chinese online sources. We found that China's GM cartoons peaked during controversial social events from the end of 2012 to 2016, which is consistent with the Baidu Media Index on GM headline news. About 85% of the cartoons involve GM food and more than half of cartoons share scary information. The mainstream media is more neutral and not only presents the dilemma in choice but also promotes genetically modified organisms (GMOs). However, social media inclines toward a more pessimistic view, providing scary information and focusing on health risks and conspiracy theories. Controversial topics have fueled the spread of political conspiracy theories. Generally, scientists supporting GMOs have been criticized under suspicion of betraying their country, and the issue of GM food in China reflects strong political views.

Genomic analyses reveal distinct genetic architectures and selective pressures in Chinese donkeys.

Donkey (Equus asinus) is an important livestock animal in China because of its draft and medicinal value. After a long period of natural and artificial selection, the variety and phenotype of donkeys have become abundant. We clarified the genetic and demographic characteristics of Chinese domestic donkeys and the selection pressures by analyzing 78 whole genomes from 12 breeds. According to population structure, most Chinese domestic donkeys showed a dominant ancestral type. However, the Chinese donkeys still represented a significant geographical distribution trend. In the selective sweep, gene annotation, functional enrichment, and differential expression analyses between large and small donkey groups, we identified selective signals, including NCAPG and LCORL, which are related to rapid growth and large body size. Our findings elucidate the evolutionary history and formation of different donkey breeds and provide theoretical insights into the genetic mechanism underlying breed characteristics and molecular breeding programs of donkey clades.

Whole Genome Scan and Selection Signatures for Climate Adaption in Yanbian Cattle.

Yanbian cattle is inhabitant of North of China, exhibiting many phenotypic features, such as long, dense body hair, and abundant intramuscular fat, designed to combat the extreme cold climate adaption. In the current study, we studied the cold tolerance of nine Yanbian cattle by whole genome resequencing and compared with African tropical cattle, N'Dama, as a control group. Yanbian cattle was aligned to the Bos taurus reference genome (ARS-UCD1.2) yielding an average of 10.8 fold coverage. The positive selective sweep analysis for the cold adaption in Yanbian cattle were analyzed using composite likelihood ratio (CLR) and nucleotide diversity (θπ), resulting in 292 overlapped genes. The strongest selective signal was found on BTA16 with potential mutation in CORT gene, a regulatory gene of primary hormone in the hypothalamic-pituitary-adrenal (HPA) axis, is reported to be associated with the cold stress, representedfour missense mutations (c.269C > T, p.Lys90Ile; c.251A > G, p.Glu84Gly; c.112C > T, p.Pro38Ser; c.86G > A, p.Pro29His). Meanwhile another gene on BTA6, showed significantly higher selective sweep signals for a cold adapted trait for hair follicle and length development, FGF5 (fibroblast growth factor 5) with a missense mutation (c.191C > T, p.Ser64Phe). Moreover, cold adapted Yanbian cattle was statistically compared with the hot adapted N'Dama cattle, a taurine cattle reported to show superior heat tolerance than zebu cattle, making them better adapted to the hot regions of Africa. XP-CLR, Fst, and θπ ratio were used to compare both breeds, yielding 487, 924, and 346 genes respectively. Among the 12 overlapped genes, (CD36) (c.638A > G, p.Lys 213Arg) involved in fat digestion and absorption plays an important role in membrane transport of long-chain fatty acid and its expression could increase in cold exposure. Henceforth, our study provides a novel genetic insights into the cold climate adaptation of Yanbian cattle and identified three candidate genes (CORT, FGF5, and CD36), which can add to an understanding of the cold climate adaptation of Yanbian cattle.

BGVD: An Integrated Database for Bovine Sequencing Variations and Selective Signatures.

Next-generation sequencing has yielded a vast amount of cattle genomic data for global characterization of population genetic diversity and identification of genomic regions under natural and artificial selection. However, efficient storage, querying, and visualization of such large datasets remain challenging. Here, we developed a comprehensive database, the Bovine Genome Variation Database (BGVD). It provides six main functionalities: gene search, variation search, genomic signature search, Genome Browser, alignment search tools, and the genome coordinate conversion tool. BGVD contains information on genomic variations comprising ~60.44 M SNPs, ~6.86 M indels, 76,634 CNV regions, and signatures of selective sweeps in 432 samples from modern cattle worldwide. Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map, using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes (ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1). Signals of selection sweep are displayed as Manhattan plots and Genome Browser tracks. To further investigate and visualize the relationships between variants and signatures of selection, the Genome Browser integrates all variations, selection data, and resources, from NCBI, the UCSC Genome Browser, and Animal QTLdb. Collectively, all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale. BGVD is publicly available at http://animal.nwsuaf.edu.cn/BosVar.

Genome-Wide Association Study Identifies Genomic Loci Associated With Neurotransmitter Concentration in Cattle.

Abnormal neurotransmitter concentration is one of the factors that affect the health status, behavioral personality, and welfare level of animals, but the genetic basis of the abnormality is still largely unknown. The objective of this study is to identify putative genomic loci associated with neurotransmitter concentration in cattle. We measured serotonin (5HT), dopamine (DA), cortisol, glutamate (Glu), and ACTH concentrations in blood serum using double-antibody sandwich ELISA in 30 Brahman cattle and 127 Yunling cattle. Interestingly, we found that ACTH concentration was positively correlated with body weight, cannon circumference, and hip width (P < 0.05). Genome-wide association study (GWAS) was performed with mixed linear models using autosomal SNPs derived from the whole-genome sequence. We identified five, five, two, three, and five suggestive loci associated with 5HT, DA, cortisol, Glu, and ACTH concentration, respectively. These 20 associated loci implicated 18 candidate genes. For Glu concentration, the most significant association locus was assigned to MCHR1, a G-coupled receptor that could modulate glutamate release. For dopamine concentration, a very strong association locus was located in the intron of SLC18A2, which is a critical mediator of dopamine dynamics. However, for ACTH concentration, a very strong association locus was assigned to HTR1F, a G protein-coupled receptor that can influence the release of ACTH. Other candidate genes of interest identified for neurotransmitter concentration were PRMT6, GADD45A, PCCA, ANGPT1, ACCS, LOC100336971, TNR, GSDMA, CNTN3, CARMIL1, CDKAL1, RBFOX1, PCDH15, and LGALS12. Our findings will provide targets for the genetic improvement of neurotransmitter-related traits in domestic cattle and basic materials for studying the mechanism of neurotransmitter synthesis, release, and transport in human and animals.

Whole-genome analyses identify loci and selective signals associated with body size in cattle.

Body size plays a key role in production, health, selection, and environmental adaptation of animals, but the genetic basis of body size variation is not clearly understood. Here, we conducted genome-wide association studies (GWAS) of 15 body size traits using autosomal single nucleotide polymorphisms (SNPs) derived from whole-genome sequences of 31 Brahman cattle and 131 Yunling cattle and identified 20 significant loci, which implicated 18 candidate genes. For ischium width, the most significant SNP was assigned to LCORL, a famous gene controlling body size. For chest width, the most significant SNP was located upstream of BMP5, a secreted ligand of transformation growth factor-beta superfamily of proteins involved in bone and cartilage development. Subsequently, we detected selective sweeps in Brahman cattle using integrated Haplotype Score, composite likelihood ratio, and nucleotide diversity. The results showed CNTNAP5 locus associated with hip cross height and LIMCH1 locus associated with forehead size were in selective signals, which were consistent with higher hip cross height and higher forehead size in Brahman cattle compared with Yunling cattle. Our findings provide genetic insights into variation and selection of body size using GWAS and selective signals and will accelerate future efforts aimed at cattle improvement.

Genomic analyses reveal distinct genetic architectures and selective pressures in buffaloes.

BACKGROUND: The domestic buffalo (Bubalus bubalis) is an essential farm animal in tropical and subtropical regions, whose genomic diversity is yet to be fully discovered. RESULTS: In this study, we describe the demographic events and selective pressures of buffalo by analyzing 121 whole genomes (98 newly reported) from 25 swamp and river buffalo breeds. Both uniparental and biparental markers were investigated to provide the final scenario. The ancestors of swamp and river buffalo diverged ∼0.23 million years ago and then experienced independent demographic histories. They were domesticated in different regions, the swamp buffalo at the border between southwest China and southeast Asia, while the river buffalo in south Asia. The domestic stocks migrated to other regions and further differentiated, as testified by (at least) 2 ancestral components identified in each subspecies. Different signals of selective pressures were also detected in these 2 types of buffalo. The swamp buffalo, historically used as a draft animal, shows selection signatures in genes associated with the nervous system, while in river dairy breeds, genes under selection are related to heat stress and immunity. CONCLUSIONS: Our findings substantially expand the catalogue of genetic variants in buffalo and reveal new insights into the evolutionary history and distinct selective pressures in river and swamp buffalo.