Animal genetics最新文献

{"title":"Genetic parameters, genome-wide associations and potential candidate genes for additive and dominance effects of tail traits in Merinoland sheep based on whole-genome sequence data in a selection experiment","authors":"Johanna Mainzer,&nbsp;Tong Yin,&nbsp;Isabella Giambra,&nbsp;Hannah Hümmelchen,&nbsp;Petra Engel,&nbsp;Henrik Wagner,&nbsp;Axel Wehrend,&nbsp;Sven König","doi":"10.1111/age.70041","DOIUrl":"10.1111/age.70041","url":null,"abstract":"<p>The aim of this study was an in-depth genomic analysis for tail length (TL), tail characteristics and body measurements in the Merinoland sheep breed considering whole-genome sequence data. Genomic analyses included the estimation of genetic parameters and dominance effects, genome-wide associations for the additive and dominance component, and the annotation of potential candidate genes. We implemented a unified selection and mating experiment to create extreme lamb groups based on breeding values for TL. The 254 lambs from the mating experiment were phenotyped at birth for TL, tail circumference, and body length (all in cm), for body weight, and X-rayed to count the number of vertebrae and to identify tail abnormalities for tail fractures, axis deviations, block vertebrae, and wedged vertebrae. Heritabilities using the variant-based relationship matrix were large for the morphological measurements TL (0.85), body length (0.93), and body weight (0.85), moderate for tail circumference (0.21), and number of vertebrae (0.29), but close to zero for tail abnormalities. Dominance variance for TL explained 14.95% of the phenotypic variation, but was close to zero for the remaining tail traits. The positive breeding value correlations indicate longer and thicker tails for taller and heavier lambs. Breeding value correlations were negative between TL with block vertebrae and wedged vertebrae. Genome-wide associations for additive-genetic and dominance effects revealed 726 significant variants, which are located close to potential candidate genes. These candidate genes have known functions on skeletal growth, and regulate the development of bone structures and of vertebrae characteristics.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12445261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Survey of functional Mendelian variants in New Zealand Huntaway and Heading dog breeds","authors":"Florence Smith,&nbsp;Thomas Lopdell,&nbsp;Melissa Stephen,&nbsp;Millicent Henry,&nbsp;Keren Dittmer,&nbsp;Hayley Hunt,&nbsp;Nick Sneddon,&nbsp;Liam Williams,&nbsp;Jack Rolfe,&nbsp;Dorian Garrick,&nbsp;Mathew D. Littlejohn","doi":"10.1111/age.70042","DOIUrl":"10.1111/age.70042","url":null,"abstract":"<p>New Zealand (NZ) Huntaway and Heading dogs are working breeds that play active roles on farms across NZ. While these breeds are common in NZ, they are not well-known elsewhere, and little is understood about their genetic make-up. Here, we used whole genome sequencing to provide a comprehensive genomic view of 249 working dogs. As first use of this resource, we report the allele frequencies of provisionally functional variants aggregated from the Online Mendelian Inheritance in Animals (OMIA) database. Of 435 “probably causal” variants, 27 segregated in our sample. Notable examples of disease variants potentially actionable for selection include those in the <i>CUBN</i>, <i>CLN8</i>, <i>SGSH</i>, <i>SOD1</i>, <i>VWF</i>, and <i>VPS13B</i> genes. These findings will enable genetic testing and selection opportunities to help improve the health and performance of future generations of these unique breeds.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12445248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring genetic diversity and population structure of Myanmar indigenous chickens using double digest restriction site-associated DNA sequencing","authors":"Su Lai Yee Mon,&nbsp;Moe Lwin,&nbsp;Aye Aye Maw,&nbsp;Lat Lat Htun,&nbsp;Saw Bawm,&nbsp;Yukio Nagano,&nbsp;Atsushi J. Nagano,&nbsp;Kotaro Kawabe,&nbsp;Yasuhiko Wada,&nbsp;Shin Okamoto,&nbsp;Takeshi Shimogiri","doi":"10.1111/age.70038","DOIUrl":"https://doi.org/10.1111/age.70038","url":null,"abstract":"<p>This study used double-digest restriction site-associated DNA sequencing to investigate the genetic diversity and population structure of eight populations of Myanmar indigenous chickens (MICs). We conducted genetic diversity and population structure analyses of indigenous chickens from Myanmar and other Asian countries and commercial chickens. A total of 20 261 autosomal SNPs were used. The expected heterozygosity of the eight populations of MICs ranged from 0.259 ± 0.175 (MYN_FCN) to 0.282 ± 0.152 (MYN_YGN), and the observed heterozygosity ranged from 0.245 ± 0.187 (MYN_FCN) to 0.265 ± 0.164 (MYN_YGN). The population structure analyses suggested that MICs possessed a genetic cluster that is limited in many chicken populations in this study. In addition, three distinct groups were found among Myanmar and Asian populations. We then identified differentially selected regions (DSRs) among these groups to understand their differences: 48 DSRs between Myanmar fighting chickens and MICs, 54 DSRs between Myanmar fighting chickens and a group of Myanmar and Asian indigenous chickens, and 48 DSRs between MICs and a group of Myanmar and Asian indigenous chickens. Gene Ontology enrichment analysis revealed certain significant genes in those group-pairs. The results revealed genetic differences between Myanmar and other Asian chickens.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.70038","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144869856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotype concordance and trait mapping efficacy comparing data from the Equine 670 K SNP array with whole genome sequence in 21 horses","authors":"Samantha L. Van Buren,&nbsp;Jessica L. Petersen,&nbsp;C. Titus Brown,&nbsp;Carrie J. Finno","doi":"10.1111/age.70037","DOIUrl":"https://doi.org/10.1111/age.70037","url":null,"abstract":"<p>With advancing genomic technologies, single-nucleotide polymorphism (SNP) arrays and whole genome sequencing (WGS) have become essential tools in equine genetic research. In this study, we assessed the concordance in SNP calls and trait-mapping efficacy by comparing data of 21 horses both genotyped on the Equine 670 K SNP array and sequenced at either ~12× or ~30× depth. Our analysis revealed that higher sequencing depths were significantly associated with fewer discordant calls between platforms. Additionally, we investigated the most frequent no-call and discordant positions and identified positions that were indels or multiallelic in the WGS. To assess the effectiveness of the 670 K SNP array vs. WGS in trait association studies, we mapped the chestnut coat color. Both technologies showed a clear peak at the expected locus, although neither association had loci reaching Bonferroni-corrected statistical significance, which was not statistically possible in this small group of horses. The findings of this study provide valuable insights for making informed decisions when selecting between SNP arrays and WGS at varying sequencing depths for equine genomic research applications.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144853680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A recessive deleterious missense variant in PEX7 causes a lethal form of chondrodysplasia in Bazadaise cattle","authors":"Cécile Grohs,&nbsp;Stéphanie Minéry,&nbsp;Sébastien Fritz,&nbsp;Mekki Boussaha,&nbsp;Aurélien Capitan","doi":"10.1111/age.70035","DOIUrl":"https://doi.org/10.1111/age.70035","url":null,"abstract":"&lt;p&gt;The term ‘bulldog calves’ colloquially refers to a heterogeneous group of skeletal malformations, typically characterized by severe craniofacial deformities reminiscent of the brachycephalic appearance of Bulldog dogs. These conditions include type II achondrogenesis, spondyloepimetaphyseal dysplasia, and rhizomelic chondrodysplasia punctata (RCDP) caused by mutations of &lt;i&gt;COL2A1&lt;/i&gt;, &lt;i&gt;ACAN&lt;/i&gt;, and &lt;i&gt;GNPAT&lt;/i&gt;, respectively (Boulling et al., &lt;span&gt;2025&lt;/span&gt;; Bourneuf et al., &lt;span&gt;2017&lt;/span&gt;; Cavanagh et al., &lt;span&gt;2007&lt;/span&gt;; Daetwyler et al., &lt;span&gt;2014&lt;/span&gt;).&lt;/p&gt;&lt;p&gt;Since 2020, four ‘bulldog calves’ (two males, two females) have been reported to the French National Observatory for Bovine Abnormalities by the breeding society of the local Bazadaise breed. All were stillborn and exhibited disproportionate dwarfism, characterized by craniofacial dysmorphism, shortened limbs with hypermobile joints, and low birth weight despite a normal gestation length (~20–25 kg vs. 40 kg; Figure 1a,b). Ear biopsies were obtained from three cases, but no specimens were available for comprehensive pathological examination due to rapid carcass disposal.&lt;/p&gt;&lt;p&gt;Pedigree analysis using the PEDIG software package (Boichard, &lt;span&gt;2002&lt;/span&gt;) identified a single common ancestor four to seven generations back across all lineages, supporting a recessive mode of inheritance (Figure 1c).&lt;/p&gt;&lt;p&gt;Homozygosity mapping using the Illumina EuroGMD SNP array (Boichard et al., &lt;span&gt;2018&lt;/span&gt;) and established methods (Boulling et al., &lt;span&gt;2025&lt;/span&gt;; Mesbah-Uddin et al., &lt;span&gt;2019&lt;/span&gt;) revealed a significant peak on chromosome 9, defined by a 74-marker haplotype homozygous in all cases and none of 223 controls (Bonferroni-adjusted &lt;i&gt;p&lt;/i&gt; &lt; 0.01; Figure 1d).&lt;/p&gt;&lt;p&gt;The whole genome of an affected calf was sequenced as described by Boulling et al. (&lt;span&gt;2025&lt;/span&gt;). After excluding variants present in a control panel of 1869 cattle from over 70 non-Bazadaise breeds (dataset described in Besnard et al., &lt;span&gt;2024&lt;/span&gt;), 16 candidate variants remained within the associated interval (NC_037336.1:73 454 255–79 825 274 bp; ARS-UCD1.2 genome assembly; Table S1). Among them, only the NC_037336.1:g.74831677G&gt;T substitution in the gene encoding peroxisomal biogenesis factor 7 (PEX7), leading to a p.Asp205Tyr amino acid change, was predicted to be deleterious (SIFT score = 0.01). Interestingly, mutations in &lt;i&gt;PEX7&lt;/i&gt; and four other genes involved in peroxisomal protein import or ether phospholipid synthesis (&lt;i&gt;PEX5&lt;/i&gt;, &lt;i&gt;AGPS&lt;/i&gt;, &lt;i&gt;FAR1&lt;/i&gt;, and &lt;i&gt;GNPAT&lt;/i&gt;) have been implicated in human RCDP (de Vet et al., &lt;span&gt;1998&lt;/span&gt;; Devi et al., &lt;span&gt;2021&lt;/span&gt;; Dodt et al., &lt;span&gt;1995&lt;/span&gt;; Motley et al., &lt;span&gt;1997&lt;/span&gt;; Ofman et al., &lt;span&gt;1998&lt;/span&gt;; Purdue et al., &lt;span&gt;1997&lt;/span&gt;).&lt;/p&gt;&lt;p&gt;Furthermore, as outlined in the introduction, our team identified a recessive &lt;i&gt;GNPAT&lt;/i&gt; variant as the cause of the RCDP subtype of bulldog calves in Aubra","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.70035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144832512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery of a regulatory polymorphism in the bovine PICALM gene associated with milk αS1-casein concentration","authors":"Mélissa Poncet,&nbsp;Maureen Féménia,&nbsp;Maxime Ben-Braiek,&nbsp;Mathieu Charles,&nbsp;Nathalie Duprat,&nbsp;Katarzyna Chałaśkiewicz,&nbsp;Arnaud Boulling,&nbsp;Hiroaki Taniguchi,&nbsp;Véronique Blanquet,&nbsp;Dominique Rocha","doi":"10.1111/age.70036","DOIUrl":"https://doi.org/10.1111/age.70036","url":null,"abstract":"","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144810945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of bovine leukocyte antigen – DRB3 genotyping using nanopore sequencing","authors":"Takenori Arai,&nbsp;Yu-ichi Kanetsuna,&nbsp;Saki Miyake,&nbsp;Saki Uehara,&nbsp;Kazuya Nagai,&nbsp;Kei-ich Matsuda,&nbsp;Toh-ichi Hirata,&nbsp;Yusuke Sakai,&nbsp;Takashi Matsuzaki,&nbsp;Shinji Yamada,&nbsp;Hirokazu Hikono,&nbsp;Kenji Murakami","doi":"10.1111/age.70033","DOIUrl":"https://doi.org/10.1111/age.70033","url":null,"abstract":"<p>The <i>bovine leukocyte antigen DRB3</i> (<i>BoLA-DRB3</i>) gene, a crucial component of major histocompatibility complex class (MHC) II, influences disease susceptibility and production traits in cattle. Conventional PCR – (Sanger)-sequence-based typing (PCR-SBT) – has limitations, including time-intensive processing and phase ambiguity issues. We developed a nanopore-sequencing-based method for <i>BoLA-DRB3</i> genotyping. The full-length gene (10.9 kbp) was amplified from blood samples of 109 Japanese Black cattle and sequenced using Oxford Nanopore Technologies’ nanopore MinION. The method achieved high-quality metrics, with a mean coverage of 99.97%, an average sequencing depth of 2599× and a mean <i>Q</i>-score of 20.5. Perfect reference sequence alignment was obtained in 92.7% (101/109) of samples. Alleles of all samples showed complete concordance with the set of PCR-SBT typing results for exon 2. The entire process was completed within 3 days (6 h of hands-on time), substantially reducing the time and cost requirements compared with other methods. This nanopore sequencing method provides accurate <i>BoLA-DRB3</i> genotyping while resolving phase ambiguity through full-length molecule analysis, presenting a potential new standard for bovine MHC genotyping.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.70033","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144767444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prediction of essential liver transcription factors in response to fat deposition in pigs based on changes in transposase-accessible chromatin signals","authors":"Katarzyna Piórkowska,&nbsp;Kacper Żukowski,&nbsp;Katarzyna Kowalska,&nbsp;Katarzyna Ropka-Molik,&nbsp;Mirosław Tyra","doi":"10.1111/age.70032","DOIUrl":"https://doi.org/10.1111/age.70032","url":null,"abstract":"<p>Pigs have been altered throughout the decades to increase the meat content in their carcasses. However, this has led to a reduction in fat levels in subcutaneous, visceral, and intramuscular fats, where intramuscular fat is crucial for flavor. The current study used combined RNA-assay for transposase-accessible chromatin (ATAC) sequencing analysis to identify key transcription factors (TFs) that might regulate important molecular mechanisms associated with fat deposition in the livers of pigs. In this study, two native Złotnicka White pig groups were used that significantly differed in terms of their fat content. RNA-seq identified 272 genes as being differentially expressed (showing &gt;1.2 fold change) and ATAC-seq identified 6333 significant peaks (differentially accessible regions [DARs]) in the transcription start site (TSS) flanking region. Ninety-eight genes overlapped between the RNA and ATAC seq results, and these differentially expressed genes–DARs were included in a subsequent motif analysis. The TRRUST and MEME tools were used to identify crucial TFs, which predicted possible binding TF motifs based on TSS ATAC peaks. The candidate TFs suggested in the present study for fat deposition in pigs are SREBP1, ATF4, KLF11, RORA, and MYC, whose DNA-binding motif sequence was enriched in DAR overlapping TSS. Moreover, for MYC, ATF4, and KLF11 TFs, DARs were identified within the TSS flanking regions. The present study aimed to pinpoint the key liver TFs that are indirectly related to fat deposition in pigs.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144767446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic imprinting at a porcine ZNF locus via a canonical imprinting mechanism","authors":"Jinsoo Ahn,&nbsp;In-Sul Hwang,&nbsp;Mi-Ryung Park,&nbsp;Seongsoo Hwang,&nbsp;In-Cheol Cho,&nbsp;Kichoon Lee","doi":"10.1111/age.70034","DOIUrl":"https://doi.org/10.1111/age.70034","url":null,"abstract":"<p>Genomic imprinting causes parent-of-origin dependent gene expression, primarily driven by a subset of germline differentially methylated regions that function as imprinting control regions at promoter-associated CpG islands. While these mechanisms have been investigated in depth in mice and humans, our understanding of the molecular basis of genomic imprinting in pigs remains limited, particularly at a non-orthologous porcine locus. This study aimed to investigate a pig locus displaying a canonical DNA methylation-dependent imprinting pattern and explore its potential involvement in transcription-coupled imprinting mechanisms. By comparing parthenogenetic and control porcine day-21 embryos, we identified a maternally methylated differentially methylated region in a previously uncharacterized pig locus, <i>LOC100520903</i> (<i>ZNF300-like</i>), which may serve as an imprinting control region. This was accompanied by a significantly higher paternal mRNA expression of <i>LOC100520903</i> in control embryos compared to parthenogenetic embryos (<i>p</i> &lt; 0.05), as detected by RNA-seq. At this locus, a previously unannotated transcript with an alternative first exon located far upstream was predominantly expressed in oocytes (supported by &gt;10 RNA-seq junction reads), alongside a promoter marked by H3K4me3 and an adjacent long terminal repeat element (<i>E</i>-value = 5.8e-62). This transcript was no longer detected from embryogenesis onward (0 reads), at which point the annotated <i>LOC100520903</i> transcripts became expressed. Concurrently, oocyte-specific DNA methylation was observed at the CpG island of the <i>LOC100520903</i> gene promoter, indicative of maternal methylation. Moreover, in the pig liver and brain, paternal monoallelic expression was consistently observed based on haplotype-tagged RNA-seq reads. Our findings provide mechanistic insights into genomic imprinting at the porcine <i>LOC100520903</i> locus.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.70034","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144751634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative analysis of cattle (Bos taurus, 2n = 60) and river buffalo (Bubalus bubalis, 2n = 50) genome assemblies reveals two evolutionary conserved inversions and invalid centromere–telomere orientation of some autosomes","authors":"Ramona Pistucci,&nbsp;Ilaria Cascone,&nbsp;Alessandra Iannuzzi,&nbsp;Sara Albarella,&nbsp;Wiktoria Kowal-Mierzwa,&nbsp;Michele Zannotti,&nbsp;Leopoldo Iannuzzi,&nbsp;Pietro Parma","doi":"10.1111/age.70031","DOIUrl":"https://doi.org/10.1111/age.70031","url":null,"abstract":"<p>This study investigates autosome evolution between river buffalo (<i>Bubablus bubalis</i>, BBU) and cattle (<i>Bos taurus</i>, BTA), two closely related species within the <i>Bovidae</i> family. Despite differences in chromosome numbers (2<i>n</i> = 60 in cattle and 2<i>n</i> = 50 in river buffalo), previous cytogenetic studies have shown high autosome similarity. However, standard banding techniques have limitations in detecting small-scale genomic rearrangements. Using molecular comparisons, this study identifies two previously undetected chromosomal inversions: a 30-Mb inversion on BBU7 (compared to BTA6) and a 4-Mb inversion on BBU14 (compared to BTA13). These findings were validated through bioinformatics analyses (genomic alignments and BLAST searches) and confirmed via fluorescence in situ hybridization technique. In addition, it has been shown that several river buffalo chromosomes are shown inverted in the genome assembly considered in this study (NDDB_SH_1). The study highlights that autosome evolution in <i>Bovidae</i> involves not only centric fusions but also cryptic intra-chromosomal rearrangements. These results contribute to a deeper understanding of genome evolution in closely related species and demonstrate the importance of high-resolution molecular techniques in uncovering hidden genomic changes.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 4","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.70031","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144716555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}