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Special Issue Conference on the 25th International Colloquium on Animal...
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Special Issue Conference on the 25th International Colloquium on Animal Cytogenetics and Genomics, Naples June 26–29, 2024

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 30 October 2025 | Viewed by 1494

Special Issue Editors

Dr. Leopoldo Iannuzzi

E-Mail Website
Guest Editor
Institute for Animal Production System in Mediterranean Environment, National Research Council, 80055 Portici, Italy
Interests: animal clinical cytogenetics; environmental cytogenetics; evolutionary animal cytognetics; molecular cytogenetics
Special Issues, Collections and Topics in MDPI journals
Dr. Sara Albarella

E-Mail Website
Guest Editor
Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137 Naples, Italy
Interests: animal cytogenetics; animal genetics; molecular basis of embryo development; congenital malformations; DNA extraction methods; disorders of sex development; biomonitoring
Special Issues, Collections and Topics in MDPI journals
Dr. Pietro Parma

E-Mail Website
Guest Editor
Department of Agricultural and Environmental Sciences, Milano University, 20131 Milano, Italy
Interests: clinical cytogenetics; molecular cytogenetics; bio-informatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The 25th International Colloquium on Animal Cytogenetics and Genomics (https://icacg2024.org/) is dedicated to the memory of Dr. James (Jim) Womack, a pioneer in gene mapping, mainly in cattle. The meeting was organized into ten sessions, beginning with the General Opening Session 1, which featured three main lectures highlighting the fields of animal cytogenetics and genomics.

The nine other sessions covered a large spectrum of the animal cytogenetics and genomics fields, such as  (a) Animal Diagnostics, (b) Advanced Genomics in Water Buffalo, (c) Comparative Cytogenetics and Genomics, (d) Mutagenesis and Biomonitoring using Cytogenetic and Genomic Tests, (e) Cytogenetics and Genomics of Non-Mammalian Vertebrates, (f) Advances in Animal Genomics and Epigenomics, (g) Cytogenetic and Genomic Characterization of Animal Biodiversity, (h) Cytogenetics and Genomics of Invertebrates, (i) Poster session covering all the aspects treated in the previous specific sessions.

Among the research studies presented, those related to animal genomics were more prevalent than those that focused solely on cytogenetics. However, several abstracts combined the two disciplines (Cytogenomics) to provide a deeper understanding of animal genomes and to better identify latent chromosome abnormalities related to fertility. Various genomic approaches were reported, aimed at improving the selection of animals for productive traits, disease resistance, and animal biodiversity.

The aim of the present Special Issue Conference is to group together many important contributions presented at the meeting in a unique volume constituting a point of reference in animal cytogenetics and genomics and, at the same time, to create a basis for further developments in these scientific fields.

The present Special Issue Conference is now open to all groups participating in the meeting for MS submissions, such as MS-review, original MS, or short communications.

Dr. Leopoldo Iannuzzi
Dr. Sara Albarella
Dr. Pietro Parma
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • animal diagnostics
  • advanced genomics in water buffalo
  • comparative cytogenetics and genomics
  • mutagenesis and biomonitoring using cytogenetic and genomic tests
  • cytogenetics and genomics of non-mammalian vertebrates
  • advances in animal genomics and epigenomics
  • cytogenetic and genomic characterization of animal biodiversity
  • cytogenetics and genomics of invertebrates

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Published Papers (3 papers)

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13 pages, 1925 KB  
Article
Cytogenetic Screening on Mediterranean Italian River Buffalo Males Intended for Reproduction and Females with Fertility Issues—A Pilot Study
by Angela Perucatti, Francesca Ciotola, Ramona Pistucci, Sara Albarella, Viviana Genualdo, Cristina Rossetti, Roberta Cimmino, Nadia Piscopo, Evaristo Di Napoli, Domenico Incarnato, Orlando Paciello, Vincenzo Peretti, Pietro Parma and Leopoldo Iannuzzi
Animals 2025, 15(18), 2654; https://doi.org/10.3390/ani15182654 - 10 Sep 2025
Viewed by 513
Abstract
In Italy, karyotype analysis is routinely performed on all young males intended for reproduction to screen for chromosome abnormalities. This practice gained prominence following the identification of a complex chromosome abnormality in a well-known bull named Magnifico and its progeny. This procedure significantly [...] Read more.
In Italy, karyotype analysis is routinely performed on all young males intended for reproduction to screen for chromosome abnormalities. This practice gained prominence following the identification of a complex chromosome abnormality in a well-known bull named Magnifico and its progeny. This procedure significantly enhances the value of the Mediterranean Italian River Buffalo breed, particularly in the context of artificial insemination both within Italy and in other countries importing semen. In the current study, 159 young Mediterranean Italian River Buffalo (MIRB) males intended for reproduction, 30 females with fertility issues, 3 young females and a male co-twin were investigated by analyzing their karyotype using both CBA- and RBA-banding. All males displayed a normal karyotype (2n = 50, XY), although one animal displayed an abnormal X-chromosome with C-band polymorphism, as it is C-band negative when this chromosome normally shows the largest C-band among all chromosomes. This result was also confirmed by the FISH-mapping technique using three bovine BAC-clones containing SAT-I, SAT-III and SAT-IV. Cytogenetic investigation showed that seven females, along with one male co-twin, were affected by freemartinism (XX/XY leukocyte chimerism) and were subsequently removed from the farm. In two of these females, clinical and necroscopic examinations showed severe damage of the internal reproductive organs. Full article
(This article belongs to the Special Issue Special Issue Conference on the 25th International Colloquium on Animal Cytogenetics and Genomics, Naples June 26–29, 2024)
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14 pages, 2090 KB  
Technical Note
A Strategy for Single-Run Sequencing of the Water Buffalo Genome: (II) Fast One-Step Assembly of Highly Continuous Chromosome Sequences
by Elvira Toscano, Leandra Sepe, Federica Di Maggio, Marcella Nunziato, Angelo Boccia, Elena Cimmino, Arcangelo Scialla, Francesco Salvatore and Giovanni Paolella
Animals 2025, 15(20), 3014; https://doi.org/10.3390/ani15203014 - 17 Oct 2025
Viewed by 215
Abstract
Genome sequencing has possibly been the greatest step in the development of advanced tools for animal genetic improvement: knowledge of gene sequences and use of haplotype markers for productivity traits can provide important improvements in yield production and optimisation of reproductive program. Next-generation [...] Read more.
Genome sequencing has possibly been the greatest step in the development of advanced tools for animal genetic improvement: knowledge of gene sequences and use of haplotype markers for productivity traits can provide important improvements in yield production and optimisation of reproductive program. Next-generation and, more recently, third-generation sequencing techniques enormously increased the ability to produce sequences from single individuals and increased the interest in exome or whole-genome sequencing as an alternative to SNP chips in breeding programs as these techniques allowed for the capture of a wider range of variations, including characterisation of rare variants, structural variations, and copy number changes. Here, we present a procedure, based on fast de novo assembly and a scaffolding step, to quickly build an almost complete genome starting from long reads obtained in a single sequencing run. The procedure, applied to sequences from five water buffaloes, was able to independently build, for each individual, an almost complete high-quality genome with highly continuous chromosome sequences; in most cases, over 90% of the length of the reference chromosome was covered by less than ten long contigs. Unlike other pipelines based on slower assemblers or which require many sequencing data, in 1–2 days, the proposed procedure can go from a single run to continuous genome assembly, supporting fast analysis of large chromosome structures, potentially useful for improving animal breeding and productivity. Full article
(This article belongs to the Special Issue Special Issue Conference on the 25th International Colloquium on Animal Cytogenetics and Genomics, Naples June 26–29, 2024)
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16 pages, 2086 KB  
Technical Note
A Strategy for Single-Run Sequencing of the Water Buffalo Genome: (I) the Use of Third-Generation Technology to Quickly Produce Long, High-Quality Reads
by Federica Di Maggio, Marcella Nunziato, Elvira Toscano, Leandra Sepe, Roberta Cimmino, Emanuela Antonella Capolongo, Alessandra Vasco, Giovanni Paolella and Francesco Salvatore
Animals 2025, 15(20), 2991; https://doi.org/10.3390/ani15202991 - 15 Oct 2025
Cited by 1 | Viewed by 228
Abstract
(1) Background: Water buffaloes (Bubalus bubalis) are important for dairy and meat production. Up to now, genomic analysis has focused on female subjects, leaving the Y chromosome essentially unknown. Advances in third-generation sequencing (TGS) made it possible to improve the study [...] Read more.
(1) Background: Water buffaloes (Bubalus bubalis) are important for dairy and meat production. Up to now, genomic analysis has focused on female subjects, leaving the Y chromosome essentially unknown. Advances in third-generation sequencing (TGS) made it possible to improve the study of complex genome sequences, such as buffalo and other mammalian species including humans. (2) Methods: In this study, we applied TGS-based long-read sequencing to generate, in one step, high-quality whole-genome sequences, which can take full advantage of a rapid bioinformatic pipeline, such as that described in the companion paper. (3) Results: Five male buffalo genomes have been fully sequenced at relatively high depth (20–40×) which, combined with the read length typical of TGS, provide the basis for important insights into male-specific genetic traits, including those linked to meat and milk production. (4) Conclusions: With the use of TGS technologies, we offer a complete strategy for fast, one-step genome sequencing which can also be applied to other farm animals with a comparably large genome. This approach can help in revealing genetic features characteristic of an animal individual beyond the simple assessment of a number of SNPs or other known sequence variations, thus supporting improved genetic selection for dairy productivity and future research on genetic variability in buffalo breeds. Full article
(This article belongs to the Special Issue Special Issue Conference on the 25th International Colloquium on Animal Cytogenetics and Genomics, Naples June 26–29, 2024)
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