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Animals
Special Issues
Genomic Prediction in Livestock
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Genomic Prediction in Livestock

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 1630

Special Issue Editor

Dr. Yiren Gu

E-Mail Website
Guest Editor
Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China
Interests: genetic breeding of pigs; functional genomics; molecular breeding

Special Issue Information

Dear Colleagues,

Genomic prediction is the process of using genetic data to predict an individual’s phenotype, which has been implemented in many livestock breeding processes to increase genetic gain and accelerate the breeding process. This Special Issue will focus on papers related to recent progress on genomic prediction, specifically in livestock, including swine, cattle, goat, and sheep. Topics may include new knowledge of genomic prediction of economic traits, applications of multi-omics data and machine learning algorithms in genomic prediction, and novel methods of genomic prediction (such as multi-trait genomic prediction).

In this Special Issue, original research articles and reviews are welcome.

Dr. Yiren Gu
Guest Editor

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

  • genomic prediction
  • livestock
  • economic traits
  • omics
  • multi-trait genomic prediction
  • GWAS

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

15 pages, 2854 KiB  
Article
Chromosome-Level Genome Assembly of the Meishan Pig and Insights into Its Domestication Mechanisms
by Huipeng Du, Jianchao Hu, Zhiyan Zhang and Zhongzi Wu
Animals 2025, 15(4), 603; https://doi.org/10.3390/ani15040603 - 19 Feb 2025
Viewed by 436
Abstract
Pigs are essential agricultural animals, and among the various breeds, the Meishan pig, a native breed of China, is renowned for its high reproductive performance. This breed has been introduced to many countries to enhance local pig breeding programs. However, there have been [...] Read more.
Pigs are essential agricultural animals, and among the various breeds, the Meishan pig, a native breed of China, is renowned for its high reproductive performance. This breed has been introduced to many countries to enhance local pig breeding programs. However, there have been limited genomic and population genetics studies focusing on Meishan pigs. We created a chromosomal-level genomic assembly using high-depth PacBio sequencing and Illumina sequencing data collected from a Meishan pig. Additionally, we analyzed whole-genome sequencing (WGS) data from Chinese boars and Meishan pigs to identify domestication selection signals within the Meishan breed. The assembled genome of the Meishan pig (MSjxau) was found to be 2.45 Gb in size, with a scaffold length of 139.17 Mb. The quality value was 37.06, and the BUSCO score was 96.2%, indicating good completeness, continuity, and accuracy. We annotated transposable elements, segmental duplication, and genes in the MSjxau genome. By combining these data with 28 publicly available genomes, we provide a high-quality structural variants resource for pigs. Furthermore, we identified 716 selective sweep intervals between Chinese wild pigs and Meishan pigs, where the selected gene PGR may be linked to the high fertility observed in Meishan pigs. Our study offers valuable genomic and variation resources for pig breeding and identifies several genes associated with the domestication of the Meishan pig. This lays the groundwork for further investigation into the genetic mechanisms behind complex traits in pigs. Full article
(This article belongs to the Special Issue Genomic Prediction in Livestock)
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16 pages, 1360 KiB  
Article
Resequencing Composite Kazakh Whiteheaded Cattle: Insights into Ancestral Breed Contributions, Selection Signatures, and Candidate Genetic Variants
by Aigerim K. Khamzina, Alexander V. Igoshin, Zhadyra U. Muslimova, Asset A. Turgumbekov, Damir M. Khussainov, Nikolay S. Yudin, Yessengali S. Ussenbekov and Denis M. Larkin
Animals 2025, 15(3), 385; https://doi.org/10.3390/ani15030385 - 29 Jan 2025
Viewed by 813
Abstract
This study investigates the genetic architecture of the Kazakh Whiteheaded (KWH) cattle, applying population genetics approaches to resequenced genomes. FST analysis of 66 cattle breeds identified breeds for admixture analysis. At K = 19, the composite KWH breed showed contributions from Hereford, [...] Read more.
This study investigates the genetic architecture of the Kazakh Whiteheaded (KWH) cattle, applying population genetics approaches to resequenced genomes. FST analysis of 66 cattle breeds identified breeds for admixture analysis. At K = 19, the composite KWH breed showed contributions from Hereford, Altai, and Kalmyk cattle. Principal component analysis and ancestry inference confirmed these patterns, with KWH genomes comprising 45% Hereford, 30% Altai, and 25% Kalmyk ancestries. Haplotype analysis revealed 73 regions under putative selection in KWH, some shared with Hereford (e.g., with the gene DCUN1D4) and some KWH-specific (e.g., with the gene SCMH1). FST analysis identified 105 putative intervals under selection, with key genes (KITLG, SLC9C1, and SCMH1) involved in coat colour and physiological adaptations. Functional enrichment using The Database for Annotation, Visualization, and Integrated Discovery (DAVID) in selected regions highlighted clusters associated with developmental processes, ubiquitination, and fatty acid metabolism. Point FST identified 42 missense variants in genes enriched in functions related to economically important traits. Local ancestry inference revealed genomic intervals with predominantly non-Hereford ancestry, including high Altai (e.g., SCAPER) and Kalmyk (e.g., SRD5A2) contributions, while Hereford-dominated regions included genes ENO1 and RERE. This work elucidates the genomic contributions and adaptive signatures of selection shaping the KWH breed, providing candidate genetic variants for breeding program improvement and enhanced genome predictions. Full article
(This article belongs to the Special Issue Genomic Prediction in Livestock)
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