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Molecular Progression of Genetics in Breeding of Farm Animals
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Molecular Progression of Genetics in Breeding of Farm Animals

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 May 2025 | Viewed by 1768

Special Issue Editor

Dr. Karel Novák

E-Mail Website
Guest Editor
Department of Genetics and Breeding, Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic
Interests: genetics; breeding of farm animals

Special Issue Information

Dear Colleagues,

Molecular breeding in farm animal species has contributed to the widespread use of the technology of genome-wide genotyping arrays. For organizational, economic, and regulatory reasons, this technology has started to be used faster than in biomedicine. However, the large-scale application of array-based genomic selection also involves a significant simplification of breeding. As a result, current developments are moving towards the widespread application of whole-genome sequencing, as can be illustrated by the example of major species. More accurate data should allow for the variability contained in commercial populations and genetic resources to be exploited more fully and efficiently. Full knowledge of functional variation across the genome also makes it possible to mitigate the negative side effects of breeding based on a limited number of economic parameters. The same challenge can be addressed by targeted resequencing and characterization of functional variation in immunity-related genes. Breeding for health traits based on this information should be a potential solution for sustainable breeding programs. This Special Issue aims to summarize the current status of applied genome sequencing in livestock species and the detailed use of variability in genes responsible for health traits.

Dr. Karel Novák
Guest Editor

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Keywords

  • farm animal
  • livestock
  • genome sequencing

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Published Papers (2 papers)

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Research

18 pages, 24816 KiB  
Article
Insights into Adaption and Growth Evolution: Genome–Wide Copy Number Variation Analysis in Chinese Hainan Yellow Cattle Using Whole–Genome Re–Sequencing Data
by Ziqi Zhong, Ziyi Wang, Xinfeng Xie, Deyou Pan, Zhiqing Su, Jinwei Fan, Qian Xiao and Ruiping Sun
Int. J. Mol. Sci. 2024, 25(22), 11919; https://doi.org/10.3390/ijms252211919 - 6 Nov 2024
Viewed by 422
Abstract
Copy number variation (CNV) serves as a crucial source of genomic variation and significantly aids in the mining of genomic information in cattle. This study aims to analyze re–sequencing data from Chinese Hainan yellow cattle, to uncover breed CNV information, and to elucidate [...] Read more.
Copy number variation (CNV) serves as a crucial source of genomic variation and significantly aids in the mining of genomic information in cattle. This study aims to analyze re–sequencing data from Chinese Hainan yellow cattle, to uncover breed CNV information, and to elucidate the resources of population genetic variation. We conducted whole–genome sequencing on 30 Chinese Hainan yellow cattle, thus generating 814.50 Gb of raw data. CNVs were called using CNVnator software, and subsequent filtering with Plink and HandyCNV yielded 197,434 high–quality CNVs and 5852 CNV regions (CNVRs). Notably, the proportion of deleted sequences (81.98%) exceeded that of duplicated sequences (18.02%), with the lengths of CNVs predominantly ranging between 20 and 500 Kb This distribution demonstrated a decrease in CNVR count with increasing fragment length. Furthermore, an analysis of the population genetic structure using CNVR databases from Chinese, Indian, and European commercial cattle breeds revealed differences between Chinese Bos indicus and Indian Bos indicus. Significant differences were also observed between Hainan yellow cattle and European commercial breeds. We conducted gene annotation for both Hainan yellow cattle and European commercial cattle, as well as for Chinese Bos indicus and Indian Bos indicus, identifying 206 genes that are expressed in both Chinese and Indian Bos indicus. These findings may provide valuable references for future research on Bos indicus. Additionally, selection signatures analysis based on Hainan yellow cattle and three European commercial cattle breeds identified putative pathways related to heat tolerance, disease resistance, fat metabolism, environmental adaptation, candidate genes associated with reproduction and the development of sperm and oocytes (CABS1, DLD, FSHR, HSD17B2, KDM2A), environmental adaptation (CNGB3, FAM161A, DIAPH3, EYA4, AAK1, ERBB4, ERC2), oxidative stress anti–inflammatory response (COMMD1, OXR1), disease resistance (CNTN5, HRH4, NAALADL2), and meat quality (EHHADH, RHOD, GFPT1, SULT1B1). This study provides a comprehensive exploration of CNVs at the molecular level in Chinese Hainan yellow cattle, offering theoretical support for future breeding and selection programs aimed at enhancing qualities of this breed. Full article
(This article belongs to the Special Issue Molecular Progression of Genetics in Breeding of Farm Animals)
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15 pages, 8438 KiB  
Article
Role of Csdc2 in Regulating Secondary Hair Follicle Growth in Cashmere Goats
by Heqing Zhu, Yingying Li, He Xu, Yuehui Ma, Göran Andersson, Erik Bongcam-Rudloff, Tiantian Li, Jie Zhang, Yan Li, Jilong Han and Min Yang
Int. J. Mol. Sci. 2024, 25(15), 8349; https://doi.org/10.3390/ijms25158349 - 30 Jul 2024
Viewed by 1060
Abstract
Cashmere goats possess two types of hair follicles, with the secondary hair follicles producing valuable cashmere fiber used for textiles. The growth of cashmere exhibits a seasonal pattern arising from photoperiod change. Transcription factors play crucial roles during this process. The transcription factor, [...] Read more.
Cashmere goats possess two types of hair follicles, with the secondary hair follicles producing valuable cashmere fiber used for textiles. The growth of cashmere exhibits a seasonal pattern arising from photoperiod change. Transcription factors play crucial roles during this process. The transcription factor, cold-shock domain, containing C2 (Csdc2) plays a crucial role in modulating cell proliferation and differentiation. Our preceding research indicated that the expression of Csdc2 changes periodically during anagen to telogen. However, the mechanisms of Csdc2 in regulating SHF growth remain unclear. Here, we found that the knockdown of Csdc2 inhibits the proliferation of dermal papilla cells. ChIP-Seq analysis showed that Csdc2 had a unique DNA binding motif in SHFs. Through conjoint analysis of ChIP-Seq and RNA-Seq, we revealed a total of 25 candidate target genes of Csdc2. Notably, we discovered a putative Csdc2 binding site within roundabout guidance receptor 2 (Robo2) on chromosome 1 of the goat genome. Furthermore, qRT-PCR and dual-luciferase reporter assay confirmed Csdc2’s positive regulatory influence on Robo2. These findings expand the research field of hair follicle transcriptional regulatory networks, offering insights into molecular breeding strategies to enhance cashmere production in goats. Full article
(This article belongs to the Special Issue Molecular Progression of Genetics in Breeding of Farm Animals)
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