Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
5.1
3.5
Journals
Genes
Special Issues
Functional Genomics and Breeding in Animals
share announcement

Functional Genomics and Breeding in Animals

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (15 April 2024) | Viewed by 5671

Special Issue Editors

Dr. Weimin Wang

E-Mail Website
Guest Editor
College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
Interests: economic trait; functional genomics; molecular breeding; genome selection; multi-omics; genomics and epigenomics
Dr. Xiang Zhou

E-Mail Website
Guest Editor
Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
Interests: pig; genome; RNA-seq; disease-resistant breeding; PRRSV
Special Issues, Collections and Topics in MDPI journals
Dr. Weiwei Wu

E-Mail Website
Guest Editor
Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, China
Interests: reproduction; biological breeding

Special Issue Information

Dear Colleagues,

Domestic animals are an economically important part of agriculture and provide an essential source of meat, wool, milk, fur, etc., for humans. To date, numerous genes and genetic variations associated with economic traits have been identified based on the strategies of candidate gene analysis and high-throughput sequencing technologies, but few major genes and causative mutations associated with complex traits have been discovered. Research on the functional genomics of animals offers opportunities to understand the genetic mechanisms that underpin complex traits of economic importance, and the identification of functional candidate genes and causative mutations are active research areas.

This Special Issue aims to present the new advances and insights on functional genomics and breeding in animals. We welcome original research articles and reviews addressing functional candidate genes or causative mutations associated with complex traits in animals (reproduction, feed efficiency, growth, meat quality and disease resistance, etc.). Contributions by experts in the field in the form of research papers and critical reviews are invited.

Dr. Weimin Wang
Dr. Xiang Zhou
Dr. Weiwei Wu
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. Genes is an international peer-reviewed open access monthly 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 2600 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

  • economic traits
  • gene expression
  • genetic markers
  • functional genomics
  • molecular breeding
  • genome selection
  • omics data

Published Papers (4 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Other

16 pages, 4161 KiB  
Article
Genetic Origin and Introgression Pattern of Pingliang Red Cattle Revealed Using Genome-Wide SNP Analyses
by Yuanqing Wang, Jun Ma, Jing Wang, Lupei Zhang, Junwei Hu, Minghao Ma, Lingyang Xu, Yan Chen, Bo Zhu, Zezhao Wang, Huijiang Gao, Junya Li and Xue Gao
Genes 2023, 14(12), 2198; https://doi.org/10.3390/genes14122198 - 11 Dec 2023
Viewed by 937
Abstract
The Pingliang red cattle, an outstanding indigenous resource in China, possesses an exceptional breeding value attributed to its tender meat and superior marbling quality. Currently, research efforts have predominantly concentrated on exploring its maternal origin and conducting conventional phenotypic studies. However, there remains [...] Read more.
The Pingliang red cattle, an outstanding indigenous resource in China, possesses an exceptional breeding value attributed to its tender meat and superior marbling quality. Currently, research efforts have predominantly concentrated on exploring its maternal origin and conducting conventional phenotypic studies. However, there remains a lack of comprehensive understanding regarding its genetic basis. To address this gap, we conducted a thorough whole-genome analysis to investigate the population structure, phylogenetic relationships, and gene flows of this breed using genomic SNP chip data from 17 bovine breeds. The results demonstrate that Pingliang red cattle have evolved distinct genetic characteristics unique to this breed, clearly distinguishing it from other breeds. Based on the analysis of the population structure and phylogenetic tree, it can be classified as a hybrid lineage between Bos taurus and Bos indicus. Furthermore, Pingliang red cattle display a more prominent B. taurus pedigree in comparison with Jinnan, Qinchuan, Zaosheng, Nanyang, and Luxi cattle. Moreover, this study also revealed closer genetic proximity within the Chinese indigenous cattle breed, particularly Qinchuan cattle, which shares the longest identical by descent (IBD) fragment with Pingliang red cattle. Gene introgression analysis shows that Pingliang red cattle have undergone gene exchange with South Devon and Red Angus cattle from Europe. Admixture analysis revealed that the proportions of East Asian taurine and Chinese indicine in the ancestry of Pingliang red cattle are approximately 52.44% and 21.00%, respectively, while Eurasian taurine, European taurine, and Indian indicine account for approximately 17.55%, 7.27%, and 1.74%. Our findings unveil distinct genetic characteristics in Pingliang red cattle and attribute their origin to B. taurus and B. indicus ancestry, as well as contributions from Qinchuan cattle, South Devon, and Red Angus. Full article
(This article belongs to the Special Issue Functional Genomics and Breeding in Animals)
►▼ Show Figures

Figure 1

15 pages, 5515 KiB  
Article
The Role of lncRNAs in Pig Muscle in Response to Cold Exposure
by Dongjie Zhang, Liang Wang, Wentao Wang and Di Liu
Genes 2023, 14(10), 1901; https://doi.org/10.3390/genes14101901 - 30 Sep 2023
Viewed by 1057
Abstract
Cold exposure is an essential factor affecting breeding efforts in cold regions. Muscle, as an important tissue for homeothermic animals, can produce heat through shivering thermogenesis (ST) and non-shivering thermogenesis (NST) under cold exposure. Long non-coding RNAs (lncRNAs) play important roles in regulating [...] Read more.
Cold exposure is an essential factor affecting breeding efforts in cold regions. Muscle, as an important tissue for homeothermic animals, can produce heat through shivering thermogenesis (ST) and non-shivering thermogenesis (NST) under cold exposure. Long non-coding RNAs (lncRNAs) play important roles in regulating gene expression. However, the regulatory mechanisms of lncRNAs and their role in the thermogenesis of pigs are unclear. We examined lncRNAs in the skeletal muscle of an indigenous pig breed, the Enshi black pig, when the pigs were exposed to acute or chronic cold. Three pigs were maintained inside a pig house (control group), three pigs were maintained outside the pig house for 55 d (chronic cold group), and three pigs were suddenly exposed to the conditions outside the pig house for 3 days (acute cold group). After the experiment, the longissimus dorsi of each pig were collected, and their lncRNA profiles were sequenced and analyzed. Each sample obtained nearly 12.56 Gb of clean data. A total of 11,605 non-coding RNAs were obtained, including 10,802 novel lncRNAs. The number of differentially expressed lncRNAs (DElncRNAs) was identified under acute cold (427) and cold acclimation (376), with 215 and 192 upregulated lncRNAs, respectively. However, only 113 lncRNAs were commonly upregulated by acute cold and cold acclimation. In addition, 65% of the target genes were trans-regulated by DElncRNAs. The target genes were enriched in signal transduction, immune system, cell growth and death pathways, and amino acid and carbohydrate metabolism. Compared to cold acclimation, acute cold stress-induced more DElncRNAs and response pathways. In conclusion, low temperatures altered the expression levels of lncRNAs and their target genes in muscle tissue. Some potential mechanisms were revealed, including ion migration and the metabolism of amino acids and carbohydrates. Full article
(This article belongs to the Special Issue Functional Genomics and Breeding in Animals)
►▼ Show Figures

Figure 1

14 pages, 4340 KiB  
Article
Distribution and Expression of Pulmonary Ionocyte-Related Factors CFTR, ATP6V0D2, and ATP6V1C2 in the Lungs of Yaks at Different Ages
by Junfeng He, Yating Wei, Yan Cui and Qian Zhang
Genes 2023, 14(3), 597; https://doi.org/10.3390/genes14030597 - 27 Feb 2023
Cited by 1 | Viewed by 1668
Abstract
In order to reveal the distribution and expression characteristics of the pulmonary ionocyte-related factors CFTR, ATP6V0D2, and ATP6V1C2 in the lungs of yaks of different ages. Explore the possible regulation of these pulmonary ionocyte-related factors in the yak lung for adaptation to high-altitude [...] Read more.
In order to reveal the distribution and expression characteristics of the pulmonary ionocyte-related factors CFTR, ATP6V0D2, and ATP6V1C2 in the lungs of yaks of different ages. Explore the possible regulation of these pulmonary ionocyte-related factors in the yak lung for adaptation to high-altitude hypoxia. The localization and expression of CTFR, ATP6V0D2, and ATP6V1C2 in the lungs of newborn, juvenile, adult, and elderly yaks were studied using immunohistochemistry, quantitative reverse transcription PCR, and Western blotting. Immunohistochemistry showed that CFTR, ATP6V0D2 and ATP6V1C2 were mainly localized in the ciliated cells and club cells of the epithelial mucosal layer of the bronchus and its branches in the lungs. For the qRT-PCR, expression of CFTR, ATP6V0D2 and ATP6V1C2 in the yak lungs varied according to age. For Western blotting, CFTR expression in the newborn group was significantly higher than in the other three groups. ATP6V0D2 expression of the adult group was significantly higher. ATP6V1C2 expression was the highest in the juvenile group (p < 0.05). This study showed that ciliated cells and club cells were related to the pulmonary ionocytes in yaks. CFTR, ATP6V0D2, and ATP6V1C2 were related to adaptations of yak lungs to high altitude hypoxia, through prevention of airway damage. Full article
(This article belongs to the Special Issue Functional Genomics and Breeding in Animals)
►▼ Show Figures

Figure 1

Other

Jump to: Research

9 pages, 1821 KiB  
Brief Report
Y-Chromosome Haplotype Report among Eight Italian Horse Breeds
by Andrea Giontella, Irene Cardinali, Francesca Maria Sarti, Maurizio Silvestrelli and Hovirag Lancioni
Genes 2023, 14(8), 1602; https://doi.org/10.3390/genes14081602 - 09 Aug 2023
Viewed by 979
Abstract
Horse domestication and breed selection processes have profoundly influenced the development and transformation of human society and civilization over time. Therefore, their origin and history have always attracted much attention. In Italy, several local breeds have won prestigious awards thanks to their unique [...] Read more.
Horse domestication and breed selection processes have profoundly influenced the development and transformation of human society and civilization over time. Therefore, their origin and history have always attracted much attention. In Italy, several local breeds have won prestigious awards thanks to their unique traits and socio-cultural peculiarities. Here, for the first time, we report the genetic variation of three loci of the male-specific region of the Y chromosome (MSY) of four local breeds and another one (Lipizzan, UNESCO) well-represented in the Italian Peninsula. The analysis also includes data from three Sardinian breeds and another forty-eight Eurasian and Mediterranean horse breeds retrieved from GenBank for comparison. Three haplotypes (HT1, HT2, and HT3) were found in Italian stallions, with different spatial distributions between breeds. HT1 (the ancestral haplotype) was frequent, especially in Bardigiano and Monterufolino, HT2 (Neapolitan/Oriental wave) was found in almost all local breeds, and HT3 (Thoroughbred wave) was detected in Maremmano and two Sardinian breeds (Sardinian Anglo-Arab and Sarcidano). This differential distribution is due to three paternal introgressions of imported stallions from foreign countries to improve local herds; however, further genetic analyses are essential to reconstruct the genetic history of native horse breeds, evaluate the impact of selection events, and enable conservation strategies. Full article
(This article belongs to the Special Issue Functional Genomics and Breeding in Animals)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-4
Back to TopTop