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Molecular Genetics and Breeding Mechanisms in Domestics Animals: 2nd Edition

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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 September 2024 | Viewed by 11182

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Dr. Guiping Zhao

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Chinese Academy of Agricultural Sciences, Beijing, China
Interests: animal genetics and breeding; immunogenetics; breeding for disease resistance; interactions between microbe and host
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Dear Colleagues,

Alongside the continuous progress of biotechnology, molecular genetics, breeding theory and methods, scientists in the field have rapidly developed high-quality germplasms. The current Special Issue on “Molecular Genetics and Breeding Mechanisms in Domestics Animals” explores and disseminates the latest research trends and achievements in the scientific field of animal molecular genetics and breeding. The Special Issue also aims to explore the achievements in the research concerning disease-resistance breeding, which is of great significance to the development of animal husbandry and human health.

We invite submissions that discuss the molecular biology, genetics and immunity of domestic animals, placing particular emphasis on the following topics:

Analysis of molecular mechanisms of character formation based on multiomics;
Genetic mechanism research about important functional genes in animals;
New breeding theory based on bio-informatics;
Effects of microbiota on immune development;
Molecular interactions between microbial products and host sensors.

Dr. Guiping Zhao
Guest Editor

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Keywords

animal genetics
animal breeding
functional genomics
multiomics analysis
molecular immunity
interactions between microbe and host

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Research

19 pages, 27849 KiB

Open AccessArticle

Combined Multi-Omics Analysis Reveals the Potential Role of ACADS in Yak Intramuscular Fat Deposition

by Fang Xu, Haibo Wang, Chunyu Qin, Binglin Yue, Youzhualamu Yang, Jikun Wang, Jincheng Zhong and Hui Wang

Int. J. Mol. Sci. 2024, 25(16), 9131; https://doi.org/10.3390/ijms25169131 - 22 Aug 2024

Viewed by 498

Abstract

The Yak (Bos grunniens) is a special breed of livestock predominantly distributed in the Qinghai–Tibet Plateau of China. Intramuscular fat (IMF) content in beef cattle is a vital indicator of meat quality. In this study, RNA-Seq and Protein-Seq were respectively employed to sequence the transcriptome and proteome of the longissimus dorsi (LD) tissue from 4-year-old yaks with significant differences in IMF content under the same fattening conditions. Five overlapping genes (MYL3, ACADS, L2HGDH, IGFN1, and ENSBGRG00000000-926) were screened using combined analysis. Functional verification tests demonstrated that the key gene ACADS inhibited yak intramuscular preadipocyte (YIMA) differentiation and proliferation, promoted mitochondrial biogenesis gene expression, and increased the mitochondrial membrane potential (MMP). Furthermore, co-transfection experiments further demonstrated that interfering with ACADS reversed the effect of PPARα agonists in promoting lipid differentiation. In conclusion, ACADS potentially inhibits lipid deposition in YIAMs by regulating the PPARα signalling pathway. These findings offer insights into the molecular mechanisms underlying yak meat quality. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Domestics Animals: 2nd Edition)

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20 pages, 5640 KiB

Open AccessArticle

Whole-Genome Resequencing Analysis of the Camelus bactrianus (Bactrian Camel) Genome Identifies Mutations and Genes Affecting Milk Production Traits

by Huaibing Yao, Zhangyuan Pan, Wanpeng Ma, Zhongkai Zhao, Zhanqiang Su and Jie Yang

Int. J. Mol. Sci. 2024, 25(14), 7836; https://doi.org/10.3390/ijms25147836 - 17 Jul 2024

Viewed by 615

Abstract

Milk production is an important trait that influences the economic value of camels. However, the genetic regulatory mechanisms underlying milk production in camels have not yet been elucidated. We aimed to identify candidate molecular markers that affect camel milk production. We classified Junggar Bactrian camels (9–10-year-old) as low-yield (<1.96 kg/d) or high-yield (>2.75 kg/d) based on milk production performance. Milk fat (5.16 ± 0.51 g/100 g) and milk protein (3.59 ± 0.22 g/100 g) concentrations were significantly lower in high-yielding camels than those in low-yielding camels (6.21 ± 0.59 g/100 g, and 3.93 ± 0.27 g/100 g, respectively) (p < 0.01). There were no apparent differences in gland tissue morphology between the low- and high-production groups. Whole-genome resequencing of 12 low- and 12 high-yield camels was performed. The results of selection mapping methods, performed using two methods (F_ST and θπ), showed that 264 single nucleotide polymorphism sites (SNPs) overlapped between the two methods, identifying 181 genes. These genes were mainly associated with the regulation of oxytocin, estrogen, ErbB, Wnt, mTOR, PI3K-Akt, growth hormone synthesis/secretion/action, and MAPK signaling pathways. A total of 123 SNPs were selected, based on significantly associated genomic regions and important pathways for SNP genotyping, for verification in 521 additional Bactrian camels. This analysis showed that 13 SNPs were significantly associated with camel milk production yield and 18 SNPs were significantly associated with camel milk composition percentages. Most of these SNPs were located in coding regions of the genome. However, five and two important mutation sites were found in the introns of CSN2 (β-casein) and CSN3 (κ-casein), respectively. Among the candidate genes, NR4A1, ADCY8, PPARG, CSN2, and CSN3 have previously been well studied in dairy livestock. These observations provide a basis for understanding the molecular mechanisms underlying milk production in camels as well as genetic markers for breeding programs aimed at improving milk production. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Domestics Animals: 2nd Edition)

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16 pages, 2456 KiB

Open AccessArticle

Whole Genome Scan Uncovers Candidate Genes Related to Milk Production Traits in Barka Cattle

by Wondossen Ayalew, Xiaoyun Wu, Getinet Mekuriaw Tarekegn, Tesfaye Sisay Tessema, Rakan Naboulsi, Renaud Van Damme, Erik Bongcam-Rudloff, Zewdu Edea, Min Chu, Solomon Enquahone, Chunnian Liang and Ping Yan

Int. J. Mol. Sci. 2024, 25(11), 6142; https://doi.org/10.3390/ijms25116142 - 2 Jun 2024

Cited by 1 | Viewed by 1737

Abstract

In this study, our primary aim was to explore the genomic landscape of Barka cattle, a breed recognized for high milk production in a semi-arid environment, by focusing on genes with known roles in milk production traits. We employed genome-wide analysis and three selective sweep detection methods (ZF_ST, θπ ratio, and ZHp) to identify candidate genes associated with milk production and composition traits. Notably, ACAA1, P4HTM, and SLC4A4 were consistently identified by all methods. Functional annotation highlighted their roles in crucial biological processes such as fatty acid metabolism, mammary gland development, and milk protein synthesis. These findings contribute to understanding the genetic basis of milk production in Barka cattle, presenting opportunities for enhancing dairy cattle production in tropical climates. Further validation through genome-wide association studies and transcriptomic analyses is essential to fully exploit these candidate genes for selective breeding and genetic improvement in tropical dairy cattle. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Domestics Animals: 2nd Edition)

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21 pages, 4347 KiB

Open AccessArticle

Integrating Multiple Database Resources to Elucidate the Gene Flow in Southeast Asian Pig Populations

by Guangzhen Li, Yuqiang Liu, Xueyan Feng, Shuqi Diao, Zhanming Zhong, Bolang Li, Jinyan Teng, Wenjing Zhang, Haonan Zeng, Xiaodian Cai, Yahui Gao, Xiaohong Liu, Xiaolong Yuan, Jiaqi Li and Zhe Zhang

Int. J. Mol. Sci. 2024, 25(11), 5689; https://doi.org/10.3390/ijms25115689 - 23 May 2024

Viewed by 758

Abstract

The domestic pig (Sus scrofa) and its subfamilies have experienced long-term and extensive gene flow, particularly in Southeast Asia. Here, we analyzed 236 pigs, focusing on Yunnan indigenous, European commercial, East Asian, and Southeast Asian breeds, using the Pig Genomics Reference Panel (PGRP v1) of Pig Genotype-Tissue Expression (PigGTEx) to investigate gene flow and associated complex traits by integrating multiple database resources. In this study, we discovered evidence of admixtures from European pigs into the genome of Yunnan indigenous pigs. Additionally, we hypothesized that a potential conceptual gene flow route that may have contributed to the genetic composition of the Diannan small-ear pig is a gene exchange from the Vietnamese pig. Based on the most stringent gene introgression scan using the fd statistic, we identified three specific loci on chromosome 8, ranging from 51.65 to 52.45 Mb, which exhibited strong signatures of selection and harbored the NAF1, NPY1R, and NPY5R genes. These genes are associated with complex traits, such as fat mass, immunity, and litter weight, in pigs, as supported by multiple bio-functionalization databases. We utilized multiple databases to explore the potential dynamics of genetic exchange in Southeast Asian pig populations and elucidated specific gene functionalities. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Domestics Animals: 2nd Edition)

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15 pages, 4340 KiB

Open AccessArticle

Identification of Susceptibility Genes Underlying Bovine Respiratory Disease in Xinjiang Brown Cattle Based on DNA Methylation

by Hang Cao, Chao Fang, Ling-Ling Liu, Frederic Farnir and Wu-Jun Liu

Int. J. Mol. Sci. 2024, 25(9), 4928; https://doi.org/10.3390/ijms25094928 - 30 Apr 2024

Cited by 1 | Viewed by 925

Abstract

DNA methylation is a form of epigenetic regulation, having pivotal parts in controlling cellular expansion and expression levels within genes. Although blood DNA methylation has been studied in humans and other species, its prominence in cattle is largely unknown. This study aimed to methodically probe the genomic methylation map of Xinjiang brown (XJB) cattle suffering from bovine respiratory disease (BRD), consequently widening cattle blood methylome ranges. Genome-wide DNA methylation profiling of the XJB blood was investigated through whole-genome bisulfite sequencing (WGBS). Many differentially methylated regions (DMRs) obtained by comparing the cases and controls groups were found within the CG, CHG, and CHH (where H is A, T, or C) sequences (16,765, 7502, and 2656, respectively), encompassing 4334 differentially methylated genes (DMGs). Furthermore, GO/KEGG analyses showed that some DMGs were involved within immune response pathways. Combining WGBS-Seq data and existing RNA-Seq data, we identified 71 significantly differentially methylated (DMGs) and expressed (DEGs) genes (p < 0.05). Next, complementary analyses identified nine DMGs (LTA, STAT3, IKBKG, IRAK1, NOD2, TLR2, TNFRSF1A, and IKBKB) that might be involved in the immune response of XJB cattle infected with respiratory diseases. Although further investigations are needed to confirm their exact implication in the involved immune processes, these genes could potentially be used for a marker-assisted selection of animals resistant to BRD. This study also provides new knowledge regarding epigenetic control for the bovine respiratory immune process. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Domestics Animals: 2nd Edition)

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15 pages, 2455 KiB

Open AccessArticle

Unveiling the Genetic Mechanism of Meat Color in Pigs through GWAS, Multi-Tissue, and Single-Cell Transcriptome Signatures Exploration

by Cheng Liu, Zitao Chen, Zhe Zhang, Zhen Wang, Xiaoling Guo, Yuchun Pan and Qishan Wang

Int. J. Mol. Sci. 2024, 25(7), 3682; https://doi.org/10.3390/ijms25073682 - 26 Mar 2024

Cited by 1 | Viewed by 1472

Abstract

Meat color traits directly influence consumer acceptability and purchasing decisions. Nevertheless, there is a paucity of comprehensive investigation into the genetic mechanisms underlying meat color traits in pigs. Utilizing genome-wide association studies (GWAS) on five meat color traits and the detection of selection signatures in pig breeds exhibiting distinct meat color characteristics, we identified a promising candidate SNP, 6_69103754, exhibiting varying allele frequencies among pigs with different meat color characteristics. This SNP has the potential to affect the redness and chroma index values of pork. Moreover, transcriptome-wide association studies (TWAS) analysis revealed the expression of candidate genes associated with meat color traits in specific tissues. Notably, the largest number of candidate genes were observed from transcripts derived from adipose, liver, lung, spleen tissues, and macrophage cell type, indicating their crucial role in meat color development. Several shared genes associated with redness, yellowness, and chroma indices traits were identified, including RINL in adipose tissue, ENSSSCG00000034844 and ITIH1 in liver tissue, TPX2 and MFAP2 in lung tissue, and ZBTB17, FAM131C, KIFC3, NTPCR, and ENGSSSCG00000045605 in spleen tissue. Furthermore, single-cell enrichment analysis revealed a significant association between the immune system and meat color. This finding underscores the significance of the immune system associated with meat color. Overall, our study provides a comprehensive analysis of the genetic mechanisms underlying meat color traits, offering valuable insights for future breeding efforts aimed at improving meat quality. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Domestics Animals: 2nd Edition)

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21 pages, 2125 KiB

Open AccessArticle

Integrated Discriminant Evaluation of Molecular Genetic Markers and Genetic Diversity Parameters of Endangered Balearic Dog Breeds

by José Manuel Alanzor Puente, Águeda Laura Pons Barro, Antonio González Ariza, María del Amparo Martínez Martínez, Juan Vicente Delgado Bermejo and Francisco Javier Navas González

Int. J. Mol. Sci. 2024, 25(5), 2706; https://doi.org/10.3390/ijms25052706 - 26 Feb 2024

Viewed by 769

Abstract

The genetic diversity analysis of six dog breeds, including Ca de Bestiar (CB), Ca de Bou (CBOU), Podenco Ibicenco (PI), Ca Rater (CR), Ca Mè (CM), and Ca de Conills (CC), reveals insightful findings. CB showcases the highest mean number of alleles (6.17) and heterozygosity values, with significant deviations from Hardy–Weinberg equilibrium (HWE) observed in five markers, indicating high intra-racial genetic diversity (average observed heterozygosity (H_o) = 0.754, expected heterozygosity (H_e) = 0.761). In contrast, CBOU presents the lowest mean number of alleles (5.05) and heterozygosity values, coupled with moderate polymorphic information content (PIC) values and a moderate level of intra-racial genetic diversity (average H_o = 0.313, H_e = 0.394). PI demonstrates moderate genetic diversity with an average of 5.75 alleles and highly informative PIC values, while CR displays robust genetic diversity with an average of 6.61 alleles and deviations from equilibrium, indicating potential risks of inbreeding (average H_o = 0.563, H_e = 0.658). CM exhibits moderate genetic diversity and deviations from equilibrium, similar to CBOU, with an average of 6.5 alleles and moderate PIC values (average H_o = 0.598, H_e = 0.676). Conversely, CC shows a wider range of allelic diversity and deviations from equilibrium (average H_o = 0.611, H_e = 0.706), suggesting a more diverse genetic background. Inter-racial analysis underscores distinct genetic differentiation between breeds, emphasizing the importance of informed breeding decisions and proactive genetic management strategies to preserve diversity, promote breed health, and ensure long-term sustainability across all breeds studied. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Domestics Animals: 2nd Edition)

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14 pages, 3212 KiB

Open AccessArticle

Molecular Genetic Characteristics of the Hoxc13 Gene and Association Analysis of Wool Traits

by Hongxian Sun, Zhaohua He, Fangfang Zhao, Jiang Hu, Jiqing Wang, Xiu Liu, Zhidong Zhao, Mingna Li, Yuzhu Luo and Shaobin Li

Int. J. Mol. Sci. 2024, 25(3), 1594; https://doi.org/10.3390/ijms25031594 - 27 Jan 2024

Cited by 1 | Viewed by 1028

Abstract

Homobox C13 (Hoxc13) is an important transcription factor in hair follicle cycle development, and its deletion had been found in a variety of animals leading to abnormal hair growth and disruption of the hair follicle system. In this study, we used immunofluorescence, immunohistochemistry, real-time fluorescence quantitative PCR (RT-qPCR), and Kompetitive Allele-Specific PCR (KASP) genotyping to investigate molecular genetic characteristics of the Hoxc13 gene in Gansu alpine fine-wool sheep. The results revealed that Hoxc13 was significantly expressed during both the anagen and catagen phases (p < 0.05). It was found to be highly expressed predominantly in the dermal papillae and the inner and outer root sheaths, showing a distinct spatiotemporal expression pattern. Two single nucleotide polymorphisms (SNPs) in the exon 1 of Hoxc13, both the individual locus genotypes and the combined haplotypes were found to be correlated with wool length (p < 0.05). It was determined the mutations led to changes in mRNA expression, in which higher expression of this gene was related with longer wool length. In summary, this unique spatiotemporal expression pattern of the Hoxc13 gene may regulate the wool length of Gansu alpine fine-wool sheep, which can be used as a molecular genetic marker for wool traits and thus improve the breed. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Domestics Animals: 2nd Edition)

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13 pages, 3184 KiB

Open AccessArticle

Identification of miRNA Associated with Trichomonas gallinae Resistance in Pigeon (Columba livia)

by Xinyi Li, Aixin Ni, Ran Zhang, Yunlei Li, Jingwei Yuan, Yanyan Sun, Jilan Chen and Hui Ma

Int. J. Mol. Sci. 2023, 24(22), 16453; https://doi.org/10.3390/ijms242216453 - 17 Nov 2023

Cited by 2 | Viewed by 1038

Abstract

Trichomonas gallinae (T. gallinae) has a great influence on the pigeon industry. Pigeons display different resistance abilities to T. gallinae, so the study of the molecular mechanism of resistance is necessary in breeding disease resistant lines. MiRNA plays important roles in the immune response, but there are still no reports of miRNA regulating trichomonosis resistance. We used small RNA sequencing technology to characterize miRNA profiles in different groups. T. gallinae was nasally inoculated in one day old squabs, and according to the infection status, the groups were divided into control (C), susceptible (S) and tolerant (T) groups. We identified 2429 miRNAs in total, including 1162 known miRNAs and 1267 new miRNAs. In a comparison among the C, S and T groups, the target genes of differentially expressed miRNAs were analyzed via GO and KEGG annotation. The results showed that the target genes were enriched in immune-response-related pathways. This indicated that the differentially expressed miRNAs had a critical influence on T. gallinae infection. Novel_miR_741, which could inhibit the expression of PRKCQ, was down-regulated in the T group compared to the C group. It was proven that a decreased novel_miR_741 expression would increase the expression of PRKCQ and increase the immune response. This study brings new insights into understanding the mechanism of trichomonosis resistance. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Domestics Animals: 2nd Edition)

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22 pages, 7702 KiB

Open AccessArticle

Whole-Transcriptome RNA Sequencing Uncovers the Global Expression Changes and RNA Regulatory Networks in Duck Embryonic Myogenesis

by Shuibing Liu, Jintao Wu, Wentao Zhang, Hongxia Jiang, Yanan Zhou, Jing Liu, Huirong Mao, Sanfeng Liu and Biao Chen

Int. J. Mol. Sci. 2023, 24(22), 16387; https://doi.org/10.3390/ijms242216387 - 16 Nov 2023

Cited by 3 | Viewed by 1435

Abstract

Duck meat is pivotal in providing high-quality protein for human nutrition, underscoring the importance of studying duck myogenesis. The regulatory mechanisms governing duck myogenesis involve both coding and non-coding RNAs, yet their specific expression patterns and molecular mechanisms remain elusive. To address this knowledge gap, we performed expression profiling analyses of mRNAs, lncRNAs, circRNAs, and miRNAs involved in duck myogenesis using whole-transcriptome RNA-seq. Our analysis identified 1733 differentially expressed (DE)-mRNAs, 1116 DE-lncRNAs, 54 DE-circRNAs, and 174 DE-miRNAs when comparing myoblasts and myotubes. A GO analysis highlighted the enrichment of DE molecules in the extracellular region, protein binding, and exocyst. A KEGG analysis pinpointed pathways related to ferroptosis, PPAR signaling, nitrogen metabolism, cell cycle, cardiac muscle contraction, glycerolipid metabolism, and actin cytoskeleton. A total of 51 trans-acting lncRNAs, including ENSAPLT00020002101 and ENSAPLT00020012069, were predicted to participate in regulating myoblast proliferation and differentiation. Based on the ceRNAs, we constructed lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA ceRNA networks involving five miRNAs (miR-129-5p, miR-133a-5p, miR-22-3p, miR-27b-3p, and let-7b-5p) that are relevant to myogenesis. Furthermore, the GO and KEGG analyses of the DE-mRNAs within the ceRNA network underscored the significant enrichment of the glycerolipid metabolism pathway. We identified five different DE-mRNAs, specifically ENSAPLG00020001677, ENSAPLG00020002183, ENSAPLG00020005019, ENSAPLG00020010497, and ENSAPLG00020017682, as potential target genes that are crucial for myogenesis in the context of glycerolipid metabolism. These five mRNAs are integral to ceRNA networks, with miR-107_R-2 and miR-1260 emerging as key regulators. In summary, this study provides a valuable resource elucidating the intricate interplay of mRNA-lncRNA-circRNA-miRNA in duck myogenesis, shedding light on the molecular mechanisms that govern this critical biological process. Full article

(This article belongs to the Special Issue Molecular Genetics and Breeding Mechanisms in Domestics Animals: 2nd Edition)

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