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Quantitative Genetics and Bioinformatics Method in Animals

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Bioinformatics".

Deadline for manuscript submissions: closed (15 November 2022) | Viewed by 22775

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Dr. Lei Zhou

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Guest Editor

National Engineering Laboratory For Animal Breeding, College of Animal Science and Techonolgy, China Agricultural University, Beijing 100193, China
Interests: pig breeding; genomic selection; genome variation and evolution; multi-omics; Bayesian method; bioinformatics

Dr. Tao Xiang

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Guest Editor

Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
Interests: genomic selection; multiple populations; crossbred performance; non-additive effects; GWAS; omics data; new phenotypes; bioinformatics

Special Issue Information

Dear Colleagues,

Bioinformatic and statistical methods are crucial in genetic and biology studies, and advanced bioinformatic and quantitative methods/tools are becoming even more important in the rapidly developing multi-omics era. In this Special Issue, we welcome the submission of research articles and review articles on topics related to the quantitative genetics and bioinformatics method for Animal Genetics and Breeding, describing novel models, tools, software and approaches in all fields of animal genetics. Research topics among the following themes are especially welcomed:

Novel models and methods in genomic selection and GWAS of animals;
Machine learning and artificial intelligence in the bioinformatics method of animals;
Novel computational methods and insights for genes, biological pathways, and networks associated with different traits in animals;
Novel approaches and methods to assemble different animals’ genome and to characterize the genome variation;
Biological omics-data (including RNA-seq, HiC, CHIP-seq, ATAC-seq etc.) analysis for different traits in animals;
New bioinformatics and statistical algorithms and software development for quantitative traits.

Dr. Lei Zhou
Dr. Tao Xiang
Guest Editors

Manuscript Submission Information

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Keywords

animal genetics
bioinformatics
quantitative genetics
genomic selection
GWAS
omics data
functional genomics
biological network
toolkits and databases

Published Papers (11 papers)

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Research

14 pages, 3309 KiB

Open AccessArticle

Comprehensive Analysis of the lncRNA–miRNA–mRNA Regulatory Network for Intramuscular Fat in Pigs

by Yanhui Zhao, Shaokang Chen, Jiani Yuan, Yumei Shi, Yan Wang, Yufei Xi, Xiaolong Qi, Yong Guo, Xihui Sheng, Jianfeng Liu, Lei Zhou, Chuduan Wang and Kai Xing

Genes 2023, 14(1), 168; https://doi.org/10.3390/genes14010168 - 7 Jan 2023

Cited by 3 | Viewed by 2206

Abstract

Intramuscular fat (IMF) is an essential trait closely related to meat quality. The IMF trait is a complex quantitative trait that is regulated by multiple genes. In order to better understand the process of IMF and explore the key factors affecting IMF deposition, we identified differentially expressed mRNA, miRNA, and lncRNA in the longissimus dorsi muscle (LD) between Songliao Black (SL) pigs and Landrace pigs. We obtained 606 differentially expressed genes (DEGs), 55 differentially expressed miRNAs (DEMs), and 30 differentially expressed lncRNAs (DELs) between the SL pig and Landrace pig. Enrichment results from GO and KEGG indicate that DEGs are involved in fatty acid metabolism and some pathways related to glycogen synthesis. We constructed an lncRNA–miRNA–mRNA interaction network with 18 DELs, 11 DEMs, and 42 DEGs. Finally, the research suggests that ARID5B, CPT1B, ACSL1, LPIN1, HSP90AA1, IRS1, IRS2, PIK3CA, PIK3CB, and PLIN2 may be the key genes affecting IMF deposition. The LncRNAs MSTRG.19948.1, MSTRG.13120.1, MSTRG.20210.1, and MSTRG.10023.1, and the miRNAs ssc-miRNA-429 and ssc-miRNA-7-1, may play a regulatory role in IMF deposition through their respective target genes. Our research provides a reference for further understanding the regulatory mechanism of IMF. Full article

(This article belongs to the Special Issue Quantitative Genetics and Bioinformatics Method in Animals)

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12 pages, 2198 KiB

Open AccessArticle

Transcription Analysis of Liver and Muscle Tissues from Landrace Finishing Pigs with Different Feed Conversion Ratios

by Zhixin Wang, Yingzhi He and Zhen Tan

Genes 2022, 13(11), 2067; https://doi.org/10.3390/genes13112067 - 8 Nov 2022

Cited by 4 | Viewed by 1452

Abstract

The efficiency of feed utilization determines the cost and economic benefits of pig production. In the present study, two pairs of full-sibling and two pairs of half-sibling female Landrace finishing pigs were selected, with each pair including individuals with different feed conversion rates, with liver and longissimus muscle tissue samples collected from each group for transcriptome analysis. A total of 561 differentially expressed genes (DEGs), among which 224 were up-regulated and 337 were down-regulated, were detected in the liver transcriptomes in the high-feed efficiency group compared to the low-feed efficiency group. The DEGs related to phosphorus and phosphate metabolism, arginine biosynthesis, chemical carcinogenesis, cytokine-cytokine receptor interaction, the biosynthesis of amino acids, and drug metabolism-cytochrome P450 in liver tissue were also associated with feed efficiency. In total, 215 DEGs were screened in the longissimus muscle tissue and were mainly related to disease and immune regulation, including complement and coagulation cascades, systemic lupus erythematosus, and prion diseases. The combination of gene expression and functional annotation results led to the identification of candidate feed efficiency-related biomarkers, such as ARG1, ARG2, GOT1, GPT2, ACAA2, ACADM, and ANGPTL4, members of cytochrome P450 family, and complement component family genes. Although the novel feed efficiency-related candidate genes need to be further evaluated by a larger sample size and functional studies, the present study identifies novel candidate biomarkers for the identification of functional SNPs underlying porcine feed efficiency. Full article

(This article belongs to the Special Issue Quantitative Genetics and Bioinformatics Method in Animals)

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12 pages, 1949 KiB

Open AccessArticle

Genetic Diversity and Population Structure of Hemiculter leucisculus (Basilesky, 1855) in Xinjiang Tarim River

by Siyuan Sun, Zhenyi Hu, Zhengyi Lu, Lu Liu, Xuan Liu, Qiong Zhou, Bin Huo, Dapeng Li and Rong Tang

Genes 2022, 13(10), 1790; https://doi.org/10.3390/genes13101790 - 4 Oct 2022

Cited by 2 | Viewed by 1563

Abstract

Hemiculter leucisculus is an invasive fish and widely distributed in the Xinjiang Tarim River. In this study, RAD-seq was used to explore the genetic diversity and population subgroup structure of H. leucisculus in the Tarim River and develop relevant Simple Sequence Repeat (SSR) markers. The study collected 40 samples distributed at four different sites of the Tarim River. A total of 7,291,260 single nucleotide polymorphisms (SNPs) were obtained. The genetic diversity results showed that the population genetic diversity level of H. leucisculus was low. The population pairwise F_ST values ranged from 0.231 to 0.258, indicating that there was moderate genetic differentiation among these populations. AMOVA showed that the genetic variation within populations accounted for 92.31% of the total variation. The principal component analysis (PCA) and neighbor joining (NJ) tree revealed that the four populations could be separated into two clusters (upper-middle and downstream populations) and the individuals from Taitema Lake (TTMH) showed differences and had a bigger geographic distance than the others. There is the probability that the H. leucisculus from Bosten Lake entered Taitema Lake to breed and then expanded into the Tarim River due to the water diversion projects in location. In addition, 147,705 SSRs loci were detected and 22,651 SSR primer pairs were developed. This study will contribute to providing valuable molecular data for the management of wild populations, marker-assisted selection and resource exploitation of H. leucisculus. Full article

(This article belongs to the Special Issue Quantitative Genetics and Bioinformatics Method in Animals)

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12 pages, 2600 KiB

Open AccessArticle

Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 Cells

by Xiaolong Li, Xiaoqian Zhang, Yandong Luo, Ru Liu, Yan Sun, Shuhong Zhao, Mei Yu and Jianhua Cao

Genes 2022, 13(9), 1515; https://doi.org/10.3390/genes13091515 - 24 Aug 2022

Cited by 1 | Viewed by 1513

Abstract

The porcine monomyeloid cell line, or 3D4/21 cells, is an effective tool to study the immune characteristics and virus infection mechanism of pigs. Due to the introduction of the neomycin resistance gene and the SV40 large T antigen gene, its genome has undergone essential changes, which are still unknown. Studying the variation in genome structure, especially the large fragments of insertions and deletions (InDels), is one of the proper ways to reveal these issues. In this study, an All-seq method was established by combining Mate-pair and Shotgun sequencing methods, and the detection and verification of large fragments of InDels were performed on 3D4/21 cells. The results showed that there were 844 InDels with a length of more than 1 kb, of which 12 regions were deletions of more than 100 kb in the 3D4/21 cell genome. In addition, compared with porcine primary alveolar macrophages, 82 genes including the CD163 had lost transcription in 3D4/21 cells, and 72 genes gained transcription as well. Further referring to the Hi-C structure, it was found that the fusion of the topologically associated domains (TADs) caused by the deletion may lead to abnormal gene function. The results of this study provide a basis for elaborating the genome structure and functional variation in 3D4/21 cells, provide a method for rapid and convenient detection of large-scale InDels, and provide useful clues for the study of the porcine immune function genome and the molecular mechanism of virus infection. Full article

(This article belongs to the Special Issue Quantitative Genetics and Bioinformatics Method in Animals)

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13 pages, 4222 KiB

Open AccessArticle

Genome-Wide Association Study Reveals Additive and Non-Additive Effects on Growth Traits in Duroc Pigs

by Yahui Xue, Shen Liu, Weining Li, Ruihan Mao, Yue Zhuo, Wenkai Xing, Jian Liu, Chuang Wang, Lei Zhou, Minggang Lei and Jianfeng Liu

Genes 2022, 13(8), 1454; https://doi.org/10.3390/genes13081454 - 16 Aug 2022

Cited by 7 | Viewed by 2008

Abstract

Growth rate plays a critical role in the pig industry and is related to quantitative traits controlled by many genes. Here, we aimed to identify causative mutations and candidate genes responsible for pig growth traits. In this study, 2360 Duroc pigs were used to detect significant additive, dominance, and epistatic effects associated with growth traits. As a result, a total number of 32 significant SNPs for additive or dominance effects were found to be associated with various factors, including adjusted age at a specified weight (AGE), average daily gain (ADG), backfat thickness (BF), and loin muscle depth (LMD). In addition, the detected additive significant SNPs explained 2.49%, 3.02%, 3.18%, and 1.96% of the deregressed estimated breeding value (DEBV) variance for AGE, ADG, BF, and LMD, respectively, while significant dominance SNPs could explain 2.24%, 13.26%, and 4.08% of AGE, BF, and LMD, respectively. Meanwhile, a total of 805 significant epistatic effects SNPs were associated with one of ADG, AGE, and LMD, from which 11 sub-networks were constructed. In total, 46 potential genes involved in muscle development, fat deposition, and regulation of cell growth were considered as candidates for growth traits, including CD55 and NRIP1 for AGE and ADG, TRIP11 and MIS2 for BF, and VRTN and ZEB2 for LMD, respectively. Generally, in this study, we detected both new and reported variants and potential candidate genes for growth traits of Duroc pigs, which might to be taken into account in future molecular breeding programs to improve the growth performance of pigs. Full article

(This article belongs to the Special Issue Quantitative Genetics and Bioinformatics Method in Animals)

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19 pages, 7709 KiB

Open AccessArticle

New Insight into the Genome-Wide Diversity and Admixture of Six Colombian Sheep Populations

by Herman Alberto Revelo, Vincenzo Landi, Diana López-Alvarez, Yineth Alexandra Palacios, Samuel R. Paiva, Concepta McManus, Elena Ciani and Luz Ángela Alvarez

Genes 2022, 13(8), 1415; https://doi.org/10.3390/genes13081415 - 9 Aug 2022

Viewed by 2058

Abstract

Creole sheep represent a strategic genetic resource for populations living in marginal areas under financial restrictions on the American continent. Six Colombian sheep breeds (two wool (BCL-Boyacá and NCL-Nariño, 12 and 14 samples) and four hair (OPCE-Ethiopian, 54 samples; OPCS-Sudan, 74 samples; OPCP-Pelibeuy, 59 samples; OPCW-Wayúu, 24 samples) were genotyped using the Illumina Ovine SNP50 BeadChip. Data was also included from international 44 breeds from International Sheep Genomics Consortium (ISGC) and from data published in previous a previous work on the Caribbean and African breeds. Although geographically separated, wool (NCL, BCL) and hair types (OPCE, OPCS, OPCW) presented little genetic differentiation (FST 0.05) at a global level but several groups of animals separated suggesting local clustering due to geographical isolation. The OPCP underwent a recent crossing with Mexican Pelibuey, explaining its differentiation. Findings in this work such as the proximity to West African Djallonké (WAD) and Barbados Black Belly (BBB), suggest different introductions of African type animals from the Caribbean region on a pre-existing genetic basis formed by animals deriving from the first importations coming from Europe in colonial times. As expected, Colombian wool breeds showed, in particular in Admixture software results, a greater genomic component in common with European breeds and in particular with Iberian ones (Churra). This study provides a basis for future research into the genetic diversity within and between the Colombian sheep breeds analysed, and scientific data for policy decisions on Farm Animal Genetic Resources (FAnGR). Full article

(This article belongs to the Special Issue Quantitative Genetics and Bioinformatics Method in Animals)

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14 pages, 2682 KiB

Open AccessArticle

Comprehensive Analysis of Differentially Expressed mRNAs, lncRNAs and circRNAs Related to Intramuscular Fat Deposition in Laiwu Pigs

by Jingxuan Li, Xueyan Zhao, Yanping Wang and Jiying Wang

Genes 2022, 13(8), 1349; https://doi.org/10.3390/genes13081349 - 27 Jul 2022

Cited by 1 | Viewed by 1756

Abstract

Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) are important classes of small noncoding RNAs that can regulate numerous biological processes. To understand the role of message RNA (mRNAs, lncRNAs and circRNAs) in the regulation of intramuscular fat (IMF) deposition, in this study the expression profiles of longissimus dorsi (LD) muscle from six Laiwu pigs (three with extremely high and three with extremely low IMF content) were sequenced based on rRNA-depleted library construction. In total, 323 differentially expressed protein-coding genes (DEGs), 180 lncRNAs (DELs) and 105 circRNAs (DECs) were detected between the high IMF and low IMF groups. Functional analysis indicated that most DEGs, and some target genes of DELs, were enriched into GO terms and pathways related to adipogenesis, suggesting their important roles in regulating IMF deposition. In addition, 12 DELs were observed to exhibit a positive relationship with stearoyl-CoA desaturase (SCD), phosphoenolpyruvate carboxykinase 1 (PCK1), and adiponectin (ADIPOQ), suggesting they are highly likely to be the target genes of DELs. Finally, we constructed a source gene-circRNA-miRNA connective network, and some of miRNA of the network have been reported to affect lipid metabolism or adipogenesis. Overall, this work provides a valuable resource for further research and helps to understand the potential functions of lncRNAs and circRNAs in IMF deposition. Full article

(This article belongs to the Special Issue Quantitative Genetics and Bioinformatics Method in Animals)

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19 pages, 1964 KiB

Open AccessArticle

Molecular Characterization of TGF-Beta Gene Family in Buffalo to Identify Gene Duplication and Functional Mutations

by Muhammad Saif-ur Rehman, Faiz-ul Hassan, Zia-ur Rehman, Iqra Ishtiaq, Saif ur Rehman and Qingyou Liu

Genes 2022, 13(8), 1302; https://doi.org/10.3390/genes13081302 - 22 Jul 2022

Cited by 6 | Viewed by 1973

Abstract

The TGF-β superfamily is ubiquitously distributed from invertebrates to vertebrates with diverse cellular functioning such as cell adhesion, motility, proliferation, apoptosis, and differentiation. The present study aimed to characterize the TGF-β gene superfamily in buffalo through evolutionary, structural, and single nucleotide polymorphism (SNPs) analyses to find the functional effect of SNPs in selected genes. We detected 32 TGF-β genes in buffalo genome and all TGF-β proteins exhibited basic nature except INHA, INHBC, MSTN, BMP10, and GDF2, which showed acidic properties. According to aliphatic index, TGF-β proteins were thermostable but unstable in nature. Except for GDF1 and AMH, TGF-β proteins depicted hydrophilic nature. Moreover, all the detected buffalo TGF-β genes showed evolutionary conserved nature. We also identified eight segmental and one tandem duplication event TGF-β gene family in buffalo, and the ratio of Ka/Ks demonstrated that all the duplicated gene pairs were under selective pressure. Comparative amino acid analysis demonstrated higher variation in buffalo TGF-β gene family, as a total of 160 amino acid variations in all the buffalo TGF-β proteins were detected. Mutation analysis revealed that 13 mutations had an overall damaging effect that might have functional consequences on buffalo growth, folliculogenesis, or embryogenesis. Full article

(This article belongs to the Special Issue Quantitative Genetics and Bioinformatics Method in Animals)

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13 pages, 957 KiB

Open AccessArticle

Population Structure and Genetic Diversity of Chinese Honeybee (Apis Cerana Cerana) in Central China

by Fang Fang, Xiasang Chen, Jie Lv, Xinyan Shi, Xiaojuan Feng, Zhen Wang and Xiang Li

Genes 2022, 13(6), 1007; https://doi.org/10.3390/genes13061007 - 2 Jun 2022

Cited by 3 | Viewed by 2388

Abstract

Central China has a rich terrain with a temperate monsoon climate and varied natural environments for the Chinese honeybee (Apis cerana cerana). However, little comprehensive research on population genetic diversity has been done in this area. A population survey of the structure and genetic diversity of Apis cerana cerana in this area is deeply needed for understanding adaptation to variable environments and providing more references for the protection of honeybee biodiversity. In this study, we present a dataset of 72 populations of Chinese honeybees collected from nine sites by whole genome sequencing in Central China. We obtained 2,790,214,878 clean reads with an average covering a depth of 22×. A total of 27,361,052 single nucleotide polymorphisms (SNPs) were obtained by mapping to the reference genome with an average mapping rate of 93.03%. Genetic evolution analysis was presented via the population structure and genetic diversity based on the datasets of SNPs. It showed that Apis cerana cerana in plains exhibited higher genetic diversity than in mountain areas. The mantel test between Apis cerana cerana groups revealed that some physical obstacles, especially the overurbanization of the plains, contributed to the differentiation. This study is conducive to elucidating the evolution of Apis cerana in different environments and provides a theoretical basis for investigating and protecting the Chinese honeybee. Full article

(This article belongs to the Special Issue Quantitative Genetics and Bioinformatics Method in Animals)

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17 pages, 3610 KiB

Open AccessArticle

Transcriptome Analysis Reveals the Differentially Expressed Genes Associated with Growth in Guangxi Partridge Chickens

by Minghui Shao, Kai Shi, Qian Zhao, Ying Duan, Yangyang Shen, Jinjie Tian, Kun He, Dongfeng Li, Minli Yu, Yangqing Lu, Yanfei Tang and Chungang Feng

Genes 2022, 13(5), 798; https://doi.org/10.3390/genes13050798 - 29 Apr 2022

Cited by 2 | Viewed by 2327

Abstract

The Guangxi Partridge chicken is a well-known chicken breed in southern China with good meat quality, which has been bred as a meat breed to satisfy the increased demand of consumers. Compared with line D whose body weight is maintained at the average of the unselected group, the growth rate and weight of the selected chicken group (line S) increased significantly after breeding for four generations. Herein, transcriptome analysis was performed to identify pivotal genes and signal pathways of selective breeding that contributed to potential mechanisms of growth and development under artificial selection pressure. The average body weight of line S chickens was 1.724 kg at 90 d of age, which showed a significant increase at 90 d of age than line D chickens (1.509 kg), although only the internal organ ratios of lung and kidney changed after standardizing by body weight. The myofiber area and myofiber density of thigh muscles were affected by selection to a greater extent than that of breast muscle. We identified 51, 210, 31, 388, and 100 differentially expressed genes (DEGs) in the hypothalamus, pituitary, breast muscle, thigh muscle, and liver between the two lines, respectively. Several key genes were identified in the hypothalamus-pituitary-muscle axis, such as FST, THSB, PTPRJ, CD36, PITX1, PITX2, AMPD1, PRKAB1, PRKAB2, and related genes for muscle development, which were attached to the cytokine–cytokine receptor interaction signaling pathway, the PPAR signaling pathway, and lipid metabolism. However, signaling molecular pathways and the cell community showed that elevated activity in the liver of line S fowl was mainly involved in focal adhesion, ECM-receptor interaction, cell adhesion molecules, and signal transduction. Collectively, muscle development, lipid metabolism, and several signaling pathways played crucial roles in the improving growth performance of Guangxi Partridge chickens under artificial selection for growth rate. These results support further study of the adaptation of birds under selective pressure. Full article

(This article belongs to the Special Issue Quantitative Genetics and Bioinformatics Method in Animals)

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22 pages, 5127 KiB

Open AccessArticle

Integrated Analysis of the ceRNA Network and M-7474 Function in Testosterone-Mediated Fat Deposition in Pigs

by Ximing Liu, Ying Bai, Ran Cui, Shuaihan He, Yao Ling, Changxin Wu and Meiying Fang

Genes 2022, 13(4), 668; https://doi.org/10.3390/genes13040668 - 10 Apr 2022

Cited by 3 | Viewed by 1930

Abstract

Castration can significantly enhance fat deposition in pigs, and the molecular mechanism of fat deposition caused by castration and its influence on fat deposition in different parts of pigs remain unclear. RNA-seq was performed on adipose tissue from different parts of castrated and intact Yorkshire pigs. Different ceRNA networks were constructed for different fat parts. GO and KEGG pathway annotations suggested that testosterone elevates cell migration and affects differentiation and apoptosis in back fat, while it predisposes animals to glycolipid metabolism disorders and increases the expression of inflammatory cytokines in abdominal fat. The interaction between M-7474, novel_miR_243 and SGK1 was verified by dual fluorescence experiments. This ceRNA relationship has also been demonstrated in porcine preadipocytes. Overexpression of M-7474 significantly inhibited the differentiation of preadipocytes compared to the control group. When 100 nM testosterone was added during preadipocyte differentiation, the expression of M-7474 was increased, and preadipocyte differentiation was significantly inhibited. Testosterone can affect preadipocyte differentiation by upregulating the expression of M-7474, sponging novel-miR-243, and regulating the expression of genes such as SGK1. At the same time, HSD11B1 and SLC2A4 may also be regulated by the corresponding lncRNA and miRNA, which ultimately affects glucose uptake by adipocytes and leads to obesity. Full article

(This article belongs to the Special Issue Quantitative Genetics and Bioinformatics Method in Animals)

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