Animal genetics最新文献_第3页

A genome-wide association study reveals candidate genes and regulatory regions associated with birth weight in pigs 全基因组关联研究揭示了与猪出生体重相关的候选基因和调控区域。

IF 1.8 3区生物学

Animal genetics Pub Date : 2024-08-13 DOI: 10.1111/age.13468

Dadong Deng, Hongtao Wang, Kun Han, Zhenshuang Tang, Xiaoping Li, Xiangdong Liu, Xiaolei Liu, Xinyun Li, Mei Yu

{"title":"A genome-wide association study reveals candidate genes and regulatory regions associated with birth weight in pigs","authors":"Dadong Deng, Hongtao Wang, Kun Han, Zhenshuang Tang, Xiaoping Li, Xiangdong Liu, Xiaolei Liu, Xinyun Li, Mei Yu","doi":"10.1111/age.13468","DOIUrl":"10.1111/age.13468","url":null,"abstract":"Piglet birth weight is associated with preweaning survival, and its related traits have been included in the breeding program. Thus, understanding its genetic basis is essential. This study identified four birth weight-associated genomic regions on chromosomes 2, 4, 5, and 7 through genome-wide association study analysis in 7286 pigs from three different pure breeds using the FarmCPU model. The genetic and phenotypic variance explained by the four candidate regions is 8.42% and 1.85%, respectively. Twenty-eight candidate genes were detected, of which APPL2, TGFBI, MACROH2A1, and SEC22B have been reported to affect body growth or development. In addition, 21 H3K4me3-enriched peaks overlapped with the birth weight-associated genomic regions were identified by integrating the genome-wide association study results with our previous ChIP-seq and RNA-seq data generated in the pig placenta, a fetal organ relevant to birth weight, and three of the regulatory regions influence TGFBI, MACROH2A1, and SEC22B expression. This study provides new insights into understanding the mechanisms for birth weight. Further investigating the variants in the regulatory regions would help identify the functional variants for birth weight in pigs.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Heterozygous DSP in-frame deletion in a poodle with syndromic ichthyosis involving additional hair and tooth abnormalities 一只贵宾犬患有综合鱼鳞病，并伴有额外的毛发和牙齿异常。

IF 1.8 3区生物学

Animal genetics Pub Date : 2024-08-13 DOI: 10.1111/age.13467

Sarah Kiener, Georg Lehner, Vidhya Jagannathan, Monika Welle, Tosso Leeb

{"title":"Heterozygous DSP in-frame deletion in a poodle with syndromic ichthyosis involving additional hair and tooth abnormalities","authors":"Sarah Kiener, Georg Lehner, Vidhya Jagannathan, Monika Welle, Tosso Leeb","doi":"10.1111/age.13467","DOIUrl":"10.1111/age.13467","url":null,"abstract":"Ichthyoses comprise a large heterogeneous group of skin disorders, characterized by generalized scaly and hyperkeratotic skin. We investigated a miniature poodle with early onset generalized scaling, dry and irregularly thickened skin, paw pad hyperkeratosis and abnormalities in hair and teeth. The clinical signs of ichthyosis were confirmed by histopathological examination, which revealed mild epidermal hyperplasia and lamellar orthokeratotic hyperkeratosis. A hereditary condition was suspected and a genetic investigation was initiated. We sequenced the whole genome of the affected dog and searched for potentially causative variants in functional candidate genes for the observed phenotype. The analysis revealed a heterozygous in-frame deletion in DSP, NC_049256.1:g.8804542_8804544del resulting from a de novo mutation event as evidenced by genotyping leukocyte DNA from both parents. The 3 bp deletion is predicted to remove one aspartic acid without disrupting the open reading frame (XM_038584124.1:c.1821_1823del, XP_038440052.1:p.(Asp608del)). The DSP gene encodes desmoplakin, a desmosomal plaque protein, responsible for cell–cell adhesion to provide resistance to mechanical stress in epidermal and cardiac tissues. We hypothesize that the deletion of one amino acid in the N-terminal globular head domain acts in a dominant negative manner and thus impairs the proper connection with other proteins. Several variants in DSP in humans and cattle have been described to result in different phenotypes associated with hair and skin abnormalities, sometimes in combination with variable cardiac and/or dental manifestations. In conclusion, we characterized a new syndromic ichthyosis phenotype in a dog and identified a de novo 3 bp deletion in the DSP gene as causal variant.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13467","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integration of ssGWAS and ROH analyses for uncovering genetic variants associated with reproduction traits in Large White pigs 整合 ssGWAS 和 ROH 分析，发现与大白猪繁殖性状相关的遗传变异。

IF 1.8 3区生物学

Animal genetics Pub Date : 2024-08-12 DOI: 10.1111/age.13465

Zhenyang Zhang, Wei Zhao, Zhen Wang, Yuchun Pan, Qishan Wang, Zhe Zhang

{"title":"Integration of ssGWAS and ROH analyses for uncovering genetic variants associated with reproduction traits in Large White pigs","authors":"Zhenyang Zhang, Wei Zhao, Zhen Wang, Yuchun Pan, Qishan Wang, Zhe Zhang","doi":"10.1111/age.13465","DOIUrl":"10.1111/age.13465","url":null,"abstract":"The low heritability of reproduction traits such as total number born (TNB), number born alive (NBA) and adjusted litter weight until 21 days at weaning (ALW) poses a challenge for genetic improvement. In this study, we aimed to identify genetic variants that influence these traits and evaluate the accuracy of genomic selection (GS) using these variants as genomic features. We performed single-step genome-wide association studies (ssGWAS) on 17 823 Large White (LW) pigs, of which 2770 were genotyped by 50K single nucleotide polymorphism (SNP) chips. Additionally, we analyzed runs of homozygosity (ROH) in the population and tested their effects on the traits. The genomic feature best linear unbiased prediction (GFBLUP) was then carried out in an independent population of 350 LW pigs using identified trait-related SNP subsets as genomic features. As a result, our findings identified five, one and four SNP windows that explaining more than 1% of genetic variance for ALW, TNB, and NBA, respectively and discovered 358 hotspots and nine ROH islands. The ROH SSC1:21814570–27186456 and SSC11:7220366–14276394 were found to be significantly associated with ALW and NBA, respectively. We assessed the genomic estimated breeding value accuracy through 20 replicates of five-fold cross-validation. Our findings demonstrate that GFBLUP, incorporating SNPs located in effective ROH (p-value < 0.05) as genomic features, might enhance GS accuracy for ALW compared with GBLUP. Additionally, using SNPs explaining more than 0.1% of the genetic variance in ssGWAS for NBA as genomic features might improve the GS accuracy, too. However, it is important to note that the incorporation of inappropriate genomic features can significantly reduce GS accuracy. In conclusion, our findings provide valuable insights into the genetic mechanisms of reproductive traits in pigs and suggest that the ssGWAS and ROH have the potential to enhance the accuracy of GS for reproductive traits in LW pigs.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141915958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genetic Eye Diseases in Animals: A Selected Review of Recent Advances 动物遗传性眼病：最新进展精选回顾》。

IF 1.8 3区生物学

Animal genetics Pub Date : 2024-07-17 DOI: 10.1111/age.13460

A. M. Komáromy, J. A. Lenstra

引用次数: 0

genomeprofile: Unveiling the genomic profile for livestock breeding through comprehensive SNP array-based genotyping 基因组概况：通过基于 SNP 阵列的全面基因分型，揭示家畜育种的基因组概况。

IF 1.8 3区生物学

Animal genetics Pub Date : 2024-07-17 DOI: 10.1111/age.13466

Ina Hulsegge, Aniek C. Bouwman, Martijn F. L. Derks

{"title":"genomeprofile: Unveiling the genomic profile for livestock breeding through comprehensive SNP array-based genotyping","authors":"Ina Hulsegge, Aniek C. Bouwman, Martijn F. L. Derks","doi":"10.1111/age.13466","DOIUrl":"10.1111/age.13466","url":null,"abstract":"In livestock breeding, single nucleotide polymorphism arrays have become a cornerstone of modern livestock breeding. SNP arrays facilitate the identification of genetic markers linked to economically important traits and provide a powerful tool for predicting breeding values. However, conventional breeding programs often overlook additional genomic features contained in the SNP array data that can provide valuable insights into the genetic diversity, copy number variation, inbreeding levels and potential challenges in breeding lines. Here we present genomeprofile, a tool using SNP array-based genomic data, offering a comprehensive profile of breeding animals including the identification of copy number variants and runs of homozygosity, and screening for aneuploidy. By integrating these features into the breeding landscape, genomeprofile enables a more comprehensive picture of genomic variation, ultimately enhancing precision breeding strategies. To illustrate the practicality and efficacy of genomeprofile, we applied the tool to a dataset of four pig breeding lines. The genomeprofile tool is a user-friendly tool that processes genotype data in finalreport or plink ped format efficiently into useful output. The output contains copy number variations, runs of homozygosity, selection signatures, aneuploidy and inbreeding per individual and across populations. This allows breeding companies and researchers to identify unique individuals or regions in the genome of interest based on routinely collected data.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13466","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multiomic meta-analysis suggests a correlation between steroid hormone-related genes and litter size in goats 多组元分析表明，山羊的类固醇激素相关基因与产仔数之间存在相关性。

IF 1.8 3区生物学

Animal genetics Pub Date : 2024-07-17 DOI: 10.1111/age.13464

Cheng-Li Liu, Hui-Long Mou, Ri-Su Na, Xiao Wang, Peng-Fei Hu, Simone Ceccobelli, Yong-Fu Huang, Guang-Xin E

{"title":"Multiomic meta-analysis suggests a correlation between steroid hormone-related genes and litter size in goats","authors":"Cheng-Li Liu, Hui-Long Mou, Ri-Su Na, Xiao Wang, Peng-Fei Hu, Simone Ceccobelli, Yong-Fu Huang, Guang-Xin E","doi":"10.1111/age.13464","DOIUrl":"10.1111/age.13464","url":null,"abstract":"Litter size is a key indicator of production performance in livestock. However, its genetic basis in goats remains poorly understood. In this work, a genome-wide selection sweep analysis (GWSA) on 100 published goat genomes with different litter rates was performed for the first time to identify candidate genes related to kidding rate. This analysis was combined with the public RNA-sequencing data of ovary tissues (follicular phase) from high- and low-yielding goats. A total of 2278 genes were identified by GWSA. Most of these genes were enriched in signaling pathways related to ovarian follicle development and hormone secretion. Moreover, 208 differentially expressed genes between groups were obtained from the ovaries of goats with different litter sizes. These genes were substantially enriched in the cholesterol and steroid synthesis signaling pathways. Meanwhile, the weighted gene co-expression network was used to perform modular analysis of differentially expressed genes. The results showed that seven modules were reconstructed, of which one module showed a very strong correlation with litter size (r = −0.51 and p-value <0.001). There were 51 genes in this module, and 39 hub genes were screened by Pearson's correlation coefficient between core genes > 0.4, correlation coefficient between module members > 0.80 and intra-module connectivity ≥5. Finally, based on the results of GWSA and hub gene Venn analysis, seven key genes (ACSS2, HECW2, KDR, LHCGR, NAMPT, PTGFR and TFPI) were found to be associated with steroid synthesis and follicle growth development. This work contributes to understanding of the genetic basis of goat litter size and provides theoretical support for goat molecular breeding.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

EquCab_Finn: A new reference genome assembly for the domestic horse, Finnhorse EquCab_Finn：家马芬马的新参考基因组组装。

IF 1.8 3区生物学

Animal genetics Pub Date : 2024-07-10 DOI: 10.1111/age.13463

Kisun Pokharel, Melak Weldenegodguad, Tiina Reilas, Juha Kantanen

引用次数: 0

Genomic analysis links the American mink Royal pastel coat phenotype to retroviral element type 1 insertion in the HPS3 gene 基因组分析将美洲水貂的皇家粉色被毛表型与 HPS3 基因中的 1 型逆转录病毒元件插入联系起来。

IF 1.8 3区生物学

Animal genetics Pub Date : 2024-07-02 DOI: 10.1111/age.13461

Andrey D. Manakhov, Nelli A. Aarakelyan, Adela V. Lapteacru, Tatiana V. Andreeva, Oleg V. Trapezov, Evgeny I. Rogaev

{"title":"Genomic analysis links the American mink Royal pastel coat phenotype to retroviral element type 1 insertion in the HPS3 gene","authors":"Andrey D. Manakhov, Nelli A. Aarakelyan, Adela V. Lapteacru, Tatiana V. Andreeva, Oleg V. Trapezov, Evgeny I. Rogaev","doi":"10.1111/age.13461","DOIUrl":"10.1111/age.13461","url":null,"abstract":"To date, only 10 of the more than 30 fur colours that had been observed in American mink (Neogale vison) have been linked to specific genes. The Royal pastel fur colour is part of a large family of brownish colours that are quite similar to one another, making breeding and selecting processes more difficult. Here we carried out whole-genome sequencing of five American minks with Royal pastel (b/b) phenotypes originating from two distinct mink populations. We identified an insertion of endogenous retroviral element type 1 (ERV1) into the first intron of the gene encoding the HPS3 protein, which regulates the trafficking of tyrosinase-containing vesicles to maturing melanosomes. With Cas9-targeted nanopore sequencing, we reconstructed the full-length sequence of the 11.7 Kb ERV1 insertion and observed hypermethylation that spread to the HPS3 gene promoter region. These findings highlight the role of HPS3 in the formation of melanosomes and melanin, as well as the genetic process regulating the intensity and spectrum of hair colour. Moreover, in mink breeding projects, these data are also useful for tracking economically important fur qualities.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Construction of a high-density linkage map and QTL detection for growth traits in South African abalone (Haliotis midae) 构建南非鲍鱼（Haliotis midae）生长性状的高密度连接图和 QTL 检测。

IF 1.8 3区生物学

Animal genetics Pub Date : 2024-06-30 DOI: 10.1111/age.13462

Thendo Stanley Tshilate, Edson Ishengoma, Clint Rhode

{"title":"Construction of a high-density linkage map and QTL detection for growth traits in South African abalone (Haliotis midae)","authors":"Thendo Stanley Tshilate, Edson Ishengoma, Clint Rhode","doi":"10.1111/age.13462","DOIUrl":"10.1111/age.13462","url":null,"abstract":"Haliotis midae is one of the most important molluscs in South African commercial aquaculture. In this study, a high-resolution integrated linkage map was constructed, and QTL identified using 2b-RADseq for genotyping SNPs in three families. The final integrated linkage map was composed by merging the individual family maps, resulting in 3290 informative SNPs mapping to 18 linkage groups, conforming to the known haploid chromosome number for H. midae. The total map spanned 1798.25 cM with an average marker interval of 0.55 cM, representing a genome coverage of 98.76%. QTL analysis, across all three families, resulted in a total of five QTL identified for growth-related traits, shell width, shell length, and total body weight. For shell width and total body weight, one QTL was identified for each trait respectively, whilst three QTL were identified for shell length. The identified QTL respectively explained between 7.20% and 11.40% of the observed phenotypic variance. All three traits were significantly correlated (r = 0.862–0.970; p < 0.01) and shared overlapping QTL. The QTL for growth traits were mapped back to the H. midae draft genome and BLAST searches revealed the identity of candidate genes, such as egf-1, megf10, megf6, tnx, sevp1, kcp, notch1, and scube2 with possible functional roles in H. midae growth. The constructed high-density linkage map and mapped QTL have given valuable insights regarding the genetic architecture of growth-related traits and will be important genetic resources for marker-assisted selection. It remains, however, important to validate causal variants through linkage disequilibrium fine mapping in future.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13462","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A metagenomic survey of the fecal microbiome of the African savanna elephant (Loxodonta africana) 非洲草原象（Loxodonta africana）粪便微生物组元基因组调查。

IF 1.8 3区生物学

Animal genetics Pub Date : 2024-06-24 DOI: 10.1111/age.13458

Louis Lategan du Preez, Elzette van der Walt, Angel Valverde, Christopher Rothmann, Frederick Wilhelm Cornelius Neser, Errol Duncan Cason

{"title":"A metagenomic survey of the fecal microbiome of the African savanna elephant (Loxodonta africana)","authors":"Louis Lategan du Preez, Elzette van der Walt, Angel Valverde, Christopher Rothmann, Frederick Wilhelm Cornelius Neser, Errol Duncan Cason","doi":"10.1111/age.13458","DOIUrl":"10.1111/age.13458","url":null,"abstract":"The African savanna elephant (Loxodonta africana) is the largest terrestrial animal on Earth and is found primarily in Southern and Eastern Africa. It is a hindgut, colonic fermenter and subsists on a diet of raw plant materials found in its grazing area. In this study the bacterial, archaeal and fungal populations of seven African savanna elephant fecal metagenomes were first characterized using amplicon sequencing. On the genus level it was observed that the p-1088-a5 gut group in the bacteriome, Methanocorpusulum and Methanobrevibacter in the archaeome and Alternaria, Aurobasidium, Didymella and Preussia in the mycome, predominated. Subsequently, metagenomic shotgun sequencing was employed to identify possible functional pathways and carbohydrate-active enzymes (CAZymes). Carbohydrate catabolic pathways represented the main degradation pathways, and the fecal metagenome was enriched in the glycohydroside (GH) class of CAZymes. Additionally, the top GH families identified – GH43, GH2, GH13 and GH3 – are known to be associated with cellulytic, hemicellulytic and pectolytic activities. Finally, the CAZymes families identified in the African savanna elephant were compared with those found in the Asian elephant and it was demonstrated that there is a unique repository of CAZymes that could be leveraged in the biotechnological context such as the degradation of lignocellulose for the production of second-generation biofuels and energy.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13458","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0