Animal genetics最新文献_第7页

Analysis of genetic variants in protein-coding genes of Aoluguya reindeer based on the whole-genome data 基于全基因组数据的 Aoluguya 驯鹿蛋白质编码基因遗传变异分析。

IF 2.4 3区生物学

Animal genetics Pub Date : 2024-02-06 DOI: 10.1111/age.13402

Wenfeng Yi, Mingyue Hu, Lulu Shi, Ting Li, Hao Sun, Lihong Qin, Shouqing Yan

引用次数: 0

H3K27ac modification and transcription characteristics of adipose and muscle tissues in Chuxiang Black pig 竹乡黑猪脂肪和肌肉组织的 H3K27ac 修饰及转录特征

IF 2.4 3区生物学

Animal genetics Pub Date : 2024-01-31 DOI: 10.1111/age.13400

Renzhuo Kuang, Zhixiang Xu, Honghong Zhou, Zhao Zhang, Hao Peng, Daoyuan Wang, Xuewen Xu, Shuhong Zhao, Yunxia Zhao, Mengjin Zhu

{"title":"H3K27ac modification and transcription characteristics of adipose and muscle tissues in Chuxiang Black pig","authors":"Renzhuo Kuang, Zhixiang Xu, Honghong Zhou, Zhao Zhang, Hao Peng, Daoyuan Wang, Xuewen Xu, Shuhong Zhao, Yunxia Zhao, Mengjin Zhu","doi":"10.1111/age.13400","DOIUrl":"10.1111/age.13400","url":null,"abstract":"The establishment of high-quality pork breeds for improving meat quality in the pig industry is needed. The Chuxiang Black (CX) pig is a new breed developed from Chinese local pigs and Western lean pigs that has a high proportion of lean meat and excellent meat quality. However, the characteristics of cis-regulatory elements in CX pigs are still unknown. In this study, cis-regulatory elements of muscle and adipose tissues in CX pigs were investigated using ChIP-seq and RNA sequencing. Compared with the reported cis-regulatory elements of muscle and adipose tissues, 1768 and 1012 highly activated enhancers and 433 and 275 highly activated promoters in CX muscle and adipose tissues were identified, respectively. Motif analysis showed that transcription factors, such as MEF2A and MEF2C, were core regulators of highly activated enhancers and promoters in muscle. Similarly, the transcription factors JUNB and CUX1 were identified as essential for highly activated enhancers and promoters in CX adipose tissue. These results enrich the resources for the analysis of cis-regulatory elements in the pig genome and provide new basic data for further meat quality improvement through breeding in pigs.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139656470","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

Smartphone-based digital phenotyping for genome-wide association study of intramuscular fat traits in longissimus dorsi muscle of pigs 基于智能手机的猪背阔肌肌肉脂肪性状全基因组关联研究数字表型。

IF 2.4 3区生物学

Animal genetics Pub Date : 2024-01-30 DOI: 10.1111/age.13401

Yang Shen, Yuxi Chen, Shufeng Zhang, Ze Wu, Xiaoyu Lu, Weizhen Liu, Bang Liu, Xiang Zhou

{"title":"Smartphone-based digital phenotyping for genome-wide association study of intramuscular fat traits in longissimus dorsi muscle of pigs","authors":"Yang Shen, Yuxi Chen, Shufeng Zhang, Ze Wu, Xiaoyu Lu, Weizhen Liu, Bang Liu, Xiang Zhou","doi":"10.1111/age.13401","DOIUrl":"10.1111/age.13401","url":null,"abstract":"Intramuscular fat (IMF) content and distribution significantly contribute to the eating quality of pork. However, the current methods used for measuring these traits are complex, time-consuming and costly. To simplify the measurement process, this study developed a smartphone application (App) called Pork IMF. This App serves as a rapid and portable phenotyping tool for acquiring pork images and extracting the image-based IMF traits through embedded deep-learning algorithms. Utilizing this App, we collected the IMF traits of the longissimus dorsi muscle in a crossbred population of Large White × Tongcheng pigs. Genome-wide association studies detected 13 and 16 SNPs that were significantly associated with IMF content and distribution, respectively, highlighting NR2F2, MCTP2, MTLN, ST3GAL5, NDUFAB1 and PID1 as candidate genes. Our research introduces a user-friendly digital phenotyping technology for quantifying IMF traits and suggests candidate genes and SNPs for genetic improvement of IMF traits in pigs.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139641460","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

Canine coat color E locus updates: Identification of a new MC1R variant causing ‘sable’ coat color in English Cocker Spaniels and a proposed update to the E locus dominance hierarchy 犬毛色 E 基因座更新：鉴定导致英国可卡犬 "黑貂色 "毛色的新 MC1R 变体，并建议更新 E 基因座的优势等级。

IF 2.4 3区生物学

Animal genetics Pub Date : 2024-01-29 DOI: 10.1111/age.13398

Leena Honkanen, Robert Loechel, Stephen Davison, Jonas Donner, Heidi Anderson

{"title":"Canine coat color E locus updates: Identification of a new MC1R variant causing ‘sable’ coat color in English Cocker Spaniels and a proposed update to the E locus dominance hierarchy","authors":"Leena Honkanen, Robert Loechel, Stephen Davison, Jonas Donner, Heidi Anderson","doi":"10.1111/age.13398","DOIUrl":"10.1111/age.13398","url":null,"abstract":"The coat color phenotype ‘sable’ occurs in the English Cocker Spaniel dog breed. It closely resembles other canine color patterns known as domino/grizzle/pied (eA allele) and grizzle/domino (eG allele) determined by variants in the melanocortin 1 receptor gene (MC1R; ‘extension’ or E locus), a key multi-allele regulator of coat color. We examined genetic variation in MC1R, and found one new non-synonymous variant, c.250G>A (p.(Asp84Asn)), consistently associated with the English Cocker Spaniel ‘sable’ phenotype. We propose calling this newly identified allele eH and further show that the eA, eH and eG (previously known as EG) alleles associate with similar phenotypes in dogs impacting genotypes regulated by beta-defensin 103 gene (CBD103; K locus) and agouti signaling protein gene (ASIP; A locus) in the absence of the EM and E alleles. This suggests that all three alleles are putative reduced-function variants of the MC1R gene. We propose the revised and updated E locus dominance hierarchy to be EM > E > eA/eH/eG > e1–3.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13398","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139568868","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

Whole genome resequencing reveals candidate genes for postaxial polydactyly in Large White pigs 全基因组重测序揭示了大白猪后轴多指畸形的候选基因。

IF 2.4 3区生物学

Animal genetics Pub Date : 2024-01-29 DOI: 10.1111/age.13399

Yongle Hao, Yunlei Song, Fei Chen, Jianhong Tang

{"title":"Whole genome resequencing reveals candidate genes for postaxial polydactyly in Large White pigs","authors":"Yongle Hao, Yunlei Song, Fei Chen, Jianhong Tang","doi":"10.1111/age.13399","DOIUrl":"10.1111/age.13399","url":null,"abstract":"Polydactyly is a genetic abnormality that affects both pig welfare and industry profits. Despite efforts to explore the genetic basis of pig polydactyly, progress remains limited. In this study, we analyzed a group of Large White pigs with postaxial polydactyly, including 29 cases and 79 controls from 24 families. High-depth sequencing was performed on 20 pigs, while low-depth sequencing was improved through imputation for the remaining pigs. A genome-wide association study (GWAS) and genetic differentiation were conducted using the resequencing dataset, resulting in the identification of 48 significantly associated SNPs and 27 candidate regions. The genetic differentiation regions on chromosomes 5 and 18, which harbored GWAS-identified SNPs, were delineated as confidence regions. The confidence region at Chr18: 1.850–1.925 Mb covers the fifth intron of LMBR1, a gene that contains an important regulatory element for SHH, known as ZRS. Mutations in this ZRS have been found to cause polydactyly in animals and humans. Therefore, we propose LMBR1 as a prospective candidate gene for postaxial polydactyly. These findings emphasize the importance of exploring the role of ZRS within LMBR1 in the pathogenesis of polydactyly in pigs.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139568956","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

Identification of genomic regions associated with resistance to gastrointestinal parasites in an indigenous sheep by single- and multiple-locus methods 通过单病灶和多病灶方法鉴定与一种土著绵羊对胃肠道寄生虫的抵抗力有关的基因组区域。

IF 2.4 3区生物学

Animal genetics Pub Date : 2024-01-10 DOI: 10.1111/age.13392

S. A. Rafat, M. Barbato, R. Hajializadeh Valilou, G. H. Moghaddam, A. Nematollahi, K. Periasamy, R. Pichler, P. Ajmone Marsan

引用次数: 0

Differential expression of ASIP transcripts reveals genetic mechanism underpinning black-tail independence from body plumage in yellow-bodied chickens ASIP转录本的差异表达揭示了黄腹鸡黑尾独立于体羽的遗传机制。

IF 2.4 3区生物学

Animal genetics Pub Date : 2024-01-09 DOI: 10.1111/age.13395

Xiaotong Zheng, Jianfei Chen, Ruixue Nie, Huanhuan Miao, Ziwei Chen, Jiaheng He, Yinku Xie, Hao Zhang

{"title":"Differential expression of ASIP transcripts reveals genetic mechanism underpinning black-tail independence from body plumage in yellow-bodied chickens","authors":"Xiaotong Zheng, Jianfei Chen, Ruixue Nie, Huanhuan Miao, Ziwei Chen, Jiaheng He, Yinku Xie, Hao Zhang","doi":"10.1111/age.13395","DOIUrl":"10.1111/age.13395","url":null,"abstract":"The genetic foundation of chicken body plumage color has been extensively studied. However, little attention has been paid to the inheritance patterns and molecular mechanisms underlying the formation of distal feather colors (tail and wingtip). Differences in these colors are common; for example, the Chinese Huiyang Beard chicken has black tail feathers, but yellow body plumage. Here, the hybrid offspring of Huiyang Beard and White Leghorn chickens were used to study the inheritance patterns of tail-feather color. The expression levels of pigment genes in differently colored feather follicles were analyzed using quantitative real-time PCR. The results showed that genetic regulation of tail-feather color was independent of body-plumage color. The Dominant White locus inhibited eumelanin synthesis in tail feathers without affecting the formation of yellow body plumage, whereas the Silver locus had the opposite effect. The expression of agouti signaling protein (ASIP) gene class 1 transcripts was significantly lower in black tail-feather follicles than in yellow body follicles, whereas tyrosinase-related protein 1 (TYRP1) gene expression was significantly higher in black tail feathers. These differentially expressed genes were confirmed to exert an effect on eumelanin and pheomelanin formation in feathers, thus influencing the regulation of chicken tail-feather color. In conclusion, this study lays the foundation for further research on the genetic mechanisms of regional differences in feather color, contributing to a better understanding of plumage pigmentation in chickens.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139401523","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

Identification of population-informative markers from high-density genotyping data through combined feature selection and machine learning algorithms: Application to European autochthonous and cosmopolitan pig breeds 通过组合特征选择和机器学习算法从高密度基因分型数据中识别种群信息标记：欧洲本土猪种和世界猪种的应用。

IF 2.4 3区生物学

Animal genetics Pub Date : 2024-01-08 DOI: 10.1111/age.13396

Giuseppina Schiavo, Francesca Bertolini, Samuele Bovo, Giuliano Galimberti, María Muñoz, Riccardo Bozzi, Marjeta Čandek-Potokar, Cristina Óvilo, Luca Fontanesi

{"title":"Identification of population-informative markers from high-density genotyping data through combined feature selection and machine learning algorithms: Application to European autochthonous and cosmopolitan pig breeds","authors":"Giuseppina Schiavo, Francesca Bertolini, Samuele Bovo, Giuliano Galimberti, María Muñoz, Riccardo Bozzi, Marjeta Čandek-Potokar, Cristina Óvilo, Luca Fontanesi","doi":"10.1111/age.13396","DOIUrl":"10.1111/age.13396","url":null,"abstract":"Large genotyping datasets, obtained from high-density single nucleotide polymorphism (SNP) arrays, developed for different livestock species, can be used to describe and differentiate breeds or populations. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this study, we applied the Boruta algorithm, a wrapper of the machine learning random forest algorithm, on a database of 23 European pig breeds (20 autochthonous and three cosmopolitan breeds) genotyped with a 70k SNP chip, to pre-select informative SNPs. To identify different sets of SNPs, these pre-selected markers were then ranked with random forest based on their mean decrease accuracy and mean decrease gene indexes. We evaluated the efficiency of these subsets for breed classification and the usefulness of this approach to detect candidate genes affecting breed-specific phenotypes and relevant production traits that might differ among breeds. The lowest overall classification error (2.3%) was reached with a subpanel including only 398 SNPs (ranked based on their mean decrease accuracy), with no classification error in seven breeds using up to 49 SNPs. Several SNPs of these selected subpanels were in genomic regions in which previous studies had identified signatures of selection or genes associated with morphological or production traits that distinguish the analysed breeds. Therefore, even if these approaches have not been originally designed to identify signatures of selection, the obtained results showed that they could potentially be useful for this purpose.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13396","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139401442","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

Genome-wide association analysis revealed new QTL and candidate genes affecting the teat number in Dutch Large White pigs 全基因组关联分析揭示了影响荷兰大白猪乳头数的新 QTL 和候选基因。

IF 2.4 3区生物学

Animal genetics Pub Date : 2024-01-08 DOI: 10.1111/age.13397

Michao Deng, Zijian Qiu, Chenxi Liu, Lijing Zhong, Xinfeng Fan, Yuquan Han, Ran Wang, Pinghua Li, Ruihua Huang, Qingbo Zhao

{"title":"Genome-wide association analysis revealed new QTL and candidate genes affecting the teat number in Dutch Large White pigs","authors":"Michao Deng, Zijian Qiu, Chenxi Liu, Lijing Zhong, Xinfeng Fan, Yuquan Han, Ran Wang, Pinghua Li, Ruihua Huang, Qingbo Zhao","doi":"10.1111/age.13397","DOIUrl":"10.1111/age.13397","url":null,"abstract":"Teat number (TNUM) is an important reproductive trait of sows, which affects the weaning survival rate of piglets. In this study, 1166 Dutch Large White pigs with TNUM phenotype were used as the research object. These pigs were genotyped by 50K SNP chip and the chip data were further imputed to the resequencing level. The estimated heritabilities of left teat number (LTN), right teat number (RTN) and total teat number (TTN) were 0.21, 0.19 and 0.3, respectively. Based on chip data, significant SNPs for RTN on SSC2, SSC5, SSC9 and SSC13 were identified using genome-wide association analysis (GWAS). Significant SNPs for TTN were identified on SSC2, SSC5 and SSC7. Based on imputed data, the GWAS identified a significant SNP (rs329158522) for LTN on SSC17, two significant SNPs (rs342855242 and rs80813115) for RTN on SSC2 and SSC9, and two significant SNPs (rs327003548 and rs326943811) for TTN on SSC5 and SSC6. Among them, four novel QTL were discovered. The Bayesian fine-mapping method was used to fine map the QTL identified in the GWAS of the imputed data, and the confidence intervals of QTL affecting LTN (SSC17: 45.22–46.20 Mb), RTN (SSC9: 122.18–122.80 Mb) and TTN (SSC5: 14.01–15.91 Mb, SSC6: 120.06–121.25 Mb) were detected. A total of 52 candidate genes were obtained. Furthermore, we identified five candidate genes, WNT10B, AQP5, FMNL3, NUAK1 and CKAP4, for the first time, which involved in breast development and other related functions by gene annotation. Overall, this study provides new molecular markers for the breeding of teat number in pigs.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13397","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139401441","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

Evaluating three strategies of genome-wide association analysis for integrating data from multiple populations 评估整合多人群数据的三种全基因组关联分析策略。

IF 2.4 3区生物学

Animal genetics Pub Date : 2024-01-07 DOI: 10.1111/age.13394

Zhanming Zhong, Guangzhen Li, Zhiting Xu, Haonan Zeng, Jinyan Teng, Xueyan Feng, Shuqi Diao, Yahui Gao, Jiaqi Li, Zhe Zhang

{"title":"Evaluating three strategies of genome-wide association analysis for integrating data from multiple populations","authors":"Zhanming Zhong, Guangzhen Li, Zhiting Xu, Haonan Zeng, Jinyan Teng, Xueyan Feng, Shuqi Diao, Yahui Gao, Jiaqi Li, Zhe Zhang","doi":"10.1111/age.13394","DOIUrl":"10.1111/age.13394","url":null,"abstract":"In livestock, genome-wide association studies (GWAS) are usually conducted in a single population (single-GWAS) with limited sample size and detection power. To enhance the detection power of GWAS, meta-analysis of GWAS (meta-GWAS) and mega-analysis of GWAS (mega-GWAS) have been proposed to integrate data from multiple populations at the level of summary statistics or individual data, respectively. However, there is a lack of comparison for these different strategies, which makes it difficult to guide the best practice of GWAS integrating data from multiple study populations. To maximize the comparison of different association analysis strategies across multiple populations, we conducted single-GWAS, meta-GWAS, and mega-GWAS for the backfat thickness of 100 kg (BFT_100) and days to 100 kg (DAYS_100) within each of the three commercial pig breeds (Duroc, Yorkshire, and Landrace). Based on controlling the genome inflation factor to one, we calculated corrected p-values (pC). In Yorkshire, with the largest sample size, mega-GWAS, meta-GWAS and single-GWAS detected 149, 38 and 20 significant SNPs (pC < 1E-5) associated with BFT_100, as well as 26, four, and one QTL, respectively. Among them, pC of SNPs from mega-GWAS was the lowest, followed by meta-GWAS and single-GWAS. The correlation of pC among the three GWAS strategies ranged from 0.60 to 0.75 and the correlation of SNP effect values between meta-GWAS and mega-GWAS was 0.74, all showing good agreement. Collectively, even though there are differences in the integration of individual data or summary statistics, integrating data from multiple populations is an effective means of genetic argument for complex traits, especially mega-GWAS versus single-GWAS.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139377129","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