Animal genetics最新文献_第10页

Functional SNPs in SYISL promoter significantly affect muscle fiber density and muscle traits in pigs SYISL启动子中的功能性SNPs显著影响猪的肌肉纤维密度和肌肉性状。

IF 2.4 3区生物学

Animal genetics Pub Date : 2023-10-25 DOI: 10.1111/age.13370

Wei Lv, Yaxin Peng, Jingjing Hu, Mingfei Zhu, Yangcang Mao, Litong Wang, Guoshui Wang, Zaiyan Xu, Wangjun Wu, Bo Zuo

{"title":"Functional SNPs in SYISL promoter significantly affect muscle fiber density and muscle traits in pigs","authors":"Wei Lv, Yaxin Peng, Jingjing Hu, Mingfei Zhu, Yangcang Mao, Litong Wang, Guoshui Wang, Zaiyan Xu, Wangjun Wu, Bo Zuo","doi":"10.1111/age.13370","DOIUrl":"10.1111/age.13370","url":null,"abstract":"Our previous studies showed that SYISL is a negative regulator of muscle growth and regeneration in mice, pigs and humans. SYISL knockout resulted in an increase in the density of muscle fibers and muscle growth. However, it is unclear whether there are natural mutations in pig SYNPO2 intron sense-overlapping lncRNA (pSYISL) that affect the expression of pSYISL and muscle growth traits. In this study, three SNPs in exons and six SNPs within the promoter of pSYISL were identified. Association analysis showed that the two SNPs in exons are significantly associated with loin muscle area (p < 0.05); the six SNPs in the promoter that show complete linkage are significantly associated with live backfat thickness and live loin muscle area in American Large White pigs. Bioinformatics and luciferase reporter assays as well as in vitro binding experiments indicated that the mutation of SNP rs702045770 (g.539G>A) leads to the loss of YY1 binding to the promoter, thus affecting the expression level of pSYISL, and we found that Jiangshan Black pigs with genotype GG have a higher expression level of pSYISL than genotype AA individuals, but the muscle fiber density was significantly lower than in genotype AA individuals. Furthermore, the association analysis showed that the carcass backfat thickness of genotype GG of SNP rs702045770 was significantly higher than that of other genotypes in (Pietrain × Duroc) × (Landrace × Yorkshire) crossbred pigs (p < 0.05). The glycolytic potential of genotype GG was significantly higher than that of other genotypes (p < 0.05). These results provide novel insight into the identification of functional SNPs in non-coding genomic regions.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50160433","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

Rapid genotyping of bovine MC1R gene c.296T>C and c.310delG haplotypes using high-resolution melting analysis 使用高分辨率熔解分析快速分型牛MC1R基因c.296T>c和c.310delG单倍型。

IF 2.4 3区生物学

Animal genetics Pub Date : 2023-10-24 DOI: 10.1111/age.13373

Rui Hong, Yi Yan, Changhong Zhu, Fuyuan Zuo, Gong-Wei Zhang

引用次数: 0

The 4 bp deletion mutation in HOXD1 gene determines the polycerate trait in Chinese Sishui fur sheep 4 HOXD1基因的bp缺失突变决定了中国泗水毛羊的多聚体性状。

IF 2.4 3区生物学

Animal genetics Pub Date : 2023-10-17 DOI: 10.1111/age.13369

Cheng Zhang, Huan Zhang, Tenggang Di, Guan Wang, Fengyi Gao, Zhiqiang Li, Ming Li, Guangli Yang

引用次数: 0

Identification of potential biomarkers associated with meat tenderness in Hanwoo (Korean cattle): An expression quantitative trait loci analysis 韩屋牛肉质嫩度相关潜在生物标志物的鉴定：表达定量性状基因座分析。

IF 2.4 3区生物学

Animal genetics Pub Date : 2023-10-12 DOI: 10.1111/age.13360

Yoonji Chung, Sun Sik Jang, Dong Hun Kang, Yeong Kuk Kim, Hyun Joo Kim, Ki Yong Chung, Inchul Choi, Seung Hwan Lee

{"title":"Identification of potential biomarkers associated with meat tenderness in Hanwoo (Korean cattle): An expression quantitative trait loci analysis","authors":"Yoonji Chung, Sun Sik Jang, Dong Hun Kang, Yeong Kuk Kim, Hyun Joo Kim, Ki Yong Chung, Inchul Choi, Seung Hwan Lee","doi":"10.1111/age.13360","DOIUrl":"10.1111/age.13360","url":null,"abstract":"Meat tenderness is considered the most important trait contributing to beef quality, level of consumer satisfaction, willingness to pay premium prices and industry profit. Genomic selection method would be helpful for genetic improvement of traits with low heritability and that are difficult to measure. The identification of core genes can aid genomic selection for complex traits with low heritability that are difficult to measure. We performed statistical analysis of associations between longissimus dorsi muscle tenderness and gene expression in 20 Hanwoo cattle, using Warner–Bratzler shear force and RNAseq data, respectively. We found a total of 166 core genes, from which six (ASAP1, CAPN5, ELN, SUMF2, TTC8 and MGAT4A) were regulated by 16 cis-expression quantitative trait loci (eQTL) SNPs. Notably, we found that a cis-eQTL SNP of the ELN gene contained an MFZ-1 binding site in its putative promoter region. These findings provide useful information for genomic prediction of beef tenderness in Hanwoo cattle.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41188904","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

Genome-wide association study using a single-step approach for teat number in Duroc, Landrace and Yorkshire pigs in Korea 韩国杜洛克、长白猪和约克郡猪乳头数量的全基因组关联研究。

IF 2.4 3区生物学

Animal genetics Pub Date : 2023-10-09 DOI: 10.1111/age.13357

Jun Park, Kyoung-Tag Do, Kyung-Do Park, Hak-Kyo Lee

{"title":"Genome-wide association study using a single-step approach for teat number in Duroc, Landrace and Yorkshire pigs in Korea","authors":"Jun Park, Kyoung-Tag Do, Kyung-Do Park, Hak-Kyo Lee","doi":"10.1111/age.13357","DOIUrl":"10.1111/age.13357","url":null,"abstract":"We investigated the genetic basis of teat number in sows, which is an important factor in their reproductive performance. We collected genotyping data from 20 353 pigs of three breeds (Duroc, Landrace and Yorkshire) using the Porcine SNP60K Bead Chip, and analyzed phenotypic data from 240 603 pigs. The heritability values of total teat number were 0.33 ± 0.02, 0.51 ± 0.01 and 0.50 ± 0.01 in Duroc, Landrace and Yorkshire pigs, respectively. A genome-wide association study was used to identify significant chromosomal regions associated with teat number in SSC7 and SSC9 in Duroc pig, SSC3, SSC7 and SSC18 in Landrace pig, and SSC7, SSC8 and SSC10 in Yorkshire pig. Among the markers, MARC0038565, located between the vertnin (VRTN) and synapse differentiation-inducing 1-like (SYNDIG1L) genes, showed the strongest association in the Duroc pig and was significant in all breeds. In Landrace and Yorkshire pigs, the most significant markers were located within the apoptosis resistant E3 ubiquitin protein ligase 1 (AREL1) and latent transforming growth factor beta-binding protein 2 (LTBP2) genes in SSC7, respectively. VRTN is a candidate gene regulating the teat number. Most markers were located in SSC7, indicating their significance in determining teat number and their potential as valuable genomic selection targets for improving this trait. Extensive linkage disequilibrium blocks were identified in SSC7, supporting their use in genomic selection strategies. Our study provides valuable insights into the genetic architecture of teat numbers in pigs, and helps identify candidate genes and genomic regions that may contribute to this economically important trait.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41181842","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

A new method for molecular sex identification in the Japanese quail (Coturnix japonica) 日本鹌鹑分子性别鉴定的新方法。

IF 2.4 3区生物学

Animal genetics Pub Date : 2023-10-09 DOI: 10.1111/age.13368

Xiaoxu Jia, Wanqiang Chen, Xiujun Tang, Junxian Lu, Yanfeng Fan, Yushi Gao

引用次数: 0

Genotyping-by-sequencing reveals a high number and quality of single nucleotide polymorphisms in guinea pigs (Cavia porcellus) from the Peruvian Andes 通过测序进行的基因分型显示，来自秘鲁安第斯山脉的豚鼠（Cavia porcellus）具有大量和高质量的单核苷酸多态性。

IF 2.4 3区生物学

Animal genetics Pub Date : 2023-10-05 DOI: 10.1111/age.13367

María Victoria Borja Lozano, Bianca Vigil Santillán, Manuel J. More Montoya, Jonathan A. Morón Barraza, Aura Liz García-Serquén, Gustavo Gutiérrez Reynoso, Claudia E. Yalta-Macedo

{"title":"Genotyping-by-sequencing reveals a high number and quality of single nucleotide polymorphisms in guinea pigs (Cavia porcellus) from the Peruvian Andes","authors":"María Victoria Borja Lozano, Bianca Vigil Santillán, Manuel J. More Montoya, Jonathan A. Morón Barraza, Aura Liz García-Serquén, Gustavo Gutiérrez Reynoso, Claudia E. Yalta-Macedo","doi":"10.1111/age.13367","DOIUrl":"10.1111/age.13367","url":null,"abstract":"Guinea pigs are a major source of animal protein for Peruvian Andean families. Despite the economic and cultural relevance of guinea pigs, their genomic characterization has been scarcely addressed. Genotyping-by-sequencing (GBS) has emerged as an affordable alternative to genotyping of livestock and native animals. Here, we report the use of GBS for single nucleotide polymorphism (SNP) discovery of traditionally raised guinea pigs from six regions of the Peruvian Andes and one group of breeding animals. The paired-end (2 × 150 bp) sequencing of 40 guinea pig DNA samples generated a mean of 6.4 million high-quality sequencing reads per sample. We obtained an average sequencing depth of 10× with an 88.5% mapping rate to the Cavia porcellus reference genome. A total of 279 965 SNPs (102 SNPs/Mbp) were identified after variant calling and quality filtering. Based on this SNP set, we assessed the genetic diversity and distance within our selected guinea pig populations. An overall average minor allele frequency of 0.13, an observed heterozygosity of 0.31, an expected heterozygosity of 0.35, and an F-value of 0.1 were obtained, while the SNP-based neighbor-joining tree suggests a closer genetic relationship between individuals from geographically close locations. We showed that GBS is a cost-effective tool for SNP discovery and genetic characterization of Peruvian guinea pig populations. Therefore, it may be considered as a suitable and affordable tool for genomic characterization of poorly studied native animal species.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41108338","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

Advances in the discovery of genetic elements underlying longissimus dorsi muscle growth and development in the pig 猪背最长肌生长发育遗传因素的发现进展。

IF 2.4 3区生物学

Animal genetics Pub Date : 2023-10-05 DOI: 10.1111/age.13365

Qingjie Zeng, Zhi-Qiang Du

{"title":"Advances in the discovery of genetic elements underlying longissimus dorsi muscle growth and development in the pig","authors":"Qingjie Zeng, Zhi-Qiang Du","doi":"10.1111/age.13365","DOIUrl":"10.1111/age.13365","url":null,"abstract":"As a major source of protein in human diets, pig meat plays a crucial role in ensuring global food security. Key determinants of meat production refer to the chemical and physical compositions or characteristics of muscle fibers, such as the number, hypertrophy potential, fiber-type conversion and intramuscular fat deposition. However, the growth and formation of muscle fibers comprises a complex process under spatio-temporal regulation, that is, the intermingled and concomitant proliferation, differentiation, migration and fusion of myoblasts. Recently, with the fast and continuous development of next-generation sequencing technology, the integration of quantitative trait loci mapping with genome-wide association studies (GWAS) has greatly helped animal geneticists to discover and explore thousands of functional or causal genetic elements underlying muscle growth and development. However, owing to the underlying complex molecular mechanisms, challenges to in-depth understanding and utilization remain, and the cost of large-scale sequencing, which requires integrated analyses of high-throughput omics data, is high. In this review, we mainly elaborate on research advances in integrative analyses (e.g. GWAS, omics) for identifying functional genes or genomic elements for longissimus dorsi muscle growth and development for different pig breeds, describing several successful transcriptome analyses and functional genomics cases, in an attempt to provide some perspective on the future functional annotation of genetic elements for muscle growth and development in pigs.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41112109","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

A whole genome scan reveals distinct features of selection in Zhaotong cattle of Yunnan province 对云南昭通牛进行全基因组扫描，发现其具有明显的选择特征。

IF 2.4 3区生物学

Animal genetics Pub Date : 2023-10-05 DOI: 10.1111/age.13363

Yang Lyu, Xiwen Guan, Xinglong Xu, Pengfei Wang, Qiaoxian Li, Manjit Panigrahi, Jicai Zhang, Ningbo Chen, Bizhi Huang, Chuzhao Lei

{"title":"A whole genome scan reveals distinct features of selection in Zhaotong cattle of Yunnan province","authors":"Yang Lyu, Xiwen Guan, Xinglong Xu, Pengfei Wang, Qiaoxian Li, Manjit Panigrahi, Jicai Zhang, Ningbo Chen, Bizhi Huang, Chuzhao Lei","doi":"10.1111/age.13363","DOIUrl":"10.1111/age.13363","url":null,"abstract":"Over the years, indigenous cattle have not only played an essential role in securing primary food sources but have also been utilized for labor by humans, making them invaluable genetic resources. The Zhaotong cattle, a native Chinese breed from the Yunnan province, possess excellent meat quality and resistance to heat and humidity. Here we used whole genome sequencing data of 104 animals to delve into the population structure, genomic diversity and potential positive selection signals in Zhaotong cattle. The findings of this study demonstrate that the genetic composition of Zhaotong cattle was primarily derived from Chinese indicine cattle and East Asian cattle. The nucleotide diversity of Zhaotong cattle was only lower than that of Chinese indicine cattle, which was much higher than that of other taurine cattle. Genome-wide selection scans detected a series of positive candidate regions containing multiple key genes related to bone development and metabolism (CA10, GABRG3, GLDN and NOTUM), meat quality traits (ALG8, LINGO2, MYO5B, PRKG1 and GABRB1), immune response (ADA2, BMF, LEF1 and PAK6) and heat resistance (EIF2AK4 and LEF1). In summary, this study supplies essential genetic insights into the genome diversity within Zhaotong cattle and provides a foundational framework for comprehending the genetic basis of indigenous cattle breeds.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41107141","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

Detection of genomic variations and selection signatures in Wagyu using whole-genome sequencing data 使用全基因组测序数据检测和牛的基因组变异和选择特征。

IF 2.4 3区生物学

Animal genetics Pub Date : 2023-10-04 DOI: 10.1111/age.13364

Lulu Shi, Mingyue Hu, Weining Lai, Wenfeng Yi, Zhengxi Liu, Hao Sun, Feng Li, Shouqing Yan

{"title":"Detection of genomic variations and selection signatures in Wagyu using whole-genome sequencing data","authors":"Lulu Shi, Mingyue Hu, Weining Lai, Wenfeng Yi, Zhengxi Liu, Hao Sun, Feng Li, Shouqing Yan","doi":"10.1111/age.13364","DOIUrl":"10.1111/age.13364","url":null,"abstract":"Wagyu is recognized for producing marbled beef with high nutritional value and flavor. Reportedly, Wagyu has been widely used to improve the meat quality of local breeds around the world. However, studies on the genetic mechanism of meat quality in Wagyu at the whole-genome level are rarely reported. Here, whole-genome sequencing data of 11 Wagyu and 115 other individuals were used to explore the genomic variations and genes under selection pressure in Wagyu. A total of 31 349 non-synonymous variants and 53 102 synonymous variants were identified in Wagyu. The population structure analysis showed that Wagyu had the closest genetic relationship with Mishima–Ushi cattle and was apparently separated from other cattle breeds. Then, composite likelihood ratio (CLR), integrated haplotype score, fixation index and cross-population composite likelihood ratio (XP-CLR) tests were performed to identify the candidate genes under positive selection in Wagyu. In total, 770 regions containing 312 genes were identified by at least three methods. Among them, 97 regions containing 27 genes were detected by all four methods. We specifically illustrate a list of interesting genes, including LRP2BP, GAA, CACNG6, CXADR, GPCPD1, KLF2, KLF13, SOX5, MYBPC1, SLC25A10, ATP8A1 and MYH15, which are associated with lipid metabolism, fat deposition, muscle development, bone development, feed intake and growth traits in Wagyu. This is the first study to explore the genomic variations and selection signatures of Wagyu at the whole-genome level. These results will provide significant help to beef cattle improvement and breeding.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41134380","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