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Single-step genome-wide association study reveals candidate genes for body mass index trait in Yunong-black pigs 单步全基因组关联研究揭示了云农黑猪体重指数性状的候选基因。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-12-23 DOI: 10.1111/age.13501
Ziyi Wu, Tengfei Dou, Jiahao Wu, Liyao Bai, Yongqian Zhang, Shengyuan Zan, Songbai Yang, Hao Zhou, Jinyi Han, Xuelei Han, Ruimin Qiao, Kejun Wang, Feng Yang, Xin-Jian Li, Xiu-Ling Li
{"title":"Single-step genome-wide association study reveals candidate genes for body mass index trait in Yunong-black pigs","authors":"Ziyi Wu,&nbsp;Tengfei Dou,&nbsp;Jiahao Wu,&nbsp;Liyao Bai,&nbsp;Yongqian Zhang,&nbsp;Shengyuan Zan,&nbsp;Songbai Yang,&nbsp;Hao Zhou,&nbsp;Jinyi Han,&nbsp;Xuelei Han,&nbsp;Ruimin Qiao,&nbsp;Kejun Wang,&nbsp;Feng Yang,&nbsp;Xin-Jian Li,&nbsp;Xiu-Ling Li","doi":"10.1111/age.13501","DOIUrl":"10.1111/age.13501","url":null,"abstract":"<p>Body mass index (BMI) can serve as a reasonable indicator of overall body fat content in pigs. This study aimed to identify underlying variants and candidate genes associated with BMI in Yunong-black pigs. A single-step genome-wide association analysis (GWAS) was performed on 1405 BMI records and 924 Yunong-black pigs genotyped using a 50 K SNP Chip. De-regressed estimated breeding values were taken as the response variable in the GWAS. The estimated heritability for BMI was 0.157. Nine significant regions were associated with BMI, accounting for 12.828% of genetic variance, with the highest region explaining 1.969% of the genetic variance. Linkage disequilibrium analysis of the nine significant regions revealed that SNPs in six single-step GWAS-identified genomic regions were all located in the linkage disequilibrium blocks. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses of the 29 protein-coding genes annotated to these regions revealed that <i>FABP2</i>, a key gene associated with BMI in human, was enriched in the fatty acid binding term and the fat digestion and absorption pathway. This study provides a better insight into the genetic architecture of the BMI trait, and offers potential molecular markers for the breeding of Yunong-black pigs.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142880923","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 TYR-iffic discovery: Identification of a second TYR variant associated with acromelanism in dogs 一项TYR流量发现:鉴定与犬肢黑症相关的第二个TYR变异。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-12-22 DOI: 10.1111/age.13496
Samantha L. Van Buren, Anushka Panjwani, Carrie J. Finno
{"title":"A TYR-iffic discovery: Identification of a second TYR variant associated with acromelanism in dogs","authors":"Samantha L. Van Buren,&nbsp;Anushka Panjwani,&nbsp;Carrie J. Finno","doi":"10.1111/age.13496","DOIUrl":"10.1111/age.13496","url":null,"abstract":"","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875731","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
Analysis of SLICK allele in African taurine and Zebu cattle breeds 非洲牛磺酸和Zebu牛品种SLICK等位基因分析。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-12-22 DOI: 10.1111/age.13499
Samrawit Gebeyehu, Bradley Heins, Tad Sonstegard, Johann Sölkner, Gábor Mészáros, Amadou Traoré, Albert Soudré
{"title":"Analysis of SLICK allele in African taurine and Zebu cattle breeds","authors":"Samrawit Gebeyehu,&nbsp;Bradley Heins,&nbsp;Tad Sonstegard,&nbsp;Johann Sölkner,&nbsp;Gábor Mészáros,&nbsp;Amadou Traoré,&nbsp;Albert Soudré","doi":"10.1111/age.13499","DOIUrl":"10.1111/age.13499","url":null,"abstract":"&lt;p&gt;The SLICK trait enhances heat tolerance by modifying physiological traits, such as improving sweating ability, and is phenotypically expressed as short and sleek coats (Davis et al., &lt;span&gt;2016&lt;/span&gt;; Olson et al., &lt;span&gt;2003&lt;/span&gt;). The SLICK coat trait in cattle is attributed to six naturally occurring truncation mutations in the prolactin receptor (PRLR) gene on bovine chromosome 20 (Flórez et al., &lt;span&gt;2020&lt;/span&gt;; Sosa et al., &lt;span&gt;2021&lt;/span&gt;). This results in frameshift mutations in the PRLR gene, particularly in exons 10 and 11, which disrupt the open reading frame, and leads to truncated receptor proteins that confer the SLICK phenotype (Davis et al., &lt;span&gt;2017&lt;/span&gt;; Porto-Neto et al., &lt;span&gt;2018&lt;/span&gt;). These mutations have been identified in many South American breeds, such as Senepol, Carora and Limonero, and the trait is inherited in an autosomal-dominant manner (Flórez et al., &lt;span&gt;2020&lt;/span&gt;; Flórez Murillo et al., &lt;span&gt;2024&lt;/span&gt;; Nicholas et al., &lt;span&gt;2024&lt;/span&gt;; Olson et al., &lt;span&gt;2003&lt;/span&gt;). The mutation was first identified in Criollo breeds: the Mexican Criollo Lechero has SLICK3 and SLICK4 at frequencies of 0.9 and 0.03; the Colombian Blanco Orejineg has SLICK1 and SLICK5 at frequencies of 0.50 and 0.38; and the Hartón del Valle has SLICK1, SLICK2, SLICK5 and SLICK6 at frequencies of 0.29, 0.18, 0.24 and 0.21 respectively (Flórez et al., &lt;span&gt;2020&lt;/span&gt;). Although the allelic frequency of the mutation is relatively low in some Criollo breeds, the autosomal-dominant inheritance pattern ensures that individuals carrying at least one copy of a SLICK allele exhibit the phenotype.&lt;/p&gt;&lt;p&gt;The SLICK allele is well documented in Criollo breeds of the Caribbean Basin, descended from Iberian taurine cattle (Flórez et al., &lt;span&gt;2020&lt;/span&gt;; Porto-Neto et al., &lt;span&gt;2018&lt;/span&gt;). The allele may also exist in African breeds because these cattle have environmental stressors similar to those of Criollo breeds. However, the specific SLICK mutation in African taurine cattle has not been identified (Xia et al., &lt;span&gt;2023&lt;/span&gt;). Although African cattle possess various tropical adaptations, it is unknown whether they exhibit the SLICK phenotype. Investigation of the presence and frequency of SLICK alleles in West African breeds is crucial for understanding the origins of these mutations and their potential application in breeding programs to enhance adaptability, productivity and resilience in tropical dairy systems. The study evaluated SLICK-causing mutations in African breeds compared with Criollo breeds. No SLICK mutations were found in a panel of 1063 genomic DNA samples from 40 breeds across 15 ecotypes, including 126 African taurine samples (Sonstegard et al., &lt;span&gt;2025&lt;/span&gt;). Genotyping of SLICK mutations (1–5) was done with iPlex assays (Geneseek, Lincoln, NE, USA). Allele frequencies were determined for four Criollo breeds (Mexican Criollo Lechero tropical, &lt;i&gt;n&lt;/i&gt; = 20; Colombian Blanco Orejinegro, &lt;i&gt;n&lt;/i","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11664028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875732","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 sequencing and assembly of feral chickens in the wild of Sulawesi, Indonesia 印度尼西亚苏拉威西岛野生野鸡的基因组测序和组装。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-12-22 DOI: 10.1111/age.13497
Hidayat Ashari, Li-Sheng Liu, Muhammad Ihsan Andi Dagong, Zheng-Fei Cai, Guo-Li Xie, Ting-Ting Yin, Ya-Ping Zhang, Jian-Lin Han, Min-Sheng Peng
{"title":"Genome sequencing and assembly of feral chickens in the wild of Sulawesi, Indonesia","authors":"Hidayat Ashari,&nbsp;Li-Sheng Liu,&nbsp;Muhammad Ihsan Andi Dagong,&nbsp;Zheng-Fei Cai,&nbsp;Guo-Li Xie,&nbsp;Ting-Ting Yin,&nbsp;Ya-Ping Zhang,&nbsp;Jian-Lin Han,&nbsp;Min-Sheng Peng","doi":"10.1111/age.13497","DOIUrl":"10.1111/age.13497","url":null,"abstract":"<p>The feralization of domestic chicken makes the conservation and management of red jungle fowl (<i>Gallus gallus</i>) more complicated and challenging. We collected two Sulawesi feral chickens, located east of the Wallace Line, for whole-genome sequencing and de novo genome assembly. Phylogenetic and <i>f4</i>-statistics analyses indicated that the Sulawesi feralized domestic chickens (<i>G. g. domesticus</i>) received gene flow from <i>G. g. gallus</i>. We integrated ~45× ultra-long Oxford Nanopore Technology reads and ~28× PacBio HiFi reads to generate a de novo genome assembly of a female Sulawesi feral chicken (GGsula) with a contig N50 of 19.88 Mbp. We characterized structural variations in GGsula, and found some were related to nervous system. Our study provides the first genome assembly of feral chickens, which is a unique genomic resource to explore the process of chicken domestication and feralization.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875776","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
The genomic landscape of short tandem repeats in cattle 牛短串联重复序列的基因组景观。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-12-18 DOI: 10.1111/age.13498
Pengfei Wang, Xin Sheng, Xiaoting Xia, Fuwen Wang, Ruizhe Li, Zulfiqar Ahmed, Ningbo Chen, Chuzhao Lei, Zhijie Ma
{"title":"The genomic landscape of short tandem repeats in cattle","authors":"Pengfei Wang,&nbsp;Xin Sheng,&nbsp;Xiaoting Xia,&nbsp;Fuwen Wang,&nbsp;Ruizhe Li,&nbsp;Zulfiqar Ahmed,&nbsp;Ningbo Chen,&nbsp;Chuzhao Lei,&nbsp;Zhijie Ma","doi":"10.1111/age.13498","DOIUrl":"10.1111/age.13498","url":null,"abstract":"<p>Short tandem repeats (STRs) are abundant and have high mutation rates across cattle genomes; however, comprehensive exploration of cattle STRs is needed. Here, we constructed a comprehensive map of 467 553 polymorphic STRs (pSTRs) constructed from 423 cattle genomes representing 59 breeds worldwide. We observed that pSTRs in coding sequences and 5′UTRs (Untranslated Regions) were under strong selective constraints and exhibited a relatively low level of diversity. Furthermore, we found that these pSTRs underwent more contraction than expansion. Population analysis showed a strong positive correlation (<i>R</i> = 1) between pSTR diversity and single nucleotide polymorphic heterozygosity. We also investigated STR differences between taurine and indicine cattle and detected 2301 highly divergent STRs, which might relate to immune, endocrine and neurodevelopmental pathways. In summary, our large-scale study characterizes the spectrum of STRs in cattle, expands the scale of known cattle STR variation and provides novel insights into differences among various cattle subspecies.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845648","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 3-bp deletion in the SLC45A2 gene is associated with loss of fleece pigmentation in black-fleeced Suffolk sheep SLC45A2基因的3个bp缺失与黑羊毛萨福克羊的羊毛色素沉着丧失有关。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-11-28 DOI: 10.1111/age.13495
R. G. Tearle, T. Chen, F. D. Brien
{"title":"A 3-bp deletion in the SLC45A2 gene is associated with loss of fleece pigmentation in black-fleeced Suffolk sheep","authors":"R. G. Tearle,&nbsp;T. Chen,&nbsp;F. D. Brien","doi":"10.1111/age.13495","DOIUrl":"10.1111/age.13495","url":null,"abstract":"<p>Sheep have naturally pigmented wool which interferes with dyeing. Selection has been carried out over many years to remove pigment, with substantial success, but most wool still contains some pigment. As an alternative to selection, it has been proposed to take a naturally occurring mutation found in black Suffolk sheep, that blocks wool pigmentation, and introgress it into other breeds. However, the nature of the mutation has not been identified, prompting us to characterise it. The Suffolk white-fleece phenotype is associated with a novel 3-bp deletion in the gene <i>SLC45A2</i>, which encodes a membrane bound transporter that mediates melanin synthesis. The deletion results in the removal of one amino acid from the protein. The assignment of this deletion as the likely causative mutation is supported by it: being homozygous in the genome of nine animals with a white fleece and not homozygous in the genomes of eight animals with a black fleece; having a high level of conservation of the encoded amino acid sequence in the region surrounding the deleted amino acid across Mammalia; and the same deletion (but in a compound heterozygous state) being found in human <i>SLC45A2</i> in a person with albinism.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749754","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 differentially expressed genes and polymorphisms related to intramuscular oleic-to-stearic fatty acid ratio in pigs 鉴定与猪肌肉内油酸与硬脂酸脂肪酸比例有关的差异表达基因和多态性。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-11-26 DOI: 10.1111/age.13491
Jesús Valdés-Hernández, Yuliaxis Ramayo-Caldas, Magí Passols, Lourdes Criado-Mesas, Anna Castelló, Armand Sánchez, Josep M. Folch
{"title":"Identification of differentially expressed genes and polymorphisms related to intramuscular oleic-to-stearic fatty acid ratio in pigs","authors":"Jesús Valdés-Hernández,&nbsp;Yuliaxis Ramayo-Caldas,&nbsp;Magí Passols,&nbsp;Lourdes Criado-Mesas,&nbsp;Anna Castelló,&nbsp;Armand Sánchez,&nbsp;Josep M. Folch","doi":"10.1111/age.13491","DOIUrl":"10.1111/age.13491","url":null,"abstract":"<p>The intramuscular oleic-to-stearic fatty acid ratio (C18:1<i>n</i>-9/C18:0) is an important indicator of the biosynthesis and desaturation of fatty acids in muscle. By using an RNA-Seq approach in muscle samples from 32 BC1_DU (25% Iberian and 75% Duroc) pigs with divergent values (high: H and low: L) of C18:1<i>n</i>-9/C18:0 fatty acids ratio, a total of 81 differentially expressed genes (DEGs) were identified. Functional analyses of DEGs indicate that mainly peroxisome proliferator-activated receptor signaling pathway (associated genes: <i>PPARG</i>, <i>SCD</i>, <i>PLIN1</i>, and <i>FABP3</i>) was overrepresented. Notably, <i>SCD</i> is directly involved in the conversion of C18:0 to C18:1<i>n</i>-9, and <i>PPARG</i> is a transcription factor regulating lipid metabolism genes, including <i>SCD</i>. However, other DEGs (e.g., <i>ACADVL</i>, <i>FADS3</i>, <i>EPHB2</i>, <i>HGFAC</i>, <i>NGFR</i>, <i>NR0B2</i>, <i>MDH1</i>, <i>MMAA</i>, <i>PPP1R1B</i>, <i>SFRP5</i>, <i>RAB30</i>, and <i>TRARG1</i>) are plausible candidate genes to explain the phenotypic differences of the C18:1<i>n</i>-9/C18:0 ratio. Interestingly, seven genetic variants within the <i>SCD</i> (including the well-known AY487830:g.2228T&gt;C SNP and other novel genotyped polymorphisms) are associated with two haplotypes. Although the haplotypes are segregating at different frequencies in the H and L groups, they do not fully explain the desaturation ratios or the <i>SCD</i> expression levels. A more complex model, including polyunsaturated fatty acids such as C18:2<i>n</i>-6, C20:4<i>n</i>-6, and C18:3<i>n</i>-3, is suggested to explain the regulation of the C18:1<i>n</i>-9/C18:0 desaturation ratio in porcine muscle.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13491","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724808","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
Identification of a de novo missense variant in the BRI3BP gene in a Holstein calf with congenital cardiac malformation and carpus valgus 在一头患有先天性心脏畸形和腕外翻的荷斯坦小牛身上发现了 BRI3BP 基因中的一个新的错义变异。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-11-26 DOI: 10.1111/age.13494
Chang He, Llorenç Grau-Roma, Robin Schmid, Irene M. Häfliger, Mireille Meylan, Cord Drögemüller, Joana G. P. Jacinto
{"title":"Identification of a de novo missense variant in the BRI3BP gene in a Holstein calf with congenital cardiac malformation and carpus valgus","authors":"Chang He,&nbsp;Llorenç Grau-Roma,&nbsp;Robin Schmid,&nbsp;Irene M. Häfliger,&nbsp;Mireille Meylan,&nbsp;Cord Drögemüller,&nbsp;Joana G. P. Jacinto","doi":"10.1111/age.13494","DOIUrl":"10.1111/age.13494","url":null,"abstract":"<p>Congenital malformations in cattle pose a diagnostic challenge with limited treatment options and are often associated with a guarded prognosis. The aim of this study was to characterize the clinicopathological phenotype of a viable calf with complex congenital heart defects and carpus valgus, and to identify a possible genetic cause using a whole genome sequencing trio approach. A 3-month-old female Holstein calf was referred for respiratory distress and congenital carpal deviation. Clinicopathologic findings included ventricular septal defect, ventricular dilatation, atrioventricular valve dysplasia, an overriding aorta, and unilateral carpus valgus. Genetic analysis revealed a private heterozygous missense variant in <i>BRI3BP</i> affecting an evolutionarily conserved residue (c.478G&gt;A; p.Val160Ile). The variant was predicted to be deleterious and was present only in the affected calf and was absent in more than 5100 sequenced bovine genomes, including both parents, indicating a de novo origin. This study implicates an important role for the uncharacterized BRI3 binding protein in cardiac and possibly also bone development. By presenting the first <i>BRI3BP</i>-related disease model, this study demonstrates the potential to gain new insights into the function of individual genes by using phenotypically well-studied spontaneous mutants in large animals, and it provides a novel candidate gene for similar conditions in humans.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11666921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724803","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
Comparative genome-wide association study of single- and multi-locus models with ontology analysis for enhancing Hanwoo cow reproductive traits 利用本体分析进行单病灶和多病灶模型的全基因组关联比较研究,以提高汉和奶牛的繁殖性状。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-11-26 DOI: 10.1111/age.13493
Ji Yeong Kim, Eun Ho Kim, Ho Chan Kang, Cheol Hyun Myung, Hyun Tae Lim
{"title":"Comparative genome-wide association study of single- and multi-locus models with ontology analysis for enhancing Hanwoo cow reproductive traits","authors":"Ji Yeong Kim,&nbsp;Eun Ho Kim,&nbsp;Ho Chan Kang,&nbsp;Cheol Hyun Myung,&nbsp;Hyun Tae Lim","doi":"10.1111/age.13493","DOIUrl":"10.1111/age.13493","url":null,"abstract":"<p>The reproductive characteristics of Hanwoo play a significant role in farm profitability by decreasing the generation interval. This study analyzed 1015 primiparous and 916 multiparous cows using a genome-wide association study with both single-locus (GEMMA, GCTA) and multi-locus models (FarmCPU, BLINK). A significant marker for age at first service was identified across all methods. For age at first conception, GEMMA identified two markers, while FarmCPU and BLINK identified 14 and two markers, respectively. Regarding age at first calving, GEMMA identified two markers, and FarmCPU and BLINK found 15 and two markers, respectively. In multiparous cows, except for days open, one marker for gestation length and two markers for calving interval were identified in the multi-locus models (FarmCPU and BLINK). Additionally, one marker for the number of services per conception was identified using GEMMA. Key candidate genes included <i>PLCB1</i> (maintaining pregnancy), <i>MUC1</i> (fetal development), and <i>ADCY5</i> (associated with fetal birth), while <i>TXNL1</i> regulates embryo implantation timing. Gene ontology functions associated with embryo implantation and placental regulation were also confirmed (GO:0046875). Although the multi-locus models identified a greater number of markers and candidate genes, there was no overlap with the results from the single-locus models. The multi-locus models showed enhanced detection power, but slight inflation in test statistics (<i>λ</i> values) necessitates cautious interpretation to avoid false positives. Thus, a combination of both models is recommended to improve reproductive efficiency in cows, providing valuable insights into the genetic aspects of reproductive traits.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724786","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 scans for signatures of selection in North African sheep reveals differentially selected regions between fat- and thin-tailed breeds 对北非绵羊选择特征的全基因组扫描揭示了肥尾绵羊和细尾绵羊之间不同的选择区域。
IF 1.8 3区 生物学
Animal genetics Pub Date : 2024-11-21 DOI: 10.1111/age.13487
Slim Ben-Jemaa, Ghazi Yahyaoui, Samia Kdidi, Afef Najjari, Johannes A. Lenstra, Salvatore Mastrangelo, Semir B. S. Gaouar, Joram M. Mwacharo, Touhami Khorchani, Mohamed H. Yahyaoui
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