Animal genetics最新文献

{"title":"A PAX3 insertion in the Celestial breed and certain feline breeding lines with dominant blue eyes","authors":"Marie Abitbol,&nbsp;Alice Couronné,&nbsp;Caroline Dufaure de Citres,&nbsp;Vincent Gache","doi":"10.1111/age.13433","DOIUrl":"10.1111/age.13433","url":null,"abstract":"<p>During the last 60 years many inherited traits in domestic outbred cats were selected and retained giving birth to new breeds characterised by singular coat or morphological phenotypes. Among them, minimal white spotting associated with blue eyes was selected by feline breeders to create the Altai, Topaz, and Celestial breeds. Various established breeds also introduced this trait in their lineages. The trait, that was confirmed as autosomal dominant by breeding data, was first described in domestic cats from Kazakhstan and Russia, in British shorthair and British longhair from Russia, and in Maine Coon cats from the Netherlands, suggesting different founding effects. Using a genome-wide association study we identified a single region on chromosome C1 that was associated with the minimal white spotting and blue eyes phenotype (also called DBE by breeders for dominant blue eyes) in the French Celestial breed. Within that region we identified <i>Paired Box 3</i> (<i>PAX3</i>) as the strongest candidate gene, since <i>PAX3</i> is a key regulator of <i>MITF</i> (<i>M</i><i>elanocyte-</i><i>I</i><i>nducing</i> <i>T</i><i>ranscription</i> <i>F</i><i>actor</i>) and <i>PAX3</i> variants have been previously identified in various species showing white spotting with or without blue eyes including the mouse and the horse. Whole genome sequencing of a Celestial cat revealed an endogenous retrovirus LTR (long terminal repeat) insertion within <i>PAX3</i> intron 4 known to contain regulatory sequences (conserved non-coding element [CNE]) involved in <i>PAX3</i> expression. The insertion is in the vicinity of CNE2 and CNE3. All 52 Celestial and Celestial-mixed cats with a DBE phenotype presented the insertion, that was absent in their 22 non-DBE littermates and in 87 non-DBE cats from various breeds. The outbred Celestial founder was also heterozygous for the insertion. Additionally, the variant was found in nine DBE Maine Coon cats related to the Celestial founder and four DBE Siberian cats with an uncertain origin. Segregation of the variant in the Celestial breed is consistent with dominant inheritance and does not appear to be associated with deafness. We propose that this NC_018730.3:g.206974029_206974030insN[395] variant represents the <i>DBE</i>^<i>CEL</i> (<i>Celestial Dominant Blue Eyes</i>) allele in the domestic cat.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13433","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140674198","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}

{"title":"A panel of tetranucleotide STR markers as an alternative approach to forensic DNA identification of wolf and dog","authors":"Aliaksandra E. Hrebianchuk,&nbsp;Nastassia S. Parfionava,&nbsp;Tatsiana V. Zabauskaya,&nbsp;Iosif S. Tsybovsky","doi":"10.1111/age.13428","DOIUrl":"10.1111/age.13428","url":null,"abstract":"<p>Commercial panels of microsatellite (STR) loci are focused on the use of DNA of the domestic dog (<i>Canis lupus familiaris</i>) and are often inapplicable for genotyping the DNA of the gray wolf (<i>Canis lupus lupus</i>). We propose a CPlex test system, including one hexa- and 12 tetranucleotide autosomal STR loci, as well as two sex loci, that is equally efficient in DNA identification of biological samples of the wolf and the dog. Analysis of molecular variance between samples revealed significant differentiation values (<i>F</i>_ST = 0.0784, <i>p</i> &lt; 0.001), which allows to use the panel to differentiate wolf and dog samples. Population subdivision coefficients (<i>θ</i>-values) were calculated for each of the 13 STR loci of the developed test system. It was shown that the values of the genotype frequency for dogs and wolves, without and with considering the <i>θ</i>-value, differ by three orders of magnitude (for dogs 8.9 × 10⁻¹⁶ and 2.1 × 10⁻¹⁴ and for wolves 1.9 × 10⁻¹⁵ and 4.5 × 10⁻¹⁴, respectively). The use of population subdivision coefficients will allow to identify the most reliable results of an expert identification study and the power of exclusion provided by the STR loci of the CPlex test system makes it possible to achieve a reliable level of evidence in forensic DNA analysis of both wolves and dogs. The test system has been validated for use in forensic identification of the dog and wolf based on biological traces found at crime scenes, as well as for individual identification and establishing biological relationship of animals of these species.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140679447","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}

{"title":"Multiplex fluorescent amplification-refractory mutation system PCR method for the detection of 10 genetic defects in Holstein cattle and its comparison with the KASP genotyping assay","authors":"Md. Yousuf Ali Khan,&nbsp;Dongmei Dai,&nbsp;Xin Su,&nbsp;Jia Tian,&nbsp;Jiamin Zhou,&nbsp;Liqin Ma,&nbsp;Yachun Wang,&nbsp;Wan Wen,&nbsp;Yi Zhang","doi":"10.1111/age.13432","DOIUrl":"10.1111/age.13432","url":null,"abstract":"<p>The common deleterious genetic defects in Holstein cattle include haplotypes 1–6 (HH1–HH6), haplotypes for cholesterol deficiency (HCD), bovine leukocyte adhesion deficiency (BLAD), complex vertebral malformation (CVM) and brachyspina syndrome (BS). Recessive inheritance patterns of these genetic defects permit the carriers to function normally, but homozygous recessive genotypes cause embryo loss or neonatal death. Therefore, rapid detection of the carriers is essential to manage these genetic defects. This study was conducted to develop a single-tube multiplex fluorescent amplification–refractory mutation system (mf-ARMS) PCR method for efficient genotyping of these 10 genetic defects and to compare its efficiency with the kompetitive allele specific PCR (KASP) genotyping assay. The mf-ARMS PCR method introduced 10 sets of tri-primers optimized with additional mismatches in the 3′ end of wild and mutant-specific primers, size differentiation between wild and mutant-specific primers, fluorescent labeling of universal primers, adjustment of annealing temperatures and optimization of primer concentrations. The genotyping of 484 Holstein cows resulted in 16.12% carriers with at least one genetic defect, while no homozygous recessive genotype was detected. This study found carrier frequencies ranging from 0.0% (HH6) to 3.72% (HH3) for individual defects. The mf-ARMS PCR method demonstrated improved detection, time and cost efficiency compared with the KASP method for these defects. Therefore, the application of mf-ARMS PCR for genotyping Holstein cattle is anticipated to decrease the frequency of lethal alleles and limit the transmission of these genetic defects.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140580602","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}

{"title":"Genome-wide association study identified five quantitative trait loci and two candidate genes for digestive traits in Suhuai pigs","authors":"Kaijun Li,&nbsp;Liming Hou,&nbsp;Taoran Du,&nbsp;Guang Pu,&nbsp;Chenxi Liu,&nbsp;Gensheng Liu,&nbsp;Juan Zhou,&nbsp;Ruihua Huang,&nbsp;Qingbo Zhao,&nbsp;Pinghua Li","doi":"10.1111/age.13430","DOIUrl":"10.1111/age.13430","url":null,"abstract":"<p>This work aimed to identify markers and candidate genes underlying porcine digestive traits. In total, 331 pigs were genotyped by 80 K Chip data or 50 K Chip data. For apparent neutral detergent fiber digestibility, a total of 19 and 21 candidate single nucleotide polymorphisms (SNP) were respectively identified using a genome-wide efficient mixed-model association algorithm and linkage-disequilibrium adjusted kinship. Among them, three quantitative trait locus (QTL) regions were identified. For apparent acid detergent fiber digestibility, a total of 16 and 17 SNPs were identified by these two methods, respectively. Of these, three QTL regions were also identified. Moreover, two candidate genes (<i>MST1</i> and <i>LATS1</i>), which are functionally related to intestinal homeostasis and health, were detected near these significant SNPs. Taken together, our results could provide a basis for deeper research on digestive traits in pigs.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140580508","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}

{"title":"Genome-wide association study identifies a novel candidate gene for egg production traits in chickens","authors":"Huimin Kang,&nbsp;Yuedan Lu,&nbsp;Weitu Zhang,&nbsp;Guohong Hua,&nbsp;Jiankang Gan,&nbsp;Xuqing Deng,&nbsp;Zhengfen Zhang,&nbsp;Hua Li","doi":"10.1111/age.13427","DOIUrl":"10.1111/age.13427","url":null,"abstract":"<p>Qingyuan partridge chicken is a renowned indigenous yellow broiler breed in China. Egg production traits are important economic traits for chickens. With the decreasing cost of whole genome resequencing, identifying candidate genes with more precision has become possible. In order to identify molecular markers and candidate genes associated with egg production traits, we conducted genome-wide association studies based on the resequencing data of 287 female Qingyuan partridge chickens. For each hen, age at first egg and egg laying rate were recorded and calculated, respectively. With a univariate linear mixed model, we detected one genome-wide significant single nucleotide polymorphism (SNP) and three chromosome-wide significant SNPs associated with egg laying rate. <i>MTA2</i> is highly likely to be a functional gene for egg laying rate. Our study identifies <i>MTA2</i> as the first time to be associated with egg laying rate. Findings in our study will advance our understanding of the genetic basis of egg production and have the potential to improve the efficiency of genomic selection in chickens.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140580500","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}

{"title":"Identification of candidate genes associated with milk production and mastitis based on transcriptome-wide association study","authors":"Sevda Hosseinzadeh,&nbsp;Seyed Abbas Rafat,&nbsp;Arash Javanmard,&nbsp;Lingzhao Fang","doi":"10.1111/age.13422","DOIUrl":"10.1111/age.13422","url":null,"abstract":"<p>Genetic research for the assessment of mastitis and milk production traits simultaneously has a long history. The main issue that arises in this context is the known existence of a positive correlation between the risk of mastitis and lactation performance due to selection. The transcriptome-wide association study (TWAS) approach endeavors to combine the expression quantitative trait loci and genome-wide association study summary statistics to decode complex traits or diseases. Accordingly, we used the <span>farmgtex</span> project results as a complete <span>bovine</span> database for mastitis and milk production. The results of colocalization and TWAS approaches were used for the detection of functional associated candidate genes with milk production and mastitis traits on multiple tissue-based transcriptome records. Also, we used the <span>david</span> database for gene ontology to identify significant terms and associated genes. For the identification of interaction networks, the <span>genemania</span> and <span>string</span> databases were used. Also, the available <i>z</i>-scores in TWAS results were used for the calculation of the correlation between tissues. Therefore, the present results confirm that <i>LYNX1</i>, <i>DGAT1</i>, <i>C14H8orf33</i>, and <i>LY6E</i> were identified as significant genes associated with milk production in eight, six, five, and five tissues, respectively. Also, <i>FBXL6</i> was detected as a significant gene associated with mastitis trait. <i>CLN3</i> and <i>ZNF34</i> genes emerged via both the colocalization and TWAS approaches as significant genes for milk production trait. It is expected that TWAS and colocalization can improve our perception of the potential health status control mechanism in high-yielding dairy cows.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140580514","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}

{"title":"The landscape of allelic expression and DNA methylation at the bovine SGCE/PEG10 locus","authors":"Yinjiao Zhang,&nbsp;Cui Zhang,&nbsp;Weina Chen,&nbsp;Haonan Huo,&nbsp;Shujing Li,&nbsp;Wenli Yu,&nbsp;Lanjie Jin,&nbsp;Kun Wang,&nbsp;Shijie Li","doi":"10.1111/age.13429","DOIUrl":"10.1111/age.13429","url":null,"abstract":"<p>Genomic imprinting is an epigenetic regulation in mammals in which a small subset of genes is monoallelically expressed dependent on their parental origin. A large imprinted domain, <i>SGCE/PEG10</i> locus, is located on human chromosome 7q21s and mouse proximal chromosome 6. However, genomic imprinting of bovine <i>SGCE/PEG10</i> cluster has not been systematically studied. In this study, we investigated allele expression of 14 genes of the <i>SGCE/PEG10</i> locus in bovine somatic tissues and term placenta using a single nucleotide polymorphism (SNP)-based sequencing method. In addition to <i>SGCE</i> and <i>PEG10</i>, two conserved paternally expressed genes in human and mice, five other genes (<i>TFPI2</i>, <i>GNG11</i>, <i>ASB4</i>, <i>PON1</i>, and <i>PON3</i>) were paternally expressed. Three genes, <i>BET1</i>, <i>COL1A2</i>, and <i>CASD1</i>, exhibited tissue-specific monoallelic expression. <i>CALCR</i> showed monoallelic expression in tissues but biallelic expression in the placenta. Three genes, <i>GNGT1</i>, <i>PPP1R9A</i>, and <i>PON2</i>, showed biallelic expression in cattle. Five differentially methylated regions (DMRs) were found to be associated with the allelic expression of <i>TFPI2</i>, <i>COL1A2</i>, <i>SGCE/PEG10</i>, <i>PON3</i>, and <i>ASB4</i> genes, respectively. The <i>SGCE/PEG10</i> DMR is a maternally hypermethylated germline DMR, but <i>TFPI2</i>, <i>COL1A2</i>, <i>PON3</i>, and <i>ASB4</i> DMRs are secondary DMRs. In summary, we identified five novel bovine imprinted genes (<i>GNG11</i>, <i>BET1</i>, <i>COL1A2</i>, <i>CASD1</i>, and <i>PON1</i>) and four secondary DMRs at the <i>SGCE/PEG10</i> locus.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140580595","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}

{"title":"A novel QTL region for pH and meat color in Duroc pigs","authors":"Eduard Molinero,&nbsp;Ramona N. Pena,&nbsp;Joan Estany,&nbsp;Roger Ros-Freixedes","doi":"10.1111/age.13426","DOIUrl":"10.1111/age.13426","url":null,"abstract":"<p>One of the most important processes that occur during the transformation of muscle to meat is the pH decline as a consequence of the post-mortem metabolism of muscle tissue. Abnormal pH declines lead to pork defects such as pale, soft, and exudative meat. There is genetic variance for ultimate pH and the role of some genes on this phenotype is well established. After conducting a genome-wide association study on ultimate pH using 526 purebred Duroc pigs, we identified associated regions on <i>Sus scrofa</i> chromosomes (SSC) 3, 8, and 15. Functional candidate genes in these regions included <i>PRKAG3</i> and <i>PHKG1</i>. The SSC8 region, at 71.6 Mb, was novel and, although no candidate causative gene could be identified, it may have regulatory effects. Subsequent analysis on 828 pigs from the same population confirmed the impact of the three associated regions on pH and meat color. We detected no interaction between the three regions. Further investigations are necessary to unravel the functional significance of the novel genomic region at SSC8. These variants could be used as markers in marker-assisted selection for improving meat quality.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13426","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140580792","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}

{"title":"Study on the origin of the Baise horse based on whole-genome resequencing","authors":"Xiaoran Lin,&nbsp;Mo Feng,&nbsp;Ying Li,&nbsp;Yu Liu,&nbsp;Min Wang,&nbsp;Yuanyuan Li,&nbsp;Tao Yang,&nbsp;Chunjiang Zhao","doi":"10.1111/age.13424","DOIUrl":"10.1111/age.13424","url":null,"abstract":"<p>The Baise horse, an indigenous horse breed mainly distributed in the Baise region of Guangxi province in southwest China, has a long history as draft animal. However, there is a lack of research regarding the origin and ancestral composition of the Baise horse. In this study, whole-genome resequencing data from 236 horses of seven Chinese indigenous horse breeds, five foreign horse breeds, and four Przewalski's horses were used to investigate the relationships between the Baise horse and other horse breeds. The results showed that foreign horse breeds had no significant impact on the formation of the Baise horse. The two southwestern horse populations, the Debao pony and the Jinjiang horse, exhibit the closest genetic affinity with the Baise horse. This is consistent with their adjacent geographical distribution. Analysis of the migration route revealed a gene flow from the Chakouyi horse into the Baise horse. In summary, our results confirm that the formation of the Baise horse did not involve participation from foreign breeds. Geographical distance emerges as a crucial factor in determining the genetic relationships with the Baise horse. Gene flows of indigenous horse breeds along ancient routes of trade activities had played a role in the formation of the Baise horse.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140580605","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}

{"title":"Whole-genome resequencing uncovers diversity and selective sweep in Kazakh cattle","authors":"Lei Xu,&nbsp;Yunyun Zhang,&nbsp;Yang Guo,&nbsp;Qiuming Chen,&nbsp;Menghua Zhang,&nbsp;Hong Chen,&nbsp;Juan Geng,&nbsp;Xixia Huang","doi":"10.1111/age.13425","DOIUrl":"10.1111/age.13425","url":null,"abstract":"<p>The Kazakh cattle in the Xinjiang Uygur Autonomous Region of China are highly adaptable and have multiple uses, including milk and meat production, and use as draft animals. They are an excellent original breed that could be enhanced by breeding and hybrid improvement. However, the genomic diversity and signature of selection underlying the germplasm characteristics require further elucidation. Herein, we evaluated 26 Kazakh cattle genomes in comparison with 103 genomes of seven other cattle breeds from regions around the world to assess the Kazakh cattle genetic variability. We revealed that the relatively low linkage disequilibrium at large SNP distances was strongly correlated with the largest effective population size among Kazakh cattle. Using population structural analysis, we next demonstrated a taurine lineage with restricted <i>Bos indicus</i> introgression among Kazakh cattle. Notably, we identified putative selected genes associated with resistance to disease and body size within Kazakh cattle. Together, our findings shed light on the evolutionary history and breeding profile of Kazakh cattle, as well as offering indispensable resources for germplasm resource conservation and crossbreeding program implementation.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140334451","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}