Animal genetics最新文献

{"title":"Intragenic MFSD8 duplication and histopathological findings in a rabbit with neuronal ceroid lipofuscinosis","authors":"Matthias Christen,&nbsp;Katharina M. Gregor,&nbsp;Ariane Böttcher-Künneke,&nbsp;Mara S. Lombardo,&nbsp;Wolfgang Baumgärtner,&nbsp;Vidhya Jagannathan,&nbsp;Christina Puff,&nbsp;Tosso Leeb","doi":"10.1111/age.13441","DOIUrl":"10.1111/age.13441","url":null,"abstract":"<p>Neuronal ceroid lipofuscinoses (NCL) are among the most prevalent neurodegenerative disorders of early life in humans. Disease-causing variants have been described for 13 different NCL genes. In this study, a refined pathological characterization of a female rabbit with progressive neurological signs reminiscent of NCL was performed. Cytoplasmic pigment present in neurons was weakly positive with Sudan black B and autofluorescent. Immunohistology revealed astrogliosis, microgliosis and axonal degeneration. During the subsequent genetic investigation, the genome of the affected rabbit was sequenced and examined for private variants in NCL candidate genes. The analysis revealed a homozygous ~10.7 kb genomic duplication on chromosome 15 comprising parts of the <i>MFSD8</i> gene, NC_013683.1:g.103,727,963_103,738,667dup. The duplication harbors two internal protein coding exons and is predicted to introduce a premature stop codon into the transcript, truncating ~50% of the wild-type <i>MFSD8</i> open reading frame encoding the major facilitator superfamily domain containing protein 8, XP_002717309.2:p.(Glu235Leufs*23). Biallelic loss-of-function variants in <i>MFSD8</i> have been described to cause NCL7 in human patients, dogs and a single cat. The available clinical and pathological data, together with current knowledge about <i>MFSD8</i> variants and their functional impact in other species, point to the <i>MFSD8</i> duplication as a likely causative defect for the observed phenotype in the affected rabbit.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 4","pages":"588-598"},"PeriodicalIF":1.8,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13441","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140847379","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":"An association weight matrix identified biological pathways associated with bull fertility traits in a multi-breed population","authors":"Wei Liang Andre Tan,&nbsp;Nicholas James Hudson,&nbsp;Laercio Ribeiro Porto Neto,&nbsp;Antonio Reverter,&nbsp;Juliana Afonso,&nbsp;Marina Rufino Salinas Fortes","doi":"10.1111/age.13431","DOIUrl":"10.1111/age.13431","url":null,"abstract":"<p>Using seven indicator traits, we investigated the genetic basis of bull fertility and predicted gene interactions from SNP associations. We used percent normal sperm as the key phenotype for the association weight matrix–partial correlation information theory (AWM-PCIT) approach. Beyond a simple list of candidate genes, AWM-PCIT predicts significant gene interactions and associations for the selected traits. These interactions formed a network of 537 genes: 38 genes were transcription cofactors, and 41 genes were transcription factors. The network displayed two distinct clusters, one with 294 genes and another with 243 genes. The network is enriched in fertility-associated pathways: steroid biosynthesis, p53 signalling, and the pentose phosphate pathway. Enrichment analysis also highlighted gene ontology terms associated with ‘regulation of neurotransmitter secretion’ and ‘chromatin formation’. Our network recapitulates some genes previously implicated in another network built with lower-density genotypes. Sequence-level data also highlights additional candidate genes relevant to bull fertility, such as <i>FOXO4</i>, <i>FOXP3</i>, <i>GATA1</i>, <i>CYP27B1</i>, and <i>EBP</i>. A trio of regulatory genes—<i>KDM5C</i>, <i>LRRK2</i>, and <i>PME—</i>was deemed core to the network because of their overarching connections. This trio probably influences bull fertility through their interaction with genes, both known and unknown as to their role in male fertility. Future studies may target the trio and their target genes to enrich our understanding of male fertility further.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 4","pages":"495-510"},"PeriodicalIF":1.8,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13431","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140832708","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":"Renal dysplasia in Leonberger dogs – An emerging recessive congenital disorder?","authors":"Anna Letko,&nbsp;Corinne Gurtner,&nbsp;Vidhya Jagannathan,&nbsp;Cord Drögemüller","doi":"10.1111/age.13439","DOIUrl":"10.1111/age.13439","url":null,"abstract":"&lt;p&gt;Renal dysplasia (RD) is a complex congenital disease characterised by abnormal differentiation of renal tissue (Greco, &lt;span&gt;2001&lt;/span&gt;). Several forms of inherited RD have been reported in various animal species, including dogs (OMIA:001135-9615). The canine RD phenotype can range from asymptomatic to severe chronic kidney disease and the genetic etiology remains unclear (Cavalera et al., &lt;span&gt;2021&lt;/span&gt;; Dillard et al., &lt;span&gt;2018&lt;/span&gt;; Safra et al., &lt;span&gt;2015&lt;/span&gt;). Similar secondary kidney damage can also result from recessive metabolic disorders such as xanthinuria, known in dogs (OMIA:001283-9615) or cattle (OMIA:001283-9913). Leonbergers globally suffer from various diseases, with cancer, orthopedic and neurological conditions being the most frequent (Letko et al., &lt;span&gt;2020&lt;/span&gt;). However, in the owner-reported health survey, 0.44% of dogs were diagnosed with ‘renal system issues’ (Letko et al., &lt;span&gt;2020&lt;/span&gt;). The underlying cause of RD has not yet been described in this breed.&lt;/p&gt;&lt;p&gt;In a litter of eight purebred Leonbergers, one puppy was diagnosed with a congenital form of RD and euthanised at 11 weeks of age owing to worsening clinical signs. For diagnosis confirmation and histopathological examination, the kidneys were collected and fixed in 10% buffered formalin and embedded in paraffin. Sections of 1.5 μm were cut and compared with a kidney sample of a control dog (Figure 1a). Histological lesions were present in both kidneys. The cortex and medulla had areas of fetal glomeruli featuring small glomeruli with peripheral nuclei and inapparent capillaries. Some tubuli appeared small and immature and were lined by closely packed cuboidal epithelial cells while others were ectatic and sometimes contained birefringent greenish crystals and occasional mineralisation. Additionally, some tubuli contained intraluminal eosinophilic droplet material. The interstitium showed multifocal areas with mild fibrosis and aggregates of lymphocytes, plasma cells, a few neutrophils and macrophages, some of which were laden with hemosiderin (Figure 1b).&lt;/p&gt;&lt;p&gt;Samples for genome sequencing of the affected dog or his littermates were not available. Therefore, parental whole-genome sequencing (WGS) data were utilised to gain insights into the genetic basis of RD. Blood samples and the DNA of the unaffected dam and sire of the case were previously donated to the Vetsuisse Biobank for diagnostic purposes. Whole-genome sequencing was performed at ~20× read depth using Illumina NovaSeq6000 and variants were called as described previously (Letko et al., &lt;span&gt;2023&lt;/span&gt;). The pedigree records supported a recessive mode of inheritance (Figure S1). Therefore, the WGS data were queried for variants heterozygous in both parents with respect to canine reference UU_Cfam_GSD_1.0. A global cohort of 1541 dogs, including 85 unrelated adult Leonbergers not known to be RD affected (Table S1), was used to evaluate allele frequency of the 1 090 859 shared v","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 4","pages":"700-701"},"PeriodicalIF":1.8,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13439","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140832978","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":"Heterozygous deletion of the NSDHL gene in an Appenzeller Mountain Dog with verrucous epidermal keratinocytic nevi","authors":"Sarah Kiener,&nbsp;Brett Wildermuth,&nbsp;Nadine M. Meertens,&nbsp;Vidhya Jagannathan,&nbsp;Tosso Leeb","doi":"10.1111/age.13436","DOIUrl":"10.1111/age.13436","url":null,"abstract":"&lt;p&gt;Dermal mosaicism can result in skin disorders with specific distribution patterns of the lesions. The most common example is X-chromosomal functional mosaicism, in which the distribution pattern results from random X-chromosome inactivation (Lyonization) (Vreeburg &amp; van Steensel, &lt;span&gt;2012&lt;/span&gt;). Three different skin patterns have been described, namely Blaschko lines, the checkerboard pattern and lateralization (Happle, &lt;span&gt;2006&lt;/span&gt;). Verrucous epidermal keratinocytic nevi (OMIA 002117) caused by variants in the X-chromosomal &lt;i&gt;NSDHL&lt;/i&gt; gene may present with any of these patterns. The encoded NAD(P)H steroid dehydrogenase-like protein is a C4 demethylase involved in post-squalene cholesterol biosynthesis. Pathogenic &lt;i&gt;NSDHL&lt;/i&gt; variants result in disruption of an essential step in cholesterol biosynthesis with a subsequent aggregation of toxic intermediates and a lack of cholesterol in the skin (Caldas &amp; Herman, &lt;span&gt;2003&lt;/span&gt;; König et al., &lt;span&gt;2000&lt;/span&gt;). In heterozygous female dogs, this presents as a cornification disorder and is inherited as an X-linked semidominant trait (Bauer et al., &lt;span&gt;2017&lt;/span&gt;; Christen et al., &lt;span&gt;2020&lt;/span&gt;; Leuthard et al., &lt;span&gt;2019&lt;/span&gt;). &lt;i&gt;NSDHL&lt;/i&gt;-associated disorders in humans cause a more severe phenotype involving congenital hemidysplasia with ichthyosiform nevus and limb defects (CHILD syndrome; König et al., &lt;span&gt;2000&lt;/span&gt;). In hemizygous males, such variants have been described as embryonic lethal (Happle et al., &lt;span&gt;1980&lt;/span&gt;).&lt;/p&gt;&lt;p&gt;A 10-month-old female intact Appenzeller Mountain Dog was presented with an 8 month history of severe, progressive hyperkeratosis of the paw pads causing lameness and a primarily left-sided multifocal hyperkeratosis of the haired skin, causing alopecia and mild pruritus. The lesions began on the left inner pinna and hind paw pads and slowly progressed to involve all four paws, although the right front was only mildly affected. Stripes of alopecia with hyperkeratosis were present on the lateral and caudal left thigh, with multiple smaller areas on the left tarsus, left lateral neck and left hip. Complete blood count, serum biochemistry and skin cytology were within normal limits and a fungal culture was negative. Multiple skin punch biopsies were taken under sedation to further pursue a diagnosis. Based on these results the paw pads were treated topically in an attempt to reduce cholesterol precursors in the skin and therefore hyperkeratosis. Two-percent ketoconazole cream and then 2% simvastatin ointment were tried successively, without improvement. The lesions on the haired skin then cleared completely with oral ketoconazole 5 mg/kg once daily but the paw pads remained quite hyperkeratotic, requiring repeated trimming (Figure 1).&lt;/p&gt;&lt;p&gt;Histopathologically, skin biopsies showed moderate to severe hyperplasia of the epidermis and infundibula of the hair follicles, forming spiked fronds (Figure 2). The infundibula of the hair fo","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"55 4","pages":"697-699"},"PeriodicalIF":1.8,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.13436","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140661445","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 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":"55 4","pages":"670-675"},"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":"55 3","pages":"440-451"},"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":"55 3","pages":"457-464"},"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":"55 3","pages":"471-474"},"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":"55 3","pages":"480-483"},"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":"55 3","pages":"430-439"},"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}