Comparison of two methods of sperm- and testis-mediated gene transfer in production of transgenic animals: A systematic review
Anim Genet. 2024 Feb 15. doi: 10.1111/age.13404. Online ahead of print.ABSTRACTTransgenic (Tg) animal technology is one of the growing areas in biology. Various Tg technologies, each with its own advantages and disadvantages, are available for generating Tg animals. These include zygote microinjection, electroporation, viral infection, embryonic stem cell or spermatogonial stem cell-mediated production of Tg animals, sperm-mediated gene transfer (SMGT), and testis-mediated gene transfer (TMGT). However, there are currently no comprehensive studies comparing SMGT and TMGT methods, selecting appropriate gene delivery carrier...
Source: Animal Genetics - February 16, 2024 Category: Genetics & Stem Cells Authors: Zeinab Dehghan Gholamhossein Darya Shayesteh Mehdinejadiani Amin Derakhshanfar Source Type: research
Towards identification of new genetic determinants for post-weaning diarrhea in piglets
This study aimed to identify new genetic loci for resistance to diarrhea based on phenotypic data. In depth clinical characterization of diarrhea was performed in 257 pigs belonging to two herds during the first 14 days post weaning. The daily diarrhea assessments were used for the classification of pigs into case and control groups. Pigs were assigned to case and control groups based only on the incidence of diarrhea in the second week of the study in order to differentiate between differences in etiology. Genome-wide association studies and metabolomics association analysis were performed in order to identify new biologi...
Source: Animal Genetics - February 12, 2024 Category: Genetics & Stem Cells Authors: Emil Ibragimov Esben Østergaard Eriksen Jens Peter Nielsen Claus B J ørgensen Merete Fredholm Peter Karlskov-Mortensen Source Type: research
Towards identification of new genetic determinants for post-weaning diarrhea in piglets
This study aimed to identify new genetic loci for resistance to diarrhea based on phenotypic data. In depth clinical characterization of diarrhea was performed in 257 pigs belonging to two herds during the first 14 days post weaning. The daily diarrhea assessments were used for the classification of pigs into case and control groups. Pigs were assigned to case and control groups based only on the incidence of diarrhea in the second week of the study in order to differentiate between differences in etiology. Genome-wide association studies and metabolomics association analysis were performed in order to identify new biologi...
Source: Animal Genetics - February 12, 2024 Category: Genetics & Stem Cells Authors: Emil Ibragimov Esben Østergaard Eriksen Jens Peter Nielsen Claus B J ørgensen Merete Fredholm Peter Karlskov-Mortensen Source Type: research
Naturally occurring genetic diseases caused by de novo variants in domestic animals
Anim Genet. 2024 Feb 7. doi: 10.1111/age.13403. Online ahead of print.ABSTRACTWith the advent of next-generation sequencing, an increasing number of cases of de novo variants in domestic animals have been reported in scientific literature primarily associated with clinically severe phenotypes. The emergence of new variants at each generation is a crucial aspect in understanding the pathology of early-onset diseases in animals and can provide valuable insights into similar diseases in humans. With the aim of collecting deleterious de novo variants in domestic animals, we searched the scientific literature and compiled repor...
Source: Animal Genetics - February 7, 2024 Category: Genetics & Stem Cells Authors: Lu ísa Azevedo Andreia P Amaro Jo ão Niza-Ribeiro M ónica Lopes-Marques Source Type: research
Analysis of genetic variants in protein-coding genes of Aoluguya reindeer based on the whole-genome data
Anim Genet. 2024 Feb 6. doi: 10.1111/age.13402. Online ahead of print.NO ABSTRACTPMID:38319118 | DOI:10.1111/age.13402 (Source: Animal Genetics)
Source: Animal Genetics - February 6, 2024 Category: Genetics & Stem Cells Authors: Wenfeng Yi Mingyue Hu Lulu Shi Ting Li Hao Sun Lihong Qin Shouqing Yan Source Type: research
H3K27ac modification and transcription characteristics of adipose and muscle tissues in Chuxiang Black pig
In this study, cis-regulatory elements of muscle and adipose tissues in CX pigs were investigated using ChIP-seq and RNA sequencing. Compared with the reported cis-regulatory elements of muscle and adipose tissues, 1768 and 1012 highly activated enhancers and 433 and 275 highly activated promoters in CX muscle and adipose tissues were identified, respectively. Motif analysis showed that transcription factors, such as MEF2A and MEF2C, were core regulators of highly activated enhancers and promoters in muscle. Similarly, the transcription factors JUNB and CUX1 were identified as essential for highly activated enhancers and p...
Source: Animal Genetics - January 31, 2024 Category: Genetics & Stem Cells Authors: Renzhuo Kuang Zhixiang Xu Honghong Zhou Zhao Zhang Hao Peng Daoyuan Wang Xuewen Xu Shuhong Zhao Yunxia Zhao Mengjin Zhu Source Type: research
Smartphone-based digital phenotyping for genome-wide association study of intramuscular fat traits in longissimus dorsi muscle of pigs
Anim Genet. 2024 Jan 30. doi: 10.1111/age.13401. Online ahead of print.ABSTRACTIntramuscular fat (IMF) content and distribution significantly contribute to the eating quality of pork. However, the current methods used for measuring these traits are complex, time-consuming and costly. To simplify the measurement process, this study developed a smartphone application (App) called Pork IMF. This App serves as a rapid and portable phenotyping tool for acquiring pork images and extracting the image-based IMF traits through embedded deep-learning algorithms. Utilizing this App, we collected the IMF traits of the longissimus dors...
Source: Animal Genetics - January 30, 2024 Category: Genetics & Stem Cells Authors: Yang Shen Yuxi Chen Shufeng Zhang Ze Wu Xiaoyu Lu Weizhen Liu Bang Liu Xiang Zhou Source Type: research
Whole genome resequencing reveals candidate genes for postaxial polydactyly in Large White pigs
In this study, we analyzed a group of Large White pigs with postaxial polydactyly, including 29 cases and 79 controls from 24 families. High-depth sequencing was performed on 20 pigs, while low-depth sequencing was improved through imputation for the remaining pigs. A genome-wide association study (GWAS) and genetic differentiation were conducted using the resequencing dataset, resulting in the identification of 48 significantly associated SNPs and 27 candidate regions. The genetic differentiation regions on chromosomes 5 and 18, which harbored GWAS-identified SNPs, were delineated as confidence regions. The confidence reg...
Source: Animal Genetics - January 29, 2024 Category: Genetics & Stem Cells Authors: Yongle Hao Yunlei Song Fei Chen Jianhong Tang Source Type: research
Canine coat color E locus updates: Identification of a new MC1R variant causing 'sable' coat color in English Cocker Spaniels and a proposed update to the E locus dominance hierarchy
We examined genetic variation in MC1R, and found one new non-synonymous variant, c.250G>A (p.(Asp84Asn)), consistently associated with the English Cocker Spaniel 'sable' phenotype. We propose calling this newly identified allele eH and further show that the eA , eH and eG (previously known as EG ) alleles associate with similar phenotypes in dogs impacting genotypes regulated by beta-defensin 103 gene (CBD103; K locus) and agouti signaling protein gene (ASIP; A locus) in the absence of the EM and E alleles. This suggests that all three alleles are putative reduced-function variants of the MC1R gene. We propose the revis...
Source: Animal Genetics - January 29, 2024 Category: Genetics & Stem Cells Authors: Leena Honkanen Robert Loechel Stephen Davison Jonas Donner Heidi Anderson Source Type: research
Identification of genomic regions associated with resistance to gastrointestinal parasites in an indigenous sheep by single- and multiple-locus methods
Anim Genet. 2024 Jan 10. doi: 10.1111/age.13392. Online ahead of print.ABSTRACTWe investigated the association between 157 SNPs located in 75 candidate genes involved in the immune system and proxy traits for resistance to gastrointestinal nematodes in sheep. A total of 211 lambs from eight flocks were sampled. Nematode eggs per gram were counted and classified as: (i) Strongyles, (ii) Nematodirus spp., (iii) Trichuris spp. and (iv) Marshallagia marshalli. Single- and multiple-locus models were used to test the marker-trait associations. Seven significant SNPs were identified on chromosomes OAR6, 15, 16, and 19. These find...
Source: Animal Genetics - January 10, 2024 Category: Genetics & Stem Cells Authors: S A Rafat M Barbato R Hajializadeh Valilou G H Moghaddam A Nematollahi K Periasamy R Pichler P Ajmone Marsan Source Type: research
Differential expression of ASIP transcripts reveals genetic mechanism underpinning black-tail independence from body plumage in yellow-bodied chickens
In conclusion, this study lays the foundation for further research on the genetic mechanisms of regional differences in feather color, contributing to a better understanding of plumage pigmentation in chickens.PMID:38194424 | DOI:10.1111/age.13395 (Source: Animal Genetics)
Source: Animal Genetics - January 9, 2024 Category: Genetics & Stem Cells Authors: Xiaotong Zheng Jianfei Chen Ruixue Nie Huanhuan Miao Ziwei Chen Jiaheng He Yinku Xie Hao Zhang Source Type: research
Differential expression of ASIP transcripts reveals genetic mechanism underpinning black-tail independence from body plumage in yellow-bodied chickens
In conclusion, this study lays the foundation for further research on the genetic mechanisms of regional differences in feather color, contributing to a better understanding of plumage pigmentation in chickens.PMID:38194424 | DOI:10.1111/age.13395 (Source: Animal Genetics)
Source: Animal Genetics - January 9, 2024 Category: Genetics & Stem Cells Authors: Xiaotong Zheng Jianfei Chen Ruixue Nie Huanhuan Miao Ziwei Chen Jiaheng He Yinku Xie Hao Zhang Source Type: research
Evaluating three strategies of genome-wide association analysis for integrating data from multiple populations
Anim Genet. 2024 Jan 7. doi: 10.1111/age.13394. Online ahead of print.ABSTRACTIn livestock, genome-wide association studies (GWAS) are usually conducted in a single population (single-GWAS) with limited sample size and detection power. To enhance the detection power of GWAS, meta-analysis of GWAS (meta-GWAS) and mega-analysis of GWAS (mega-GWAS) have been proposed to integrate data from multiple populations at the level of summary statistics or individual data, respectively. However, there is a lack of comparison for these different strategies, which makes it difficult to guide the best practice of GWAS integrating data fr...
Source: Animal Genetics - January 8, 2024 Category: Genetics & Stem Cells Authors: Zhanming Zhong Guangzhen Li Zhiting Xu Haonan Zeng Jinyan Teng Xueyan Feng Shuqi Diao Yahui Gao Jiaqi Li Zhe Zhang Source Type: research
Identification of population-informative markers from high-density genotyping data through combined feature selection and machine learning algorithms: Application to European autochthonous and cosmopolitan pig breeds
In this study, we applied the Boruta algorithm, a wrapper of the machine learning random forest algorithm, on a database of 23 European pig breeds (20 autochthonous and three cosmopolitan breeds) genotyped with a 70k SNP chip, to pre-select informative SNPs. To identify different sets of SNPs, these pre-selected markers were then ranked with random forest based on their mean decrease accuracy and mean decrease gene indexes. We evaluated the efficiency of these subsets for breed classification and the usefulness of this approach to detect candidate genes affecting breed-specific phenotypes and relevant production traits tha...
Source: Animal Genetics - January 8, 2024 Category: Genetics & Stem Cells Authors: Giuseppina Schiavo Francesca Bertolini Samuele Bovo Giuliano Galimberti Mar ía Muñoz Riccardo Bozzi Marjeta Čandek-Potokar Cristina Óvilo Luca Fontanesi Source Type: research
Genome-wide association analysis revealed new QTL and candidate genes affecting the teat number in Dutch Large White pigs
In this study, 1166 Dutch Large White pigs with TNUM phenotype were used as the research object. These pigs were genotyped by 50K SNP chip and the chip data were further imputed to the resequencing level. The estimated heritabilities of left teat number (LTN), right teat number (RTN) and total teat number (TTN) were 0.21, 0.19 and 0.3, respectively. Based on chip data, significant SNPs for RTN on SSC2, SSC5, SSC9 and SSC13 were identified using genome-wide association analysis (GWAS). Significant SNPs for TTN were identified on SSC2, SSC5 and SSC7. Based on imputed data, the GWAS identified a significant SNP (rs329158522) ...
Source: Animal Genetics - January 8, 2024 Category: Genetics & Stem Cells Authors: Michao Deng Zijian Qiu Chenxi Liu Lijing Zhong Xinfeng Fan Yuquan Han Ran Wang Pinghua Li Ruihua Huang Qingbo Zhao Source Type: research
