Genetic variants and haplotype combination in the bovine CRTC3 affected conformation traits in two Chinese native cattle breeds (Bos Taurus)

Wu, Sen; Ning, Yue; Raza, Sayed Haidar Abbas; Zhang, Chengtu; Zhang, Le; Chen, Gong; Wang, Hongbao; Schreurs, Nicola M.; Liu, Zan

doi:10.1016/j.ygeno.2018.11.028

Cited by 13 publications

(10 citation statements)

References 43 publications

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“…These studies indicated that Jiaxian Red originated from the crossbreeding between taurine and indicine cattle. Studies attempting to explain the growth and meat quality of Jiaxian Red cattle have focused on single gene SNPs (single nucleotide polymorphisms), such as MYLK4 [13], TRPV1 and TRPA1 [14], and CRTC3 [15]. However, there has been no previous studies using WGS data to identify genes under the selection pressure of this breed.…”

Section: Introductionmentioning

confidence: 99%

Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

Xia

Zhang

et al. 2021

BMC Genomics

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Background Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. Results The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6). Conclusion We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.

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Section: Introductionmentioning

confidence: 99%

Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

Xia

Zhang

et al. 2021

BMC Genomics

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“…There are many genes that have been reported to be associated with the economic traits of cattle (Li et al, 2010;Pausch et al, 2017;Raza et al, 2018;Sun et al, 2018;Cheng et al, 2020). In particular, genes such as MYLK4 (Zheng et al, 2019), CRTC3 (Wu et al, 2018), LEPR (Guo et al, 2008), and LHX4 (Ren et al, 2010) have been reported to be associated with the growth traits of Chinese cattle breeds. As body size is one the most important economic/growth traits for the modern breeding industry, it is valuable to investigate the genetic dynamics of this trait.…”

Section: Discussionmentioning

confidence: 99%

Whole Transcriptome Analysis Identifies the Taxonomic Status of a New Chinese Native Cattle Breed and Reveals Genes Related to Body Size

et al. 2020

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Wandong (WD) cattle has recently been identified as a new Chinese native cattle breed by the National Commission for Livestock and Poultry Genetic Resources. The population size of this breed is less than 10,000. WD cattle and Dabieshan (DB) cattle are sympatric but are raised in different ecological environments, on mountains and plains, respectively, and the body sizes of these two breeds are markedly different. Blood samples were obtained from 8 adult female WD cattle and 7 adult female DB cattle (24 months old). The total RNA was extracted from leukocyte cells, and sequencing experiments were conducted on the Illumina HiSeq TM 4000 platform. After the removal of one outlier sample from the WD cattle breed as determined by principal component analysis (PCA), phylogenetic and population structure analyses indicated that WD and DB cattle formed a distinct Central China cattle group and showed evidence of hybridization between Bos. taurus and Bos. indicus. The immune-regulator CD48 (P = 1.3E-6) was associated with breed-specific traits according to loss-offunction variant enrichment analysis. In addition, 113 differentially expressed genes were identified between the two breeds, many of which are associated with the regulation of body growth, which is the major difference between the two breeds. This study showed that WD cattle belong to the group of hybrids between Bos. Taurus and Bos. indicus, and one novel gene associated with breed traits and multiple differentially expressed genes between these two closely related breeds was identified. The results provide insights into the genetic mechanisms that underlie economically important traits, such as body size, in cattle.

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“…CREB-regulated transcription co-activator 3 (CRTC3) is an essential protein in lipid homeostasis [89] and is regarded as a member of the CREB co-activator class (CREB-regulated transcription coactivators CRTC) [50]. CRTC3 is placed on chromosome 21 in cattle and is contained in 15 exons and 14 introns.…”

Section: Gene Polymorphism Vs Slaughter Value and Beef Qualitymentioning

confidence: 99%

“…For meat quality in native Chinese beef cattle, there were four SNPs, two in introns (SNP1: g.62652 A > G and SNP4: g.91297C > T) and two in exons (SNP2 g.62730C > T and SNP3: g.66478G > C) with an influence on carcass characteristics [50]. These SNPs primarily expressed in CRTC3 which is located on chromosome 21.…”

Section: Gene Polymorphism Vs Slaughter Value and Beef Qualitymentioning

confidence: 99%

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Advances of Molecular Markers and Their Application for Body Variables and Carcass Traits in Qinchuan Cattle

Raza

Khan

Abdelnour

et al. 2019

Genes

Self Cite

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This review considers the unique characteristics of Chinese cattle and intramuscular fat content (IMF) as factors influencing meat quality, including tenderness, flavor, and juiciness of meat. Due to its nutritional qualities, meat contributes to a healthy and balanced diet. The intramuscular fat content and eating quality of beef are influenced by many factors, which can generally be divided into on-farm and pre-slaughter factors (breed, sex of cattle, age at slaughter, housing system, diet, and pre-slaughter handling) and postmortem factors (post-slaughter processing, chilling temperature, and packaging). Meat quality traits can also be influenced by the individual genetic background of the animal. Worldwide, the function of genes and genetic polymorphisms that have potential effects on fattening of cattle and beef quality have been investigated. The use of DNA markers is recognized as a powerful and efficient approach to achieve genetic gain for desirable phenotypic characteristics, which is helpful for economic growth. The polymorphisms of the SIRT4, SIRT6, SIRT7, CRTC3, ABHD5, KLF6, H-FABP, and ELOVL6 genes for body and growth characteristics of cattle, and also for beef quality, are considered with the aim of highlighting the significance of beef intramuscular fat content, and that growth, body, and meat quality characteristics are polygenically regulated.

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Genetic variants and haplotype combination in the bovine CRTC3 affected conformation traits in two Chinese native cattle breeds (Bos Taurus)

Cited by 13 publications

References 43 publications

Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

Whole Transcriptome Analysis Identifies the Taxonomic Status of a New Chinese Native Cattle Breed and Reveals Genes Related to Body Size

Advances of Molecular Markers and Their Application for Body Variables and Carcass Traits in Qinchuan Cattle

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