Exploring genotype–phenotype relationships of the<i>CRABP2</i>gene on growth traits in beef cattle

Wen, Yifan; Li, Zheng; Niu, Hongyu; Zhang, Guoliang; Zhang, Guimin; Ma, Yihan; Tian, Yi-Ran; Liu, Yanrong; Yang, Peng; Yang, Di-Yi; Lei, Chuzhao; Dang, Ruihua; Qi, Xinglei; Chen, Hong; Huang, Bizhi; Huang, Yongzhen

doi:10.1080/10495398.2018.1531015

Cited by 3 publications

(3 citation statements)

References 31 publications

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“…The r 2 -values above 1/3 (r 2 >0.33) indicate that LD was sufficiently strong for mapping [ 15 ]. The mean r 2 indicated that LD among the g.5070C>A, g.5076T>C, and g.5148A>C sites was strong, and this may be attributed to the lower recombination and higher genotypic variation at these sites [ 23 ].…”

Section: Discussionmentioning

confidence: 99%

Genetic variants of the growth differentiation factor 8 affect body conformation traits in Chinese Dabieshan cattle

et al. 2022

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Objective: The growth differentiation factor 8 (GDF8) gene plays a key role in bone formation, resorption, and skeletal muscle development in mammals. Here, we studied the genetic variants of GDF8 and their contribution to body conformation traits in Chinese Dabieshan cattle.Methods: Single nucleotide polymorphisms were identified in the bovine GDF8 gene by DNA sequencing. Phylogenetic analysis, motif analysis, and genetic diversity analysis were conducted using bioinformatics software. Association analysis between five SNPs, haplotype combinations, and body conformation traits was conducted in 380 individuals.Results: GDF8 was highly conserved in seven species, and the GDF8 sequence of cattle was most similar to the sequences of sheep and goat based on the phylogenetic analysis. The motif analysis showed that there were 12 significant motifs in GDF8. Genetic diversity analysis indicated that the polymorphism information content of the five studied SNPs was within 0.25 to 0.5. Haplotype analysis revealed that a total of 12 different haplotypes and those with a frequency of < 0.05 were excluded. Linkage disequilibrium analysis showed that there was a strong linkage (r 2 > 0.330) between the following SNPs: g.5070C > A, g.5076T > C, and g.5148A > C. Association analysis indicated that these five SNPs were associated with some of the body conformation traits (p < 0.05), and the animals with haplotype combination H1H1 (-GGGGCCTTAA-) had greater wither height, hip height, heart girth, abdominal girth, and pin bone width than the other animals (p < 0.05) in Dabieshan cattle. Conclusion:Overall, our results indicate that the genetic variants of GDF8 affected the body conformation traits of Chinese Dabieshan cattle, and the GDF8 gene could make a strong candidate gene in Dabieshan cattle breeding programs.

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Section: Discussionmentioning

confidence: 99%

Genetic variants of the growth differentiation factor 8 affect body conformation traits in Chinese Dabieshan cattle

et al. 2022

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“…The r 2 -values, among the g.10670A > C, g.10684C > G, and g.10763A > G sites, and between g.10667A > C and g.10699A > G sites, were sufficiently strong for mapping. The results may be caused by the lower recombination and higher genotypic variation at these sites [29].…”

Section: Discussionmentioning

confidence: 99%

Polymorphisms of the Growth Hormone Releasing Hormone Receptor Gene Affect Body Conformation Traits in Chinese Dabieshan Cattle

Zhao

Jin

Liu

et al. 2022

Animals

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This study was performed to expose the polymorphisms of the growth hormone-releasing hormone receptor gene in Chinese Dabieshan cattle, evaluate its effect on body conformation traits, and find potential molecular markers in Chinese cattle. The GHRHR structure and the phylogenetic tree were analyzed using bioinformatics software. The polymorphism of the GHRHR gene in 486 female cattle was genotyped by PCR-RFLP and DNA sequencing, and the association between SNPs and body conformation traits of Chinese Dabieshan cattle was analyzed by one-way ANOVA in SPSS software. GHRHR was often conserved in nine species, and its sequence of cattle was closest to sheep and goats. Six polymorphic SNPs were identified, g.10667A > C and g.10670A > C were missense mutation. The association analysis indicated that the six SNPs significantly influenced the body conformation traits of Chinese Dabieshan cattle (p < 0.05). Six haplotypes were identified and Hap1 (-CAACGA-) had the highest frequency (36.10%). The Hap3/5 (-GCCCCCGGAAGG-) exhibited a significantly greater wither height (WH), hip height (HH), heart girth (HG), and hip width (HW) (p < 0.05). Overall, the polymorphisms of GHRHR affected the body conformation traits of Chinese Dabieshan cattle, and the GHRHR gene could be used as a molecular marker in Dabieshan cattle breeding programs.

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“…Another region on Chr 10, detected with nSL on both the merged SNP chip-WGS dataset and WGS dataset alone, included the FLRT2 gene, which is related to embryonic development (Haines et al, 2006) and has been associated with calf birth weight by a GWAS in Holstein (Cole et al, 2014). The gene CRABP2 in the Chr 3 region has been also related to growth traits in beef cattle (Wen et al, 2020). Finally, the Chr15 region includes a cluster of olfactory receptor genes (OR2D2, OR2D3, OR10A4, and 0R6A2), a family that is implicated in appetite regulation (Soria-Gomez et al, 2014) and for which genome-wide copy number variants have been associated with 10 diverse production traits in Holstein cattle (Zhou et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed

et al. 2021

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Gene banks, framed within the efforts for conserving animal genetic resources to ensure the adaptability of livestock production systems to population growth, income, and climate change challenges, have emerged as invaluable resources for biodiversity and scientific research. Allele frequency trajectories over the few last generations contain rich information about the selection history of populations, which cannot be obtained from classical selection scan approaches based on present time data only. Here we apply a new statistical approach taking advantage of genomic time series and a state of the art statistic (nSL) based on present time data to disentangle both old and recent signatures of selection in the Asturiana de los Valles cattle breed. This local Spanish originally multipurpose breed native to Asturias has been selected for beef production over the last few generations. With the use of SNP chip and whole-genome sequencing (WGS) data, we detect candidate regions under selection reflecting the effort of breeders to produce economically valuable beef individuals, e.g., by improving carcass and meat traits with genes such as MSTN, FLRT2, CRABP2, ZNF215, RBPMS2, OAZ2, or ZNF609, while maintaining the ability to thrive under a semi-intensive production system, with the selection of immune (GIMAP7, GIMAP4, GIMAP8, and TICAM1) or olfactory receptor (OR2D2, OR2D3, OR10A4, and 0R6A2) genes. This kind of information will allow us to take advantage of the invaluable resources provided by gene bank collections from local less competitive breeds, enabling the livestock industry to exploit the different mechanisms fine-tuned by natural and human-driven selection on different populations to improve productivity.

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Exploring genotype–phenotype relationships of theCRABP2gene on growth traits in beef cattle

Cited by 3 publications

References 31 publications

Genetic variants of the growth differentiation factor 8 affect body conformation traits in Chinese Dabieshan cattle

Genetic variants of the growth differentiation factor 8 affect body conformation traits in Chinese Dabieshan cattle

Polymorphisms of the Growth Hormone Releasing Hormone Receptor Gene Affect Body Conformation Traits in Chinese Dabieshan Cattle

Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed

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