Genetic variants in the SIRT6 transcriptional regulatory region affect gene activity and carcass quality traits in indigenous Chinese beef cattle (Bos taurus)

Gui, Linsheng; Raza, Sayed Haidar Abbas; Garcia, Matthew; Sun, Yonggang; Ullah, Irfan; Han, Yin-cang

doi:10.1186/s12864-018-5149-0

Cited by 15 publications

(5 citation statements)

References 29 publications

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“…The relative expression levels of the KAT2B gene were calculated via 2 −∆∆Ct method [ 21 ]. The mRNA expression levels of KAT2B in tissues were analyzed through GraphPad Prism 6 software.…”

Section: Methodsmentioning

confidence: 99%

KAT2B Gene Polymorphisms Are Associated with Body Measure Traits in Four Chinese Cattle Breeds

Lin

Chen

et al. 2022

Animals

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Identifying molecular markers related to growth characteristics or meat quality is significant for improving beef cattle breeds. K(lysine) acetyltransferase 2B (KAT2B) is a transcriptional co-activator regulating the acetylation modification of histones, which may be involved in the development and metabolism of muscle and adipose. However, investigations of KAT2B genetic variations in Chinese native cattle are still limited. This study aimed to identify crucial single nucleotide polymorphisms (SNPs) influencing the body measurements of Chinese native cattle. Biological evolution and conservation analysis showed that KAT2B was highly conserved among the ruminants. By qPCR assay, KAT2B gene expression was found to be spatiotemporally specific in bovine tissues such as adipose and liver. By the RFLP-PCR method, three SNPs of KAT2B (g.T61908C, g.T62131C, and g.C73406T) were identified in 827 individuals of four Chinese cattle breeds, including Qinchuan (n = 658), Fu (n = 52), Yak (n = 48), and Chaidam (n = 69) cattle. Association analysis between these KAT2B polymorphisms and the body measurements of Chinese native cattle revealed significant observations. The genetic effects of g.T61908C, g.T62131C, and g.C73406T on the associated phenotypes were illustrated in each breed. In Qinchuan cattle, g.T62131C was significantly associated with better body height, chest width, hip width, and withers height, for which TC and/or TT were the advantageous genotype. In Fu cattle, TT genotype of g.T61908C was associated to better body length, while individuals with TT or CC of g.T62131C showed higher circumference of cannon bone than those with TC genotype. In Yak, individuals with TT genotype of g.C73406T had heavier body weight. In Chaidam cattle, TC genotype of g.C73406T was associated to superior body weight, while CC genotype of g.C73406T was associated to superior chest girth and circumference of cannon bone. These findings suggest that KAT2B gene polymorphisms can be used as the molecular markers for the early molecular marker-assisted selection in beef cattle breeding programs.

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Section: Methodsmentioning

confidence: 99%

KAT2B Gene Polymorphisms Are Associated with Body Measure Traits in Four Chinese Cattle Breeds

Lin

Chen

et al. 2022

Animals

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“…It is regulated by the synergistic action of transcription factors (TFs) and regulatory proteins, and plays an important role in the accuracy and diversity of the transmission of genetic information [25,[33][34][35]. Transcription factor ACSL1 belong to the long-chain adipocyte-acid CoA family, which can catalyze the conversion of long-chain adipocyte acids into acyl coenzyme A in active form, which is used to synthesize cell lipids and is degraded by β-oxidation [36][37][38][39][40]. In addition, PPARα participates in lipid metabolism and inflammatory reaction [41].…”

Section: Discussionmentioning

confidence: 99%

The Molecular Characteristics of the FAM13A Gene and the Role of Transcription Factors ACSL1 and ASCL2 in Its Core Promoter Region

Liang

Raza

et al. 2019

Genes

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The gene family with sequence similarity 13 member A (FAM13A) has recently been identified as a marker gene in insulin sensitivity and lipolysis. In this study, we first analyzed the expression patterns of this gene in different tissues of adult cattle and then constructed a phylogenetic tree based on the FAM13A amino acid sequence. This showed that subcutaneous adipose tissue had the highest expression in all tissues except lung tissue. Then we summarized the gene structure. The promoter region sequence of the gene was successfully amplified, and the −241/+54 region has been identified as the core promoter region. The core promoter region was determined by the unidirectional deletion of the 5’ flanking promoter region of the FAM13A gene. Based on the bioinformatics analysis, we examined the dual luciferase activity of the vector constructed by the mutation site, and the transcription factors ACSL1 and ASCL2 were found as transcriptional regulators of FAM13A. Moreover, electrophoretic mobility shift assay (EMSA) further validated the regulatory role of ACSL1 and ASCL2 in the regulation of FAM13A. ACSL1 and ASCL2 were finally identified as activating transcription factors. Our results provide a basis for the function of the FAM13A gene in bovine adipocytes in order to improve the deposition of fat deposition in beef cattle muscle.

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“…involved in growth regulation is confirmed by identification of additional notable candidate genes with known effect on body size and/or carcass traits, including Grb10 on BTA 4 [84][85][86], PDGFRA, MAD2L and UBE2K on BTA 6 [87][88][89][90], SIRT6 on BTA 7 [91][92][93], and ACAT1, KDELC2 on BTA 15 [94][95][96] in Yaroslavl breed, and EGR1, HSPA9 on BTA 7 [97,98], and CDH15, DPEP1, GAS8, GALNS, and MC1R on BTA 18 [30,[99][100][101][102] in Kholmogor breed. The second overlapping genomic region under positive selection in Yaroslavl, Kholmogor and Holstein breeds containing TNFRSF1B, MFN2, PLOD1, KIAA2013, NPPB, NPPA, CLCN6, MTHFR, AGTRAP, FBXO2, MTOR, ANGPTL7, EXOSC10, and MASP2 genes was found on BTA16 (Table 3, S6 Table).…”

Section: Plos Onementioning

confidence: 99%

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

et al. 2020

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Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.

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Genetic variants in the SIRT6 transcriptional regulatory region affect gene activity and carcass quality traits in indigenous Chinese beef cattle (Bos taurus)

Cited by 15 publications

References 29 publications

KAT2B Gene Polymorphisms Are Associated with Body Measure Traits in Four Chinese Cattle Breeds

KAT2B Gene Polymorphisms Are Associated with Body Measure Traits in Four Chinese Cattle Breeds

The Molecular Characteristics of the FAM13A Gene and the Role of Transcription Factors ACSL1 and ASCL2 in Its Core Promoter Region

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

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