Associations between polymorphisms of SLC22A7, NGFR, ARNTL and PPP2R2B genes and Milk production traits in Chinese Holstein

Jia, Ruike; Fu, Yihan; Xu, Lingna; Li, Houcheng; Li, Yanhua; Liu, Lin; Ma, Zhuo; Sun, Dongxiao; Han, Bo

doi:10.1186/s12863-021-01002-0

Cited by 7 publications

(6 citation statements)

References 62 publications

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“…As the most complex trait in dairy cow production, milk production trait is regulated by many genes and environmental factors. Some nucleotide polymorphisms may be caused by a large (Fu et al, 2022;Jia et al, 2021;Potu et al, 2022) have discussed that SNPs in milk production candidate functional genes can significantly affect milk production traits of dairy cows. In addition, by adding functional gene information of target traits with large genetic effects to expand SNP marker data, the accuracy of genome breeding value prediction can be improved (de Las et al, 2020;Ye et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

“…Scientific evaluation of population genetic structure can provide reference for genetic evaluation, protection and utilization of high‐quality resource populations of Holstein. At present, a large number of studies (Fu et al., 2022; Jia et al., 2021; Potu et al., 2022) have discussed that SNPs in milk production candidate functional genes can significantly affect milk production traits of dairy cows. In addition, by adding functional gene information of target traits with large genetic effects to expand SNP marker data, the accuracy of genome breeding value prediction can be improved (de Las et al., 2020; Ye et al., 2022).…”

Section: Discussionmentioning

confidence: 99%

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Polymorphism of ADAM12, DPP6 and PRKN genes and their associations with milk production traits in Holstein

Li,

Hu,

Feng

et al. 2023

Reprod Domestic Animals

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Milk production traits as the most important economic traits of dairy cows, they directly reflect the benefits of breeding and the economic benefits of pasture. In this study, A disintegrin and metalloproteinase‐12 (ADAM12), Parkinson's disease gene 2 (PRKN) and dipeptidyl peptidase‐like protein subtype 6 (DPP6) polymorphism in 384 Chinese Holstein cows were detected by time‐of‐flight mass spectrometry and through statistical analysis using software such as Popgene 32, SAS 9.4 and Origin 2022, the relationship between single nucleotide polymorphisms (SNPs) of three genes with four milk production traits such as daily milk yield (DMY), milk fat percentage (MFP), milk protein percentage (MPP) and somatic cell score (SCS) was verified at molecular level. The results showed that four polymorphic loci (116,467,133, 116,604,487, 116,618,268 and 116,835,111) of DPP6 gene, two polymorphic loci (97,665,052 and 97,159,837) of PRKN gene and two polymorphic loci (45,542,714 and 45,553,888) of ADAM12 gene were detected. PRKN‐97665052, DPP6‐116467133, ADAM12‐45553888, DPP6‐116604487 and DPP6‐116835111 were all in Hardy–Weinberg equilibrium state (p > .05). ADAM12‐45542714, PRKN‐97159837 and PRKN‐97665052 were moderately polymorphic (0.25 ≤ PIC <0.50) in Holstein. It is evident that the selection potential and genetic variation of these five loci are relatively large, and the genetic richness is relatively high. The correlation analysis of different genotypes between these eight loci and milk production traits of Holstein showed that ADAM12‐45542714 and DPP6‐116835111 (p < .01) had an extremely significant effects on the DMY of Chinese Holstein in Ningxia, while PRKN‐97665052 had an extremely significant effect on MFP (p < .01). The effect of PRKN‐97665052 and DPP6‐116467133 on MPP of Holstein were extremely significant (p < .01). DPP6‐116618268 had an extremely significant effect on the SCS of Holstein in Ningxia (p < .01), and AA genotype individuals showed a higher SCS than GG genotype individuals; the other two loci (ADAM12‐45553888 and DPP6‐116604487) had no significant effects on milk production traits of Holstein (p > .05). In addition, through the joint analysis of DPP6, PRKN and ADAM12 gene loci, it was found that the interaction effect between the three gene loci could significantly affect the DMY, SCS (p < .01) and MPP (p < .05). In conclusion, several different loci of DPP6, PRKN and ADAM12 genes can affect the milk production traits of Holstein to different degrees. PRKN, DPP6 and ADAM12 genes can be used as potential candidate genes for milk production traits of Holstein for marker‐assisted selection, providing theoretical basis for breeding of Holstein.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Polymorphism of ADAM12, DPP6 and PRKN genes and their associations with milk production traits in Holstein

Li,

Hu,

Feng

et al. 2023

Reprod Domestic Animals

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“…For the GL trait, a number of candidate genes located within 20 kb of genome-wide significant and suggestive significant SNPs were identified in both lines. Among them, the PPP2R2B gene had a genetic significant effect on milk production traits in Chinese Holstein [ 67 ]. This gene may be associated with sperm motility in Duroc pigs as a candidate gene [ 68 ].…”

Section: Discussionmentioning

confidence: 99%

GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data

Wang

Shi

et al. 2022

IJMS

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Total number born (TNB), number of stillborn (NSB), and gestation length (GL) are economically important traits in pig production, and disentangling the molecular mechanisms associated with traits can provide valuable insights into their genetic structure. Genotype imputation can be used as a practical tool to improve the marker density of single-nucleotide polymorphism (SNP) chips based on sequence data, thereby dramatically improving the power of genome-wide association studies (GWAS). In this study, we applied Beagle software to impute the 50 K chip data to the whole-genome sequencing (WGS) data with average imputation accuracy (R2) of 0.876. The target pigs, 2655 Large White pigs introduced from Canadian and French lines, were genotyped by a GeneSeek Porcine 50K chip. The 30 Large White reference pigs were the key ancestral individuals sequenced by whole-genome resequencing. To avoid population stratification, we identified genetic variants associated with reproductive traits by performing within-population GWAS and cross-population meta-analyses with data before and after imputation. Finally, several genes were detected and regarded as potential candidate genes for each of the traits: for the TNB trait: NOTCH2, KLF3, PLXDC2, NDUFV1, TLR10, CDC14A, EPC2, ORC4, ACVR2A, and GSC; for the NSB trait: NUB1, TGFBR3, ZDHHC14, FGF14, BAIAP2L1, EVI5, TAF1B, and BCAR3; for the GL trait: PPP2R2B, AMBP, MALRD1, HOXA11, and BICC1. In conclusion, expanding the size of the reference population and finding an optimal imputation strategy to ensure that more loci are obtained for GWAS under high imputation accuracy will contribute to the identification of causal mutations in pig breeding.

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“…Therefore, many researchers try to find the key genes/loci that have significant impacts on milk production traits through candidate gene analysis, genome-wide association analysis and omics data analysis strategies ( Schennink et al, 2009 ; Canovas et al, 2013 ; Cui et al, 2014 ; Liang et al, 2017 ; Bhat et al, 2020 ). Studies have shown that the milk production traits of dairy cows can be significantly affected by SNPs in the genes ( Jiang et al, 2010 ; Dux et al, 2018 ; Han et al, 2019a ; Han et al, 2019b ; Clancey et al, 2019 ; Jia et al, 2021 ; Du et al, 2022 ; Fu et al, 2022 ; Ye et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic marker identification of SEC13 gene for milk production traits in Chinese holstein

Jia

Sun

et al. 2023

Front. Genet.

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SEC13 homolog, nuclear pore and COPII coat complex component (SEC13) is the core component of the cytoplasmic COPII complex, which mediates material transport from the endoplasmic reticulum to the Golgi complex. Our preliminary work found that SEC13 gene was differentially expressed in dairy cows during different stages of lactation, and involved in metabolic pathways of milk synthesis such as citric acid cycle, fatty acid, starch and sucrose metabolisms, so we considered that the SEC13 might be a candidate gene affecting milk production traits. In this study, we detected the polymorphisms of SEC13 gene and verified their genetic effects on milk yield and composition traits in a Chinese Holstein cow population. By sequencing the whole coding and partial flanking regions of SEC13, we found four single nucleotide polymorphisms (SNPs). Subsequent association analysis showed that these four SNPs were significantly associated with milk yield, fat yield, protein yield or protein percentage in the first and second lactations (p ≤.0351). We also found that two SNPs in SEC13 formed one haplotype block by Haploview4.2, and the block was significantly associated with milk yield, fat yield, fat percentage, protein yield or protein percentage (p ≤ .0373). In addition, we predicted the effect of SNP on 5′region on transcription factor binding sites (TFBSs), and found that the allele A of 22:g.54362761A>G could bind transcription factors (TFs) GATA5, GATA3, HOXD9, HOXA10, CDX1 and Hoxd13; and further dual-luciferase reporter assay verified that the allele A of this SNP inhibited the fluorescence activity. We speculate that the A allele of 22:g.54362761A>G might inhibit the transcriptional activity of SEC13 gene by binding the TFs, which may be a cause mutation affecting the formation of milk production traits in dairy cows. In summary, we proved that SEC13 has a significant genetic effect on milk production traits and the identified significant SNPs could be used as candidate genetic markers for GS SNP chips development; on the other hand, we verified the transcriptional regulation of 22:g.54362761A>G on SEC13 gene, providing research direction for further function validation tests.

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Associations between polymorphisms of SLC22A7, NGFR, ARNTL and PPP2R2B genes and Milk production traits in Chinese Holstein

Cited by 7 publications

References 62 publications

Polymorphism of ADAM12, DPP6 and PRKN genes and their associations with milk production traits in Holstein

Polymorphism of ADAM12, DPP6 and PRKN genes and their associations with milk production traits in Holstein

GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data

Genetic marker identification of SEC13 gene for milk production traits in Chinese holstein

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