The copy number variation of DMBT1 gene effects body traits in two Chinese cattle breeds

Li, Zheng; Xu, Jie; Liu, Xian; Zhang, Zijing; Zhong, Jialin; Wen, Yifan; Yao, Zhilei; Yang, Peng; Wang, Eryao; Chen, Fuying; Huang, Wenyuan; Qi, Zengfang; Yang, Guojie; Lei, Chuzhao; Chen, Hong; Ru, Baorui; Huang, Yongzhen

doi:10.1007/s13205-022-03124-3

Cited by 4 publications

(4 citation statements)

References 27 publications

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“…Although related issues have been extensively studied through SNPs, there have been few reports on CNVR-based selection signals for adaptation to disease resistance in humans and animals [ 65 , 66 ]. In the present study, we highlighted genes ( CATHL3 and DMBT ) that overlapped highly differentiated CNVRs between SM and other duck populations.…”

Section: Discussionmentioning

confidence: 99%

“…Similarly, DMBT1, a member of the scavenger receptor cysteine-rich super family, is considered to play a role in tumorigenesis and pathogen defense [ 70 ]. A DMBT1 -harbored SNP selection signal provides evidence of a bovine tuberculosis (bTB) susceptibility gene in cattle breeds [ 65 ]. SM inhabits a mountainous area that has been relatively closed to transportation for a long time, acting as a natural barrier to some extent.…”

Section: Discussionmentioning

confidence: 99%

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Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing

Li,

Quan,

Liu

et al. 2024

BMC Genomics

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Background Specific pathogen-free ducks are a valuable laboratory resource for waterfowl disease research and poultry vaccine development. High throughput sequencing allows the systematic identification of structural variants in genomes. Copy number variation (CNV) can explain the variation of important duck genetic traits. Herein, the genome-wide CNVs of the three experimental duck species in China (Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)) were characterized using resequencing to determine their genetic characteristics and selection signatures. Results We obtained 4,810 CNV regions (CNVRs) by merging 73,012 CNVs, covering 4.2% of the duck genome. Functional analysis revealed that the shared CNVR-harbored genes were significantly enriched for 31 gene ontology terms and 16 Kyoto Encyclopedia of Genes and Genomes pathways (e.g., olfactory transduction and immune system). Based on the genome-wide fixation index for each CNVR, growth (SPAG17 and PTH1R), disease resistance (CATHL3 and DMBT1), and thermoregulation (TRPC4 and SLIT3) candidate genes were identified in strongly selected signatures specific to JD, SM, and SX, respectively. Conclusions In conclusion, we investigated the genome-wide distribution of experimental duck CNVs, providing a reference to establish the genetic basis of different phenotypic traits, thus contributing to the management of experimental animal genetic resources.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing

Li,

Quan,

Liu

et al. 2024

BMC Genomics

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“…However, in cattle, the DMBT1 was found to be involved with facial dysplasia syndrome in Holstein cattle [39]. A recent study revealed a CNV within the DMBT1 gene to be present in two Chinese breeds that were also associated with growth, specifically body length [53]. An interesting finding was the high level of expression of the DMBT1 gene in tuberculosis susceptible tissues [53].…”

Section: Discussionmentioning

confidence: 99%

Copy Number Variation Discovery in South African Nguni-Sired and Bonsmara-Sired Crossbred Cattle

Kooverjee

Soma

Nest

et al. 2023

Animals

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Crossbreeding forms part of Climate-Smart beef production and is one of the strategies to mitigate the effects of climate change. Two Nguni-sired and three Bonsmara-sired crossbred animals underwent whole genome sequencing. Following quality control and file preparation, the sequence data were investigated for genome-wide copy number variation (CNV) using the panelcn.MOPS tool. A total of 355 CNVs were identified in the crossbreds, of which 274 were unique in Bonsmara-sired crossbreds and 81 unique in the Nguni-sired crossbreds. Genes that differed in copy number in both crossbreds included genes related to growth (SCRN2, LOC109572916) and fertility-related factors (RPS28, LOC1098562432, LOC109570037). Genes that were present only in the Bonsmara-sired crossbreds included genes relating to lipid metabolism (MAF1), olfaction (LOC109569114), body size (HES7), immunity (LOC10957335, LOC109877039) and disease (DMBT1). Genes that were present only in the Nguni-sired crossbreds included genes relating to ketosis (HMBOX1) and amino acid transport (LOC109572916). Results of this study indicate that Nguni and Bonsmara cattle can be utilized in crossbreeding programs as they may enhance the presence of economically important traits associated with both breeds. This will produce crossbred animals that are good meat producers, grow faster, have high fertility, strong immunity and a better chance of producing in South Africa’s harsh climate conditions. Ultimately, this study provides new genetic insights into the adaptability of Nguni and Bonsmara crossbred cattle.

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“…As CNVRs usually work through regulation effects or dose effects [ 43 , 44 ], we analyzed the RNA expression profiles of some individuals with different CNVR dosages. Interestingly, we found that one of the PELP1 ASs, named ENSSSCT00000019597, was significantly differently expressed in CNV150-variant individuals.…”

Section: Discussionmentioning

confidence: 99%

Copy Number Variations Contribute to Intramuscular Fat Content Differences by Affecting the Expression of PELP1 Alternative Splices in Pigs

Wei

Shu

Wang

et al. 2022

Animals

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Intramuscular fat (IMF) is a key meat quality trait. Research on the genetic mechanisms of IMF decomposition is valuable for both pork quality improvement and the treatment of obesity and type 2 diabetes. Copy number variations (CNVs) are a type of variant that may influence meat quality. In this study, a total of 1185 CNV regions (CNVRs) including 393 duplicated CNVRs, 432 deleted CNVRs, and 361 CNVRs with both duplicated and deleted status were identified in a pig F2 resource population using next-generation sequencing data. A genome-wide association study (GWAS) was then performed between CNVs and IMF, and a total of 19 CNVRs were found to be significantly associated with IMF. QTL colocation analysis indicated that 3 of the 19 CNVRs overlapped with known QTLs. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3′UTR end of the proline, as well as glutamate and the leucine rich protein 1 (PELP1) gene may affect the expression of PELP1 alternative splices. Sequence alignment and Alphafold2 structure prediction results indicated that the two alternative splices of PELP1 have a 23 AA sequence variation and a helix-fold structure variation. This region is located in the region of interaction between PELP1 and other proteins which have been reported to be significantly associated with fat deposition or insulin resistance. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affects the structure of the PELP1 protein. In conclusion, we found some CNVRs, especially CNV150, located in PELP1 that affect IMF. These findings suggest a novel mechanistic approach for meat quality improvement in animals and the potential treatment of insulin resistance in human beings.

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The copy number variation of DMBT1 gene effects body traits in two Chinese cattle breeds

Cited by 4 publications

References 27 publications

Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing

Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing

Copy Number Variation Discovery in South African Nguni-Sired and Bonsmara-Sired Crossbred Cattle

Copy Number Variations Contribute to Intramuscular Fat Content Differences by Affecting the Expression of PELP1 Alternative Splices in Pigs

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