Genome-wide detection of copy number variations in polled yak using the Illumina BovineHD BeadChip

Chen, Jia; Wang, Hongbo; Li, Chen; Wu, Xiaoyun; Zan, Linsen; Ding, Xuezhi; Guo, Xian; Bao, Pengjia; Pei, Jie; Chen, Min; Liang, Chunnian; Yan, Ping

doi:10.1186/s12864-019-5759-1

Cited by 19 publications

(14 citation statements)

References 86 publications

(85 reference statements)

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“…The statistics demonstrate that weaning weights are significantly correlated with CNV2 type. Interestingly, this is in agreement with the conclusion of previous studies [28]. This phenomenon may be due to the function of the CADM2 gene, which plays an important role in maintaining the synaptic circuitry of the central nervous system [50], and can mediate leptin sensitivity, thermogenesis and energy metabolism [51].…”

Section: Discussionsupporting

confidence: 92%

“…To explain why this CNV has such an uncommon influence on phenotype, firstly the CADM2 gene had been reported to overlap a QTL region that is correlated with body weight (weaning and yearling) [28]. Secondly, body weight and energy metabolism are maintained by the central nervous system and previous studies have identified that CADM2 is expressed more abundantly in different regions of the brain than in any other tissue [52].…”

Section: Discussionmentioning

confidence: 99%

“…In recent years, several functional CNV regions have been discovered and validated in the yak, utilizing an NGS-based method [25][26][27]. In addition to this, in a previous association study, CNVRs throughout the yak genome have been constructed using SNP arrays which indicate that the cell adhesion molecule 2 (CADM2, also known as SynCAM2, Igsf4d and Nectin-like molecule 3) gene overlaps with a portion of CNVR29 and CNVR30 [28]. Variants of the CADM2 gene have been previously identified to play a pivotal role in the human body mass index (BMI) values by means of the central nervous system [29][30][31].…”

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confidence: 99%

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Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak

Chen

et al. 2019

Animals

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Simple Summary: Cell adhesion molecule 2 (CADM2), also known as synaptic cell adhesion molecule 2 (SYNCAM2), is the mediator of synaptic signals enriched in the brain. Overlaps between copy number variation (CNV) regions in CADM2 and quantitative trait loci (QTL) related to body weight have been clarified in a previous study. In this study, two loci were amplified in the CADM2 gene (CNV1: 235,915 bp, exon 1 and partial intron 1; CNV2: 60,430 bp, intron 9) to explore the relationship between CNV types in the CADM2 gene and growth traits in 350 Ashidan yaks. Association analysis illustrated that no significant effect was found on growth traits in CNV1. However, the CNV2 mutation had a significant effect on body weight at the sixth month (p < 0.05). Individuals with the gain-type copy number variation CNV2 were significantly superior to those with loss-or normal-type in terms of body weight (p < 0.05). In summary, this study confirmed that CADM2-CNVs affect growth traits in yaks, and may be candidate genes for successful yak breeding and genetics projects.Abstract: Copy number variation (CNV) is currently accepted as a common source of genetic variation. It is reported that CNVs may influence the resistance to disease and complex economic traits, such as residual feed intake, muscle formation, and fat deposition in livestock. Cell adhesion molecule 2 (CADM2) is expressed widely in the brain and adipose tissue and can regulate body weight through the central nervous system. Growth traits are important economic traits for animal selection. In this study, we aimed to explore the effect of CADM2 gene copy number variants on yak growth traits. Here, two CNVs in the CADM2 gene were investigated using the quantitative polymerase chain reaction (qPCR), and the association of the CNVs with growth traits in yak was analyzed using statistical methods by SPSS software. Differences were considered significant if the p value was < 0.05. Statistical analysis indicated significant association of CADM2-CNV2 with the body weight of the Chinese Ashidan yak. A significant effect of CNV2 (p < 0.05) was found on body weight at 6 months. In CNV2, the gain-type copy number variation exhibited greater performance than the other variants, with greater body weight observed at 6 months (p < 0.05). To the best of our knowledge, this is the first attempt to investigate the function of CADM2-CNVs and their association with growth traits in animals. This may be a useful candidate marker in marker-assisted selection of yaks.Animals 2019, 9, 1008 2 of 11 polymorphisms (RFLP), single nucleotide polymorphisms (SNP), indels (Insertion/Deletion) and structural variations, such as inversions, duplications and deletions. To date, SNPs are used extensively for complex economic disease traits in livestock [2][3][4][5]. More than 99% of indels are less than 50 bp in length [6,7], and some long insertions and deletions are returned into the concept of structural variation [8]. As a genetic marker, indels have great potential whether in growth and reproduction...

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak

Chen

et al. 2019

Animals

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“…So far the researches about hair follicle growth in yak mainly focused on the expression pattern of several genes such as BMP2, TGF-β and HSP70 [21][22][23], there were no systematic molecular study involved in HFs cycle on yak was reported. The hair growth pattern of yak is similar to goat, in addition, the harsh living environment with cold and oxygen-thin air makes yak some unique traits, such as the high altitude adaptation [24], skin is the important protective barrier against cold and harsh environment, the study of lncRNAs influencing on the HFs may also broaden our knowledge on alpine adaptation of yak.…”

Section: Introductionmentioning

confidence: 97%

Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak

Zhang

Bao

Jia

et al. 2020

Preprint

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Background: Long non coding RNA (lncRNA) as important regulator has been demonstrated playing an indispensable role in the biological process of hair follicles (HFs) growth. However, their function and expression profile in hair cycling of yak are yet unknown. It only a few functional lncRNAs have been identified, partly due to the low sequence conservation and lack of identified conserved properties in lncRNAs. Here, lncRNA-seq was employed to detect the expression profile of lncRNAs during HFs cycle of yak, and the sequence conservation between yak and cashmere goat during HFs cycle was analyzed. Result: Totally 2884 lncRNAs were identified in five phases (Jan. Mar. Jun. Aug. and Oct.) during HFs cycle of yak. We then performed differential expression analysis between three phases (Jan. Mar. and Oct.) finding that 198 differently expressed lncRNAs (DELs) were obtained in Oct-vs-Jan, 280 DELs were obtained in Jan-vs-Mar, and 340 DELs were obtained in Mar-vs-Oct. Subsequently, the nearest genes of DELs were used to explore the potential function of lncRNAs by GO and KEGG enrichment analysis, several critical pathways involved in HFs development such as Wnt signaling pathway, VEGF signaling pathway and Signaling pathways regulating pluripotency of stem cells were enriched. To further screen key lncRNAs influencing in HFs cycle, twenty-four sequence conserved DELs were obained via comparison analysis of partial DELs with previously published lncRNA-seq data of cashmere goat in HFs cycle by NCBI blast-2.9.0+, and the limited degree of sequence conservation of lncRNAs were observed. Conclusion: Our study expanded the knowledge about lncRNAs affecting on hair cycling, and the finding related to sequence conservation properties of lncRNAs between two species at the specific trait- HFs cycle will likely provide valuable insights into the study of lncRNAs functionality and mechanism.

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“…The hair growth pattern of yak is similar to that of goats. Also, the harsh living environment with cold and oxygenthin air gives yak some unique traits, such as the high altitude adaptation [24]. The skin is an important protective barrier against a cold and harsh environment.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak

Zhang

Bao

Jia

et al. 2020

Preprint

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Background: Long non-coding RNA (lncRNA) as an important regulator has been demonstrated playing an indispensable role in the biological process of hair follicles (HFs) growth. However, their function and expression profile in the HFs cycle of yak are yet unknown. Only a few functional lncRNAs have been identified, partly due to the low sequence conservation and lack of identified conserved properties in lncRNAs. Here, lncRNA-seq was employed to detect the expression profile of lncRNAs during the HFs cycle of yak, and the sequence conservation of two datasets between yak and cashmere goat during the HFs cycle was analyzed. Results: A total of 2884 lncRNAs were identified in 5 phases (Jan., Mar., Jun., Aug., and Oct.) during the HFs cycle of yak. Then, differential expression analysis between 3 phases (Jan., Mar., and Oct.) was performed, revealing that 198 differentially expressed lncRNAs (DELs) were obtained in the Oct.-vs-Jan. group, 280 DELs were obtained in the Jan.-vs-Mar. group, and 340 DELs were obtained in Mar.-vs-Oct. group. Subsequently, the nearest genes of lncRNAs were searched as the potential target genes and used to explore the function of DELs by GO and KEGG enrichment analysis. Several critical pathways involved in HFs development such as Wnt signaling pathway, VEGF signaling pathway, and Signaling pathways regulating pluripotency of stem cells, were enriched. To further screen key lncRNAs influencing the HFs cycle, 24 DELs with differ degree of sequence conservation were obtained via a comparative analysis of partial DELs with previously published lncRNA-seq data of cashmere goat in the HFs cycle using NCBI BLAST-2.9.0+, and 3 DELs of them were randomly selected for further detailed analysis of the sequence conservation properties. Conclusions: This study revealed the expression pattern and potential function of lncRNAs during HFs cycle of yak, which would expand the knowledge about the role of lncRNAs in the HFs cycle. The findings related to sequence conservation properties of lncRNAs in the HFs cycle between the two species may provide valuable insights into the study of lncRNA functionality and mechanism. Keywords: Hair follicle cycling, lncRNA, NCBI blast-2.9.0+, Yak

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Genome-wide detection of copy number variations in polled yak using the Illumina BovineHD BeadChip

Cited by 19 publications

References 86 publications

Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak

Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak

Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak

Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak

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