Two Different Copy Number Variations of the SOX5 and SOX8 Genes in Yak and Their Association with Growth Traits

Chen, Min; Bao, Qi; Bao, Pengjia; Guo, Xian; Liang, Chunnian; Yan, Ping

doi:10.3390/ani12121587

Cited by 6 publications

(2 citation statements)

References 41 publications

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“…The SOX5 gene was necessary for the formation and development of bones (Lefebvre et al, 2001). Zhang et al demonstrated that the copy number variation of SOX5 was associated with growth traits in yak (Zhang et al, 2022). MYBPC1 , one of the subtypes of myosin‐binding protein C, has been demonstrated to be located within genomic regions of quantitative trait loci (QTL) that are associated with growth‐related traits (Offer et al, 1973; Takasuga et al, 2007).…”

Section: Figurementioning

confidence: 99%

Detection of genomic variations and selection signatures in Wagyu using whole‐genome sequencing data

Shi,

Hu,

Lai

et al. 2023

Animal Genetics

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Wagyu is recognized for producing marbled beef with high nutritional value and flavor. Reportedly, Wagyu has been widely used to improve the meat quality of local breeds around the world. However, studies on the genetic mechanism of meat quality in Wagyu at the whole‐genome level are rarely reported. Here, whole‐genome sequencing data of 11 Wagyu and 115 other individuals were used to explore the genomic variations and genes under selection pressure in Wagyu. A total of 31 349 non‐synonymous variants and 53 102 synonymous variants were identified in Wagyu. The population structure analysis showed that Wagyu had the closest genetic relationship with Mishima–Ushi cattle and was apparently separated from other cattle breeds. Then, composite likelihood ratio (CLR), integrated haplotype score, fixation index and cross‐population composite likelihood ratio (XP‐CLR) tests were performed to identify the candidate genes under positive selection in Wagyu. In total, 770 regions containing 312 genes were identified by at least three methods. Among them, 97 regions containing 27 genes were detected by all four methods. We specifically illustrate a list of interesting genes, including LRP2BP, GAA, CACNG6, CXADR, GPCPD1, KLF2, KLF13, SOX5, MYBPC1, SLC25A10, ATP8A1 and MYH15, which are associated with lipid metabolism, fat deposition, muscle development, bone development, feed intake and growth traits in Wagyu. This is the first study to explore the genomic variations and selection signatures of Wagyu at the whole‐genome level. These results will provide significant help to beef cattle improvement and breeding.

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Section: Figurementioning

confidence: 99%

Detection of genomic variations and selection signatures in Wagyu using whole‐genome sequencing data

Shi,

Hu,

Lai

et al. 2023

Animal Genetics

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“…Yak (Bos grunniens) is the main livestock living on the Qinghai–Tibet Plateau and its surrounding areas [ 1 ]. It can provide meat, milk, hair and fuel for people in pastoral areas, and is closely related to the life of people in the plateau area [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

Analysis of Copy Number Variation in the Whole Genome of Normal-Haired and Long-Haired Tianzhu White Yaks

Meng

Bao

et al. 2022

Genes

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Long-haired individuals in the Tianzhu white yak population are a unique genetic resource, and have important landscape value. Copy number variation (CNV) is an important source of phenotypic variation in mammals. In this study, we used resequencing technology to detect the whole genome of 10 long-haired Tianzhu white yaks (LTWY) and 10 normal-haired Tianzhu white yaks (NTWY), and analyzed the differences of CNV in the genome of LTWYs and NTWYs. A total of 110268 CNVs were identified, 2006 CNVRs were defined, and the distribution map of these CNVRs on chromosomes was constructed. The comparison of LTWYs and NTWYs identified 80 differential CNVR-harbored genes, which were enriched in lipid metabolism, cell migration and other functions. Notably, some differential genes were identified as associated with hair growth and hair-follicle development (e.g., ASTN2, ATM, COL22A1, GK5, SLIT3, PM20D1, and SGCZ). In general, we present the first genome-wide analysis of CNV in LTWYs and NTWYs. Our results can provide new insights into the phenotypic variation of different hair lengths in Tianzhu white yaks.

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Early Growth and Development and Nonlinear Model Fitting Analysis of Ashidan Yak

Meng

Bao

et al. 2023

Animals

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Understanding animal growth plays an important role in improving animal genetics and breeding. In order to explore the early growth and development law of Ashidan yak, the body weight (BW), wither height (WH), body oblique length (BL) and chest girth (CG) of 260 female Ashidan yaks were measured. These individuals grew under grazing conditions, and growth traits were measured at 6, 12, 18 and 30 months of age. Then the absolute growth and relative growth of Ashidan yak were calculated, and five nonlinear models (Logistic model, Gompertz model, Brody model, von Bertalanffy model and Richards model) were used to fit the growth curve of Ashidan yak. The fitting effect of the model was evaluated according to MSE, AIC and BIC. The results showed that the growth rate of Ashidan yak was the fastest from 12 to 18 months old, and the growth was slow or even stagnant from 6 to 12 months old. The AIC and BIC values of the Richards model were the lowest among the five models, with an AIC value of 4543.98 and a BIC value of 4563.19. The Richards model estimated body weight at 155.642 kg. In summary, the growth rate of female Ashidan yak changes with the seasons, growing faster in warm seasons and slower in cold seasons. Richards model is the best model to describe the growth curve of female Ashidan yak in five nonlinear models.

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Two Different Copy Number Variations of the SOX5 and SOX8 Genes in Yak and Their Association with Growth Traits

Cited by 6 publications

References 41 publications

Detection of genomic variations and selection signatures in Wagyu using whole‐genome sequencing data

Detection of genomic variations and selection signatures in Wagyu using whole‐genome sequencing data

Analysis of Copy Number Variation in the Whole Genome of Normal-Haired and Long-Haired Tianzhu White Yaks

Early Growth and Development and Nonlinear Model Fitting Analysis of Ashidan Yak

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