Association between the copy number variation of<i>CCSER1</i>gene and growth traits in Chinese<i>Capra hircus</i>(goat) populations

Xu, Zongbin; Wang, Xianwei; Song, Xingya; An, Qi; Wang, Dahui; Zhang, Zijing; Ding, Xiaoting; Yao, Zhilei; Wang, Eryao; Liu, Xian; Ru, Baorui; Xu, Zejun; Huang, Yongzhen

doi:10.1080/10495398.2022.2025818

Cited by 9 publications

(9 citation statements)

References 43 publications

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“…Another gene, SDCCAG8 , also serves as a potential regulator of reproductive phenomena, such as fecundity and litter size in goats ( Seifi et al, 2021 ). In the case of body growth, GALNTL6 was found to be among the top overlapping genes related to meat quality and carcass traits in chickens ( Xu et al, 2023 ). Copy number variations in the CCSER1 gene are linked to body growth traits, especially chest girth, in the Chinese goat population ( Fu et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Comprehensive whole-genome resequencing unveils genetic diversity and selective signatures of the Xiangdong black goat

Liu,

Li,

Luo

et al. 2024

Front. Genet.

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Xiangdong black goats, indigenous to Hunan Province, China, exhibit remarkable adaptation to challenging environments and possess distinct black coat coloration alongside exceptional meat quality attributes. Despite their significance, comprehensive genomic investigations of this breed have been notably lacking. This study involved a comprehensive examination of population structure, genomic diversity, and regions of selection in Xiangdong black goats utilizing whole-genome sequencing data from 20 samples of this breed and 139 published samples from six other Chinese goat breeds. Our genomic analysis revealed a total of 19,133,125 biallelic single nucleotide polymorphisms (SNPs) within the Xiangdong black goat genome, primarily located in intergenic and intronic regions. Population structure analysis indicated that, compared with Jintang, Guizhou and Chengdu goats, Xiangdong black goats exhibit a reduced level of genetic differentiation but exhibit relatively greater divergence from Jining goats. An examination of genetic diversity within Xiangdong black goats revealed a moderate level of diversity, minimal inbreeding, and a substantial effective population size, which are more reflective of random mating patterns than other Chinese goat breeds. Additionally, we applied four distinct selective sweep methods, namely, the composite likelihood ratio (CLR), fixation index (FST), θπ ratio and cross-population extended haplotype homozygosity (XP-EHH), to identify genomic regions under positive selection and genes associated with fundamental biological processes. The most prominent candidate genes identified in this study are involved in crucial aspects of goat life, including reproduction (CCSER1, PDGFRB, IFT88, LRP1B, STAG1, and SDCCAG8), immunity (DOCK8, IL1R1, and IL7), lactation and milk production (SPP1, TLL1, and ERBB4), hair growth (CHRM2, SDC1, ITCH, and FGF12), and thermoregulation (PDE10A). In summary, our research contributes valuable insights into the genomic characteristics of the Xiangdong black goat, underscoring its importance and utility in future breeding programs and conservation initiatives within the field of animal breeding and genetics.

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Section: Discussionmentioning

confidence: 99%

Comprehensive whole-genome resequencing unveils genetic diversity and selective signatures of the Xiangdong black goat

Liu,

Li,

Luo

et al. 2024

Front. Genet.

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“…In addition to the genomic regions showing differentiation between GIFTw and other strains, a region on Oni12 (21.33–21.69) showed differentiation between the FAST population and other populations, suggesting the possibility of selection related to the development of the FAST strain. One of the three annotated genes in this region, CCSER1 , has been identified as associated with growth and feed efficiency in several studies of terrestrial livestock (Xia et al, 2021 ; Xu et al, 2022 ; Xue et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Oreochromis niloticus) populations

Barría

Peñaloza

Papadopoulou

et al. 2023

Evolutionary Applications

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Nile tilapia (Oreochromis niloticus) is among the most farmed finfish worldwide, distributed across different environmental conditions. Its wide distribution has mainly been facilitated by several breeding programs and widespread dissemination of genetically improved strains. In the first Nile tilapia study exploiting a whole‐genome pooled sequencing (Poolseq) approach, we identified the genetic structure and signatures of selection in diverse, farmed Nile tilapia populations, with a particular focus on the GIFT strain, developed in the 1980s, and currently managed by WorldFish (GIFTw). We also investigated important farmed strains from The Philippines and Africa. Using both SNP array data and Poolseq SNPs, we characterized the population structure of these samples. We observed the greatest separation between the Asian and African populations and greater admixture in the Asian populations than in the African ones. We also established that the SNP array data were able to successfully resolve relationships between these diverse Nile tilapia populations. The Poolseq data identified genomic regions with high levels of differentiation (FST) between GIFTw and the other populations. Gene ontology terms associated with mesoderm development were significantly enriched in the genes located in these regions. A region on chromosome Oni06 was genetically differentiated in pairwise comparisons between GIFTw and all other populations. This region contains genes associated with muscle‐related traits and overlaps with a previously published QTL for fillet yield, suggesting that these traits may have been direct targets for selection on GIFT. A nearby region was also identified using XP‐EHH to detect genomic differentiation using the SNP array data. Genomic regions with high or extended homozygosity within each population were also identified. This study provides putative genomic landmarks associated with the recent domestication process in several Nile tilapia populations, which could help to inform their genetic management and improvement.

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“…These genetic variations in livestock species can also influence breeding outcomes, with economically important traits such as meat quality and carcass weight being the primary focus of these analyses. CNVs in the SERPINA3-1 [ 27 ], DYNC1I2 [ 28 ], PLA2G2A [ 29 ], and SYT11 [ 30 ] genes can influence beef cattle growth traits, while CNVs in the CCSER1 [ 31 ], MYLK4 [ 32 ], PIGY [ 33 ], and KAT6A [ 34 ] genes can influence sheep and goat growth traits.…”

Section: Discussionmentioning

confidence: 99%

Copy Number Variations in the MICALL2 and MOGAT2 Genes Are Associated with Ashidan Yak Growth Traits

Liu

Huang

Dai

et al. 2022

Animals

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Copy number variations (CNVs) are a result of genomic rearrangement affecting DNA regions over 1 kb in length, and can include inversions, translocations, deletions, and duplications. The molecule interacting with CasL-like protein 2 (MICALL2) gene is primarily associated with mitochondrial protein targeting and exhibits predicted stress fiber colocalization. The monoacylglycerol O-acyltransferase 2 (MOGAT2) gene encodes an enzyme responsible for catalyzing diacylglycerol synthesis from 2-monoacylglycerol and fatty acyl-CoA. For this study, blood samples were obtained from 315 yaks, and the body weight, body length, withers height, and chest girth of these animals were measured at 6, 12, 18, and 30 months of age. Genomic DNA was harvested from the collected blood samples, and CNVs in these samples were detected by qPCR. The resultant data were compared using ANOVAs, revealing significant associations between MICALL2 gene CNVs and body weight at 6 months of age (p < 0.05), body length and chest girth at 30 months of age (p < 0.05), and withers height at 18 months of age (p < 0.01) in Ashidan yaks. Similarly, MOGAT2 CNVs were significantly associated with body weight at 6 and 30 months of age (p < 0.05), and with withers height at 18 months of age (p < 0.01) in these Ashidan yaks. MICALL2 and MOGAT2 gene expression was further analyzed in yak tissue samples, revealing that MICALL2 was most highly expressed in the adipose tissue, whereas MOGAT2 was most highly expressed in the lung. These results thus confirmed the relationship between CNVs in the MICALL2 and MOGAT2 genes and Ashidan yak growth traits, providing a valuable gene locus that can be leveraged for future marker-assisted yak breeding efforts.

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Association between the copy number variation ofCCSER1gene and growth traits in ChineseCapra hircus(goat) populations

Cited by 9 publications

References 43 publications

Comprehensive whole-genome resequencing unveils genetic diversity and selective signatures of the Xiangdong black goat

Comprehensive whole-genome resequencing unveils genetic diversity and selective signatures of the Xiangdong black goat

Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Oreochromis niloticus) populations

Copy Number Variations in the MICALL2 and MOGAT2 Genes Are Associated with Ashidan Yak Growth Traits

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