Genome‐wide selection signal analysis of Australian Boer goat reveals artificial selection imprinting on candidate genes related to muscle development

Yang, Bo; Yuan, Ying; Zhou, Dong‐Ke; Ma, Yue; Mahrous, Karima F.; Wang, S.‐Z.; He, Yanan; Duan, Xinghai; Zhang, W.‐Y.; Guang‐Xin, E

doi:10.1111/age.13092

Cited by 15 publications

(10 citation statements)

References 57 publications

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“…Among these candidate genes, some were involved in ovarian function ( PPP2R5C , CDC25A , ESR1 , RPS26 , and SERPINBs ); seasonal reproduction ( DIO3 , BTG1 , and CRYM ); and metabolism ( OSBPL8 , SLC39A5 , and SERPINBs ) [ 36 ]. In addition, Yang et al [ 37 ] used whole-genome sequencing data from 46 Australian Boer goats to detect SNPs and identify genomic regions associated with muscle development. Finally, 30 candidate genes (e.g., JAK2 , KCNQ1 , PDE5A , PDLIM5 , and TBX5 ) directly associated with muscle development were obtained.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study of Body Conformation Traits by Whole Genome Sequencing in Dazu Black Goats

Sun

Fang

et al. 2022

Animals

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Identifying associations between genetic markers and economic traits has practical benefits for the meat goat industry. To better understand the genomic regions and biological pathways contributing to body conformation traits of meat goats, a genome-wide association study was performed using Dazu black goats (DBGs), a Chinese indigenous goat breed. In particular, 150 DBGs were genotyped by whole-genome sequencing, and six body conformation traits, including body height (BH), body length (BL), cannon circumference (CC), chest depth (CD), chest width (CW), and heart girth (HG), were examined. In total, 53 potential SNPs were associated with these body conformation traits. A bioinformatics analysis was performed to evaluate the genes located close to the significant SNPs. Finally, 42 candidate genes (e.g., PSTPIP2, C7orf57, CCL19, FGF9, SGCG, FIGN, and SIPA1L) were identified as components of the genetic architecture underlying body conformation traits. Our results provide useful biological information for the improvement of growth performance and have practical applications for genomic selection in goats.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study of Body Conformation Traits by Whole Genome Sequencing in Dazu Black Goats

Sun

Fang

et al. 2022

Animals

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“…Subsequently, excellent growth performance is one of the important goals of Boer goat breeding. Therefore, investigating the selective genes between different breeding stages of Boer goats may help elucidate the genetic basis of muscle development [15]. Notably, some genes identified in this study attracted the attention of the authors.…”

Section: Discussionmentioning

confidence: 89%

“…C, San Diego, CA, US) and whole genome sequencing was performed by Illumina NovaSeq 6000 × Ten platform (BGI, Shenzhen, China), the sequencing depth, for BH animals, was expected around 10×. The genome datasets of total 30 Australian Boer goats (AS) from our previous study [15] and 30 African indigenous goats (AF) were obtained from NCBI SRA database (PRJNA671542), respectively (Table S1).…”

Section: Animals Genome Sequencing and Data Acquisitionmentioning

confidence: 99%

Genome-Wide Selective Analysis of Boer Goat to Investigate the Dynamic Heredity Evolution under Different Stages

Yuan

Zhang

Liu

et al. 2022

Animals

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Boer goats, as kemp in meat-type goats, are selected and bred from African indigenous goats under a long period of artificial selection. Their advantages in multiple economic traits, particularly their plump growth, have attracted worldwide attention. The current study displayed the genome-wide selection signature analyses of South African indigenous goat (AF), African Boer (BH), and Australian Boer (AS) to investigate the hereditary basis of artificial selection in different stages. Four methods (principal component analysis, nucleotide diversity, linkage disequilibrium decay, and neighbor-joining tree) implied the genomic diversity changes with different artificial selection intensities in Boer goats. In addition, the θπ, FST, and XP-CLR methods were used to search for the candidate signatures of positive selection in Boer goats. Consequently, 339 (BH vs. AF) and 295 (AS vs. BH) candidate genes were obtained from SNP data. Especially, 10 genes (e.g., BMPR1B, DNER, ITGAL, and KIT) under selection in both groups were identified. Functional annotation analysis revealed that these genes are potentially responsible for reproduction, metabolism, growth, and development. This study used genome-wide sequencing data to identify inheritance by artificial selection. The results of the current study are valuable for future molecular-assisted breeding and genetic improvement of goats.

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“…A total of 127 publicly available goat genome datasets were downloaded from the NCBI Sequence Read Archive (SRA), including 46 Australian Boer goats from our previous study ( Yang et al, 2021 ) and 81 other goats (45 African, 16 European, and 20 Asian goats) as the control group (Supplementary Table S1).…”

Section: Methodsmentioning

confidence: 99%

A 1.1 Mb duplication CNV on chromosome 17 contributes to skeletal muscle development in Boer goats

Yuan¹,

Zhang²,

Yang³

et al. 2023

Zoological Research

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The Boer goat is one of the top meat breeds in modern animal husbandry and has attracted widespread attention for its unique growth performance. However, the genetic basis of muscle development in the Boer goat remains obscure. In this study, we identified specific structural variants in the Boer goat based on genome-wide selection signals and analyzed the basis of the molecular heredity of related candidate genes in muscle development. A total of 9 959 autosomal copy number variations (CNVs) were identified through selection signal analysis in 127 goat genomes. Specifically, we confirmed that the highest signal CNV (HSV) was a chromosomal arrangement containing an approximately 1.11 Mb (CHIR17: 60062304–61171840 bp) duplicated fragment inserted in reverse orientation and a 5 362 bp deleted region (CHIR17:60145940–60151302 bp) with overlapping genes (e.g., ARHGAP10 , NR3C2 , EDNRA , PRMT9 , and TMEM184C ). The homozygous duplicated HSV genotype (+/+) was found in 96% of Boer goats but was not detected in Eurasian goats and was only detected in 4% of indigenous African goats. The expression network of three candidate genes ( ARHGAP10 , NR3C2 , and EDNRA ) regulating dose transcription was constructed by RNA sequencing. Results indicated that these genes were involved in the proliferation and differentiation of skeletal muscle satellite cells (SMSCs) and their overexpression significantly increased the expression of SAA3 . The HSV of the Boer goat contributed to superior skeletal muscle growth via the dose effects of overlapping genes.

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Genome‐wide selection signal analysis of Australian Boer goat reveals artificial selection imprinting on candidate genes related to muscle development

Cited by 15 publications

References 57 publications

Genome-Wide Association Study of Body Conformation Traits by Whole Genome Sequencing in Dazu Black Goats

Genome-Wide Association Study of Body Conformation Traits by Whole Genome Sequencing in Dazu Black Goats

Genome-Wide Selective Analysis of Boer Goat to Investigate the Dynamic Heredity Evolution under Different Stages

A 1.1 Mb duplication CNV on chromosome 17 contributes to skeletal muscle development in Boer goats

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