Genome-wide selection signatures analysis of litter size in Dazu black goats using single-nucleotide polymorphism

Guang‐Xin, E; Duan, Xinghai; Zhang, Jiahua; Huang, Yongfu; Zhao, Yongju; Na, Risu; Zhao, Zhongquan; Ma, Yue; Chu, Mingxing; Basang, Wangdui; Zhu, Yanbin; An, Tian-Wu; Luo, Xiaolin; Han, Yilin; Zeng, Yan

doi:10.1007/s13205-019-1869-3

Cited by 20 publications

(12 citation statements)

References 40 publications

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“…There have been several genomic studies of DBGs to date; however, these studies are limited by small sample sizes. Genome-wide selection signatures in 31 DBGs from two groups with differences in fecundity revealed that LRP1B and GRID2 showed significantly different patterns of linkage disequilibrium [ 40 ]. In addition, E et al [ 41 ] classified CNVs according to the previous results and reported three differentially expressed genes ( LOC108633278 , PPP1R12A , and YIPF4 ) between the high-yield and low-yield groups.…”

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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“…Thus, to establish optimal breeding programs, plenty of candidate genes, as well as their genetic variations should be appropriately used [4][5][6][7]. Maker-assisted selection (MAS) can satisfy the need to screen crucial genes and consider the relation between their polymorphisms and growth-related traits [8][9][10][11]. Herein, establishing a MAS system and performing candidate genes analyses will speed up the development of goat breeding [12][13][14][15].…”

Section: Introductionmentioning

confidence: 99%

Myostatin (MSTN) Gene Indel Variation and Its Associations with Body Traits in Shaanbei White Cashmere Goat

Feng

Wang

et al. 2020

Animals

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Myostatin (MSTN) gene, also known as growth differentiation factor 8 (GDF8), is a member of the transforming growth factor-beta super-family and plays a negative role in muscle development. It acts as key points during pre- and post-natal life of amniotes that ultimately determine the overall muscle mass of animals. There are several studies that concentrate on the effect of a 5 bp insertion/deletion (indel) within the 5’ untranslated region (5’ UTR) of goat MSTN gene in goats. However, almost all sample sizes were below 150 individuals. Only in Boer goats, the sample sizes reached 482. Hence, whether the 5 bp indel was still associated with the growth traits of goats in large sample sizes which were more reliable is not clear. To find an effective and dependable DNA marker for goat rearing, we first enlarged the sample sizes (n = 1074, Shaanbei White Cashmere goat) which would enhance the robustness of the analysis and did the association analyses between the 5 bp indel and growth traits. Results uncovered that the 5 bp indel was significantly related to body height, height at hip cross, and chest width index (p < 0.05). In addition, individuals with DD genotype had a superior growing performance than those with the ID genotype. These findings suggested that the 5 bp indel in MSTN gene are significantly associated with growth traits and the specific genotype might be promising for maker-assisted selection (MAS) of goats.

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“…In this study, we screened numerous genes related to reproduction and growth. Specifically, PDGFRB gene insertion, deletions and indels were associated with improved litter size in goats ( E et al, 2019 ). Previously, the role of the LRP1B gene as a potential candidate gene for reproductive traits in Dazu black goats was revealed ( Tao et al, 2021 ).…”

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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Genome-wide selection signatures analysis of litter size in Dazu black goats using single-nucleotide polymorphism

Cited by 20 publications

References 40 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

Myostatin (MSTN) Gene Indel Variation and Its Associations with Body Traits in Shaanbei White Cashmere Goat

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

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