Whole-genome selective scans detect genes associated with important phenotypic traits in goat (Capra hircus)

Wan, Xing; Jing, Jia-Nan; Wang, Dongfeng; Lv, Feng‐Hua

doi:10.3389/fgene.2023.1173017

Cited by 3 publications

(2 citation statements)

References 52 publications

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“…These separate studies in pigs demonstrate that RELL1 is likely an important gene for embryonic development. An SNP highly associated with early puberty of a tropical species of cattle (Bos indicus) was located most proximally to the RELL1 gene [97], and RELL1 was associated with prolificacy in goats in a separate study [98], further supporting a role of RELL1 for development. Knocking down expression of the transcription factor ZBED1 results in both increased apoptosis, and increased expression of several genes including RELT, in a choriocarcinoma cell line induced to differentiate into trophoblasts [60].…”

Section: Reproduction and Developmentmentioning

confidence: 82%

The RELT Family of Proteins: An Increasing Awareness of Their Importance for Cancer, the Immune System, and Development

Cusick,

Alcaide,

Shi

2023

Biomedicines

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This review highlights Receptor Expressed in Lymphoid Tissues (RELT), a Tumor Necrosis Factor Superfamily member, and its two paralogs, RELL1 and RELL2. Collectively, these three proteins are referred to as RELTfms and have gained much interest in recent years due to their association with cancer and other human diseases. A thorough knowledge of their physiological functions, including the ligand for RELT, is lacking, yet emerging evidence implicates RELTfms in a variety of processes including cytokine signaling and pathways that either promote cell death or survival. T cells from mice lacking RELT exhibit increased responses against tumors and increased inflammatory cytokine production, and multiple lines of evidence indicate that RELT may promote an immunosuppressive environment for tumors. The relationship of individual RELTfms in different cancers is not universal however, as evidence indicates that individual RELTfms may be risk factors in certain cancers yet appear to be protective in other cancers. RELTfms are important for a variety of additional processes related to human health including microbial pathogenesis, inflammation, behavior, reproduction, and development. All three proteins have been strongly conserved in all vertebrates, and this review aims to provide a clearer understanding of the current knowledge regarding these interesting proteins.

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Section: Reproduction and Developmentmentioning

confidence: 82%

The RELT Family of Proteins: An Increasing Awareness of Their Importance for Cancer, the Immune System, and Development

Cusick,

Alcaide,

Shi

2023

Biomedicines

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“…In developing countries like Ethiopia, enormous goat genetic resources are present [4], among which there are approximately 30.2 million heads of goat population in Ethiopia [5]. These indigenous goat populations have generally developed certain valuable genetic merits, such as the ability to perform better under low input conditions, greater disease tolerance, high adaptive ability to heat stresses and specialized important traits [6]. Moreover, selection for environmental adaptation and marketable traits may have differently shaped the genomes of these goat breeds [7].…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity, Population Structure and Selection Signature in Begait Goats Revealed by Whole-Genome Sequencing

Gebreselase,

Nigussie,

Wang

et al. 2024

Animals

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Goats belong to a group of animals called small ruminants and are critical sources of livelihood for rural people. Genomic sequencing can provide information ranging from basic knowledge about goat diversity and evolutionary processes that shape genomes to functional information about genes/genomic regions. In this study, we exploited a whole-genome sequencing data set to analyze the genetic diversity, population structure and selection signatures of 44 individuals belonging to 5 Ethiopian goat populations: 12 Aberegalle (AB), 5 Afar (AF), 11 Begait (BG), 12 Central highlands (CH) and 5 Meafure (MR) goats. Our results revealed the highest genetic diversity in the BG goat population compared to the other goat populations. The pairwise genetic differentiation (FST) among the populations varied and ranged from 0.011 to 0.182, with the closest pairwise value (0.003) observed between the AB and CH goats and a distant correlation (FST = 0.182) between the BG and AB goats, indicating low to moderate genetic differentiation. Phylogenetic tree, ADMIXTURE and principal component analyses revealed a classification of the five Ethiopian goat breeds in accordance with their geographic distribution. We also found three top genomic regions that were detected under selection on chromosomes 2, 5 and 13. Moreover, this study identified different candidate genes related to milk characteristics (GLYCAM1 and SRC), carcass (ZNF385B, BMP-7, PDE1B, PPP1R1A, FTO and MYOT) and adaptive and immune response genes (MAPK13, MAPK14, SCN7A, IL12A, EST1 DEFB116 and DEFB119). In conclusion, this information could be helpful for understanding the genetic diversity and population structure and selection scanning of these important indigenous goats for future genetic improvement and/or as an intervention mechanism.

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Characterization of runs of homozygosity islands in American mink using whole‐genome sequencing data

Davoudi,

Do,

Rathgeber

et al. 2024

J Animal Breeding Genetics

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The genome‐wide analysis of runs of homozygosity (ROH) islands can be an effective strategy for identifying shared variants within a population and uncovering important genomic regions related to complex traits. The current study performed ROH analysis to characterize the genome‐wide patterns of homozygosity, identify ROH islands and annotated genes within these candidate regions using whole‐genome sequencing data from 100 American mink (Neogale vison). After sequence processing, variants were called using GATK and Samtools pipelines. Subsequent to quality control, 8,373,854 bi‐allelic variants identified by both pipelines remained for further analysis. A total of 34,652 ROH segments were identified in all individuals, among which shorter segments (0.3–1 Mb) were abundant throughout the genome, approximately accounting for 84.39% of all ROH. Within these segments, we identified 63 ROH islands housing 156 annotated genes. The genes located in ROH islands were associated with fur quality (EDNRA, FGF2, FOXA2 and SLC24A4), body size/weight (MYLK4, PRIM2, FABP2, EYS and PHF3), immune capacity (IL2, IL21, PTP4A1, SEMA4C, JAK2, CCNA2 and TNIP3) and reproduction (ADAD1, KHDRBS2, INSL6, PGRMC2 and HSPA4L). Furthermore, Gene Ontology and KEGG pathway enrichment analyses revealed 56 and 9 significant terms (FDR‐corrected p‐value < 0.05), respectively, among which cGMP‐PKG signalling pathway, regulation of actin cytoskeleton, and calcium signalling pathway were highlighted due to their functional roles in growth and fur characteristics. This is the first study to present ROH islands in American mink. The candidate genes from ROH islands and functional enrichment analysis suggest possible signatures of selection in response to the mink breeding targets, such as increased body length, reproductive performance and fur quality. These findings contribute to our understanding of genetic characteristics, and provide complementary information to assist with implementation of breeding strategies for genetic improvement in American mink.

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Whole-genome selective scans detect genes associated with important phenotypic traits in goat (Capra hircus)

Cited by 3 publications

References 52 publications

The RELT Family of Proteins: An Increasing Awareness of Their Importance for Cancer, the Immune System, and Development

The RELT Family of Proteins: An Increasing Awareness of Their Importance for Cancer, the Immune System, and Development

Genetic Diversity, Population Structure and Selection Signature in Begait Goats Revealed by Whole-Genome Sequencing

Characterization of runs of homozygosity islands in American mink using whole‐genome sequencing data

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