Genome-Wide Association Study of Potential Meat Quality Trait Loci in Ducks

Guo, Qixin; Huang, Lan; Bai, Hao; Wang, Zhixiu; Bi, Yue; Chen, Guohong; Jiang, Yong; Chang, Guobin

doi:10.3390/genes13060986

Cited by 12 publications

(7 citation statements)

References 55 publications

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“…The coiled-coil serine rich protein 1 or CCSER1 gene on OAR6, which encodes a proline-rich protein, plays an important role in mitosis and cell division and has been linked to several human cancers [ 125 ]. SNPs in the intronic region of this gene have been associated with male fertility traits in sheep, such as ejaculate quality [ 126 ], and together with the TIGD2 gene with growth and carcass traits in cattle [ 127 ], body weight in salmon [ 128 ], and meat quality traits in ducks [ 129 ]. The TIGD2 gene has also been associated with resistance to disease and bacterial infection in cattle [ 85 ], making it an important candidate in our study.…”

Section: Discussionmentioning

confidence: 99%

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

Lukic,

Curik,

Drzaic

et al. 2023

J Animal Sci Biotechnol

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Background The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type. Results We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis. Conclusions Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.

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Section: Discussionmentioning

confidence: 99%

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

Lukic,

Curik,

Drzaic

et al. 2023

J Animal Sci Biotechnol

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“…Hopefully, newly developed biotechnologies can greatly advance this field: (1) Omics analyses could help identify sex-associated genes and explore their regulation mechanism at various levels. (2) Genomewide association studies (GWASs) could establish the relationships between special traits (such as sex) and genes (or SNPs) through re-sequence analyses [43,44]. (3) The CRISPR system can contribute to gene function characterization through gene gain (or loss) of function [45].…”

Section: Future Investigations Of Gjsox9 In G Japonicusmentioning

confidence: 99%

gjSOX9 Cloning, Expression, and Comparison with gjSOXs Family Members in Gekko japonicus

Huang,

Zhao,

et al. 2023

CIMB

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SOX9 plays a crucial role in the male reproductive system, brain, and kidneys. In this study, we firstly analyzed the complete cDNA sequence and expression patterns for SOX9 from Gekko japonicus SOX9 (gjSOX9), carried out bioinformatic analyses of physiochemical properties, structure, and phylogenetic evolution, and compared these with other members of the gjSOX family. The results indicate that gjSOX9 cDNA comprises 1895 bp with a 1482 bp ORF encoding 494aa. gjSOX9 was not only expressed in various adult tissues but also exhibited a special spatiotemporal expression pattern in gonad tissues. gjSOX9 was predicted to be a hydrophilic nucleoprotein with a characteristic HMG-Box harboring a newly identified unique sequence, “YKYQPRRR”, only present in SOXE members. Among the 20 SOX9 orthologs, gjSOX9 shares the closest genetic relationships with Eublepharis macularius SOX9, Sphacrodactylus townsendi SOX9, and Hemicordylus capensis SOX9. gjSOX9 and gjSOX10 possessed identical physicochemical properties and subcellular locations and were tightly clustered with gjSOX8 in the SOXE group. Sixteen gjSOX family members were divided into six groups: SOXB, C, D, E, F, and H with gjSOX8, 9, and 10 in SOXE among 150 SOX homologs. Collectively, the available data in this study not only facilitate a deep exploration of the functions and molecular regulation mechanisms of the gjSOX9 and gjSOX families in G. japonicus but also contribute to basic research regarding the origin and evolution of SOX9 homologs or even sex-determination mode in reptiles.

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“…Based on the maturity of sequencing technologies, diverse genomic studies have been performed to identify genomic loci affecting meat quality in pigs. Especially, several population-level studies using short read data, such as population genomic analyses [ 5 – 7 ] and genome-wide association studies [ 8 – 10 ], have identified plentiful regions and genes associated with the traits at the whole-genome level.…”

Section: Introductionmentioning

confidence: 99%

Identification and characterization of structural variants related to meat quality in pigs using chromosome-level genome assemblies

Kwon,

Park,

et al. 2024

BMC Genomics

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Background Many studies have been performed to identify various genomic loci and genes associated with the meat quality in pigs. However, the full genetic architecture of the trait still remains unclear in part because of the lack of accurate identification of related structural variations (SVs) which resulted from the shortage of target breeds, the limitations of sequencing data, and the incompleteness of genome assemblies. The recent generation of a new pig breed with superior meat quality, called Nanchukmacdon, and its chromosome-level genome assembly (the NCMD assembly) has provided new opportunities. Results By applying assembly-based SV calling approaches to various genome assemblies of pigs including Nanchukmacdon, the impact of SVs on meat quality was investigated. Especially, by checking the commonality of SVs with other pig breeds, a total of 13,819 Nanchukmacdon-specific SVs (NSVs) were identified, which have a potential effect on the unique meat quality of Nanchukmacdon. The regulatory potentials of NSVs for the expression of nearby genes were further examined using transcriptome- and epigenome-based analyses in different tissues. Conclusions Whole-genome comparisons based on chromosome-level genome assemblies have led to the discovery of SVs affecting meat quality in pigs, and their regulatory potentials were analyzed. The identified NSVs will provide new insights regarding genetic architectures underlying the meat quality in pigs. Finally, this study confirms the utility of chromosome-level genome assemblies and multi-omics analysis to enhance the understanding of unique phenotypes.

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Genome-Wide Association Study of Potential Meat Quality Trait Loci in Ducks

Cited by 12 publications

References 55 publications

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

gjSOX9 Cloning, Expression, and Comparison with gjSOXs Family Members in Gekko japonicus

Identification and characterization of structural variants related to meat quality in pigs using chromosome-level genome assemblies

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