Integration of transcriptome sequencing and whole genome resequencing reveal candidate genes in egg production of upright and pendulous-comb chickens

Cai, Danfeng; Wang, Zhijun; Zhou, Zhen; Lin, Duo; Ju, Xing; Nie, Qinghua

doi:10.1016/j.psj.2023.102504

Cited by 14 publications

(11 citation statements)

References 59 publications

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“…The Protein Kinase B alpha ( AKT1 ), localized within the genomic region of 51.54 to 51.64Mb on GGC5, was identified through genome-wide selective sweep analysis by ( Liu et al, 2016 ), AKTI is involved in immune function regulation, as well as sensory organ development and neurogenesis processes ( Brazil and Hemmings, 2001 ). The Ca 2+ /Calmodulin-Dependent Protein Kinase 1D ( CAMK1D ), situated between positions of 6.36 to 6.46 Mb on GGC1, has been proposed as a potential candidate gene contributing to differences observed in comb size and egg-laying performance among chicken populations ( Cai et al, 2023 ). The Golgin B1 ( GOLGB1 ) located on 0.03 to 0.13Mb of GGC1 functions within the Golgi apparatus.…”

Section: Results and Disscussionmentioning

confidence: 99%

Weighted single-step GWAS identified candidate genes associated with carcass traits in a Chinese yellow-feathered chicken population

Pan,

Qi,

et al. 2024

Poultry Science

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Section: Results and Disscussionmentioning

confidence: 99%

Weighted single-step GWAS identified candidate genes associated with carcass traits in a Chinese yellow-feathered chicken population

Pan,

Qi,

et al. 2024

Poultry Science

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“…Exploring the mechanisms of reproductive trait-related genes in poultry is crucial to improve the reproductive performance of poultry. The selection of four pendulous-comb and four upright-comb chickens at 217 days of age for RNA-seq and whole genome resequencing identified CAMK1D, CLSTN2, MAST2, PIK3C2G, TBC1D1, STK3, ADGRB3, and PPARGC1A as potential candidate genes for egg production [ 34 ]. The whole genome resequencing analysis identified 37 SNPs on GGA20 that were associated with egg production in chickens, and gene annotation revealed 37 SNPs were identified in the BMP7 gene [ 35 ].…”

Section: Application Of Whole Genome Resequencing In Chickensmentioning

confidence: 99%

Whole Genome Resequencing Helps Study Important Traits in Chickens

Xiong

Liu

Rao

2023

Genes

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The emergence of high-throughput sequencing technology promotes life science development, provides technical support to analyze many life mechanisms, and presents new solutions to previously unsolved problems in genomic research. Resequencing technology has been widely used for genome selection and research on chicken population structure, genetic diversity, evolutionary mechanisms, and important economic traits caused by genome sequence differences since the release of chicken genome sequence information. This article elaborates on the factors influencing whole genome resequencing and the differences between these factors and whole genome sequencing. It reviews the important research progress in chicken qualitative traits (e.g., frizzle feather and comb), quantitative traits (e.g., meat quality and growth traits), adaptability, and disease resistance, and provides a theoretical basis to study whole genome resequencing in chickens.

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“…Extensive studies on the genetic mechanisms of head tissues have been conducted in other poultry species. In chickens, the comb is a fleshy protuberance found on the top of the head [8], and significant differences in egg-laying performance and growth rate were observed between Pea Comb (PC) and Single Comb (UC) chickens [9,10]. The genes BMP2 and CHADL are related to chicken comb size, whereas STK32A, PIK3R1, and EDN1 regulate the development of the chicken comb [11].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Profiling Unveils Key Genes Regulating the Growth and Development of Yangzhou Goose Knob

Xu,

Fan,

et al. 2024

IJMS

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Goose is one of the most economically valuable poultry species and has a distinct appearance due to its possession of a knob. A knob is a hallmark of sexual maturity in goose (Anser cygnoides) and plays crucial roles in artificial selection, health status, social signaling, and body temperature regulation. However, the genetic mechanisms influencing the growth and development of goose knobs remain completely unclear. In this study, histomorphological and transcriptomic analyses of goose knobs in D70, D120, and D300 Yangzhou geese revealed differential changes in tissue morphology during the growth and development of goose knobs and the key core genes that regulate goose knob traits. Observation of tissue sections revealed that as age increased, the thickness of the knob epidermis, cuticle, and spinous cells gradually decreased. Additionally, fat cells in the dermis and subcutaneous connective tissue transitioned from loose to dense. Transcriptome sequencing results, analyzed through differential expression, Weighted Gene Co-expression Network Analysis (WGCNA), and pattern expression analysis methods, showed D70-vs.-D120 (up-regulated: 192; down-regulated: 423), D70-vs.-D300 (up-regulated: 1394; down-regulated: 1893), and D120-vs.-D300 (up-regulated: 1017; down-regulated: 1324). A total of 6243 differentially expressed genes (DEGs) were identified, indicating varied expression levels across the three groups in the knob tissues of D70, D120, and D300 Yangzhou geese. These DEGs are significantly enriched in biological processes (BP) such as skin morphogenesis, the regulation of keratinocyte proliferation, and epidermal cell differentiation. Furthermore, they demonstrate enrichment in pathways related to goose knob development, including ECM–receptor interaction, NF-kappa B, and PPAR signaling. Through pattern expression analysis, three gene expression clusters related to goose knob traits were identified. The joint analysis of candidate genes associated with goose knob development and WGCNA led to the identification of key core genes influencing goose knob development. These core genes comprise WNT4, WNT10A, TCF7L2, GATA3, ADRA2A, CASP3, SFN, KDF1, ERRFI1, SPRY1, and EVPL. In summary, this study provides a reference for understanding the molecular mechanisms of goose knob growth and development and provides effective ideas and methods for the genetic improvement of goose knob traits.

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Integration of transcriptome sequencing and whole genome resequencing reveal candidate genes in egg production of upright and pendulous-comb chickens

Cited by 14 publications

References 59 publications

Weighted single-step GWAS identified candidate genes associated with carcass traits in a Chinese yellow-feathered chicken population

Weighted single-step GWAS identified candidate genes associated with carcass traits in a Chinese yellow-feathered chicken population

Whole Genome Resequencing Helps Study Important Traits in Chickens

Transcriptome Profiling Unveils Key Genes Regulating the Growth and Development of Yangzhou Goose Knob

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