Rongchao Ji

Jiangsu Agri-animal Husbandry Vocational College

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Sun GuoBo

Scientific Institute of Pearl River Water Resources Protection

Xiaohui Mu

Chinese Academy of Fishery Sciences

Mengli Zhao

Scientific Institute of Pearl River Water Resources Protection

Xiao‐Ming Li

Zhejiang University

Hongchang Zhao

Jiangsu Agri-animal Husbandry Vocational College

Jun Wang

Ministry of Agriculture and Rural Affairs

Chao Chen

Second Xiangya Hospital of Central South University

Jian Wang

Qilu Hospital of Shandong University

Gansheng Zhang

Jiangsu Agri-animal Husbandry Vocational College

Guangliang Gao

Chongqing Academy of Animal Science

Cooperative Institutions

Jiangsu Agri-animal Husbandry Vocational College

Yangzhou University

Scientific Institute of Pearl River Water Resources Protection

Shanghai Jiao Tong University

Chinese Academy of Medical Sciences & Peking Union Medical College

Fudan University

Chinese Academy of Sciences

Central South University

Jilin University

Sichuan University

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Effects of Choline on Reproductive Performance, Egg Quality, and Ovarian Morphological Development in Breeding Geese

Wenfeng Liu Jian Wang Jun Wang Rongchao Ji Zhiyue Wang

10.2139/ssrn.4969871

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Identification of differentially expressed genes and signaling pathways in Gaoyou duck ovary at different physiological stages

Frontiers in Veterinary Science (2023)

Lei Zhang Jun Xie Sun GuoBo Rongchao Ji Xiaoming Li

Introduction Gaoyou duck is famous in China and abroad for its good production of double-yolk eggs. However, there has been no systematic research on the egg-laying characteristics of the Gaoyou duck, which limits the development and utilization of breed resource. Methods To identify the essential genes related to ovarian development, the transcriptome profiles of the ovaries of Gaoyou ducks at different physiological stages were analyzed. The transcriptome profiles of the ovaries of Gaoyou ducks at 150 d (before laying), 240 d (egg laying) and 500 d (nesting) were constructed, and the differentially expressed genes (DEGs) underwent GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses. Results The 6 randomly selected DEGs were verified by real-time fluorescent quantitative PCR that their relative expression was consistent with the transcriptional expression profile. Furthermore, KEGG analysis found that 8 candidate signaling pathways were essential for ovarian development, including the MAPK signaling pathway, Progesterone-mediated oocyte maturation, Cell adhesion molecules (CAMs), NOD-like receptor signaling pathway, ECM-receptor interaction, Focal adhesion, TGF-beta signaling path-way and Phagosome. Finally, 5 key DEGs were identified to participate in ovarian development, including TGIF1, TGFBR2, RAF1, PTK2 and FGF10. Discussion Our findings reveal the mechanisms under-lying the molecular regulation of related genes in Gaoyou duck ovarian development.

KEGG

10.3389/fvets.2023.1190998

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Effect of cage rearing pattern on expression of PRL and PRLR genes in Black Muscovy Duck.

Guizhou nongye kexue (2018)

Xiaoming Li Sun GuoBo Bian You-qing Zhang GanSheng Rongchao Ji

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Additional file 1 of Genome-wide selective signatures mining the candidate genes for egg laying in goose

Figshare (2023)

Hongchang Zhao Sun GuoBo Xiaohui Mu Xiao‐Ming Li Jun Wang

Supplementary Material 1: Table S1. The statistical table of sequencing results for each sample.

Laying

10.6084/m9.figshare.24761447

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Comparative study of polymorphism in breeds and generations based on duck a-fabp gene.

He'nan nongye kexue (2016)

Biao Dong Qin HaoRong Jian Wang Sun GuoBo Rongchao Ji

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Ovarian transcriptome profile from pre-laying period to broody period of Xupu goose

Poultry Science (2021)

Haorong Qin Xiao‐Ming Li Jian Wang Sun GuoBo Xiaohui Mu

Xupu goose, a breed from Hunan province, produces high quality and quantity of meat and liver. However, its egg production rate is low, with poor reproductive traits but strong broody performance. These characteristics decrease the economic value of Xupu goose significantly. Here, RNA-seq was used to analyze the transcriptome changes of ovaries of Xupu goose at different stages to explore the molecular mechanism of reproduction from the pre-laying period to the broody period. A total of 258 genes were differentially expressed in the 3 stages. These genes are associated with inflammation, reproduction, mutual recognition and adhesion between cells, and cytoskeleton formation, and so on. In particular, we report, for the first time, the expression patterns of MRP126, serglycin, TXNIP, and FZD2 during the pre-laying, egg-laying, and broody periods of goose ovaries. Functional analysis by GO annotation revealed that GO terms were mainly involved in actin, cell signal transduction and regulation, and cellular components. Three pathways, including focal adhesion (gga04510), ECM-receptor interaction (gga04512), and N-Glycan biosynthesis (gga00510), were significantly enriched in the three groups. These findings provide a basis for further exploration of profiles of goose ovaries to improve egg production of Xupu goose.

10.1016/j.psj.2021.101403

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Genome-wide selective signatures mining the candidate genes for egg laying in goose

BMC Genomics (2023)

Hongchang Zhao Sun GuoBo Xiaohui Mu Xiao‐Ming Li Jun Wang

Improving the egg production of goose is a crucial goal of breeding, because genetics is the key factor affecting egg production. Thus, we sequenced the genomes of 55 Chinese indigenous geese from six breeds, which were divided into the high egg-laying group (ZE, HY, and SC) and low egg-laying group (ZD, LH, and ST). Based on the results of the inter-population selection signal analysis, we mined the selected genome regions in the high egg-laying germplasm population to identify the key candidate genes affecting the egg-laying traits.According to the whole-genome sequencing data, the average sequencing depth reached 11.75X. The genetic relationships among those six goose breeds coincided with the breed's geographical location. The six selective signal detection results revealed that the most selected regions were located on Chr2 and Chr12. In total, 12,051 single-nucleotide polymorphism (SNP) sites were selected in all six methods. Using the enrichment results of candidate genes, we detected some pathways involved in cell differentiation, proliferation, and female gonadal development that may cause differences in egg production. Examples of these pathways were the PI3K-Akt signaling pathway (IGF2, COMP, and FGFR4), animal organ morphogenesis (IGF2 and CDX4), and female gonad development (TGFB2).On analyzing the genetic background of six local goose breeds by using re-sequencing data, we found that the kinship was consistent with their geographic location. 107 egg-laying trait-associated candidate genes were mined through six selection signal analysis. Our study provides a critical reference for analyzing the molecular mechanism underlying differences in reproductive traits and molecular breeding of geese.

Candidate gene

10.1186/s12864-023-09852-x

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Telomere-to-telomere genome assembly of the goose Anser cygnoides

Scientific Data (2024)

Hongchang Zhao Hao Zhou Sun GuoBo Biao Dong Wenqi Zhu

Abstract Our study presents the assembly of a high-quality Taihu goose genome at the Telomere-to-Telomere (T2T) level. By employing advanced sequencing technologies, including Pacific Biosciences HiFi reads, Oxford Nanopore long reads, Illumina short reads, and chromatin conformation capture (Hi-C), we achieved an exceptional assembly. The T2T assembly encompasses a total length of 1,197,991,206 bp, with contigs N50 reaching 33,928,929 bp and scaffold N50 attaining 81,007,908 bp. It consists of 73 scaffolds, including 38 autosomes and one pair of Z/W sex chromosomes. Importantly, 33 autosomes were assembled without any gap, resulting in a contiguous representation. Furthermore, gene annotation efforts identified 34,898 genes, including 436,162 RNA transcripts, encompassing 806,158 exons, 743,910 introns, 651,148 coding sequences (CDS), and 135,622 untranslated regions (UTR). The T2T-level chromosome-scale goose genome assembly provides a vital foundation for future genetic improvement and understanding the genetic mechanisms underlying important traits in geese.

Sequence assembly

10.1038/s41597-024-03567-8

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Whole-genome re-sequencing association study on body size traits at 10-weeks of age in Chinese indigenous geese

Frontiers in Veterinary Science (2024)

Sun GuoBo Hongchang Zhao Xiaohui Mu Xiao‐Ming Li Jun Wang

To investigate the genetic factors underlying marketed body size traits in Chinese local geese, we conducted a comprehensive study involving nine body size traits in 251 samples at 10 weeks of age from five local breeds: Taihu goose (TH), Sichuan goose (SC), Guangfeng goose (GF), Xupu goose (XP), and Youjiang goose (YJ). Genotyping data were obtained through whole-genome re-sequencing, followed by a genome-wide association analysis utilizing the fixed and random model circulating probability unification (FarmCPU) approach. Our findings revealed 88 significant SNPs associated with body size traits, with 16 SNPs surpassing the genome-wide significance threshold (

Genome-wide Association Study

Genetic Association

10.3389/fvets.2024.1506471

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Genome-wide selective signatures mining the candidate genes for egg laying in goose

Research Square (Research Square) (2023)

Hongchang Zhao Sun GuoBo Xiaohui Mu Xiao‐Ming Li Jun Wang

Abstract Background Improving the egg production of goose is a crucial goal of breeding, because genetics is the key factor affecting egg production. Thus, we sequenced the genomes of 55 Chinese indigenous geese from six breeds, which were divided into the high egg-laying group (ZE, HY, and SC) and low egg-laying group (ZD, LH, and ST). Based on the results of the inter-population selection signal analysis, we explored the selected genome regions in the high egg-laying germplasm population to identify the key candidate genes affecting the egg-laying traits. Results According to the whole-genome sequencing data, the average sequencing depth reached 11.75X. The genetic relationships among those six goose breeds coincided with the breed’s geographical location. The six selective signal detection results revealed that the most selected regions were located on chromosomes 2 and 12. In total, 12,051 single-nucleotide polymorphism (SNP) sites were selected in all six methods. Using the enrichment results of candidate genes, we detected some pathways involved in cell differentiation, proliferation, and female gonadal development that may cause differences in egg production. Examples of these pathways were the PI3K-Akt signaling pathway ( IGF2 , COMP , and FGFR4 ), animal organ morphogenesis ( IGF2 and CDX4 ), and female gonad development ( TGFB2 ). Conclusion On analyzing the genetic background of six local goose breeds by using re-sequencing data, we found that the kinship was consistent with their geographic location. Some egg-laying trait-associated candidate genes were mined through selection signal analysis. Our study provides a critical reference for analyzing the molecular mechanism underlying differences in reproductive traits and molecular breeding of geese.

Candidate gene

10.21203/rs.3.rs-3183250/v1

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