Chromosome-level genome and population genomics reveal evolutionary characteristics and conservation status of Chinese indigenous geese

Ouyang, Jing; Zheng, Sumei; Huang, Min; Tang, Hongbo; Qiu, Xiaohui; Chen, Shoujin; Wang, Zhangzhang; Zhou, Zhongdong; Gao, Yuren; Xiong, Yanpeng; Zeng, Guohua; Huang, Jian; He, Jiugen; Ren, Jun; Chen, Hao; Yan, Xueming

doi:10.1038/s42003-022-04125-x

Cited by 9 publications

(10 citation statements)

References 91 publications

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“…Chinese domestic geese other than Yili geese are genetically closely related to swan geese, while Yili geese and two European domestic geese (Landaise geese and Roman geese) are genetically close to greylag geese; these findings suggest that Chinese domestic geese (except Yili) may originate from swan geese while Yili geese, Landaise geese, and Roman geese may originate from greylag geese. This is supported by previous population analyses [ 9 , 10 , 11 ]. In the European group, we note that the Rhine goose had almost half admixed background with Chinese domestic geese, and it constituted a separate population but was genetically closely related to Chinese domestic breeds.…”

Section: Discussionsupporting

confidence: 90%

“…It is one of the first domesticated poultry: Chinese domestic goose was domesticated over 7000 years ago [ 7 ], and European domestic goose was domesticated approximately 5000 years ago [ 8 ]. It seems to be an indisputable fact that there are two origins for domestic geese [ 9 , 10 , 11 ]: Chinese domestic geese (except Yili geese) originate from the swan goose ( Anser cygnoides ), and European domestic geese and Yili geese originate from the greylag goose ( Anser anser ). However, these results are not conclusive because there are still many goose breeds not included in these studies.…”

Section: Introductionmentioning

confidence: 99%

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Population Structure and Selection Signatures of Domestication in Geese

Chen

Cao

et al. 2023

Biology

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The goose is an economically important poultry species and was one of the first to be domesticated. However, studies on population genetic structures and domestication in goose are very limited. Here, we performed whole genome resequencing of geese from two wild ancestral populations, five Chinese domestic breeds, and four European domestic breeds. We found that Chinese domestic geese except Yili geese originated from a common ancestor and exhibited strong geographical distribution patterns and trait differentiation patterns, while the origin of European domestic geese was more complex, with two modern breeds having Chinese admixture. In both Chinese and European domestic geese, the identified selection signatures during domestication primarily involved the nervous system, immunity, and metabolism. Interestingly, genes related to vision, skeleton, and blood-O2 transport were also found to be under selection, indicating genetic adaptation to the captive environment. A forehead knob characterized by thickened skin and protruding bone is a unique trait of Chinese domestic geese. Interestingly, our population differentiation analysis followed by an extended genotype analysis in an additional population suggested that two intronic SNPs in EXT1, an osteochondroma-related gene, may plausibly be sites responsible for knob. Moreover, CSMD1 and LHCGR genes were found to be significantly associated with broodiness in Chinese domestic geese and European domestic geese, respectively. Our results have important implications for understanding the population structure and domestication of geese, and the selection signatures and variants identified in this study might be useful in genetic breeding for forehead knob and reproduction traits.

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Section: Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Population Structure and Selection Signatures of Domestication in Geese

Chen

Cao

et al. 2023

Biology

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“…The remaining high‐quality paired‐end reads were mapped to the Xingguo Grey reference genome (Ouyang et al, 2022) using the burrows–wheeler aligner (version 0.7.8) with the command line ‘BWA mem ‐t 8 ‐k 32 ‐M’. To reduce mismatches generated by PCR amplification before sequencing, duplicated reads were removed with the help of samtools (Li et al, 2009; Li & Durbin, 2009).…”

Section: Methodsmentioning

confidence: 99%

“…Questions about where and when the domestication occurred, the associated genetic changes and the subsequent history of domestic geese remain largely unresolved. Recent studies have revealed complex genetic relationships between wild and domesticated populations and the development of advanced genetic sequencing technologies have allowed researchers to study the genomes of geese in unprecedented detail, unlocking new insights into the evolutionary history of these birds (Heikkinen et al, 2015; Ouyang et al, 2022; Ren et al, 2016). Through comparative genomic analysis, previous studies have identified several domestication selection genes, such as PRKAB1 and PRKAG2 , which are related to growth and development, feed intake and meat feed efficiency, as well as pathways involved in growth reproductive metabolism regulation (Liu et al, 2021; Zhou et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Genomic signatures reveal selection in Chinese and European domesticated geese

Zhang,

Li,

Tang

et al. 2023

Animal Genetics

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The Swan goose and Greylag goose are species of geese native to East Asia and Europe, respectively, and are widely believed to be the ancestors of Chinese and European domesticated geese. The Yili goose (YL) and European domestic geese originated from the Greylag goose, but the history of domestication is unclear. In this study, we sequenced and analyzed the genome of the YL goose and the Hortobagy goose to combine with other previously sequenced goose populations for in‐depth analysis. The population genetic variations in Stone geese, East Zhejiang White Geese, Taihu geese and Zi geese were also identified and compared. The results showed that admixture gene flow existed in the YL geese population, which was introgressed by Chinese geese, suggesting that gene flow events were frequent and widespread among domesticated geese. Further selected sweep analysis identified candidate genes and metabolic pathways that may be related to the differences in morphology. Several genes such as TGFBR3L, CMYA5, FOXD1, ARHGEF28 and SUCLG2 are associated with growth, reproduction and fertility traits. The results of this study will help to understand the genetic characteristics of domestic geese and the genes affecting important traits and provide a basis for the improved breed of domestic geese.

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“…Xi et al discovered a significant correlation between the presence of a 14 bp insertion mutation in exon 3 of the EDNRB2 gene and the white feather phenotype observed in Sichuan Gang geese [5]. Yang et al and Ouyang et al also reported an association between the same 14 bp insertion mutation in the EDNRB2 gene and the white feather phenotype found in swan geese [9,10]. Ren et al screened 26 genes related to goose feather color formation, including KITLG, MITF, TYRO3, and KIT [11].…”

Section: Introductionmentioning

confidence: 97%

Identification of Differentially Expressed Genes and microRNAs in the Gray and White Feather Follicles of Shitou Geese

Guo,

Chen,

Luo

et al. 2024

Animals

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The Shitou goose, a highly recognized indigenous breed with gray plumage originating from Chaozhou Raoping in Guangdong Province, China, is renowned for being the largest goose species in the country. Notably, during the pure breeding process of Shitou geese, approximately 2% of the offspring in each generation unexpectedly exhibited white plumage. To better understand the mechanisms underlying white plumage color formation in Shitou geese, we conducted a comparative transcriptome analysis between white and gray feather follicles, aiming to identify key genes and microRNAs that potentially regulate white plumage coloration in this unique goose breed. Our results revealed a number of pigmentation genes, encompassing TYR, TYRP1, EDNRB2, MLANA, SOX10, SLC45A2, GPR143, TRPM1, OCA2, ASIP, KIT, and SLC24A5, which were significantly down-regulated in the white feather follicles of Shitou geese. Among these genes, EDNRB2 and KIT emerged as the most promising candidate genes for white plumage coloration in Shitou geese. Additionally, our analysis also uncovered 46 differentially expressed miRNAs. Of these, miR-144-y may play crucial roles in the regulation of feather pigmentation. Furthermore, the expression of novel-m0086-5p, miR-489-y, miR-223-x, miR-7565-z, and miR-3535-z exhibits a significant negative correlation with the expression of pigmentation genes including TYRP1, EDNRB2, MLANA, SOX10, TRPM1, and KIT, suggesting these miRNAs may indirectly regulate the expression of these genes, thereby influencing feather color. Our findings provide valuable insights into the genetic mechanisms underlying white plumage coloration in Shitou geese and contribute to the broader understanding of avian genetics and coloration research.

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Chromosome-level genome and population genomics reveal evolutionary characteristics and conservation status of Chinese indigenous geese

Cited by 9 publications

References 91 publications

Population Structure and Selection Signatures of Domestication in Geese

Population Structure and Selection Signatures of Domestication in Geese

Genomic signatures reveal selection in Chinese and European domesticated geese

Identification of Differentially Expressed Genes and microRNAs in the Gray and White Feather Follicles of Shitou Geese

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