Whole genome sequencing of a wild swan goose population

Ni, Hongyu; Zhang, Yonghong; Yang, Yuwei; Yin, Yijing; Xie, Hengli; Zheng, Jinlei; Dong, Lei; Diao, Jizhe; Wang, Meng; Lv, Zhichao; Yan, Shouqing; Li, Yumei; Sun, Hao; Sun, Xueqi

doi:10.3389/fgene.2023.1038606

Cited by 2 publications

(2 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The genome‐wide LD of XHF geese decayed to r 2 = 0.2 at a physical distance of about 11 kb, and that of Zi geese decayed to r 2 = 0.2 at a physical distance of about 2.5 kb (Figure S2). According to a previous study, the genome‐wide LD of swan geese decayed to r 2 = 0.2 at a physical distance of about 200 bp (Ni et al., 2023). We found that the decay rate of swan geese is faster than that of XHF geese and Zi geese.…”

Section: Figurementioning

confidence: 96%

Integrated analysis of whole genome and transcriptome sequencing uncovers genetic differences between Zi goose and Xianghai flying goose

Ni,

Zhang,

Yang

et al. 2023

Animal Genetics

Self Cite

View full text Add to dashboard Cite

Zi goose is a famous indigenous breed originating from northeast China with high annual egg production. Xianghai flying goose is a composite breed and is bred by crosses of the wild swan goose and the Zi goose. Our previous study revealed significant differences in muscle fiber characteristics between the two populations. Here, we aimed to reveal the underlying genetic basis of the above phenotype differences through whole‐genome and transcriptome analysis. A total of 20 blood samples (10 Zi geese and 10 Xianghai flying geese) were used for whole genome sequencing, and eight breast muscle tissue samples (four Zi geese and four Xianghai flying geese) were used for RNA sequencing. Using the FST and XP‐EHH analysis, some highly differentiated genome regions annotated with egg production (RORB, WNT4, BMPR1B) and breast muscle development (WNT7B) between the two populations were detected. RNA‐sequencing analysis revealed differentially expressed genes related to muscle development (IGF1, PAX7). Moreover, several genes were detected by both genome and transcriptome analysis, and some of them were reported to be associated with muscle growth (SLIT2, PREX1) and intramuscular fat (COL6A1). These findings will help researchers better understand the genetic basis related to egg production and muscle development in geese.

show abstract

Section: Figurementioning

confidence: 96%

Integrated analysis of whole genome and transcriptome sequencing uncovers genetic differences between Zi goose and Xianghai flying goose

Ni,

Zhang,

Yang

et al. 2023

Animal Genetics

Self Cite

View full text Add to dashboard Cite

show abstract

“…The genetic diversity of organisms is the basis for ensuring the survival and evolution of breeds and is of great significance for evolutionary polymorphism analyses, genetic relationship analyses, germplasm resource optimization, and the protection of existing breeds [7]. Currently, microsatellite markers and whole genome sequencing methods are used to study the genetic diversity and population structure of endangered goose breeds [8][9][10]. Wen et al also used whole genome sequencing to reveal the origin breeds of Chinese domestic geese [11].…”

Section: Introductionmentioning

confidence: 99%

Analysis of Genetic Diversity and Population Structure of Endemic Endangered Goose (Anser cygnoides) Breeds Based on Mitochondrial CYTB

Qi,

Fan,

et al. 2024

Animals

View full text Add to dashboard Cite

The analysis of the genetic diversity and historical dynamics of endemic endangered goose breeds structure has attracted great interest. Although various aspects of the goose breed structure have been elucidated, there is still insufficient research on the genetic basis of endemic endangered Chinese goose breeds. In this study, we collected blood samples from Lingxiang White (LX), Yan (YE), Yangjiang (YJ), Wuzong (WZ), Xupu (XP), and Baizi (BZ) geese (Anser cygnoides) and used Sanger sequencing to determine the partial sequence of the cytochrome b (CYTB) gene in a total of 180 geese. A total of 117 polymorphic sites were detected in the 707 bp sequence of the mtDNA CYTB gene after shearing and correction, accounting for approximately 16.55% of the entire sequence. The AT content (51.03%) of the processed sequence was slightly higher than the GC content (48.97%), indicating a preference for purine bases. The YJ, YE, and WZ breeds had the highest population genetic diversity, with a haplotype diversity greater than 0.9 (Hd > 0.9) and average population nucleotide difference of 8.01 (K > 8.01). A total of 81 haplotypes were detected and divided into six major branches. Among the six goose breeds, there were frequent genetic exchanges among LX, YJ, YE, and WZ geese (Nm > 15.00). We analyzed the distribution of base-mismatch differences in goose breeds and tested their historical dynamics for neutrality in Tajima’s D and Fu’s Fs. For YJ and WZ geese, Tajima’s D > 0, but the difference was not significant (p > 0.05). The actual values for the two breeds exhibited multimodal Poisson distributions. The population patterns of the WZ and YJ geese are purportedly relatively stable, and the breeds have not experienced population expansions or bottleneck effects, which is consistent with the neutrality test results. This study provides new insights into the diverse genetic origins and historical dynamics that sustain endemic endangered goose breeds.

show abstract

Whole genome sequencing of a wild swan goose population

Cited by 2 publications

References 8 publications

Integrated analysis of whole genome and transcriptome sequencing uncovers genetic differences between Zi goose and Xianghai flying goose

Integrated analysis of whole genome and transcriptome sequencing uncovers genetic differences between Zi goose and Xianghai flying goose

Analysis of Genetic Diversity and Population Structure of Endemic Endangered Goose (Anser cygnoides) Breeds Based on Mitochondrial CYTB

Contact Info

Product

Resources

About