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

Abstract

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.

Potential regulator of meat quality in geese: C1QTNF1 implications on cell proliferation and muscle growth

“…Among them, C1QTNF1 with relatively high expression and under strong selection between the XHF geese and Zi geese populations, the mutation location and selection intensity of the C1QTNF1 are shown in Figure 1 A. The RT-qPCR assay results indicated that the expression level of the C1QTNF1 gene in breast muscle tissue of Zi geese than that of XHF geese, and the results of the test were consistent with the transcriptome data in previous study ( Ni et al, 2023 ) ( Figure 1 B).…”

“…In the previous study, cross population extended haplotype homozogysity ( XP-EHH ) and RNA-Seq technology was used to analyze DEGs affecting meat quality of Xianghai flying geese and Zi geese and to screen key regulatory genes and pathways related to meat quality traits through enrichment analysis with the GO and KEGG database in order to find a more accurate molecular marker ( Ni et al, 2023 ). This integrated analysis of multi-omics data overcame the limitations of single-omics, and accessed the genetic information of organisms in different dimensions, which is an effective solution to address biological problems nowadays.…”

“…Based on the previous integrated analysis between the genome and breast muscle transcriptome of XHF geese and Zi geese, the highly differentially candidate genes which containing mutation sites located in the CDS region were identified ( Ni et al, 2023 ), and the information of candidate genes whose mutation sites are located in the CDS region are summarized in Table 2 . Among them, C1QTNF1 with relatively high expression and under strong selection between the XHF geese and Zi geese populations, the mutation location and selection intensity of the C1QTNF1 are shown in Figure 1 A.…”

“…Quantitative and qualitative changes in genes affect muscle characteristics, the information on variation obtained from a multi-omics approach will be more comprehensive and accurate. In previous investigation, we utilized an integrated analysis of the genome and transcriptome of the breast muscle to ascertain the primary candidate gene C1QTNF1 , which showed a strong under-selection signal and significant gene expression levels between XHF geese and Zi geese ( Ni et al, 2023 ). Further validation of the regulatory role of C1QTNF1 at the cellular level will help to elucidate the molecular mechanisms of goose muscle development.…”