Whole Genome Resequencing Identifies Single-Nucleotide Polymorphism Markers of Growth and Reproduction Traits in Zhedong and Zi Crossbred Geese

Abstract

The broodiness traits of domestic geese are a bottleneck that prevents the rapid development of the goose industry. To reduce the broodiness of the Zhedong goose and thus improve it, this study hybridized it with the Zi goose, which has almost no broody behavior. Genome resequencing was performed for the purebred Zhedong goose, as well as the F2 and F3 hybrids. The results showed that the F1 hybrids displayed significant heterosis in growth traits, and their body weight was significantly greater than those of the other groups. The F2 hybrids showed significant heterosis in egg-laying traits, and the number of eggs laid was significantly greater than those of the other groups. A total of 7,979,421 single-nucleotide polymorphisms (SNPs) were obtained, and three SNPs were screened. Molecular docking results showed that SNP11 located in the gene NUDT9 altered the structure and affinity of the binding pocket. The results suggested that SNP11 is an SNP related to goose broodiness. In the future, we will use the cage breeding method to sample the same half-sib families to accurately identify SNP markers of growth and reproductive traits.

Keywords: brooding; goose; laying cycles; molecular docking; whole genome resequencing.

Figure 1

Schematic diagram of Zhedong and Zi crossbred goose experiment. Purebred Zhedong geese were introduced in Xiangshan County in 2016 and 2019. The Zi goose is a local variety in Heilongjiang. The F1, F2 and F3 hybrids were obtained through hybridization, and some experimental populations were selected to measure body weight and laying rate as well as for whole genome resequencing analysis. If the primary generation Zhedong goose was homozygous for site AA, then gene type AB and AA could appear in the F2 and F3 generations. However, BB type was not possible.

Figure 2

Changes in the goose egg-laying trait and body weight in different generations. (A) Heat map of goose egg-laying data of different generations. The different colors represent different laying rates, and the abscissa is initially dated 21 February. The end time is 3 July; the total number of days is 133. On 29 February 2020, the experimental group did not start laying eggs. (B) Growth data of different generations of geese (0–4 weeks) (C) Growth data of different generations of geese (6–8 weeks) (D) Growth data of different generations of geese (10–12 weeks). The body weight of the F3 hybrids shows significant differences at 2 weeks and 12 weeks. The different letters indicate significant differences. The green bar represents SE. Body-weight unit: g.

Figure 2

Changes in the goose egg-laying trait and body weight in different generations. (A) Heat map of goose egg-laying data of different generations. The different colors represent different laying rates, and the abscissa is initially dated 21 February. The end time is 3 July; the total number of days is 133. On 29 February 2020, the experimental group did not start laying eggs. (B) Growth data of different generations of geese (0–4 weeks) (C) Growth data of different generations of geese (6–8 weeks) (D) Growth data of different generations of geese (10–12 weeks). The body weight of the F3 hybrids shows significant differences at 2 weeks and 12 weeks. The different letters indicate significant differences. The green bar represents SE. Body-weight unit: g.

Figure 2

Changes in the goose egg-laying trait and body weight in different generations. (A) Heat map of goose egg-laying data of different generations. The different colors represent different laying rates, and the abscissa is initially dated 21 February. The end time is 3 July; the total number of days is 133. On 29 February 2020, the experimental group did not start laying eggs. (B) Growth data of different generations of geese (0–4 weeks) (C) Growth data of different generations of geese (6–8 weeks) (D) Growth data of different generations of geese (10–12 weeks). The body weight of the F3 hybrids shows significant differences at 2 weeks and 12 weeks. The different letters indicate significant differences. The green bar represents SE. Body-weight unit: g.

Figure 2

Changes in the goose egg-laying trait and body weight in different generations. (A) Heat map of goose egg-laying data of different generations. The different colors represent different laying rates, and the abscissa is initially dated 21 February. The end time is 3 July; the total number of days is 133. On 29 February 2020, the experimental group did not start laying eggs. (B) Growth data of different generations of geese (0–4 weeks) (C) Growth data of different generations of geese (6–8 weeks) (D) Growth data of different generations of geese (10–12 weeks). The body weight of the F3 hybrids shows significant differences at 2 weeks and 12 weeks. The different letters indicate significant differences. The green bar represents SE. Body-weight unit: g.

Figure 3

Screening and analysis of candidate SNPs. (A) Gene Ontology (GO) analysis for 3.370 candidate SNPs. (B) Level two GO analysis of candidate SNPs. (C) KEGG enrichment of candidate SNPs. (D) Distribution statistics of candidate SNPs on chromosome positions. (E) Classified statistics of candidate SNPs distributed in the exon.

Figure 3

Screening and analysis of candidate SNPs. (A) Gene Ontology (GO) analysis for 3.370 candidate SNPs. (B) Level two GO analysis of candidate SNPs. (C) KEGG enrichment of candidate SNPs. (D) Distribution statistics of candidate SNPs on chromosome positions. (E) Classified statistics of candidate SNPs distributed in the exon.

Figure 3

Screening and analysis of candidate SNPs. (A) Gene Ontology (GO) analysis for 3.370 candidate SNPs. (B) Level two GO analysis of candidate SNPs. (C) KEGG enrichment of candidate SNPs. (D) Distribution statistics of candidate SNPs on chromosome positions. (E) Classified statistics of candidate SNPs distributed in the exon.

Figure 3

Screening and analysis of candidate SNPs. (A) Gene Ontology (GO) analysis for 3.370 candidate SNPs. (B) Level two GO analysis of candidate SNPs. (C) KEGG enrichment of candidate SNPs. (D) Distribution statistics of candidate SNPs on chromosome positions. (E) Classified statistics of candidate SNPs distributed in the exon.

Figure 4

SNP3 and SNP4 affect the NUP37 protein. The structure of the NUP37 protein was unchanged due to SNP3 and SNP4. The 304th amino acid of SNP3 in the upper right corner is Ile, and in the lower right corner is Met. The 298th amino acid of SNP4 in the upper left corner is Phe, and in the lower left corner is Val.

Figure 5

SNP11 affects NUDT9 molecular docking. SNP11 does not affect the structure of the NUDT9 protein. To display the docking of amino acids, different angles were rotated. The left side shows 218 Thr combined with ADPR. The right side shows 218 Ala combined with ADPR. The combination box has changed.