Genome-Wide Association Study to Identify SNPs and Haplotypes Associated with Reproductive Performance and Egg Quality Traits in Geese

Abstract

Background: Geese are one of the most economically important waterfowl worldwide. However, suboptimal reproductive performance hinders the development of the goose rearing industry. With the increasing public concern surrounding animal health and the regulation of the goose rearing industry, reproductive performance and egg quality have become a major focus for researchers. To promote the accuracy of selective breeding and identify important candidate genes associated with reproductive performance and egg quality traits, we examined the birth body weight (BBW), egg number at 48 weeks (EN48), egg number at 60 weeks (EN60) and egg yolk color (EYC) among 209 Sichuan White geese using a genome-wide association study (GWAS).Results: In this study, we obtained 2.896 Tb of raw whole-genome sequencing data with a mean depth coverage of 12.44. A total of 9,279,339 single nucleotide polymorphisms (SNPs) were identified in the goose genome. The GWAS analysis showed that 26 SNPs were significantly associated with the examined birth body weight (BBW), egg number in 48- and 60-week-old geese (EN48 and EN60) traits and egg yolk color (EYC), respectively. Notably, two genomic regions, a 28.85 kb genomic region (4512855bp ~ 4541709bp) on chromosome 35, and 294.57kb genomic region (21069009 b ~ 21363580 bp) located on chromosome 5, were significantly associated with egg number in 48- and 60-week-old geese (EN40 and EN60) egg yolk color (EYC), respectively. In addition, we performed the MALDI-TOP MS method to detected SNPs and haplotypes markers for EN48, EN60 and EYC traits were identified in the candidate gene TMEM161A, CALCR, TFPI2, and GLP1R, respectivelyConclusions: The SNPs, haplotypes markers and genes identified in this study can be used for marker-assisted selection of reproductive performance and egg quality traits in geese, promoting the accuracy of selective breeding. In addition, the identified candidate genes significantly associated with the traits provide a foundation for a better understanding of the mechanisms underlying reproduction and egg quality in geese.

Standing genetic variation andde novomutations underlie parallel evolution of island bird phenotypes

“…The karyotype distribution of the putative inversion identified on Chromosome 28 was associated with body size but was conflated with geographic population structure. The function of genes inside this region varied widely, some of them are involved in immunity, others in cholesterol metabolism and some are even directly linked to fitness proxies in birds (Krist 2011), like egg qual-ity (Gao et al 2021). However, it is unclear whether they contributed to the evolution of large body sizes in Southern Melanesia.…”

The Effects of Three-way Cross Strategy on the Gander Reproductive Performance

“…But compared to chickens and ducks, geese exhibit the poorest reproductive performance which severely impedes the development of the industry and limits the income of the farmers. To improve the reproductive performance of the geese, animal breeders have tried several ways from the aspects of the environment (Wang et al, 2005;Chang et al, 2016), nutrition (Zhang et al 2020) and genetic background (Gao et al 2021). Based on the previous studies, the crossbreeding strategy has become the most promising way for improving reproductive performance to the maximum extent.…”

“…Though more attention has been paid to the egg-laying performance of geese (Zhang et al, 2020;Gao et al, 2021;Guo et al, 2019;Zhu et al, 2017), the performance of ganders is more crucial such as sperm quality. The factors affecting sperm quality include ejaculate volume, sperm concentration and viability which determine to a great degree the hatchability and fertility (Lukaszewicz et al, 2003;Kowalczyk et al, 2012).…”