Sichuan White is a popular Chinese goose breed reared for both meat and eggs. While egg laying and egg quality traits have been studied intensively in avians, including chickens[29, 30], ducks[15, 31], and quail[32], few studies have examined traits other than those associated with egg laying in the goose genome [13].
In the current study, a GWAS using 209 geese identified 27 SNPs significantly correlated with BBW, EN48, EN60 and EYC traits. As one of the most economically important traits, BBW is a major focus of goose breeding and has been correlated with a number of other performance traits in birds[33]. A SNP located within SMAP2 (stromal membrane-associated protein 2) was significantly associated with BW. In mammals, SMAP2 is necessary for formation in spermiogenesis[34], with SMAP2-deficient mice displaying male infertility[35], globozoospermia[36], asthenozoospermia[36], and abnormal acrosome formation[36]. Therefore, SMAP2 may be essential for reproduction in geese, regulating the BBW trait.
It is noteworthy that four SNPs situated within TMEM161A were grouped into a haplotype block, and association analyses confirmed that both the SNPs and the haplotype were significantly associated with EN48 and EN60. TMEM161A, also known as an adaptive response to oxidative stress protein 29 (AROS-29), is involved in several cellular processes, including the adaptive response to oxidative stress [37], the response to ultraviolet radiation, and the response to retinoic acid, and is a negative regulator of the intrinsic apoptotic signaling pathway in response to DNA damage and a positive regulator of the DNA repair response. In birds, retinoic acid promotes embryo development and egg production and can regulate egg number [38, 39]. Sichuan White geese display seasonal reproduction as an adaption to migration habit of the domesticate from wild goose and are therefore sensitive UV radiation. Because TMEM161A plays a key role in the response to UV light[40], it is possible that the artificial selection pressures resulting from the intensification of animal production systems contributed to the appearance of the four SNPs in TMEM161A, satisfying the demand for increased egg production and aiding in adaptation to the production environment. Mover, we also identified the other 5 candidate genes for the EN48 or EN60 traits, PGM2L (Glucose 1,6-bisphosphate synthase), DP13B (DCC-interacting protein 13-beta), DP13B (DCC-interacting protein 13-beta), RTJK (RNA-directed DNA polymerase from mobile element jockey), S2542 (Mitochondrial coenzyme A transporter SLC25A42). Previous studies have identified many candidate genes corresponding to reproductive traits in geese [41]. However, the positional candidate genes for egg number identified in the current study did not overlap with these genes. The egg number trait in poultry is quantitative and is regulated by numerous genes as well as the environment[42]. The positional candidate genes and SNPs identified here were all associated with egg production and micro-effect control of the examined traits. In addition, previous studies have examined a range of different breeds raised under diverse conditions, resulting in differences in the artificial selection pressures among studies that would undoubtedly influence egg number. Further, while the population sizes used in these studies were sufficient to draw goose breed-specific conclusions, they were not large enough to make species-wide predictions.
The biology pathway analysis of the candidate genes for EN48 and EN60 highly enrich in the response to radiation (GO:0009314), response to light stimulus (GO:0009416), cellular response to hormone stimulus (GO:0032870), response to and peptide hormone (GO:0043434) (Table 3). As we known, goose is the seasonal breeding goose were regulated by the light and the reproduction actives were controlled by the cycling reproduction hormones. We speculated that the candidate genes for EN48 or EN60 were response to the light or the reproduction hormones, involving in to regulate the reproduction activities, the mechanism needed to be further studied.
EYC is a crucial economic egg quality character because consumers associate yolk color with nutrition in [43]. Studies have shown that EYC is affected by genetic [44], environmental [45], housing [46], and dietary [47] factors. In the current study, twelve SNPs were significantly associated with EYC in Sichuan White geese. It is worth noting that five of these SNPs were constructed into a haplotype, resulting in the identification of positional candidate genes CALCR (calcitonin receptor), TFPI2 (tissue factor pathway inhibitor 2), and GLP1R (glucagon-like peptide 1 receptor). CALCR is a receptor that binds the peptide hormone calcitonin, and is involved in calcium homeostasis, bone formation and metabolism, and lipid metabolism[48, 49]. GLP1R, a member of the glucagon receptor family of G protein-coupled receptors, is involved in the control of blood sugar levels by enhancing insulin secretion[50]. Interestingly, CALCR and GLP1R regulate peptides that have anorexic effects, suppressing long-term food intake and promoting significant weight loss [51, 52]. TFPI-2 belongs to the Kunitz-type family of protease inhibitors and regulates matrix metalloproteinase activation and extracellular matrix degradation. Deficiency in this gene in mice accelerate the development of atherosclerotic lesions[53]. In addition, over-expression of TFPI-2 strongly inhibits the proliferation and migration of vascular smooth muscle cells, and affects smooth muscle cell proliferation and migration [53, 54]. Therefore, these positional candidate genes may control the EYC trait by affecting food intake or lipid metabolism in geese. EYC is a quantitative trait in birds and is regulated by many genes in poultry[55]. In agreement with previous studies, we also identified multiple other positional candidate genes corresponding to the twelve SNPs, including MBB1A (Myb-binding protein 1A-like protein), CB042 (uncharacterized protein C2orf42), CACB2, (voltage-dependent L-type calcium channel subunit beta-2), CCM2 (cerebral cavernous malformations protein 2 homolog), and ZBT46 (zinc finger and BTB domain-containing protein 46), the effects of which on EYC require further study.
The GO pathway analysis revealed that the regulation of epidermal growth factor-activated receptor activity (GO:0007176), regulation of epidermal growth factor receptor signaling pathway (GO:0042058) was remarkably enriched for EYC traits in goose. the two GO terms modulate the EGF-activated receptor activity. In mammal or birds, EGF-like growth factors play an important role in the ovulatory follicle[56], maturation of the cumulus-oocyte complex[57], oocyte maturation and development[58]. One of the key factors affected the EYC were genetic[59]. We propose that the candidate genes for EYC traits the EGF-activated receptor factors, might regulated the process of oocyte maturation and development, and determined the EYC traits in goose.