Genome-Wide Association Study-Based Identification of SNPs and Haplotypes Associated With Goose Reproductive Performance and Egg Quality

Abstract

Geese are one of the most economically important waterfowl. However, the low reproductive performance and egg quality of geese hinder the development of the goose industry. The identification and application of genetic markers may improve the accuracy of beneficial trait selection. To identify the genetic markers associated with goose reproductive performance and egg quality traits, we performed a genome-wide association study (GWAS) for body weight at birth (BBW), the number of eggs at 48 weeks of age (EN48), the number of eggs at 60 weeks of age (EN60) and egg yolk color (EYC). The GWAS acquired 2.896 Tb of raw sequencing data with an average depth of 12.44× and identified 9,279,339 SNPs. The results of GWAS showed that 26 SNPs were significantly associated with BBW, EN48, EN60, and EYC. Moreover, five of these SNPs significantly associated with EN48 and EN60 were in a haplotype block on chromosome 35 from 4,512,855 to 4,541,709 bp, oriented to TMEM161A and another five SNPs significantly correlated to EYC were constructed in haplotype block on chromosome 5 from 21,069,009 to 21,363,580, which annotated by TMEM161A, CALCR, TFPI2, and GLP1R. Those genes were enriched in epidermal growth factor-activated receptor activity, regulation of epidermal growth factor receptor signaling pathway. The SNPs, haplotype markers, and candidate genes identified in this study can be used to improve the accuracy of marker-assisted selection for the reproductive performance and egg quality traits of geese. In addition, the candidate genes significantly associated with these traits may provide a foundation for better understanding the mechanisms underlying reproduction and egg quality in geese.

Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation

“…The practical value of Belyaev’s concept has been realized in a huge collection of commercial fur colors—e.g., “Amber-gold pastel,” “Ashen,” “Beige,” “Black crystal,” “Cobalt,” “Ermine-like,” “Peach,” ““Pearl,” Platinum,” “Purple,” “Silver sable-like,” “Steel-blue,” and “Straw,”—rarely or never seen in the wild [ 6 ]. The concept’s fundamental importance has found confirmation in a large variety of breeds of dogs [ 7 ], cats [ 8 ], pigs [ 9 ], cows [ 10 ], horses [ 11 ], sheep [ 12 ], goats [ 13 ], chickens [ 14 ], ducks [ 15 ], geese [ 16 ], and other domestic animals [ 17 ] as well as in artificial shelters and additional feeding for wild animals in wildlife for saving them [ 18 ]. On the basis of Belyaev’s concept [ 1 ], a laboratory model of animal domestication by humans has been created using outbred lines of tame and aggressive rats artificially bred [ 19 ] for performance on a standard glove test [ 20 ].…”

Identification and Validation of Marketing Weight-Related SNP Markers Using SLAF Sequencing in Male Yangzhou Geese

“…In additional, one SNP in exon three of Myostatin gene was detected in Landes and Kielecka geese breeds [49]. Recently, a total of 26 SNPs and 14 annotated genes significantly associated with quality traits and egg production were identified in Sichuan white geese by GWAS [50].…”

Identification of the differentially expressed genes in the leg muscles of Zhedong white geese (Anser cygnoides) reared under different photoperiods

“…China is the largest producer and consumer of goose meat globally. However, owing to the lack of a scientific breeding method, the breeding cycle of geese is longer than that of other poultry, which seriously restricts the development of the goose industry ( Gao et al, 2021a ). Therefore, exploring scientific methods to improve muscle development and meat quality of Chinese local geese is a useful way to overcome the current predicament.…”