Identification of SNPs and INDELS associated with duck egg quality traits through a genome-wide association analysis.

Autor:	Zhang M; College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, PR China., Lu L; Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China., Li Y; College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, PR China., Wu Q; College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, PR China., Liu Y; College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, PR China., Liu H; Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, PR China., Tang H; Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, PR China., Lin R; Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, 364031, PR China., Chen H; Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, 364031, PR China., Zeng T; Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China., Tian Y; Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China., Yan Y; College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, PR China., Wei Y; College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, PR China., Ren C; College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, PR China., Li W; College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, PR China., Liu M; College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, PR China., Yu J; College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, PR China., Liu J; College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, PR China., Lin X; College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, PR China., Zeng G; College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, PR China., Cheng C; College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, PR China., Jiang X; Fujian Provincial Animal Husbandry Headquarters, Fuzhou, Fujian 350003, PR China., Sun Y; College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, PR China. Electronic address: boysun2010@163.com.
Jazyk:	angličtina
Zdroj:	Poultry science [Poult Sci] 2024 Dec; Vol. 103 (12), pp. 104459. Date of Electronic Publication: 2024 Oct 29.
DOI:	10.1016/j.psj.2024.104459
Abstrakt:	Egg quality traits are economically important in the poultry industry. To explore the genetic architecture and identify potential candidate genes, a genome-wide association study (GWAS) was performed for 13 egg quality traits using data from whole-genome sequencing of 299 Longyan Shan-ma female ducks, including 12 quantitative traits and one qualitative trait, eggshell color (ESC; white, light green, green). From estimation of pedigree genetic parameters, heritability (h 2 ) ranged from 0.022 to 0.996 for the 12 quantitative traits, with the highest h 2 (0.996) for eggshell color a* value (ESCA) and the lowest h 2 (0.022) for egg yolk percentage relative to EW. A total of 8,874 single nucleotide polymorphism (SNP)-based significant associations (1.0 × 10 -6 ) and 247 insertion-deletion (indel)-based significant associations (1.00 × 10 -5 ) were identified, including 5,980 SNPs and 159 indel markers. From 5,924 SNPs and 143 indels associated with ESC traits, 181 potential candidate genes were identified, and most significant SNPs and indels (P < 1.0 × 10 -20 ) were located at 1.86 Mb (44.29-46.15 Mb) on chromosome 4. The top SNP (chr4:45325309:C>A; P = 7.97 × 10 -43 ) and the top indel (chr4:45299595:delTTCCACTCCAC; P = 4.20 × 10 -36 ) for the ESC a* value were within two known ESC candidate genes; ATP-binding cassette subfamily G member 2 (ABCG2) and protein kinase cGMP-dependent 2 (PRKG2). Of 56 SNPs and 16 indels associated with other egg quality traits, 46 potential candidate genes were identified including synapse differentiation-inducing 1-like (SYNDIG1L) for EW, and core histone macro-H2A.1 (LOC101795967) and neurogenin 1 (NEUROG1) for egg shape index; and four genes including collagen type VI alpha 3 chain (COL6A3), lysine demethylase 7A (KDM7A), LOC101802169, and sperm-associated antigen 16 (SPAG16) for egg yolk weight and the percentage of yolk to total egg weight. Of the 46 genes, the molecular functions of 22 are related to protein binding, indicating important roles in the formation of egg quality traits. Our findings provide new insight into the genetic basis of egg quality traits in ducks. Competing Interests: Declaration of competing interest Authors declare that they have no competing interests. (Copyright © 2024. Published by Elsevier Inc.)
Databáze:	MEDLINE
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