Identification of SNPs and INDELS associated with duck egg quality traits through a genome-wide association analysis
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 duck...
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Elsevier
2024-12-01
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| author | Min Zhang Lizhi Lu Yan Li Qiong Wu Yanhui Liu Hongfei Liu Hehe Tang Rulong Lin Hongping Chen Tao Zeng Yong Tian Yuting Yan Yanning Wei Chenyu Ren Wenfu Li Min Liu Jie Yu Jiawen Liu Xin Lin Guanghua Zeng Chunmei Cheng Xiaobing Jiang Yanfa Sun |
| author_facet | Min Zhang Lizhi Lu Yan Li Qiong Wu Yanhui Liu Hongfei Liu Hehe Tang Rulong Lin Hongping Chen Tao Zeng Yong Tian Yuting Yan Yanning Wei Chenyu Ren Wenfu Li Min Liu Jie Yu Jiawen Liu Xin Lin Guanghua Zeng Chunmei Cheng Xiaobing Jiang Yanfa Sun |
| author_sort | Min Zhang |
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| description | 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 (h2) ranged from 0.022 to 0.996 for the 12 quantitative traits, with the highest h2 (0.996) for eggshell color a* value (ESCA) and the lowest h2 (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. |
| format | Article |
| id | doaj-art-be4a5bdad7884b11bc79f583cceba710 |
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| spelling | doaj-art-be4a5bdad7884b11bc79f583cceba7102025-08-20T01:55:37ZengElsevierPoultry Science0032-57912024-12-011031210445910.1016/j.psj.2024.104459Identification of SNPs and INDELS associated with duck egg quality traits through a genome-wide association analysisMin Zhang0Lizhi Lu1Yan Li2Qiong Wu3Yanhui Liu4Hongfei Liu5Hehe Tang6Rulong Lin7Hongping Chen8Tao Zeng9Yong Tian10Yuting Yan11Yanning Wei12Chenyu Ren13Wenfu Li14Min Liu15Jie Yu16Jiawen Liu17Xin Lin18Guanghua Zeng19Chunmei Cheng20Xiaobing Jiang21Yanfa Sun22College 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 ChinaInstitute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR ChinaCollege 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 ChinaCollege 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 ChinaCollege 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 ChinaInstitute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, PR ChinaInstitute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, PR ChinaLongyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, 364031, PR ChinaLongyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, 364031, PR ChinaInstitute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR ChinaInstitute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR ChinaCollege 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 ChinaCollege 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 ChinaCollege 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 ChinaCollege 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 ChinaCollege 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 ChinaCollege 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 ChinaCollege 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 ChinaCollege 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 ChinaCollege 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 ChinaCollege 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 ChinaFujian Provincial Animal Husbandry Headquarters, Fuzhou, Fujian 350003, PR ChinaCollege 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; Corresponding author at: College of Life Science, Longyan University, No. 1 Dongxiao North Road, Xinluo District, Longyan, Fujian 364012, PR China.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 (h2) ranged from 0.022 to 0.996 for the 12 quantitative traits, with the highest h2 (0.996) for eggshell color a* value (ESCA) and the lowest h2 (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.http://www.sciencedirect.com/science/article/pii/S003257912401037XLongyan Shan-ma duckEgg quality traitGWASSNPIndel |
| spellingShingle | Min Zhang Lizhi Lu Yan Li Qiong Wu Yanhui Liu Hongfei Liu Hehe Tang Rulong Lin Hongping Chen Tao Zeng Yong Tian Yuting Yan Yanning Wei Chenyu Ren Wenfu Li Min Liu Jie Yu Jiawen Liu Xin Lin Guanghua Zeng Chunmei Cheng Xiaobing Jiang Yanfa Sun Identification of SNPs and INDELS associated with duck egg quality traits through a genome-wide association analysis Poultry Science Longyan Shan-ma duck Egg quality trait GWAS SNP Indel |
| title | Identification of SNPs and INDELS associated with duck egg quality traits through a genome-wide association analysis |
| title_full | Identification of SNPs and INDELS associated with duck egg quality traits through a genome-wide association analysis |
| title_fullStr | Identification of SNPs and INDELS associated with duck egg quality traits through a genome-wide association analysis |
| title_full_unstemmed | Identification of SNPs and INDELS associated with duck egg quality traits through a genome-wide association analysis |
| title_short | Identification of SNPs and INDELS associated with duck egg quality traits through a genome-wide association analysis |
| title_sort | identification of snps and indels associated with duck egg quality traits through a genome wide association analysis |
| topic | Longyan Shan-ma duck Egg quality trait GWAS SNP Indel |
| url | http://www.sciencedirect.com/science/article/pii/S003257912401037X |
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