Genome-wide association analysis of the primary feather growth traits of duck: identification of potential Loci for growth regulation

Ma, Shengchao; Li, Pengcheng; Liu, Hehe; Yang, Xi; Xu, Qian; Qi, Jingjing; Wang, Jianmei; Li, Liang; Wang, Jiwen; Hu, Jiwei; He, Hua; Han, Chunchun; Bai, Lili

doi:10.1016/j.psj.2022.102243

Cited by 7 publications

(9 citation statements)

References 57 publications

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“…Plumage traits are controlled by numerous genes and molecular pathways, making them very complex to comprehend. The differences among feather color patterns are important in analyzing these molecular pathways [ 8 ]. In ducks, feather coloration is an economic and well-recognized trait.…”

Section: Discussionmentioning

confidence: 99%

“…Using Burrows–Wheeler alignment (BWA aln, version 0.7.12), the clean reads were mapped to the duck reference genome (ZJU 1.0) using default parameters. After mapping, single-nucleotide polymorphism (SNP) calling was performed using genome analysis toolkit (GATK) 3.5 [ 1 , 8 ]. The SNPs were further filtered using VCFtools (version 0.1.15) based on the following criteria: (1) SNPs with minor allele frequency > 0.05 and a major allele frequency < 0.99; (2) the maximum missing rate was <0.1; and (3) SNPs with only 2 alleles.…”

Section: Methodsmentioning

confidence: 99%

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Genome-Wide Association Studies Reveal Candidate Genes Associated with Pigmentation Patterns of Single Feathers of Tianfu Nonghua Ducks

Twumasi,

Wang,

et al. 2023

Animals

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In modern advanced genetics and breeding programs, the study of genes related to pigmentation in ducks is gaining much attention and popularity. Genes and DNA mutation cause variations in the plumage color traits of ducks. Therefore, discovering related genes responsible for different color traits and pigment patterns on each side of the single feathers in Chinese ducks is important for genetic studies. In this study, we collected feather images from 340 ducks and transported them into Image Pro Plus (IPP) 6.0 software to quantify the melanin content in the feathers. Thereafter, a genome-wide association study was conducted to reveal the genes responsible for variations in the feather color trait. The results from this study revealed that the pigmented region was larger in the male ducks as compared to the female ducks. In addition, the pigmented region was larger on the right side of the feather vane than on the left side in both dorsal and ventral feathers, and a positive correlation was observed among the feather color traits. Further, among the annotated genes, WNT3A, DOCK1, RAB1A, and ALDH1A3 were identified to play important roles in the variation in pigmented regions of the various feathers. This study also revealed that five candidate genes, including DPP8, HACD3, INTS14, SLC24A1, and DENND4A, were associated with the color pigment on the dorsal feathers of the ducks. Genes such as PRKG1, SETD6, RALYL, and ZNF704 reportedly play important roles in ventral feather color traits. This study revealed that genes such as WNT3A, DOCK1, RAB1A, and ALDH1A3 were associated with different pigmentation patterns, thereby providing new insights into the genetic mechanisms of single-feather pigmentation patterns in ducks.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Genome-Wide Association Studies Reveal Candidate Genes Associated with Pigmentation Patterns of Single Feathers of Tianfu Nonghua Ducks

Twumasi,

Wang,

et al. 2023

Animals

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“…Finally, a total of 19,628,941 SNPs were obtained by VCFtools for GWAS analysis. The specific methods and statistical results have been sorted out by our research group in the early stage [ 44 ].…”

Section: Methodsmentioning

confidence: 99%

Genome-wide association analysis explores the genetic loci of amino acid content in duck’s breast muscle

Wang,

Lu,

et al. 2024

BMC Genomics

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Background Amino acids are the basic components of protein and an important index to evaluate meat quality. With the rapid development of genomics, candidate regions and genes affecting amino acid content in livestock and poultry have been gradually revealed. Hence, genome-wide association study (GWAS) can be used to screen candidate loci associated with amino acid content in duck meat. Result In the current study, the content of 16 amino acids was detected in 358 duck breast muscles. The proportion of Glu to the total amino acid content was relatively high, and the proportion was 0.14. However, the proportion of Met content was relatively low, at just 0.03. By comparative analysis, significant differences were found between males and females in 3 amino acids, including Ser, Met, and Phe. In addition, 12 SNPs were significantly correlated with Pro content by GWAS analysis, and these SNPs were annotated by 7 protein-coding genes; 8 significant SNPs were associated with Tyr content, and these SNPs were annotated by 6 protein-coding genes. At the same time, linkage disequilibrium (LD) analysis was performed on these regions with significant signals. The results showed that three SNPs in the 55–56 Mbp region of chromosome 3 were highly correlated with the leader SNP (chr3:55526954) that affected Pro content (r2 > 0.6). Similarly, LD analysis showed that there were three SNPs in the 21.2–21.6 Mbp region of chromosome 13, which were highly correlated with leader SNP (chr13:21421661) (r2 > 0.6). Moreover, Through functional enrichment analysis of all candidate genes. The results of GO enrichment analysis showed that several significant GO items were associated with amino acid transport function, including amino acid transmembrane transport and glutamine transport. The results further indicate that these candidate genes are closely associated with amino acid transport. Among them, key candidate genes include SLC38A1. For KEGG enrichment analysis, CACNA2D3 and CACNA1D genes were covered by significant pathways. Conclusion In this study, GWAS analysis found a total of 28 significant SNPs affecting amino acid content. Through gene annotation, a total of 20 candidate genes were screened. In addition, Through LD analysis and enrichment analysis, we considered that SERAC1, CACNA2D3 and SLC38A1 genes are important candidate genes affecting amino acid content in duck breast muscle.

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“…Our team has reported this data on candidate genes for feather color in Nonghua ducks and male mallard ducks. ( Ma et al, 2023 ; Wang et al, 2023 ).…”

Section: Methodsmentioning

confidence: 99%

Identification of candidate genes affecting the tibia quality in Nonghua duck

Lu,

Wei,

Yang

et al. 2024

Poultry Science

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Genome-wide association analysis of the primary feather growth traits of duck: identification of potential Loci for growth regulation

Cited by 7 publications

References 57 publications

Genome-Wide Association Studies Reveal Candidate Genes Associated with Pigmentation Patterns of Single Feathers of Tianfu Nonghua Ducks

Genome-Wide Association Studies Reveal Candidate Genes Associated with Pigmentation Patterns of Single Feathers of Tianfu Nonghua Ducks

Genome-wide association analysis explores the genetic loci of amino acid content in duck’s breast muscle

Identification of candidate genes affecting the tibia quality in Nonghua duck

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