Genome-wide association analysis reveals regulatory genes for the metabolite synthesis of 2-acetyl-1-pyrroline in aromatic coconut (<i>Cocos nucifera</i> L.)

Hao Ding; Xiang Lv; Guangzhen Zhou; Xiaomei Liu; Xiwei Sun; Jing Li; Amjad Iqbal; Yaodong Yang

doi:10.1016/j.jgg.2024.12.002

Volume 52 Issue 2

Feb. 2025

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Genome-wide association analysis reveals regulatory genes for the metabolite synthesis of 2-acetyl-1-pyrroline in aromatic coconut (Cocos nucifera L.)

doi: 10.1016/j.jgg.2024.12.002

a. Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339, China;
b. Hainan Coconut International Joint Research Center, Wenchang, Hainan 571339, China;
c. Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, Hainan 570228, China;
d. Department of Food Science & Technology, Abdul Wali Khan University Mardan, 23200, Pakistan

Received Date: 2024-09-04
Accepted Date: 2024-12-02
Rev Recd Date: 2024-11-30

Available Online: 2025-07-11

Publish Date: 2024-12-13

Abstract

Abstract

Coconut (Cocos nucifera L.) is a key tropical economic tree valued for its fruit flavor, particularly 2-acetyl-1-pyrroline (2AP), a vital aroma metabolite. To enhance high-aromatic coconut breeding efforts, it is essential to deeply understand the hereditary factors governing the production of 2AP. In this study, a genome-wide association analysis identifies 32 loci that exhibit significant associations with 2AP content based on single nucleotide polymorphism (SNP) variations from 168 aromatic coconut germplasm resources. Transcriptome analysis then pinpoints 22 candidate genes near significant loci involved in 2AP metabolism. Proteins encoded by these genes are involved in amino acid metabolism, glycolysis, and secondary metabolism. Among these, Asparagine synthetase coding gene ASN1, Gamma-glutamylcysteine synthetase coding gene GSH1, and UbiA prenyltransferase coding gene UBIA are enriched in the linkage region constructed by significant locus Chr04_61490504. In particular, the SNP mutation of CnASN1 leads to amino acid changes in the functional region of the coding protein, potentially resulting in differences in 2AP content among haplotype populations. Identifying variations in related candidate genes, particularly the gene CnASN1, provides molecular markers closely associated with 2AP synthesis for coconut breeding and offers further insights into the metabolic mechanisms of 2AP.
- Aromatic coconut,
- 2AP,
- SNP,
- Genome-wide association study (GWAS),
- Haplotype analysis

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