Identification of the CaFAB2 Gene Family in Coffea arabica and Its Potential Role in Seed Fatty Acid Synthesis
ZHANG Zhen-Wei1, DONG Xiang-Shu2, YANG Jing1, QI Mei-Jun1, WANG Bu-Tian1, SHI Xue-Dong1, HUANG Wen-Long1, LI Xue-Jun1, GE Yu1,*
1 College of Tropical Crops, Yunnan Agricultural University, Pu'er 665099, China; 2 Institute of Plant Resources, Yunnan University, Kunming 650504, China
Abstract：The quality of Coffea arabica beans is the primary objective of breeding new varieties of C. arabica with high quality, among these, the aroma of coffee bean is the key factor to evaluate the quality of C. arabica bean, and fatty acid is one of the precursors to form volatile aroma components of C. arabica bean. Stearoyl-ACP desaturase (FAB) is an essential enzyme involved in unsaturated fatty acid synthesis in plants, and its desaturation function significantly influences the proportion and unsaturation level of fatty acids. Through Blast comparison analysis, 4 members of the CaFAB2 gene family within the C. arabica genome were identified in this study. Further investigation illuminated that these 4 CaFAB2 genes consisted of 381~415 amino acids with molecular weights ranging from 43 936.6 to 47 693.4 D. Besides, these 4 genes also had isoelectric points greater than 7 and exhibited hydrophilic characteristics with instability indices from 29.55 to 42.67 but less than 100 fat index values. And the total average coefficients were all negative, so they were hydrophilic proteins. The proteins of 4 CaFAB2 genes were localized in chloroplasts. Through gene family analysis, it was found that the conserved motif of the CaFAB2 gene family was identical to that of the FAB2 gene family of Arabidopsis thaliana, and the distribution position was highly similar, with the domain PLN00179. Additionally, it was observed that 2 offspring genes corresponded to 1 parental gene between C. eugenoedes and Coffea canephora regarding the presence of CaFAB2 genes in the genome structure of C. arabica. Furthermore, the fatty acid contents were mainly composed of linoleic acid, palmitic acid, oleic acid, and stearic acid during 4 developmental stages of C. arabica seeds, and these 4 compounds indicated the same trend characterized by initial decrease followed by gradual increase. The transcriptome sequencing and real-time fluorescence quantitative PCR analyse revealed a positive correlation between CaFAB2.3 and oleic acid synthesis, while the CaFAB2.1 and CaFAB2.3 primarily participated in early palmitic acid synthesis in the 4 developmental stages of C. arabica seeds. This study provides a theoretical foundation for further investigation on variation tendency and biosynthesis of fatty acids in C. arabica, and offered novel insights into the identification and regulatory mechanisms of CaFAB2 genes in C. arabica.
张振伟, 董相书, 杨婧, 杞美军, 王步天, 施学东, 黄文龙, 李学俊, 葛宇. 小粒咖啡CaFAB2基因家族的鉴定及其在种子脂肪酸合成中的潜在作用[J]. 农业生物技术学报, 2025, 33(1): 79-91.
ZHANG Zhen-Wei, DONG Xiang-Shu, YANG Jing, QI Mei-Jun, WANG Bu-Tian, SHI Xue-Dong, HUANG Wen-Long, LI Xue-Jun, GE Yu. Identification of the CaFAB2 Gene Family in Coffea arabica and Its Potential Role in Seed Fatty Acid Synthesis. 农业生物技术学报, 2025, 33(1): 79-91.
[1] 曹宁, 董春娟, 尚庆茂. 2016. 外源水杨酸对低温下黄瓜幼苗CsFAD的表达调控[J]. 园艺学报, 43(10): 1941-1952. (Cao N, Dong C J, Shang Q M.2016. Effects of exogenous salicylic acid on the expression of CsFAD genes in Cucumber seedlings under low temperature[J]. Acta Horticulturae Sinica, 43(10): 1941-1952.) [2] 陈虹, 潘存德, 王蓓, 等. 2016. 核桃种子发育主要营养物质积累之间的关系及脂肪酸动态变化[J]. 河北农业大学学报, 39(01): 57-62, 74. (Chen H, Pan C D, Wang B, et al.2016. The relationship among nutrients' accumulation and dynamic changes of fatty acids in seed development of walnut[J]. Journal of Agricultural University of Hebei, 39(01): 57-62, 74.) [3] 迟晓元, 郝翠翠, 潘丽娟, 等. 2016. 不同花生品种脂肪酸组成及其积累规律的研究[J]. 花生学报, 45(03): 32-36. (Chi X Y, Hao C C, Pan L J.et al.2016. Fatty acid accumulation pattern in different types of peanut[J]. Journal of Peanut Science, 45(03): 32-36.) [4] 董聪慧, 董文江, 程金焕, 等. 2022. 咖啡豆烘焙过程中油脂脂肪酸组成、挥发性风味及活性成分的演变规律[J]. 食品科学, 43(24): 210-222. (Dong C H, Dong W J, Cheng J H, et al.2022. Evolution of fatty acid composition, volatile flavors and bioactive ingredients of coffee oil during coffee bean roasting[J]. Food Science, 43(24): 210-222.) [5] 胡荣锁, 董文江, 宗迎, 等. 2018. 5个产区咖啡果皮成分分析与营养评价[J]. 热带作物学报, 39(05): 987-992. (Hu R S, Dong W J, Zong Y, et al.2018. Analysis and evaluation of nutritional components of coffee peel from five different growing regions[J]. Chinese Journal of Tropical Crops, 39(05): 987-992.) [6] 李晓丹, 吴刚, 武玉花, 等. 2007. 大豆种子发育过程中脂肪酸积累模式研究[J]. 大豆科学, 26(04): 506-510. (Li X D, Wu G, Wu Y H, et al.2007. The accumulation pattern of fatty acids during the development of soybean seeds[J]. Soybean Science, 26(04): 506-510.) [7] 李晓丹, 肖玲, 吴刚, 等. 2008. 芝麻种子发育过程中脂肪酸积累模式的研究[J]. 中国油料作物学报, 30(01): 84-89. (Li X D, Xiao L, Wu G, et al.2008. Accumulation pattern of fatty acids during the seed development of sesame (Sesamum indicum L.)[J]. Chinese Journal of Oil Crop Sciences, 30(01): 84-89.) [8] 刘浩, 鲁清, 李海芬, 等. 2019. 花生硬脂酰-ACP酸脱饱和基因FAB2表达的分子机制[J]. 作物学报, 45(11): 1638-1648. (Liu H, Lu Q, Li H F, et al.2019. Molecular mechanism of stearoyl-ACP desaturase gene FAB2 expression in peanut[J]. Acta Agronomica Sinica, 45(11): 1638-1648.) [9] 马建江, 吴嫚, 裴文锋, 等. 2015. 棉花种子发育过程中脂肪及脂肪酸积累模式研究[J]. 棉花学报, 27(02): 95-103. (Ma J J, Wu M, Pei W F, et al.2015. Accumulation patterns of fat and fatty acids during cotton seed development[J]. Cotton Science, 27(02): 95-103.) [10] 屈淑平, 常影, 秦俊芬, 等. 2011. 籽用南瓜种子发育过程中脂肪酸积累模式[J]. 中国油料作物学报, 33(06): 628-631. (Qu S P, Chang Y, Qin J F, et al.2011. Accumulation pattern of fatty acids during pumpkin (Cucurbita maxima Duch) seed development[J]. Chinese Journal of Oil Crop Sciences, 33(06): 628-631.) [11] 陶宇, 卢选康, 严鑫等. 2024. 227个花生品种主要油脂性状的遗传多样性分析[J]. 花生学报, 53(01): 1-9. (Tao Y, Lu X K, Yan X, et al.2024. Genetic diversity analysis of major lipid traits in 227 peanut cultivars[J]. Journal of Peanut Science, 53(01): 1-9.) [12] 闫林, 黄丽芳, 王晓阳, 等. 2019a. 基于ISSR标记的咖啡资源遗传多样性分析[J]. 热带作物学报, 40(02): 300-307. (Yan L, Huang L F, Wang X Y, et al.2019a. Genetic diversity of coffee germplasms by ISSR markers[J]. Chinese Journal of Tropical Crops, 40(02): 300-307.) [13] 闫林, 黄丽芳, 王晓阳, 等. 2019b. 咖啡种质资源遗传多样性的ISSR分析[J]. 南方农业学报, 50(03): 491-499. (Yan L, Huang L F, Wang X Y, et al.2019b. Genetic diversity of coffee gemeplasms by ISSR analysis[J]. Journal of Southern Agriculture, 50(03): 491-499.) [14] 杨婧, 李学俊, 张宝琼, 等. 2024. 咖啡AP2基因家族鉴定及其与脂肪酸合成相关基因表达[J]. 分子植物育种, 1-18. (Yang J, Li X J, Zhang B Q, et al.2024. Identification of AP2 gene family in coffea canephor and gene expression analysis related to fatty acid[J]. Molecular Plant Breeding, 1-18.) [15] 杨丽, 陈虹, 潘存德, 等. 2017. 核桃种子油脂转化期转录组分析[J]. 果树学报, 34(09): 1084-1094. (Yang L, Chen H, Pan C D, et al.2017. Transcriptome analysis for walnut seed during oil synthesis period[J]. Journal of Fruit Science, 34(09): 1084-1094.) [16] 周菲. 2020. 向日葵油酸合成上游基因HaFAB2克隆与表达分析[J]. 东北农业大学学报, 51(11): 23-31. (Zhou F.2020. Cloning and expression analysis of HaFAB2, an upstream gene for oleic acid synthesis in sunflower[J]. Journal of Northeast Agricultural University, 51(11): 23-31.) [17] Bailey T L, Johnson J, Grant C E, et al.2015. The MEME suite[J]. Nucleic Acids Research, 43(W1): W39-W49. [18] Chi X, Yang Q, Lu Y, et al.2011. Genome-wide analysis of fatty acid desaturases in soybean (Glycine max)[J]. Plant Molecular Biology Reporter, 29: 769-783. [19] Ding Z T, Shen J Z, Pan L L, et al.2016. CsSAD: A fatty acid desaturase gene involved in abiotic resistance in Camellia sinensis (L.)[J]. Genetics and Molecular Research, 15(1): 15017512. [20] Freitas N C, Barreto H G, Fernandes-Brum C N, et al.2017. Validation of reference genes for qPCR analysis of Coffea arabica L. somatic embryogenesis-related tissues[J]. Plant Cell, Tissue and Organ Culture (PCTOC), 3(128): 663-678. [21] Hajiahmadi Z, Abedi A, Wei H, et al.2020. Identification, evolution, expression, and docking studies of fatty acid desaturase genes in wheat (Triticum aestivum L.)[J]. BMC genomics, 21: 1-20. [22] Kachroo A, Shanklin J, Whittle E, et al.2007. The Arabidopsis stearoyl-acyl carrier protein-desaturase family and the contribution of leaf isoforms to oleic acid synthesis[J]. Plant Molecular Biology, 63: 257-271. [23] Kodama H, Horiguchi G, Nishiuchi T, et al.1995. Fatty acid desaturation during chilling acclimation is one of the factors involved in conferring low-temperature tolerance to young tobacco leaves[J]. Plant Physiology, 107(4): 1177-1185. [24] Li D, LI H, FENG H, et al.2024. Unveiling kiwifruit TCP genes: Evolution, functions, and expression insights[J]. Plant Signaling & Behavior, 19(1): 2338985 [25] Liu C, Yang N, Yang Q, et al.2019a. Enhancing Robusta coffee aroma by modifying flavour precursors in the green coffee bean[J]. Food Chemistry, 281: 8-17. [26] Liu C, Yang Q, Linforth R, et al.2019b. Modifying Robusta coffee aroma by green bean chemical pre-treatment[J]. Food Chemistry, 272: 251-257. [27] Lu S, Wang J, Chitsaz F, et al.2020. CDD/SPARCLE: The conserved domain database in 2020[J]. Nucleic Acids Research, 48(D1): D265-D268. [28] Marchler-Bauer A, Bo Y, Han L, et al.2017. CDD/SPARCLE: Functional classification of proteins via subfamily domain architectures[J]. Nucleic Acids Research, 45(D1): D200-D203. [29] Mehari B, Redi‐Abshiro M, Chandravanshi B S, et al.2019. GC‐MS profiling of fatty acids in green coffee (Coffea arabica L.) beans and chemometric modeling for tracing geographical origins from Ethiopia[J]. Journal of the Science of Food and Agriculture, 99(8): 3811-3823. [30] Sun J, Bie X M, Wang N, et al.2020. Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat[J]. BMC Plant Biology, 20: 1-14. [31] Wang J, Chitsaz F, Derbyshire M K, et al.2024. The conserved domain database in 2023[J]. Nucleic Acids Research, 51(D1): D384-D388. [32] Wang J, Shao Y, Yang X, et al.2023. Heterogeneous expression of stearoyl-acyl carrier protein desaturase genes SAD1 and SAD2 from Linum usitatissimum enhances seed oleic acid accumulation and seedling cold and drought tolerance capability in Brassica napus[J]. Journal of Integrative Agriculture, 23(6): 1864-1878 [33] Worku M, De Meulenaer B, Duchateau L, et al.2018. Effect of altitude on biochemical composition and quality of green arabica coffee beans can be affected by shade and postharvest processing method[J]. Food Research International, 105: 278-285. [34] Xie J, Chen Y, Cai G, et al.2023. Tree visualization by one table (tvBOT): A web application for visualizing, modifying and annotating phylogenetic trees[J]. Nucleic Acids Research, 51(W1): W587-W592. [35] Zhang P, Burton J W, Upchurch R G, et al.2008. Mutations in a Δ9-stearoyl-ACP-desaturase gene are associated with enhanced stearic acid levels in soybean seeds[J]. Crop Science, 48(6): 2305-2313. [36] Zhu M, Long Y, Ma Y, et al.2021. Comparison of chemical and fatty acid composition of green coffee bean (Coffea arabica L.) from different geographical origins[J]. LWT-Food Science and Technology, 140: 110802.
