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Mining transcriptome data to identify genes and pathways related to lemon taste using supervised and unsupervised data learning methods
Horticulture, Environment, and Biotechnology ( IF 2.5 ) Pub Date : 2021-02-19 , DOI: 10.1007/s13580-021-00337-y
Zahra Zinati , Sima Sazegari , Hosein Amin , Ahmad Tahmasebi

There is a dearth of studies on the genes engaged in citrus taste. Unraveling the major genes involved in pathways related to the taste of citrus (sweet or acidic) is highly important for developing new genotypes with favorable taste. Pivotal genes linked to citrus taste can be extracted through mining a large number of expression data. To attain this objective, 10 different attribute weighting algorithms (AWAs) were applied on the expression data from three lemon (Citrus limon) genotypes differing in terms of fruit acidity. As a result, a total of 170 probe sets were identified by more than eight AWAs as the most discriminative probe sets. Subsequently, principal component analysis and hierarchical clustering heatmaps were implemented for validation of the 170 top-ranked probe sets. Noticeably, the identified top 170 probe sets significantly contributed to accurate discrimination between sweet and acidic lemon samples, which indicate the significance and accuracy of prediction of probe sets. According to the results, some genes like citrate synthase, malate dehydrogenase, proton-pumping ATPase, and flavanone 3-hydroxylase had distinct roles in differentiation of the studied genotypes and acidity. Among all of the genes, malate dehydrogenase was the most informative. To the best of our knowledge, this is the first report on identifying the most important genes contributing to lemon taste using supervised and unsupervised data learning methods.



中文翻译:

使用监督和非监督数据学习方法挖掘转录组数据以识别与柠檬味相关的基因和途径

缺乏有关柑橘味基因的研究。揭示与柑橘味(甜味或酸性味)有关的途径中涉及的主要基因对于开发具有良好味觉的新基因型非常重要。可以通过挖掘大量表达数据来提取与柑橘味相关的关键基因。为实现此目标,对来自三个柠檬(柑桔)的表达数据应用了10种不同的属性加权算法(AWA))的基因型在水果酸度方面有所不同。结果,通过八个以上的AWA将总共170个探针集识别为最具判别性的探针集。随后,实施了主成分分析和层次聚类热图,以验证170个排名最高的探针组。值得注意的是,确定的前170个探针组显着有助于准确区分甜柠檬和酸性柠檬样品,这表明了预测探针组的重要性和准确性。根据结果​​,柠檬酸合酶,苹果酸脱氢酶,质子泵ATP酶和黄烷酮3-羟化酶等基因在所研究基因型和酸度的区分中具有独特的作用。在所有基因中,苹果酸脱氢酶是最有用的。据我们所知,

更新日期:2021-02-19
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