首页|Gene expression,transcription factor binding and histone modification predict leaf adaxial-abaxial polarity related genes

Gene expression,transcription factor binding and histone modification predict leaf adaxial-abaxial polarity related genes

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Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process re-mains unclear.To uncover critical genes involved in leaf ad-abaxial patterning,we applied a combination of in silico prediction using machine learning(ML)and experimental analysis.A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground truth.Gene expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(ChIP-seq)was used as input,enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription factors.Parallel to this,available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial sides.Based on these analyses,we obtained a set of 111 novel genes which are involved in leaf ad-abaxial specialization.To explore implications for vegetable crop breeding,we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell transcriptomics.The results demonstrated the utility of our computational approach for predicting candidate genes in crop species.Our findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development,with demonstrable breeding applications.

Machine learningLeaf polarityArabidopsis thalianaBrassica rapaTranscription factor

Wei Sun、Zhicheng Zhang、Guusje Bonnema、Xiaowu Wang、Aalt Dirk Jan van Dijk

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State Key Laboratory of Vegetable Biobreeding,Institute of Vegetables and Flowers,Chinese Academy of Agricultural Sciences,Beijing 100081,China

Sino-Dutch Joint Lab of Vegetable Genomics,Beijing 100081,China

Bioinformatics Group,Wageningen University and Research,6708 PB Wageningen,the Netherlands

Plant Breeding,Wageningen University and Research,6708 PB Wageningen,the Netherlands

Biosystems Data Analysis,Swammerdam Institute for Life Sciences,University of Amsterdam,1090 GE Amsterdam,the Netherlands

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National Key Research and Development Program of ChinaCentral Publicinterest Scientific Institution Basal Research FundAgricultural Science and Technology Innovation Program(ASTIP)China Scholarship Council

2022YFF1003003Y2023PT16202103250097

2024

10.1016/j.hpj.2024.06.002

园艺学报(英文版)

园艺学报(英文版)

CSTPCD
ISSN：
年,卷(期)：2024.10(4)
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