数字农科院2.0

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

文献类型： 外文期刊

作者： Sun, Wei;Zhang, Zhicheng;Bonnema, Guusje;Wang, Xiaowu;vanDijk, Aalt Dirk Jan

作者机构：

关键词： Machine learning;Leaf polarity;Arabidopsis thaliana;Brassica rapa;Transcription factor

期刊名称： HORTICULTURAL PLANT JOURNAL

ISSN： 2095-9885

年卷期： 2024 年 10 卷 4 期

页码：

收录情况： SCIE（2024版） ; ; CSCD（2023-2024年度） ; ; 科技核心（2024版） ; ; 农林核心（2020版）

摘要： Leaf adaxial-abaxial (ad-abaxial) polarity is crucial for leaf morphology and function, but the genetic machinery governing this process remains 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.

分类号：

  • 相关文献

[1]Multiple copies of eukaryotic translation initiation factors in Brassica rapa facilitate redundancy, enabling diversification through variation in splicing and broad-spectrum virus resistance. Nellist, Charlotte F.,Jenner, Carol E.,Moore, Jonathan D.,Barker, Guy C.,Walsh, John A.,Qian, Wei,Zhang, Shujiang,Wang, Xiaowu,Sun, Rifei,Briggs, William H.. 2014

[2]The impact of genorne triplication on tandem gene evolution in Brassica rapa. Fang, Lu,Cheng, Feng,Wu, Jian,Wang, Xiaowu. 2012

[3]AtTGA4, a bZIP transcription factor, confers drought resistance by enhancing nitrate transport and assimilation in Arabidopsis thaliana. Zhong, Li,Li, Weiwei,Xu, Zhaoshi,Zhou, Yongbin,Li, Liancheng,Chen, Ming,Ma, Youzhi,Zhong, Li,Chen, Dandan,Min, Donghong.

[4]Protein-DNA interactions in the promoter region of the gene encoding diapause hormone and pheromone biosynthesis activating neuropeptide of the cotton bollworm, Helicoverpa armigera. Hong, B,Zhang, ZF,Tang, SM,Yi, YZ,Zhang, TY,Xu, WH.

[5]Production and characterization of intertribal somatic hybrids of Raphanus sativus and Brassica rapa with dye and medicinal plant Isatis indigotica. Tu, Yuqin,Sun, Jian,Liu, Yan,Ge, Xianhong,Zhao, Zhigang,Yao, Xingcheng,Li, Zaiyun,Sun, Jian. 2008

[6]Carotenoid biosynthetic genes in Brassica rapa: comparative genomic analysis, phylogenetic analysis, and expression profiling. Li, Peirong,Zhang, Shujiang,Zhang, Shifan,Li, Fei,Zhang, Hui,Cheng, Feng,Wu, Jian,Wang, Xiaowu,Sun, Rifei. 2015

[7]Regulation of bolting and identification of the alpha-tubulin gene family in Brassica rapa L. ssp pekinensis. Zhang, Y. W.,Jin, D.,Xu, C.,Zhang, L.,Guo, M. H.,Zhang, Y. W.,Fang, Z. Y.. 2016

[8]Development of gene-based markers for the Turnip mosaic virus resistance gene retr02 in Brassica rapa. Li, Guo-Liang,Qian, Wei,Zhang, Shu-Jiang,Zhang, Shi-Fan,Li, Fei,Zhang, Hui,Wu, Jian,Wang, Xiao-Wu,Sun, Ri-Fei.

[9]Chromosome elimination, addition and introgression in intertribal partial hybrids between Brassica rapa and Isatis indigotica. Tu, Yuqin,Sun, Jian,Ge, Xianhong,Li, Zaiyun,Sun, Jian.

[10]Design of a Brassica rapa core collection for association mapping studies. Zhao, Jianjun,Del Carpio, Dunia Pino,Basnet, Ram Kumar,Zhang, Ningwen,Li, Fei,Bucher, Johan,Visser, Richard G. F.,Bonnema, Guusje,Zhao, Jianjun,Artemyeva, Anna,Gao, Jie,Li, Fei,Wang, Xiaowu.

[11]IDENTITIES AND RELATIONSHIPS AMONG CHINESE VEGETABLE BRASSICAS AS DETERMINED BY RANDOM AMPLIFIED POLYMORPHIC DNA MARKERS. REN, JP,MCFERSON, JR,LI, RG,KRESOVICH, S,LAMBOY, WF.

[12]Genetic Diversity of European and Chinese Oilseed Brassica rapa Cultivars from Different Breeding Periods. Zhao Yong-guo,Lu Chang-ming,Zhao Yong-guo,Zhao Yong-guo,Atta, Ofori. 2009

[13]Three genes encoding AOP2, a protein involved in aliphatic glucosinolate biosynthesis, are differentially expressed in Brassica rapa. Zhang, Jifang,Liu, Zhiyuan,Liang, Jianli,Wu, Jian,Cheng, Feng,Wang, Xiaowu.

[14]Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa. Cheng, Feng,Sun, Chao,Wu, Jian,Liang, Jianli,Cai, Chengcheng,Wang, Xiaowu,Schnable, James,Woodhouse, Margaret R.,Freeling, Michael.

[15]Anthocyanin profile characterization and quantitative trait locus mapping in zicaitai (Brassica rapa L. ssp chinensis var. purpurea). Guo, Ning,Wu, Jian,Zheng, Shuning,Cheng, Feng,Liu, Bo,Liang, Jianli,Cui, Yang,Wang, Xiaowu.

[16]The Brassica rapa FLC homologue FLC2 is a key regulator of flowering time, identified through transcriptional co-expression networks. Xiao, Dong,Zhao, Jian J.,Basnet, Ram K.,Zhang, Ning W.,Bucher, Johan,Lin, Ke,Bonnema, Guusje,Xiao, Dong,Hou, Xi L.,Zhao, Jian J.,Basnet, Ram K.,Bonnema, Guusje,Carpio, Dunia P. D.,Cheng, Feng,Wang, Xiao W.,Bonnema, Guusje. 2013

[17]Expression profiling reveals functionally redundant multiple-copy genes related to zinc, iron and cadmium responses in Brassica rapa. Li, Jimeng,Liu, Bo,Cheng, Feng,Wang, Xiaowu,Wu, Jian,Li, Jimeng,Aarts, Mark G. M..

[18]Characterization of FAE1 in the zero erucic acid germplasm of Brassica rapa L.. Yan, Guixin,Li, Dan,Cai, Mengxian,Gao, Guizhen,Chen, Biyun,Xu, Kun,Li, Jun,Li, Feng,Wang, Nian,Qiao, Jiangwei,Li, Hao,Zhang, Tianyao,Wu, Xiaoming.

[19]Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa. Tong, Chaobo,Yu, Jingyin,Huang, Junyan,Dong, Caihua,Hua, Wei,Liu, Shengyi,Wang, Xiaowu,Wu, Jian,Li, Wanshun. 2013

[20]The Fate of Arabidopsis thaliana Homeologous CNSs and Their Motifs in the Paleohexaploid Brassica rapa. Subramaniam, Sabarinath,Freeling, Michael,Wang, Xiaowu,Pires, J. Chris. 2013

作者其他论文 更多>>