Transcriptome Analysis for Screening Key Genes Related to Regulating Branching Ability in Apple
[Background]The number of branches on an apple tree plays a pivotal role in its environmental adaptability,growth,survival,and resource competition.In production practice,the apple cultivars with more branches can better meet the needs of pruning and shaping,not only do they facilitate timely adjustments to the tree's structure based on local conditions,but also they ensure a uniform distribution of fruit-bearing branches,thereby guaranteeing both fruit quantity and quality.[Objective]In this study,by using the top buds and lateral buds of more-branched cultivar Huaxing and fewer-branched cultivar Huashuo at the same developmental stage,the transcriptome sequencing was carried out to identify key genes regulating the ability of branching,as well as to elucidate the potential mechanism underlying branching phenotype,and finally to provide the theoretical basis for improving the branching ability and yield of apple.[Method]The lateral and terminal buds of Huashuo and Huaxing were sampled for RNA-seq.By differential expressed gene(DEG)and analysis and weighted gene co-expression network(WGCNA)analysis,the core candidate genes that were responsible for branch number difference were identified and further demonstrated their function by Arabidopsis transformation.[Result]A total of 2 920 DEGs were identified from the comparison between the terminal buds,while 5 127 DEGs were screened out from the comparison between the lateral buds.DEGs were mainly enriched in phytohormone signaling pathway.Notably,the auxin signaling pathway,and strigolactone signaling pathway seemed to have the closest connection with the branching ability of apple with the related genes encoding MdIAA3,MAX2,TCP,and JAZ,which showed significant differences between lateral buds.Furthermore,DEGs annotated to cell cycle and cell wall modification families,such as CYC(Cyclins),CDK(Cyclin-dependent kinase),and EXPA(Expansin),also demonstrated a positive correlation with apple branching ability.In addition,those candidate genes obtained from WGCNA analysis also showed high possibility of getting involved in branch number regulation.Heterologous transformation of Arabidopsis with MdIAA3 could significantly enhance the overall growth,increased pod number and branching number of Arabidopsis.[Conclusion]Through comprehensive research,13 candidate regulatory genes were identified that potentially played a crucial role in transcriptional regulation for branch number.MdIAA3 was ectopically expressed in Arabidopsis,which significantly promoted plant growth and branching ability.It was plausible that these genes regulated branching through processes,such as cell differentiation and development,cell wall modification,auxin,and strigolactone signaling pathway.
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