转录组分析筛选调控苹果分枝能力的关键基因

doi:10.3864/j.issn.0578-1752.2024.10.011

Abstract

Abstract:

【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.

Key words: apple, branching ability, transcriptome analysis, KEGG, plant hormone, MdIAA3

ZHANG HaiQing, ZHANG HengTao, GAO QiMing, YAO JiaLong, WANG YaRong, LIU ZhenZhen, MENG XiangPeng, ZHOU Zhe, YAN ZhenLi. Transcriptome Analysis for Screening Key Genes Related to Regulating Branching Ability in Apple[J].Scientia Agricultura Sinica, 2024, 57(10): 1995-2009.

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References 60

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样本 Sample	原始序列数据 Raw reads	过滤后数据 Clean reads	比对到基因组 Total map	碱基质量值 Q20 (%)	碱基质量值 Q30 (%)	GC占比 GC (%)
HSD1	46230010	45481100	40805210(89.72%)	96.07	89.95	45.42
HSD2	47417824	46744010	42366223(90.63%)	96.57	90.97	46.07
HSD3	50614470	49588586	44958745(90.66%)	96.64	91.07	46.12
HSC1	41885282	40719076	36228477(88.97%)	96.07	90.07	46.07
HSC2	45343404	44619430	40058699(89.78%)	96.72	91.30	45.85
HSC3	41242840	40301052	36008246(89.35%)	96.45	90.78	45.93
HXD1	46239534	45644466	41374789(90.65%)	95.94	89.81	46.15
HXD2	46475308	45429544	41069245(90.40%)	96.46	90.81	46.43
HXD3	45253168	44460432	40627835(91.38%)	96.88	91.66	46.50
HXC1	42828110	42435144	38346254(90.36%)	96.29	90.44	45.92
HXC2	46425522	45877734	41220790(89.85%)	95.96	89.79	45.53
HXC3	46221574	45743482	41406160(90.52%)	96.67	91.20	45.61

Transcriptome Analysis for Screening Key Genes Related to Regulating Branching Ability in Apple

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