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

摘要/Abstract

摘要：

【背景】苹果分枝数量的多少对于树体适应环境、生长生存、竞争资源都具有十分重要的作用。在实际生产过程中，多分枝的苹果品种更能满足整形修剪的需求，其不仅有利于果农因地制宜适时调整树体结构，塑造便于机械化采收的树形；而且对于调整结果枝均匀分布、保证结果量和果实品质都至关重要。【目的】本研究拟通过对同一发育时期的多分枝品种‘华星’和少分枝品种‘华硕’的顶芽、侧芽分别进行转录组测序，挖掘影响苹果分枝能力的关键基因，解析候选基因通过介导激素通路调控苹果分枝能力的潜在机理，为提高苹果分枝能力及产量提供理论依据。【方法】分别对‘华硕’和‘华星’的侧芽及顶芽进行转录组测序，通过差异表达基因（DEG）分析并借助加权基因共表达网络分析（weighted gene co-expression network analysis，WGCNA）等生物信息学手段，筛选引起分枝数量差异的核心候选基因，并通过在拟南芥中异源过表达候选基因对筛选结果准确性进行验证。【结果】在‘华硕’和‘华星’的顶芽之间比对共得到2 920个差异表达基因，而‘华硕’和‘华星’侧芽间比较共筛选到5 127个差异表达基因。DEGs主要富集在植物激素信号传导通路中，生长素信号通路和独脚金内酯信号通路与苹果分枝能力关系最密切，相关编码MdIAA3、MAX2、TCP、JAZ等家族的基因在两个品种侧芽间的差异十分显著。编码CYC（cyclins）、CDK（cyclin-dependent kinase）、EXPA（expansin）等细胞周期、细胞壁修饰相关基因家族的DEGs也与苹果分枝能力呈正相关。进一步通过WGCNA分析得到候选基因CAD、EXPA、CYC、JAZ、SAUR的互作网络关系，这些基因可能在苹果分枝能力的调控过程中具有一定作用。对MdIAA3异源转化拟南芥后，发现MdIAA3明显增加了拟南芥长势、结荚数、分枝数。【结论】通过转录组分析，筛选到13个调控基因可作为苹果分枝能力控制的潜在基因，MdIAA3在拟南芥中异位表达，明显促进了植株长势和分枝能力；苹果分枝能力的调控主要涉及细胞的分化与发育，细胞壁修饰，生长素、独脚金内酯信号传导等过程。

关键词: 苹果, 分枝能力, 转录组分析, KEGG, 植物激素, MdIAA3

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

张海青, 张恒涛, 高启明, 姚家龙, 王亚荣, 刘珍珍, 孟祥鹏, 周喆, 阎振立. 转录组分析筛选调控苹果分枝能力的关键基因[J]. 中国农业科学, 2024, 57(10): 1995-2009.

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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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