Comparative RNA-Seq profiling of berry development between table grape 'Kyoho' and its early-ripening mutant 'Fengzao'.
Comparative RNA-Seq profiling of berry development between table grape 'Kyoho' and its early-ripening mutant 'Fengzao'.
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食用葡萄“巨峰”与其早熟突变体“丰早”浆果发育的比较 RNA 测序分析
DOI：
10.1186/s12864-016-3051-1
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发表时间：
2016-10-12
期刊：
影响因子：
4.4
通讯作者：
Zhong GY
中科院分区：
文献类型：
--
作者：
Guo DL;Xi FF;Yu YH;Zhang XY;Zhang GH;Zhong GY
早熟是水果作物一个重要的理想属性。“Kyoho”是许多亚洲国家流行的食用葡萄品种。‘凤藻’是‘京花’的芽突变体，比‘京花’早熟近30天。为了鉴定控制‘丰早’果实早期发育和成熟的基因，比较了两个品种在果实果皮和果肉组织8个不同发育阶段的RNA-Seq谱。使用Illumina HiSeq系统获得了‘Kyoho’和‘Fenzhao’之间浆果发育的RNA-Seq图谱，并使用各种统计方法进行了分析。使用qRT-PCR验证了几个选定基因的表达模式。从‘Fengzao’和‘Kyoho’不同浆果发育阶段的40个RNA文库中获得约4.47亿个RNA- seq序列。这些序列分别在果肉和果皮组织中定位到23,178和22,982个基因。虽然‘丰早’和‘Kyoho’中的大多数基因在不同的浆果发育阶段具有相似的表达模式，但也有许多基因仅在‘丰早’或‘Kyoho’中检测到表达。比较‘丰早’和‘京好’的平均表达量，我们发现肉组织中有10个基因和果皮组织中有22个基因在FDR≤0.05时存在差异表达。其中最引人注目的是VIT_214s0030g00950（一种超氧化物歧化酶基因）。该ROS相关基因在不同浆果发育阶段的果皮和果肉组织中的表达水平均低于‘Fengzao’，只有在vsamicraison中例外。VIT_200s0238g00060 （TMV抗性蛋白n-like）和VIT_213s0067g01100（抗病蛋白at3g14460-like）是两个品种在果皮和果肉组织中差异表达的另外两个值得注意的基因。GO功能分类和DEGs的KEGG富集分析表明，两个品种的果肉和果皮组织中与胁迫和ROS相关的基因活性发生了变化。使用qRT-PCR成功验证了几个感兴趣的差异表达基因。比较分析揭示了‘Kyoho’及其早熟突变体‘Fengzao’发育果实中存在几十个差异表达的基因。对这些差异表达基因的进一步分析表明，与ROS及其发病机制相关的基因活性可能参与了‘丰藻’早熟的形成。本文的在线版本（doi:10.1186/s12864-016-3051-1）包含补充材料，可供授权用户使用。
Early ripening is an important desirable attribute for fruit crops. ‘Kyoho’ is a popular table grape cultivar in many Asian countries. ‘Fengzao’ is a bud mutant of ‘Kyoho’ and ripens nearly 30 days earlier than ‘Kyoho’. To identify genes controlling early fruit development and ripening in ‘Fengzao’, RNA-Seq profiles of the two cultivars were compared at 8 different berry developmental stages in both berry peel and flesh tissues. RNA-Seq profiling of berry development between ‘Kyoho’ and ‘Fenzhao’ were obtained using the Illumina HiSeq system and analyzed using various statistical methods. Expression patterns of several selected genes were validated using qRT-PCR. About 447 millions of RNA-Seq sequences were generated from 40 RNA libraries covering various different berry developmental stages of ‘Fengzao’ and ‘Kyoho’. These sequences were mapped to 23,178 and 22,982 genes in the flesh and peel tissues, respectively. While most genes in ‘Fengzao’ and ‘Kyoho’ shared similar expression patterns over different berry developmental stages, there were many genes whose expression were detected only in ‘Fengzao’ or ‘Kyoho’. We observed 10 genes in flesh tissue and 22 genes in peel tissue were differentially expressed at FDR ≤ 0.05 when the mean expression of ‘Fengzao’ and ‘Kyoho’ were compared. The most noticeable one was VIT_214s0030g00950 (a superoxide dismutase gene). This ROS related gene showed lower expression levels in ‘Fengzao’ than ‘Kyoho’ in both peel and flesh tissues across various berry developmental stages with the only exception at véraison. VIT_200s0238g00060 (TMV resistance protein n-like) and VIT_213s0067g01100 (disease resistance protein at3g14460-like) were the two other noticeable genes which were found differentially expressed between the two cultivars in both peel and flesh tissues. GO functional category and KEGG enrichment analysis of DEGs indicated that gene activities related to stress and ROS were altered between the two cultivars in both flesh and peel tissues. Several differentially expressed genes of interest were successfully validated using qRT-PCR. Comparative profiling analysis revealed a few dozens of genes which were differentially expressed in the developing berries of ‘Kyoho’ and its early ripening mutant ‘Fengzao’. Further analysis of these differentially expressed genes suggested that gene activities related to ROS and pathogenesis were likely involved in contributing to the early ripening in ‘Fengzao’. The online version of this article (doi:10.1186/s12864-016-3051-1) contains supplementary material, which is available to authorized users.