Guo Da-Long, Xi Fei-Fei, Yu Yi-He, Zhang Xiao-Yu, Zhang Guo-Hai, Zhong Gan-Yuan
College of Forestry, Henan University of Science and Technology, Luoyang, 471003, Henan Province, China.
USDA-Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY, 14456, USA.
BMC Genomics. 2016 Oct 12;17(1):795. doi: 10.1186/s12864-016-3051-1.
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'.
早熟是水果作物的一个重要优良特性。“巨峰”是许多亚洲国家广受欢迎的鲜食葡萄品种。“丰早”是“巨峰”的芽变品种，比“巨峰”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，在两个品种的浆果果皮和果肉组织的8个不同发育阶段比较了RNA测序图谱。
使用Illumina HiSeq系统获得“巨峰”和“丰早”浆果发育的RNA测序图谱，并采用多种统计方法进行分析。使用qRT-PCR验证了几个选定基因的表达模式。
从40个RNA文库中生成了约4.47亿条RNA测序序列，这些文库涵盖了“丰早”和“巨峰”不同的浆果发育阶段。这些序列分别映射到果肉和果皮组织中的23178个和22982个基因。虽然“丰早”和“巨峰”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，但有许多基因仅在“丰早”或“巨峰”中表达。当比较“丰早”和“巨峰”的平均表达时，我们观察到果肉组织中有10个基因，果皮组织中有22个基因在FDR≤0.05时差异表达。最显著的一个是VIT_214s0030g00950（一种超氧化物歧化酶基因）。在各个浆果发育阶段，这个与活性氧相关的基因在“丰早”的果皮和果肉组织中的表达水平均低于“巨峰”，仅在转色期除外。VIT_200s0238g00060（类烟草花叶病毒抗性蛋白n）和VIT_213s0067g01100（类抗病蛋白at3g14460）是另外两个在两个品种的果皮和果肉组织中均差异表达的显著基因。对差异表达基因的GO功能分类和KEGG富集分析表明，两个品种在果肉和果皮组织中与胁迫和活性氧相关的基因活性均发生了改变。使用qRT-PCR成功验证了几个感兴趣的差异表达基因。
比较图谱分析揭示了几十个在“巨峰”及其早熟突变体“丰早”的发育浆果中差异表达的基因。对这些差异表达基因的进一步分析表明，与活性氧和发病机制相关的基因活性可能参与了“丰早”的早熟过程。
