Skip to main content
ARS Home » Northeast Area » Geneva, New York » Grape Genetics Research Unit (GGRU) » Research » Publications at this Location » Publication #328652
Title: Comparative RNA-Seq profiling of berry development between table grape ‘Kyoho’ and its early-ripening mutant ’Fengzao’

Author
item GUO, DA-LONG - Henan Institute Of Science And Technology
item XI, FEI-FEI - Henan Institute Of Science And Technology
item YU, YI-HE - Henan Institute Of Science And Technology
item ZHANG, XIAO-YU - Henan Institute Of Science And Technology
item ZHANG, GUO=HAI - Henan Institute Of Science And Technology
item Zhong, Gan-Yuan

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/20/2016
Publication Date: 11/5/2016
Citation: Guo, D., Xi, F., Yu, Y., Zhang, X., Zhang, G., Zhong, G. 2016. Comparative RNA-Seq profiling of berry development between table grape ‘Kyoho’ and its early-ripening mutant ’Fengzao’. BMC Genomics. 17(1):795. doi:10/1186/s12864-016-3051-1.

Interpretive Summary: Early ripening is an important attribute for many fruit species. ‘Kyoho’ is a popular table grape cultivar grown in many Asian countries. ‘Fengzao’ is a bud sport of ‘Kyoho’ and ripens nearly 30 days earlier than ‘Kyoho’. To identify genes controlling early fruit development and ripening in ‘Fengzao’, mRNA profiles of the two cultivars were compared at 8 different berry developmental stages in both berry peel and flesh tissues. As expected, certain genes showed differential expression levels and patterns in ‘Fengzao’ compared with ‘Kyoho’. Further analysis suggested that stress- and pathogen-responsive genes might play critical roles in and/or significantly respond to the early ripening of ‘Fengzao’. Some genes responsible for cell wall degradation and plasma membrane might be involved as well.

Technical Abstract: About 447 millions of RNA-Seq sequences were generated from 40 RNA libraries covering 8 different berry developmental stages of table grape ‘Kyoho’ and its early ripening bud mutant ‘Fengzao’. 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 expressed only in ‘Fengzao’ or ‘Kyoho’. In addition, several dozen genes 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) which showed overall lower expression level in ‘Fengzao’ than ‘Kyoho’ in both peel and flesh tissues except at the véraison stage. 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 in both peel and flesh tissues. Gene Ontology functional category and KEGG enrichment analyses of differentially expressed genes indicated that gene activities related to ROS and pathogenesis were altered between the two cultivars in both flesh and peel tissues. Several differentially expressed genes were validated using qRT-PCR. The discovery of a relatively small number of key genes underlying the ripening difference in the wild and mutant types provides valuable targets in future studies of the genetic control of early fruit ripening in grapes.