Resequencing and transcriptomic analysis reveal differences in nitrite reductase in jujube fruit (Ziziphus jujuba Mill.)

Na Li,Liulin Li,Yuqin Song,Jie Li,Xinxin Feng,Ruijie Hao

doi:10.1186/s13007-021-00776-9

Abstract

BackgroundJujube is a typical fruit tree species from China. ‘Muzao’, a cracking-susceptible cultivar, and ‘Linhuang No. 1’, a cracking-resistant cultivar, were selected in a previous study as contrasting research materials. Whole-genome resequencing and transcriptomic analysis of ‘Linhuang No. 1’ and ‘Muzao’ allowed the identification of differentially expressed genes with different gene structures between the two cultivars and could be helpful in explaining the differences and similarities between the two cultivars.ResultsResequencing identified 664,129 polymorphic variable sites between ‘Linhuang No. 1’ and ‘Muzao’. To determine the genetic relationship among ‘Linhuang No. 1’, ‘Muzao’ and the jujube genome reference cultivar ‘Dongzao’, the characteristic polymorphic variable sites were analysed by principal component analysis. The genetic relationship between ‘Linhuang No. 1’ and ‘Muzao’ was closer than that of either variety and ‘Dongzao’. Nineteen differentially expressed genes were identified by combining transcriptomic analysis with resequencing analysis. LOC107427052 (encoding a nitrite reductase) was identified by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis for further study. The identified insertion was not in the domain region of the LOC107427052 gene coding sequence (CDS) region and was verified by the finding that the insertion did not affect translation of the protein. The LOC107427052 gene expression levels, nitrite reductase activities and nitrite contents of ‘Muzao’ were significantly higher than the corresponding values of ‘Linhuang No. 1’ at the young fruit stage. There was no significant difference in the quantity of the product of nitrite reductase, namely, ammonia, between the two cultivars.ConclusionsThe present study was the first to explore the differences between different jujube cultivars (‘Linhuang No. 1’ and ‘Muzao’) by combining genome resequencing and transcriptomics. LOC107427052 (encoding a nitrite reductase) was characterized by KEGG enrichment analysis. The insertion in the CDS region of the LOC107427052 gene provides a new direction for the study of nitrogen metabolism in jujube. Our study has laid a foundation for the comparative analysis of nitrite metabolism between the jujube cultivars ‘Linhuang No. 1’ and ‘Muzao’.

Highlights

Jujube is a typical fruit tree species from China [1]
The results showed that there was no significant difference in the nitrite reductase activities between ‘Linhuang No 1’ and ‘Muzao’ at the later stage of fruit development; the nitrite reductase activities of ‘Linhuang No 1’ and ‘Muzao’ were 0.75 U/g fresh weight (FW) and 0.93 U/g FW (p < 0.05) at the fullred stage, respectively
The present study was the first to explore the differences between different jujube cultivars (‘Linhuang No 1’ and ‘Muzao’) by combining genome resequencing and transcriptomics

Summary

Introduction

Jujube is a typical fruit tree species from China [1]. Jujube is valued as a traditional herbal medicine as well as a popular fruit, eaten fresh or dried, and is cultivated on 2 million hectares in China alone, with an annual production of approximately 7.36 million tons in 2018 (https://data.stats.gov.cn/easyquery.htm?cn=E0103).Jujube cv. ‘Muzao’ is one of the most widely cultivated jujube. Due to the wide cultivation area of the jujube tree crop (Ziziphus jujuba Mill.), there are many varieties and geographical types of jujube, each varying in terms of fruit shape, individual fruit weight, drying rate, nutrient composition and fruit characteristics [3]. ‘Linhuang No 1’ is a dry jujube cultivar selected from ‘Muzao’ that has fruit characteristics similar to those of ‘Muzao’. Compared with ‘Muzao’, ‘Linhuang No 1’ shows greater resistance to fruit cracking [4]. ‘Linhuang No 1’ has become a valuable genotype for scientific research into the mechanism of fruit cracking. Jujube is a typical fruit tree species from China. ‘Muzao’, a cracking-susceptible cultivar, and ‘Linhuang No 1’, a cracking-resistant cultivar, were selected in a previous study as contrasting research materials. Whole-genome resequencing and transcriptomic analysis of ‘Linhuang No 1’ and ‘Muzao’ allowed the identification of differentially expressed genes with different gene structures between the two cultivars and could be helpful in explaining the differences and similarities between the two cultivars

Methods

Results

Discussion

Conclusion