Plant Molecular Biology

, Volume 96, Issue 4–5, pp 493–507 | Cite as

Genome-wide genetic variation and comparison of fruit-associated traits between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina)

  • Tian-Jia Liu
  • Yong-Ping Li
  • Jing-Jing Zhou
  • Chun-Gen Hu
  • Jin-Zhi Zhang


Key message

The comprehensive genetic variation of two citrus species were analyzed at genome and transcriptome level. A total of 1090 differentially expressed genes were found during fruit development by RNA-sequencing.


Fruit size (fruit equatorial diameter) and weight (fresh weight) are the two most important components determining yield and consumer acceptability for many horticultural crops. However, little is known about the genetic control of these traits. Here, we performed whole-genome resequencing to reveal the comprehensive genetic variation of the fruit development between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina). In total, 5,865,235 single-nucleotide polymorphisms (SNPs) and 414,447 insertions/deletions (InDels) were identified in the two citrus species. Based on integrative analysis of genome and transcriptome of fruit, 640,801 SNPs and 20,733 InDels were identified. The features, genomic distribution, functional effect, and other characteristics of these genetic variations were explored. RNA-sequencing identified 1090 differentially expressed genes (DEGs) during fruit development of kumquat and Clementine mandarin. Gene Ontology revealed that these genes were involved in various molecular functional and biological processes. In addition, the genetic variation of 939 DEGs and 74 multiple fruit development pathway genes from previous reports were also identified. A global survey identified 24,237 specific alternative splicing events in the two citrus species and showed that intron retention is the most prevalent pattern of alternative splicing. These genome variation data provide a foundation for further exploration of citrus diversity and gene–phenotype relationships and for future research on molecular breeding to improve kumquat, Clementine mandarin and related species.


Alternative splicing events Citrus Genome resequencing Genetic variation InDels SNPs 



This research was supported by the National Natural Science Foundation of China (Grant Nos. 31471863, 31372046, 31672110 and 31772252).

Author Contributions

JJZ, CGH, JZZ conceived the research plan and supervised the experiments, TJL and YPL performed the experiments and analyzed the data, JJZ and JZZ drafted the manuscript. All authors read and approved the final manuscript.

Supplementary material

11103_2018_712_MOESM1_ESM.jpg (2.5 mb)
Figure S1. The average fruit size and weight of Clementine mandarin and kumquat at maturity. (JPG 2577 KB)
11103_2018_712_MOESM2_ESM.jpg (1.1 mb)
Figure S2. Evolutionary comparisons of Clementine mandarin and kumquat with other citrus genomes. The resequencing data of some citrus from a previous study (Wu et al. 2014), including sour orange (SRX372786), sweet orange (SRX372703), low-acid pumelo (SRX372702), Chandler pumelo (SRX372688), Willowleaf mandarin (SRX372685), W. Murcott mandarin (SRX372687), Ponkan mandarin (SRX372665), and Clementine mandarin (SRX371962). The SNPhylo software package was used with the SNP data set from these species to generate a maximum-likelihood phylogenetic tree with default parameters. Blue indicates the citrus species in this study. (JPG 1164 KB)
11103_2018_712_MOESM3_ESM.jpg (3.1 mb)
Figure S3. Landscape of the genome variation of Clementine mandarin vs. kumquat. (JPG 3196 KB)
11103_2018_712_MOESM4_ESM.jpg (897 kb)
Figure S4.The expression pattern of fruit-development-related genes from previous reports were investigated by real-time PCR. Relative transcript levels are calculated by real-time PCR with β-actin as the standard. Data are means ± SE of four separate measurements. (JPG 897 KB)
11103_2018_712_MOESM5_ESM.jpg (170 kb)
Figure S5. The alternative splicing pattern of three selected genes at different developmental stages of Clementine mandarin and kumquat. (JPG 169 KB)
11103_2018_712_MOESM6_ESM.xlsx (2.8 mb)
Supplementary material 6 (XLSX 2831 KB)


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© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  1. 1.Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry ScienceHuazhong Agricultural UniversityWuhanChina

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