Advertisement

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
Article
  • 430 Downloads

Abstract

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.

Abstract

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.

Keywords

Alternative splicing events Citrus Genome resequencing Genetic variation InDels SNPs 

Notes

Acknowledgements

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)

References

  1. Alpert K, Grandillo S, Tanksley S (1995) fw 2.2: a major QTL controlling fruit weight is common to both red-and green-fruited tomato species. Theor Appl Genet 91:994–1000PubMedGoogle Scholar
  2. Azzi L, Deluche C, Gevaudant F, Frangne N, Delmas F, Hernould M, Chevalier C (2015) Fruit growth-related genes in tomato. J Exp Bot 66:1075–1086CrossRefPubMedGoogle Scholar
  3. Bai H, Cao Y, Quan J, Dong L, Li Z, Zhu Y, Zhu L, Dong Z, Li D (2013) Identifying the genome-wide sequence variations and developing new molecular markers for genetics research by re-sequencing a landrace cultivar of Foxtail Millet. PLoS ONE 8:e73514CrossRefPubMedPubMedCentralGoogle Scholar
  4. Barchi L, Lanteri S, Portis E, Acquadro A, Valè G, Toppino L, Rotino GL (2011) Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genom 12:304CrossRefGoogle Scholar
  5. Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A (2010) Manipulation of FASTQ data with galaxy. Bioinformatics 26:1783–1785CrossRefPubMedPubMedCentralGoogle Scholar
  6. Brunner AM, Nilsson O (2004) Revisiting tree maturation and floral initiation in the poplar functional genomics era. New Phytol 164:43–51CrossRefGoogle Scholar
  7. Cao K, Zheng ZJ, Wang LR, Liu X, Zhu GR, Fang WC, Cheng SF, Zeng P, Chen CW, Wang XW, Xie M, Zhong X, Wang XL, Zhao P, Bian C, Zhu YL, Zhang JH, Ma GS, Chen CX, Li YJ, Hao FG, Li Y, Huang GD, Li YX, Li HY, Guo J, Xu X, Wang J (2014) Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops. Genome Biol 15:415PubMedPubMedCentralGoogle Scholar
  8. Cheng Y-J, Guo W-W, Yi H-L, Pang X-M, Deng X (2003) An efficient protocol for genomic DNA extraction from Citrus species. Plant Mol Biol Reporter 21:177–178CrossRefGoogle Scholar
  9. Choi H-S (2005) Characteristic odor components of kumquat (Fortunella japonica Swingle) peel oil. J Agric Food Chem 53:1642–1647CrossRefPubMedGoogle Scholar
  10. Choi Y, Sims GE, Murphy S, Miller JR, Chan AP (2012) Predicting the functional effect of amino acid substitutions and indels. PLoS ONE 7:e46688CrossRefPubMedPubMedCentralGoogle Scholar
  11. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu XY, Ruden DM (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w(1118); iso-2; iso-3. Fly 6:80–92CrossRefPubMedPubMedCentralGoogle Scholar
  12. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676CrossRefPubMedGoogle Scholar
  13. Cong B, Liu J, Tanksley SD (2002) Natural alleles at a tomato fruit size quantitative trait locus differ by heterochronic regulatory mutations. Proc Natl Acad Sci USA 99:13606–13611CrossRefPubMedPubMedCentralGoogle Scholar
  14. Cuenca J, Aleza P, Garcia-Lor A, Ollitrault P, Navarro L (2016) Fine mapping for identification of citrus alternaria brown spot candidate resistance genes and development of new SNP markers for marker-assisted selection. Front Plant Sci 7:1948PubMedPubMedCentralGoogle Scholar
  15. Datta S, Datta S, Kim S, Chakraborty S, Gill RS (2010) Statistical analyses of next generation sequence data: a partial overview. J Proteomics Bioinform 3:183CrossRefPubMedPubMedCentralGoogle Scholar
  16. De FP, Stegmeir T, Cabrera A, Van Der Knapp E, Rosyara UR, Sebolt AM, Dondini L, Dirlewanger E, Querogarcia J, Campoy JA (2013) Cell number regulator genes in Prunus provide candidate genes for the control of fruit size in sweet and sour cherry. Mol Breeding 32:311–326CrossRefGoogle Scholar
  17. Deikman J, Fischer RL (1988) Interaction of a DNA binding factor with the 5′-flanking region of an ethylene-responsive fruit ripening gene from tomato. EMBO J 7:3315–3320PubMedPubMedCentralGoogle Scholar
  18. Foissac S, Sammeth M (2007) ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Res 35:W297–W299CrossRefGoogle Scholar
  19. Gillaspy G, Bendavid H, Gruissem W (1993) Fruits: a developmental perspective. Plant Cell 5:1439–1451CrossRefPubMedPubMedCentralGoogle Scholar
  20. Giovannoni JJ (2004) Genetic regulation of fruit development and ripening. Plant Cell 16:S170–S180CrossRefGoogle Scholar
  21. Grandillo S, Ku HM, Tanksley SD (1999) Identifying the loci responsible for natural variation in fruit size and shape in tomato. Theor Appl Genet 99:978–987CrossRefGoogle Scholar
  22. Hirakawa H, Shirasawa K, Ohyama A, Fukuoka H, Aoki K, Rothan C, Sato S, Isobe S, Tabata S (2013) Genome-wide SNP genotyping to infer the effects on gene functions in tomato. DNA Res 20:221–233CrossRefPubMedPubMedCentralGoogle Scholar
  23. Jain M, Moharana KC, Shankar R, Kumari R, Garg R (2014) Genomewide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance. Plant Biotechnol J 12:253–264CrossRefPubMedGoogle Scholar
  24. Jiao WB, Huang D, Xing F, Hu YB, Deng XX, Xu Q, Chen LL (2013) Genome-wide characterization and expression analysis of genetic variants in sweet orange. Plant J 75:954–964CrossRefPubMedGoogle Scholar
  25. Jones AM, Im K-H, Savka MA, Wu M-J, DeWitt NG, Shillito R, Binns AN (1998) Auxin-dependent cell expansion mediated by overexpressed auxin-binding protein 1. Science 282:1114–1117CrossRefPubMedGoogle Scholar
  26. Khan MRG, Ai XY, Zhang JZ (2013) Genetic regulation of flowering time in annual and perennial plants. Wiley Interdisc Rev 5:347–359CrossRefGoogle Scholar
  27. Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360CrossRefPubMedPubMedCentralGoogle Scholar
  28. Kobayashi M, Nagasaki H, Garcia V, Just D, Bres C, Mauxion J-P, Le Paslier M-C, Brunel D, Suda K, Minakuchi Y (2013) Genome-wide analysis of intraspecific DNA polymorphism in ‘Micro-Tom’, a model cultivar of tomato (Solanum lycopersicum). Plant Cell Physiol 55:445–454CrossRefPubMedGoogle Scholar
  29. Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER (2013) The next-generation sequencing revolution and its impact on genomics. Cell 155:27–38CrossRefPubMedPubMedCentralGoogle Scholar
  30. Koyasako A, Bernhard R (1983) Volatile constituents of the essential oil of kumquat. J Food Sci 48:1807–1812CrossRefGoogle Scholar
  31. Krizek BA (1999) Ectopic expression of AINTEGUMENTA in Arabidopsis plants results in increased growth of floral organs. Dev Genet 25:224–236CrossRefPubMedGoogle Scholar
  32. Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26:589–595CrossRefPubMedPubMedCentralGoogle Scholar
  33. Li S-B, Xie Z-Z, Hu C-G, Zhang J-Z (2016) A review of auxin response factors (ARFs) in plants. Front Plant Sci 7:47PubMedPubMedCentralGoogle Scholar
  34. Lijavetzky D, Cabezas JA, Ibáñez A, Rodríguez V, Martínez-Zapater JM (2007) High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology. BMC Genomics 8:424CrossRefPubMedPubMedCentralGoogle Scholar
  35. Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550CrossRefPubMedPubMedCentralGoogle Scholar
  36. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303CrossRefPubMedPubMedCentralGoogle Scholar
  37. Mizukami Y, Fischer RL (2000) Plant organ size control: AINTEGUMENTA regulates growth and cell numbers during organogenesis. Proc Natl Acad Sci USA 97:942–947CrossRefPubMedPubMedCentralGoogle Scholar
  38. Monforte AJ, Diaz A, Caño-Delgado A, Van Der Knapp E (2014) The genetic basis of fruit morphology in horticultural crops: lessons from tomato and melon. J Exp Bot 65:4625–4637CrossRefPubMedGoogle Scholar
  39. Montanari S, Saeed M, Knabel M, Kim Y, Troggio M, Malnoy M, Velasco R, Fontana P, Won K, Durel CE, Perchepied L, Schaffer R, Wiedow C, Bus V, Brewer L, Gardiner SE, Crowhurst RN, Chagne D (2013) Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in european pear and interspecific Pyrus hybrids. PLoS ONE 8:e77022CrossRefPubMedPubMedCentralGoogle Scholar
  40. Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, Krabichler B, Speicher MR, Zschocke J, Trajanoski Z (2013) A survey of tools for variant analysis of next-generation genome sequencing data. Briefings Bioinform 15:256–278CrossRefGoogle Scholar
  41. Paran I, Knaap EVD (2007) Genetic and molecular regulation of fruit and plant domestication traits in tomato and pepper. J Exp Bot 58:3841–3152CrossRefPubMedGoogle Scholar
  42. Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol 33:290–295CrossRefPubMedPubMedCentralGoogle Scholar
  43. Ren Y, Zhao H, Kou Q, Jiang J, Guo S, Zhang H, Hou W, Zou X, Sun H, Gong G (2012) A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome. PLoS ONE 7:e29453CrossRefPubMedPubMedCentralGoogle Scholar
  44. Schoof H, Lenhard M, Haecker A, Mayer KF, Jürgens G, Laux T (2000) The stem cell population of Arabidopsis shoot meristems in maintained by a regulatory loop between the CLAVATA and WUSCHEL genes. Cell 100:635–644CrossRefPubMedGoogle Scholar
  45. Schuster SC (2007) Next-generation sequencing transforms today’s biology. Nature 5:16–18Google Scholar
  46. Shen S, Park JW, Lu Z-x, Lin L, Henry MD, Wu YN, Zhou Q, Xing Y (2014) rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci 111:E5593–E5601Google Scholar
  47. Stower H (2013) Population genomics: characterizing indels. Nat Rev Genet 14:302–302Google Scholar
  48. Sun L, Zhang Q, Xu Z, Yang W, Guo Y, Lu J, Pan H, Cheng T, Cai M (2013) Genome-wide DNA polymorphisms in two cultivars of mei (Prunus mume sieb. et zucc.). BMC Genet 14:98CrossRefPubMedPubMedCentralGoogle Scholar
  49. Tan FC, Swain SM (2006) Genetics of flower initiation and development in annual and perennial plants. Physiol Plant 128:8–17CrossRefGoogle Scholar
  50. Tan FC, Swain SM (2007) Functional characterization of AP3, SOC1 and WUS homologues from citrus (Citrus sinensis). Physiol Plant 131:481–495CrossRefPubMedGoogle Scholar
  51. Tanksley SD (2004) The genetic, developmental, and molecular bases of fruit size and shape variation in tomato. Plant Cell 16:S181–S189CrossRefGoogle Scholar
  52. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protocols 7:562–578CrossRefPubMedGoogle Scholar
  53. Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, Ruiz M, Scalabrin S, Terol J, Takita MA, Labadie K, Poulain J, Couloux A, Jabbari K, Cattonaro F, Del Fabbro C, Pinosio S, Zuccolo A, Chapman J, Grimwood J, Tadeo FR, Estornell LH, Munoz-Sanz JV, Ibanez V, Herrero-Ortega A, Aleza P, Perez-Perez J, Ramon D, Brunel D, Luro F, Chen CX, Farmerie WG, Desany B, Kodira C, Mohiuddin M, Harkins T, Fredrikson K, Burns P, Lomsadze A, Borodovsky M, Reforgiato G, Freitas-Astua J, Quetier F, Navarro L, Roose M, Wincker P, Schmutz J, Morgante M, Machado MA, Talon M, Jaillon O, Ollitrault P, Gmitter F, Rokhsar D (2014) Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol 32:656–662CrossRefPubMedPubMedCentralGoogle Scholar
  54. Xing L, Zhang D, Song X, Weng K, Shen Y, Li Y, Zhao C, Ma J, An N, Han M (2016) Genome-wide sequence variation identification and floral-associated trait comparisons based on the re-sequencing of the ‘Nagafu No. 2’ and ‘Qinguan’ varieties of apple (Malus domestica Borkh.). Front Plant Sci 7:908PubMedPubMedCentralGoogle Scholar
  55. Zeballos JL, Abidi W, Gimenez R, Monforte AJ, Moreno MA, Gogorcena Y (2016) Mapping QTLs associated with fruit quality traits in peach [Prunus persica (L.) Batsch] using SNP maps. Tree Genet Genomes 12:37CrossRefGoogle Scholar
  56. Zhang JZ, Li ZM, Yao JL, Hu CG (2009) Identification of flowering-related genes between early flowering trifoliate orange mutant and wild-type trifoliate orange (Poncirus trifoliata L. Raf.) by suppression subtraction hybridization (SSH) and macroarray. Gene 430:95–104CrossRefPubMedGoogle Scholar
  57. Zhang G, Sebolt AM, Sooriyapathirana SS, Wang D, Bink MC, Olmstead JW, Iezzoni AF (2010) Fruit size QTL analysis of an F1 population derived from a cross between a domesticated sweet cherry cultivar and a wild forest sweet cherry. Tree Genet Genomes 6:25–36CrossRefGoogle Scholar
  58. Zhang JZ, Liu SR, Hu CG (2016) Identifying the genome-wide genetic variation between precocious trifoliate orange and its wild type and developing new markers for genetics research. DNA Res 23:403–414CrossRefPubMedPubMedCentralGoogle Scholar
  59. Zheng LY, Guo XS, He B, Sun LJ, Peng Y, Dong SS, Liu TF, Jiang SY, Ramachandran S, Liu CM, Jing HC (2011) Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol 12:R114CrossRefPubMedPubMedCentralGoogle Scholar
  60. Zou X, Shi C, Austin RS, Merico D, Munholland S, Marsolais F, Navabi A, Crosby WL, Pauls KP, Yu K (2013) Genome-wide single nucleotide polymorphism and insertion-deletion discovery through next-generation sequencing of reduced representation libraries in common bean. Mol Breed 33:769–778CrossRefGoogle Scholar

Copyright information

© 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

Personalised recommendations