Czech J. Genet. Plant Breed., 2017, 53(3):97-106 | DOI: 10.17221/43/2016-CJGPB

Comparative transcriptomic analysis reveals a series of single nucleotide polymorphism between red- and white-fleshed loquats (Eriobotrya japonica)Original Paper

Shuxia SUN1, 2, Jing LI1, 2, Dong CHEN1, 2, Hongjiang XIE1, 2, Meiyan TU1, 2, Liu JIA1, 2, Guoliang JIANG1, 2*
1 Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan Province, P.R. China
2 Southwestern Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement, Ministry of Agriculture, Chengdu, Sichuan Province, P.R. China

Loquat (Eriobotrya japonica) is an economically important crop and red-fleshed cultivars have a much higher carotenoid content than white-fleshed cultivars. We used Illumina RNA-seq technology to gain a global overview of the loquat transcriptome from a mixture of fruit samples at different developmental stages for both red-fleshed and white-fleshed loquat. A total of 94.98 million paired-end short reads were obtained and 61 586 unigenes were generated from de novo assembly with an average length of 817 bp. Among these unigenes, 44 710 unigenes were annotated by blast against Nr, Swissprot, GO, COG and KEGG databases. For these annotated unigenes, 123 biosynthesis pathways were predicted by mapping these unigenes to the reference canonical pathways and 41 unigenes were predicted to be involved in carotenoid biosynthesis. RT-qPCR analysis showed that the expression level of the LCYB gene was higher in red-fleshed loquat and the CRTRB gene had a higher expression level in white-fleshed loquat. Comparative analysis of the two transcriptomes revealed 2396 single nucleotide polymorphisms (SNPs) between red- and white-fleshed loquats. The majority of SNPs identified between the two loquat cultivars were nonsense mutations and one out of eleven SNPs in candidate genes involved in carotenoid biosynthesis was a sense mutation. This suggests that the analysis based on transcriptomes can reveal key genes related to the carotenoid biosynthesis and more carotene in red-fleshed loquat cultivars may result from both more carotene produced by the higher expression of LCYB genes and less carotene converted because of the low expression of the CRTRB gene. All these results from the transcriptome analysis will be useful for the elucidation of genetic differences between red- and white-fleshed loquat fruits and further functional analysis for genes responsible for carotenoid accumulation.

Keywords: carotenoid biosynthesis; expression analysis; SNP; transcriptome

Published: September 30, 2017  Show citation

ACS AIP APA ASA Harvard Chicago Chicago Notes IEEE ISO690 MLA NLM Turabian Vancouver
SUN S, Jing L, CHEN D, XIE H, Meiyan T, JIA L, JIANG G. Comparative transcriptomic analysis reveals a series of single nucleotide polymorphism between red- and white-fleshed loquats (Eriobotrya japonica). Czech J. Genet. Plant Breed. 2017;53(3):97-106. doi: 10.17221/43/2016-CJGPB.
Share...
Download citation
  • BibTeX (.bib)
  • Bookends (.ris)
  • EasyBib (.ris)
  • EndNote (.enw)
  • EndNote 8 (.xml)
  • ISI WoS (.isi)
  • Medlars (.medlars)
  • Mendeley (.ris)
  • MODS (.xml)
  • Papers (.ris)
  • RefWorks (.txt)
  • RefManager (.ris)
  • RIS (.ris)
  • MS Word (.xml)
  • Zotero (.ris)
    • Open full article

    Supplementary files:

    Download file43-2016 Chen Table S1.xlsx

    File size: 11.34 kB

    Download file43-2016 Chen Table S2.xlsx

    File size: 92.38 kB

    Download file43-2016 Chen Table S3.xlsx

    File size: 11.72 kB

    Download fileChen_Figure S1_ESM.pdf

    File size: 939.61 kB

    References

    1. Bertrand M. (2010): Carotenoid biosynthesis in diatoms. Photosynthesis Research, 106: 89-102. Go to original source... Go to PubMed...
    2. Fan H., Xiao Y., Yang Y., Xia W., Mason A.S., Xia Z., Qiao F., Zhao S., Tang H. (2013): RNA-Seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches. PLoS ONE, 8: e59997. Fu X., Feng C., Wang C., Yin X., Lu P., Grierson D., Xu C., Chen K. (2014): Involvement of multiple phytoene synthase genes in tissue- and cultivar-specific accumulation of carotenoids in loquat. Journal of Experimental Botany, 65: 4679-4689. Go to original source... Go to PubMed...
    3. Gomez-Garcia M., Ochoa-Alejo N. (2013): Biochemistry and molecular biology of carotenoid biosynthesis in chili peppers (Capsicum spp.). International Journal of Molecular Sciences, 14: 19025-19053. Go to original source... Go to PubMed...
    4. Gulledge A.A., Roberts A.D., Vora H., Patel K., Loraine A.E. (2012): Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a. American Journal of Botany, 99: 219-231. Go to original source... Go to PubMed...
    5. Gupta V., Estrada A.D., Blakley I., Reid R., Patel K., Meyer M.D., Andersen S.U., Brown A.F., Lila M.A., Loraine A.E. (2015): RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing. Gigascience, 4: 5. Go to original source... Go to PubMed...
    6. Haas B.J., Papanicolaou A., Yassour M., Grabherr M., Blood P.D., Bowden J., Couger M.B., Eccles D., Li B., Lieber M., Macmanes M.D., Ott M., Orvis J., Pochet N., Strozzi F., Weeks N., Westerman R., William T., Dewey C.N., Henschel R., Leduc R.D., Friedman N., Regev A. (2013): De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols, 8: 1494-1512. Go to original source... Go to PubMed...
    7. Hyun T.K., Lee S., Rim Y., Kumar R., Han X., Lee S.Y., Lee C.H., Kim J.Y. (2014): De-novo RNA sequencing and metabolite profiling to identify genes involved in anthocyanin biosynthesis in Korean black raspberry (Rubus coreanus Miquel). PLoS ONE, 9: e88292. Go to original source... Go to PubMed...
    8. Lei X., Xiao Y., Xia W., Mason A.S., Yang Y., Ma Z., Peng M. (2014): RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF) mediated gene expression pattern in Elaeis guineensis compared to other species. PLoS ONE, 9: e114482. Go to original source... Go to PubMed...
    9. Li X., Xu H., Feng J., Zhou X., Chen J. (2015): Mining of genic SNPs and diversity evaluation of landraces in loquat. Scientia Horticulturae, 195: 82-88. Go to original source...
    10. Li X.Y., Xu H.X., Chen J.W. (2014): Rapid identification of red-flesh loquat cultivars using EST-SSR markers based on manual cultivar identification diagram strategy. Genetics and Molecular Research, 13: 3384-3394. Go to original source... Go to PubMed...
    11. Lu S., Li L. (2008): Carotenoid metabolism: biosynthesis, regulation, and beyond. Journal of Integrative Plant Biology, 50: 778-785. Go to original source... Go to PubMed...
    12. McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., Kernytsky A., Garimella K., Altshuler D., Gabriel S., Daly M., DePristo M.A. (2010): The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20: 1297-1303. Go to original source... Go to PubMed...
    13. Rodriguez-Concepción M., Stange C. (2013): Biosynthesis of carotenoids in carrot: an underground story comes to light. Archives of Biochemistry and Biophysics, 539: 110-116. Go to original source... Go to PubMed...
    14. Shin S., Zheng P., Fazio G., Mazzola M., Main D., Zhu Y. (2016): Transcriptome changes specifically associated with apple (Malus domestica) root defense response during Pythium ultimum infection. Physiological and Molecular Plant Pathology, 94: 16-26. Go to original source...
    15. Shulaev V., Sargent D.J., Crowhurst R.N., Mockler T.C., Folkerts O., Delcher A.L., Jaiswal P., Mockaitis K., Liston A., Mane S.P., Burns P., Davis T.M., Slovin J.P., Bassil N., Hellens R.P., Evans C., Harkins T., Kodira C., Desany B., Crasta O.R., Jensen R.V., Allan A.C., Michael T.P., Setubal J.C., Celton J.M., Rees D.J., Williams K.P., Holt S.H., Ruiz Rojas J.J., Chatterjee M., Liu B., Silva H., Meisel L., Adato A., Filichkin S.A., Troggio M., Viola R., Ashman T.L., Wang H., Dharmawardhana P., Elser J., Raja R., Priest H.D., Bryant D.W., Fox S.E., Givan S.A., Wilhelm L.J., Naithani S., Christoffels A., Salama D.Y., Carter J., Lopez G.E., Zdepski A., Wang W., Kerstetter R.A., Schwab W., Korban S.S., Davik J., Monfort A., Denoyes-Rothan B., Arus P., Mittler R., Flinn B., Aharoni A., Bennetzen J.L., Salzberg S.L., Dickerman A.W., Velasco R., Borodovsky M., Veilleux R.E., Folta K.M. (2011): The genome of woodland strawberry (Fragaria vesca). Nature Genetics, 43: 109-116. Go to original source... Go to PubMed...
    16. Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., Kalyanaraman A., Fontana P., Bhatnagar S.K., Troggio M., Pruss D., Salvi S., Pindo M., Baldi P., Castelletti S., Cavaiuolo M., Coppola G., Costa F., Cova V., Dal Ri A., Goremykin V., Komjanc M., Longhi S., Magnago P., Malacarne G., Malnoy M., Micheletti D., Moretto M., Perazzolli M., Si-Ammour A., Vezzulli S., Zini E., Eldredge G., Fitzgerald L.M., Gutin N., Lanchbury J., Macalma T., Mitchell J.T., Reid J., Wardell B., Kodira C., Chen Z., Desany B., Niazi F., Palmer M., Koepke T., Jiwan D., Schaeffer S., Krishnan V., Wu C., Chu V.T., King S.T., Vick J., Tao Q., Mraz A., Stormo A., Stormo K., Bogden R., Ederle D., Stella A., Vecchietti A., Kater M.M., Masiero S., Lasserre P., Lespinasse Y., Allan A.C., Bus V., Chagne D., Crowhurst R.N., Gleave A.P., Lavezzo E., Fawcett J.A., Proost S., Rouze P., Sterck L., Toppo S., Lazzari B., Hellens R.P., Durel C.E., Gutin A., Bumgarner R.E., Gardiner S.E., Skolnick M., Egholm M., Van de Peer Y., Salamini F., Viola R. (2010): The genome of the domesticated apple (Malus × domestica Borkh.). Nature Genetics, 42: 833-839. Go to original source... Go to PubMed...
    17. Verde I., Abbott A.G., Scalabrin S., Jung S., Shu S., Marroni F., Zhebentyayeva T., Dettori M.T., Grimwood J., Cattonaro F., Zuccolo A., Rossini L., Jenkins J., Vendramin E., Meisel L.A., Decroocq V., Sosinski B., Prochnik S., Mitros T., Policriti A., Cipriani G., Dondini L., Ficklin S., Goodstein D.M., Xuan P., Del Fabbro C., Aramini V., Copetti D., Gonzalez S., Horner D.S., Falchi R., Lucas S., Mica E., Maldonado J., Lazzari B., Bielenberg D., Pirona R., Miculan M., Barakat A., Testolin R., Stella A., Tartarini S., Tonutti P., Arus P., Orellana A., Wells C., Main D., Vizzotto G., Silva H., Salamini F., Schmutz J., Morgante M., Rokhsar D.S. (2013): The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nature Genetics 45: 487-494. Go to original source... Go to PubMed...
    18. Wang Z., Gerstein M., Snyder M. (2009): RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics, 10: 57-63. Go to original source... Go to PubMed...
    19. Wu J., Wang Z., Shi Z., Zhang S., Ming R., Zhu S., Khan M.A., Tao S., Korban S.S., Wang H., Chen N.J., Nishio T., Xu X., Cong L., Qi K., Huang X., Wang Y., Zhao X., Deng C., Gou C., Zhou W., Yin H., Qin G., Sha Y., Tao Y., Chen H., Yang Y., Song Y., Zhan D., Wang J., Li L., Dai M., Gu C., Shi D., Wang X., Zhang H., Zeng L., Zheng D., Wang C., Chen M., Wang G., Xie L., Sovero V., Sha S., Huang W., Zhang M., Sun J., Xu L., Li Y., Liu X., Li Q., Shen J., Paull R.E., Bennetzen J.L. (2013): The genome of the pear (Pyrus bretschneideri Rehd.). Genome Research, 23: 396-408. Go to original source... Go to PubMed...
    20. Xia W., Mason A.S., Xiao Y., Liu Z., Yang Y., Lei X., Wu X., Ma Z., Peng M. (2014): Analysis of multiple transcriptomes of the African oil palm (Elaeis guineensis) to identify reference genes for RT-qPCR. Journal of Biotechnology, 184: 63-73. Go to original source... Go to PubMed...
    21. Xu H.M., Kong X.D., Chen F., Huang J.X., Lou X.Y., Zhao J.Y. (2015): Transcriptome analysis of Brassica napus pod using RNA-Seq and identification of lipid-related candidate genes. BMC Genomics, 16: 858. Go to original source... Go to PubMed...
    22. Yan J., Kandianis C.B., Harjes C.E., Bai L., Kim E.-H., Yang X., Skinner D.J., Fu Z., Mitchell S., Li Q., Fernandez M.G.S., Zaharieva M., Babu R., Fu Y., Palacios N., Li J., DellaPenna D., Brutnell T., Buckler E.S., Warburton M.L., Rocheford T. (2010): Rare genetic variation at Zea mays crtRB1 increases β-carotene in maize grain. Nature Genetics, 42: 322-327. Go to original source... Go to PubMed...
    23. Zhou C., Xu C., Sun C., Li X., Chen K. (2007): Carotenoids in white- and red-fleshed loquat fruits. Journal of Agricultural and Food Chemistry, 55: 7822-7830. Go to original source... Go to PubMed...

    This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY NC 4.0), which permits non-comercial use, distribution, and reproduction in any medium, provided the original publication is properly cited. No use, distribution or reproduction is permitted which does not comply with these terms.


    Return to the content