Abstract
Traditionally, coffee is propagated by seed. However, in recent years, the propagation of plants derived from somatic embryos has become increasingly important. The genetic homogeneity of plants derived from somatic embryos must be assessed before large-scale propagation. In this study, the genetic uniformity of somatic embryo–derived and seed-derived plants obtained from the same mother plant in two arabica hybrid coffee cultivars was examined using sequence-related amplified polymorphism (SRAP) and start codon-targeted (SCoT) markers, as well as the sequencing of seven functional genes. In both cultivars, the analysis of molecular markers revealed a remarkable genetic similarity of 93 to 98% between the plants derived from somatic embryos and those derived from seeds compared to the mother plant. Sequence analysis confirmed that the large subunit of ribulose-1,5-biphosphate carboxylase and mitochondrial ribosomal protein had the highest sequence similarity of all the genes studied. Among the five nuclear genes analyzed, the pathogenesis-related protein 1A-like gene showed the lowest sequence variability while the zinc finger protein gene showed the highest sequence variability compared to the NAC25, UDP-glycosyltransferase, and light-inducing protein chloroplastic-like genes. The presence of variable frequency of single-nucleotide polymorphisms (SNPs) and insertions and deletions (indels) created the overall sequence polymorphism across different genes. There was no substantial difference in sequence variability between plants derived from somatic embryos and those grown from seeds. This study represents the first comparative analysis of the genetic homogeneity of somatic embryo–derived and seed-derived plants of self-fertilized arabica coffee cultivars.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data Availability
All data generated or analyzed during this study are included in this published article (and its supplementary information files).
References
Annonymous, (2014) Coffee guide-a manual of coffee cultivation. Published by Director of Research, Central Coffee Research Institute, Coffee Research Station, Chickmagalur District, Karanataka, India
Bajaj P, Bhasin M, Varadarajan R (2023) Molecular bases for strong phenotypic effects of single-site synonymous substitutions in the E.coli ccdB toxin gene. bioRxiv 532503 https://doi.org/10.1101/2023.03.13.532503
Bednarek PT, Orłowska R (2020) Plant tissue culture environment as a switch-key of (epi)genetic changes. Plant Cell Tiss Org Cult 140:245–257. https://doi.org/10.1007/s11240-019-01724-1
Bertrand B, Alpizar E, Lara L, SantaCreo R, Hidalgo M, Quijano JM, Montagnon C, Georget F, Etienne H (2011) Performance of Coffea arabica F1 hybrids in agroforestry and full-sun cropping systems in comparison with American pure line cultivars. Euphytica 181:147–158. https://doi.org/10.1007/s10681-011-0372-7
Biswas P, Nandy S, Dey A, Tikendra L, Nongdam P (2022) Molecular markers in assessing genetic clonal fidelity for in vitro propagated endangered medicinal plants. In: Kumar A, Choudhury B, Dayanandan S, Khan ML (eds) Molecular genetics and genomics tools in biodiversity conservation. Springer, Singapore https://doi.org/10.1007/978-981-16-6005-4_6
Boatwright JL, Sapkota S, Kresovich S (2023) Functional genomic effects of InDels using Bayesian genome-phenome wide association studies in sorghum. Front Genet 14:1143395. https://doi.org/10.3389/fgene.2023.1143395
Bohry D, Ramos HCC, Dos Santos PHD, Boechat MSB, Arêdes FAS, Pirovani AAV, Pereira MG (2021) Discovery of SNPs and InDels in papaya genotypes and its potential for marker assisted selection of fruit quality traits. Sci Rep 11:292. https://doi.org/10.1038/s41598-020-79401-z
Bolívar-González A, Molina-Bravo R, Solano-Sánchez W, Araya-Valverde E, Suzana T, Suzuki I, Gatica-Arias PLFP, A, (2023) SNP markers found in non-coding regions can distinguish among low-variant genotypes of arabica and other coffee species. Genet Resour Crop Evol 70:1215–1228. https://doi.org/10.1007/s10722-022-01498-0
Buhr F, Jha S, Thommen M, Mittelstaet J, Kutz F, Schwalbe H, Rodnina MV, Komar AA (2016) Synonymous codons direct cotranslational folding towards different protein conformations. Mol Cell 61:341–351. https://doi.org/10.1016/j.molcel.2016.01.008
Bychappa M, Mishra MK, Jingade P, Huded AKC (2019) Genomic alterations in coding region of tissue culture plants of Coffea arabica obtained through somatic embryogenesis revealed by molecular markers. Plant Cell Tiss Org Cult 139:91–103. https://doi.org/10.1007/s11240-019-01666-8
Campos NA, Panis B, Carpentier SC (2017) Somatic embryogenesis in coffee: the evolution of biotechnology and the integration of omics technologies offer great opportunities. Front Plant Sci 8:1460. https://doi.org/10.3389/fpls.2017.01460
Chen N, Shao Q, Lu Q, Li X, Xiao Gao Y, Q, (2023) Research progress on function of NAC transcription factors in tomato (Solanum lycopersicum L.). Euphytica 219:22. https://doi.org/10.1007/s10681-023-03153-w
Chen Y, Wang B, Chen J, Wang X, Wang R, Peng S, Chen L, Ma L, Luo J (2015) Identification of Rubisco rbcL and rbcS in Camellia oleifera and their potential as molecular markers for selection of high tea oil cultivars. Front Plant Sci 6:189. https://doi.org/10.3389/fpls.2015.00189
Cloutier S, Landry BS (1994) Molecular markers applied to plant tissue culture. In Vitro Cell Div Bio - Plant 30:32–39
Collard BCY, Mackill DJ (2009) Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol Bio Rep 27:86–93. https://doi.org/10.1007/s11105-008-0060-5
Cortaga CQ, Lachica JAP, Lantican DV, Ocampo ETM (2022) Genome-wide SNP and InDel analysis of three Philippine mango species inferred from whole-genome sequencing. J Genet Eng Biotechnol 20:46. https://doi.org/10.1186/s43141-022-00326-3
Dakal TC, Kala D, Dhiman G, Yadav V, Krokhotin A, Dokholyan NV (2017) Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene. Sci Rep 7:6525. https://doi.org/10.1038/s41598-017-06575-4
Ducos JP, Alenton R, Reano JF, Kanchanomai C, Deshayes A, Pétiard V (2003) Agronomic performance of Coffea canephora P. trees derived from large-scale somatic embryo production in liquid medium. Euphytica 131:215–223. https://doi.org/10.1023/A:1023915613158
Engelken J, Funk C, Adamska I (2012) The extended light-harvesting complex (LHC) protein superfamily: classification and evolutionary dynamics. Functional genomics and evolution of photosynthetic systems (eds) R. Burnap and W. Vermaas (Dordrecht: Springer), 265–284 https://doi.org/10.1007/978-94-007-1533-2_11
Etienne, H (2005) Somatic embryogenesis protocol: coffee (Coffea arabica L. and C. P.). In: S.M. Jain and P.K. Gupta (Eds.). Protocol for somatic embryogenesis in woody plants. Springer, the Netherlands. pp 167–179 https://doi.org/10.1007/1-4020-2985-3_14
Etienne H, Breton D, Breitler J-C, Bertrand B, Déchamp E, Awada R, Marraccini P, Léran S, Alpizar E, Campa C, Courtel P, Georget F, Ducos J-P (2018) Coffee somatic embryogenesis: how did research, experience gained and innovations promote the commercial propagation of elite clones from the two cultivated species? Front Plant Sci 9:1630. https://doi.org/10.3389/fpls.2018.01630
Garcia C, de Almeida FAA, Costa M, Britto D, Valle R, Royaert S, Marelli JP (2019) Abnormalities in somatic embryogenesis caused by 2,4-D: an overview. Plant Cell Tiss Organ Cult 137:193–212. https://doi.org/10.1007/s11240-019-01569-8
Gharabli H, Della Gala V, Welner DH (2023) The function of UDP-glycosyltransferases in plants and their possible use in crop protection. Biotechnol Adv 67:108182. https://doi.org/10.1016/j.biotechadv.2023.108182
Hall RD, Trevisan F, de Vos RCH (2022) Coffee berry and green bean chemistry – opportunities for improving cup quality and crop circularity. Food Res Intl. https://doi.org/10.1016/j.foodres.2021.110825
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acid Symp Ser 41:95–98
Hosein FN, Austin N, Maharaj S, Johnson W, Rostant L, Ramdass AC, Rampersad SN (2017) Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad. Ecol Evol 7:7311–7333. https://doi.org/10.1002/ece3.3220
Huded AKC, Jingade P, Bychappa M, Mishra MK (2020) Genetic diversity and population structure analysis of coffee (Coffea canephora) germplasm collections in Indian gene bank employing SRAP and SCoT markers. Int J Fruit Sci 20(sup2):S757–S784. https://doi.org/10.1080/15538362.2020.1768618
International Coffee Organization (ICO) Coffee report and outlook, December 2023. https://icocoffee.org/documents/cy202324/Coffee_Report_and_Outlook_December_2023_ICO.pdf. Accessed 12-04-2024
Jingade P, Huded A, Kosaraju B, Mishra M (2019) Diversity genotyping of Indian coffee (Coffea arabica L) germplasm accessions by using SRAP markers. J Crop Improv 33:327–345. https://doi.org/10.1080/15427528.2019.1592050
Kakimzhanova A, Dyussembekova D, Nurtaza A, Yessimseitova A, Shevtsov A, Lutsay V, Ramankulov Y, Kabieva S (2022) An efficient micropropagation system for the vulnerable wild apple species, Malus sieversii, and confirmation of its genetic homogeneity. Erwerbs-Obstbau 65:621–632. https://doi.org/10.1007/s10341-022-00720-8
Kittichotsatsawat Y, Jangkrajarng V, Tippayawong KY (2021) Enhancing coffee supply chain towards sustainable growth with big data and modern agricultural technologies. Sustainability 13: 10.3390/su130 84593
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096
Landey RB, Cenci A, Georget F, Bertrand B, Camayo G, Dechamp E, Herrera JC, Santoni S, Lashermes P, Simpson J, Etienne H (2013) High genetic and epigenetic stability in Coffea arabica plants derived from embryogenic suspensions and secondary embryogenesis as revealed by AFLP, MSAP and the phenotypic variation. PLoS ONE 8:e56372. https://doi.org/10.1371/journal.pone.0056372
Landey RB, Cenci A, Guyot R, Bertrand B, Georget F, Dechamp E et al (2015) Assessment of genetic and epigenetic changes during cell culture ageing in coffee and relations with somaclonal variation. Plant Cell Tiss Org Cult 3:517–531. https://doi.org/10.1007/s11240-015-0772-9
Larsen B, Migicovsky Z, Jeppesen AA, Gardner KM, Toldam-Andersen TB, Myles S, Ørgaard M, Petersen MA, Pedersen C (2019) Genome-wide association studies in apple reveal loci for aroma volatiles, sugar composition, and harvest date. Plant Genome 12 https://doi.org/10.3835/plantgenome2018.12.0104
Lee H, Popodi E, Tang H, Foster PL (2012) Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proc Natl Acad Sci USA 109:E2774–E2783. https://doi.org/10.1073/pnas.1210309109
Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor App Genet 103:455–461. https://doi.org/10.1007/s001220100570
Librado P, Rozas J (2009) DNASP V5: a software for comprehensive analysis of DNA polymorphism data. Bioinfrom 25:1451–1452. https://doi.org/10.1093/bioinformatics/btp187
Liu YH, Xu Y, Zhang M, Cui Y, Sze SH, Smith CW, Xu S, Zhang HB (2020) Accurate prediction of a quantitative trait using the genes controlling the trait for gene-based breeding in cotton. Front Plant Sci 11:583277. https://doi.org/10.3389/fpls.2020.583277
Mekbib Y, Tesfaye K, Dong X, Saina JK, Hu GW, Wang QF (2022) Whole-genome resequencing of Coffea arabica L. (Rubiaceae) genotypes identify SNP and unravels distinct groups showing a strong geographical pattern. BMC Plant Biol 22:69. https://doi.org/10.1186/s12870-022-03449-4
Milbourne D, Meyer R, Bradshaw JE, Baird E, Bonar N, Provan J, Powell W, Waugh R (1997) Comparison of PCR based marker systems for the analysis of genetic relationships in cultivated potato. Mol Breed 3:127–136. https://doi.org/10.1023/A:1009633005390
Mishra MK (2019) Genetic resources and breeding of coffee (Coffea spp.) In: Jameel M. Al-Khayri, S. Mohan Jain and Dennis V. Johnson (Editors) Advances in plant breeding strategies, Vol. 4 Nut and Industrial Crops. Springer Publisher. pp. 475–515 https://doi.org/10.1007/978-3-030-23112-5
Mishra MK, Huded AKC, Jingade P, Muniswamy B (2022a) Molecular characterization and genetic structure analysis of Coffea arabica and Coffea canephora cultivars from India using SCoT markers. Ecol Genet Genom 23:100117. https://doi.org/10.1016/j.egg.2022.100117
Mishra MK, Jingade P, Huded AKC (2022) DNA barcoding analysis and phylogenetic relationships of Indian wild coffee species. Turk J Bot 46:2. https://doi.org/10.55730/1300-008X.2675
Mishra MK, Jingade P, Huded AKC, Muniswamy B (2023) Assessment of genetic homogeneity of somatic embryo-derived plants and seed-derived plants of a robusta coffee cultivar using molecular markers and functional genes sequencing. Plant Cell Tiss Org Cult 153:319–332. https://doi.org/10.1007/s11240-023-02468-9
MK Mishra, A Slater, 2012 Recent advances in the genetic transformation of coffee. Hindawi Publishing Corporation, Biotechnology Research International https://doi.org/10.1155/2012/580857
Muniswamy B, Kosaraju B, Mishra MK, Yenugula R (2017) Field performance and genetic fidelity of micropropagated plants of Coffea canephora (Pierre ex A. Froehner). Open Life Sci 12:1–11. https://doi.org/10.1515/biol-2017-0001
Muñoz-Espinoza C, Di Genova A, Sánchez A, Correa J, Espinoza A, Meneses C, Maass A, Orellana A, Hinrichsen P (2020) Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches. BMC Plant Biol 20:365. https://doi.org/10.1186/s12870-020-02564-4
Prevost A, Wilkinson MJ (1999) A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet 98:107–112. https://doi.org/10.1007/s001220051046
Rahman FU, Khan IA, Aslam A, Liu R, Sun L, Wu Y, Aslam MM, Khan AU, Li P, Jiang J, Fan X, Liu C, Zhang Y (2022) Transcriptome analysis reveals pathogenesis-related gene 1 pathway against salicylic acid treatment in grapevine (Vitis vinifera L) Front Genet 13 https://doi.org/10.3389/fgene.2022.1033288
Rajkumar MS, Garg R, Jain M (2022) Genome-wide discovery of DNA polymorphisms via resequencing of chickpea cultivars with contrasting response to drought stress. Physiol Plant 174:e13611. https://doi.org/10.1111/ppl.13611
Rajput S, Agrawal V (2020) Micropropagation of Atropa acuminate Royle ex Lindl. (a critically endangered medicinal herb) through root callus and evaluation of genetic fidelity, enzymatic and non-enzymatic antioxidant activity of regenerants. Acta Physiol Plant 42:160. https://doi.org/10.1007/s11738-020-03145-6
Rani V, Singh KP, Shiran M, Nandy S, Goel S, Sreenath HL, Raina SN (2000) Evidence for new nuclear and mitochondrial genome organizations among high frequency somatic embryogenesis-derived plants of allotetraploid Coffea arabica L. (Rubiaceae). Plant Cell Rep 19:1013–1020. https://doi.org/10.1007/s002990000228
Robles P, Quesada V (2017) Emerging roles of mitochondrial ribosomal proteins in plant development. Int J Mol Sci 18:2595. https://doi.org/10.3390/ijms18122595
Rohlf FJ (1995) NTSYS-pc numerical taxonomy and multivariate analysis system version 2.02. Exterior software, Setauket, New York
Seninde DR, Chambers E IV (2020) Coffee flavor: A review. Beverages 6:44. https://doi.org/10.3390/beverages6030044
Silvarolla MB, Mazzafera P, Fazuoli LC (2004) Plant biochemistry: a naturally decaffeinated arabica coffee. Nature 429:826. https://doi.org/10.1038/429826a
Sneath PH, Sokal RR (1973) Numerical taxonomy: the principles and practice of numerical classification. 1st Edition, W. H. Freeman, San Francisco.
Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526. https://doi.org/10.1093/oxfordjournals.molbev.a040023
Tao T, Huang Q, Zuo Z, Lu Y, Su X, Xu Y, Li P, Xu C, Yang Z (2022) Nucleotide polymorphisms of the maize ZmFWL7 gene and their association with ear-related traits. Front Genet 13:960529. https://doi.org/10.3389/fgene.2022.960529
Tran HTM, Furtado A, Vargas CAC, Smyth H, Slade-Lee L, Henry R (2018) SNP in the Coffea arabica genome associated with coffee quality. Tree Genet Genome 14:72
Uma S, Karthic R, Kalpana S, Backiyarani S, Kumaravel M, Saranya S, Saraswathi MS, Durai P (2023) An efficient embryogenic cell suspension culture system through secondary somatic embryogenesis and regeneration of true-to-type plants in banana cv Sabri (silk subgroup AAB). Plant Cell Tiss Org Cult 155:313–322. https://doi.org/10.1007/s11240-023-02570-y
Van Loon VC, VanStrien EA (1999) The families of pathogenesis-related proteins, their activities, and comparative analysis of PR-1 type proteins. Physiol Mol Plant Pathol 55:85–97
Wei Y, Mu H, Xu G, Wang Y, Li Y, Li S, Wang L (2021) Genome-wide analysis and functional characterization of the UDP-glycosyltransferase family in grapes. Horticulturae 7:204. https://doi.org/10.3390/horticulturae7080204
Wojcik OM, Nailwal TK, Pande V (2022) Callus induction and multiple shoot proliferation from nodal explants of Mansonia altissima: confirmation of genetic stability using ISSR and RAPD markers. In Vitro Cell Dev Biol - Plant 58:479–488. https://doi.org/10.1007/s11627-021-10249-2
Wu Z, Waneka G, Broz AK, King CR, Sloan DB (2020) MSH1 is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes. Proc Natl Acad Sci USA 117:16448–16455. https://doi.org/10.1073/pnas.2001998117
Yadav LK, Wilde HD (2022) Identification and bioinformatic characterization of rare variants of Rhododendron canescens architecture genes. Euphytica 218:66. https://doi.org/10.1007/s10681-022-03019-7
Yuce K, Ozkan AI (2020) Cys2His2 zinc finger proteins boost survival ability of plants against stress conditions. In (Ed.), Plant stress physiology. Intech Open. https://doi.org/10.5772/intechopen.92590
Author information
Authors and Affiliations
Contributions
MKM conceived and designed the experiment, regenerated the somatic embryo–derived plantlets, and participated in data curing. BM participated in the tissue culture and field establishment of somatic embryo–derived and seed-derived plants. PJ and AKH performed molecular marker experiments and provided analysis tools. MKM prepared and edited the manuscript. All authors discussed and approved the final manuscript. AKH and PJ have made equal contributions to the manuscript.
Corresponding author
Ethics declarations
Conflict of Interest
The authors declare no competing interests.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Mishra, M.K., Huded, A.K.C., Jingade, P. et al. Comparative genetic assessment of somatic embryo– and seed-derived plants of two arabica hybrid coffee cultivars using SRAP and SCoT molecular markers and organellar and nuclear genes sequencing. In Vitro Cell.Dev.Biol.-Plant (2024). https://doi.org/10.1007/s11627-024-10436-x
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s11627-024-10436-x