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Research Article

Genetic Diversity and Population Structure Analysis of Coffee (Coffea canephora) Germplasm Collections in Indian Gene Bank Employing SRAP and SCoT Markers

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References

  • Agarwal, A., V. Gupta., S.U. Haq., P.K. Jatav., S.L. Kothari., and S. Kachhwaha. 2018. Assessment of genetic diversity in 29 rose germplasms using SCoT marker. J. King Saud. Univ. Sci. doi: 10.1016/j.jksus.2018.04.022.
  • Anagbogu, C.F., R. Bhattacharjee., C. Ilori., P. Tongyoo., K.E. Dada., A.A. Muyiwa., P. Gepts., and D.M. Beckles. 2019. Genetic diversity and re-classification of coffee (Coffea canephora Pierre ex A. Froehner) from South Western Nigeria through genotyping-by-sequencing-single nucleotide polymorphism analysis. Genet. Resour. Crop Evol 66(3):685–696. doi:10.1007/s10722-019-00744-2.
  • Anderson, J.A., G.A. Churchill., J.E. Sutrique., S.D. Tanksley, and M.E. Sorrells. 1993. Optimizing parental selection for genetic linkage maps. Genome 36(1):181–186. doi: 10.1139/g93-024.
  • Anonymous. 2014. Coffee Guide: A manual of coffee cultivation. Published by Central Coffee Research Institute, Karnataka, India.
  • Arif, M., N.W. Zaidi., Y.P. Singh., Q. Haq., and U.S. Singh. 2009. A comparative analysis of ISSR and RAPD markers for study of genetic diversity in Shisham (Dalbergia sissoo). Plant Mol. Biol. Rep. 27(4):488–495. doi: 10.1007/s11105-009-0097-0.
  • Bhattacharyya, P., S. Kumaria., S. Kumar., and P. Tandon. 2013. Start codon targeted (SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl, an endangered medicinal orchid species. Gene 529:21–26. doi: 10.1016/j.gene.2013.07.096.
  • Bhawna, M.Z., L. Arya., and M. Verma. 2017. Use of SCoT markers to assess the gene flow and population structure among two different population of bottle gourd. Plant Gene 9:80–86. doi: 10.1016/j.plgene.2016.09.001.
  • Bikila, A.B., N.S. Sakiyama., and E.T. Caixeta. 2017. SNPs based molecular diversity of Coffea canephora. J. Microbiol. Exp 5. doi: 10.15406/jmen.2017.05.00136.
  • Botstein, D., R.L. White, M.H. Skolnick., and R.M. Davies. 1980. Construction of a genetic map in man using restricted length polymorphism. Am. J. Hum. Genet. 32(3):314–331.
  • Chen, C., E. Durand., F. Forbes., and O. Francois. 2007. Bayesian clustering algorithms ascertaining spatial population structure: A new computer program and a comparison study. Mol. Ecol. Notes. 7(5):747–756. doi: 10.1111/j.1471-8286.2007.01769.x.
  • Collard, B.C.Y., and D.J. Mackill. 2009. Start codon targeted (SCoT) polymorphism: A simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol. Biol. Rep 27(1):86–93. doi: 10.1007/s11105-008-0060-5.
  • Cubry, P., D.F. Bellis., D. Pot., P. Musoli., and T. Leroy. 2013. Global analysis of Coffea canephora Pierre ex Froehner (Rubiaceae) from the Guineo-Congolese region reveals impacts from climatic refuges and migration effects. Genet. Resour. Crop Evol. 60(2):483–501. doi: 10.1007/s10722-012-9851-5.
  • Davis, A.P., H. Chadburn, J. Moat., R. O’Sullivan, S. Hargreaves, and E.N. Lughadha. 2019. High extinction risk for wild coffee species and implications for coffee sector sustainability. Sci. Adv. 5(1):eaav3473. doi: 10.1126/sciadv.aav3473.
  • Earl, D.A., and B.M. Vonholdt. 2012. STRUCTURE Harvester: A website and program for visualizing structure output and implementing the evanno method. Conserv. Genet. Resour. 4(2):359–361. doi: 10.1007/s12686-011-9548-7.
  • Etminan, A., A.P. Aboughadareh., A. Noori., A.A. Rad., L. Shooshtari., Z. Mahdavian., and M.Y. Khanian. 2018. Genetic relationships and diversity among wild Salvia accessions revealed by ISSR and SCoT markers. Biotechnol. Biotec. Eqp 32(3):610–617. doi: 10.1080/13102818.2018.1447397
  • Evanno, G., S. Regnaut., and J. Goudet. 2005. Detecting the number of clusters of individuals using the software structure: a simulation study. Mol. Ecol. 14(8):2611–2620. doi: 10.1111/mec.2005.14.issue-8.
  • Ferrao, L.F.V., E.T. Caixeta., F.F. Souza., and E.M. Zambolin. 2013. Comparative study of different molecular markers for classifying and establishing genetic relationships in Coffea canephora Plant Syst. Evol 299:225–238. doi: 10.1007/s00606-012-0717-2.
  • Garavito, A., M. Christophe., R. Guyot, and B. Bertrand. 2016. Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico. BMC Plant Biol. 16(1):242. doi: 10.1186/s12870-016-0933-y.
  • Garrido-Cardenas, J.A., C. Mesa-Valle., and F. Manzano-Agugliaro. 2018. Trends in plant research using molecular markers. Planta 247(3):543–557. doi: 10.1007/s00425-017-2829-y.
  • Ghislain, M., D. Zhang., D. Fajardo., Z. Huaman., and R. Hijmans. 1999. Marker-assisted sampling of the cultivated andean potato Solanum Phureja collection using RAPD markers. Genet. Resour. Crop Evo. 46(6):547–555. doi: 10.1023/A:1008724007888.
  • Gomez, C., S. Dussert., P. Hamon., S. Hamon., A. de Kochko., and V. Poncet. 2009. Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone: Cumulative impact of ancient climatic changes and recent human activities. BMC Plant Biol. 9:167. doi: 10.1186/1471-2148-9-167.
  • International Coffee Organization (ICO) Report. 2017. Coffee market ends 2017/18 in surplus. https://icocoffeeorg.tumblr.com/post/178884744500/coffee-market-ends-201718-in-surplus.
  • Jaccard, P. 1908. Nouvelles recherches sur la distribution florale. Bull. Société vaudoise Sci. Nat. 44:223–270. doi: 10.5169/seals-268384.
  • Jiang, L.F., X. Qi., X.Q. Zhang., L.K. Huang., X. Ma., and W.G. Xie. 2014. Analysis of diversity and relationships among orchardgrass (Dactylis glomerata L.) accessions using start codon-targeted markers. Genet. Mol. Res. 13(2):4406–4418. doi: 10.4238/2014.June.11.4.
  • Jingade, P., A.K. Huded., B. Kosaraju., and M.K. Mishra. 2019. Diversity genotyping of Indian coffee (Coffea arabica L.) germplasm accessions by using SRAP markers. J. Crop Improv 33(3):327–345. doi: 10.1080/15427528.2019.1592050.
  • Kesawat, M.S., and B.D. Kumar. 2009. Molecular Markers: It’s Application in Crop Improvement. J. Crop Sci. Biotechnol. 12(4):169–181. doi: 10.1007/s12892-009-0124-6.
  • Kumar, M., G.P. Mishra., R. Singh., P.K. Naik., S. Dwivedi., Z. Ahmad., and S.B. Singh. 2009. Genetic variability studies among apricot populations from cold arid desert of Ladakh using DNA markers. Indian J. Hort. 66(2):147–153.
  • Leroy, T., D.F. Bellis., H. Legnate., P. Musoli., A. Kalonji., R.G.L. Solorzano., and P. Cubry. 2014. Developing core collections to optimize the management and the exploitation of diversity of the coffee Coffea canephora. Genetica 142(3):185–199. doi: 10.1007/s10709-014-9766-5.
  • Li, G., and C.F. Quiros. 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. Appl. Genet. 103(2–3):455–461. doi: 10.1007/s001220100570.
  • Li, P., X. Zhan., Q. Que., W. Qu., M. Liu., K. Ouyang., J. Li., X. Deng., Z. Junjie., B. Liao., et al. 2015. genetic diversity and population structure of Toona Ciliata Roem. Based on sequence-related amplified polymorphism (SRAP) markers. Forests 6(12):1094–1106. doi: 10.3390/f6041094.
  • Liao, B., F. Wang., L. Chen., P. Li., K. Ouyang., R. Pian., M. Liu., Q. Que., X. Zhou., W. Xi., et al. 2016. Population structure and genetic relationships of Melia Taxa in China assayed with sequence- related amplified polymorphism (SRAP) markers. Forests 7(12):81. doi: 10.3390/f7040081.
  • Linos, A., N. Nikoloudakis., A. Katsiotis., and M. Hagidimitriou. 2014. Genetic structure of the greek olive germplasm revealed by RAPD, ISSR and SSR Markers. Sci. Hort 175(C):33–43. doi: 10.1016/j.scienta.2014.05.034.
  • Luo, C., X He., and H Chen., S, J, Ou., M, P, Gao., J, S, Brown., C, T, Tondo., R, J. Schnell., 2011. Genetic diversity of mango cultivars estimated using SCoT and ISSR markers, Biochemical Systematics and Ecology, 39 (4–6),676-684, https://doi.org/10.1016/j.bse.2011.05.023
  • Milbourne, D., R. Meyer., J.E. Bradshaw., E. Baird., N. Bonar., J. Provan., W. Powell., and R. Waugh. 1997. Comparison of PCR based marker systems for the analysis of genetic relationships in cultivated potato. Mol. Breeding 3(2):127–136. doi: 10.1023/A:1009633005390.
  • Mishra, M.K., and A. Slater. 2012. Recent Advances in the Genetic Transformation of Coffee. Hindawi Publishing Corporation. Biotechnol Res Int 2012:1–17. doi: 10.1155/2012/580857.
  • Mishra, M.K., P. Tornincasa, B. de-Nardi, E. Asquini., R. Dreos, L.D. Terra, R. Rathinavelu., P. Rovelli, A. Pallavicini., and G. Graziosi. 2011a. Genome organization in coffee as revealed by EST PCR-RFLP, SNPs and SSR Analysis. J. Crop Sci. Biotechnol 14(1):25–37. doi: 10.1007/s12892-010-0035-6.
  • Mishra, M.K., S. Nishani., and Jayarama. 2011b. Genetic relationship among indigenous coffee species from India Using RAPD, ISSR, and SRAP marker analysis. Biharean Biol 5(1):17–24. doi: 10.2298/ABS1103667M.
  • Mishra, M.K., S. Nishani., M. Gowda., D. Padmajyothi., N. Suresh., H.L. Sreenath., and Y. Raghuramulu. 2014. Genetic diversity among Ethiopian Coffee (Coffea arabica L.) collections available in Indian gene bank using sequence related amplified polymorphism markers. Plant Breed. Seed Sci 70(1):29–40. doi: 10.1515/plass-2015-0011.
  • Mulpuri, S., T. Muddanuru., and G. Francis. 2013. Start codon targeted (SCoT) polymorphism in toxic and non-toxic accessions of Jatropha curcas L. and development of a codominant SCAR marker. Plant Sci. 207:117–127. doi: 10.1016/j.plantsci.2013.02.013.
  • Ogutu, C., T. Fang., L. Yan, L. Wang., W. Lu., L. Huang., X. Wang., B. Ma., X. Deng., A. Owiti., et al. 2016. Characterization and utilization of microsatellites in the Coffea canephora genome to assess genetic association between wild species in Kenya and cultivated coffee. Tree Genet. Genomes 12(3):54. doi: 10.1007/s11295-016-1014-y.
  • Paliwal, R., R. Singh., A. Singh., S. Kumar., A. Kumar., and R.S. Majumdar. 2013. Molecular Characterization of Giloe (Tinospora cordifolia Willd. Miers ex Hook. F. and Thoms.) accessions using Start Codon Targeted (SCoT) markers. Int. J. Med. Arom. Plants 3:413–422.
  • Peakall, R., and P.E. Smouse. 2012. GenAlEx 6.5: Genetic Analysis in Excel. Population genetic software for teaching and research-an update. J. Bioinform. 28(19):2537–2539. doi: 10.1093/bioinformatics/bts460.
  • Powell, W, M Morgante, C Andre, M Hanafey, J Vogel, S Tingey, and A Rafalski. 1996. The comparison of rflp, rapd, aflp and ssr (microsatellite) markers for germplasm analysis. Molecular Breeding 2:225-238. doi:10.1007/BF00564200.
  • Prakash, N.S., M.C. Combes., S. Dussert., S. Naveen., and P. Lashermes. 2005. Analysis of genetic diversity in Indian robusta coffee genepool (Coffea canephora) in comparison with a representative core collection using SSRs and AFLPs. Genet. Resour. Crop Evol. 52(3):333–343. doi: 10.1007/s10722-003-2125-5.
  • Prevost, A., and M.J. Wilkinson. 1999. A new system of comparing PCR primers applied to ISSR finger printing of potato cultivars. Theor. Appl. Genet. 98(1):107–112. doi: 10.1007/s001220051046.
  • Pritchard, J.K., P. Stephens., and P. Donnelly. 2000. Inference of population structure using multi locus genotype data. Genetics 155(2):945–959.
  • Que, Y., Y. Pan., Y. Lu., C. Yang., Y. Yang., N. Huang., and L. Xu. 2014. Genetic analysis of diversity within a Chinese local sugarcane germplasm based on start codon targeted polymorphism. BioMed Res. Int. 2014:1–10. doi: 10.1155/2014/468375.
  • Rajesh, M.K., A.A. Sabana., K.E. Rachana., S. Rahman., B.A. Jerard., and A. Karun. 2015. Genetic relationship and diversity among coconut (Cocos nucifera L.) accessions revealed through SCoT analysis. 3 Biotech 5(6):999–1006. doi: 10.1007/s13205-015-0304-7.
  • Rajwade, A.E., R.S. Arora., N.Y. Kadoo., A.M. Harsulkar., P.B. Ghorpade., and V.S. Gupta. 2010. Relatedness of Indian Flax Genotypes (Linum usitatissimum L.): an inter-simple sequence repeat (ISSR) primer assay. Mol. Biotechnol 45(2):161–170. doi: 10.1007/s12033-010-9256-7.
  • Ram, A.S., M.S. Sreenivasan., and R. Naidu. 1994. Exploitation of coffee germplasm in India – II. Diploid species. J. Coffee Res. 24:107–114.
  • Rohlf, F.J. 1995. NTSYS-pc numerical taxonomy and multivariate analysis system version 2.02. Exterior software, Setauket, New York.
  • Shangguo, F., Y. Zhu., Y. Chenliang., K. Jiao., M. Jiang., J. Lu., C. Shen., Q. Ying., and H. Wang. 2018. Development of species-specific SCAR markers, based on a SCoT analysis, to authenticate physalis (Solanaceae) Species. Front. Genet 9:192. https://www.frontiersin.org/article/10.3389/fgene.2018.00192.
  • Singh, A., R. Avtar., D. Singh., O. Sangwan., and P. Balyan. 2013. Genetic variability, character association and path analysis for seed yield and component traits under two environments in indian mustard. J. Oilseed Brassica 4(1):43–48.
  • Solorzano, R.G.L., D.F. Bellis., T. Leroy., L. Plaza., H. Guerrero., C. Subia., D. Calderon., F. Fernandez., I. Garzon., D. Lopez., et al. 2017. Revealing the diversity of introduced coffea canephora Germplasm in Ecuador: towards a national strategy to improve robusta. Sci. World J. 2017:1–12. doi: 10.1155/2017/1248954.
  • Sonia, C., and T. Gopalakrishna. 2007. Comparative assessment of REMAP and ISSR marker assays for genetic polymorphism studies in Magnaporthe grisea. Curr. Sci 93:688–692. https://www.jstor.org/stable/24099392.
  • Souframanien, J., and T. Gopalakrishna. 2004. A comparative analysis of genetic diversity in blackgram genotypes using RAPD and ISSR markers. Theor. Appl. Genet 109(8):1687–1693. doi: 10.1007/s00122-004-1797-3.
  • Sousa, T.V., E.T. Caixeta, E.R. Alkimim., A.C.B. de Oliveira., A.A. Pereira., N.S. Sakiyama., M.F.J. de Resende., and L. Zambolim. 2017. Population structure and genetic diversity of coffee progenies derived from Catuaí and Híbrido de Timor revealed by genome-wide SNP marker. Tree Genet. Genomes 13(6):124. doi: 10.1007/s11295-017-1208-y.
  • Tamaki, I., and M. Okada. 2014. Genetic admixing of two evergreen oaks, Quercus acuta and Q. sessilifolia (Subgenus Cyclobalanopsis), Is the result of interspecific introgressive hybridization. Tree Genet. Genomes 10(4):989–999. doi: 10.1007/s11295-014-0737-x.
  • Tatikonda, L., S.P. Wani., S. Kannan., N. Beerelli., K. Sreedevi., D.A. Hoisington., P. Devi., and R.K. Varshney. 2010. AFLP-based molecular characterization of an elite germplasm collection of Jatropha curcas L, a biofuel plant. Plant Sci. 176(4):505–513. doi: 10.1016/j.plantsci.2009.01.006.
  • Thudi, M., R. Manthena., S.P. Wani., L. Tatikonda., D.A. Hoisington., and R.V. Varshney. 2010. Analysis of Genetic Diversity in Pongamia [Pongamia pinnata (L) Pierrre] using AFLP Markers. J. Plant Biochem. Biot 19(2):209–216. doi: 10.1007/BF03263342.
  • Tshilenge, P., K.K. Nkongolo., M. Mehes., and A. Kalonji. 2009. Genetic variation in Coffea canephora L. (Var. Robusta) accessions from the founder gene pool evaluated with ISSR and RAPD. Afr. J. Biotechnol 8(3):380–390. http://www.academicjournals.org/AJB.
  • Wang, Y., S Li., X Zhang., Y Wang., and C Zhang. 2016. Isolation and analysis of differentially expressed genes during ovule abortion in the seedless grape, scientia horticulturae. 211(376–383):. https://doi.org/10.1016/j.scienta.2016.09.014.
  • Wei, Y.L., X. He., C. Luo., and H. Chen. 2012. Genetic diversity of Podocarpus by SCoT markers. Guangxi Zhiwu/Guihaia 32(1):90–93.
  • Zhang, J.Y., D.L. Guo., Y. Gong., C.H. Liu., M. Li., and G.H. Zhang. 2011. Optimization of start codon targeted polymorphism PCR (SCoT-PCR) system in Vitis vinifera. J. Fruit Sci. 28:209–214.
  • Zhang, Y., X. Zhang., X. Chen., W. Sun., and L. Jiao. 2018. Genetic diversity and structure of tea plant in Qinba area in China by three types of molecular markers. Hereditas 22:155. doi: 10.1186/s41065-018-0058-4.
  • Zitouna, N., M. Gharbi., H. Chennaoui., A. Touati., I. Fadhlaoui., N. Trifi-Farah., and S. Marghali. 2015. Characterization of Sulla Species via SRAP Markers: Polymorphism and Systematic Analyses. Merit Res. J. Agri. Sci. Soil Sci 3(6):089–097. http://meritresearchjournals.org/asss/index.htm.

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