Genetic Variability of Access of the Active Germplasm Bank of Coffea canephora of Incaper in Southern Espírito Santo

Document Type: Research Article

Authors

1 Development and Innovation Institute, Technical Assistance and Rural Extension of Espírito Santo, Rodovia Joao Domingo Zago, Brazil

2 Brazilian Agricultural Research Corporation Institute, Technical Assistance and Rural Extension of Espírito Santo, Brazil

3 Itapemirim City Hall, ES. Former Pos Doctor Junior CNPq fellow and Consorcio Pesquisa Café in INCAPER

4 Technical Assistance and Rural Extension of Espírito Santo and research coordinator of Brazilian College Multivix

5 Research Coffee Consortium Scholarship of Southern Center, Development and Innovation Institute, Technical Assistance, and Rural Extension of Espírito Santo

10.22080/jgr.2020.19162.1194

Abstract

This study aimed to analyze the genetic variability of 323 accessions of the Active Germplasm Bank (BAG) of Coffea canephora of the Institute for Research, Technical Assistance and Rural Extension of Espírito Santo (Incaper) using 38 quantitative phenotypic characters. The standardized average Euclidean distance between the accessions was estimated to generate a statistical distance matrix and, from this, the groupings were performed using the Tocher and UPGMA. Concerning the studied accessions, the amplitude of the data set for each characteristic, and the possibility of selection were visualized. The accuracy of data collection was verified by the Variation Index with values below 10% for most of the characters, except for characters such as number of rosettes in the upper plagiotropic branch, number of grains in the smallest orthotropic branch, and number of grains per rosette on the upper plagiotropic branch. Using the Tocher method, 25 groups were recognized, 10 of which were formed by only one accession. The hierarchical grouping highlighted the lack of duplicates and accessions 173 (ES 1-B) as the most genetically distant. The analysis of the relative contribution of each character distinguished fresh matter and dry matter of orthotropic branches thrown by plants susceptible to pruning as fundamental for the differentiation of accessions and important in future studies of diversity as they are responsible for about 83% of the phenotypic variability of the study. There were no duplicates among the evaluated accessions and there are heterotic groups and distinct accessions in the BAG that can be used in hybridization programs or per se to obtain new cultivars. The pairs of the most similar and dissimilar accessions were 45 (148/86) and 320 (IAC37) with a statistical distance of 0.0713 and 173 (ES 1-B) and 270 (403-Marilândia) with a distance of 0.4765, respectively.

Keywords


Alkimim ER, Caixeta ET, Sousa TV, Silva FL, Sakiyama NS, Zambolim L. 2018. High-throughput targeted genotyping using next-generation sequencing applied in Coffea canephora breeding. Euphytica 214:50 doi:10.1007/s10681-018-2126-2.
Anagbogu CF, Bhattacharjee R, Ilori C, Tongyoo P, Dada KE, Muyiwa AA, Gepts P, Beckles DM. 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 Ev 66: 685-696.
Archana RS, Sudha Rani M, Vishnu Vardhan KM, Fareeda G. 2018. Genetic diversity studies among rice (Oryza sativa L.) genotypes for grain yield, yield components and nutritional traits in rice. Int J Chem Studies 6: 134-137.
Berthaud, J. 1986. Les resources génétique pour l’amélioration des caféiers africains diploides. Evaluation de la richesse génétique des populations sylvestres et de ses mécanismes organisateurs. Conséquences pour l’application. University of Paris, Pais, Orstrom.
Bramel P, Krishnan S, Horna D, Lainoff B, Montagnon C .2017. Global conservation strategy for coffee genetic resources. Crop Trust, World Coffee Res., Portland, OR. Available at: https://worldcoffeeresearch.org/documents/42/Coffee_Strategy_Low_Res.pdf.
Carmona PAO, Peixoto JR, Amaro GB, Mendonça M. 2015. Genetic divergence of sweet potato accessionsions based on morpho-agronomic descriptors of the roots. Hortic Bras 33: 241-250.
Cecon PR, Silva FF, Ferreira A, Ferrao RG, Carneiro APS, Detmann E, Faria PN, Morais TSS. 2008. Análise de medidas repetidas na avaliaçao de clones de café 'Conilon'. Pesq Agropec Bras. 43: 1171-1176.
Companhia Nacional de Abastecimento. 2020. Acampamento da safra brasileira: café. v. 6, n. 1, p. 1-62, Brasília: Conab, jan.
Cosme S, Cuevas HE, Zhang D, Oleksyk TK, Irish BM. 2016. Genetic diversity of naturalized cacao (Theobroma cacao L.) in Puerto Rico. Tree Genet Genomes 12: 1-13.
Covre AM, Canal L, Partelli FL, Alexandre RS, Ferreira A, Vieira HD. 2016. Development of clonal seedlings of promising conilon coffee (Coffea canephora) genotypes. Aust J Crop Sci 10: 385-392.
Cruz CD, Regazzi AJ, Carneiro PCS. 2012. Modelos biométricos aplicados ao melhoramento genético. Viçosa: Ed. da UFV, 514p.
Cruz CD. 2013. Genes: a software package for analysis in experimental statistics and quantitative genetics.Acta Sci Agron 35: 271-276.
Cruz CD. 2016. Genes Software -extended and integrated with the R, Matlab and Selegen. Acta Sci Agron 38: 547-552.
Cubry P, Bellis F, Pot D, Musoli P, Leroy T. 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 Ev 60: 483-501.
Dalcomo JM, Vieira HD, Ferreira A, Lima WL, Ferrao RG, Fonseca AFA, Ferrao MAG, Partelli FL. 2015. Evaluation of genetic divergence among clones of conilon coffee after scheduled cycle pruning. Genet Mol Res 14: 15417-15426.
Davis AP, Chadburn H, Moat J, Sullivan RO, Hargreaves S, Lughadha EN. 2019. High extinction risk for wild coffee species and implications for coffee sector sustainability. Sci Adv 5: 1-9.
Davis AP, Govaerts R, Bridson DM, Stoffelen P. 2006. An annotated taxonomic conspectus of the genus Coffea (Rubiaceae). Bot J Linn Soc 152: 465-512.
Davis AP, Tosh J, Ruch N, Fay MF. 2011. Growing coffee: Psilanthus (Rubiaceae) subsumed on the basis of plastid and nuclear DNA sequences; implications for the size, morphology, distribution and evolutionary history of Coffea. Bot J Linn Soc 167: 357-377.
Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G, Lashermes P. 2014. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 345: 1181-1184.
Falconer DS. 1981. Introdução à Genética Quantitativa (Tradução de Silva, MA e Silva, JC). Universidade Federal de Viçosa, Viçosa, MG, p.279
Ferrao MAG, Fonseca AFA, Ferrao RG, Barbosa WM, Souza EMR. 2009. Genetic divergence in conilon coffee revealed by RAPD markersCrop Breed Appl Biot 9: 67-74.
Ferrao MAG, Ferrao RG, Fonseca AFA, Verdim Filho AC, Volpi PS. 2015. Origem, dispersão geográfica, taxonomia e diversidade genética de Coffea canephora. Café conilon. Vitória: Incaper, 66-91.
Ferrao MAG, Fonseca AFA, Ferrao RG, Volpi PS, Verdin Filho AC, Riva-Souza EM, Comerio M, Kaulz M. 2017b. Variabilidade genética de progênies híbridas de Coffea canephora. In: congresso brasileiro de melhoramento de plantas, 9., 2017, Foz do Iguaçu. Melhoramento de plantas: projetando o futuro. Foz do Iguaçu: SBMP, 2017.
Ferrao MAG, Ferrao RG, Fonseca AFA, Verdim Filho AC, Volpi PS. 2019. Origin, geographical dispersion, taxonomy and genetic diversity of Coffea canephora. In: Ferrão RG, Fonseca AFA, Ferrão MAG, De Muner LH, eds. Café Conilon, segunda edição atualizada e ampliada. Vitória: DCM/Incaper Press, 85-109.
Ferrao MAG, Fonseca AFA, Barbosa WM, Ferrao RG. 2005. Variabilidade genética em Coffea canephora com base em marcadores RAPD. In: Embrapa Café-Artigo em anais de congresso (ALICE) 2005. in: simpósio de pesquisa dos cafés do brasil, 4., 2005, Londrina. Anais... Brasília, DF: Embrapa Café, 2005.
Ferrao RG, Fonseca AFA, Ferrao MAG, Muner LH. 2017b. Café Conilon, segunda ediçao atualizada e ampliada. Vitória: DCM/Incaper, 784p.
Fonseca AFA.  1999. Análises biométricas em café conilon (Coffea canephora Pierre).
Fonseca AFA, Sediyama T, Cruz CD, Sakiyama NS, Ferrao MAG, Ferrao RG, Bragança SM. 2006. Divergência genética em café conilon. Pesqu. Agropecu. Bras. Pesquisa Agropecuária Brasileira 41: 599-605.
International Coffee Organization (ICO). 2018. Trade Statistics. Available at: www.ico.org/ trade_statistics.asp.
Laliberté B, Cryer NC, Daymond AJ, End MJ, Engels JM, Eskes A, Gilmour M, Lachenaud P, Phillips-Mora W, Turnbull CJ, Umaharan P. 2012. A global strategy for the conservation and use of cacao genetic resources, as the foundation for a sustainable cocoa economy.
Lebot V, Melteras M, Pilecki A, Labouisse JP. 2020. Chemometric evaluation of cocoa (Theobroma cacao L.) and coffee (Coffea spp.) germplasm using HPTLC. Genet Resour Crop Ev 67: 895-911.
Marraccini P, Vinecky F, Alves GSC, Ramos HJO. 2012. Differentially expressed genes and proteins upon drought acclimation in tolerant and sensitive genotypes of Coffea canephora. J Exp Bot 63: 4191-4212.
Montagnon C, Leroy T, Yapo AB. 1992. Diversité génotypique et phénotypique de quelques groupes de caféiers (Coffea canephora Pierre) em collection. Conséquences sur leur utilisation em sélection. Café CacaoThé 36: 187-198.
Musoli P, Cubry P, Aluka P, Billot C, Dufour M, Bellis F, Pot D, Bieysse D, Charrier A, Leroy T. 2009. Genetic differentiation of wild and cultivated populations: diversity of Coffea canephora Pierre in Uganda. Genome 52: 634-646.
Prezotti LC, Oliveira JA, Gomes JA, Dadalto GG. 2013. Manual de recomendação de calagem e adubação para o Estado do Espírito Santo: 5ª aproximação.
Team Rc. 2019. R: A language and environment for statistical computing v. 3.5. 1. Vienna, Austria: foundation for statistical computing.
Rabbani MA, Iwabuchi A, Murakami Y, Suzuki T, Takayangi K. 1998. Phenotypic variation and the relationship among mustard (Brassica juncea L.) germplasm from Pakistan. Euphytica 101: 357-366.
Rahman MS, Islam SMS. 2020. Genetic diversity analysis based on morphological characters in mulberry (Morus spp.) J Biosci 28: 111-119.
RAO RC. 1952. Advanced statistical methods in biometric research.
Rocha RB, Santos DV, Ramalho AR, Teixeira AL. 2014. Characterization and use of genetic variability of bank active germplasm Coffea canephora Pierre ex Froehner. Coffee Sci 8:478-485.
Silva FL, Baffa DCF, Rezende JC, Oliveira ACB, Pereira AA, Cruz CD. 2015. Genetic variability among robusta coffee genotypes in the state of Minas Gerais. Coffee Sci 10: 20-27.
Silvestrini M, Maluf MP, Silvarolla MB, Guerreiro-Filho O, Medina-Filho HP, Vanini MMT, Oliveira AS, Gaspari-Pezzopane C, Fazuoli LC. 2008. Genetic diversity of a Coffea germplasm collection assessed by RAPD markers. Genet Resour Crop Ev 55: 901-910.
Singh D. 1981. The relative importance of characters affecting genetic divergence. Indian J Genet Pl Br 41: 237-245.
Solórzano RGL, Bellis F, Leroy T, Plaza L, Guerrero H, Subia C, Calderón D, Fernández F, Garzón I, Lopez D, Vera D. 2017. Revealing the diversity of introduced Coffea canephora germplasm in ecuador: towards a national strategy to improve robusta. Sci World J 2017: 1-12.
Souza FF, Caixeta ET, Ferrao LFV, Pena GF, Sakiyama NS, Zambolim EM, Zambolim L, Cruz CD. 2013. Molecular diversity in Coffea canephora germplasm conserved and cultivated in Brazil. Crop Breed Appl Biot 13: 221-227.
Souza FF, Queiroz MA, Dias RCS. 2005. Divergência genética em linhagens de melancia. Hortic Bras 23: 179-183.
USDA 2019. United States department of agriculture. Production, Supply and Distribuition. Available at: https://apps.fas.usda. gov/psdonline/app/index.html#/app/downloads.