Genetic Characterization Of Early Generation Lines Using SNPS Makers And Agronomic Traits For Resistance To Striga Improvement In Maize
Abstract
The characterization of a greater number of lines hence potentially increase the efficiency of maize breeding programs. This study aims to assess the genetic variation and relationships existing within a population of 177 lines and the two parental lines, using 8,883 SNPs markers obtained from sequencing genotyping (GBS) and four agronomic traits. Two hundred S1 lines and four checks including the two parents have been evaluated under Striga hermonthica infestation in Benin Republic and Nigeria for two years during 2018 and 2019 growing seasons using 51 x 4 lattice design with two replicates. The UPGMA phylogeny, was used to group the progenies based on their genetic similarity. The tested lines have displayed high genetic variability for all the agronomic traits. Analysis molecular revealed that the polymorphism information content has been varied from 0.047 to 0.50, with average of 0.37, and 63% of the SNP makers were highly polymorphic. The population has displayed a moderate diversity with average genetic diversity of 0.44. The estimated genetic distance has been varied from 0.01 to 0.79 and the highest distance has been observed between the two parental lines. UPGMA clustering based on the Gower dissimilarity matrix grouped the 177 lines into two clusters (I and II) at 30% genetic similarity threshold. The estimated genetic distances between lines showed that all the progenies were genetically related to the two parental lines; and have the potential to provide new favorable alleles for the development of high-performing, Striga-resistant and/or Striga-tolerant maize populations.
Keywords
Full Text:
PDFReferences
Prasanna, B. M., Cairns, J.E., Zaidi. H., Beyene, Y., Makumbi, D.,Gowda, M., Magorokosho, C., · Zaman Allah, M., Olsen, M.,· Das, A., Worku, M., Gethi, J., Vivek, B. S., Nair, S. K., Rashid, Z., · Vinayan, M. T., Issa, A.B.,· Dhliwayo, F.S.V. T., and Zhang, X. (2021). Beat the stress: breeding for climate resilience in maize for the tropical rainfed environment. Theoretical and Applied Genetics, https://doi.org/10.1007/s00122-021-03773-7.
Badu-Apraku B. and Fakorede M.A.B. (2017). Maize in Sub-Saharan Africa: Importance and Production Constraints. In: Advances in genetic enhancement of early and extra-early maize for Sub-Saharan Africa. Switzerland: Springer. DOI 10.1007/978-3-319-64852-1_1.
Prasanna, B.M., Palacios-Rojas, N., Hossain, F., Muthusamy, V., Menkir,A., Dhliwayo, T., Ndhlela, T., San Vicente, F., Nair, S.K., Vivek,B.S., Zhang,X., Olsen, M., and Fan, X. (2020). Molecular Breeding for Nutritionally Enriched Maize: Status and Prospects. Front. Genet. 10:1392. doi: 10.3389/fgene.2019.01392.
FAOSTAT. (2020). FAO, Rome. Available at: www.faostat.org (accessed 15 June 2021).
Shiferaw, B., Prasanna, B.M., Hellin, J., andBänziger, M. (2011). Crops that feed the world 6. Past successes and future challenges to the role played by maize in global food security. Food Secur 3:307–327. https://doi.org/10.1007/s12571-011-0140-5.
Kim, S. K., Adetimirin, V. O., Thé, C., and Dossou, R. (2002). Yield losses in maize due to Striga hermonthica in West and Central Africa. International Journal of Pest Management, 48(3), 211–217. https://doi. org/10.1080/09670870110117408.
Kamara, A.Y., Menkir, A., Chikoye, D., Solomon, R., Tofa, A.I., and Omoigui, L.O. (2020). Seed dressing maize with imazapyr to control Striga hermonthica in farmers’ fields in the savannas of Nigeria. Agriculture, 56: 620–632.
Menkir A, Crossa J, Meseka S, Bossey B, Muhyideen O, Riberio PF, Coulibaly M, Yacoubou A-M, Olaoye G and Haruna A (2020) Stacking Tolerance to Drought and Resistance to a Parasitic Weed in Tropical Hybrid Maize for Enhancing Resilience to Stress Combinations. Front. Plant Sci. 11:166, 1-16. doi: 10.3389/fpls.2020.00166.
Cairns, J.E., and Prasanna, B.M. (2018). Developing and deploying climateresilient maize varieties in the developing world. Curr Opin Plant Biol 45:226–230. https://doi.org/10.1016/j.pbi.2018.05.004.
Menkir, A. (2006). Assessment of reactions of diverse maize inbred lines to Striga hermonthica (Del.) Benth. Plant Breeding, 125:131–139.
Menkir, A., Kling, J. G., Badu-Apraku, B., and Ibikunle, O. (2006). Registration of 26 tropical maize germplasm lines with resistance to Striga hermonthica. Crop Science, 46: 1007–1009.
Sserumaga, J.P., Makumbi, D., Ji, H., Njoroge, K., Muthomi, J.W., Chemining’wa, G.N., Si-myung, L., Asea, G., and Kim, H. (2014). Molecular characterization of tropical maize inbred lines using microsatellite DNA markers. Maydica, 59, 267–274.
Mafakheri, K., Bihamta, M.R., and Abbasi, A.R. (2017). Assessment of genetic diversity in cowpea (Vigna unguiculata L.) germplasm using morphological and molecular characterisation. Cogent Food Agric. 3:1-20. https://doi.org/10.1080/23311932.2017.
Westman, A.L. and Kresovich, S., (1997). Use of molecular marker techniques for description of plant genetic variation. In: Biotechnology and plant genetic resources. Callow JL, Ford-Lloyd BV, Newburry HJ eds. CAB Int 9-4.
Legesse, B.W., Myburg, A.A., Pixley, K.V., Botha, A.M. (2006). Genetic diversity of African maize inbred lines revealed by SSR markers. Hereditas 18: 415-423.
Govindaraj, M., Vetriventhan, M., Srinivasan, M. (2015). Importance of genetic diversity assessment in crop plants and its recent advances: An overview of its analytical perspectives. Genet. Res. Int. 431487.
Choukan, R., Hossainzadeh, A., Ghannadha, M.R., Talei, A.R., Mohammadi, S.A., andWarburton, M.L. (2006). Use of SSR data to determine relationships and potential heterotic groupings within medium to late maturing Iranian maize inbred lines. Field Crop Res. 95: 221-222.
Nyombayire, A., Derera,J., Sibiya,J., Gasura, E., and Ngaboyisonga, C. (2016). Genetic diversity among maize inbred lines selected for the mid-altitudes and highlands of Rwanda. Maydica, 61: 1-7.
Mengesha, W.A., Menkir, A., Nnanna,U., Meseka, S., Farinola,A., Germa,G., and Gedil,M., (2017). Genetic diversity of tropical maize inbred lines combining resistance to Striga hermonthica with drought tolerance using SNP markers. Plant Breeding 136: 338–343.
Bawa, A., Abdulai, M. S., and Addai, I. K. (2015). Evaluation of inbred lines and hybrid maize (Zea mays L.) for tolerance to Striga hermonthica (Del.) Benth in the guinea savanna agro-ecological zone of Ghana. American Journal of Agricultural and Biological Science, 10(3), 128–136. https://doi.org/10.3844/ajabssp.2015.128.136.
Sam, O.A., Muyideen, O.O., Oluyinka, J.I., Melaku,G., Anthony,O.J. and Amudalat, B.O.(2019). Assessment of genetic diversity among low nitrogen-tolerant early generation maize inbred lines using SNP markers, South African Journal of Plant and Soil, 1–8, DOI: 10.1080/02571862.2018.153701.
Belalia, N., Lupini, A., Djemel, A., Morsli, A., Mauceri, A., Lotti, C., Khelifi-Slaoui, M., Khelifi, L., and Sunseri, F. (2019. Analysis of genetic diversity and population structure in Saharan maize (Zea mays L.) populations using phenotypic traits and SSR markers. Genet. Resour. Crop Evol. 66, 243–257.
Giordani, W., Scapim, C.A., Ruas, P.M., Ruas, C.D., Contreras-Soto, R., Coan, M., Fonseca, I.C., Gonçalves, L.S (2019). Genetic diversity, population structure and AFLP markers associated with maize reaction to southern rust. Bragantia, 78, 183–196. 2.
Badu-Apraku, B., Garcia-Oliveira, A.L., Petroli, C. D., Hearne, S., Adewale S.A., and Gedil M. (2021). Genetic diversity and population structure of early and extra-early maturing maize germplasm adapted to sub-Saharan Africa. BMC Plant Biology; 21:96, 1-15 https://doi.org/10.1186/s12870-021-02829-6.
Wu, Y., Vicente, S.F., Huang, K., Dhliwayo,T., Costich, D.E., Semagn,K., Sudha,N., Olsen, M., Prasanna,M.B., Zhang,X., and Babu, R. (2016). Molecular characterization of CIMMYT maize inbred lines with genotyping-by-sequencing SNPs. Theoretical and Applied Genetics, 129: 753–765.
Xu,C., Ren, Y., Jian,Y., Guo, Z., Zhang, Y., Xie, C., Fu,J., Wang, H., Wang,G., Xu, Y., Li,P., Cheng Zou, P. (2017). Development of a maize 55 K SNP array with improved genome coverage for molecular breeding. Molecular Breeding, 37: 20.
Kasoma, C., Hussein S., Mark D. L., Shayanowako A. I.T., and Mathew I. (2021). Revealing the genetic diversity of maize (Zea mays L.) populations by phenotypic traits and DArTseq markers for variable resistance to fall armyworm. Genet Resour Crop Evol. 68:243–259 https://doi.org/10.1007/s10722-020-00982-9.
Badu-Apraku, B., Adewale S., Agre P., Gedil, M., & Asiedu R.(2020a). Identification of QTLs Controlling Resistance/Tolerance to Striga hermonthica in an Extra-Early Maturing Yellow Maize Population. Agronomy, 10:1-18.
Saghai-Maroof, M.A., Soliman, K.M., Jorgensen, R.A., Allard, R.W. (1984) Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc. Natl. Acad. Sci. USA, 81, 8014–8018.
Elshire, R.J., Glaubitz, J.C.; Sun, Q.; Poland, J.A.; Kawamoto, K.; Buckler, E.S.; Mitchell, S.E. A robust (2011). Simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 6, e19379.
Glaubitz, J.C., Casstevens, T.M., Lu, F.,Harriman, J.,Elshire, R.J.,Sun, Q., Buckler, E.S. (2014). TASSEL-GBS: A high capacity genotyping by sequencing analysis pipeline. PLoS ONE, 9, e90346.
Vargas, M.; Combs, E.; Alvarado, G.; Atlin, G.; Mathews, K.; Crossa, J. (2013). META: A suite of SAS programs to analyze multienvironment breeding trials. Agron. J. 105, 9–11.
Wickham, H. (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, https://ggplot2.tidyverse.org.
Liu, K., and Muse S. V. (2005). Power marker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21, 2128— 2129.
Botstein, D. R., White R. L., Skolnick, M., and Davis,R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32, 314—333.
Rogers, J. S. (1972). Measures of genetic similarity and genetic distance. Studies in Genetics, VII. Univ. Texas Publ., Texas. 7213, 145—153.
Tamura, K., Peterson, D., Peterson,N., Stecher, G., Nei, M., and Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731—2739.
Nda, H. A., Akanvou, L., Pokou, N.D. , Akanza, K. P., Kouakou, C. K. and Zoro, B. I. A. (2016). Genetic diversity and population structure of maize landraces from Côte d’Ivoire. Afr. J. Biotechnol. Vol. 15(44), pp. 2507-2516, DOI: 10.5897/AJB2016.15678.
Kwabena Darkwa, Kwabena Darkwa, Bunmi Olasanmi, Kolade, O., Pierre Mournet, Antonio Lopez-Montes, David Dekoeyer, Patrick Adebola, Lava P. Kumar, Robert Asiedu, and Asrat Asfaw (2020). A SNP-Based Linkage Map and QTL Identification for resistance to Yam Anthracnose Disease (YAD) in Water Yam (Discorea alata), Research Square, 1-24. https://doi.org/10.21203/rs.3.rs-26806/v1.
Menkir, A., Makumbi, D.,and Franco, J. (2012). Assessment of reaction patterns of hybrids to Striga hermonthica (Del.) Benth. under artificial infestation in Kenya and Nigeria. Crop Sci. 52, 2528–2537.
Menkir, A., and Meseka, S. (2019). Genetic improvement in resistance to Striga in tropical maize hybrids. Crop Sci. 59, 2484–2497.
Badu-Apraku, B., Adewale, S., Agre P., Gedil, M., Toyinbo, J., & Asiedu R. (2020b). Identification of QTLs for grain yield and other traits in tropical maize under Striga infestation. PLoS ONE,15: 1-20.
Makumbi, D., Diallo, A., Kanampiu, F., Mugo,S., & Karaya, H. (2015). Agronomic performance and genotype × environment interaction of herbicide resistant maize varieties in eastern Africa. Crop Sci 55:541-555. doi.org/10.2135/cropsci2014.08.0593.
Oyekale, S.A., Badu-Apraku, B., Adetimirin, V.O., Unachukwu, N., & Gedil, M. (2021). Development of Extra-Early Provitamin a Quality Protein Maize Inbreds with Resistance/Tolerance to Striga hermonthica and Soil Nitrogen Stress. Agronomy, 11, 891: 1-23. https://doi.org/10.3390/ agronomy11050891.
Wu,X., Li,Y., Li, X., Li,C., Shi,Y., Song,Y., Zhzng, Z., Li,Y., and Wang, T.(2015). Analysis of genetic differentiation and genomic variation to reveal potential regions of importance during maize improvement. BMC Plant Biol. 15(1):25, 1-13.
Novoselović, D., Bentley,A.R., Šimek,R., Dvojković,K., Sorrells,M.E., Gosman N, et al. (2016). Characterizing Croatian wheat germplasm diversity and structure in a European context by DArT markers. Front Plant Sci. 7:184.
Adu, G.B., Badu-Apraku, B., Akromah, R., Garcia-Oliveira,A.L., Awuku, F.J., Gedil, M. (2019).Genetic diversity and population structure of early-maturing tropical maize inbred lines using SNP markers. PLoS One.14(4): e0214810.
Badu-Apraku, B., Garcia-Oliveira, A.L. , Petroli, C. D., Hearne, S. , Adewale, S.A. and Gedil, M. (2021). Genetic diversity and population structure of early and extra-early maturing maize germplasm adapted to sub-Saharan Africa, BMC Plant Biology 21:96, 1-15.
Obeng-Bio,E., Badu-Apraku, B., Ifie,B.E., Danquah A., Takyiwaa,B.E., Dadzie, M.A., Noudifoulè, G.,T., and Talabi,A.,O., (2020). Genetic diversity among early provitamin A quality protein maize inbred lines and the performance of derived hybrids under contrasting nitrogen environments. BMC Genetics, 21:78, 1-13. https://doi.org/10.1186/s12863-020-00887-7.
Wu, X., Wang, A., Guo, X., Liu, P., Zhu, Y., Li, X., and Chen, Z. (2019). Genetic characterization of maize germplasm derived from Suwan population and temperate resources, Hereditas, 156:2, 1-8. https://doi.org/10.1186/s41065-018-0077-1.
Elston, R.C. (2005). Genetic markers. Encyclopedia of Biostatistics, John Wiley and Sons Ltd.
Garcia, A.A., Benchimol, L.L., Barbosa, A.M., Geraldi, I.O., Souza, C.L., and Souza, A.P.D. (2004). Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines. Genet Mol Biol 27:579–588.
Mangelsdorf, P.C., and Jones,D.F. (1926). The expression of mendelian factorsin the gametophyte of maize. Genetics, 11, 423-455.
DOI: http://dx.doi.org/10.52155/ijpsat.v27.2.3271
Refbacks
- There are currently no refbacks.
Copyright (c) 2021 Abdoul-Madjidou Yacoubou, Nouhoun Zoumarou Wallis, Nnanna Unachukwu, Hafiz Adio Salami, Narcisse S. HOUNFODJI, Agre Paterne
This work is licensed under a Creative Commons Attribution 4.0 International License.