Grouping and clustering of maize Lancaster germplasm inbreds according to the results of SNP-analysis
AbstractThe objective of this article is the grouping and clustering of maize inbred lines based on the results of SNP-genotyping for the verification of a separate cluster of Lancaster germplasm inbred lines. As material for the study, we used 91 maize (Zea mays L.) inbred lines, including 31 Lancaster germplasm lines and 60 inbred lines of other germplasms (23 Iodent inbreds, 15 Reid inbreds, 7 Lacon inbreds, 12 Mix inbreds and 3 exotic inbreds). The majority of the given inbred lines are included in the Dnipro breeding programme. The SNP-genotyping of these inbred lines was conducted using BDI-III panel of 384 SNP-markers developed by BioDiagnostics, Inc. (USA) on the base of Illumina VeraCode Bead Plate. The SNP-markers of this panel are biallelic and are located on all 10 maize chromosomes. Their range of conductivity was >0.6. The SNP-analysis was made in completely automated regime on Illumina BeadStation equipment at BioDiagnostics, Inc. (USA). A principal component analysis was applied to group a general set of 91 inbreds according to allelic states of SNP-markers and to identify a cluster of Lancaster inbreds. The clustering and determining hierarchy in 31 Lancaster germplasm inbreds used quantitative cluster analysis. The share of monomorphic markers in the studied set of 91 inbred lines equaled 0.7%, and the share of dimorphic markers equaled 99.3%. Minor allele frequency (MAF) > 0.2 was observed for 80.6% of dimorphic markers, the average index of shift of gene diversity equaled 0.2984, PIC on average reached 0.3144. The index of gene diversity of markers varied from 0.1701 to 0.1901, pairwise genetic distances between inbred lines ranged from 0.0316–0.8000, the frequencies of major alleles of SNP-markers were within 0.5085–0.9821, and the frequencies of minor alleles were within 0.0179–0.4915. The average homozygosity of inbred lines was 98.8%. The principal component analysis of SNP-distances confirmed the isolation of the Lancaster group within the general set of analyzed inbred lines. Two-dimensional component analysis showed that the first principal component (PCA1) accounted for 36.0% of total variation and divided the investigated set of 91 inbred lines into two fractions, while all the inbred lines which are considered Lancaster based on pedigree information were included in one of the fractions. The second principal component (PCA2), which accounted for 12.1% of total variation, separated most of the Lancaster germplasm inbred lines from the others in this fraction, although the overlapping of the locations of Lancaster and non-Lancaster inbred lines was observed. Qualitative cluster analysis of 31 Lancaster germplasm inbred lines allowed to identify two clusters: the first one includes 23 inbred lines of Ukrainian selection and the well known Mo17 inbred line (77.4% of total number of analysed lines) inbred line, and the second cluster included 6 inbred lines of Ukrainian selection and the well known Oh43 inbred line (22.6% of total number of analysed lines) inbred line. The isolation of two clusters within Lancaster germplasm indicates the genetic diversity in this plasm. The evaluation of genome similarities through allelic states of SNP-markers can successfully be used for classification and systematization of the gene pool of maize genetic resources.
Bennetzen, J. L., & Hake, E. S. A. (2009). Handbook of maize. Genetic and genomics. New York. Springer Science.
Brereton, R. G. (2003). Chemometrics: Data analysis for the laboratory and chemical plant. Wiley, Chichester.
Dao, A., Sanou, J., Mitchell, S. E., Gracen, V., & Danquah, E. Y. (2014). Genetic diversity among INERA maize inbred lines with single nucleotide polymor phism (SNP) markers and their relationship with CIMMYT, IITA, and temperate lines. BMC Genetics, 15, 127–140.
Derkach, K. V., Abraimova, O. E., & Satarova, T. M. (2016). Reguljacіja morfo genezu in vitro u lіnіj kukurudzi grupi Lankaster [Regulation of in vitro morphogenesis in maize inbreds of the Lancaster group]. Visnyk of Dnipro petrovsk Universitet. Biology, Ecology, 24(2), 253–257 (in Ukrainian).
Dzjubec’kij, B. V., Bodenko, N. A., Fed’ko, M. M., & Gusak, J. V. (2012). Stvorennja seredn’opіznіh gіbridіv kukurudzi na bazі plazmi Lankaster (С103) [Creation of medium-late hybrids of corn based on Lancaster germplasm (С103)]. Bjuleten’ Іnstitutu Sіl’s’kogo Gospodarstva Stepovoji Zony NAAN Ukrayiny, 3, 8–11 (in Ukrainian).
Elshire, R. J., Acharya, C. B., Mitchell, S. E., Flint-Garcia, S. A., McMullen, M. D., Holland, J. B., Buckler, E. S., & Gardner, C. A. (2013). Comprehen sive genotyping of the USA national maize inbreds seed bank. Genome Biology, 14(6), R55.
Li, X., Jian, Y., Xie, C., Wu, J., Xu, Y., & Zou, C. (2017). Fast diffusion of domesticated maize to temperate zones. Scientific Reports, 7, 2077–2089.
Lu, Y., Yan, J., Guimarães, C. T., Taba, S., Hao, Z., Gao, S., Chen, S., Li, J., Zhang, S., Vivek, B. S., Magorokosho, C., Mugo, S., Makumbi, D., Parento ni, S. N., Shah, T., Rong, T., Crouch, J. H., & Xu, Y. (2009). Molecular characterization of global maize breeding germplasm based in genome-wide single nucleotide polymorphisms. Theoretical and Applied Genetics, 120(1), 93–115.
Mikić, S., Kondić-špika, A., Brbaklić, L., Stanisavljević, D., Ćeran, M., Trkulja, D., & Mitrović, B. (2017). Molecular and phenotypic characterisation of diverse temperate maize inbred lines in Southeast Europe. Zemdirbyste-Agriculture, 104(1), 31–40.
Nelson, P. T., Krakowsky, M. D., Coles, N. D., Holland, J. B., Bubeck, D. M., Smith, J. S. C., & Goodman, M. M. (2016). Genetic characterization of the North Carolina State University Maize Lines. Crop Science, 56, 259–275.
Romay, M. C., Millard, M. J., Glaubitz, J. C., Peiffer, J. A., Swarts, K. L., Casste vens, T. M., Elshire, R. J., Acharya, C. B., Mitchell, S. E., Flint-Garcia, S. A., McMullen, M. D., Holland, J. B., Buckler, E. S., & Gardner, C. A. (2013). Comprehensive genotyping of the USA national maize inbreds seed bank. Genome Biology, 14(6), R55.
Schaefer, C. M., & Bernardo, R. (2013). Population structure and single nucleotide polymorphism diversity of historical Minnesota maize inbreds. Crop Science, 53(4), 1529–1536.
Semagn, K., Magorokosho, C., Vivek, B. S., Makumbi, D., Beyene, Y., Mugo, S., Prasanna, B. M., & Warburton, M. L. (2012). Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers. BMC Genomics, 13, 113–124.
Sivolap, J. M., Kozhuhova, N. J., & Kalendar’, R. N. (2011). Variabel’nost’ i spe cifichnost’ genomov sel’skohozjajstvennyh rastenij [Variability and specifici ty of genomes of agricultural plants]. Astroprint, Odessa (in Russian).
Smith, S. D., Murray, S. C., & Heffner, E. (2015). Molecular analysis of genetic diversity in a Texas maize (Zea mays L.) breeding program. Maydica, 60, 1–8.
Venkatramana, P., Carlson, C., Blackstad, M., Bialozynski, R., Schultz, Q., & Kaufman, B. (2010). Development and characterization of single nucleotide polymorphism (SNP) panel for marker assisted backcrossing in corn. Seed Technology, 32(2), 153–154.
Wen, W., Franco J., Chavez-Tovar, V. H., Yan, J., & Taba, S. (2012). Genetic characterization of a core set of a tropical maize race Tuxpeño for further use in maize improvement. PLoS One, 7(3), e32626.
Wu, X., Li, Y., Shi, Y., Song, Y., Wang, T., Huang, Y., & Li, Y. (2014). Fine genetic characterization of elite maize germplasm using high-throughput SNP genotyping. Theoretical and Applied Genetics, 127, 621–631.
Wu, Y., San Vicente, F., Huang, K., Dhliwayo, T., Costich, D. E., Semagn, K., & 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., & Zou, C. (2017). Development of a maize 55 K SNP array with improved genome coverage for molecular breeding. Molecular Breeding, 37(3), 20–34.
Zhang, X., Zhang, H., Li, L., Lan, H., Ren, Z., Liu, D., Wu, L., Liu, H., Jaqueth, J., Li, B., Pan, G., & Gao, S. (2016). Characterizing the popula tion structure and genetic diversity of maize breeding germplasm in Southwest China using genome-wide SNP markers. BMC Genomics, 17(1), 697–704.
Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons «Attribution» 4.0 License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.