Grouping and clustering of maize Lancaster germplasm inbreds according to the results of SNP-analysis


  • K. V. Derkach Institute of Grain Crops of National Academy of Agrarian Science of Ukraine
  • T. M. Satarova Oles Honchar Dnipro National University
  • V. V. Borysova Institute of Grain Crops of National Academy of Agrarian Science of Ukraine
  • V. Y. Cherchel Institute of Grain Crops of National Academy of Agrarian Science of Ukraine
  • B. V. Dzyubeckiy Institute of Grain Crops of National Academy of Agrarian Science of Ukraine
Keywords: Zea mays, markers of single nucleotide polymorphism of DNA, principal component analysis, cluster analysis

Abstract

The 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. 

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Published
2017-08-03
How to Cite
Derkach, K., Satarova, T., Borysova, V., Cherchel, V., & Dzyubeckiy, B. (2017). Grouping and clustering of maize Lancaster germplasm inbreds according to the results of SNP-analysis. Regulatory Mechanisms in Biosystems, 8(3), 343-348. https://doi.org/https://doi.org/10.15421/021753

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