Microsatellite analysis of the correlation between molecular and morphological traits in assorted maize inbred lines

Abstract

The success in identifying heterosis in hybrid maize (Zea mays L.) breeding depends on the availability of reliable genetic diversity among maize inbred lines. Conventional methods of breeding have been boosted by the availability and efficiency of molecular markers. Coupling simple sequence repeat (SSR) markers with morphological markers provides thorough starting information for new inbred lines, especially from different genetic backgrounds. Furthermore, recent evidences that the environment can influence the epigenetic structure of the genome have necessitated morphological screening of crops during breeding programmes. This study used 28 agronomic traits and 14 SSR markers which are distributed uniformly in ten (1-10) inbred lines, namely EM11-133, EM12-210, OSU23i, CML395, CML202, CML442, CML444, CML208, CML312 and CML204 from Kenya, International Centre for the Improvement of Maize and Wheat (CIMMYT), and another (OSU 23i) from USA. The aim was to investigate their morphological and genetic diversity, categorise the inbred lines into useful groups based on the molecular profiles and morphological traits, and lastly determine the level of phenotype-genotype correlation. The dissimilarity calculated using SSR markers had a mean morphological dissimilarity of 0.895403, an r value of -0.1421 and a p -0.9840. The dissimilarity between the molecular and morphological traits was 0.860465. Comparison between the molecular and morphological data had a dissimilarity matrix with an r -0.2323 and a p value of 0.0120. This was probably due to intrinsic synteny in maize genome. The dendrograms generated with hierarchical Unweighted Pair Group Method with Arithmetic mean (UPGMA) cluster analysis of the Jaccard's similarity coefficient matrices revealed four major clusters. The Co-ancestry distance showed six tied groups with the Kenya cluster showing some differentiation with Exact Tests for population differentiation with a p = 0.0513. The American inbred line (OSU 23i) segregated alone, while the Kenya lines (EM11-133 and EM12-210) had close homology with the CIMMYT inbred lines (CMLs). A total of 2.0 alleles were detected among the inbred lines using bulk DNA samples and 14 SSR loci. Clustering analysis based on the genetic similarity coefficients separated the inbred lines into 4 groups with the American inbred line seeming to be genotypically more diverse from the others.Key Words: Genetic diversity, molecular markers, SSR, Zea mays RÉSUMÉLe succès dans l'identification des hétérosis de maïs hybrides (Zea mays L.) dépend de la disponibilité d'une diversité génétique fiable dans les lignées endogames du maïs. Les méthodes conventionnelles de l'hybridation avaient été améliorées par la disponibilité et l'efficacité des marqueurs moléculaires. Le couplage des marqueurs simples de sequence répétée (SSR) avec les marqueurs morphologiques fournit des informations fondamentales précises pour les nouvelles lignées endogames, principalement de différente constitution génétique. En outre, les recentes évidences selon...

Phenotypic characterization of elite quality protein maize (QPM) inbred lines adapted to tropical-highlands and the association studies using SSR markers

“…In agreement to this finding, Dagne (2008) reported a low correlation coefficient (r= 0.09) between morphological and SSR-based genetic distance measures among 35 QPM inbred lines using 40 SSR markers. Karanja et al (2009) found a correlation coefficient of 0.2323 with p value of 0.012 between SSR and morphological data in assorted maize inbred lines. Amelework et al (2016) also reported that there was no significant relationship between molecular and morphological distances in a study conducted using 30 SSRs and 36 sorghum genotypes.…”

“…Morphological and molecular markers and pedigree analyses are widely used in germplasm characterization and to establish genetic diversity and relationship in crop plants (Warburton et al, 2005). Morphoagronomic traits are among the earliest markers widely used in germplasm characterization, management and utilization (Smith and Smith, 1992;Karanja et al, 2009;Sow et al, 2014). Abu-Alrub et al (2006) used kernel characteristics as the best descriptors followed by ear traits for classifying Peruvian highland maize germplasm.…”

Diversity and path coefficient analysis of Southern African maize hybrids

“…These results are also supported by Shahrokhi and Khavarikhorasani (2013), who reported on the effectiveness of phenotypic traits as they grouped 28 maize hybrids into four clusters. Furthermore, Karanja et al (2009) reported that both phenotypic traits and SSR markers were effective in clustering inbred lines. Pedigree analysis placed 119 inbred maize lines into eight and SSR markers resulted in clustering the inbred lines into 10 groups (Reid et al, 2011).…”

Analysis of genetic diversity among tropical and subtropical maize inbred lines using SSR markers

“…In this study, mean of alleles per locus was considerably lower than reported earlier in the maize. Karanja et al, (2009) reported 2.0 averages of alleles using 14 loci. The SSRs used in this study were tri-repeat motifs (thirty nine loci), di and tetra-repeat (one locus each) whereas; information of one repeat motif was not available at MaizeGDB.…”