Abstract
Association mapping is a powerful approach to detect associations between traits of interest and genetic markers based on linkage disequilibrium in molecular plant breeding. The aim of this study was the identification of single nucleotide polymorphisms (SNPs) and SilicoDArT markers associated with yield traits and morphological features in maize. Plant material constituted inbred lines. The field experiment with inbred lines was established on 10 m2 plots in a set of complete random blocks in three replicates. We observed 22 quantitative traits. Association mapping was performed in this study using a method based on the mixed linear model with the population structure estimated by eigenanalysis (principal component analysis applied to all markers) and modeled by random effects. As a result of mapping, 969 markers (346 SNPs and 623 SilocoDArT) were selected from 49,911 identified polymorphic molecular markers, which were significantly associated with the analyzed morphological features and yield structure traits. Markers associated with five or six traits were selected during further analyses, including SilicoDArT 4591115 (anthocyanin coloration of anthers, length of main axis above the highest lateral branch, cob length, number of grains per cob, weight of fresh grains per cob and weight of fresh grains per cob at 15% moisture), SilicoDArT 7059939 (anthocyanin coloration of glumes of cob, time of anthesis—50% of flowering plants, time of silk emergence—50% of flowering plants, anthocyanin coloration of anthers and cob diameter), SilicoDArT 5587991 (anthocyanin coloration of glumes of cob, time of anthesis—50% of flowering plants, anthocyanin coloration of anthers, curvature of lateral branches and number of rows of grain). The two genetic similarity dendrograms between the inbred lines were constructed based on all significant SNPs and SilicoDArT markers. On both dendrograms lines clustered according to the kernel structure (flint, dent) and origin. The selected markers may be useful in predicting hybrid formulas in a heterosis culture. The present study demonstrated that molecular SNP and Silico DArT markers could be used in this species to group lines in terms of origin and lines with incomplete origin data. They can also be useful in maize in predicting the hybrid formula and can find applications in the selection of parental components for heterosis crossings.
Highlights
Modern maize breeding is to create new cultivars with improved traits [1]
The development of new genotyping methods based on hybridization markers or next-generation sequencing technology (NGS) makes them increasingly applied in basic research
The availability of a large number of single nucleotide polymorphisms (SNPs) markers or the reproducibility of DArT technology and their decreasing costs make modern methods to be used in economically important plants in applied research, such as identification of trait markers or even selection at the level of entire genomes, when the criterion of time is more important than the initial financial expenditure
Summary
The breeding based largely on the use of the heterosis phenomenon (F1 hybrid vigor), occurring as a result of crossing two inbred lines with the highest combining ability. High-yielding hybrids are obtained with traits that exceed parental lines. The reasons for the occurrence of heterosis are not clearly determined, there are many hypotheses explaining this phenomenon, e.g., the hypothesis of overdomination or domination. It is believed that heterosis is associated with the genetic distance between parental forms, determined by DNA polymorphism, adequate selection of parental components becomes a key element in the breeding process [1]. Intensive research have been conducted on the possible use of molecular markers in the selection of parental lines for heterosis crosses [2,3,4]. Markers based on single nucleotide polymorphisms (SNPs) are increasingly used for this purpose [5]
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