RAPD and Internal Transcribed Spacer Sequence Analyses Reveal Zea nicaraguensis as a Section Luxuriantes Species Close to Zea luxurians

Abstract

Genetic relationship of a newly discovered teosinte from Nicaragua, Zea nicaraguensis with waterlogging tolerance, was determined based on randomly amplified polymorphic DNA (RAPD) markers and the internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA using 14 accessions from Zea species. RAPD analysis showed that a total of 5,303 fragments were produced by 136 random decamer primers, of which 84.86% bands were polymorphic. RAPD-based UPGMA analysis demonstrated that the genus Zea can be divided into section Luxuriantes including Zea diploperennis, Zea luxurians, Zea perennis and Zea nicaraguensis, and section Zea including Zea mays ssp. mexicana, Zea mays ssp. parviglumis, Zea mays ssp. huehuetenangensis and Zea mays ssp. mays. ITS sequence analysis showed the lengths of the entire ITS region of the 14 taxa in Zea varied from 597 to 605 bp. The average GC content was 67.8%. In addition to the insertion/deletions, 78 variable sites were recorded in the total ITS region with 47 in ITS1, 5 in 5.8S, and 26 in ITS2. Sequences of these taxa were analyzed with neighbor-joining (NJ) and maximum parsimony (MP) methods to construct the phylogenetic trees, selecting Tripsacum dactyloides L. as the outgroup. The phylogenetic relationships of Zea species inferred from the ITS sequences are highly concordant with the RAPD evidence that resolved two major subgenus clades. Both RAPD and ITS sequence analyses indicate that Zea nicaraguensis is more closely related to Zea luxurians than the other teosintes and cultivated maize, which should be regarded as a section Luxuriantes species.

Phylogeny, Floral Evolution, and Inter-Island Dispersal in Hawaiian Clermontia (Campanulaceae) Based on ISSR Variation and Plastid Spacer Sequences

“…In general, however, many investigators have found that phylogenies based on such arbitrarily amplified markers are highly concordant with, but better resolved than those based on plastid or ITS sequences and/or restriction sites ([29], [31]–[36] for AFLPs, [28], [37] for RAPDs, [38]–[40] for ISSRs). Rieseberg [27] found that 91% of 220 RAPD markers used to study interspecific relationships in Helianthus appeared to reflect homologous markers; Ipek et al [30] found that 95% of AFLP amplicons in garlic were identical or highly homologous to the typical marker for that band.…”

The effect of different genome and cytoplasm on meiotic pairing in maize newly synthetic polyploids

“…In some allopolyploids, the different genomes from parents may occur divergent changes and different degrees of diplodization (Liu and Wendel 2002), probably due to the discrepant stability of parental genome. In this study, Z. perennis genome is more stable than that of maize in four allopolyploids, and possible explanations for our observations include: (a) the phylogenetic analysis shows that Z. perennis is more primitive than maize (Wang et al 2011), therefore, the inherent stability probably exist in Z. perennis genome as a result from long-term evolution; (b) recent studies demonstrate maize genome has tetraploid origin (Gonzalez and Poggio 2011), ''A'' and ''B'' genome probably exist partial homology (Molina et al 2012); (c) for the two allotriploids, the haploid genome of maize can hardly perform the homologous chromosome paring; (d) different genomes in one nucleus may lead to the disordered expression of Phs1 and Pam1, which play important roles on chromosome paring (Molina et al 2012).…”

“…The results suggest Z. perennis cytoplasm may give a relatively relaxed environment especially for maize genome. The possible reasons include: (a) the presence of foreign nuclear genome in cytoplasm from the male parent can result in nuclear-cytoplasm incompatibility (Wang et al 2010;Cui et al 2012) and maternal enzymatic system may treat the male chromosomes as exogenous intruders (Hu et al 2013), thus, gene structure variation, aneuploidy and chromosomes structure variation as well as meiosis confusion can potentially occur, comparing to Z. perennis cytoplasm, maize cytoplasm probably has a stronger defense system; (b) Z. perennis is more primitive than maize (Wang et al 2011), and the cytoplasm may have a greater containment than maize; (c) Z. perennis cytoplasm probably has a less negative influence on Phs1 and Pam1 than maize cytoplasm. Additional, interactions can occur between nuclear and cytoplasm followed by loss of genes from both nuclear genome and plasmon (Rand et al 2004), which suggests genome stability also may be affected by interactions between different genome composition and cytoplasm (Cui et al 2012), different results in allotriploids and allotetraploids conform to this speculation.…”

Molecular Characterization of two Maize Hybrids Based on Primer Bias

“…An improved de novo assembly and annotation of a maize reference genome have been recently conducted [14]. To investigate the wide diversity of maize genotypes, few studies on ITS sequencing [15,16] and microsatellites or simple sequence repeats [17,18] have been published. The phylogenetic relationships of Zea species inferred from ITS sequences were demonstrated to be highly concordant with Random Amplified Polymorphic DNA (RAPD) evidence [16,19].…”

“…To investigate the wide diversity of maize genotypes, few studies on ITS sequencing [15,16] and microsatellites or simple sequence repeats [17,18] have been published. The phylogenetic relationships of Zea species inferred from ITS sequences were demonstrated to be highly concordant with Random Amplified Polymorphic DNA (RAPD) evidence [16,19]. The main objective of this study was to identify a molecular marker or a haplotype-specific signature sequence that can be used to distinguish the genomes of two Egyptian maize hybrids, M10 and M321M321.…”