Molecular Diversity, Structure and Domestication of Grasses

Over the last 10,000 years, crop domestication has been the single most important human cultural development. Grasses are prominent among these crops, and provide the vast majority of the world\u27s food. Similar traits have been selected during the domestication and breeding of these critically important grasses, and since they share a similar complement of genes, the same set of genes may have been selected. Even though the process of domestication occurred over the same 5000 to 10,000 year period, the domesticated grasses have major differences in genome structure, diversity, and life history. Molecular investigations of grass domestication have succeeded in identifying progenitor species and are beginning to catalog genetic resources. Additionally, research is now elucidating some of the basic processes by which crops have evolved over the last few millennia. In this review, we discuss our present knowledge of molecular diversity among the grass crops and relate that diversity to the genes involved in domestication and to yield gains. Understanding the connection between diversity and genome structure will be critical to future crop breeding

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

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

Nucleotide diversity and molecular evolution of the WAG-2 gene in common wheat (Triticum aestivum L) and its relatives

In this work, we examined the genetic diversity and evolution of the WAG-2 gene based on new WAG-2 alleles isolated from wheat and its relatives. Only single nucleotide polymorphisms (SNP) and no insertions and deletions (indels) were found in exon sequences of WAG-2 from different species. More SNPs and indels occurred in introns than in exons. For exons, exons+introns and introns, the nucleotide polymorphism π decreased from diploid and tetraploid genotypes to hexaploid genotypes. This finding indicated that the diversity of WAG-2 in diploids was greater than in hexaploids because of the strong selection pressure on the latter. All dn/ds ratios were < 1.0, indicating that WAG-2 belongs to a conserved gene affected by negative selection. Thirty-nine of the 57 particular SNPs and eight of the 10 indels were detected in diploid species. The degree of divergence in intron length among WAG-2 clones and phylogenetic tree topology suggested the existence of three homoeologs in the A, B or D genome of common wheat. Wheat AG-like genes were divided into WAG-1 and WAG-2 clades. The latter clade contained WAG-2, OsMADS3 and ZMM2 genes, indicating functional homoeology among them

The use and limits of ITS data in the analysis of intraspecific variation in Passiflora L. (Passifloraceae)

The discovery and characterization of informative intraspecific genetic markers is fundamental for evolutionary and conservation genetics studies. Here, we used nuclear ribosomal ITS sequences to access intraspecific genetic diversity in 23 species of the genus Passiflora L. Some degree of variation was detected in 21 of these. The Passiflora and Decaloba (DC.) Rchb. subgenera showed significant differences in the sizes of the two ITS regions and in GC content, which can be related to reproductive characteristics of species in these subgenera. Furthermore, clear geographical patterns in the spatial distribution of sequence types were identified in six species. The results indicate that ITS may be a useful tool for the evaluation of intraspecific genetic variation in Passiflora

Phylogeography of the wild subspecies of Zea mays

Z. mays ssp. parviglumis and ssp. mexicana are the closest wild relatives to domesticated maize. Using isozyme and chloroplast evidence, this study examined how populations of these subspecies are related to one another, and how geography has structured the relationships between them. As some lines of evidence indicate that ssp. mexicana is a derived clade of ssp. parviglumis, dispersal, isolation by distance (IBD), and altitudinal hypotheses were tested to explain the genetic differentiation of ssp. mexicana and parviglumis populations. Simple dispersal hypotheses explained most of this genetic variation, while IBD and altitudinal models explained very little of the variation. The origin of this dispersal appeared to be the middle and lower elevation regions of Guerrero. These dispersal events are discussed in light of Late Pleistocene and Holocene climate change and maize domestication