Precise utilization of wild genetic resources to improve the resistance of their cultivated relatives to environmental growth limiting factors, such as salinity stress and diseases, requires a clear understanding of their genomic relationships. Although seriously criticized, analyzing these relationships in tribe Triticeae has largely been based on meiotic chromosome pairing in hybrids of wide crosses, a specialized and labourious strategy. In this study, DArTseq, an efficient genotyping-by-sequencing platform, was applied to analyze the genomes of 34 Triticeae species. We reconstructed the phylogenetic relationships among diploid and polyploid Aegilops and Triticum species, including hexaploid wheat. Tentatively, we have identified the diploid genomes that are likely to have been involved in the evolution of five polyploid species of Aegilops, which have remained unresolved for decades. Explanations which cast light on the progenitor of the A genomes and the complex genomic status of the B/G genomes of polyploid Triticum species in the Emmer and Timopheevi lineages of wheat have also been provided. This study has, therefore, demonstrated that DArTseq genotyping can be effectively applied to analyze the genomes of plants, especially where their genome sequence information are not available.

BackgroundThe tertiary gene pool of bread wheat, to which Leymus racemosus belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it. Continuous enrichment of public databases with useful information regarding these species is, therefore, needed to provide insights on their genome structures and aid successful utilization of their genes to develop improved wheat cultivars for effective management of environmental stresses.ResultsWe generated de novo DNA and mRNA sequence information of L. racemosus and developed 110 polymorphic PCR-based markers from the data, and to complement the PCR markers, DArT-seq genotyping was applied to develop additional 9990 SNP markers. Approximately 52% of all the markers enabled us to clearly genotype 22 wheat-L. racemosus chromosome introgression lines, and L. racemosus chromosome-specific markers were highly efficient in detailed characterization of the translocation and recombination lines analyzed. A further analysis revealed remarkable transferability of the PCR markers to three other important Triticeae perennial species: L. mollis, Psathyrostachys huashanica and Elymus ciliaris, indicating their suitability for characterizing wheat-alien chromosome introgressions carrying chromosomes of these genomes.ConclusionThe efficiency of the markers in characterizing wheat-L. racemosus chromosome introgression lines proves their reliability, and their high transferability further broadens their scope of application. This is the first report on sequencing and development of markers from L. racemosus genome and the application of DArT-seq to develop markers from a perennial wild relative of wheat, marking a paradigm shift from the seeming concentration of the technology on cultivated species. Integration of these markers with appropriate cytogenetic methods would accelerate development and characterization of wheat-alien chromosome introgression lines.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0603-1) contains supplementary material, which is available to authorized users.

Background Cowpea is a dryland crop with potential to improve food security in sub-Saharan Africa, where it is mostly produced and consumed. Contemporary plant improvement technologies, including genome editing, marker-assisted selection, and optimized transformation protocols, are being deployed to improve cowpea characteristics. Integrating speed breeding with these technologies would accelerate genetic gain in cowpea breeding. There are established speed breeding protocols for other important legumes, such as soybean, peanut, and chickpea, but none has been previously reported for cowpea. Results With the aid of regulated growth conditions in two different chamber types, as well as the cultivation of new plant generations from seeds of oven-dried immature pods, we developed and validated, for the first time, an efficient speed breeding protocol that accommodates approximately seven to eight breeding generations per year for 3 cowpea genotypes. The 3 cowpea genotypes were evaluated under controlled growth conditions in light-emitting diode and metal halide lamp chambers to determine the effect of CO2 supplementation on flowering and maturation durations, optimum conditions for plant growth, cross pollination, and pod development. Elevated CO2 concentration had no influence on either flowering time or pod development. Adequate temperature, relative humidity and light intensity improved plant development and the rate of successful hand pollination, and  cultivating seeds of 11-day-old immature pods oven-dried at 39 °C for 2 days resulted in at least a 62% reduction in the time between pollination and sowing of the next plant generation. The plants cultivated from seeds of the oven-dried immature pods showed no defect at any stage of development. Conclusions Using the speed breeding protocol developed in this study, cowpea breeding cycles can be increased from the traditional one cycle per year in the field to as many as 8 generations per year in regulated growth chamber conditions. This protocol has no special technical requirements; hence, it can be implemented in any standard growth chamber. This would fast-track development, testing, validation, and utilization of improved cowpea cultivars.

Ocimum basilicum is widely distributed in the tropical and subtropical regions of the world, with greatest variability in Africa and India. It is valued in many countries for its culinary, medicinal, industrial and religious importance. Although cytogenetic entries on the plant have been made in other geographical locations of the world, in Nigeria, such entries, prior to this report, have been limited if not completely unavailable. In this analysis, axillary buds, obtained from growing plants, were used to conduct mitotic study. Results from this study showed chromosome counts of 2n = 48 and 60, thus bringing to light the existence of chromosome number variation and the possibility of polyploidy at different levels in the plant species in this agro-ecological zone. This research has, therefore, established that at least there are two cytotypes in the population of Ocimum basilicum growing in the humid forest vegetation zone of Nigeria. Analysis of the two cytotypes revealed asymmetrical karyotypes, indicative of advancement in the evolutionary trend of the plant species.