DArTseq-based analysis of genomic relationships among species of tribe Triticeae

Offiong U Edet,Yasir S A Gorafi,Hisashi Tsujimoto,Shuhei Nasuda

doi:10.1038/s41598-018-34811-y

Offiong U Edet, Yasir S A Gorafi + Show 2 more

Open Access

https://doi.org/10.1038/s41598-018-34811-y

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Abstract

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.

Highlights

Triticeae is one of the most economically important tribes of the grass family, Poaceae, and includes such globally significant species as bread wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), and rye (Secale cereale L.)
To determine the putative progenitors of each of the polyploid species of Aegilops, SilicoDArT markers in the diploid genomes of all the Aegilops species were used as genome analyzers (Table 1)
The progenitors of the polyploid species were estimated based on the proportions of diploid markers that are retained in each polyploid genome

Summary

Introduction

Triticeae is one of the most economically important tribes of the grass family, Poaceae, and includes such globally significant species as bread wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), and rye (Secale cereale L.). Chromosome pairing is affected by diverse factors, and the reliability of failed chromosome pairing as an indicator of genome dissimilarity has been questioned[9,10,11] Molecular cytogenetic methods such as C-banding, fluorescence in situ hybridization and genomic in situ hybridization have helped to generate useful information on genome differences and phylogenetic relationships in the Triticeae[1,2,3,12,13]. The choice of which data to use depends on the research objective Using both types of data, we clarified the extent of genomic similarity among Aegilops species in different sections and clusters and the evolutionary relationships between diploid and polyploid species in Aegilops and Triticum species. The consistency of the outcomes of this study with previous reports and the flexibility of DArTseq genotyping make this marker system suitable for routine applications to analyze plant genomes

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