A bioinformatics approach to define the Eps-D1 subtelomeric chromosomal deletion in bread wheat (Triticum aestivum).

Abstract

Flowering time is one of the critical determinants of yields in flowering plants. The flowering time in bread wheat (Triticum aestivum) is directly determined by vernalization, photoperiod response and earliness per se (Eps). Previous studies on earliness per se regions revealed that Spark and Cadenza carry a large subtelomeric chromosomal deletion on the long arm of chromosome 1D (1DL) which caused a five-day early flowering relative to varieties with an intact 1DL named Eps-D1. This study used a bioinformatics approach to define the proximal end of Eps-D1. The known genes from the proximal end TaBradi2g14730 (inside the deletion) and TaBradi2g14790 (outside the deletion) were used to establish the Aegilops tauschii (wheat donor of the D genome) DNA sequence in-between. Sequence analysis bioinformatic tools were used to establish the Aegilops tauschii contig that was used for defining the proximal end of the deletion. Brachypodium distachyon synteneous genes which are collinear with the genes in the 1DL deletion were used to map the Aegilops tauschii contig. Approximately 130000 bases are between TaBradi2g14730 and TaBradi2g14790. It should now be easy to design 1DL genome specific primers to determine where exactly the proximal end of the deletion starts. These results are novel and there is no report in literature where this method was used. The results are a solid foundation for further studies and research on Eps-D1. This method can be used to define other deletions on other wheat chromosomes and is applicable to all other crops in general