Abstract
Bread wheat (Triticum aestivum, 2n = 6x = 42, AABBDD) has a complex allohexaploid genome, which makes it difficult to differentiate between the homoeologous sequences and assign them to the chromosome A, B, or D subgenomes. The chromosome-based draft genome sequence of the ‘Chinese Spring’ common wheat cultivar enables the large-scale development of polymerase chain reaction (PCR)-based markers specific for homoeologs. Based on high-confidence ‘Chinese Spring’ genes with known functions, we developed 183 putative homoeolog-specific markers for chromosomes 4B and 7B. These markers were used in PCR assays for the 4B and 7B nullisomes and their euploid synthetic hexaploid wheat (SHW) line that was newly generated from a hybridization between Triticum turgidum (AABB) and the wild diploid species Aegilops tauschii (DD). Up to 64% of the markers for chromosomes 4B or 7B in the SHW background were confirmed to be homoeolog-specific. Thus, these markers were highly transferable between the ‘Chinese Spring’ bread wheat and SHW lines. Homoeolog-specific markers designed using genes with known functions may be useful for genetic investigations involving homoeologous chromosome tracking and homoeolog expression and interaction analyses.
Highlights
The number of plant genomes that have been sequenced since the release of the Arabidopsis thaliana genome sequence in 2000 continues to grow
Because very few ancestor lines of T. turgidum and Ae. tauschii were involved in the generation of bread wheat, a considerable amount of genetic variation in the two ancestor species is missing from modern bread wheat populations
The synthetic hexaploid wheat (SHW) lines enable the simultaneous re-use of T. turgidum and Ae. tauschii, and have been preferentially used by several research groups to enhance the genetic diversity of bread wheat [8,9,21,22]
Summary
The number of plant genomes that have been sequenced since the release of the Arabidopsis thaliana genome sequence in 2000 continues to grow. Recent genome comparisons have advanced our understanding of the evolution and structure of plant genomes, and the resulting information has been used to improve crop quality and production. Bread wheat (Triticum aestivum, 2n = 6x = 42, AABBDD) is a vital crop in terms of food security, providing nearly 20% of the calories and protein consumed by the global population [1]. The study of its genetics has been impeded by its complex and large hexaploid genome that contains a high proportion of repetitive DNA [2,3].
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