The karyotype of Aegilops geniculata and its use to identify both addition and substitution lines of wheat

BACKGROUND: The annual allotetraploid species Aegilops geniculata harbors a number of traits relevant for wheat improvement. An effective cytogenetic method has yet to be developed to distinguish between each of its 14 chromosomes. RESULTS: A fluorescence in situ hybridization (FISH) approach was adopted to describe the karyotype of Ae. geniculata. Each of its 14 chromosomes was unequivocally recognized using a cocktail of three probes, namely pTa-713, (AAC)(5) and pTa71. FISH karyotyping was then used to detect and characterize selections from an Ae. geniculata × bread wheat wide cross of a chromosome 1M(g) disomic addition line and three 4M(g)(4B) substitution lines. The identity of the addition line was confirmed by the presence of Glu-M1, detected both using an SDS-PAGE separation of endosperm proteins and by applying a PCR assay directed at the Glu-M1 locus. The status of the substitution lines was validated by genotyping using a wheat single nucleotide polymorphism chip. CONCLUSION: FISH karyotyping based on pTa-713, (AAC)(5) and pTa71 will be useful for determining the contribution of Ae. geniculata to derivatives of an Ae. geniculata × wheat wide cross. SNP chip-based genotyping is effective for confirming the status of whole chromosome wheat/alien substitution lines. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13039-019-0428-2) contains supplementary material, which is available to authorized users.