A linkage map of Aegilops biuncialis reveals significant genomic rearrangements compared to bread wheat

Goatgrasses with U- and M-genomes are important sources of new alleles for wheat breeding to maintain yield and quality under extreme conditions. However, the introgression of beneficial traits from wild Aegilops species into wheat has been limited by poor knowledge of their genomes and scarcity of molecular tools. Here, we present the first linkage map of allotetraploid Aegilops biuncialis Vis., developed using 224 F₂ individuals derived from a cross between MvGB382 and MvGB642 accessions. The map comprises 5663 DArTseq markers assigned to 15 linkage groups corresponding to 13 chromosomes. Chromosome 1M^b could not be constructed due to a lack of recombination caused by rearrangements in the MvGB382 accession. The genetic map spans 2518 cM with an average marker density of 2.79 cM. The skeleton map contains 920 segregating markers, divided between the M^b sub-genome (425 markers) and the U^b sub-genome (495 markers). Chromosomes of the M^b sub-genome, originating from Aegilops comosa Sm. in Sibth. et Sm., show well-preserved collinearity with Triticum aestivum L. chromosomes. In contrast, chromosomes of the U^b sub-genome, originating from Aegilops umbellulata Zhuk., exhibit a varying degree of collinearity, with 1U^b, 3U^b, and 5U^b retaining a substantial level of collinearity with Triticum aestivum, while 2U^b, 4U^b, 6U^b, and 7U^b show significant rearrangements. A quantitative trait locus affecting fertility was identified near the centromere on the long arm of chromosome 3M^b, explaining 23.5% of the variance. The genome structure of Aegilops biuncialis, highlighted by the genetic map, provides insights into the speciation within the species and will support alien gene transfer into wheat.