Identification and Specific KASP Marker Development for Durum Wheat T2DS-2AS.2AL Translocation Line YL-429 with Wax Inhibitor Gene IW2

Non-glaucous wheat can reduce solar light reflection in low-light cultivation regions, enhancing photosynthetic efficiency and potentially increasing yield. In previous work, a non-glaucous cuticular line, YL-429, was discovered in derivatives of pentaploid hybrids by crossing the synthetic wheat LM/AT23 (non-glaucous cuticular) with its tetraploid donor parent LM (glaucous) and selfing to F₇ generations. In the present study, multicolor fluorescence in situ hybridization was used to characterize the karyotype of the YL-429 line; genome resequencing was performed to identify the breakpoint of the 2D-2A chromosome translocation of YL-429; and bulk sequencing analysis was conducted to detect the SNP in the translocated fragment and accordingly develop specific kompetitive allele-specific PCR markers for use in breeding. The line YL-429 was preliminarily determined as a 2DS and 2AS translocation (LM T2DS-2AS.2AL) line through karyotyping. Genome alignment identified an approximately 13.8 Mb segment, including the wax inhibitor gene <i>Iw2</i>, in the telomeric region of the 2DS chromosome arm replacing an approximately 16.1 Mb segment in that of the 2AS chromosome arm. According to the bulk DNA sequencing data, 27 specific KASP markers were developed for detecting the translocated fragment from the 2DS of <i>Aegilops tauschii</i>. The LM T2DS-2AS.2AL translocation line YL-429 could be helpful in improving the photosynthesis of durum wheat cultivated in low-light cultivation regions. The developed markers can assist the screening of the T2DS-2AS.2AL translocation in breeding.