The in silico identification and characterization of a bread wheat/Triticum militinae introgression line

Abstract

The capacity of the bread wheat (Triticum aestivum) genome to tolerate introgression from related genomes can be exploited for wheat improvement. A resistance to powdery mildew expressed by a derivative of the cross-bread wheat cv. Tähti × T. militinae (Tm) is known to be due to the incorporation of a Tm segment into the long arm of chromosome 4A. Here, a newly developed in silico method termed rearrangement identification and characterization (RICh) has been applied to characterize the introgression. A virtual gene order, assembled using the GenomeZipper approach, was obtained for the native copy of chromosome 4A; it incorporated 570 4A DArTseq markers to produce a zipper comprising 2132 loci. A comparison between the native and introgressed forms of the 4AL chromosome arm showed that the introgressed region is located at the distal part of the arm. The Tm segment, derived from chromosome 7G, harbours 131 homoeologs of the 357 genes present on the corresponding region of Chinese Spring 4AL. The estimated number of Tm genes transferred along with the disease resistance gene was 169. Characterizing the introgression's position, gene content and internal gene order should not only facilitate gene isolation, but may also be informative with respect to chromatin structure and behaviour studies.

Keywords: GenomeZipper; alien introgression; chromosome rearrangement; chromosome translocation; comparative analysis; linkage drag.

Figure 1

The bivariate flow karyotype of T. militinae. Mitotic chromosomes at metaphase were stained with DAPI and GAA microsatellites were labelled with FITC. A set of 13 distinct clusters were obtained (shown boxed). Cluster #8 harbours the Tm chromosome (7G) which was the origin of the introgression segment present in line 8.1. Cluster #4 harbours a putative homoeolog of 7G and based on its width and shape most likely comprises a mixture of two distinct chromosomes.

Figure 2

Variation in homoeologous gene density along the various 4A‐CS chromosome segments compared to their homoeologous chromosomes. The structure of native 4A‐CS chromosome is represented at the bottom with syntenic blocks with rice genome shown in different colours (red = Os3; blue = OS11; green = Os6). (a) The 4A homoeologous gene density compared to 4B and 4D chromosomes, (b) comparison with the 5BL and 5DL chromosome arms and (c) comparison with chromosome arms 7AS and 7DS is shown as homoeologous genes frequency histogram. Homoeologous regions are characterized by a high average frequency (denoted by the horizontal lines). The lower average frequency shown by the group 7 chromosomes reflects a significantly lower sequencing coverage.

Figure 3

Variation in homologous gene density between 4A‐CS chromosome and 4AL‐TM telosome. The structure of native 4A‐CS chromosome is represented at the bottom with syntenic blocks with rice genome shown in different colours (red = Os3; blue = OS11; green = Os6). The homologous gene density along the 4A‐CS zipper compare to 4AL‐TM assembly is shown with the black line. The segment of the Tm introgression overlaps the 7BS translocation in 4AL (red highlight). The equivalent region on the 4AL‐CS telosome harbours 357 genes, only 131 have homologous genes on the Tm segment. The dark blue bar represents approximate localization of the QPm‐tut‐4A locus.