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

Abstract

SummaryThe 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.

Divergence between bread wheat and Triticum militinae in the powdery mildew resistance QPm.tut-4A locus and its implications for cloning of the resistance gene

“…Majority of these were developed using GenomeZipper and 4AL-specific BAC clones. Besides markers owm16 and owm39 , polymorphism was inferred using the 4AL-7G and 4AL CS survey sequences (Abrouk et al 2017 , IWGSC 2014 ). Segregation patterns observed in the extended CS × 8.1 mapping population were used to establish marker order.…”

“…Valárik et al 2006 ). The GenomeZipper and chromosome-specific survey sequences (Abrouk et al 2017 , Hernandez et al 2012 , IWGSC 2014 ) were particularly effective in this context, but use was also made of sequence scaffolds developed in the tetraploid wheat T. dicoccoides (Avni et al 2017 ) and the BAC contigs defining the chromosome 4AL physical map (IWGSC 2018 ). Initially, these resources allowed the genetic length of the target to be narrowed to just 0.012 cM (Fig.…”

“…The informativeness of a potential marker was first assessed via an in silico inspection of the chromosome-specific survey sequences of 4AL-7G (Abrouk et al 2017 ) and the chromosome survey sequences (CSS) of 4AL CS generated by IWGSC ( 2014 ). The choice of sequences was governed by the need to saturate the genetic map of the QPm.tut - 4A region, so it was based on a virtual gene order of the chromosome 4A represented by GenomeZippers (Abrouk et al 2017 , Hernandez et al 2012 ). 4AL CSS scaffolds obtained from the GenomeZipper delimited by the markers flanking the QPm.tut - 4A segment were aligned with 4AL-7G sequence scaffolds using the BlastN algorithm (Altschul et al 1990 ).…”

“…Tähti background, the resistance decreases the number of secondary haustoria formed by the pathogen and enhances host cell apoptosis (Islamov et al 2015 ). The gene (or genes) present within QPm.tut - 4A , which acts in a race non-specific manner (Jakobson et al 2012 ), is located in T. militinae itself on chromosome 7G (Abrouk et al 2017 ). In a hybrid between wild-type bread wheat and the introgression line, little recombination occurs between the T. militinae segment and the segment of chromosome 4AL which has been replaced in line 8.1.…”

Targeted sequencing of the short arm of chromosome 6V of a wheat relative Haynaldia villosa for marker development and gene mining

“…Thus, the introgression of alien chromatin harboring traits of interest by chromosome engineering remains a priority. However, due to linkage drag, this strategy often introduces favorable traits together with deleterious loci, compromising yield and quality [43]. Thus, advanced chromosome engineering is needed to minimize alien chromatin during alien introgression breeding.…”