Genomics of Wild Relatives and Alien Introgressions

Abstract

Alien introgression breeding is an attractive approach to recover genetic variation that was lost during wheat domestication and breeding. New alleles and genes may be introduced from wild relatives from the tribe Triticeae, which exhibit large genetic variation and many potentially useful traits. Although a range of wheat-alien introgression lines has been developed, apart from the 1BL.1RS translocation, only a few commercial wheat cultivars benefitted from alien introgression. This is a consequence of poor knowledge of genome structure of wild donors, limited ability to control chromosome behavior during meiosis in interspecific hybrids and introgression lines, difficulties in eliminating unwanted chromatin transferred simultaneously with genes of interest, as well as a lack of tools permitting large-scale production and characterization of introgression lines. Recent advances in molecular and flow cytogenetics and genomics are bound to change the situation. New insights into the meiotic recombination raise the hopes for the ability to control its frequency and distribution. The progress in comparative genome analysis provides clues about the genome collinearity between wild species and wheat, making it possible to assess chances for chromosome recombination and predict its outcomes. Genomics tools enable massive and high-resolution screening of hybrids and their progenies and characterize their genomes, including the development of markers linked to traits of interest. Until recently, little attention has been paid to the function of introgressed genes and their interaction with the host genome. However, also this has been changing and all these achievements make the breeding of improved wheat cultivars using wild germplasm a realistic goal. Keywords (separated by "-") Wheat breeding-Alien gene function-Chromosome flow sorting-Chromosome genomics-Epigenetic modifications-Genome sequencing-Interspecific hybridization-Molecular cytogenetics-Molecular markers AUTHOR QUERIES

Dissecting the U, M, S and C genomes of wild relatives of bread wheat (Aegilops spp.) into chromosomes and exploring their synteny with wheat

“…tauschii, respectively) (Kilian et al, 2011;Shangguan et al, 2013). Slicing the genomes into single chromosomes provides a powerful approach to perform structural and functional genome analysis Rey et al, 2015).…”

“…The efficiency of introgression breeding and the development of high-density genetic maps of Aegilops is limited by small number of molecular markers suitable for highthroughput screening (Zhang et al, 1998). In recent decades, wheat-specific RFLP (Restriction Fragment Length Polymorphism), SSR (Simple Sequence Repeat), AFLP (Amplified Fragment Length Polymorphism) and Conserved Orthologous Set (COS) markers were tested in Aegilops species (Peil et al, 1998;Schneider et al, 2010;Rey et al, 2015). Nagy et al (2006) used S-SAP (Sequence-Specific Amplification Polymorphism) technology to produce 14 and 30 genome-specific markers for Ae.…”

“…More recently, Diversity Arrays Technology (DArT) markers and microarray hybridization-based sequence-independent marker systems were used to develop a high-density genetic map of wheat 9 wild emmer (Peleg et al, 2008). The advent of next generation sequencing (NGS) technologies led to the development of SNP-based platforms for wheat genotyping (Rey et al, 2015). However, low representation of wild wheat relatives in the SNP design may limit the utility of these platforms in alien introgression breeding (Winfield et al, 2016) and new genomic resources need to be generated from wild relatives of wheat.…”

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

“…Typically, introgression events have involved the transfer of a substantially sized donor chromosome segment, which, along with the target, probably bears gene(s), which impact negatively on the host's fitness (a phenomenon also called 'linkage drag') (Gill et al, 2011;Qi et al, 2007;Zamir, 2001). For this reason, very few introgression lines are represented in commercial cultivars (Rey et al, 2015). The prime means of reducing the length of an introgressed segment is to induce recombination with its homoeologous region (Niu et al, 2011).…”

Cytomolecular discrimination of the Am chromosomes of Triticum monococcum and the A chromosomes of Triticum aestivum using microsatellite DNA repeats

“…Fluorescence in situ hybridization (FISH) with repetitive DNA probes results in chromosome-specific hybridization patterns, making this technique an excellent tool for the karyotypic analysis of cereals (Mukai et al 1993;Pedersen and Langridge 1997). One of the most popular combinations of probes for the cytomolecular analysis of wheat consists of the satellite repeats pSc119.2, Afa family and pTa71 (Rey et al 2015). Unfortunately, these probes only produced a small number of weak diagnostic signals on the A genome chromosomes of wheat.…”