Sequence Elimination and Cytosine Methylation Are Rapid and Reproducible Responses of the Genome to Wide Hybridization and Allopolyploidy in Wheat

Abstract

Interspecific or intergeneric hybridization, followed by chromosome doubling, can lead to the formation of new allopolyploid species. Recent studies indicate that allopolyploid formation is associated with genetic and epigenetic changes, although little is known about the type of changes that occur, how rapidly they occur, and the type of sequences involved. To address these matters, we have surveyed F1 hybrids between diploid species from the wheat (Aegilops and Triticum) group and their derived allotetraploids by screening a large number of loci using amplified fragment length polymorphism and DNA gel blot analysis and by assaying the extent of cytosine methylation. We found that sequence elimination is one of the major and immediate responses of the wheat genome to wide hybridization or allopolyploidy, that it affects a large fraction of the genome, and that it is reproducible. In one cross between Ae. sharonensis ؋ Ae. umbellulata , 14% of the loci from Ae. sharonensis were eliminated compared with only 0.5% from Ae. umbellulata, with most changes occurring in the F1 hybrid. In contrast, crosses between Ae. longissima ؋ T. urartu showed that sequence elimination was more frequent after chromosome doubling. Alterations in cytosine methylation occurred in ‫ف‬ 13% of the loci, either in the F1 hybrid or in the allopolyploid. For eight of nine bands that were isolated, the sequences that underwent elimination corresponded to low-copy DNA, whereas alterations in methylation patterns affected both repetitive DNA sequences, such as retrotransposons, and low-copy DNA in approximately equal proportions.

Allopolyploidy-Induced Rapid Genome Evolution in the Wheat (Aegilops–Triticum) Group

“…However, the loss of the hybridization fragment(s) found here and in other works Liu et al, 1998a;Shaked et al, 2001) was observed in all enzymes that produced diagnosable polymorphism. Moreover, we checked hybrids and allopolyploids with methylation-sensitive and -insensitive isoschizomeric restriction enzymes and found the same RFLP profiles (data not shown).…”

“…Altered patterns of DNA methylation have been shown to be a frequent outcome in new allopolyploids (Song et al, 1995;Liu et al, 1998b;Shaked et al, 2001). However, the loss of the hybridization fragment(s) found here and in other works Liu et al, 1998a;Shaked et al, 2001) was observed in all enzymes that produced diagnosable polymorphism.…”

“…Although the molecular mechanism of sequence elimination is not known (for discussion, see Shaked et al, 2001), a number of rules and characteristics of this process can be derived from our results. An obvious and critical question arising from the results of Feldman et al (1997) and Liu et al (1997Liu et al ( , 1998aLiu et al ( , 1998b is whether findings from synthetic allopolyploids, which were produced by colchicine treatment of F1 plants, can be extended to natural allopolyploids.…”

“…One could argue that a particular set of sequences (CSSs and GSSs) was analyzed in this work, thus explaining the differences. In a related study, Shaked et al (2001) analyzed a random set of loci in the same allopolyploids that are described in this work. They found that sequence elimination is the major response of the wheat genome to allopolyploidization, and their results confirm the nonrandom nature of sequence elimination.…”

Genomewide Variation in an Introgression Line of Rice-Zizania Revealed by Whole-Genome re-Sequencing

“…It has been established that hybridization between genetically differentiated species or ecotypes may induce structural genomic changes (e.g., rearrangement) in the hybrids [1-7]. To address the genetic consequences of inter-specific hybridization, a larger number of studies have investigated the genetic variation patterns and molecular modes of the resultant hybrids.…”