Genetic and epigenetic variations induced by wheat-rye 2R and 5R monosomic addition lines.

BACKGROUND: Monosomic alien addition lines (MAALs) can easily induce structural variation of chromosomes and have been used in crop breeding; however, it is unclear whether MAALs will induce drastic genetic and epigenetic alterations. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, wheat-rye 2R and 5R MAALs together with their selfed progeny and parental common wheat were investigated through amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP) analyses. The MAALs in different generations displayed different genetic variations. Some progeny that only contained 42 wheat chromosomes showed great genetic/epigenetic alterations. Cryptic rye chromatin has introgressed into the wheat genome. However, one of the progeny that contained cryptic rye chromatin did not display outstanding genetic/epigenetic variation. 78 and 49 sequences were cloned from changed AFLP and MSAP bands, respectively. Blastn search indicated that almost half of them showed no significant similarity to known sequences. Retrotransposons were mainly involved in genetic and epigenetic variations. Genetic variations basically affected Gypsy-like retrotransposons, whereas epigenetic alterations affected Copia-like and Gypsy-like retrotransposons equally. Genetic and epigenetic variations seldom affected low-copy coding DNA sequences. CONCLUSIONS/SIGNIFICANCE: The results in the present study provided direct evidence to illustrate that monosomic wheat-rye addition lines could induce different and drastic genetic/epigenetic variations and these variations might not be caused by introgression of rye chromatins into wheat. Therefore, MAALs may be directly used as an effective means to broaden the genetic diversity of common wheat

Numbers of lost and new bands in progeny compared with their parental plants.

*<p>‘–’indicates no comparison was done.</p

Method of AFLP was used to analyze the ten parental wheat plants.

<p>AFLP fingerprints of genomic DNA of ten ‘Mianyang 11’ plants displayed by selective primer combination <i>Eco</i>R I-ACG+ <i>Mse</i> I-CAA. M, DNA marker. 1–10, ten single ‘Mianyang 11’ plants.</p

Types of polymorphic methylated sites in the ten progeny of ‘Mianyang11’.

*<p>HPS, hypermethylation polymorphism site; DPS, demethylation polymorphism site; UPS, unpone.0054057.g001.tifcertain polymorphism site.</p>**<p>The numbers were obtained by comparing ‘Mianyang11’ with each of its ten progeny.</p

Sequences of AFLP and MSAP adapters and primers used in this study.

<p>Sequences of AFLP and MSAP adapters and primers used in this study.</p

Criteria by which patterns of polymorphic methylated sites were judged.

*<p>EM, <i>Eco</i>R I+<i>Msp</i> I; EH, <i>Eco</i>R I+<i>Hpa</i> II; -, band absent; +, band present.</p

Method of AFLP was used to analyze the 11 materials in present study.

<p>AFLP fingerprints of genomic DNA of the 11 materials displayed by selective primer combination <i>Eco</i>R I-AAC+ <i>Mse</i> I-CTG. MY11, ‘Mianyang11’.</p

Method of MSAP was used to analyze the 11 materials in present study.

<p>MSAP fingerprints of genomic DNA of the 11 materials and variation of methylation pattern displayed by selective primer combination <i>Eco</i>R I-AAC+ <i>Hpa</i> II/<i>Msp</i> I-TCGA. EM, <i>Eco</i>R I+<i>Msp</i> I; EH, <i>Eco</i>R I+<i>Hpa</i> II; MY11, ‘Mianyang11’.</p