Structural chromosome rearrangements and polymorphisms identified in Chinese wheat cultivars by high-resolution multiplex oligonucleotide FISH

Abstract

High-resolution multiplex oligonucleotide FISH revealed the frequent occurrence of structural chromosomal rearrangements and polymorphisms in widely grown wheat cultivars and their founders. Over 2000 wheat cultivars including 19 founders were released and grown in China from 1949 to 2000. To understand the impact of breeding selection on chromosome structural variations, high-resolution karyotypes of Chinese Spring (CS) and 373 Chinese cultivars were developed and compared by FISH (fluorescence in situ hybridization) using an oligonucleotide multiplex probe based on repeat sequences. Among them, 148 (39.7%) accessions carried 14 structural rearrangements including three single translocations (designated as T), eight reciprocal translocations (RT), one pericentric inversion (perInv), and two combined variations having both the deletion and single translocations. Five rearrangements were traced to eight founders, including perInv 6B detected in 57 cultivars originating from Funo, Abbondanza, and Fan 6, T 1RS∙1BL in 47 cultivars derived from the Lovrin series, RT 4AS∙4AL-1DS/1DL∙1DS-4AL in 31 varieties from Mazhamai and Bima 4, RT 1RS∙7DL/7DS∙1BL in three cultivars was from Aimengniu, and RT 5BS∙5BL-5DL/5DS∙5DL-5BL was only detected in Youzimai. In addition to structural rearrangements, 167 polymorphic chromosome blocks (defined as unique signal patterns of oligonucleotide repeat probes distributed within chromosomes) were identified, and 59 were present in one or more founders. Some specific types were present at high frequencies indicating selective blocks in Chinese wheat varieties. All cultivars and CS were clustered into four groups and 15 subgroups at chromosome level. Common block patterns occurred in the same subgroup. Origin, geographic distribution, probable adaptation to specific environments, and potential use of these chromosomal rearrangements and blocks are discussed.

Discovery of powdery mildew resistance gene candidates fromAegilops biuncialischromosome 2Mbbased on transcriptome sequencing

“…After GISH, the hybridization signals were washed off with PBS (phosphate-buffered saline). Eight single-strand oligonucleotides were then used as probes for dual-color ND-FISH [36,39]. The eight oligonucleotides includes Oligo-pAs1-1, Oligo-pAs1-3, Oligo-pAs1-4, Oligo-pAs1-6, Oligo-AFA-3, Oligo-AFA-4, Oligo-pSc119.2-1 and Oligo-(GAA) 10.…”

Identification of large-scale genomic rearrangements during wheat evolution and the underlying mechanisms

“…Allopolyploid genome plasticity, together with heterosis, may play an important role in the success of some allopolyploid lineages, relative to their diploid progenitors (Feldman and Levy 2012;Van de Peer et al 2017). Large-scale genomic rearrangements between wheat allopolyploids (Devos et al 1995;Badaeva et al 2007;Jorgensen et al 2017;Huang et al 2018;Thind et al 2018) and between wheat allopolyploids and their progenitor species Huo et al 2018) were previously identified. However, the mechanisms involved in such rearrangements remain largely unknown.…”

Identification and characterization of large-scale genomic rearrangements during wheat evolution

“…Large-scale genomic rearrangements between wheat allopolyploids [25][26][27][28][29] and between wheat allopolyploids and their progenitor species [30,31] were previously identified. The mechanism(s) of DNA sequence elimination, including deletion of TE-containing sequences following allopolyploidization events, has yet to be identified.…”