Characterization of Chromosomal Rearrangement in New Wheat—Thinopyrum intermedium Addition Lines Carrying Thinopyrum—Specific Grain Hardness Genes

Abstract

The wild species, Thinopyrum intermedium. (Genome StStJSJSJJ), serves as a valuable germplasm resource providing novel genes for wheat improvement. In the current study, non-denaturing fluorescence in situ hybridization (ND-FISH) with multiple probes and comparative molecular markers were applied to characterize two wheat-Th. intermedium chromosome additions. Sequential ND-FISH with new labeled Th. intermedium specific oligo-probes were used to precisely determine the chromosomal constitution of Th. intermedium, wheat—Th. intermedium partial amphiploids and addition lines Hy36 and Hy37. The ND-FISH results showed that the added JS-St translocated chromosomes in Hy36 had minor Oligo-5S ribosomal DNA (rDNA) signals at the short arm, while a pair of J-St chromosomes in Hy37 had major Oligo-pTa71 and minor Oligo-5S rDNA signals. The 90K SNP array and PCR-based molecular markers that mapped on wheat linkage group 5 and 3 facilitated the identification of Thinopyrum chromosome introgressions in the addition lines, and confirmed that added chromosomes in Hy36 and Hy37 were 5JSS.3StS and 5JS.3StS, respectively. Complete coding sequences at the paralogous puroindoline-a (Pina) loci from Th. intermedium were cloned and localized on the short arm of chromosome 5JS of Hy36. Line Hy36 showed a reduction in the hardness index, which suggested that Th. intermedium-specific Pina gene sequences may be associated with the softness trait in wheat background. The molecular cytogenetic identification of novel wheat—Th. intermedium derivatives indicated that the frequent chromosome rearrangement occurred in the progenies of wheat-Thinopyrum hybridization. The new wheat-Thinopyrum derived lines may increase the genetic diversity for wheat breeding.

Genome-Wide Distribution of Novel Ta-3A1 Mini-Satellite Repeats and Its Use for Chromosome Identification in Wheat and Related Species

“…The Ta-3A1 probe has been used to precisely identify the chromosomal breakage points in wheat-Th. intermedium introgression lines [68,69]. FISH specific hybridization sites by Ta-3A1 on Secale, Dasypyrum, and Aegilops chromosomes can also trace specific chromatin in wheat-alien introgression lines.…”

Diversified Chromosome Rearrangements Detected in a Wheat‒Dasypyrum breviaristatum Substitution Line Induced by Gamma-Ray Irradiation

“…Furthermore, synthesized tandem repeat-based oligos are equally efficient for the identification of wheat and alien chromosomes [32]. Moreover, oligo probes including Oligo-B and Oligo-D for distinguishing wheat B- and D-genomes [33], Oligo-pDb12H for targeting Dasypyrum chromosomes have also been developed [34]. These oligo probes have allowed researchers to easily identify some specific chromosomal rearrangements and reciprocal translocations involving the three sub-genomes of wheat and Dasypyrum genome through ND-FISH analysis.…”

Development of Specific Thinopyrum Cytogenetic Markers for Wheat-Wheatgrass Hybrids Using Sequencing and qPCR Data

“…The development of cytogenetic markers is a tedious process that requires long and laborious FISH testing of various probes before a suitable probe is found. In many cytogenetic studies aimed at molecular-cytogenetic characterization of wheat–wheatgrass hybrids, the classical FISH probes such as 45S rDNA, pAs1, pSc119.2, and pTa71 are applied [ 32 , 37 , 38 , 39 , 40 , 41 , 42 ]. However, the development of new Thinopyrum -specific probes is necessary as it would enable the precise identification of chromosome rearrangements in amphidiploids and introgression lines and can be used in evolutionary studies of Triticeae [ 40 , 43 , 48 , 49 ].…”

“…One of the basic approaches in the study of WWGHs and introgression lines, along with molecular markers, remains cytogenetic studies with common and specific probes [ 21 , 37 , 38 , 39 , 40 , 41 , 42 ]. This approach enables the discrimination of related subgenomes in amphidiploids, visualization of chromosomal composition, and identification of rearrangements.…”