Copy number variation of TdDof controls solid-stemmed architecture in wheat

Abstract

Stem solidness is an important agronomic trait of durum (Triticum turgidum L. var. durum) and bread (Triticum aestivum L.) wheat that provides resistance to the wheat stem sawfly. This dominant trait is conferred by the SSt1 locus on chromosome 3B. However, the molecular identity and mechanisms underpinning stem solidness have not been identified. Here, we demonstrate that copy number variation of TdDof, a gene encoding a putative DNA binding with one finger protein, controls the stem solidness trait in wheat. Using map-based cloning, we localized TdDof to within a physical interval of 2.1 Mb inside the SSt1 locus. Molecular analysis revealed that hollow-stemmed wheat cultivars such as Kronos carry a single copy of TdDof, whereas solid-stemmed cultivars such as CDC Fortitude carry multiple identical copies of the gene. Deletion of all TdDof copies from CDC Fortitude resulted in the loss of stem solidness, whereas the transgenic overexpression of TdDof restored stem solidness in the TdDof deletion mutant pithless1 and conferred stem solidness in Kronos. In solid-stemmed cultivars, increased TdDof expression was correlated with the down-regulation of genes whose orthologs have been implicated in programmed cell death (PCD) in other species. Anatomical and histochemical analyses revealed that hollow-stemmed lines had stronger PCD-associated signals in the pith cells compared to solid-stemmed lines, which suggests copy number-dependent expression of TdDof could be directly or indirectly involved in the negative regulation of PCD. These findings provide opportunities to manipulate stem development in wheat and other monocots for agricultural or industrial purposes.

Comparative Analysis of Coding and Non-Coding Features within Insect Tolerance Loci in Wheat with Their Homologs in Cereal Genomes

“…In this study, we focused on two crucial wheat pathogens, Wheat Stem Sawfly (WSS; Cephus cinctus Norton) and Orange Wheat Blossom Midge (OWBM, Sitodiplosis mosellana), and explored the content and organization of coding and non-coding features on multiple resistance loci across cereal genomes. The focus of this study is not the causal or candidate genes, which have recently been firmly established for two of the loci already [17,23], but rather to provide a comparative overview of Each number indicates the number of miRNA families identified in each cereal species that are shared (or not) with the others. Three miRNA families were shown to be shared among all analyzed species, whereas eight miRNAs were conserved in wheat, barley, and rye.…”

“…Stem solidness trait has been utilized as the primary defense strategy against WSS in wheat. The causal gene, TdDof, of the major QTL on chromosome 3BL controlling stem solidness was recently identified and characterized [17]. When this QTL and homologous regions in related Poaceae species were compared, a high level of synteny was observed (Figure 1).…”

“…The causal gene, TdDof, residing within the major QTL on the long arm of chromosome 3B (Qss.msub-3BL in hexaploid bread and SSt1 in tetraploid wheat; 3BL-QTL hereafter, for simplicity) that confers stem solidness in wheat has been recently identified [17]. In order to understand how this locus has been broadly shaped in cereal genomes, molecular markers defining the 3BL-QTL [12] were first mapped to the 3B chromosomes in Triticum aestivum cv.…”

“…Copy number variation, where the presence of additional copies coupled with increased expression of this gene, has been shown to positively regulate stem solidness [17].…”

Development and Identification of Four New Synthetic Hexaploid Wheat Lines with Solid Stems

“…The synergistic two-way interaction between SSt1 and other secondary QTLs on the chromosome resulted in a higher rate of solid stems than when SSt1 was used alone 32 . The solidity of the stem was complementary to many factors 33 , and the additive effect of the SSt1 resistance allele in durum wheat produced stem solidness three times that of common wheat, with an additive effect 32,33 . TRITD3Bv1G280530 in solid-stemmed and hollow-stemmed durum wheat differed in copy number and was most likely to be a candidate gene in the SSt1 interval 34 .…”