Separating homeologs by phasing in the tetraploid wheat transcriptome

Abstract Polyploidy occurs prevalently and plays an important role during plant speciation and evolution. This phenomenon suggests polyploidy could develop novel features that enable them to adapt wider range of environmental conditions compared with diploid progenitors. Bread wheat (Triticum aestivum L., BBAADD) is a typical allohexaploid species and generally exhibits greater salt tolerance than its tetraploid wheat progenitor (BBAA). However, little is known about the underlying molecular basis and the regulatory pathway of this trait. Here, we show that the histone acetyltransferase TaHAG1 acts as a crucial regulator to strengthen salt tolerance of hexaploid wheat. Salinity-induced TaHAG1 expression was associated with tolerance variation in polyploidy wheat. Overexpression, silencing and CRISPR-mediated knockout of TaHAG1 validated the role of TaHAG1 in salinity tolerance of wheat. TaHAG1 contributed to salt tolerance by modulating ROS production and signal specificity. Moreover, TaHAG1 directly targeted a subset of genes that are responsible for hydrogen peroxide production, and enrichment of TaHAG1 triggered increased H3 acetylation and transcriptional upregulation of these loci under salt stress. In addition, we found the salinity-induced TaHAG1-mediated ROS production pathway is involved in salt tolerance difference of wheat accessions with varying ploidy. Our findings provide insight into the molecular mechanism of how an epigenetic regulatory factor facilitates adaptability of polyploidy wheat and highlights this epigenetic modulator as a strategy for salt tolerance breeding in bread wheat.

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Function and evolution of allelic variation of Sr13 conferring resistance to stem rust in tetraploid wheat ( Triticum turgidum L.)

The Plant Journal ◽

10.1111/tpj.15263 ◽

2021 ◽

Author(s):

Baljeet K. Gill ◽

Daryl L. Klindworth ◽

Matthew N. Rouse ◽

Jinglun Zhang ◽

Qijun Zhang ◽

...

Keyword(s):

Stem Rust ◽

Triticum Turgidum ◽

Allelic Variation ◽

Tetraploid Wheat

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The Independent Domestication of Timopheev’s Wheat: Insights from Haplotype Analysis of the Brittle rachis 1 (BTR1-A) Gene

Genes ◽

10.3390/genes12030338 ◽

2021 ◽

Vol 12 (3) ◽

pp. 338

Author(s):

Moran Nave ◽

Mihriban Taş ◽

John Raupp ◽

Vijay K. Tiwari ◽

Hakan Ozkan ◽

...

Keyword(s):

Promoter Region ◽

Haplotype Analysis ◽

Common Ancestor ◽

Triticum Turgidum ◽

Tetraploid Wheat ◽

Wheat Species ◽

Loss Of Function ◽

Brittle Rachis ◽

Gene Level ◽

Large Panel

Triticum turgidum and T. timopheevii are two tetraploid wheat species sharing T. urartu as a common ancestor, and domesticated accessions from both of these allopolyploids exhibit nonbrittle rachis (i.e., nonshattering spikes). We previously described the loss-of-function mutations in the Brittle Rachis 1 genes BTR1-A and BTR1-B in the A and B subgenomes, respectively, that are responsible for this most visible domestication trait in T. turgidum. Resequencing of a large panel of wild and domesticated T. turgidum accessions subsequently led to the identification of the two progenitor haplotypes of the btr1-A and btr1-B domesticated alleles. Here, we extended the haplotype analysis to other T. turgidum subspecies and to the BTR1 homologues in the related T. timopheevii species. Our results showed that all the domesticated wheat subspecies within T. turgidum share common BTR1-A and BTR1-B haplotypes, confirming their common origin. In T. timopheevii, however, we identified a novel loss-of-function btr1-A allele underlying a partially brittle spike phenotype. This novel recessive allele appeared fixed within the pool of domesticated Timopheev’s wheat but was also carried by one wild timopheevii accession exhibiting partial brittleness. The promoter region for BTR1-B could not be amplified in any T. timopheevii accessions with any T. turgidum primer combination, exemplifying the gene-level distance between the two species. Altogether, our results support the concept of independent domestication processes for the two polyploid, wheat-related species.

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Genetically Divergent Types of the Wheat Leaf Fungus Puccinia triticina in Ethiopia, a Center of Tetraploid Wheat Diversity

Phytopathology ◽

10.1094/phyto-10-15-0247-r ◽

2016 ◽

Vol 106 (4) ◽

pp. 380-385 ◽

Cited By ~ 10

Author(s):

J. A. Kolmer ◽

M. A. Acevedo

Keyword(s):

Leaf Rust ◽

Common Wheat ◽

Hexaploid Wheat ◽

Rust Fungus ◽

Tetraploid Wheat ◽

Low Frequency ◽

Puccinia Triticina ◽

Leaf Rust Resistance ◽

Virulence Phenotype ◽

Wheat Leaf

Collections of Puccinia triticina, the wheat leaf rust fungus, were obtained from tetraploid and hexaploid wheat in the central highlands of Ethiopia, and a smaller number from Kenya, from 2011 to 2013, in order to determine the genetic diversity of this wheat pathogen in a center of host diversity. Single-uredinial isolates were derived and tested for virulence phenotype to 20 lines of Thatcher wheat that differ for single leaf rust resistance genes and for molecular genotypes with 10 simple sequence repeat (SSR) primers. Nine virulence phenotypes were described among the 193 isolates tested for virulence. Phenotype BBBQJ, found only in Ethiopia, was predominantly collected from tetraploid wheat. Phenotype EEEEE, also found only in Ethiopia, was exclusively collected from tetraploid wheat and was avirulent to the susceptible hexaploid wheat ‘Thatcher’. Phenotypes MBDSS and MCDSS, found in both Ethiopia and Kenya, were predominantly collected from common wheat. Phenotypes CCMSS, CCPSS, and CBMSS were found in Ethiopia from common wheat at low frequency. Phenotypes TCBSS and TCBSQ were found on durum wheat and common wheat in Kenya. Four groups of distinct SSR genotypes were described among the 48 isolates genotyped. Isolates with phenotypes BBBQJ and EEEEE were in two distinct SSR groups, and isolates with phenotypes MBDSS and MCDSS were in a third group. Isolates with CCMSS, CCPSS, CBMSS, TCBSS, and TCBSQ phenotypes were in a fourth SSR genotype group. The diverse host environment of Ethiopia has selected and maintained a genetically divergent population of P. triticina.

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Composition of and variation in high- and low-molecular weight glutenin subunits, and omega gliadins in Ethiopian tetraploid wheat germplasm

Plant Genetic Resources ◽

10.1079/pgr2006110 ◽

2006 ◽

Vol 4 (2) ◽

pp. 134-143 ◽

Cited By ~ 7

Author(s):

Faris Hailu ◽

Eva Johansson ◽

Arnulf Merker ◽

Getachew Belay ◽

Harjit-Singh ◽

...

Keyword(s):

Molecular Weight ◽

Tetraploid Wheat ◽

Glutenin Subunit ◽

Low Molecular Weight ◽

Glutenin Subunits ◽

Hmw Glutenin Subunits ◽

Lmw Glutenin Subunits ◽

Hmw Glutenin ◽

Omega Gliadins ◽

High Degree

A collection of 120 Ethiopian tetraploid wheat accessions was analysed for high-molecular weight (HMW) glutenin subunit, low-molecular weight (LMW) glutenin subunit and omega gliadin composition by SDS–PAGE. For the HMW glutenin subunits, a new allelic variant, 2****, was detected which has not been previously described at the Glu-A1 locus. A high proportion of Glu-A1x banding pattern was observed in durum wheat. For the Glu-B1 locus four different banding patterns were detected. Among those HMW glutenin subunits, 7+8 were the most common, while subunits 14+15 and 6+8 were found to be rare. A high degree of variation was evident for the LMW glutenin subunits and D-zone omega gliadins. The association of the composition of the gluten with quality has been discussed. This wide variation can be used in improving the quality of wheat and to widen its genetic base.

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Wheat in the Mediterranean revisited – tetraploid wheat landraces assessed with elite bread wheat Single Nucleotide Polymorphism markers

BMC Genetics ◽

10.1186/1471-2156-15-54 ◽

2014 ◽

Vol 15 (1) ◽

pp. 54 ◽

Cited By ~ 16

Author(s):

Hugo R Oliveira ◽

Jenny Hagenblad ◽

Matti W Leino ◽

Fiona J Leigh ◽

Diane L Lister ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Bread Wheat ◽

Tetraploid Wheat ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Wheat Landraces ◽

The Mediterranean

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Characterization of nematode resistance gene analogs in tetraploid wheat

Plant Science ◽

10.1016/s0168-9452(02)00336-9 ◽

2003 ◽

Vol 164 (1) ◽

pp. 71-75 ◽

Cited By ~ 4

Author(s):

Maria Rosaria Cortese ◽

Elena Fanelli ◽

Carla De Giorgi

Keyword(s):

Resistance Gene ◽

Tetraploid Wheat ◽

Nematode Resistance ◽

Resistance Gene Analogs ◽

Nematode Resistance Gene

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Molecular characterization and chromosome-specific TRAP-marker development for Langdon durum D-genome disomic substitution lines

Genome ◽

10.1139/g06-114 ◽

2006 ◽

Vol 49 (12) ◽

pp. 1545-1554 ◽

Cited By ~ 17

Author(s):

J. Li ◽

D.L. Klindworth ◽

F. Shireen ◽

X. Cai ◽

J. Hu ◽

...

Keyword(s):

Triticum Turgidum ◽

Tetraploid Wheat ◽

Substitution Lines ◽

Genome Chromosome ◽

D Genome ◽

Single Chromosome ◽

B Genome ◽

The Individual ◽

Trap Marker

The aneuploid stocks of durum wheat ( Triticum turgidum L. subsp. durum (Desf.) Husnot) and common wheat ( T. aestivum L.) have been developed mainly in ‘Langdon’ (LDN) and ‘Chinese Spring’ (CS) cultivars, respectively. The LDN-CS D-genome chromosome disomic substitution (LDN-DS) lines, where a pair of CS D-genome chromosomes substitute for a corresponding homoeologous A- or B-genome chromosome pair of LDN, have been widely used to determine the chromosomal locations of genes in tetraploid wheat. The LDN-DS lines were originally developed by crossing CS nulli-tetrasomics with LDN, followed by 6 backcrosses with LDN. They have subsequently been improved with 5 additional backcrosses with LDN. The objectives of this study were to characterize a set of the 14 most recent LDN-DS lines and to develop chromosome-specific markers, using the newly developed TRAP (target region amplification polymorphism)-marker technique. A total of 307 polymorphic DNA fragments were amplified from LDN and CS, and 302 of them were assigned to individual chromosomes. Most of the markers (95.5%) were present on a single chromosome as chromosome-specific markers, but 4.5% of the markers mapped to 2 or more chromosomes. The number of markers per chromosome varied, from a low of 10 (chromosomes 1A and 6D) to a high of 24 (chromosome 3A). There was an average of 16.6, 16.6, and 15.9 markers per chromosome assigned to the A-, B-, and D-genome chromosomes, respectively, suggesting that TRAP markers were detected at a nearly equal frequency on the 3 genomes. A comparison of the source of the expressed sequence tags (ESTs), used to derive the fixed primers, with the chromosomal location of markers revealed that 15.5% of the TRAP markers were located on the same chromosomes as the ESTs used to generate the fixed primers. A fixed primer designed from an EST mapped on a chromosome or a homoeologous group amplified at least 1 fragment specific to that chromosome or group, suggesting that the fixed primers might generate markers from target regions. TRAP-marker analysis verified the retention of at least 13 pairs of A- or B-genome chromosomes from LDN and 1 pair of D-genome chromosomes from CS in each of the LDN-DS lines. The chromosome-specific markers developed in this study provide an identity for each of the chromosomes, and they will facilitate molecular and genetic characterization of the individual chromosomes, including genetic mapping and gene identification.

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