scholarly journals Genome-level identification of cell wall invertase genes in wheat for the study of drought tolerance

2012 ◽  
Vol 39 (7) ◽  
pp. 569 ◽  
Author(s):  
Hollie Webster ◽  
Gabriel Keeble ◽  
Bernard Dell ◽  
John Fosu-Nyarko ◽  
Y. Mukai ◽  
...  
Keyword(s):  
Cell Wall ◽  
Drought Tolerance ◽  
Aegilops Tauschii ◽  
Sequence Divergence ◽  
Wheat Chromosome ◽  
Triticum Aestivum L ◽  
Pollen Sterility ◽  
Cell Wall Invertase ◽  
D Genome ◽  
Specific Expression

In wheat (Triticum aestivum L.) drought-induced pollen sterility is a major contributor to grain yield loss and is caused by the downregulation of the cell wall invertase gene IVR1. The IVR1 gene catalyses the irreversible hydrolysis of sucrose to glucose and fructose, the essential energy substrates which support pollen development. Downregulation of IVR1 in response to drought is isoform specific and shows variation in temporal and tissue-specific expression. IVR1 is now prompting interest as a candidate gene for molecular marker development to screen wheat germplasm for improved drought tolerance. The aim of this study was to define the family of IVR1 genes to enable: (1) individual isoforms to be assayed in gene expression studies; and (2) greater accuracy in IVR1 mapping to the wheat genetic map and drought tolerance QTL analysis. Using a cell wall invertase-specific motif as a probe, wheat genomics platforms were screened for the presence of unidentified IVR1 isoforms. Wheat genomics platforms screened included the IWGSC wheat survey sequence, the wheat D genome donor sequence from Aegilops tauschii Coss, and the CCG wheat chromosome 3B assembly: contig506. Chromosome-specific sequences homologous to the query motif were isolated and characterised. Sequence annotation results showed five previously unidentified IVR1 isoforms exist on multiple chromosome arms and on all three genomes (A, B and D): IVR1–3A, IVR1–4A, IVR1–5B, IVR1.2–3B and IVR1-5D. Including three previously characterised IVR1 isoforms (IVR1.1–1A, IVR1.2–1A and IVR1.1–3B), the total number of isoform gene family members is eight. The IVR1 isoforms contain two motifs common to cell wall invertase (NDPN and WECPDF) and a high degree of conservation in exon 4, suggesting conservation of functionality. Sequence divergence at a primary structure level in other regions of the gene was evident amongst the isoforms, which likely contributes to variation in gene regulation and expression in response to water deficit within this subfamily of IVR1 isoforms in wheat.

scholarly journals Genomic patterns of introgression in interspecific populations created by crossing wheat with its wild relative

2019 ◽  
Author(s):  
Moses Nyine ◽  
Elina Adhikari ◽  
Marshall Clinesmith ◽  
Katherine W. Jordan ◽  
Allan K. Fritz ◽  
...  
Keyword(s):  
Aegilops Tauschii ◽  
Allelic Diversity ◽  
Sequence Divergence ◽  
Snp Markers ◽  
D Genome ◽  
Entire Genome ◽  
Wild Allele ◽  
Negative Epistasis ◽  
The Hill ◽  
Genomic Patterns

AbstractIntrogression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for this population and a diverse panel of 116 Ae. tauschii accessions by complexity-reduced genome sequencing were used to detect introgression based on the identity-by-descent analysis. Overall, introgression frequency positively correlated with recombination rate, with a high incidence of introgression at the ends of chromosomes and low in the pericentromeric regions, and was negatively related to sequence divergence between the parental genomes. Reduced introgression in the pericentromeric low-recombining regions spans nearly 2/3 of each chromosome arm, suggestive of the polygenic nature of introgression barriers that could be associated with multilocus negative epistasis between the alleles of wild and cultivated wheat. On the contrary, negative selection against the wild allele of Tg, controlling free-threshing trait and located in the high-recombining chromosomal region, led to reduced introgression only within ∼10 Mbp region around Tg. These results are consistent with the effect of selection on linked variation described by the Hill-Robertson effect, and offer insights into the introgression population development for crop imrpovement to ensure retention of introgressed diversity across entire genome.

scholarly journals Comparative Mapping of Genes for Brittle Rachis in Triticum

2011 ◽  
Vol 41 (No. 2) ◽  
pp. 39-44 ◽  
Author(s):  
N. Watanabe ◽  
N. Takesada ◽  
Y. Fujii ◽  
P. Martinek
Keyword(s):  
Triticum Turgidum ◽  
Aegilops Tauschii ◽  
Dominant Gene ◽  
Introgression Line ◽  
Triticum Aestivum L ◽  
Grass Species ◽  
Brittle Rachis ◽  
D Genome ◽  
Adaptive Value ◽  
Group 3

The brittle rachis phenotype is of adaptive value in wild grass species because it causes spontaneous spike shattering. The genes on the homoeologous group 3 chromosomes determine the brittle rachis in Triticeae. A few genotypes with brittle rachis have also been found in the cultivated Triticum. Using microsatellite markers, the homoeologous genes for brittle rachis were mapped in hexaploid wheat (Triticum aestivum L.), durum wheat (Triticum turgidum L. conv. durum /Desf./) and Aegilops tauschii Coss. On chromosome 3AS, the gene for brittle rachis, Br<sub>2</sub>, was linked with the centromeric marker, Xgwm32, at the distance of 13.3 cM. Br<sub>3 </sub>was located on chromosome 3BS and linked with the centromeric marker,<br />Xgwm72 (14.2 cM). Br<sub>1 </sub>was located on chromosome 3DS. The distance from the centromeric marker Xgdm72 was 23.6 cM. The loci Br<sub>1</sub>, Br<sub>2</sub> and Br<sub>3</sub> determine disarticulation of rachides above the junction of the rachilla with the rachis so that a fragment of rachis is attached below each spikelet. The rachides of Ae. tauschii are brittle at every joint, so that the mature spike disarticulates into barrel type. The brittle rachis was determined by a dominant gene, Br<sup>t</sup>, which was linked to the centromeric marker, Xgdm72 (19.7 cM), on chromosome 3DS. A D-genome introgression line, R-61, was derived from the cross Bet Hashita/Ae. tauschii, whose rachis disarticulated as a wedge type. The gene for brittle rachis of R-61, tentatively designated as Br<sup>61</sup>, was distally located on chromosome 3DS, and was linked with the centromeric marker, Xgdm72 (27.5 cM). We discussed how the brittle rachis of R-61 originated genetically. &nbsp; &nbsp;

Tapetal development and abiotic stress: a centre of vulnerability

2012 ◽  
Vol 39 (7) ◽  
pp. 553 ◽  
Author(s):  
Roger W. Parish ◽  
Huy A. Phan ◽  
Sylvana Iacuone ◽  
Song F. Li
Keyword(s):  
Cell Wall ◽  
Abiotic Stress ◽  
Oryza Sativa L ◽  
Triticum Aestivum L ◽  
Pollen Abortion ◽  
Cell Wall Invertase ◽  
Developmental Program ◽  
Specific Effects ◽  
Hexose Sugars ◽  
Microspore Stage

Many self-fertilising crops are particularly sensitive to abiotic stress at the reproductive stage. In rice (Oryza sativa L.) and wheat (Triticum aestivum L.), for example, abiotic stress during meiosis and the young microspore stage indicates the tapetum is highly vulnerable and that the developmental program appears to be compromised. Tapetal hypertrophy can occur as a consequence of cold and drought stress, and programmed cell death (PCD) is delayed or inhibited. Since the correct timing of tapetal PCD is essential for pollen reproduction, substantial losses in grain yield occur. In wheat and rice, a decrease in tapetal cell wall invertase levels is correlated with pollen abortion and results in the amount of hexose sugars reaching the tapetum, and subsequently the developing microspores, being severely reduced (‘starvation hypothesis’). ABA and gibberellin levels may be modified by cold and drought, influencing levels of cell wall invertase(s) and the tapetal developmental program, respectively. Many genes regulating tapetal and microspore development have been identified in Arabidopsis thaliana (L.) Heynh. and rice and the specific effects of abiotic stresses on the program and pathways can now begin to be assessed.

scholarly journals Long non-coding RNAs in wild wheat progenitors

2018 ◽  
Author(s):  
Alice Pieri ◽  
Mario Enrico Pè ◽  
Edoardo Bertolini
Keyword(s):  
Aegilops Tauschii ◽  
Noncoding Rnas ◽  
Reproductive Organs ◽  
Long Noncoding Rnas ◽  
D Genome ◽  
Specific Expression ◽  
Wild Wheat ◽  
Organ Specific ◽  
Species Specific ◽  
And Function

AbstractTriticum urartu and Aegilops tauschii are the diploid progenitors of the hexaploid Triticum aestivum (AuAuBBDD), donors of the Au and D genome respectively. In this work we investigate the long noncoding RNAs (lncRNAs) component of the genomes of these two wild wheat relatives. Sixty-eight RNA-seq libraries generated from several organs and conditions were retrieved from public databases. We annotated and characterized 14,515 T. urartu and 20,908 Ae. tauschii bona-fide lncRNA transcripts that show features similar to those of other plant and animal counterparts. Thousands of lncRNAs were found significantly modulated in different organs and exhibited organ specific expression, with a predominant accumulation in the spike, fostering the hypothesis of their crucial role in reproductive organs. Most of the organ-specific lncRNAs were found associated with transposable elements (TEs), indicating the possible role of TEs in lncRNA origin, differentiation and function. The majority of T. urartu and Ae. tauschii lncRNAs appear to be species-specific; nevertheless, we found some lncRNAs conserved between the two wheat progenitors, highlighting the presence and conservation of exonic splicing enhancers sites in multi-exon conserved lncRNAs. In addition, we found cases of lncRNA conservation and their cis regulatory regions spanning the wheat pre-domestication and post-domestication period. Altogether, these results represent the first comprehensive genome-wide encyclopedia of lncRNAs in wild wheat relatives, and they provide clues as to the hidden regulatory pathway mediated by long noncoding RNAs in these largely unexplored wheat progenitors.

scholarly journals Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative

2020 ◽  
Vol 10 (10) ◽  
pp. 3651-3661 ◽  
Author(s):  
Moses Nyine ◽  
Elina Adhikari ◽  
Marshall Clinesmith ◽  
Katherine W. Jordan ◽  
Allan K. Fritz ◽  
...  
Keyword(s):  
Crop Improvement ◽  
Aegilops Tauschii ◽  
Allelic Diversity ◽  
Sequence Divergence ◽  
Snp Markers ◽  
D Genome ◽  
Entire Genome ◽  
Wild Allele ◽  
The Hill ◽  
Genomic Patterns

Introgression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for this population and a diverse panel of 116 Ae. tauschii accessions by complexity-reduced genome sequencing were used to detect introgression based on the identity-by-descent analysis. Overall, introgression frequency positively correlated with recombination rate, with a high incidence of introgression at the ends of chromosomes and low in the pericentromeric regions, and was negatively related to sequence divergence between the parental genomes. Reduced introgression in the pericentromeric low-recombining regions spans nearly 2/3 of each chromosome arm, suggestive of the polygenic nature of introgression barriers that could be associated with multilocus negative epistasis between the alleles of wild and cultivated wheat. On the contrary, negative selection against the wild allele of Tg, controlling free-threshing trait and located in the high-recombining chromosomal region, led to reduced introgression only within ∼10 Mbp region around Tg. These results are consistent with the effect of selection on linked variation described by the Hill-Robertson effect, and offer insights into the introgression population development for crop improvement to maximize retention of introgressed diversity across entire genome.

The efficacy of Cot-based gene enrichment in wheat (Triticum aestivum L.)

Genome ◽  
2005 ◽  
Vol 48 (6) ◽  
pp. 1120-1126 ◽  
Author(s):  
Didier Lamoureux ◽  
Daniel G Peterson ◽  
Wanlong Li ◽  
John P Fellers ◽  
Bikram S Gill
Keyword(s):  
Triticum Aestivum ◽  
Bread Wheat ◽  
Aegilops Tauschii ◽  
Triticum Aestivum L ◽  
D Genome ◽  
Genomic Libraries ◽  
Gene Space ◽  
Fold Enrichment ◽  
Gene Enrichment ◽  
Fold Reduction

We report the results of a study on the effectiveness of Cot filtration (CF) in the characterization of the gene space of bread wheat (Triticum aestivum L.), a large genome species (1C = 16 700 Mb) of tremendous agronomic importance. Using published Cot data as a guide, 2 genomic libraries for hexaploid wheat were constructed from the single-stranded DNA collected at Cot values > 1188 and 1639 M·s. Compared with sequences from a whole genome shotgun library from Aegilops tauschii (the D genome donor of bread wheat), the CF libraries exhibited 13.7-fold enrichment in genes, 5.8-fold enrichment in unknown low-copy sequences, and a 3-fold reduction in repetitive DNA. CF is twice as efficient as methylation filtration at enriching wheat genes. This research suggests that, with improvements, CF will be a highly useful tool in sequencing the gene space of wheat.Key words: gene enrichment, renaturation kinetics, gene-rich regions, bread wheat.

Control of alien gene expression for aluminum tolerance in wheat

Genome ◽  
1990 ◽  
Vol 33 (1) ◽  
pp. 9-12 ◽  
Author(s):  
J. P. Gustafson ◽  
K. Ross
Keyword(s):  
Gene Expression ◽  
Triticum Aestivum ◽  
Chinese Spring ◽  
Aluminum Tolerance ◽  
Wheat Chromosome ◽  
Triticum Aestivum L ◽  
D Genome ◽  
Chinese Spring Wheat ◽  
Secale Cereale L ◽  
Alien Gene

The expression of aluminum tolerance from rye (Secale cereale L.) when present in a wheat (Triticum aestivum L. em. Thell.) background has been observed to be much lower than that in rye itself. By crossing each of the ditelocentric lines of 'Chinese Spring' wheat with a tolerant rye, the effects of the presence or absence of each arm of wheat on the expression of rye aluminum tolerance could be established. Of 42 wheat chromosome arms, 18 affected the expression of rye aluminum tolerance. Tolerance was increased over that observed in the euploid wheat–rye hybrid when arms 4AL, 5AL, 6AL, 7BS, 7BL, and 3DS were absent. Tolerance was reduced when arms 2AL, 5AS, 6BS, 1DS, 1DL, 2DL, 4DL, 5DS, 5DL, 6DL, 7DS, and 7DL were absent. Thus, the control of aluminum tolerance expression from rye in a wheat background was evidently under the influence of genes located on a number of wheat chromosome arms, with a few arms tending to enhance expression and many others tending to reduce it. In fact, 5AS of 'Chinese Spring' enhances expression, while 5AL suppresses it. The D genome of bread wheat appears to have the most pronounced effect on the expression of rye aluminum tolerance.Key words: rye, activator genes, suppressor genes, alien manipulation.

Tissue-Specific Expression and Drought Responsiveness of Cell-Wall Invertase Genes of Rice at Flowering

2005 ◽  
Vol 59 (6) ◽  
pp. 945-964 ◽  
Author(s):  
X. M. Ji ◽  
M. Raveendran ◽  
R. Oane ◽  
A. Ismail ◽  
R. Lafitte ◽  
...  
Keyword(s):  
Cell Wall ◽  
Cell Wall Invertase ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression

scholarly journals Traits to Differentiate Lineages and Subspecies of Aegilops tauschii, the D Genome Progenitor Species of Bread Wheat

Diversity ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 217
Author(s):  
Mazin Mahjoob Mohamed Mahjoob ◽  
Tai-Shen Chen ◽  
Yasir Serag Alnor Gorafi ◽  
Yuji Yamasaki ◽  
Nasrein Mohamed Kamal ◽  
...  
Keyword(s):  
Entire Range ◽  
Aegilops Tauschii ◽  
Triticum Aestivum L ◽  
High Quality ◽  
D Genome ◽  
Physiological Diversity ◽  
Phylogenetic Cluster ◽  
High Quality Snps ◽  
Genome Donor ◽  
Passport Data

Aegilops tauschii Coss., the D genome donor of hexaploid wheat (Triticum aestivum L.), is the most promising resource used to broaden the genetic diversity of wheat. Taxonomical studies have classified Ae. tauschii into two subspecies, ssp. tauschii and ssp. strangulata. However, molecular analysis revealed three distantly related lineages, TauL1, TauL2 and TauL3. TauL1 and TauL3 includes the only ssp. tauschii, whereas TauL2 includes both subspecies. This study aimed to clarify the phylogeny of Ae. tauschii and to find the traits that can differentiate between TauL1, TauL2 and TauL3, or between ssp. tauschii and ssp. strangulata. We studied the genetic and morpho-physiological diversity in 293 accessions of Ae. tauschii, covering the entire range of the species. A total of 5880 high-quality SNPs derived from DArTseq were used for phylogenetic cluster analyses. As a result, we observed wide morpho-physiological variation in each lineage and subspecies. Despite this variation, no key traits can discriminate lineages or subspecies though some traits were significantly different. Of 124 accessions previously lacking the passport data, 66 were allocated to TauL1, 57 to TauL2, and one to TauL3.

scholarly journals Genome-Wide Investigation of Spliceosomal SM/LSM Genes in Wheat (Triticum aestivum L.) and Its Progenitors

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1429
Author(s):  
Ruiting Gao ◽  
Ning Su ◽  
Wenqiu Pan ◽  
Qiaoyu Bao ◽  
Zhen Li ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Aegilops Tauschii ◽  
Enrichment Analysis ◽  
Wheat Chromosome ◽  
Triticum Aestivum L ◽  
Triticum Dicoccoides ◽  
Regulatory Elements ◽  
Salt Tolerance Gene

The SSM/SLSM (spliceosomal Smith (SM)/SM-like (LSM)) genes are the central components of the spliceosome in eukaryotes, which play an important role in regulating RNA splicing, participating in diverse biological processes. Although it has been detected in Arabidopsis and rice etc. plants, the members and significance of the SSM/SLSM gene family in wheat are still not reported. In this study, we identified the SSM/SLSM genes in wheat and its progenitors at genome-scale, where 57 SSM/SLSM genes were identified in wheat, together with 41, 17and 19 found in Triticum dicoccoides, Triticum urartu, and Aegilops tauschii. Furthermore, their phylogenetic relationship, gene structures, conserved motifs, and cis-regulatory elements were systematically analyzed. By synteny analysis, good collinearity of SSM/SLSM genes was found among bread wheat and its progenitors’ genomes, and the distribution of SMD2 genes in wheat chromosome 5A, 4B and 4D located in the 4AL-5AL-7BS chromosome model, due to the translocation. Then, the positively selected genes were further investigated based on the non-synonymous to synonymous (dN/dS) analysis of the orthologous pairs. Finally, the expression profiles of the SSM/SLSM genes were detected using RNA-seq datasets, and eight stress-responsive candidate genes were selected to validate their expression through qPCR (real-time quantitative polymerase chain reaction). According to the co-expression network analysis, the correlation between the LSM7-7A gene and related genes was illustrated through Gene Ontology (GO) enrichment analysis. Furthermore, the LSM7-7A gene was related to the Arabidopsis homologous salt tolerance gene RCY1. This investigation systematically identified the complete candidates of SSM/SLSM genes and their characters in wheat and its progenitors, and provided clues to a better understanding of their contribution during the wheat polyploidy process.

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