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Mapping quantitative trait loci for resistance to Pratylenchus thornei from synthetic hexaploid wheat in the International Triticeae Mapping Initiative (ITMI) population

Mapping quantitative trait loci for resistance to Pratylenchus thornei from synthetic hexaploid wheat in the International Triticeae Mapping Initiative (ITMI) population

Abstract. Root-lesion nematode (Pratylenchus thornei) is a serious pathogen of wheat in many countries. The International Triticeae Mapping Initiative (ITMI) population of recombinant inbred lines (RILs) was assessed for resistance to P. thornei to determine the chromosome locations of the resistance genes. The ITMI population is derived from a cross between the resistant synthetic hexaploid wheat W-7984 and a susceptible bread wheat cultivar Opata 85. Two years of phenotypic data for resistance to P. thornei were obtained in replicated glasshouse trials. Quantitative trait locus (QTL) analysis was performed using available segregation and map data for 114 RILs. A QTL on chromosome 6DS showed consistent effects for reduced nematode numbers (partial resistance) across years and accounted for 11% and 23% of the phenotypic variation. A second QTL for P. thornei resistance on chromosome 2BS accounted for an additional 19% and 5%. Restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) markers associated with the QTLs are physically located in regions rich in major genes at the distal ends of the short chromosome arms of 6D and 2B. SSR markers with potential for marker-assisted selection of P. thornei resistance effective in different genetic backgrounds have been identified.
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Effects of NaCl on protein profiles of tetraploid and hexaploid wheat species and their diploid wild progenitors

Effects of NaCl on protein profiles of tetraploid and hexaploid wheat species and their diploid wild progenitors

was higher than the increased proteins; and (c) the proteins changed in Ae. speltoides (B) were diminished or disappeared as a result of NaCl stress. In this sense, it is suggested that most of the decreased and disappeared LMW proteins may be salt sensitive in different degree. Also, this case may be explained with an increase in activities of protein hydrolyzing enzymes during the NaCl stress treatment. Parida et al. (2002) re- ported that the decrement in total soluble protein content of leaves as a result of the NaCl treatment might have resulted from an adverse effect of NaCl on the synthesis of certain LMW proteins. In addition, some researchers reported that the contents of two LMW proteins in hexaploid wheat, and 17 LMW and four IMW in tetraploid wheat decreased, while one LMW protein in hexaploid wheat and four LMW proteins in tetraploid wheat disappeared in the presence of NaCl (Elshintinawy and Elshourbagy 2001, Yıldız 2007).
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Heterosis and Combing Ability in F1  Population of Hexaploid Wheat  (Triticum Aestivum L )

Heterosis and Combing Ability in F1 Population of Hexaploid Wheat (Triticum Aestivum L )

Breeding efforts have resulted in various varieties of hexaploid wheat, having improved yield and grain cha- racters. Varieties and advanced lines with different morphological and economic characteristics are now availa- ble as breeding stock. For further progress, knowledge of breeding behavior, particularly of combining ability and type of gene action for the various traits, is necessary. The estimates of combining ability variances and ef- fects can give an indication of the relative magnitude of genetic variance. Besides doing haphazard crosses, it is necessary to execute only high performing ones. In this context, combining ability provides a guideline for se- lecting elite parents and desirable cross combinations to be used in formulation of a systematic breeding project for rapid improvement. Griffing’s approach has been greatly popular among various breeders, indicating greater role of additive gene action in the inheritance of grain yield and its components [8]. It is also reported that in the inheritance of productive tillering some dominance is involved [9]. It is reported that mean squares for GCA are highly significant for yield and yield components [10]; SCA is non-significant for all the traits [11]. Significant differences are reported for general combining ability and specific combining ability of all the characters [12]. It is also reported that all investigated features are determined by additive gene action [13]; the parents LU26S and 4072 are good general combiners [14]. Most of these studies revealed that a large part of total genetic variability for yield and its components was associated with the GCA effects, a measure of additive genetic variance.
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RIBOSOMAL RNA CISTRON MULTIPLICITY AND NUCLEOLAR ORGANIZERS IN HEXAPLOID WHEAT

RIBOSOMAL RNA CISTRON MULTIPLICITY AND NUCLEOLAR ORGANIZERS IN HEXAPLOID WHEAT

However, in stocks lacking chromosome lA, which ap- pears to possess a n essentially inactive organizer in hexaploid wheat as judged by the absence of changes in nucleolar nu[r]

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Detection of QTLs for important agronomical traits in hexaploid wheat using association analysis

Detection of QTLs for important agronomical traits in hexaploid wheat using association analysis

Maccaferri M., Sanguineti M.C., Corneti S., Ortega J.L.A., Salem M.B., Bort J., Deambrogio E., Garcia del Moral L.F., Demontis A., El-Ahmed A., Maalouf F., Machlab H., Martos V., Moragues M., Motawaj J., Nachit M., Nserallah N., Ouabbou H., Royo C., Slama A., Tuberosa R. (2008): Quantitative trait loci for grain yield and adaptaion of durum wheat (Triticum durum Desf.) across a wide range of water availability. Genetics, 178: 489–511.

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A genome wide survey of DNA methylation in hexaploid wheat

A genome wide survey of DNA methylation in hexaploid wheat

Gene expression changes are often associated with meth- ylated regions rather than single methylated nucleotides. To survey differentially methylated regions (DMRs) across the genome it is preferable to analyze tiled windows across it, typically of 1000 bp [19]. As this analysis is based on fragmented gene regions rather than whole genome se- quence, we summarized methylation per extended bait probe and compared these figures between the sub- genomes of wheat to identify DMRs. We used Methylkit for this analysis and focused only on regions that were identified between sub-genomes with a q value below 0.01 using the Fisher's exact test. The three sub-genomes were compared and a region selected if a single genome was at least 25 % more methylated than the other two. In the 12 ° C sample 11 DMRs were found to be specific to genome A, 15 specific to genome B and 4 specific to genome D; these figures were 7, 18 and 5, respectively, for the 27 °C sample. Similar to the enriched GO terms for uni-genome methylation, sub-genome A ’s densely methylated gene regions relate to metabolic processes, sub-genome B’s relate to metabolic processes, binding and membrane association and sub-genome D’s relate to zinc ion trans-membrane transport. Sixteen DMRs are conserved between the two temperatures. All DMRs are detailed in Table S6 in Additional file 1.
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CHROMOSOMAL LOCATION OF GENES CONTROLLING FLAVONOID PRODUCTION IN HEXAPLOID WHEAT

CHROMOSOMAL LOCATION OF GENES CONTROLLING FLAVONOID PRODUCTION IN HEXAPLOID WHEAT

Two-dimensional paper chromatography was performed on methanol ex- tracts of leaves of hexaploid bread wheat, Triticum aestivum L. cultivar Chinese Spring, and of the a[r]

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Phenotyping pipeline reveals major seedling root growth QTL in hexaploid wheat

Phenotyping pipeline reveals major seedling root growth QTL in hexaploid wheat

two-thirds the mean of some landraces (Waines and Ehdaie, 2007). The Reduced height (Rht) genes, which control shoot height in wheat and are present in many modern cultivars, have been reported to reduce root proliferation (Bai et  al., 2013). This has prompted the proposal that optimization of RSA should form the basis of a second Green Revolution to produce the increase in below-ground resource capture and yield required to meet the needs of the increasing global pop- ulation (Lynch, 2007). Furthermore, optimization of RSA may be a promising avenue to enhance nitrogen (N) uptake efficiency and hence reduce N fertilizer requirements with associated environmental and economic benefits (Foulkes et al., 2009).
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LINKAGE STUDIES INVOLVING TWO CHROMOSOMAL MALE-STERILITY MUTANTS IN HEXAPLOID WHEAT

LINKAGE STUDIES INVOLVING TWO CHROMOSOMAL MALE-STERILITY MUTANTS IN HEXAPLOID WHEAT

Thus, the Cornerstone and Probus mutants, presumed to be terminal deletions of 4Aa, induce 81% and 58%, respectively, desynapsis of the bivalent involving telocentric 4Aa; howe[r]

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DOSAGE EFFECT OF THE SPELTA GENE q OF HEXAPLOID WHEAT

DOSAGE EFFECT OF THE SPELTA GENE q OF HEXAPLOID WHEAT

spelta background a speltoid mutation would presumably give rise to an extreme spelta phenotype.. spelta differs from most uulgare varieties more than the speltoid mu[r]

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HERITABILITY ESTIMATES IN F2 SEGREGATING POPULATION IN HEXAPLOID WHEAT (TRITICUM AESTIVUM L.)

HERITABILITY ESTIMATES IN F2 SEGREGATING POPULATION IN HEXAPLOID WHEAT (TRITICUM AESTIVUM L.)

Wheat (Triticum aestivum L.) is grown widely across almost all around the world, representing about 30% of the cereal cultivation area, providing 20% of the calories for the human population (Khan et al., 2015). Since the advent of Green solution, wheat yields have increased in many reg- ions of the world (Fang et al., 2017). It has been predicted that till 2050 research attentions towards wheat will be fast as to face the challenge of feed- ing a population of 9 billion (Rajaram and Braun, 2008). Moreover, several environmental constrai- nts especially high-temperature effects and water deficit are responsible for serious threat in wheat production (Flexas et al., 2004; Prasad et al., 2009). Pakistan positions among the top countries
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STUDY OF KARYOTYPE AND NUCLEOLAR ORGANIZER REGIONS (NORS)IN WILD, SYNTHETIC AND CULTIVATED WHEATS

STUDY OF KARYOTYPE AND NUCLEOLAR ORGANIZER REGIONS (NORS)IN WILD, SYNTHETIC AND CULTIVATED WHEATS

Nucleolus organizer regions are a very important landmark for recognition and identification of chromosomes in plant species. Ag-NOR banding has been vastly used to analyze nucleolus activity in diploid and polyploidy plants, interspecific hybrids and chromosome addition lines (Fukui and Nakayama, 1997). The method of staining nucleolus organizing regions (NORs) of chromosomes with silver nitrate (the silver- staining procedure) is also suitable for estimation of rDNA transcription rate in plants. For example, this approach has been used for the estimation of NOR activity in onion leaves and wheat roots treated with plant growth (Fatkhutdinova et al., 2002). In hexaploid wheat, three chromosome pairs (IB, 6B, and 5D) are known to possess nucleolar activity; however, usually only 1B and 6B show a secondary constriction (Cermeno et al., 1984). Each diploid Triticeae species has either one or two chromosome pairs with NORs, which are present in different locations on the chromosomes of homoelogous groups 1, 5 and 6. These major NORs contain from hundreds to thousands of 18S-26S rRNA repeated gene units and their expression can be visualized by their nucleolus organizing activity and Ag-NOR banding (Badaeva et al., 1996).
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QTL Positioning of Thousand Wheat Grain Weight in Qaidam Basin

QTL Positioning of Thousand Wheat Grain Weight in Qaidam Basin

TGW is an important agronomic trait that influences the yield and milling quality of wheat. In this paper, after having investigated the phenotype of TGW from 114 ITMI recombinant inbred gene- alogies in 4 years in Qaidam Basin, a typical plateau oasis agricultural area, and having combined 1410 molecular markers, 7 major QTL loci of the thousand gain weight were screened out with the aid of QTL network software. These loci included qTgw1B (42.6 cm), qTgw2A (77.9 cm), qTgw2D1 (25.4 cm), qTgw2D2 (51.8 cm), qTgw6A1 (56.1 cm), qTgw6A2 (62.2 cm) and qTgw7A (75.7 cm) with their genetic contribution rates between 3.29% - 19.36%. There were two epistatic effect loci 2A-2D and 2A-6B with their genetic contribution rates as 2.3% and 5.3% respectively. The quan- titative genetic locus positioning of thousand hexaploid wheat grain weight in Qaidam Basin can assist us in better understanding the genetic regulatory network formed by TGW, and can also provide a theoretical basis for improving thousand wheat grain weight in this ecological area.
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Tempos of Gene Locus Deletions and Duplications and Their Relationship to Recombination Rate During Diploid and Polyploid Evolution in the Aegilops-Triticum Alliance

Tempos of Gene Locus Deletions and Duplications and Their Relationship to Recombination Rate During Diploid and Polyploid Evolution in the Aegilops-Triticum Alliance

earlier (A khunov et al. 2003a). Briefly, an EST unigene was hybridized with a set of Chinese Spring disomic substitution lines in which each Chinese Spring chromosome was indi- vidually replaced by its Lophopyrum elongatum homeologue (D vorak 1980; D vorak and C hen 1984; T uleen and H art 1988) and a set of barley disomic addition lines (I slam et al. 1981). Each such EST unigene was also hybridized with a panel of genetically diverse lines of T. urartu, Ae. tauschii, and Ae. speltoides. Designations and origins of these lines are described in A khunov et al. (2003a). These data were used to validate each tentative perturbation of synteny found in the wheat EST database to determine whether the perturbation was due to gene locus deletion or gene locus duplication and when the event originated relative to the divergence of barley, L. elongatum, and the three wheat genomes and the conver- gence of the A and B genomes in tetraploid wheat and the A, B, and D genomes in hexaploid wheat. For each paralogous set with perturbed synteny, it was determined which locus was the ancestral locus of the paralogous set (A khunov et al. 2003a). Deletions and duplications that originated during a time interval from the divergence of T. urartu and Ae. tauschii to the origin of polyploid wheat were used for measuring rates at the diploid level. Deletions and duplications that originated since the origin of tetraploid wheat in the A genome and since the origin of hexaploid wheat in the D genome were used for measuring rates at the polyploid level (supplementary Table S1 at http://www.genetics.org/supplemental/). By this pro- cess we achieved an exhaustive analysis of orthology and recent evolutionary history for a total of 3159 loci in the A and D genomes. The B-genome deletions and duplications were not considered here because the cross-pollinating habit and resulting heterozygosity of Ae. speltoides, a diploid reference species for the wheat B genome, would have greatly compli- cated these inferences.
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DNA COMPARISONS AMONG SOME BIOTYPES OF WHEAT

DNA COMPARISONS AMONG SOME BIOTYPES OF WHEAT

squarrosa (thought to carry the D genome of hexaploid wheat), tetraploid wheat (thought to carry the A and B genomes of hexaploid wheat) and hexaploid wheat (A, B and D geno[r]

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Diversity of agronomic and morphological traits in a mutant population of bread wheat studied in the Healthgrain program

Diversity of agronomic and morphological traits in a mutant population of bread wheat studied in the Healthgrain program

The similarity between the frequency of visible phenotypes in the mutagenised population of wheat reported here and those in barley suggest that both species are equally sensitive to mutation. However, as described above, the nucleotide mutation frequencies of the different populations are distinctly different, with wheat populations tolerating 10–20 times higher mutation frequencies than barley. Thus, hexaploid wheat can be seen to be much more tolerant of mutations than diploid barley. Indeed, it is likely that even higher rates of mutagenesis may be achievable in wheat: in diploid species such as barley, the main factor limiting the mutation rate appears to be the fertility of the mutagenised plants, presumably due to mutations in single copy genes that are lethal in the haploid state. In wheat, complementation of similar potentially lethal mutations by orthologous normal copies reduces the level of infertility. Thus the main Table 5 Correlations between breadmaking quality parameters and agronomic and morphological properties
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Salt tolerance classification in wheat genotypes using reducing sugar accumulation and growth characteristics

Salt tolerance classification in wheat genotypes using reducing sugar accumulation and growth characteristics

Abstract: The aim of the present study was to assess inter and intra-specific variations in Triticum groups. Local hexaploid bread wheat and Synthetic Elites and Durum where characterized based on growth abilities and amount of reducing sugar accumulated under 200 mM NaCl salinity. Further, the role of reducing sugar accumulation in adaptive process of different Triticum groups towards salinity was also measured. Identification of inter-specific and intra-specific variation with in the gene pool is of greater importance for breeding salt tolerant varieties. Salt tolerant genotypes tend to accumulate more carbohydrates under salt stress and prevent plants from oxidative damage. Wide differences observed between Triticum groups under salt stress for shoot length, shoot weight and reducing sugar content. Salt stress reduced shoot length and weight in both Local hexaploids and Synthetic elites but effect was more pronounced in Local hexaploid wheat. Kharchia and LU-26 were identified as salt tolerant standard genotypes which showed significant increase in reducing sugar content where as salt stress induced reduction in amount of reducing sugars of local hexaploid genotypes. Performance of salinity tester genotypes and synthetic elite and durum genotypes was less affected by salinity and prominent increase in reducing sugar content has been observed in comparison to local hexaploid genotypes. High values for salt tolerance indices were also observed for salinity tester set and synthetic elite and durum wheat genotypes. It may be concluded from the above findings that wheat genotypes like Kharchia, LU-26, Durum 155 and SE 88 with highest accumulation of reducing sugar content under stress could be used in breeding programs to develop salt tolerant germplasm and accumulation of reducing sugars under stress conditions could be a useful bio-marker for selecting tolerant wheat genotypes.
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Identification of Low Molecular Weight Glutenin Alleles by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF-MS) in Common Wheat (Triticum aestivum L.)

Identification of Low Molecular Weight Glutenin Alleles by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF-MS) in Common Wheat (Triticum aestivum L.)

A total of 60 hexaploid wheat lines with known LMW-GS compositions were used to establish characteristic MALDI-TOF peak pattern for each LMW-GS allele. Aroona and its 16 substitu- tion lines with different Glu-3 alleles detected by protein mobility were sourced from South Australian Research & Development Institute Grain Quality Research Laboratory and were ini- tially used to gain allele specific spectrum peak patterns (Table 1). A collection of 18 interna- tional reference varieties [21] and 25 hexaploid gene deletant lines with different Glu-3 alleles defined by SDS-PAGE were then used to verify the patterns obtained from the Aroona lines. The final allele patterns were put into use to analyze another 202 hexaploid wheat lines, includ- ing commercial cultivars and advanced breeding lines.
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A whole genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

A whole genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

An intuitive explanation for this result is that chro- mosome sorting only simplifies the separation of ho- meologous sequences in genic or low-copy regions. By contrast, the most common transposable elements occur so abundantly even in only a single chromosome arm that they thwart attempts to assemble them correctly with short reads only. In light of this limited utility of a chromosome-by-chromosome shotgun approach, on- going and future genome sequencing projects in other highly repetitive and/or polyploid cereal crops, such as rye and oats, may adopt a simpler, straight-forward whole-genome strategy to construct a draft sequence assembly instead of establishing elaborate protocols for efficient flow-sorting and subsequent chromosome-wise shotgun assembly. Likewise, it may be feasible to con- struct a genome-wide physical map of the wheat genome using sequence-based fingerprinting methods [50] that can distinguish between fragments from homeologous loci. These considerations do not diminish the impor- tance of clone-based approaches to achieving the ulti- mate goal of a finished sequence for hexaploid wheat, the long-term aim of the IWGSC [51].
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A Chromosome Bin Map of 2148 Expressed Sequence Tag Loci of Wheat Homoeologous Group 7

A Chromosome Bin Map of 2148 Expressed Sequence Tag Loci of Wheat Homoeologous Group 7

The objectives of this study were to develop a high-density chromosome bin map of homoeologous group 7 in hexaploid wheat (Triticum aestivum L.), to identify gene distribution in these chromosomes, and to perform comparative studies of wheat with rice and barley. We mapped 2148 loci from 919 EST clones onto group 7 chromosomes of wheat. In the majority of cases the numbers of loci were significantly lower in the centromeric regions and tended to increase in the distal regions. The level of duplicated loci in this group was 24% with most of these loci being localized toward the distal regions. One hundred nineteen EST probes that hybridized to three fragments and mapped to the three group 7 chromosomes were designated landmark probes and were used to construct a consensus homoeologous group 7 map. An additional 49 probes that mapped to 7AS, 7DS, and the ancestral translocated segment involving 7BS also were designated landmarks. Landmark probe orders and comparative maps of wheat, rice, and barley were produced on the basis of corresponding rice BAC/PAC and genetic markers that mapped on chromosomes 6 and 8 of rice. Identification of landmark ESTs and development of consensus maps may provide a framework of conserved coding regions predating the evolution of wheat genomes.
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