Physical Mapping of Bread Wheat Chromosome 5A: An Integrated Approach

Barabaschi, Delfina; Magni, Federica; Volante, Andrea; Gadaleta, Ágata; Šimková, Hana; Scalabrin, Simone; Prazzoli, M.L.; Bagnaresi, Paolo; Lacrima, Katia; Michelotti, V.; Desiderio, Francesca; Orrù, Luigi; Mazzamurro, Valentina; Fricano, Agostino; Mastrangelo, Anna Maria; Tononi, Paola; Vitulo, Nicola; Jurman, Irena; Frenkel, Zeev; Cattonaro, Federica; Morgante, Michèle; Blanco, Antonio; Doležel, Jaroslav; Delledonne, Massimo; Stanca, A. M.; Cattivelli, Luigi; Valè, Giampiero

doi:10.3835/plantgenome2015.03.0011

Cited by 12 publications

(17 citation statements)

References 114 publications

(131 reference statements)

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“…Forty‐three markers of the RSH‐consensus map are included in the 5AS neighbour map (Barabaschi et al ., ) as well. We compared marker order and relative distance between RSH‐consensus map and the 5AS neighbour map.…”

Section: Resultsmentioning

confidence: 90%

“…Comparison of markers order and relative distances reported in (a) physical deletion bin map, (b) RSH ‐consensus and (c) 5A neighbour map (Barabaschi et al ., ). Only markers analysed across all three maps are included.…”

Section: Resultsmentioning

confidence: 97%

“…Accordingly, the repressed recombination rate and the low number of polymorphic markers in centromeric regions caused a strong disproportion between cM and actual physical distances (Table ). Markers order was in good agreement among NI‐RIL map, deletion bin map and radiation maps; by contrast, discrepancies in the marker order were observed when comparing mapping results with the recently published 5A neighbour map (Figure ) generated to support anchoring of fingerprinting contigs of the chromosome 5A high‐quality physical map (Barabaschi et al ., ). The discrepancies are probably due to the fact that the neighbour map was constructed combining mapping results of ten different genetic maps and this approach was most likely not sufficient to put in agreement with the genetic order and physical bin location of markers in proximal regions.…”

Section: Discussionmentioning

confidence: 97%

“…Mapping results with the NI‐RIL population and of the two panels were compared. Finally, the RH map was compared to the recently published 5A consensus genetic map (called ‘neighbour map’) (Barabaschi et al ., ).…”

Section: Introductionmentioning

confidence: 97%

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High‐resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harbouring the Fusarium head blight resistance QTLQfhs.ifa‐5A

Buerstmayr

Steiner

Wagner

et al. 2017

Plant Biotechnology Journal

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SummaryThe Qfhs.ifa‐5A allele, contributing to enhanced Fusarium head blight resistance in wheat, resides in a low‐recombinogenic region of chromosome 5A close to the centromere. A near‐isogenic RIL population segregating for the Qfhs.ifa‐5A resistance allele was developed and among 3650 lines as few as four recombined within the pericentromeric C‐5AS1‐0.40 bin, yielding only a single recombination point. Genetic mapping of the pericentromeric region using a recombination‐dependent approach was thus not successful. To facilitate fine‐mapping the physically large Qfhs.ifa‐5A interval, two gamma‐irradiated deletion panels were generated: (i) seeds of line NIL3 carrying the Qfhs.ifa‐5A resistance allele in an otherwise susceptible background were irradiated and plants thereof were selfed to obtain deletions in homozygous state and (ii) a radiation hybrid panel was produced using irradiated pollen of the wheat line Chinese Spring (CS) for pollinating the CS‐nullisomic5Atetrasomic5B. In total, 5157 radiation selfing and 276 radiation hybrid plants were screened for deletions on 5AS and plants containing deletions were analysed using 102 5AS‐specific markers. Combining genotypic information of both panels yielded an 817‐fold map improvement (cR/cM) for the centromeric bin and was 389‐fold increased across the Qfhs.ifa‐5A interval compared to the genetic map, with an average map resolution of 0.77 Mb/cR. We successfully proved that the RH mapping technique can effectively resolve marker order in low‐recombining regions, including pericentromeric intervals, and simultaneously allow developing an in vivo panel of sister lines differing for induced deletions across the Qfhs.ifa‐5A interval that can be used for phenotyping.

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Section: Resultsmentioning

confidence: 90%

Section: Resultsmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 97%

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High‐resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harbouring the Fusarium head blight resistance QTLQfhs.ifa‐5A

Buerstmayr

Steiner

Wagner

et al. 2017

Plant Biotechnology Journal

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“…In order to understand if also for P5CS different isoforms are present in durum wheat, the PCR products were cloned and the sequenced cDNA clones were used as a query in a BLASTN search for all wheat A and B chromosomes with the GrainGenes 2.0 database (http://wheat.pw.usda.gov/GG2/index.shtml) and URGI database (https://wheat-urgi.versailles.inra.fr/) (Barabaschi et al, 2015). T. durum is, in fact, an allotetraploid plant with a AABB genome (2 n = 4 x = 28) formed through hybridization between two separate but related diploid species, T. monococcum or T. urartu (AA, 2 n = 14) and T. searsii or T. speltoides (BB, 2 n = 14).…”

Section: Resultsmentioning

confidence: 99%

Durum Wheat Roots Adapt to Salinity Remodeling the Cellular Content of Nitrogen Metabolites and Sucrose

et al. 2017

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Plants are currently experiencing increasing salinity problems due to irrigation with brackish water. Moreover, in fields, roots can grow in soils which show spatial variation in water content and salt concentration, also because of the type of irrigation. Salinity impairs crop growth and productivity by inhibiting many physiological and metabolic processes, in particular nitrate uptake, translocation, and assimilation. Salinity determines an increase of sap osmolality from about 305 mOsmol kg−1 in control roots to about 530 mOsmol kg−1 in roots under salinity. Root cells adapt to salinity by sequestering sodium in the vacuole, as a cheap osmoticum, and showing a rearrangement of few nitrogen-containing metabolites and sucrose in the cytosol, both for osmotic adjustment and oxidative stress protection, thus providing plant viability even at low nitrate levels. Mainly glycine betaine and sucrose at low nitrate concentration, and glycine betaine, asparagine and proline at high nitrate levels can be assumed responsible for the osmotic adjustment of the cytosol, the assimilation of the excess of ammonium and the scavenging of ROS under salinity. High nitrate plants with half of the root system under salinity accumulate proline and glutamine in both control and salt stressed split roots, revealing that osmotic adjustment is not a regional effect in plants. The expression level and enzymatic activities of asparagine synthetase and Δ1-pyrroline-5-carboxylate synthetase, as well as other enzymatic activities of nitrogen and carbon metabolism, are analyzed.

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Wheat Chromosomal Resources and Their Role in Wheat Research

Šimková,

Cápal,

Doležel

2023

Compendium of Plant Genomes

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Bread wheat (Triticum aestivum L.) is grown on more area of land than any other crop, and its global significance is challenged only by rice. Despite the socioeconomic importance, the wheat genome research was lagging behind other crops for a long time. It was mainly a high complexity of the genome, polyploidy and a high content of repetitive elements that were laying obstacles to a thorough genome analysis, gene cloning and genome sequencing. Solution to these problems came in the beginning of the new millennium with the emergence of chromosome genomics—a new approach to studying complex genomes after dissecting them into smaller parts—single chromosomes or their arms. This lossless complexity reduction, enabled by flow-cytometric chromosome sorting, reduced the time and cost of the experiment and simplified downstream analyses. Since the approach overcomes difficulties due to sequence redundancy and the presence of homoeologous subgenomes, the chromosomal genomics was adopted by the International Wheat Genome Sequencing Consortium (IWGSC) as the major strategy to sequence bread wheat genome. The dissection of the wheat genome into single chromosomes enabled the generation of chromosome survey sequences and stimulated international collaboration on producing a reference-quality assembly by the clone-by-clone approach. In parallel, the chromosomal resources were used for marker development, targeted mapping and gene cloning. The most comprehensive approaches to gene cloning, such as MutChromSeq and assembly via long-range linkage, found their use even in the post-sequencing era. The chapter provides a two-decade retrospective of chromosome genomics applied in bread wheat and its relatives and reports on the chromosomal resources generated and their applications.

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Physical Mapping of Bread Wheat Chromosome 5A: An Integrated Approach

Cited by 12 publications

References 114 publications

High‐resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harbouring the Fusarium head blight resistance QTLQfhs.ifa‐5A

High‐resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harbouring the Fusarium head blight resistance QTLQfhs.ifa‐5A

Durum Wheat Roots Adapt to Salinity Remodeling the Cellular Content of Nitrogen Metabolites and Sucrose

Wheat Chromosomal Resources and Their Role in Wheat Research

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