Structural and functional partitioning of bread wheat chromosome 3B

Choulet, Frédéric; Alberti, Adriana; Theil, Sébastien; Glover, Natasha; Barbe, Valérie; Daron, Josquin; Pingault, Lise; Sourdille, Pierre; Couloux, Arnaud; Paux, Etienne; Leroy, Philippe; Mangenot, Sophie; Guilhot, Nicolas; Gouis, Jacques Le; Balfourier, François; Alaux, Michaël; Jamilloux, Véronique; Poulain, Julie; Durand, Céline; Bellec, Arnaud; Gaspin, Christine; Šafář, Jan; Doležel, Jaroslav; Rogers, Jane; Vandepoele, Klaas; Aury, Jean‐Marc; Mayer, Klaus; Bergès, Hélène; Quesneville, Hadi; Wincker, Patrick; Feuillet, Catherine

doi:10.1126/science.1249721

Cited by 540 publications

(659 citation statements)

References 120 publications

Supporting

Mentioning

609

Contrasting

Unclassified

Order By: Relevance

“…In total, 774 SNPs and 61 SSRs from chromosome 3B (Table S4) were used on the CsRe population, from which 466 SNPs were derived from Rimbert et al (2017), 214 from Choulet et al (2014), 88 transferred from Axiom 420K Array (Rimbert et al 2017), and six from previous studies of recombination (Saintenac et al 2011). Then, 540 SNPs and 9 SSRs were retained to refine CO localization.…”

Section: Genotyping Data and Genetic Mappingmentioning

confidence: 99%

“…According to our strategy, we used scaffold information resulting in mapping/detection of markers along the chromosome 3B pseudomolecule (Choulet et al 2014) to locate and refine the CO position between two markers present on the same scaffold. This strategy allows access to a confident physical position at scaffold scale.…”

Section: Co Detectionmentioning

confidence: 99%

“…For chromosome 3B, two fully overlapping sets of 276 and 356 lines were randomly selected to genotype 5778 (Axiom Array) and 1280 (KASPar) SNPs, respectively. The whole population was genotyped with only 96 SNPs to roughly identify the recombinants along the chromosome 3B pseudomolecule (Choulet et al 2014). For whole-genome analysis, 430 lines (including the preceding sets) were randomly selected to genotype 280,226 (Axiom Array) public SNPs, from which 53,287 were used to construct a dense genetic map (Rimbert et al 2017).…”

Section: Plant Materialsmentioning

confidence: 99%

“…In all eukaryotes studied so far, the distribution of COs is not homogeneous along the chromosomes (Lukaszewski and Curtis 1993;Tenaillon et al 2002;Saintenac et al 2009;Mayer et al 2012;Pan et al 2012;Choulet et al 2014;Choi and Henderson 2015;Mercier et al 2015). For cultivated crops, this implies a decrease of the breeding power in regions showing low CO rates (Rodgers-Melnick et al 2015).…”

mentioning

confidence: 99%

“…Only one hotspot was reported in the promoter of the TaHGA3 gene on chromosome 3B (Saintenac et al 2011), and this hotspot was associated to an NCO event covering 453-1098 bp. Recently, the reference sequence of chromosome 3B and the draft assemblies of the 20 other chromosomes were published (Choulet et al 2014;International Wheat Genome Sequencing Consortium 2014), offering the opportunity to precisely characterize recombination hotspots at the wholegenome scale.…”

mentioning

confidence: 99%

See 4 more Smart Citations

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

et al. 2017

Self Cite

View full text Add to dashboard Cite

During meiosis, crossovers (COs) create new allele associations by reciprocal exchange of DNA. In bread wheat (Triticum aestivum L.), COs are mostly limited to subtelomeric regions of chromosomes, resulting in a substantial loss of breeding efficiency in the proximal regions, though these regions carry 60-70% of the genes. Identifying sequence and/or chromosome features affecting recombination occurrence is thus relevant to improve and drive recombination. Using the recent release of a reference sequence of chromosome 3B and of the draft assemblies of the 20 other wheat chromosomes, we performed fine-scale mapping of COs and revealed that 82% of COs located in the distal ends of chromosome 3B representing 19% of the chromosome length. We used 774 SNPs to genotype 180 varieties representative of the Asian and European genetic pools and a segregating population of 1270 F 6 lines. We observed a common location for ancestral COs (predicted through linkage disequilibrium) and the COs derived from the segregating population. We delineated 73 small intervals (,26 kb) on chromosome 3B that contained 252 COs. We observed a significant association of COs with genic features (73 and 54% in recombinant and nonrecombinant intervals, respectively) and with those expressed during meiosis (67% in recombinant intervals and 48% in nonrecombinant intervals). Moreover, while the recombinant intervals contained similar amounts of retrotransposons and DNA transposons (42 and 53%), nonrecombinant intervals had a higher level of retrotransposons (63%) and lower levels of DNA transposons (28%). Consistent with this, we observed a higher frequency of a DNA motif specific to the TIR-Mariner DNA transposon in recombinant intervals. KEYWORDS recombination; meiosis; bread wheat; linkage disequilibrium; transposon; hotspot; sequence motif M EIOTIC recombination is a process that allows reshuffling of diversity by the reciprocal exchange of DNA called a crossover (CO). This phenomenon is conserved in most eukaryotes (for a review see Mercier et al. 2015) and follows the formation of a double-strand break (DSB) of DNA generated by the topoisomerase SPO11 complex. However, the number of DSBs is at least 10-to 50-fold greater than the number of COs which rarely exceeds three per bivalent chromosome per meiosis (Mercier et al. 2015). This paucity of COs per meiosis with regards to the number of DSBs suggests the existence of a tight control and regulation of recombination in plants that promote DSB repair in a manner that does not lead to COs. For example, the study of the two helicases AtFANCM and RECQ4 (AtRECQ4A and AtRECQ4B) (Crismani et al. 2012;Knoll et al. 2012;Girard et al. 2014;Séguéla-Arnaud et al. 2015) revealed three-and sixfold CO frequency increases in the Atfancm single mutant and the Atrecq4a/Atrecq4b double mutant, respectively, compared to the wild type. These increases result from additional COs from the class-II pathway which suggests that FANCM and RECQ4 prevent CO formation and direct recombination intermediates towar...

show abstract

Section: Genotyping Data and Genetic Mappingmentioning

confidence: 99%

Section: Co Detectionmentioning

confidence: 99%

Section: Plant Materialsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

Tuning of meristem maturation rate increases yield in multiple Triticum aestivum cultivars

et al. 2022

View full text Add to dashboard Cite

Breeding programs aim to improve crop yield and environmental stability for enhanced food security. The principal methodology in breeding for stable yield gain relies on the indirect selection of beneficial genetics by yield evaluation across diverse environmental conditions. This methodology requires substantial resources while delivering a slow pace of yield gain and environmental adaptation. Alternative methods are required to accelerate gain and adaptation, becoming even more imperative in a changing climate. New molecular tools and approaches can enable accelerated creation and deployment of multiple alleles of genes identified to control key traits. With the advent of tools that enable breeding by targeted allelic selection, identifying gene targets associated with an improved crop performance ideotype will become crucial. Previous studies have shown that altered photoperiod regimes increase yield in wheat (Triticum aestivum). In the current study, we have employed such treatments to study the resulting yield ideotype in five spring wheat cultivars. We found that the photoperiod treatment creates a yield ideotype arising from delayed spike establishment rates that are accompanied by increased early shoot expression of TARGET OF EAT1 (TaTOE1) genes. Genes identified in this way could be used for ideotype‐based improve crop performance through targeted allele creation and selection in relevant environments.

show abstract

Distinct metabolic changes between wheat embryo and endosperm during grain development revealed by 2D‐DIGE‐based integrative proteome analysis

Cao

Zhu

et al. 2016

Proteomics

View full text Add to dashboard Cite

Two Chinese bread wheat cultivars, Jinghua 9 and Zhongmai 175, distinct in grain weight and dough quality, were used to study proteome changes in the embryo and endosperm during grain development using a two-dimensional difference gel electrophoresis (2D-DIGE)-based proteomics approach. In total, 138 and 127 differentially expressed protein (DEP) spots representing 116 and 113 unique DEPs were identified in the embryo and endosperm, respectively. Among them, 54 (31%) DEPs were commonly present in both organs while 62 (35%) and 59 (34%) DEPs occurred only in the embryo and endosperm, respectively. Embryonic DEPs are primarily stress-related proteins and involved in carbohydrate and lipid metabolism, while those from the endosperm are related primarily to carbohydrate metabolism and storage. Principal component analysis (PCA) indicated that the proteome differences in the endosperm caused by different cultivars were greater than those by development stages, while the differences in the embryo showed the opposite pattern. Protein-protein interaction (PPI) analysis revealed a complex network centered primarily on enzymes involved in carbohydrate and protein metabolism. The transcriptional levels of fourteen important DEPs encoding genes showed high similarity between organs and cultivars. In particular, some key DEPs of the endosperm, such as phosphoglucomutase, ADP-glucose pyrophosphorylase (AGPase), and sucrose synthase (SUS), showed significantly upregulated expression, indicating their key roles in starch biosynthesis and grain yield. Moreover, upregulated expression of some storage proteins in the endosperm could improve wheat bread-making quality.

show abstract

Structural and functional partitioning of bread wheat chromosome 3B

Cited by 540 publications

References 120 publications

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

Tuning of meristem maturation rate increases yield in multiple Triticum aestivum cultivars

Distinct metabolic changes between wheat embryo and endosperm during grain development revealed by 2D‐DIGE‐based integrative proteome analysis

Contact Info

Product

Resources

About