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Positional cloning of the rice male sterility gene ms-IR36, widely used in the inter-crossing phase of recurrent selection schemes

Frouin Julien, Filloux Denis, Taillebois James E., Grenier Cécile, Montes Fabienne, De Lamotte Frédéric, Verdeil Jean-Luc, Courtois Brigitte, Ahmadi Nourollah. 2014. Positional cloning of the rice male sterility gene ms-IR36, widely used in the inter-crossing phase of recurrent selection schemes. Molecular Breeding, 33 (3) : pp. 555-567.

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Quartile : Q1, Sujet : HORTICULTURE / Quartile : Q1, Sujet : AGRONOMY / Quartile : Q2, Sujet : PLANT SCIENCES / Quartile : Q3, Sujet : GENETICS & HEREDITY

Abstract : The monogenetic recessive male-sterile gene ms-IR36 is widely used to facilitate the inter-crossing phase of recurrent selection in rice (Oryza sativa), but its segregation within the progeny disturbs other breeding phases. Marker-assisted early identification of msms and Msms seedlings would help overcome this drawback. Using successively bulked segregant analysis and large F2 populations, we mapped the ms-IR36 gene to a 33-kb region on the short arm of chromosome 2 that includes 10 candidate genes. Sequencing of these candidates together with checking rice genome annotations and expression databases allowed the target to be narrowed down to one candidate gene already isolated and characterized as the tapetum degeneration retardation (TDR) gene and reported to be involved in tapetal programmed cell death. Comparison of the sequence of the TDR gene between male-sterile (MS) and male-fertile (MF) IR36 plants detected one non-synonymous nucleotide substitution affecting the active domain of the encoded protein. Perfect co-segregation was observed between polymorphism at this nucleotide (SNP) and the MS/MF phenotype of 946 F2 plants. Spatial modelling of the active domain of the candidate protein reinforced the candidate status of the only SNP identified. Histological characterization of anther development in MS IR36 revealed defects identical to the ones observed in mutants used for the isolation and characterization of the TDR gene: delayed/non-degradation of tapetum tissue and collapse of the haploid microspores. We concluded that ms-IR36 corresponded to the TDR gene with a different mutation from the earlier one described in the same gene. No significant linkage drag was associated with ms-IR36. A SNP-based marker that enables simple early identification of MS plants and MF plants with the Msms genotype was designed. (Résumé d'auteur)

Mots-clés Agrovoc : Oryza sativa, Clonage, Sélection récurrente, Gène, Infertilité mâle, Anthère, Développement biologique, Séquence nucléotidique, Marqueur génétique, Polymorphisme génétique, Ségrégation

Mots-clés complémentaires : Séquencage

Classification Agris : F30 - Plant genetics and breeding
F63 - Plant physiology - Reproduction

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Frouin Julien, CIRAD-BIOS-UMR AGAP (FRA)
  • Filloux Denis, CIRAD-BIOS-UMR BGPI (FRA)
  • Taillebois James E., CIRAD-BIOS-UMR AGAP (BRA)
  • Grenier Cécile, CIRAD-BIOS-UMR AGAP (COL)
  • Montes Fabienne, CIRAD-BIOS-UMR AGAP (FRA)
  • De Lamotte Frédéric, INRA (FRA)
  • Verdeil Jean-Luc, CIRAD-BIOS-UMR AGAP (FRA)
  • Courtois Brigitte, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-2118-7102
  • Ahmadi Nourollah, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-0072-6285

Source : Cirad - Agritrop (https://agritrop.cirad.fr/572512/)

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