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

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

Bulked sample analysis in genetics, genomics and crop improvement

“…The examples of BSA based on DNA/RNA/chip are summarized in Table . The method has been used to study a dozen of recessive mutants in maize (Liu et al ., ), leaf rust in wheat (Forrest et al ., ), sulphur and selenium contents in Arabidopsis thaliana (Becker et al ., ), salt resistance in cotton (Rodriguez‐Uribe et al ., ), bean common mosaic virus in common bean (Bello et al ., ), Phytophthora root rot in pepper (Liu et al ., ) and photosynthetic traits in poplar (Wang et al ., ).…”

The Gametic Non-Lethal Gene Gal on Chromosome 5 Is Indispensable for the Transmission of the Co-Induced Semidwarfing Gene d60 in Rice

“…On the other hand, the monogenetic male-sterile gene including the photoperiod-sensitive male sterile (PGMS) and thermosensitive male sterile are useful to facilitate the production of F 1 seeds [70] or the intercrossing phase of recurrent selection. Several genes for PGMS and thermosensitive male sterile were mapped or isolated [71][72][73]. However, their monogenetic inheritance and the expression of male sterility are certainly distinguished from the complementary sterility caused by the two genes d60 and gal.…”

Breeding for Outcrossing Ability in Rice, to Enhance Seed Production for Hybrid Rice Cropping

“…It is based on ms-IR36 MS-facilitated recurrent selection (RS), which has been extensively used to breed inbred lines [27,[31][32][33]. The ms-IR36 gene cloned by Frouin et al [26], facilitates marker-assisted screening of ms,Ms plants during the vegetative stage. Recurrent selection is a widely used breeding procedure for the improvement of allogamous crops [34,35].…”

“…The program is based on the use of a monogenic recessive gene ms-IR36 that does not interact with environmental factors and displays stable expression and Mendelian segregation [24][25][26]. The homozygous plants for the recessive allele (ms,ms) are fully male sterile while the heterozygous (Ms,ms) and homozygous (Ms,Ms) plants for the dominant allele are fully male fertile.…”