Cécile Grenier

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

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.

Progress in varietal improvement for increasing upland rice productivity in the tropics

Abstract Enhancing rice yield in upland rice systems through genetic improvement remains a major challenge in the tropics. This review aims to provide the trends on upland rice cultivation over the last 30 years and recent distribution of upland rice in the tropics, and to report progress in studies on genetic improvement for enhancing productivity in Africa, Asia, and Latin America. While upland rice cultivation area has reduced in Asia and Latin America over the last 30 years, the area in Africa has increased. The current share of upland rice area in total rice area is related to rainfall and gross national income per capita, especially in Africa, and higher share is associated with lower rice self-sufficiency at national level. Breeding programs in Asia and Latin America have developed high-yielding varieties using indica materials as parents. In Africa, New Rice for Africa (NERICA) varieties were developed from crosses between improved tropical japonica and Oryza glaberrima. However, recent studies report that there is scope for improving existing NERICA using upland indica materials from Asia. In highlands of Africa, there are ongoing breeding programs using japonica varieties, such as the Nepalese Chhomrong Dhan. Key important plant traits used in the breeding programs are not largely different across regions, especially intermediate plant height and tillering capacity (which may be related to weed-suppressive ability), and high harvest index. In conclusion, we propose an international network for breeding upland rice with accelerating seed exchange across regions that could enhance upland rice productivity through genetic improvement.

Correction: Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding.

[This corrects the article DOI: 10.1371/journal.pone.0136594.].

DHOEM: a statistical simulation software for simulating new markers in real SNP marker data.

BackgroundNumerous simulation tools based on specific assumptions have been proposed to simulate populations. Here we present a simulation tool named DHOEM (densification of haplotypes by loess regression and maximum likelihood) which is free from population assumptions and simulates new markers in real SNP marker data. The main objective of DHOEM is to generate a new population, which incorporates real and simulated SNP by statistical learning from an initial population, which match the realized features of the latter.ResultsTo demonstrate DHOEM’s abilities, we used a sample of 704 haplotypes for 12 chromosomes with 8336 SNP from a synthetic population, used for breeding upland rice in Latin America. The distributions of allele frequencies, pairwise SNP LD coefficients and data structures, before and after marker densification of the associated marker data set, were shown to be in relatively good agreement at moderate degrees of marker densification. DHOEM is a user-friendly tool that allows the user to specify the level of marker density desired, with a user defined minor allele frequency (MAF) limit, which is produced in a reasonable computation time.ConclusionsDHOEM is a user-friendly and useful tool for simulation and methodological studies in quantitative genetics and breeding.