Physiological field evaluation for drought tolerance. Field phenotyping methods for the development of the new synthetic population

The Cirad/CIAT collaborative project has developed a breeding program based on the recurrent selection (RS) for an eco-efficiency use of water. Selection was primarily based on yield and, in the course of the selection process, screening methods were refined with additional secondary relevant traits (morpho-pheno-physiological traits). The infrared (IR) thermography measures the plant canopy temperature, which gives an indication of the plant water status through leaf surface cooling capacity by transpiration along environmental conditions. We developed large scale phenotyping methods, adapting the IR technology to field conditions, to evaluate response to drought among synthetic populations. An experiment was conducted during the 2008/2009 dry season in the Santa Rosa CIAT research station in Villavicencio (Colombia) to adjust the phenotyping method based on IR thermography and to evaluate 400 S1 lines and 1000 S0 plants derived from synthetic populations. This evaluation method allowed us to identify interesting progenitors to be integrated in the population improvement scheme with the goal to develop and diffuse improved material, populations or lines, with increased resilience to drought for various rainfed ecosystems in Latin America and the Caribbean (LAC). (Résumé d'auteur

High throughput phenotyping methods for screening rice germplasm under water limited field conditions

A Cirad project (Orytage) involving NARS and IRC aims at developing an international phenotyping network for rice adaptations to drought and thermal stresses in the context of gene discovery and genetic mapping. Relevant association mapping depend on improved methods for high quality and high throughput phenotyping in the field. In case of drought the Infrared thermography was used to phenotype the plant transpiration capacity in relation with carbon isotopic discrimination, soil moisture and atmosphere demand. Two hundreds varieties representative of the Oryza sativa japonica group were phenotyped under drought condition at the Villavicencio CIAT experimental station (Colombia) during the dry season 2009/2010. Irrigation was suspended for two weeks at vegetative stage (45-60 DAS). Drought response was evaluated based on canopy temperature with an infra-red thermographic camera. The methodology was improved by CWSI (crop water stress index) calculated to normalize canopy temperatures against micro-meteorological weather fluctuations, and complemented with delta 13C measurements indicative of water use efficiency (WUE). Leaf temperature at vegetative stage exhibited strong and significant varietal differences that were negatively correlated with soil moisture content. This phenotyping approach permitted identifying genotypes with good maintenance of transpiration capacity (and thus sustained growth) under drought stress, related mainly to limited water extraction and/or greater root depth. The integration of high throughput phenotyping with genetic association study on a japonica rice variety panel, present a significant advance in order to identify genomic regions of interest and polymorphisms for marker development (ongoing). This will eventually permit developing efficient marker-assisted selection (MAS) approaches. (Résumé d'auteur

High throughput phenotyping method for water use efficiency in rice under field conditions : [Abstract, P 6.04]

A collaborative CIAT/Cirad project aims to create new improved upland rice germplasm for drought tolerance based on population improvement through recurrent selection (RS). In the framework of a multidisciplinary team (ecophysiology, molecular genetics and breeding), we seek to enhance this breeding strategy through the integration of marker-assisted breeding tools. This requires improving methods for high throughput phenotyping in the field. Four hundreds lines selected from diverse recurrent populations were screened under drought conditions in Villavicencio CIAT experimental station (Colombia) during the dry season 2008/2009. Drought stress was applied for two weeks at panicle initiation stage. Drought response under water deficit at flowering stage was evaluated based on soil moisture and canopy temperature at flowering with an infra-red thermographic camera and final grain yield. Leaf temperature at/around flowering stage exhibited strongly significant varietal differences that were negatively correlated with soil moisture content and yield. This phenotyping approach permitted identifying genotypes that display good maintenance of transpiration (and thus sustained growth) under drought stress, related mainly to limited water extraction and/or greater root depth; it also enabled identifying genotypes that have high transpirationrates (and thus higher potential growth rates) under irrigated control conditions. Selecting suitable combinations of both characteristics is expected to help identifying drought tolerant material with high yield potential. The methodology will be further improved by (1) including on each thermographic photo a wet/dry object to normalize canopy temperatures against weather fluctuations for situations where micro-meteorological backup is not available, and (2) sampling leaf material for complementary delta 13C measurements indicative of transpiration efficiency (TE). The integrated methodology is being implemented in RS breeding schemes and in parallel in a genetic association study on a japonica rice variety panel, in order to identify promising genomic regions and polymorphisms for marker development. This will eventually permit developing efficient marker-assisted recurrent selection (MARS) approaches. (Texte intégral

Exploiting genetic resources for developing rice germplasm with eco-efficient water use

The Cirad/CIAT rice collaborative project focuses on the development and enhancement of rice composite populations (CPs) through recurrent selection (RS) breeding. Our goal is to develop and diffuse improved material for various rainfed ecosystems in Latin America and the Caribbean (LAC). Our breeding strategy is based on the development of broadbase populations; their improvement thought RS and the exploitation of their genetic wealth for line development. From a base population, four CP were derived, some subjected to selections under acid soils conditions (savannas of Colombian Llanos), others selected under the conditions of Bolivian rice agriculture. We used 16 SSR loci to assess the genetic diversity within these populations and estimate genetic differentiation between them. We applied large scale phenotyping method adapted to field conditions to evaluate the response to drought. Through thermographic infra-red technology (IR) we screened S1 progenies extracted from each population which were exposed to a 15-day drought period at flowering stage. Allelic variability measured in the four CP revealed high levels of neutral diversity. The genetic diversity expressed in terms of number of observed alleles per locus (Na) and Shannon diversity index (I), was high within the populations (Na > 3.133, and I = 0.693 to I = 0.800). Significant allelic and genotypic differentiations were found at most loci. A total of six alleles were found with frequency > 5% and unique to a particular population. IR screening showed that the CPs hold favorable alleles for resilience to drought. S1 lines with cool canopy temperatures during the dry period indicated good capacity to maintain transpiration and thus sustained growth under water stress conditions. These lines are potential progenitors to develop a new population with increased eco-efficiency to water use. Besides showing the genetic wealth retained in these CP, our work presents an advance towards the integration of highthroughput phenotyping and use of molecular markers for improving RS breeding strategy. Our objective is not limited to integrating disciplines; the outcomes of the project, both methodologies and germplasm, are shared among our network of rice breeders from LAC.(Texte intégral

Accuracy of genomic selection in a rice synthetic population developed for recurrent selection.

Genomic selection is a promising breeding strategy for rapid improvement of complex traits. We investigated the accuracy of genomic estimate breeding values (GEBV) through cross validation in a synthetic population (SP) of broad genetic diversity developed for upland rice breeding for Latin America, through recurrent selection (RS). Three hundred and three S4 lines extracted from a SP that has undergone several RS cycles were phenotyped for flowering time (FL), plant height (PH) and grain weight per plant (GW), and genotyped with an average density of one marker per 22.9 kb, using genotyping by sequencing. Cross validation was performed hundred times, for four ratios of training and validation population sizes (TP/VP), using ridge regression best linear unbiased prediction (RR-BLUP), least absolute shrinkage and selection operator (LASSO) and Bayesian linear regression methods (BL). Accuracy was estimated as the correlation between GEBV and true breeding value. Linkage disequilibrium was high (average r²>0.5 at 20 kb; r²>0.25 at 1.5 Mb distance). Accuracy of GEBV increased with the size of the training population, regardless of the model. For FL and TP/VP varying from 150/153 to 270/33, the GEBV accuracy ranged from r=0.20 (0.05) to r=0.22 (0.15) under RR-BLUP, from r=0.19 (0.09) to r=0.28 (0.17) under LASSO, and from r=0.28 (0.03) to r=0.32 (0.17) under BL, before marker selection based on alleles frequency. GEBV accuracy was more sensitive to markers' allele frequency than to the total number of markers. The best selected S4 will be recombined and their progenies tested for GEBV accuracy across generations. (Résumé d'auteur

Collaborative project between CIAT and Cirad rice improvement through the use of synthetic populations

The Cirad/CIAT rice collaborative project focuses on the development and enhancement of rice synthetic populations through recurrent selection (RS) with the goal to develop and diffuse improved material, populations or lines, for various rainfed ecosystems in Latin America and the Caribbean (LAC). Our breeding strategy is based on the development of broad-base populations, their improvement thought recurrent cycles of selection and recombination, and the exploitation of their genetic wealth for line development through conventional breeding. Within our network of rice breeders from LAC, we released improved material as part of the breeding activities for upland rice in Colombia and shared germplasm of interest to LAC collaborators as part of prebreeding activities. We are developing large scale phenotyping methods adapted to field conditions to evaluate response to drought among synthetic populations. The thermographic infra-red technology was assessed for screening large number of families, as well as for single-plant evaluation within large populations. This evaluation method allowed us to identify interesting progenitors to develop new population with increased resilience to drought. Allelic variability measured in several synthetic populations revealed high level of neutral diversity. These activities are part of a much broader mission on the management of synthetic populations for more efficient use of RS breeding and for the development of a marker assisted recurrent selection program. (Résumé d'auteur

Actividad 2. Mejoramiento de polblaciones compositas. Arroz de secano para el ecosistema de sabanas : Informe anual 2001. Septiembre 2000 - Septiembre 2001

Desde 1996, acudiendo a las recomendaciones del CIAT, los proyectos arroz del CIAT y del CIAT/CIRAD, han disminuido las actividades de mejoramiento convencional por cruces entre "Japonica" Oryza sativa y "Japonica" Oryza sativa. Se están concentrando en la ampliación de la base genética del arroz de secano. El desarrollo de poblaciones de arroz con amplia base genética y el mejoramiento de las mismas por selección recurrente son nuevas estrategias de mejoramiento para alcanzar el objetivo. La creación de las poblaciones fue facilitado por la utilización del gene recesivo de androesterilidad (ms) encontrado en un mutante de la variedad IR 36. Poblaciones compositas de sitio especifico fueran creadas con los Programas Nacionales con los cuales el proyecto esta colaborando. En Colombia, poblaciones compositas fueran mejoradas utilizando dos métodos de selección recurrente. A cada etapa del mejoramiento, plantas fértiles fueran seleccionadas. Estas son consideradas como punto de partida para el desarrollo de líneas segregantes y fijas a través del método pedigrí. En 2001, mas del 90% de las líneas bajo selección provienen de las poblaciones recurrentes. Las líneas mas avanzadas están siendo evaluadas en ensayos de rendimiento en Colombia. Resultados alentadores están por venir. Palabras claves: Poblaciones de arroz, base genética, androesterilidad, mejoramiento, selección recurrente, líneas promisorias. (Résumé d'auteur

Actividad 1. Mejoramiento convencional. Arroz de secano para el ecosistema de sabanas : Informe anual 2001. Septiembre 2000 - Septiembre 2001

El mejoramiento convencional permitió el desarrollo y liberación de variedades modernas de arroz de secano en América latina (Bolivia, Brasil y Colombia). Los proyectos de CIAT y de CIRAD/CIAT están ahora concentrándose en la ampliación de la base genética del arroz de secano. Cruces ínter específicos entre Oryza sativa y el arroz cultivado en Africa Oryza glaberrima y especies silvestres relacionadas es una de las nuevas estrategias para alcanzar este obj etivo. Desde 1996, ninguno cruce convencional "Japonica" Oryza sativa por "Japonica" Oryza sativa" ha sido realizado. Pero como todavía contamos con líneas segregantes de cruces anteriores, se sigue evaluando y multiplicando en Colombia para su posterior entrega a los Programas Nacionales de América Latina y del Caribe (ALC). (Résumé d'auteur