Genetic bases of resistance to the rice hoja blanca disease deciphered by a quantitative trait locus approach.

Rice hoja blanca (RHB) is one of the most serious diseases in rice-growing areas in tropical Americas. Its causal agent is RHB virus (RHBV), transmitted by the planthopper Tagosodes orizicolus Müir. Genetic resistance is the most effective and environment-friendly way of controlling the disease. So far, only 1 major quantitative trait locus (QTL) of Oryza sativa ssp. japonica origin, qHBV4.1, that alters the incidence of the virus symptoms in 2 Colombian cultivars has been reported. This resistance has already started to be broken, stressing the urgent need for diversifying the resistance sources. In the present study, we performed a search for new QTLs of O. sativa indica origin associated with RHB resistance. We used 4 F2:3-segregating populations derived from indica-resistant varieties crossed with a highly susceptible japonica pivot parent. Besides the standard method for measuring disease incidence, we developed a new method based on computer-assisted image processing to determine the affected leaf area (ALA) as a measure of symptom severity. Based on the disease severity and incidence scores in the F3 families under greenhouse conditions and SNP genotyping of the F2 individuals, we identified 4 new indica QTLs for RHB resistance on rice chromosomes 4, 6, and 11, namely, qHBV4.2WAS208, qHBV6.1PTB25, qHBV11.1, and qHBV11.2, respectively. We also confirmed the wide-range action of qHBV4.1. Among the 5 QTLs, qHBV4.1 and qHBV11.1 had the largest effects on incidence and severity, respectively. These results provide a more complete understanding of the genetic bases of RHBV resistance in the cultivated rice gene pool and can be used to develop marker-aided breeding strategies to improve RHB resistance. The power of joint- and meta-analyses allowed precise mapping and candidate gene identification, providing the basis for positional cloning of the 2 major QTLs qHBV4.1 and qHBV11.1.

Genome Analysis and Pathobiology of Cassava-Infecting Torradoviruses Containing a Putative Maf/HAM1 Pyrophosphatase Domain.

Next generation sequencing has been used to identify and characterize the full genome sequence of a cassava-infecting torradovirus, revealing the presence of a Maf/HAM1 domain downstream of the RNA-dependent RNA-polymerase (RdRp) domain in RNA1 in all isolates sequenced. A similar domain is also found in unrelated potyvirids infecting Euphorbiaceae hosts in the Americas and cassava in Africa. Even though cassava torrado-like virus (CsTLV) could not be mechanically transmitted to a series of herbaceous hosts, it can be efficiently transmitted by bud graft-inoculation to different cassava landraces. Our bioassays show that CsTLV has a narrow host range. Crystal-like structures of isometric virus-like particles were observed in cells of plants with single infection by CsTLV, and consistently induced chlorotic leaf spots and affected root yields significantly. Moreover, CsTLV infection induces changes in the accumulation of total sugars in storage roots. Field surveys indicated the presence of CsTLV in the main cassava growing regions of Colombia, and the occurrence of two different cassava-infecting torradovirus species. Profiles of small RNAs of 21 to 24 nucleotides in length, derived from CsTLV RNAs targeted by cassava RNA silencing defense mechanisms, are also reported.

COMPARACIÓN MORFO-AGRONÓMICA Y MOLECULAR DE CATORCE VARIEDADES DE ARROZ (Oryza sativa) CON LAS LÍNEAS QUE DIERON SU ORIGEN / Morpho-agronomic and molecular comparison of fourteen varieties of rice (Oryza sativa) with the lines that gave them the origin

RESUMEN Con el objetivo de determinar las diferencias morfo-agronómicas y de calidad, y la diversidad genética entre 14 variedades de arroz de América Latina con sus respectivas líneas de origen, se estableció un estudio (Bloques completos al azar, con 28 genotipos, tres repeticiones y dos siembras en el tiempo), en el cual se midieron 25 variables morfo-agronómicas y de calidad de grano. El análisis molecular se hizo mediante un arreglo de 96 marcadores tipo SNP de alta capacidad de discriminación para arroces Indica. El análisis estadístico se hizo combinando los datos de las dos siembras porque no hubo diferencias estadísticas entre ellas. Además, se analizaron en conjunto los datos moleculares con los morfo-agronómicos y de calidad, usando el índice de Gower para generar una matriz de similitud. Mediante el programa SAS se analizaron los datos agronómicos y moleculares tanto en forma independiente como en conjunto. Los resultados mostraron que, de las 14 variedades, ocho se agruparon con su línea de origen y hubo una variedad que se agrupó con una línea hermana de su ancestro. Los resultados fueron consistentes cuando el análisis de datos se hizo independientemente o combinado. Dada la amplia diversidad encontrada dentro de las variedades y que ninguna fue homocigota al 100 % no se pudieron establecer los perfiles genéticos distintivos de ellas, por lo que se debe hacer la purificación de las variedades para establecer su huella genética.

ABSTRACT This research aimed to determine the morpho-agronomic, grain quality, and molecular differences between 14 rice varieties and their ancestors. These rice varieties from Latin America were tested for 25 variables in a randomized complete block design with 28 genotypes, two planting dates, and three replications. The molecular analysis was done using an array of 96 SNP markers with a high discrimination capacity for Indica rice. A combined statistical analysis was done because there were no statistical differences between the planting dates. Also, molecular, morpho-agronomic, and grain quality data were analyzed together, using the Gower index to generate a similarity matrix. Agronomic and molecular data were analyzed both, together and independently, through the SAS program. Results showed that eight varieties were grouped with their respective ancestor, and one variety was grouped with a sibling of their ancestor and was consistent in all the analyses. However, given the wide heterozygosity found within the varieties, distinctive genetic profiles could not be established; the varieties must be purified to establish their genetic footprint.

Genetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean.

Rice (Oryza sativa L.)grain quality is a set of complex interrelated traits that include grain milling, appearance, cooking, and edible properties. As consumer preferences in Latin America and the Caribbean evolve, determining what traits best capture regional grain quality preferences is fundamental for breeding and cultivar release. In this study, a genome-wide association study (GWAS), marker-assisted selection (MAS), and genomic selection (GS) were evaluated to help guide the development of new breeding strategies for rice grain quality improvement. For this purpose, 284 rice lines representing over 20 yr of breeding in Latin America and the Caribbean were genotyped and phenotyped for 10 different traits including grain milling, appearance, cooking, and edible quality traits. Genetic correlations among the 10 traits ranged from -0.83 to 0.85. A GWAS identified 19 significant marker/trait combinations associated with eight grain quality traits. Four functional markers, three located in the Waxy and one in the starch synthase IIa genes, were significantly associated with six grain-quality traits. These markers individually explained 51-75% of the phenotypic variance depending on the trait, clearly indicating their potential utility for MAS. Cross-validation studies to evaluate predictive abilities of four different GS models for each of the 10 quality traits were conducted and predictive abilities ranged from 0.3 to 0.72. Overall, the machine learning model random forest had the highest predictive abilities and was especially effective for traits where large effect quantitative trait loci were identified. This study provides the foundation for deploying effective molecular breeding strategies for grain quality in Latin American rice breeding programs.

Understanding the complexity of disease-climate interactions for rice bacterial panicle blight under tropical conditions.

Bacterial panicle blight (BPB) caused by Burkholderia glumae is one of the main concerns for rice production in the Americas since bacterial infection can interfere with the grain-filling process and under severe conditions can result in high sterility. B. glumae has been detected in several rice-growing areas of Colombia and other countries of Central and Andean regions in Latin America, although evidence of its involvement in decreasing yield under these conditions is lacking. Analysis of different parameters in trials established in three rice-growing areas showed that, despite BPB presence, severity did not explain the sterility observed in fields. PCR tests for B. glumae confirmed low infection in all sites and genotypes, only 21.4% of the analyzed samples were positive for B. glumae. Climate parameters showed that Montería and Saldaña registered maximum temperature above 34°C, minimum temperature above 23°C, and Relative Humidity above 80%, conditions that favor the invasion model described for this pathogen in Asia. Our study found that in Colombia, minimum temperature above 23°C during 10 days after flowering is the condition that correlates with disease incidence. Therefore, this correlation, and the fact that Montería and Saldaña had a higher level of infected samples according to PCR tests, high minimum temperature, but not maximum temperature, seems to be determinant for B. glumae colonization under studied field conditions. This knowledge is a solid base line to design strategies for disease control, and is also a key element for breeders to develop strategies aimed to decrease the effect of B. glumae and high night-temperature on rice yield under tropical conditions.