Alejandro del Pozo

Increased Genomic Prediction Accuracy in Wheat Breeding Through Spatial Adjustment of Field Trial Data

In crop breeding, the interest of predicting the performance of candidate cultivars in the field has increased due to recent advances in molecular breeding technologies. However, the complexity of the wheat genome presents some challenges for applying new technologies in molecular marker identification with next-generation sequencing. We applied genotyping-by-sequencing, a recently developed method to identify single-nucleotide polymorphisms, in the genomes of 384 wheat (Triticum aestivum) genotypes that were field tested under three different water regimes in Mediterranean climatic conditions: rain-fed only, mild water stress, and fully irrigated. We identified 102,324 single-nucleotide polymorphisms in these genotypes, and the phenotypic data were used to train and test genomic selection models intended to predict yield, thousand-kernel weight, number of kernels per spike, and heading date. Phenotypic data showed marked spatial variation. Therefore, different models were tested to correct the trends observed in the field. A mixed-model using moving-means as a covariate was found to best fit the data. When we applied the genomic selection models, the accuracy of predicted traits increased with spatial adjustment. Multiple genomic selection models were tested, and a Gaussian kernel model was determined to give the highest accuracy. The best predictions between environments were obtained when data from different years were used to train the model. Our results confirm that genotyping-by-sequencing is an effective tool to obtain genome-wide information for crops with complex genomes, that these data are efficient for predicting traits, and that correction of spatial variation is a crucial ingredient to increase prediction accuracy in genomic selection models.

Wheat genotypic variability in grain yield and carbon isotope discrimination under Mediterranean conditions assessed by spectral reflectance.

A collection of 368 advanced lines and cultivars of spring wheat (Triticum aestivum L.) from Chile, Uruguay, and CIMMYT (Centro Internacional de Mejoramiento de Maíz y Trigo), with good agronomic characteristics were evaluated under the Mediterranean conditions of central Chile. Three different water regimes were assayed: severe water stress (SWS, rain fed), mild water stress (MWS; one irrigation around booting), and full irrigation (FI; four irrigations: at tillering, flag leaf appearance, heading, and middle grain filling). Traits evaluated were grain yield (GY), agronomical yield components, days from sowing to heading, carbon isotope discrimination (Δ(13) C) in kernels, and canopy spectral reflectance. Correlation analyses were performed for 70 spectral reflectance indices (SRI) and the other traits evaluated in the three trials. GY and Δ(13) C were the traits best correlated with SRI, particularly when these indices were measured during grain filling. However, only GY could be predicted using a single regression, with Normalized Difference Moisture Index (NDMI2: 2,200; 1,100) having the best fit to the data for the three trials. For Δ(13) C, only individual regressions could be forecast under FI (r(2): 0.25-0.37) and MWS (r(2): 0.45-0.59) but not under SWS (r(2): 0.03-0.09). NIR-based SRI proved to be better predictors than those that combine visible and NIR wavelengths.

Restoration and rehabilitation of mixed espinales in central Chile: 10-year report and appraisal.

A synthesis of progress achieved thus far is provided for a 10 - year research and development program aimed at the ecological and economic rehabilitation of agroecosystems in the unirrigated portions of the central valley of Chiles Mediterranean climate region. We review our data on (1) revised management techniques aimed at restoring the gross superstructure and former levels of diversity and productivity of a mixed espinales formation; (2) selection and utilization of ecotypes of the naturalized annual Medicago polymorpha L. and the N2-fixing microsymbiont Rhizobium meliloti, for gradual improvement of espinal soil fertility; and (3) studies of the outstandingly well adapted and fast growing Canary Island tree Chamaecytisus proliferus (L. fil.) Link ssp. palmensis (Christ) Kunkel (Tagasaste), which along with about three dozen other woody nitrogen - fixing legume and several nonlegume multipurpose trees, was considered to be of potential value for deep soil layer rehabilitation combined with economic ...

Influence of conservation tillage and soil water content on crop yield in dryland compacted alfisol of Central Chile

En Chile, las zonas de clima mediterraneo se caracterizan por suelos altamente degradados y compactados por erosion, lo que requiere el uso de sistemas de labranza conservacionista para mitigar la erosion hidrica, asi como incrementar el contenido de agua en el suelo. Se evaluo una rotacion avena (Avena sativa L. cv. Supernova-INIA) - trigo (Triticum aestivum L. cv. Pandora-INIA) establecida bajo los siguientes sistemas conservacionistas: cero labranza (Nt), Nt + curvas de nivel (Nt+Cp), Nt + franjas vivas (Nt+Bh) y Nt + subsolado (Nt+Sb), las que fueron comparadas al sistema de labranza convencional (Ct), para evaluar su influencia en el contenido de agua en el suelo (SWC) en el perfil (10 a 110 cm profundidad), la compactacion del suelo y su interaccion con el rendimiento del cultivo. Las parcelas experimentales fueron establecidas 3 anos seguidos (2007 al 2009) en un Alfisol compactado. Al final de la temporada, el SWC disminuyo 44 a 51% en los sistemas conservacionistas y 60% en el sistema convencional. El sistema de labranza y la profundidad tuvieron un efecto significativo (p < 0.05) en el SWC; Nt+Sb presento un menor contenido de agua entre los 10 y 30 cm y similar al resto de los sistemas conservacionistas entre los 50 y 110 cm, sin embargo, superior a Ct. Aunque los sistemas conservacionistas mostraron un mayor SWC, la alta compactacion afecto los rendimientos. Cero labranza + subsolado redujo la compactacion del suelo e incremento significativamente el rendimiento en grano (similar a Ct en las temporadas 2008 y 2009). Estos resultados nos muestran que la eleccion de un sistema conservacionista en suelos compactados de la region mediterranea, requiere mejorar la estructura del suelo para obtener mejores rendimientos e incrementar el contenido de agua en el suelo.

Involvement of nitrogen and cytokinins in photosynthetic acclimation to elevated CO2 of spring wheat

Acclimation of photosynthetic capacity to elevated CO₂ involves a decrease of the leaf Rubisco content. In the present study, it was hypothesized that nitrogen uptake and partitioning within the leaf and among different aboveground organs affects the down-regulation of Rubisco. Given the interdependence of nitrogen and cytokinin signals at the whole plant level, it is also proposed that cytokinins affect the nitrogen economy of plants under elevated CO₂, and therefore the acclimatory responses. Spring wheat received varying levels of nitrogen and cytokinin in field chambers with ambient (370 μmol mol⁻¹) or elevated (700 μmol mol⁻¹) atmospheric CO₂. Gas exchange, Rubisco, soluble protein and nitrogen contents were determined in the top three leaves in the canopy, together with total nitrogen contents per shoot. Growth in elevated CO₂ induced decreases in photosynthetic capacity only when nitrogen supply was low. However, the leaf contents of Rubisco, soluble protein and total nitrogen on an area basis declined in elevated CO₂ regardless of nitrogen supply. Total nitrogen in the shoot was no lower in elevated than ambient CO₂, but the fraction of this nitrogen located in flag and penultimate leaves was lower in elevated CO₂. Decreased Rubisco: chlorophyll ratios accompanied losses of leaf Rubisco with CO₂ enrichment. Cytokinin applications increased nitrogen content in all leaves and nitrogen allocation to senescing leaves, but decreased Rubisco contents in flag leaves at anthesis and in all leaves 20 days later, together with the amount of Rubisco relative to soluble protein in all leaves at both growth stages. The results suggest that down regulation of Rubisco in leaves at elevated CO₂ is linked with decreased allocation of nitrogen to the younger leaves and that cytokinins cause a fractional decrease of Rubisco and therefore do not alleviate acclimation to elevated CO₂.

Using Ridge Regression Models to Estimate Grain Yield from Field Spectral Data in Bread Wheat (Triticum Aestivum L.) Grown under Three Water Regimes

Plant breeding based on grain yield (GY) is an expensive and time-consuming method, so new indirect estimation techniques to evaluate the performance of crops represent an alternative method to improve grain yield. The present study evaluated the ability of canopy reflectance spectroscopy at the range from 350 to 2500 nm to predict GY in a large panel (368 genotypes) of wheat (Triticum aestivum L.) through multivariate ridge regression models. Plants were treated under three water regimes in the Mediterranean conditions of central Chile: severe water stress (SWS, rain fed), mild water stress (MWS; one irrigation event around booting) and full irrigation (FI) with mean GYs of 1655, 4739, and 7967 kg∙ha−1, respectively. Models developed from reflectance data during anthesis and grain filling under all water regimes explained between 77% and 91% of the GY variability, with the highest values in SWS condition. When individual models were used to predict yield in the rest of the trials assessed, models fitted during anthesis under MWS performed best. Combined models using data from different water regimes and each phenological stage were used to predict grain yield, and the coefficients of determination (R2) increased to 89.9% and 92.0% for anthesis and grain filling, respectively. The model generated during anthesis in MWS was the best at predicting yields when it was applied to other conditions. Comparisons against conventional reflectance indices were made, showing lower predictive abilities. It was concluded that a Ridge Regression Model using a data set based on spectral reflectance at anthesis or grain filling represents an effective method to predict grain yield in genotypes under different water regimes.

Genetic Progress in Winter Wheat Cultivars released in Chile from 1920 to 2000

El trigo (Triticum aestivum L.) es el cultivo mas importante en Chile en terminos de superficie sembrada y areas geograficas en las cuales se siembra, cubriendo una gran diversidad de condiciones climaticas. Este estudio evaluo los cambios de varias caracteristicas agronomicas de variedades de trigo de invierno liberadas en el pais entre 1920 y 2000. Un total de 117 genotipos de trigos de invierno, que representa 45 cultivares antiguos y 72 cultivares modernos, se evaluaron en un clima humedo de tipo mediterraneo, en condiciones de riego, en el ano 2003. Los cultivares antiguos corresponden a aquellos liberados antes del ano 1960 y los modernos a los liberados despues del ano 1960. Mediante un analisis de componentes principales (CP) usando 10 caracteristicas agronomicas, permitio separar claramente los cultivares modernos de los antiguos. Al comparar los cultivares modernos con los antiguos se determino que la altura de la planta se ha reducido un 25,6%, pero en otras caracteristicas se produjo un aumento, como el indice de cosecha (21,1%), numero de granos por espiga (42,6%), valor de sedimentacion (103%) y la dureza del grano (32,0%). La variacion en la altura de la planta se correlaciono negativamente con el indice de cosecha (r = -0,30, p < 0,001). El rendimiento de grano, una caracteristica no incluida en el analisis de PC, estuvo altamente correlacionado con el segundo PC (r = 0,81, p < 0,0001). Correlaciones significativas (p < 0,01) se encontraron entre el ano de la liberacion de los cultivares y las caracteristicas agronomicas: altura de planta (r = -0,82), indice de cosecha (r = 0,40), numero de granos por espiga (0,69), valor de sedimentacion (r = 0,64), y peso del grano (r = -0,46). Estas correlaciones fueron en su mayoria una consecuencia de ausencia o presencia de genes de enanismo en el germoplasma. Finalmente el avance en rendimiento, calculado a partir de datos de rendimiento de ensayos en los que se probaron entre 15 y 25 cultivares y lineas avanzadas de trigo de invierno evaluados casi todos los anos entre 1965 y hasta 2001, no mostro ningun aumento en el rendimiento entre 1965 y 1975, pero si un aumento de 246 kg ha-1 por ano entre 1976 y 1998, lo que representa un incremento anual de 2,6%.

Productivity and Persistence of Yellow Serradela (Ornithopus compressus L.) and Biserrula (Biserrula pelecinus L.) in the Mediterranean Climate Region of Central Chile

The production and sustainability of non-irrigated pastures in the Mediterranean climate region of central Chile is currently limited by the low diversity of valuable species and cultivars of annual forage legumes, able to persist in zones with highly variable annual rainfall, and low fertility or poorly drained soils. In this work, DM production, seed yield, hardseededness and pasture persistence were evaluated for cultivars of yellow serradella (Ornithopus compressus L.) and biserrula (Biserrula pelecinusL.),�infieldexperimentsconductedinthesubhumidportion� of the Mediterranean climate region of Chile. Burr medic (Medicago polymorpha L.) and sub clover (Trifolium subterraneum L.) were used as a reference plants. A remarkable DM production and seed yield were observed in biserrula (cvs. Mor96 and Casbah), and in some cultivars of yellow serradella (e.g. Madeira, Santorini); biserrula produced by far the largest number of seeds per m 2 . As was expected for species that produce very high levels of hard-seeds, the regeneration of biserrula and serradella was low in second growing season, but plant density and productivity were high in the third growing season. The use of biserrula and serradela in monoculture or in mixture with other annual legumes, either in pasture-crop rotation or permanent pasture, would contribute to the improvement of the prevailing productive systems in the Mediterranean climate region of central Chile.

SNP-Based QTL Mapping of 15 Complex Traits in Barley under Rain-Fed and Well-Watered Conditions by a Mixed Modeling Approach

This study identified single nucleotide polymorphism (SNP) markers associated with 15 complex traits in a breeding population of barley (Hordeum vulgare L.) consisting of 137 recombinant chromosome substitution lines (RCSL), evaluated under contrasting water availability conditions in the Mediterranean climatic region of central Chile. Given that markers showed a very strong segregation distortion, a quantitative trait locus/loci (QTL) mapping mixed model was used to account for the heterogeneity in genetic relatedness between genotypes. Fifty-seven QTL were detected under rain-fed conditions, which accounted for 5–22% of the phenotypic variation. In full irrigation conditions, 84 SNPs were significantly associated with the traits studied, explaining 5–35% of phenotypic variation. Most of the QTL were co-localized on chromosomes 2H and 3H. Environment-specific genomic regions were detected for 12 of the 15 traits scored. Although most QTL-trait associations were environment and trait specific, some important and stable associations were also detected. In full irrigation conditions, a relatively major genomic region was found underlying hectoliter weight (HW), on chromosome 1H, which explained between 27% (SNP 2711-234) and 35% (SNP 1923-265) of the phenotypic variation. Interestingly, the locus 1923-265 was also detected for grain yield at both environmental conditions, accounting for 9 and 18%, in the rain-fed and irrigation conditions, respectively. Analysis of QTL in this breeding population identified significant genomic regions that can be used for marker-assisted selection (MAS) of barley in areas where drought is a significant constraint.

Physiological Traits Associated with Wheat Yield Potential and Performance under Water-Stress in a Mediterranean Environment

Different physiological traits have been proposed as key traits associated with yield potential as well as performance under water stress. The aim of this paper is to examine the genotypic variability of leaf chlorophyll, stem water-soluble carbohydrate content and carbon isotope discrimination (Δ13C), and their relationship with grain yield (GY) and other agronomical traits, under contrasting water conditions in a Mediterranean environment. The study was performed on a large collection of 384 wheat genotypes grown under water stress (WS, rainfed), mild water stress (MWS, deficit irrigation), and full irrigation (FI). The average GY of two growing seasons was 2.4, 4.8, and 8.9 Mg ha−1 under WS, MWS, and FI, respectively. Chlorophyll content at anthesis was positively correlated with GY (except under FI in 2011) and the agronomical components kernels per spike (KS) and thousand kernel weight (TKW). The WSC content at anthesis (WSCCa) was negatively correlated with spikes per square meter (SM2), but positively correlated with KS and TKW under WS and FI conditions. As a consequence, the relationships between WSCCa with GY were low or not significant. Therefore, selecting for high stem WSC would not necessary lead to genotypes of GY potential. The relationship between Δ13C and GY was positive under FI and MWS but negative under severe WS (in 2011), indicating higher water use under yield potential and MWS conditions.