Field evaluation of upland rice lines selected for QTLs controlling root traits

A marker-assisted back-cross (MABC) programme was used to introgress four root quantitative trait loci (QTLs) from the tropical japonica rice variety Azucena into the Indian upland rice variety, Kalinga III. Previously we tested the products for root traits and reported that the introgressed QTL9 (on chromosome 9) significantly increased root length in the new genetic background. Here we describe field testing for agronomic traits in near-isogenic lines (NILs) that differ for introgressed QTLs. Four NILs were selected and characterised in replicated field experiments in eastern and western India over 3 years. They were tested by upland farmers in a target population of environments (TPE) in three states of eastern India, over 2 years. NILs out-performed Kalinga III for grain and straw yield and there was interaction between the genotypes and the environment (G × E). No effect was found for the root QTL9 on grain or straw yield, however, the presence of several introgressions significantly improved both traits. Some of this effect was due to introgression of Azucena alleles at non-target regions. Overall, the Azucena introgressions increased straw yield more than grain yield. While it has yet to be demonstrated whether this effect is due to improved root systems, this finding fits with the assumption that introgressed genes are involved in partitioning of biomass to the roots and stems, rather than to the grain. The NILs could replace Kalinga III for cultivation in medium upland environments in eastern India.     

Dynamic patterns of components of genotype × environment interaction for pod yield of peanut over multiple years: A simulation approach

The relative importance of the genotype × year (G × Y), genotype × location (G × L) and genotype × location × year (G × L × Y) interactions has significant implications on the testing strategy of crop breeding lines. The goal of this study was to examine the dynamic patterns of these three interactions for pod yield of peanut using a crop simulation model. Pod yields of 17 peanut lines in the early-rainy, mid-rainy and dry seasons at 112 locations covering all peanut production areas in Thailand were simulated for 30 years (1972–2002) with the Cropping System Model (CSM)-CROPGRO-Peanut. Combined analyses of variance were preformed for individual seasons and for overall seasons, with the number of year incrementally increasing from 2 to 30, and the relative contributions of the individual sources of variation were determined. This procedure was repeated four times with different starting years. The results showed that the environmental effects accounted for the major proportion of the total yield variation, followed by the genotype effects, while the genotype × environment (G × E) effects were rather small. The contributions of the individual sources changed as the number of years in the analysis changed. Increasing number of years in the analyses resulted in an increase in the magnitude of the G × Y and G × L × Y interactions, but a decline in the G × L contribution. The contributions of the G × Y and G × L interactions were greater and more fluctuated in the dry season, while those of the G × L × Y interactions were greater in the mid-rainy season. Notable increases in the G × Y interaction in the dry season were observed in certain years. The decline in the G × L interaction with increasing number of years was closely associated with the increase in the G × L × Y interaction, and both became stable when 6 or more years were included. Several cross-over in the ranks of peanut lines for mean pod yield in two contrasting years were also observed for the mid-rainy season. These results raise a question on the effectiveness of the strategy for using locations to replace years in varietal testing that is normally employed by breeders. The practical limit of multi-year evaluation of crop breeding lines could be overcome by the use of a crop simulation model.     

Optimal numbers of environments to assess slopes of joint regression for grain yield,grain protein yield and grain protein concentration under nitrogen constraint in winter wheat

Plant breeders are interested in rationally reducing the number of testing environments for breeding new genotypes adapted to diverse conditions. One way to characterize the adaptation of a genotype is to use the joint regression model. Our objectives were to estimate the stability for grain yield (GY), grain protein yield (GPY) and grain protein content (GPC) of a set of wheat genotypes grown under varying nitrogen conditions and then to determine optimal numbers of environments for assessing the slopes of joint regression.     

Adaptation,diversity, and exploitation of global white lupin (Lupinus albus L.) landrace genetic resources

White lupin requires grain yield improvement to realize its potential as a high-protein grain crop. Some 121 entries representing 13 germplasm pools (11 landrace pools from European countries and from regions of North and East Africa, West Asia and Atlantic islands, and one winter-type and one spring-type variety pools) were evaluated in three major agroclimatic conditions, i.e., Mediterranean and subcontinental climate in Italy under autumn sowing and suboceanic climate in France under spring sowing, with the aim to assess: (i) the variation among and within germplasm pools for grain yield and 13 major morphophysiological traits; (ii) the impact of evaluation environments on entry characteristics; and (iii) the relation of wide- and specific-adaptation responses with morphophysiological traits. Indications on top-yielding genetic resources, entry morphophysiological traits and association of these traits with grain yield were largely environment-specific. Germplasm pools summarized a fairly high portion of genotypic and genotype × environment (GE) interaction variation, indicating their usefulness as a criterion for locating genetic resources with specific characteristics. Adaptive responses of germplasm pools and individual entries, modeled through Additive Main effects and Multiplicative Interaction analysis, highlighted the outstanding agronomic value for specific agroclimatic conditions of a few landrace germplasm pools in comparison with variety pools. Overall within-pool diversity for morphophysiological traits and adaptive response was largest in the landrace pools from Italy, Turkey, East Africa and West Asia. Only flowering time and individual seed weight exhibited high genetic correlations between environments for entry response, suggesting caution in inferring accession characteristics from evaluation data obtained in environments very different from those targeted by possible germplasm users. Optimal flowering time was early in the spring-sown environment, intermediate in the Mediterranean environment, and late (associated with winter survival) in the subcontinental-climate environment. Owing to the association of phenology with several other traits, germplasm ordination for adaptation pattern and for overall morphophysiological variation were very similar. Pod fertility emerged among the seed yield components because of its correlation with grain yield in each environment combined with fairly low GE interaction. Beside contributing to the ecogeographic classification of landrace germplasm, our results can support breeding programs of Europe and Mediterranean-climate regions in defining useful genetic resources, adaptation strategies and adaptive traits. Genetic resources from Madeira & Canaries (high-yielding across environments), Italy (featuring high adaptive and morphophysiological diversity) and a few other regions are of special interest for breeding in targeted definite agroclimatic conditions.     

Response to two cycles of divergent selection for grain yield under drought stress in four rice breeding populations

Drought is a major production constraint in rainfed rice (Oryza sativa L.). Lack of effective selection criteria is a major limitation hampering progress in breeding for drought tolerance. In an earlier report, we showed in two populations that one cycle of direct selection was effective in increasing grain yield under stress. In the present study, we retested the efficiency of direct selection for grain yield under drought stress in rice using four populations derived from crossing upland-adapted, drought-tolerant varieties (Apo, Vandana) to high-yielding, lowland-adapted, drought-susceptible varieties (IR64, IR72). Each population was subjected to two cycles of divergent selection either under drought stress in upland or under nonstress conditions in lowland conditions. Following selection, approximately 40 high-yielding lines selected under each protocol from each population, along with a set of unselected lines, were evaluated in a series of selection response trials over a range of moisture levels. Significant response to direct selection under stress was realized in 9 out of 15 combinations of populations and stress environments, and in 6 of the 7 severe stress trials. Averaging over all the populations and stress environments, the stress-selected lines had a yield advantage of 25 and 37% over nonstress-selected and random lines, respectively. In contrast to this, under nonstress, the nonstress-selected lines had an average yield advantage of only 7 and 13% over stress-selected and random lines, respectively. Direct selection in managed stress trials during dry seasons gave significant response (25% on average relative to indirect selection in nonstress conditions) under naturally occurring wet season stress. In addition, direct selection under stress in upland gave an average gain of 16 and 45% over nonstress-selected and random lines, respectively, under stress in lowland. The yield advantage of the stress-selected lines appears to result mainly from maintenance of higher harvest index. These results show that direct selection for grain yield under stress is effective and does not reduce yield potential. Overall, this is the first report in rice demonstrating that (a) selection under managed drought stress in the dry season can result in yield gains under natural stress in the wet season, and (b) that selection under upland drought stress can, at least under the conditions of the present study, result in gains under lowland drought conditions.     

Genotypic variation for grain and stover yield of dryland (rabi) sorghum in India 2. A characterisation of genotype × environment interactions

Genotype-by-environment interactions (GEI) have been identified as an important component of the genotypic variation for grain and stover yield traits of rabi sorghum varieties and hybrids in India. It has been argued that obtaining an understanding of the causes of these GEI is an important step to identify the scope for genetic improvement of grain and stover yield by conventional breeding. Pattern analysis was used to investigate the regional structure of the GEI for the four traits grain yield, stover yield, days-to-flower, and plant height, measured on the varieties and hybrids tested over 10 years in the All India Coordinated Sorghum Improvement Program (AICSIP). There was evidence that regional differences accounted for part of the GEI for grain yield and days-to-flower but not for stover yield and plant height. Cluster analysis was used to group the locations included in the ACSIP experiments. The five-group level was chosen to examine the causes of GEI among the location groups. Hypotheses were proposed for the observed regional grouping of trials for grain yield. One group of trials consisted of predominantly irrigated trials, the other four groups differed in the timing and intensity of drought stress imposed on the entries. This retrospective analysis provides a basis for testing the hypothesised contributions of environmental variation in water availability to regional GEI for grain and stover yield. If these hypotheses are substantiated, the current multi-environment testing strategy used for the AICSIP trials could be modified to ensure adequate sampling of the five regional groups identified by the retrospective pattern analysis.     

Influence of the soil physical environment on rice (Oryza sativa L.) response to drought stress and its implications for drought research

Plant performance under drought stress is not solely defined by an inadequate water supply but by an interaction among many factors, including climatic, edaphic, and biological factors. An important interacting factor affecting root growth, and therefore the ability of a plant to access and take up water, is the soil physical environment. Soil penetration resistance can restrict, or even halt, root system growth. For rice, a soil penetration resistance of 1.4 MPa is sufficient to inhibit root system expansion. This review describes the effects of the soil physical environment on root growth and its interaction with drought stress. A large variation in soil penetration resistance exists among rainfed rice-growing areas of South and Southeast Asia and within experimental stations used for managed-drought field phenotyping. This variability may influence genotypic performance across experimental sites/countries and the response of crop genotypes to drought stress. A case study is presented in which differences in the soil physical environment may partially elucidate differences in experimental results between two field studies conducted at different locations. These results highlight the need for increased knowledge of environmental interactions to allow the outputs of genomics to increase drought tolerance at the field level.     

Lucerne shoot and root traits associated with adaptation to favourable or drought-stress environments and to contrasting soil types

Cultivar × location interaction for lucerne forage yield across northern Italy is large, repeatable and associated with summer drought-stress level and soil type. The objectives of this study were: (i) to investigate the genotypic factors associated with cultivar adaptive responses to drought-stress and soil factors; (ii) to identify adaptive traits exploitable for selection of widely adapted or specifically adapted material. Aerial dry matter (DM) over 12 harvests and shoot traits of 13 landraces and four varieties were evaluated in four artificial environments created by the factorial combination of drought-stress level (almost nil or high) and soil type (sandy-loam or silty-clay) (Exp. 1). Aerial and root DM over four or five harvests were evaluated in metal containers 55 cm × 12 cm × 75 cm deep for the factorial combinations of three varieties by two drought-stress levels by two soil types (Exp. 2), or six landraces by two drought-stress levels (Exp. 3). Cultivar × environment interaction was detected for forage yield, plant mortality after the second summer, leaflet size and stem weight. The environments of Exp. 1 reproduced well the variety adaptive responses across agricultural environments. The relationship of cultivar forage yield with shoot traits was environment-specific, i.e.: (i) strictly negative with plant mortality, in no-stress environments (where mortality and plant competition were severe); (ii) positive with stem number per plant and autumn-winter growth, in stress environments; (iii) positive with stem dry weight, in ‘stress/sandy-loam soil’; and (iv) positive with leaflet size, in ‘no-stress/sandy-loam soil’. Cultivars specifically adapted to no-stress or sandy-loam conditions showed consistently greater root DM across three soil layers than material with opposite adaptive response. Entry yields tended to inverse genetic correlation between two environments which represented contrasting geographical subregions and were characterized by different combinations of traits associated with higher yield, i.e.: (i) higher root biomass, lower plant mortality and larger leaflets, for ‘no-stress/sandy-loam soil’; and (ii) more stems per plant and greater autumn-winter growth, for ‘stress/silty-clay soil’. The difficulty of yield-based selection for wide adaptation may hardly be overcome by selection based on adaptive traits. Adaptive trait-based selection for specific adaptation may be envisaged especially for ‘stress/silty-clay soil’ conditions, for which the relevant traits are inexpensive to record, not correlated, and not subject to cultivar × environment interaction.     

Genetic analysis and validation of quantitative trait loci associated with reproductive-growth traits and grain yield under drought stress in a doubled haploid line population of rice (Oryza sativa L.)

Drought is a major constraint for rice production and yield stability in rainfed ecosystems, especially when it occurs during the reproductive stage. Combined genetic and physiological analysis of reproductive-growth traits and their effects on yield and yield components under drought stress is important for dissecting the biological bases of drought resistance and for rice yield improvement in water-limited environments. A subset of a doubled haploid (DH) line population of CT9993-5-10-1-M/IR62266-42-6-2 was evaluated for variation in plant water status, phenology, reproductive-growth traits, yield and yield components under reproductive-stage drought stress and irrigated (non-stress) conditions in the field. Since this DH line population was previously used in extensive quantitative trait loci (QTLs) mapping of various drought resistance component traits, we aimed at identifying QTLs for specific reproductive-growth and yield traits and also to validate the consensus QTLs identified earlier in these DH lines using meta-analysis. DH lines showed significant variation for plant water status, reproductive-growth traits, yield and yield components under drought stress. Total dry matter, number of panicles per plant, harvest index, panicle harvest index, panicle fertility, pollen fertility, spikelet fertility and hundred grain weight had significant positive correlations with grain yield under drought stress. A total of 46 QTLs were identified for the various traits under stress and non-stress conditions with phenotypic effect ranging from 9.5 to 35.6% in this study. QTLs for panicle exsertion, peduncle length and pollen fertility, identified for the first time in this study, could be useful in marker-assisted breeding (MAB) for drought resistance in rice. A total of 97 QTLs linked to plant growth, phenology, reproductive-growth traits, yield and its components under non-stress and drought stress, identified in this study as well as from earlier published information, were subjected to meta-analysis. Meta-analysis identified 23 MQTLs linked to plant phenology and production traits under stress conditions. Among them, four MQTLs viz., 1.3 for plant height, 3.1 for days to flowering, 8.1 for days to flowering or delay in flowering and 9.1 for days to flowering are true QTLs. Consensus QTLs for reproductive-growth traits and grain yield under drought stress have been identified on chromosomes 1 and 9 using meta-QTL analysis in these DH lines. These MQTLs associated with reproductive-growth, grain yield and its component traits under drought stress could be useful targets for drought resistance improvement in rice through MAB and/or map-based positional analysis of candidate genes.     

Adaptation of landrace and variety germplasm and selection strategies for lucerne in the Mediterranean basin

Lucerne (Medicago sativa L.) can enhance the economic and environmental sustainability of crop-livestock systems in the western Mediterranean basin, but requires improved adaptation to stressful environments because of a predicted shortage of irrigation water and climate change. This study reports on three-year dry matter yields of five landraces from Morocco, Italy and Tunisia and seven varieties from France, Italy, Australia and USA assessed across 10 agricultural environments of Algeria, Tunisia, Morocco and Italy of which four were rainfed, one was continuously irrigated (oasis management), and five were irrigated but adopted a nine-week suspension of irrigation during summer. Our objectives were targeting cultivars to specific environments, and assisting regional breeding programmes in defining adaptation strategies, genetic resources and opportunities for international co-operation. The crop persisted well in all environments, but environment mean yield was strictly associated (P < 0.01) with annual and spring-summer (April–September) water available. Rainfed cropping implied 42% lower yield with 61% less spring-summer water available relative to irrigation with withheld summer water across three sites hosting both managements. All of these sites showed genotype × management interaction (at least P < 0.10). Cross-over genotype × environment (GE) interaction between top-yielding cultivars occurred across the 10 environments. Total number of harvests (range: 9–23), soil salinity as measured by electrical conductivity (range: 0.20–6.0 dS m⁻¹), and average spring-summer water available (range: 102–932 mm) were selected as significant (P < 0.05) environmental covariates in a factorial regression model explaining 53% of GE interaction variation. This model was exploited for targeting cultivars as a function of site-specific levels of these factors. Its indications agreed largely with those of an additive main effects and multiplicative interaction model with two GE interaction principal components. An Italian landrace exhibited specific adaptation to severely drought-prone environments, whereas landraces from north Africa were not adapted to such environments. One Moroccan landrace was specifically adapted to high number of harvests (partly reflecting frequent mowing). One variety selected for salt tolerance, and one Moroccan landrace, were specifically adapted to salt-stress environments. Environment classification as a function of GE interaction effects indicated three groups which may be object of specific breeding: (i) rainfed or irrigated environments featuring limited spring-summer water available (<350 mm), nil or low soil salinity, and moderate to low number of harvests; (ii) salt-stress environments; and (iii) environments characterized by high number of harvests.     

Genotype × environment interaction for zinc and iron concentration of wheat grain in eastern Gangetic plains of India

Zinc and iron are important micronutrients for human health for which widespread deficiency occurs in many regions of the world including South Asia. Breeding efforts for enriching wheat grains with more zinc and iron are in progress in India, Pakistan and CIMMYT (International Maize and Wheat Improvement Centre). Further knowledge on genotype × environment interaction of these nutrients in the grain is expected to contribute to better understand the magnitude of this interaction and the potential identification of more stable genotypes for this trait. Elite lines from CIMMYT were evaluated in a multilocation trial in the eastern Gangetic plains (EGP) of India to determine genotype × environment (GE) interactions for agronomic and nutrient traits. Agronomic (yield and days to heading) data were available for 14 environments, while zinc and iron concentration of grains for 10 environments. Soil and meteorological data of each of the locations were also used. GE was significant for all the four traits. Locations showed contrasting response to grain iron and zinc. Compared to iron, zinc showed greater variation across locations. Maximum temperature was the major determinant for the four traits. Zinc content in 30–60 cm soil depth was also a significant determinant for grain zinc as well as iron concentration. The results suggest that the GE was substantial for grain iron and zinc and established varieties of eastern Gangetic plains India are not inferior to the CIMMYT germplasm tested. Hence, greater efforts taking care of GE interactions are needed to breed iron and zinc rich wheat lines.