Ahmed Amri

Focused identification of germplasm strategy (FIGS) detects wheat stem rust resistance linked to environmental variables

Recent studies have shown that novel genetic variation for resistance to pests and diseases can be detected in plant genetic resources originating from locations with an environmental profile similar to the collection sites of a reference set of accessions with known resistance, based on the Focused Identification of Germplasm Strategy (FIGS) approach. FIGS combines both the development of a priori information based on the quantification of the trait-environment relationship and the use of this information to define a best bet subset of accessions with a higher probability of containing new variation for the sought after trait(s). The present study investigates the development strategy of the a priori information using different modeling techniques including learning-based techniques as a follow up to previous work where parametric approaches were used to quantify the stem rust resistance and climate variables relationship. The results show that the predictive power, derived from the accuracy parameters and cross-validation, varies depending on whether the models are based on linear or non-linear approaches. The prediction based on learning techniques are relatively higher indicating that the non-linear approaches, in particular support vector machine and neural networks, outperform both principal component logistic regression and generalized partial least squares. Overall there are indications that the trait distribution of resistance to stem rust is confined to certain environments or areas, whereas the susceptible types appear to be limited to other areas with some degree of overlapping of the two classes. The results also point to a number of issues to consider for improving the predictive performance of the models.

Evaluation of durum wheat experimental lines under different climate and water regime conditions of Iran

In the Mediterranean region, grain yield of durum wheat is frequently limited by both high temperature and drought during grain filling. A total of six sets of paired trials, including 18 durum experimental lines and two durum and bread wheat landraces, were conducted in the field under three moderate (no stress), warm (stress) and cold (stress) climate conditions and two different water regimes [i.e. rain-fed (terminal stress) and two supplemental irrigations (no stress)] conditions for two cropping seasons (2005–06 and 2006–07) in Iran. Several stress indices (i.e. drought, heat, and cold) obtained from grain yield data under different climate and water regime conditions were used to analyse relationships between genotypic grain yield data of 20 genotypes and their tolerance to different stresses. The additive main effect and multiplicative interaction (AMMI) analysis was also used to capture a large portion of the genotype by environment (GE) interaction sum of squares and to separate main and interaction effects. The combined ANOVA revealed significant differences between locations, water regimes (rain-fed v. irrigation) and their effects in discriminating among the genotypes. The genotypic yields in both rain-fed and irrigated conditions were positively associated (P < 0.01) at the moderate and warm locations; but were adversely correlated (P < 0.05) at cold locations, suggesting that a high-yield potential under two supplemental irrigations does not necessarily result in improved yield under rain-fed conditions. The results verified that grain yield increased in response to irrigation, but some genotypes were more sensitive to environmental differences depending on year and location. Relative reduction of grain yield due to drought was a promising trait to improve drought tolerance indirectly in warm and moderate locations. Estimates of broad-sense heritability also varied with climate conditions. Based on principal component analysis (PCA), the different stress indices tended to discriminate genotypes in dissimilar fashions. The results also indicate that it was possible to identify superior genotypes based on single and multiple abiotic stresses (drought, heat and cold). The genotypes G4 and G5 had general tolerance to the three abiotic stresses while the G19 and G15 were tolerant to drought and cold stresses and G18 and G17 were tolerant to heat stress. According to AMMI biplot analysis, the genotypes G4 and G9 were the best in terms of both mean yield and minimal GE interaction, indicating that selecting for improved yield may increase yield in a wide range of environments.

In Situ Conservation

The Mediterranean Basin, especially the coastline and the semi-arid and arid rangelands, have in the recent past and are currently suffering acutely from human activities that result in genetic erosion. As discussed in earlier chapters, these activities include: increasing industrialization, pollution, urbanization, inadvertent fires, increasing tourism, improper soil use and management, inappropriate animal production systems, and the general over-exploitation of natural resources. Soil erosion, loss of arable land, scarcity of water resources, loss of genetic diversity in terms of taxa and genetic variation are becoming a major concern to the sustainability of agriculture in the region. In fact, most of the national resources are already over-exploited in this region and urgent action is needed to slow the speed of degradation of the ecosystems and to stop desertification. For example, the desertified areas of rangeland, rainfed agriculture and irrigated land currently extend over 90%, 83% and 36% of their total respective areas and are increasing, showing the fragility of the predominant ecosystems in the region (ICARDA 1997).

Exploring and Mobilizing the Gene Bank Biodiversity for Wheat Improvement.

Identifying and mobilizing useful genetic variation from germplasm banks to breeding programs is an important strategy for sustaining crop genetic improvement. The molecular diversity of 1,423 spring bread wheat accessions representing major global production environments was investigated using high quality genotyping-by-sequencing (GBS) loci, and gene-based markers for various adaptive and quality traits. Mean diversity index (DI) estimates revealed synthetic hexaploids to be genetically more diverse (DI= 0.284) than elites (DI = 0.267) and landraces (DI = 0.245). GBS markers discovered thousands of new SNP variations in the landraces which were well known to be adapted to drought (1273 novel GBS SNPs) and heat (4473 novel GBS SNPs) stress environments. This may open new avenues for pre-breeding by enriching the elite germplasm with novel alleles for drought and heat tolerance. Furthermore, new allelic variation for vernalization and glutenin genes was also identified from 47 landraces originating from Iraq, Iran, India, Afghanistan, Pakistan, Uzbekistan and Turkmenistan. The information generated in the study has been utilized to select 200 diverse gene bank accessions to harness their potential in pre-breeding and for allele mining of candidate genes for drought and heat stress tolerance, thus channeling novel variation into breeding pipelines. This research is part of CIMMYT’s ongoing ‘Seeds of Discovery’ project visioning towards the development of high yielding wheat varieties that address future challenges from climate change.

Pattern analysis of genotype-by-environment interaction for grain yield in durum wheat

Pattern analysis, cluster and ordination techniques, was applied to grain yield data of 20 durum wheat genotypes grown in 19 diversified environments during 2005-07 to identify patterns of genotype (G), environment (E) and genotype-by-environment (G × E) interaction in durum multi-environment trials (METs). Main effects due to E, G and G x E interaction were highly significant, and 0·85 of the total sum of squares (SS) was accounted for by E. Of the remaining SS, the G x E interaction was almost 12 times the contribution of G alone. The knowledge of environmental and genotype classification helped to reveal several patterns of G x E interaction. This was verified by ordination analysis of the G x E interaction matrix. Grouping of environments, based on genotype performance, resulted in the separation of different types of environments. Pattern analysis confirmed the cold and warm mega-environments, and allowed the discrimination and characterization of adaptation of genotypes. However, several patterns of G x E interaction in Irans regional durum yield trials were further discerned within these mega-environments. The warm environments tended to be closer to one another, suggesting that they discriminate among durum genotypes similarly, whereas cold environments tended to diverge more. The dwarf and early maturing breeding lines from ICARDA with low to medium yields and high contribution to G x E interaction were highly adapted to warm environments, whereas the tall and later maturing genotypes with low to high yields were highly adapted to the cold environments of Iran.

Chlorophyll fluorescence parameters and drought tolerance in a mapping population of winter bread wheat in the highlands of Iran

The usefulness of fluorescence parameters as drought tolerance selection criteria for winter bread wheat in the highlands of Iran was studied. A population of 142 recombinant inbred lines, derived from a cross between two common wheat varieties, Azar2 (winter type) and 87Zhong291 (facultative type), was used to analyze the correlation between grain yield and chlorophyll fluorescence parameters at the grain-filling stage under drought stress and supplementary irrigation conditions during 2006–2007 and 2007–2008 seasons at Maragheh experiment station of the Dryland Agricultural Research Institute (DARI) using a RCBD with three replications. The results showed significant differences among the lines in the grain yield and all fluorescence parameters under rainfed and irrigation conditions. The values of chlorophyll content, F0, Fm, Fv, Fv/Fm, LWP, YPEC, NPQ, and PI in the drought-tolerant genotypes were significantly higher than those in drought-sensitive genotypes under drought stress. Significant differences were observed between slope coefficients under drought, but not under supplementary irrigation conditions except NPQ (P = 5%). It was concluded that chlorophyll content, F0, Fm, Fv, Fv/Fm, LWP, YPEC, NPQ, and PI could be used as additional indicators in screening wheat germplasm for drought tolerance.

Genetic gap analysis of wild Hordeum taxa

To facilitate the updating of in situ and ex situ conservation strategies for wild taxa of the genus Hordeum L., a combined ecogeographic survey and gap analysis was undertaken. The analysis was based on the Global Inventory of Barley Plant Genetic Resources held by ICARDA plus additional datasets, resulting in a database containing 17,131 wild Hordeum accessions. The analysis concluded that a genetic reserve should be established in the Mendoza Province of Argentina, as this is the most species-rich area globally for Hordeum . A network of reserves should also be set up across the Fertile Crescent in Israel, Palestine, Syria, Jordan, Lebanon and Turkey to provide effective conservation within the centres of diversity for gene pools 1B ( Hordeum vulgare subsp. spontaneum (C. Koch) Thell.) and 2 ( Hordeum bulbosum L.). The majority of the species were deemed under-collected, so further collecting missions are required worldwide where possible. Although ex situ and in situ conservation strategies have been developed, there needs to be further investigation into the ecological environments that Hordeum species occupy to ensure that any adaptive traits expressed are fully conserved. Additionally, studies are required to characterize existing collections and test the viability of rare species accessions held in genebanks to determine whether further ex situ collections are required alongside the proposed in situ conservation.

Grain yield stability of spring safflower (Carthamus tinctorius L.)

The additive main effect and multiplicative interaction (AMMI) model and the phenotypic stability parameters, ecovalence (W2), regression coefficient (b), coefficient of determination (R2), coefficient of variation (CV), stability variance (S2), AMMI stability value (ASV), and TOP (proportion of environments in which a genotype ranked in the top third), were used to evaluate simultaneously the yield performance and stability of 17 spring safflower genotypes and to evaluate 26 rainfed environments during 2003–05 in Iran. These parameters were designated as Type-A and Type-B for genotypes and environments, respectively. Among Type-B parameters, Spearman’s rank correlation showed that the AMMI stability value (ASVj), ecovalence (Wj2), genotypic variance (Sj2), and coefficient of variation (CVj) were significantly and positively associated (P < 0.01), indicating that one of these parameters can be used as an alternative to the others, but were significantly and negatively correlated with the genotypic selectivity (bj) parameter. The results showed that none of the Type-A statistics per se was useful for selecting high-yielding and stable genotypes. Based on these parameters, the genotypes G9, G10, and G11 combined high and stable yields while the highest yielding genotypes G1 and G17 were the most instable. Type-A and Type-B stability parameters are useful to identify genotypes with specific and large adaptations and the contrasting environments with high contribution to genotype × environment interaction.

Genetic Diversity within a Global Panel of Durum Wheat (Triticum durum) Landraces and Modern Germplasm Reveals the History of Alleles Exchange

Durum wheat is the 10th most important crop in the world, and its use traces back to the origin of agriculture. Unfortunately, in the last century only part of the genetic diversity available for this species has been captured in modern varieties through breeding. Here, the population structure and genetic diversity shared among elites and landraces collected from 32 countries was investigated. A total of 370 entries were genotyped with Axiom 35K array to identify 8,173 segregating single nucleotide polymorphisms (SNPs). Of these, 500 were selected as highly informative with a PIC value above 0.32 and used to test population structure via DAPC, STRUCTURE, and neighbor joining tree. A total of 10 sub-populations could be identified, six constituted by modern germplasm and four by landraces of different geographical origin. Interestingly, genomic comparison among groups indicated that Middle East and Ethiopia had the lowest level of allelic diversity, while breeding programs and landraces collected outside these regions were the richest in rare alleles. Further, phylogenetic analysis among landraces indicated that Ethiopia might represent a second center of origin of durum wheat, rather than a second domestication site as previously believed. Together, the analyses carried here provide a global picture of the available genetic diversity for this crop and shall guide its targeted use by breeders.

Graphic Analysis of Trait Relations and Genotype Evaluation in Durum Wheat

Trait profiles of genotypes and trait relations are frequently influenced by unpredictable conditions in the Mediterranean rainfed regions. Thus, genotype selection should be based on multiple traits in variable environments within the target region. This study was conducted to (i) examine the performance of 13 durum (Triticum turgidum L. var. durum Desf.) genotypes (11 breeding lines and two checks) and one bread wheat (Triticum aestivum L.) genotype on the basis of multiple traits, including grain yield and (ii) determine the effects of different growing environments on trait relations and broad-sense heritability (h2 BS) of various traits. The genotype-by-trait (GT) biplot analysis was applied to data from the 14 genotypes grown under drought and irrigated conditions for two years. Combined ANOVA showed that the main effects relative to year, location, genotype and their interactions were significant for most of the studied traits. Year-wise and combined GT-biplots indicated that the relationships among the studied traits were not consistent across environments, but they facilitated visual genotype comparisons and selection in each environment. Grain yield, in contrast to other traits, consistently showed wide variation across environments. The genotypes with high grain yield appeared to have high biomass, high harvest index, low grain weight and intermediate time to flowering and maturity. The genotypes with higher grain weight flowered and matured earlier. The estimates of h2 BS from single- and multi-environment trials varied from one environment to another and from trait to trait. The GT biplot was a useful tool for exploring multiple trait data, trait profiles of the genotypes and can help in determination of contrasting genotypes based on the trait(s) for improving genetic materials in durum wheat breeding program.