Hamid Khazaei

The FIGS (Focused Identification of Germplasm Strategy) Approach Identifies Traits Related to Drought Adaptation in Vicia faba Genetic Resources

Efficient methods to explore plant agro-biodiversity for climate change adaptive traits are urgently required. The focused identification of germplasm strategy (FIGS) is one such approach. FIGS works on the premise that germplasm is likely to reflect the selection pressures of the environment in which it developed. Environmental parameters describing plant germplasm collection sites are used as selection criteria to improve the probability of uncovering useful variation. This study was designed to test the effectiveness of FIGS to search a large faba bean (Vicia faba L.) collection for traits related to drought adaptation. Two sets of faba bean accessions were created, one from moisture-limited environments, and the other from wetter sites. The two sets were grown under well watered conditions and leaf morpho-physiological traits related to plant water use were measured. Machine-learning algorithms split the accessions into two groups based on the evaluation data and the groups created by this process were compared to the original climate-based FIGS sets. The sets defined by trait data were in almost perfect agreement to the FIGS sets, demonstrating that ecotypic differentiation driven by moisture availability has occurred within the faba bean genepool. Leaflet and canopy temperature as well as relative water content contributed more than other traits to the discrimination between sets, indicating that their utility as drought-tolerance selection criteria for faba bean germplasm. This study supports the assertion that FIGS could be an effective tool to enhance the discovery of new genes for abiotic stress adaptation.

A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.)

Summary Faba bean (Vicia faba L.) is a globally important nitrogen‐fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence‐based consensus map was used to explore synteny with the most closely related crop species, lentil and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2‐cM interval of Vf chromosome 2 which was highly colinear with Mt3. The obvious candidate gene from 78 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40‐1 gene controlling anthocyanin production in Medicago and resequencing of the Vf orthologue showed a putative causative deletion of the entire 5′ end of the gene.

Carbon isotope discrimination and water use efficiency in Iranian diploid, tetraploid and hexaploid wheats grown under well-watered conditions

Carbon isotope discrimination (Δ) has been proposed as physiological criterion to select C3 crops for yield and water use efficiency. The relationships between carbon isotope discrimination (Δ), water use efficiency for grain and biomass production (WUEG and WUEB, respectively) and plant and leaf traits were examined in 20 Iranian wheat genotypes including einkorn wheat (Triticum monococcum L. subsp. monococcum) accessions, durum wheat (T. turgidum L. subsp. durum (Desf.) Husn.) landraces and bread wheat (T. aestivum L. subsp. aestivum) landraces and improved cultivars, grown in pots under well-watered conditions. Carbon isotope discrimination was higher in diploid than in hexaploid and tetraploid wheats and was negatively associated with grain yield across species as well as within bread wheat. It was also positively correlated to stomatal frequency. The highest WUEG and grain yield were noted in bread wheat and the lowest in einkorn wheat. Einkorn and bread wheat had higher WUEB and biomass than durum wheat. WUEG and WUEB were significantly negatively associated to Δ across species as well as within bread and durum wheat. The variation for WUEG was mainly driven by the variation for harvest index across species and by the variation for Δ within species. The quantity of water extracted by the crop, that was closely correlated to root mass, poorly influenced WUEG. Environmental conditions and genetic variation for water use efficiency related traits appear to highly determine the relationships between WUEG and its different components (water consumed, transpiration efficiency and carbon partitioning).

Genetic Diversity of Cultivated Lentil (Lens culinaris Medik.) and Its Relation to the World's Agro-ecological Zones

Assessment of genetic diversity and population structure of germplasm collections plays a critical role in supporting conservation and crop genetic enhancement strategies. We used a cultivated lentil (Lens culinaris Medik.) collection consisting of 352 accessions originating from 54 diverse countries to estimate genetic diversity and genetic structure using 1194 polymorphic single nucleotide polymorphism (SNP) markers which span the lentil genome. Using principal coordinate analysis, population structure analysis and UPGMA cluster analysis, the accessions were categorized into three major groups that prominently reflected geographical origin (worlds agro-ecological zones). The three clusters complemented the origins, pedigrees, and breeding histories of the germplasm. The three groups were (a) South Asia (sub-tropical savannah), (b) Mediterranean, and (c) northern temperate. Based on the results from this study, it is also clear that breeding programs still have considerable genetic diversity to mine within the cultivated lentil, as surveyed South Asian and Canadian germplasm revealed narrow genetic diversity.

Do faba bean ( Vicia faba L.) accessions from environments with contrasting seasonal moisture availabilities differ in stomatal characteristics and related traits

Drought is a major constraint to faba bean (Vicia faba L.) production, and there are many mechanisms by which leaves can regulate water loss. Our primary objective was to test if the origin of the faba bean accessions, from drought-prone and non-drought-prone environments, was associated with differences in measurable aspects of stomatal morphology and physiology related to water use. Two sets, each consisting of 201 faba bean accessions, were chosen from environments with contrasting seasonal moisture profiles following the focused identification of germplasm strategy (FIGS), and then screened under well watered conditions. From these, two subsets of 10 accessions each were chosen to test for differences in response to drought. Parameters related to stomatal function and water status were measured. The dry-adapted set had bigger stomata, higher leaf relative water content (LRWC) and cooler leaves under well watered conditions. Stomatal density and stomatal area per unit area of leaflet were negatively correlated with gas exchange parameters and positively correlated with intrinsic water use efficiency. Drought caused stomatal densities to increase in the dry set while stomatal length decreased in both sets. The moisture deficit was sufficient to decrease gas exchange in both sets to similar levels, but the dry-adapted set maintained warmer leaves and a higher LRWC that showed no significant correlations with leaf morphology or gas exchange, demonstrating more effective stomatal regulation. The results also support that collection site data from the environment where genetic resources are collected can be used as indicators of adaptive traits in an herbaceous annual species.

Does water-use efficiency explain the relationship between carbon isotope discrimination and wheat grain yield?

Carbon isotope discrimination (^) has been suggested as an efficient indirect selection criterion in breeding programmes for various crop plants and traits, including grain yield (e.g., Rebetzke et al., 2002, 2006; Xu et al., 2007b) and water-use efficiency (e.g., Griffiths, 1993). To be efficient indeed, however, its relationship with such a trait should be strong and stable, at least for particular conditions (e.g., water stress), although acrossenvironment stability would be more favourable. In this paper we study wheat grain yield and its relationship with leaf ^ in growth-chamber conditions. Our particular interest lies in relating this relationship with the relationship between these two traits and water-use efficiency (WUE), hoping to discover new phenomena underlying the influence of ^ on grain yield. A negative correlation between ^ and WUE in wheat has been reported (e.g., Farquhar & Richards, 1984; Ehdaie & Waines, 1994; Monneveux et al., 2005), suggesting that genotypes showing low ^ values might be more efficient in water use (Rafi et al., 1992); this is especially to be expected in pot studies (see Araus et al., 2003, and citations therein). As Xu et al. (2007a) show, relationships between wheat grain yield and ^ vary from strongly negative to strongly positive (see, e.g., Xu et al., 2007b, for citations concerning water regimes). Even though, as the authors claim, these differences come from different organs sampled to measure ^, the time of sampling, and environmental conditions, this situation is alarming and may show that ^ is not as good an indirect selection criterion as has been proclaimed. On the other hand, it might be a good criterion, but environment-specific, in which case its interpretations should also be environment-specific; this would mean that in some environments ^ will work while in others it will not work well as the indirect selection criterion. What is more, it is likely that in one year its relation with grain yield (GY) will be strong (and positive), while in another weak or even negative (see Xu et al., 2007b). In this paper we discuss the usefulness of ^ as a possible indirect selection criterion for breeding high-yielding genotypes, and show that the relationship between ^ and GY may mainly come from the relationship between ^ and WUE and that between WUE and GY.

Marker–Trait Association Analysis of Iron and Zinc Concentration in Lentil ( Medik.) Seeds

First study to provide knowledge on genetics of biofortification in lentils. SNP markers associated with seed Fe and Zn concentration were identified in lentils. MAS to enhance breeding programs aiming to fight global micronutrient malnutrition.

Development and validation of a robust, breeder-friendly molecular marker for the vc - locus in faba bean

Faba bean (Vicia faba L.) is a valuable feed and food crop with potential for development globally as a staple protein crop. Its consumption is limited by the anti-nutritional factors vicine and convicine (v-c) in its seeds. A single gene (vc-) confers the low v-c phenotype in faba bean. Time-consuming and laborious quantitative chemical analysis is currently used in breeding programs to detect v-c concentration. Molecular markers within or linked to the vc- gene could facilitate rapid and cost-effective screening of early generation breeding populations for low v-c concentration. The large and complex faba bean genome has been an impediment to the progress of development of molecular breeding strategies. Here, we report a high-throughput low-cost KASP (Kompetitive Allele Specific PCR) marker for low v-c concentration in faba bean. The KASP assay successfully distinguished low and high v-c lines of faba bean. This marker is a significant and valuable molecular tool for faba bean breeding programs aiming to reduce v-c from faba beans worldwide.

Quantification of vicine and convicine in faba bean seeds using hydrophilic interaction liquid chromatography

Faba bean (Vicia faba L.) provides environmental and health benefits; however, the presence of the pyrimidine glycosides vicine and convicine (v-c) in its seeds limits consumption. Low v-c genotypes have been introduced, but the convicine levels in these genotypes have not been quantified. To improve detection, the polar nature of v-c was exploited by implementing hydrophilic interaction liquid chromatography (HILIC). A sample preparation method using a two-step extraction was developed for use with UV and/or tandem mass spectrometry (SRM) detection. The HILIC-UV method was suitable for over three orders of magnitude, covering the range of v-c concentrations in faba bean seeds across all genotypes tested. The linear range of HILIC-SRM was slightly less (∼3 orders of magnitude), but improved sensitivity and selectivity make it more suitable for quantifying low v-c samples. The analysis of 13 genotypes suggests that v-c concentrations in faba bean seeds may be independent quantitative traits.

In silico evaluation of plant genetic resources to search for traits for adaptation to climate change

Plant genetic resources display patterns resulting from ecological and co-evolutionary processes. Such patterns are instrumental in tracing the origin and diversity of crops and locating adaptive traits. With climate change and the anticipated increase in demand for food, new crop varieties will be needed to perform under unprecedented climatic conditions. In the present study, we explored genetic resources patterns to locate traits of adaptation to drought and to maximize the utilization of plant genetic resources lacking ex ante evaluation for emerging climate conditions. This approach is based on the use of mathematical models to predict traits as response variables driven by stochastic ecological and co-evolutionary processes. The high congruence of metrics between model predictions and empirical trait evaluations confirms in silico evaluation as an effective tool to manage large numbers of crop accessions lacking ex ante evaluation. This outcome will assist in developing cultivars adaptable to various climatic conditions and in the ultimate use of genetic resources to sustain agricultural productivity under conditions of climate change.