Miloudi Nachit

Quantitative Trait Loci for Grain Yield and Adaptation of Durum Wheat (Triticum durum Desf.) Across a Wide Range of Water Availability

Grain yield is a major goal for the improvement of durum wheat, particularly in drought-prone areas. In this study, the genetic basis of grain yield (GY), heading date (HD), and plant height (PH) was investigated in a durum wheat population of 249 recombinant inbred lines evaluated in 16 environments (10 rainfed and 6 irrigated) characterized by a broad range of water availability and GY (from 5.6 to 58.8 q ha−1). Among the 16 quantitative trait loci (QTL) that affected GY, two major QTL on chromosomes 2BL and 3BS showed significant effects in 8 and 7 environments, with R2 values of 21.5 and 13.8% (mean data of all 16 environments), respectively. In both cases, extensive overlap was observed between the LOD profiles of GY and PH, but not with those for HD. QTL specific for PH were identified on chromosomes 1BS, 3AL, and 7AS. Additionally, three major QTL for HD on chromosomes 2AS, 2BL, and 7BS showed limited or no effects on GY. For both PH and GY, notable epistasis between the chromosome 2BL and 3BS QTL was detected across several environments.

Association mapping in durum wheat grown across a broad range of water regimes

Association mapping was used to dissect the genetic basis of drought-adaptive traits and grain yield (GY) in a collection of 189 elite durum wheat accessions evaluated in 15 environments highly different for water availability during the crop cycle (from 146 to 711 mm) and GY (from 9.9 to 67.3 q ha(-1)). For highly heritable traits (e.g. heading date, kernel weight, etc.) several significant experiment-wise marker-trait associations were detected across five or more (up to 13 for kernel weight) environments, with R(2) values ranging from ca. 5 to 10%. As to GY, significant associations (R(2) from 2.5 to 4.2%) were mostly detected in one environment only (56 markers), while decreasing rapidly from two to five environments (from 20 to three markers, respectively) and with only one marker (Xbarc197 on chr. 5A) found significant in six environments (ranging from low- to high-yielding). These results are probably due to the complex genetic basis of GY and its interaction with environmental conditions. The number of markers significantly affecting GY decreased considerably under drought conditions, suggesting a limited effectiveness of association mapping to identify loci for GY under low-moisture conditions, most likely because different genotypes can attain similar phenotypes via different morpho-physiological traits and corresponding gene networks. Our study confirmed the role of major loci for phenology previously described in biparental mapping populations, highlighted a novel set of loci for drought-adaptive traits, and provided information on the agronomic value of the alleles at such loci across a broad range of soil moisture conditions.

Chlorophyll fluorescence as a selection criterion for grain yield in durum wheat under Mediterranean conditions

Abstract The relationships between different fast (non-modulated) chlorophyll fluorescence parameters measured in the field and yield were studied in durum wheat (Triticum durum Desf.) grown in a Mediterranean region (Northwest Syria) under three different water regimes. A set of 144 genotypes were cultivated in two rainfed trials (hereafter referred to as environments), 125 of which were also grown under supplementary irrigation. Fluorescence measurements were made on attached flag leaf blades about 3 weeks after anthesis in the three environments, plus a further set of measurements, two weeks after, in the irrigation environment. The photochemical capacity of Photosystem (PS) II was measured by means of the ratio of variable to maximum chlorophyll fluorescence ( F v F m ). In addition, the changes in variable (Fv = Fm − F0) fluorescence, the absolute values F0, Fm, and the half-time of the increase from F0 to F m (t 1 2 ) were also determined. Growing environment was found to have a strong effect on yield and all the fluorescence parameters. Except for F v F m , genotype effect was also significant (P ⩽ 0.001) within environments. Interaction between genotype and environment was only significant for grain yield. F0 showed the highest broad-sense heritability (h2 = 0.745), followed very closely by Fm (h2 = 0.729), t 1 2 (h 2 = 0.721) and Fv (h2 = 0.679), whereas F v F m showed much lower heritability (h2 = 0.143) and grain yield an intermediate value (h2 = 0.506). The pattern of changes in chlorophyll fluorescence parameters between the irrigation and the driest environments paralleled those associated with ageing in the former. Thus, mean values of F v F m , Fm, and t 1 2 decreased and F0 increased with ageing or in the driest environment. Across genotypes fluorescence parameters changed in a coordinated manner different from that caused by environment or ontogeny. High-yielding genotypes showed lower t 1 2 , accompanied by higher F0 and Fm. The parameter which showed the best genetic correlation with grain yield was t 1 2 (r = −0.92), followed by F0 (r = 0.88), Fm (r = 0.74) and Fv (r = 0.71), whereas F v F v (r = 0.34) was the parameter least correlated. The coordinated pattern of changes in fluorescence parameters across genotypes suggest that the more productive genotypes are those which can avoid or escape the development of drought stress during grain filling. The observed correlations of t 1 2 and F0 with phenological parameters (days from planting to heading or maturity) or indicators of water status of the crop (carbon isotope discrimination of kernels) support this conclusion.

Genomic approaches for designing durum wheat ready for climate change with a focus on drought

Climate change is projected to have a significant impact on temperature and precipitation profiles in the Mediterranean basin. The incidence and severity of drought will become commonplace and this will reduce the productivity of rain-fed crops such as durum wheat. Genetic diversity is the material basis for crop improvement and plant breeding has exploited naturally occurring variation to deliver cultivars with improved resistance to abiotic stresses. The coupling of new genomic tools, technologies, and resources with genetic approaches is essential to underpin wheat breeding through marker-assisted selection and hence mitigate climate change. Improvements in crop performance under abiotic stresses have primarily targeted yield-related traits and it is anticipated that the application of genomic technologies will introduce new target traits for consideration in wheat breeding for resistance to drought. Many traits relating to the plants response and adaptation to drought are complex and multigenic, and quantitative genetics coupled with genomic technologies have the potential to dissect complex genetic traits and to identify regulatory loci, genes and networks. Full realization of our abilities to manipulate metabolism, transduction pathways, and transcription factors for crop improvement ultimately relies on our basic understanding of the regulation of plant networks at all levels of function.

A panel of elite accessions of durum wheat (Triticum durum Desf.) suitable for association mapping studies

The effectiveness of association mapping (AM) based on linkage disequilibrium (LD) is currently beingtestedinanumberofcrops.AnimportantprerequisitefortheapplicationofAMistheavailabilityofcollectionsofaccessionswithasuitablelevelofgeneticvariationfortargettraitsandwith limited spurious LD due to the presence of population structure. Herein, the results of a genomewide molecular characterization of a collection of elite durum wheat accessions well-adapted to Mediterranean environments are presented. Ninety-seven highly polymorphic simple sequence repeats and 166 amplified fragment length polymorphism markers were used to characterize 189 durum accessions, mainly cultivars and advanced breeding lines. Genome-wide significant and sizeable LD indices at a centimorgan scale were observed, while LD mainly decayed within 10cM. On the other hand, effects due to spurious LD were notably lower than those previously observed in a durum wheat collection sampling durum gene pools of more diverse origin.

Phenotypic variation in boron-toxicity tolerance at seedling stage in durum wheat (Triticum durum)

SummaryNineteen durum wheat landraces, cultivars or advanced lines of different origins in West Asia and North Africa (WANA), and three barley and two bread wheat varieties were evaluated for their boron (B) toxicity tolerance. Seedlings were grown at five levels of soluble soil B in a plastic house under controlled temperatures. Significant differences existed between the durum wheat entries in days-to-symptom appearance and foliar symptom score. Under the highest soil B treatment, large differences existed between entries for dry weight per plant (P<0.05) but differences were non-significant for shoot B concentrations. Days-to-symptom appearance was highly correlated with symptom score, which was not correlated with shoot B concentrations. Boron toxicity symptom scores of the durum wheat entries ranged from the sensitive barley check to the moderately sensitive bread wheat check. As expected, days-to-symptom appearance decreased and symptom severity increased as the soil B concentrations increased.The result of this study supported the preliminary finding that small, though statistically significant, variation in B toxicity symptom scores exist in durum wheat. The higher CV of symptom scores found here was mainly due to one sensitive entry, Cakmak. If Cakmak was excluded from the analysis, the CV would be reduced by half, to 10%. Durum wheat genotypes which are more tolerant to B toxicity should be sought. Based on the results of this study, and of soil surveys and information collected in WANA, germplasm collected from Algeria, Iraq, Libya, Syria, and the Anatolian Plateau of Turkey should be screened first.

Photosynthetic and developmental traits associated with genotypic differences in durum wheat yield across the mediterranean basin

The relationships between various morphophysiological traits and yield were studied in durum wheat (Triticum durum Desf.) grown in Mediterranean conditions. Two sets of 22 genotypes were used. One was developed for semi-humid environments (TA-genotypes) and was cultivated in 22 trials around the Mediterranean basin with a mean yield across genotypes and environments of 4925 kg/ha. The other set was developed for drier conditions (CA-genotypes) and was cultivated in 15 trials, with a mean yield of 3501 kg/ha. Morphophysiological traits for each set were evaluated in 2 trials with contrasting water regimes conducted in north-eastern Spain: Lleida-rainfed (LR) and Lleida-irrigation (LI). Two kinds of traits were evaluated: developmental traits, including early vigour, plant height, and phenology (days from planting to heading and to maturity); and traits related to photosynthetic performance such as canopy temperature and chlorophyll content of the flag leaf, both measured during grain filling, and carbon isotope discrimination of mature grains. All the traits, measured in both Lleida trials, were related to the mean yield of the same genotypes across all the sites where they were cultivated. Yield measured at either of the 2 environments at Lleida was a much poorer predictor of genotype differences in mean yield than most of the traits. Nevertheless, the kind of environment where the morphophysiological traits were evaluated affected the performance of these traits as yield predictors. The combination of significant traits measured in the better environment (LI) explained 71% and 55% of genotype variability in yield within TA- and CA-genotypes, respectively, but only 56% and 27% when they were evaluated at LR. On the other hand, growing conditions of the yield trials was the main factor determining the best combination of traits. For TA-genotypes, larger yields were associated with shorter plants and higher carbon isotope discrimination (Δ) of grains, and to a lesser extent with higher early vigour and lower canopy temperature, whereas phenological traits made no contribution to explaining genotype differences in yield. For the CA-genotypes, higher yields were related to an earlier heading date or alternatively to a higher chlorophyll content during grain filling. A higher Δ in mature kernels also seems to be a positive trait.

Identification of SNP Mutations in DREB1, HKT1, and WRKY1 Genes Involved in Drought and Salt Stress Tolerance in Durum Wheat (Triticum turgidum L. var durum)

Tolerance mechanisms to salinity and drought stress are quite complex. Plants have developed a complex and elaborate signaling network that ensures their adaptation to this stress. For example, salinity tolerance is thought to be due to three main factors: Na(+) exclusion, tolerance to Na(+) in the tissues and osmotic tolerance. Recently, many transcription factors for tolerance to salt and drought stresses have been identified. In this study, multialignments of conserved domains in DREB1, WRKY1 transcription factors (TFs), and HKT-1 have been utilized to design specific primers in order to identify functional single nucleotide polymorphisms (SNPs). These primers have been used to probe on several genotypes of durum wheat that are differentially tolerant to salt and drought stress; they were grown in increasing concentrations of NaCl. The selected portions have been analyzed using high-resolution melting curve (HRM) technology that currently represents one of the most recent and powerful tools for detecting SNP and INDEL mutations. Analyzing the amplification profiles, observed in the resulting melting curves, samples corresponding to different treatment conditions were selected, sequenced, and aligned with the homolog sequences present in gene databases to identify and characterize potential SNP and INDEL mutations. The PCR amplicons, containing single and double SNPs, produced distinctive HRM profiles. By sequencing the polymerase chain reaction (PCR) products, several SNPs have been identified and validated. All the discovered mutations were able to generate changes in amino acid sequences of the corresponding proteins. Most of the identified SNPs were found in salt and drought tolerant durum wheat genotypes. These varieties are of great value for durum wheat breeding works.

Systems Responses to Progressive Water Stress in Durum Wheat

Durum wheat is susceptible to terminal drought which can greatly decrease grain yield. Breeding to improve crop yield is hampered by inadequate knowledge of how the physiological and metabolic changes caused by drought are related to gene expression. To gain better insight into mechanisms defining resistance to water stress we studied the physiological and transcriptome responses of three durum breeding lines varying for yield stability under drought. Parents of a mapping population (Lahn x Cham1) and a recombinant inbred line (RIL2219) showed lowered flag leaf relative water content, water potential and photosynthesis when subjected to controlled water stress time transient experiments over a six-day period. RIL2219 lost less water and showed constitutively higher stomatal conductance, photosynthesis, transpiration, abscisic acid content and enhanced osmotic adjustment at equivalent leaf water compared to parents, thus defining a physiological strategy for high yield stability under water stress. Parallel analysis of the flag leaf transcriptome under stress uncovered global trends of early changes in regulatory pathways, reconfiguration of primary and secondary metabolism and lowered expression of transcripts in photosynthesis in all three lines. Differences in the number of genes, magnitude and profile of their expression response were also established amongst the lines with a high number belonging to regulatory pathways. In addition, we documented a large number of genes showing constitutive differences in leaf transcript expression between the genotypes at control non-stress conditions. Principal Coordinates Analysis uncovered a high level of structure in the transcriptome response to water stress in each wheat line suggesting genome-wide co-ordination of transcription. Utilising a systems-based approach of analysing the integrated wheat’s response to water stress, in terms of biological robustness theory, the findings suggest that each durum line transcriptome responded to water stress in a genome-specific manner which contributes to an overall different strategy of resistance to water stress.

Near infrared reflectance spectroscopy as a potential surrogate method for the analysis of D13C in mature kernels of durum wheat

Carbon isotope discrimination (Δ13C) in grain is a potentially useful trait in breeding programs that aim to increase the yield of wheat and other cereals. Near infrared reflectance spectroscopy (NIRS) is used in routine assays to determine grain and flour quality. This study assesses the ability of NIRS to predict Δ13C in mature kernels of durum wheat. Plants were grown in north-west Syria as this location provided 3 distinct Mediterranean trials that covered a wide range for Δ13C values in grains (from about 12.9‰ to 17.6‰). We measured the spectral reflectance signature between 1100 and 2500 nm in samples from the same flour used in the conventional (i.e. mass spectrometry) determinations of Δ13C. By using principal components regression and partial least squares regression (PLSR), a model of the association between conventional laboratory analysis and these spectra was produced. Global regressions, which included samples from all 3 trials, and local models, which used samples from only one trial, were built and then validated with sample sets not included in calibration procedures. In global models, strong significant correlations (P < 0.001) were found between NIRS-predicted Δ13C and measured Δ13C values. PLSR gave r 2 values of 0.86 and 0.82 for calibration and validation sets, respectively. Although less strongly correlated, all local models selected for a subset of samples with significantly higher Δ13C values. Local models also performed well when selecting samples from the other 2 trials. The advantages and possible limitations of NIRS are further discussed.