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 plant's 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.

Photoperiod insensitive Ppd-A1a mutations in tetraploid wheat (Triticum durum Desf.)

Variation in photoperiod response plays an important role in adapting crops to agricultural environments. In hexaploid wheat, mutations conferring photoperiod insensitivity (flowering after a similar time in short or long days) have been mapped on the 2B (Ppd-B1) and 2D (Ppd-D1) chromosomes in colinear positions to the 2H Ppd-H1 gene of barley. No A genome mutation is known. On the D genome, photoperiod insensitivity is likely to be caused by deletion of a regulatory region that causes misexpression of a member of the pseudo-response regulator (PRR) gene family and activation of the photoperiod pathway irrespective of day length. Photoperiod insensitivity in tetraploid (durum) wheat is less characterized. We compared pairs of near-isogenic lines that differ in photoperiod response and showed that photoperiod insensitivity is associated with two independent deletions of the A genome PRR gene that cause altered expression. This is associated with induction of the floral regulator FT. The A genome deletions and the previously described D genome deletion of hexaploid wheat remove a common region, suggesting a shared mechanism for photoperiod insensitivity. The identification of the A genome mutations will allow characterization of durum wheat germplasm and the construction of genotypes with novel combinations of photoperiod insensitive alleles.

QTL analysis of pasta quality using a composite microsatellite and SNP map of durum wheat

Bright yellow color, firmness and low cooking loss are important factors for the production of good-quality pasta products. However, the genetic factors underlying those traits are still poorly understood. To fill this gap we developed a population of 93 recombinant inbred lines (RIL) from the cross between experimental line UC1113 (intermediate pasta quality) with the cultivar Kofa (excellent pasta quality). A total of 269 markers, including 23 SNP markers, were arranged on 14 linkage groups covering a total length of 2,140 cM. Samples from each RIL from five different environments were used for complete pasta quality testing and the results from each year were used for QTL analyses. The combined effect of different loci, environment and their interactions were analyzed using factorial ANOVAs for each trait. We identified major QTLs for pasta color on chromosomes 1B, 4B, 6A, 7A and 7B. The 4B QTL was linked to a polymorphic deletion in the Lpx-B1.1 lipoxygenase locus, suggesting that it was associated with pigment degradation during pasta processing. The 7B QTL for pasta color was linked to the Phytoene synthase 1 (Psy-B1) locus suggesting difference in pigment biosynthesis. QTLs affecting pasta firmness and cooking loss were detected on chromosomes 5A and 7B, and in both cases they were overlapping with QTL for grain protein content and wet gluten content. These last two parameters were highly correlated with pasta firmness (R > 0.71) and inversely correlated to cooking loss (R < -0.37). The location and effect of other QTLs affecting grain size and weight, gluten strength, mixing properties, and ash content are also discussed.

A major QTL for durable leaf rust resistance widely exploited in durum wheat breeding programs maps on the distal region of chromosome arm 7BL

A recombinant inbred line (RIL) population and a set of advanced lines from multiple crosses were used to investigate the leaf rust (Puccinia triticina Eriks.) resistance carried by the durum wheat cultivar Creso and its derivatives (Colosseo and Plinio). One hundred seventy-six RILs from the cross Colosseo x Lloyd were tested under artificial rust inoculation in the field. The response at the seedling stage was also investigated. A major QTL (QLr.ubo-7B.2) for leaf rust resistance controlling both the seedling and the adult open field based-response was mapped on 7BL, with the favourable allele inherited from Colosseo. QLr.ubo-7B.2 showed R2 and LOD peak values for the area under disease progress curve (AUDPC) equal to 72.9% and 44.5, respectively. The presence and location of QLr.ubo-7B.2 was validated by a linkage disequilibrium-based test using two-year field data of 62 advanced lines from 21 crosses with Creso, Colosseo or Plinio as resistance donors. QLr.ubo-7B.2 maps in a gene-dense region (7BL10-0.78-1.00) carrying several genes/QTLs in wheat and barley for resistance to rusts and other fungal diseases.

Translational research impacting on crop productivity in drought-prone environments

Conventional breeding for drought-prone environments (DPE) has been complemented by using exotic germplasm to extend crop gene pools and physiological approaches that consider water uptake (WU), water-use efficiency (WUE), and harvest index (HI) as drivers of yield. Drivers are associated with proxy genetic markers, such as carbon-isotope discrimination for WUE, canopy temperature for WU, and anthesis-silking interval for HI in maize. Molecular markers associated with relevant quantitative trait loci are being developed. WUE has also been increased through combining understanding of root-to-shoot signaling with deficit irrigation. Impacts in DPE will be accelerated by combining proven technologies with promising new strategies such as marker-assisted selection, and genetic transformation, as well as conservation agriculture that can increase WU while averting soil degradation.

Novel throughput phenotyping platforms in plant genetic studies

Unraveling the genetic basis of complex traits in plants is limited by the lack of appropriate phenotyping platforms that enable high-throughput screening of many genotypes in multilocation field trials. Near-infrared spectroscopy on agricultural harvesters and spectral reflectance of plant canopies have recently been reported as promising components of novel phenotyping platforms. Understanding the genetic basis of complex traits is now within reach with the use of these new techniques.