Identification of genomic regions determining the phenological development leading to floral transition in wheat (Triticum aestivum L.)

Association mapping of autumn-seeded rye (Secale cereale L.) reveals genetic linkages between genes controlling winter hardiness and plant development

Winter field survival (WFS) in autumn-seeded winter cereals is a complex trait associated with low temperature tolerance (LTT), prostrate growth habit (PGH), and final leaf number (FLN). WFS and the three sub-traits were analyzed by a genome-wide association study of 96 rye (Secale cereal L.) genotypes of different origins and winter-hardiness levels. A total of 10,244 single nucleotide polymorphism (SNP) markers were identified by genotyping by sequencing and 259 marker-trait-associations (MTAs; p < 0.01) were revealed by association mapping. The ten most significant SNPs (p < 1.49e−04) associated with WFS corresponded to nine strong candidate genes: Inducer of CBF Expression 1 (ICE1), Cold-regulated 413-Plasma Membrane Protein 1 (COR413-PM1), Ice Recrystallization Inhibition Protein 1 (IRIP1), Jasmonate-resistant 1 (JAR1), BIPP2C1-like protein phosphatase, Chloroplast Unusual Positioning Protein-1 (CHUP1), FRIGIDA-like 4 (FRL4-like) protein, Chalcone Synthase 2 (CHS2), and Phenylalanine Ammonia-lyase 8 (PAL8). Seven of the candidate genes were also significant for one or several of the sub-traits supporting the hypothesis that WFS, LTT, FLN, and PGH are genetically interlinked. The winter-hardy rye genotypes generally carried additional allele variants for the strong candidate genes, which suggested allele diversity was a major contributor to cold acclimation efficiency and consistent high WFS under varying field conditions.

The Relationships between Plant Developmental Traits and Winter Field Survival in Rye (Secale cereale L.)

Overwintering cereals accumulate low temperature tolerance (LTT) during cold acclimation in the autumn. Simultaneously, the plants adjust to the colder season by making developmental changes at the shoot apical meristem. These processes lead to higher winter hardiness in winter rye varieties (Secale cereale L.) adapted to Northern latitudes as compared to other cereal crops. To dissect the winter-hardiness trait in rye, a panel of 96 genotypes of different origins and growth habits was assessed for winter field survival (WFS), LTT, and six developmental traits. Best Linear Unbiased Estimates for WFS determined from five field trials correlated strongly with LTT (r = 0.90, p < 0.001); thus, cold acclimation efficiency was the major contributor to WFS. WFS also correlated strongly (p < 0.001) with final leaf number (r = 0.80), prostrate growth habit (r = 0.61), plant height (r = 0.34), but showed weaker associations with top internode length (r = 0.30, p < 0.01) and days to anthesis (r = 0.25, p < 0.05). The heritability estimates (h²) for WFS-associated traits ranged from 0.45 (prostrate growth habit) to 0.81 (final leaf number) and were overall higher than for WFS (h² = 0.48). All developmental traits associated with WFS and LTT are postulated to be regulated by phytohormone levels at shoot apical meristem.

Marker-based crop model-assisted ideotype design to improve avoidance of abiotic stress in bread wheat

Wheat phenology allows escape from seasonal abiotic stresses including frosts and high temperatures, the latter being forecast to increase with climate change. The use of marker-based crop models to identify ideotypes has been proposed to select genotypes adapted to specific weather and management conditions and anticipate climate change. In this study, a marker-based crop model for wheat phenology was calibrated and tested. Climate analysis of 30 years of historical weather data in 72 locations representing the main wheat production areas in France was performed. We carried out marker-based crop model simulations for 1019 wheat cultivars and three sowing dates, which allowed calculation of genotypic stress avoidance frequencies of frost and heat stress and identification of ideotypes. The phenology marker-based crop model allowed prediction of large genotypic variations for the beginning of stem elongation (GS30) and heading date (GS55). Prediction accuracy was assessed using untested genotypes and environments, and showed median genotype prediction errors of 8.5 and 4.2 days for GS30 and GS55, respectively. Climate analysis allowed the definition of a low risk period for each location based on the distribution of the last frost and first heat days. Clustering of locations showed three groups with contrasting levels of frost and heat risks. Marker-based crop model simulations showed the need to optimize the genotype depending on sowing date, particularly in high risk environments. An empirical validation of the approach showed that it holds good promises to improve frost and heat stress avoidance.

Quantitative Trait Loci Associated with Phenological Development, Low-Temperature Tolerance, Grain Quality, and Agronomic Characters in Wheat (Triticum aestivum L.)

Plants must respond to environmental cues and schedule their development in order to react to periods of abiotic stress and commit fully to growth and reproduction under favorable conditions. This study was initiated to identify SNP markers for characters expressed from the seedling stage to plant maturity in spring and winter wheat (Triticum aestivum L.) genotypes adapted to western Canada. Three doubled haploid populations with the winter cultivar ‘Norstar’ as a common parent were developed and genotyped with a 90K Illumina iSelect SNP assay and a 2,998.9 cM consensus map with 17,541 markers constructed. High heritability’s reflected large differences among the parents and relatively low genotype by environment interactions for all characters considered. Significant QTL were detected for the 15 traits examined. However, different QTL for days to heading in controlled environments and the field provided a strong reminder that growth and development are being orchestrated by environmental cues and caution should be exercised when extrapolating conclusions from different experiments. A QTL on chromosome 6A for minimum final leaf number, which determines the rate of phenological development in the seedling stage, was closely linked to QTL for low-temperature tolerance, grain quality, and agronomic characters expressed up to the time of maturity. This suggests phenological development plays a critical role in programming subsequent outcomes for many traits. Transgressive segregation was observed for the lines in each population and QTL with additive effects were identified suggesting that genes for desirable traits could be stacked using Marker Assisted Selection. QTL were identified for characters that could be transferred between the largely isolated western Canadian spring and winter wheat gene pools demonstrating the opportunities offered by Marker Assisted Selection to act as bridges in the identification and transfer of useful genes among related genetic islands while minimizing the drag created by less desirable genes.

The expression of CBF genes at Fr-2 locus is associated with the level of frost tolerance in Bulgarian winter wheat cultivars

The regulation of the majority of cold-regulated genes in plants is mediated by CBF (C-repeat binding factors) transcription factor family. Natural differences in frost tolerance (FT) of wheat have been mapped to the Fr-2 (Frost Resistance-2) locus on chromosome group 5 and are associated with variation in threshold induction temperatures and/or transcript levels of CBF genes.

This study used real-time reverse-transcription polymerase chain reaction (qRT-PCR) to compare the relative expression levels of four T. aestivum CBF genes (TaCBF15.2, TaCBFA19, TaCBFA2 and TaCBFD21) in crown tissue of two Bulgarian hexaploid winter wheat cultivars (Milena and Russalka) with distinct levels of low-temperature (LT) tolerance but same vernalization requirement, and the spring cultivar Chinese Spring.

The transcription profiles of the selected TaCBF genes showed that they are induced by cold treatment at 2 °C. Analysis of transcript abundance revealed that the four TaCBF genes were expressed at higher levels in the frost tolerant Milena than in the susceptible Russalka. Largest differences (fivefold and fourfold) in expression levels between both winter cultivars were observed in two of the analysed genes, TaCBF15.2 and TaCBFA19, respectively. The higher steady-state expression levels of TaCBF genes before the onset of the LT treatment in Milena, combined with stronger induction by cold treatment, suggest that these molecular responses to LT are associated with superior FT development capacity.

The results expand our understanding of the molecular mechanisms underlying LT acclimation in Bulgarian wheat and can be used for development of functional markers for improvement of FT wheat-breeding programmes.

Linkage disequilibrium and genome-wide association mapping in tetraploid wheat (Triticum turgidum L.)

Association mapping is a powerful tool for the identification of quantitative trait loci through the exploitation of the differential decay of linkage disequilibrium (LD) between marker loci and genes of interest in natural and domesticated populations. Using a sample of 230 tetraploid wheat lines (Triticum turgidum ssp), which included naked and hulled accessions, we analysed the pattern of LD considering 26 simple sequence repeats and 970 mostly mapped diversity array technology loci. In addition, to validate the potential for association mapping in durum wheat, we evaluated the same genotypes for plant height, heading date, protein content, and thousand-kernel weight. Molecular and phenotypic data were used to: (i) investigate the genetic and phenotypic diversity; (ii) study the dynamics of LD across the durum wheat genome, by investigating the patterns of LD decay; and (iii) test the potential of our panel to identify marker–trait associations through the analysis of four quantitative traits of major agronomic importance. Moreover, we compared and validated the association mapping results with outlier detection analysis based on population divergence. Overall, in tetraploid wheat, the pattern of LD is extremely population dependent and is related to the domestication and breeding history of durum wheat. Comparing our data with several other studies in wheat, we confirm the position of many major genes and quantitative trait loci for the traits considered. Finally, the analysis of the selection signature represents a very useful complement to validate marker–trait associations.

Genetic basis of qualitative and quantitative resistance to powdery mildew in wheat: from consensus regions to candidate genes

Background

Powdery mildew (Blumeria graminis f. sp. tritici) is one of the most damaging diseases of wheat. The objective of this study was to identify the wheat genomic regions that are involved in the control of powdery mildew resistance through a quantitative trait loci (QTL) meta-analysis approach. This meta-analysis allows the use of collected QTL data from different published studies to obtain consensus QTL across different genetic backgrounds, thus providing a better definition of the regions responsible for the trait, and the possibility to obtain molecular markers that will be suitable for marker-assisted selection.

Results

Five QTL for resistance to powdery mildew were identified under field conditions in the durum-wheat segregating population Creso × Pedroso. An integrated map was developed for the projection of resistance genes/ alleles and the QTL from the present study and the literature, and to investigate their distribution in the wheat genome. Molecular markers that correspond to candidate genes for plant responses to pathogens were also projected onto the map, particularly considering NBS-LRR and receptor-like protein kinases. More than 80 independent QTL and 51 resistance genes from 62 different mapping populations were projected onto the consensus map using the Biomercator statistical software. Twenty-four MQTL that comprised 2–6 initial QTL that had widely varying confidence intervals were found on 15 chromosomes. The co-location of the resistance QTL and genes was investigated. Moreover, from analysis of the sequences of DArT markers, 28 DArT clones mapped on wheat chromosomes have been shown to be associated with the NBS-LRR genes and positioned in the same regions as the MQTL for powdery mildew resistance.

Conclusions

The results from the present study provide a detailed analysis of the genetic basis of resistance to powdery mildew in wheat. The study of the Creso × Pedroso durum-wheat population has revealed some QTL that had not been previously identified. Furthermore, the analysis of the co-localization of resistance loci and functional markers provides a large list of candidate genes and opens up a new perspective for the fine mapping and isolation of resistance genes, and for the marker-assisted improvement of resistance in wheat.

FR-H3: a new QTL to assist in the development of fall-sown barley with superior low temperature tolerance

Fall-sown barley will be increasingly important in the era of climate change due to higher yield potential and efficient use of water resources. Resistance/tolerance to abiotic stresses will be critical, and foremost among the abiotic stresses is low temperature. Simultaneous gene discovery and breeding will accelerate the development of agronomically relevant fall-sown barley germplasm with resistance to low temperature. We developed two doubled haploid mapping populations using two lines from the University of Nebraska (NE) and one line from Oregon State University (OR): NB3437f/OR71 (facultative × facultative) and NB713/OR71 (winter × facultative). Both were genotyped with a custom 384 oligonucleotide pool assay (OPA). QTL analyses were performed for low temperature tolerance (LTT) and vernalization sensitivity (VS). The role of VRN-H2 in VS was confirmed and a novel alternative winter allele at VRN-H3 was discovered in the Nebraska germplasm. FR-H2 was identified as a probable determinant of LTT and a new QTL, FR-H3, was discovered on chromosome 1H that accounted for up to 48 % of the phenotypic variation in field survival at St. Paul, MN, USA. The discovery of FR-H3 is a significant advancement in barley LTT genetics and will assist in developing the next generation of fall-sown varieties.

Genetics of flowering time in bread wheat Triticum aestivum: complementary interaction between vernalization-insensitive and photoperiod-insensitive mutations imparts very early flowering habit to spring wheat

Time to flowering in the winter growth habit bread wheat is dependent on vernalization (exposure to cold conditions) and exposure to long days (photoperiod). Dominant Vrn-1 (Vrn-A1, Vrn-B1 and Vrn-D1) alleles are associated with vernalization independent spring growth habit. The semidominant Ppd-D1a mutation confers photoperiod-insensitivity or rapid flowering in wheat under short day and long day conditions. The objective of this study was to reveal the nature of interaction between Vrn-1 and Ppd-D1a mutations (active alleles of the respective genes vrn-1 and Ppd-D1b). Twelve Indian spring wheat cultivars and the spring wheat landrace Chinese Spring were characterized for their flowering times by seeding them every month for five years under natural field conditions in New Delhi. Near isogenic Vrn-1 Ppd-D1 and Vrn-1 Ppd-D1a lines constructed in two genetic backgrounds were also phenotyped for flowering time by seeding in two different seasons. The wheat lines of Vrn-A1a Vrn-B1 Vrn-D1 Ppd-D1a, Vrn-A1a Vrn-B1 Ppd-D1a and Vrn-A1a Vrn-D1 Ppd-D1a (or Vrn-1 Ppd-D1a) genotypes flowered several weeks earlier than that of Vrn-A1a Vrn-B1 Vrn-D1 Ppd-D1b, Vrn-A1b Ppd-D1b and Vrn-D1 Ppd-D1b (or Vrn-1 Ppd-D1b) genotypes. The flowering time phenotypes of the isogenic vernalization-insensitive lines confirmed that Ppd-D1a hastened flowering by several weeks. It was concluded that complementary interaction between Vrn-1 and Ppd-D1a active alleles imparted super/very-early flowering habit to spring wheats. The early and late flowering wheat varieties showed differences in flowering time between short day and long day conditions. The flowering time in Vrn-1 Ppd-D1a genotypes was hastened by higher temperatures under long day conditions. The ambient air temperature and photoperiod parameters for flowering in spring wheat were estimated at 25°C and 12 h, respectively.

Genome-wide association analysis to identify chromosomal regions determining components of earliness in wheat

The modification of flowering date is considered an important way to escape the current or future climatic constraints that affect wheat crops. A better understanding of its genetic bases would enable a more efficient and rapid modification through breeding. The objective of this study was to identify chromosomal regions associated with earliness in wheat. A 227-wheat core collection chosen to be highly contrasted for earliness was characterized for heading date. Experiments were conducted in controlled conditions and in the field for 3 years to break down earliness in the component traits: photoperiod sensitivity, vernalization requirement and narrow-sense earliness. Whole-genome association mapping was carried out using 760 molecular markers and taking into account the five ancestral group structure. We identified 62 markers individually associated to earliness components corresponding to 33 chromosomal regions. In addition, we identified 15 other significant markers and seven more regions by testing marker pair interactions. Co-localizations were observed with the Ppd-1, Vrn-1 and Rht-1 candidate genes. Using an independent set of lines to validate the model built for heading date, we were able to explain 34% of the variation using the structure and the significant markers. Results were compared with already published data using bi-parental populations giving an insight into the genetic architecture of flowering time in wheat.

Genetic control of duration of pre-anthesis phases in wheat (Triticum aestivum L.) and relationships to leaf appearance, tillering, and dry matter accumulation

The duration of pre-anthesis developmental phases is of interest in breeding for improved adaptation and yield potential in temperate cereals. Yet despite numerous studies on the genetic control of anthesis (flowering) time and floral initiation, little is known about the genetic control of other pre-anthesis phases. Furthermore, little is known about the effect that changes in the duration of pre-anthesis phases could have on traits related to leaf appearance and tillering, or dry matter accumulation before terminal spikelet initiation (TS). The genetic control of the leaf and spikelet initiation phase (LS; from sowing to TS), the stem elongation phase (SE; from TS to anthesis), and, within the latter, from TS to flag leaf appearance and from then to anthesis, was studied in two doubled-haploid, mapping bread wheat populations, Cranbrook × Halberd and CD87 × Katepwa, in two field experiments (ACT and NSW, Australia). The lengths of phases were estimated from measurements of both TS and the onset of stem elongation. Dry weight per plant before TS, rate of leaf appearance, tillering rate, maximum number of tillers and number of leaves, and dry weight per plant at TS were also estimated in the Cranbrook × Halberd population. More genomic regions were identified for the length of the different pre-anthesis phases than for total time to anthesis. Although overall genetic correlations between LS and SE were significant and positive, independent genetic variability between LS and SE, and several quantitative trait loci (QTLs) with different effects on both phases were found in the two populations. Several of these QTLs (which did not seem to coincide with reported major genes) could be of interest for breeding purposes since they were only significant for either LS or SE. There was no relationship between LS and the rate of leaf appearance. LS was strongly and positively correlated with dry weight at TS but only slightly negatively correlated with early vigour (dry weight before TS). Despite significant genetic correlations between LS and some tillering traits, shortening LS so as to lengthen SE without modifying total time to anthesis would not necessarily reduce tillering capacity, as QTLs for tillering traits did not coincide with those QTLs significant only for LS or SE. Therefore, the study of different pre-anthesis phases is relevant for a better understanding of genetic factors regulating developmental time and may offer new tools for fine-tuning it in breeding for both adaptability and yield potential.

Deciphering the genetics of flowering time by an association study on candidate genes in bread wheat (Triticum aestivum L.)

Earliness is very important for the adaptation of wheat to environmental conditions and the achievement of high grain yield. A detailed knowledge of key genetic components of the life cycle would enable an easier control by the breeders. The objective of the study was to investigate the effect of candidate genes on flowering time. Using a collection of hexaploid wheat composed of 235 lines from diverse geographical origins, we conducted an association study for six candidate genes for flowering time and its components (vernalization sensitivity and earliness per se). The effect on the variation of earliness components of polymorphisms within the copies of each gene was tested in ANOVA models accounting for the underlying genetic structure. The collection was structured in five groups that minimized the residual covariance. Vernalization requirement and lateness tend to increase according to the mean latitude of each group. Heading date for an autumnal sowing was mainly determined by the earliness per se. Except for the Constans (CO) gene orthologous of the barley HvCO3, all gene polymorphisms had a significant impact on earliness components. The three traits used to quantify vernalization requirement were primarily associated with polymorphisms at Vrn-1 and then at Vrn-3 and Luminidependens (LD) genes. We found a good correspondence between spring/winter types and genotypes at the three homeologous copies of Vrn-1. Earliness per se was mainly explained by polymorphisms at Vrn-3 and to a lesser extent at Vrn-1, Hd-1 and Gigantea (GI) genes. Vernalization requirement and earliness as a function of geographical origin, as well as the possible role of the breeding practices in the geographical distribution of the alleles and the hypothetical adaptive value of the candidate genes, are discussed.