A population of wheat multiple synthetic derivatives: an effective platform to explore, harness and utilize genetic diversity of Aegilops tauschii for wheat improvement

A new winter wheat genetic resource harbors untapped diversity from synthetic hexaploid wheat

KEY MESSAGE

The NIAB_WW_SHW_NAM population, a large nested association mapping panel, is a useful resource for mapping QTL from synthetic hexaploid wheat that can improve modern elite wheat cultivars. The allelic richness harbored in progenitors of hexaploid bread wheat (Triticum aestivum L.) is a useful resource for addressing the genetic diversity bottleneck in modern cultivars. Synthetic hexaploid wheat (SHW) is created through resynthesis of the hybridisation events between the tetraploid (Triticum turgidum subsp. durum Desf.) and diploid (Aegilops tauschii Coss.) bread wheat progenitors. We developed a large and diverse winter wheat nested association mapping (NAM) population (termed the NIAB_WW_SHW_NAM) consisting of 3241 genotypes derived from 54 nested back-cross 1 (BC1) populations, each formed via back-crossing a different primary SHW into the UK winter wheat cultivar 'Robigus'. The primary SHW lines were created using 15 T. durum donors and 47 Ae. tauschii accessions that spanned the lineages and geographical range of the species. Primary SHW parents were typically earlier flowering, taller and showed better resistance to yellow rust infection (Yr) than 'Robigus'. The NIAB_WW_SHW_NAM population was genotyped using a single nucleotide polymorphism (SNP) array and 27 quantitative trait loci (QTLs) were detected for flowering time, plant height and Yr resistance. Across multiple field trials, a QTL for Yr resistance was found on chromosome 4D that corresponded to the Yr28 resistance gene previously reported in other SHW lines. These results demonstrate the value of the NIAB_WW_SHW_NAM population for genetic mapping and provide the first evidence of Yr28 working in current UK environments and genetic backgrounds. These examples, coupled with the evidence of commercial wheat breeders selecting promising genotypes, highlight the potential value of the NIAB_WW_SHW_NAM to variety improvement.

Strategies for breeding crops for future environments

The green revolution successfully increased agricultural output in the early 1960s by relying primarily on three pillars: plant breeding, irrigation, and chemical fertilization. Today, the need to reduce the use of chemical fertilizers, water scarcity, and future environmental changes, together with a growing population, requires innovative strategies to adapt to a new context and prevent food shortages. Therefore, scientists from around the world are directing their efforts to breed crops for future environments to sustainably produce more nutritious food. Herein, we propose scientific avenues to be reinforced in selecting varieties, including crop wild relatives, either for monoculture or mixed cropping systems, taking advantage of plant-microbial interactions, while considering the diversity of organisms associated with crops and unlocking combinatorial nutritional stresses.

Heat Stress-Tolerant Quantitative Trait Loci Identified Using Backcrossed Recombinant Inbred Lines Derived from Intra-Specifically Diverse Aegilops tauschii Accessions

In the face of climate change, bringing more useful alleles and genes from wild relatives of wheat is crucial to develop climate-resilient varieties. We used two populations of backcrossed recombinant inbred lines (BIL1 and BIL2), developed by crossing and backcrossing two intra-specifically diverse Aegilops tauschii accessions from lineage 1 and lineage 2, respectively, with the common wheat cultivar 'Norin 61'. This study aimed to identify quantitative trait loci (QTLs) associated with heat stress (HS) tolerance. The two BILs were evaluated under heat stress environments in Sudan for phenology, plant height (PH), grain yield (GY), biomass (BIO), harvest index (HI), and thousand-kernel weight (TKW). Grain yield was significantly correlated with BIO and TKW under HS; therefore, the stress tolerance index (STI) was calculated for these traits as well as for GY. A total of 16 heat-tolerant lines were identified based on GY and STI-GY. The QTL analysis performed using inclusive composite interval mapping identified a total of 40 QTLs in BIL1 and 153 QTLs in BIL2 across all environments. We detected 39 QTLs associated with GY-STI, BIO-STI, and TKW-STI in both populations (14 in BIL1 and 25 in BIL2). The QTLs associated with STI were detected on chromosomes 1A, 3A, 5A, 2B, 4B, and all the D-subgenomes. We found that QTLs were detected only under HS for GY on chromosome 5A, TKW on 3B and 5B, PH on 3B and 4B, and grain filling duration on 2B. The higher number of QTLs identified in BIL2 for heat stress tolerance suggests the importance of assessing the effects of intraspecific variation of Ae. tauschii in wheat breeding as it could modulate the heat stress responses/adaptation. Our study provides useful genetic resources for uncovering heat-tolerant QTLs for wheat improvement for heat stress environments.

Mining Aegilops tauschii genetic diversity in the background of bread wheat revealed a novel QTL for seed dormancy

Due to the low genetic diversity in the current wheat germplasm, gene mining from wild relatives is essential to develop new wheat cultivars that are more resilient to the changing climate. Aegilops tauschii, the D-genome donor of bread wheat, is a great gene source for wheat breeding; however, identifying suitable genes from Ae. tauschii is challenging due to the different morphology and the wide intra-specific variation within the species. In this study, we developed a platform for the systematic evaluation of Ae. tauschii traits in the background of the hexaploid wheat cultivar 'Norin 61' and thus for the identification of QTLs and genes. To validate our platform, we analyzed the seed dormancy trait that confers resistance to preharvest sprouting. We used a multiple synthetic derivative (MSD) population containing a genetic diversity of 43 Ae. tauschii accessions representing the full range of the species. Our results showed that only nine accessions in the population provided seed dormancy, and KU-2039 from Afghanistan had the highest level of seed dormancy. Therefore, 166 backcross inbred lines (BILs) were developed by crossing the synthetic wheat derived from KU-2039 with 'Norin 61' as the recurrent parent. The QTL mapping revealed one novel QTL, Qsd.alrc.5D, associated with dormancy explaining 41.7% of the phenotypic variation and other five unstable QTLs, two of which have already been reported. The Qsd.alrc.5D, identified for the first time within the natural variation of wheat, would be a valuable contribution to breeding after appropriate validation. The proposed platform that used the MSD population derived from the diverse Ae. tauschii gene pool and recombinant inbred lines proved to be a valuable platform for mining new and important QTLs or alleles, such as the novel seed dormancy QTL identified here. Likewise, such a platform harboring genetic diversity from wheat wild relatives could be a useful source for mining agronomically important traits, especially in the era of climate change and the narrow genetic diversity within the current wheat germplasm.

Genetic Improvement and Application Practices of Synthetic Hexaploid Wheat

Synthetic hexaploid wheat (SHW) is a useful genetic resource that can be used to improve the performance of common wheat by transferring favorable genes from a wide range of tetraploid or diploid donors. From the perspectives of physiology, cultivation, and molecular genetics, the use of SHW has the potential to increase wheat yield. Moreover, genomic variation and recombination were enhanced in newly formed SHW, which could generate more genovariation or new gene combinations compared to ancestral genomes. Accordingly, we presented a breeding strategy for the application of SHW-the 'large population with limited backcrossing method'-and we pyramided stripe rust resistance and big-spike-related QTLs/genes from SHW into new high-yield cultivars, which represents an important genetic basis of big-spike wheat in southwestern China. For further breeding applications of SHW-derived cultivars, we used the 'recombinant inbred line-based breeding method' that combines both phenotypic and genotypic evaluations to pyramid multi-spike and pre-harvest sprouting resistance QTLs/genes from other germplasms to SHW-derived cultivars; consequently, we created record-breaking high-yield wheat in southwestern China. To meet upcoming environmental challenges and continuous global demand for wheat production, SHW with broad genetic resources from wild donor species will play a major role in wheat breeding.

Exome-wide variation in a diverse barley panel reveals genetic associations with ten agronomic traits in Eastern landraces

Barley (Hordeum vulgare ssp. vulgare) was one of the first crops to be domesticated and is adapted to a wide range of environments. Worldwide barley germplasm collections possess valuable allelic variations that could further improve barley productivity. Although barley genomics has offered a global picture of allelic variation among varieties and its association with various agronomic traits, polymorphisms from East Asian varieties remain scarce. In this study, we analyzed exome polymorphisms in a panel of 274 barley varieties collected worldwide, including 137 varieties from East Asian countries and Ethiopia. We revealed the underlying population structure and conducted genome-wide association studies for ten agronomic traits. Moreover, we examined genome-wide associations for traits related to grain size such as awn length and glume length. Our results demonstrate the value of diverse barley germplasm panels containing Eastern varieties, highlighting their distinct genomic signatures relative to Western subpopulations.

Ensuring Nutritional Security in India through Wheat Biofortification: A Review

Undernourishment of nutrients, also known as hidden hunger, affects over 2 billion populace globally. Even though stunting among children below five years of age has decreased in India in the last ten years, India is home to roughly thirty percent of the world's population of stunted pre-schoolers. A significant improvement has been witnessed in the targeted development and deployment of biofortified crops; approximately 20 million farm households from developing counties benefit from cultivating and consuming biofortified crops. There is ample scope for including biofortified varieties in the seed chain, ensuring nutritional security. Wheat is a dietary staple in India, typically consumed as wholemeal flour in the form of flatbreads such as chapatti and roti. Wheat contributes to nearly one fifth of global energy requirements and can also provide better amounts of iron (Fe) and zinc (Zn). As a result, biofortified wheat can serve as a medium for delivery of essential micronutrients such as Fe and Zn to end users. This review discusses wheat biofortification components such as Fe and Zn dynamics, its uptake and movement in plants, the genetics of their buildup, and the inclusion of biofortified wheat varieties in the seed multiplication chain concerning India.

Genome-wide association study reveals distinct genetic associations related to leaf hair density in two lineages of wheat-wild relative Aegilops tauschii

Wild relatives of modern crops represent a promising source of genetic variation that can be mined for adaptations to climate change. Aegilops tauschii, the D-sub-genome progenitor of bread wheat (Triticum aestivum), constitutes a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Leaf hairiness plays an essential biological role in plant defense against biotic and abiotic stress. We investigated the natural variation in leaf hair density (LHD) among 293 Ae. tauschii accessions. Genome-wide association studies were performed for LHD with 2430 and 3880 DArTseq derived single nucleotide polymorphism (SNP) markers in two lineages of this species, TauL1 and TauL2, respectively. In TauL1, three marker-trait associations (MTAs) were located on chromosome 2D, whereas in TauL2, eight MTAs were identified, two associations were localized on each of the chromosomes 2D, 3D, 5D, and 7D. The markers explained phenotypic variation (R2) from 9 to 13% in TauL1 and 11 to 36% in TauL2. The QTLs identified in chromosomes 2D and 5D might be novel. Our results revealed more rapid and independent evolution of LHD in TauL2 compared to TauL1. The majority of LHD candidate genes identified are associated with biotic and abiotic stress responses. This study highlights the significance of intraspecific diversity of Ae. tauschii to enhance cultivated wheat germplasm.

Identification of Glu-D1 Alleles and Novel Marker-Trait Associations for Flour Quality and Grain Yield Traits under Heat-Stress Environments in Wheat Lines Derived from Diverse Accessions of Aegilops tauschii

Heat stress during grain filling is considered one of the major abiotic factors influencing wheat grain yield and quality in arid and semi-arid regions. We studied the effect of heat stress on flour quality and grain yield at moderate and continuous heat stress under natural field conditions using 147 lines of wheat multiple synthetic derivatives (MSD) containing Aegilops tauschii introgressions. The study aimed to identify the marker-trait associations (MTAs) for the quality traits and grain yield under heat-stress conditions and identify stress-resilient germplasm-combining traits for good flour quality and grain yield. The MSD lines showed considerable genetic variation for quality traits and grain yield under heat-stress conditions; some lines performed better than the recurrent parent, Norin 61. We identified two MSD lines that consistently maintained relative performance (RP) values above 100% for grain yield and dough strength. We found the presence of three high-molecular-weight glutenin subunits (HMW-GSs) at the Glu-D1 locus derived from Ae. tauschii, which were associated with stable dough strength across the four environments used in this study. These HMW-GSs could be potentially useful in applications for future improvements of end-use quality traits targeting wheat under severe heat stress. A total of 19,155 high-quality SNP markers were used for the genome-wide association analysis and 251 MTAs were identified, most of them on the D genome, confirming the power of the MSD panel as a platform for mining and exploring the genes of Ae. tauschii. We identified the MTAs for dough strength under heat stress, which simultaneously control grain yield and relative performance for dough strength under heat-stress/optimum conditions. This study proved that Ae. tauschii is an inexhaustible resource for genetic mining, and the identified lines and pleiotropic MTAs reported in this study are considered a good resource for the development of resilient wheat cultivars that combine both good flour quality and grain yield under stress conditions using marker-assisted selection.

Enhancing Wheat Flour Quality Through Introgression of High-Molecular-Weight Glutenin Subunits From Aegilops tauschii Accessions

Narrow genetic diversity in the wheat gene pool restricts the improvement of wheat quality traits. Aegilops tauschii possesses valuable genetic diversity that can be used to improve not only biotic and abiotic stresses in arid regions but also wheat yield and quality. Our study, which used 392 multiple synthetic derivatives (MSD) panel developed with Ae. tauschii Coss. introgressions, had three main aims: to explore the genetic diversity of high-molecular-weight glutenin subunits (HMW-GS), to investigate the dough strength and the relationship between protein content and grain yield, and to identify lines with a good flour quality. A wide range of allelic diversity was observed at the Glu-D1 locus, reflecting the impact of the different introgressed portions of Ae. tauschii, and a wide variation was found in dough strength even between lines having the same composition of HMW-GS. We report a negative impact on dough strength of subunit 5t+10t from Ae. tauschii and a relatively positive impact of subunit 2t+12.1t. We identified four MSD lines with significantly enhanced flour quality. Regressing the grain yield of the MSD lines against protein content showed no correlation between the two traits and identified lines with comparable grain yield to the recurrent parent and higher protein content. The identified MSD lines could provide a valuable genetic resource for enhancing the end-use quality of flour without any loss in productivity.

Harnessing the diversity of wild emmer wheat for genetic improvement of durum wheat

The multiple derivative lines (MDLs) characterized in this study offer a promising strategy for harnessing the diversity of wild emmer wheat for durum and bread wheat improvement. Crop domestication has diminished genetic diversity and reduced phenotypic plasticity and adaptation. Exploring the adaptive capacity of wild progenitors offer promising opportunities to improve crops. We developed a population of 178 BC₁F₆ durum wheat (Triticum turgidum ssp. durum) lines by crossing and backcrossing nine wild emmer wheat (T. turgidum ssp. dicoccoides) accessions with the common durum wheat cultivar 'Miki 3'. Here, we describe the development of this population, which we named as multiple derivative lines (MDLs), and demonstrated its suitability for durum wheat breeding. We genotyped the MDL population, the parents, and 43 Sudanese durum wheat cultivars on a Diversity Array Technology sequencing platform. We evaluated days to heading and plant height in Dongola (Sudan) and in Tottori (Japan). The physical map length of the MDL population was 9 939 Mb with an average of 1.4 SNP/Mb. The MDL population had greater diversity than the Sudanese cultivars. We found high gene exchange between the nine wild emmer accessions and the MDL population, indicating that the MDL captured most of the diversity in the wild emmer accessions. Genome-wide association analysis identified three loci for days to heading on chromosomes 1A and 5A in Dongola and one on chromosome 3B in Tottori. For plant height, common genomic loci were found on chromosomes 4A and 4B in both locations, and one genomic locus on chromosome 7B was found only in Dongola. The results revealed that the MDLs are an effective strategy towards harnessing wild emmer wheat diversity for wheat genetic improvement.

Genomic analysis for heat and combined heat-drought resilience in bread wheat under field conditions

KEY MESSAGE

GWAS on a bread wheat panel with high D genome diversity identified novel alleles and QTLs associated with resilience to combined heat and drought stress under natural field conditions. As heat (H) and drought stresses occur concurrently under field conditions, studying them separately offers limited opportunities for wheat improvement. Here, a wheat diversity panel containing Aegilops tauschii introgressions was evaluated under H and combined heat-drought (HD) stresses to identify quantitative trait loci (QTLs) associated with resilience to the stresses, and to assess the practicability of harnessing Ae. tauschii diversity for breeding for combined stress resilience. Using genome-wide analysis, we identified alleles and QTLs on chromosomes 3D, 5D, and 7A controlling grain yield (GY), kernel number per spike, and thousand-kernel weight, and on 3D (521-549 Mbp) controlling GY alone. A strong marker-trait association (MTA) for GY stability on chromosome 3D (508.3 Mbp) explained 20.3% of the variation. Leaf traits-canopy temperature, vegetation index, and carbon isotope composition-were controlled by five QTLs on 2D (23-96, 511-554, and 606-614 Mbp), 3D (155-171 Mbp), and 5D (407-413 Mbp); some of them were pleiotropic for GY and yield-related traits. Further analysis revealed candidate genes, including GA20ox, regulating GY stability, and CaaX prenyl protease 2, regulating canopy temperature at the flowering stage, under H and HD stresses. As genome-wide association studies under HD in field conditions are scarce, our results provide genomic landmarks for wheat breeding to improve adaptation to H and HD conditions under climate change.

Frequent numerical and structural chromosome changes in early generations of synthetic hexaploid wheat

Modern hexaploid wheat (Triticum aestivum L.; AABBDD) evolved from a hybrid of tetraploid wheat (closely related to Triticum turgidum L. ssp. durum (Desf.) Husn., AABB) and goatgrass (Aegilops tauschii Coss., DD). Variations in chromosome structure and ploidy played important roles in wheat evolution. How these variations occurred and their role in expanding the genetic diversity in modern wheat is mostly unknown. Synthetic hexaploid wheat (SHW) can be used to investigate chromosome variation that occurs during the early generations of existence. SHW lines derived by crossing durum wheat 'Langdon' with twelve Ae. tauschii accessions were analyzed using oligonucelotide probe multiplex fluorescence in situ hybridization (FISH) to metaphase chromosomes and SNP markers. Cluster analysis based on SNP markers categorized them into three groups. Among 702 plants from the S8 and S9 generations, 415 (59.12%) carried chromosome variations involving all 21 chromosomes but with different frequencies for each chromosome and sub-genome. Total chromosome variation frequencies varied between lines, but there was no significant difference among the three groups. The non-random chromosome variations in SHW lines detected in this research may be an indication that similar variations occurred in the early stages of wheat polyploidization and played important roles in wheat evolution.

Transpiration response of two bread wheat lines differing in drought resilience and their backcross parent under dry-down conditions

Improving wheat productivity in drylands largely depends on how plants manage limited water resources. Using fraction of transpirable soil water threshold (FTSWTh) and drought stress response function, we characterized the water conservation traits of two wheat multiple synthetic derivative lines (MSD53 and MSD345) which both contain introgressed segments from Aegilops tauschii but differ in drought resilience. The lines and their backcross parent, 'Norin 61', were subjected to dry-down conditions. MSD53 had a higher FTSWTh for transpiration decrease than 'Norin 61' and MSD345. In terms of drought stress response function, MSD53 had the lowest threshold suction, suggesting a lower drought resilience capacity compared with MSD345. However, MSD53 exhibited an effective-water-use trait whereas MSD345 exhibited a water-saving trait under dry-down conditions. These results are consistent with the reported higher yield of MSD53 in comparison with MSD345 under drought stress in Sudan, and demonstrate that high FTSWTh supports effective water use for improved agricultural productivity in drylands. The differences in water conservation traits between the two MSD lines may be attributed to variation in introgressed segments, which can be further explored for drought resilience breeding.

Sensitivities to temperature and evaporative demand in wheat relatives

There is potential sources of alleles and genes currently locked into wheat-related species that could be introduced into wheat breeding programs for current and future hot and dry climates. However, neither the intra- nor the inter-specific diversity of the responses of leaf growth and transpiration to temperature and evaporative demand have been investigated in a large diversity of wheat-related species. By analysing 12 groups of wheat-related sub-species, we questioned the n-dimensional structure of the genetic diversity for traits linked to plant vegetative structures and development, leaf expansion and transpiration together with their responses to "non-stressing" range of temperature and evaporative demand. In addition to provide new insight on how genome type, ploidy level, phylogeny and breeding pressure together structure this genetic diversity, this study provides new mathematical formalisms and the associated parameters of trait responses in the large genetic diversity of wheat-related species. This potentially allow crop models predicting the impact of this diversity on yield, and indicate potential sources of varietal improvement for modern wheat germplasms, through interspecific crosses.

Genetic variation in drought resilience-related traits among wheat multiple synthetic derivative lines: insights for climate resilience breeding

Twenty-four wheat lines, developed by Aegilops tauschii Coss. introgressions and previously selected for heat or salinity stress tolerance, were evaluated under a drought-rewatering-drought cycle for two years. The objective was to select breeding lines that are resilient to more than one abiotic stress. The experiment was designed in alpha lattice with three replications. Drought was imposed by withholding water during flowering. The results revealed considerable genetic variability in physio-agronomic traits, reflecting the variation in the introgressed segments. High heritability estimates (above 47%) were recorded for most traits, including days to 50% heading, plant height, and thousand-grain weight, indicating the genetic control of these traits which may be useful for cultivar development. The trait-trait correlations within and between water regimes highlighted a strong association among the genetic factors controlling these traits. Some lines exhibited superior performance in terms of stress tolerance index and mean productivity compared with their backcross parent and elite cultivars commonly grown in hot and dry areas. Graphical genotyping revealed unique introgressed segments on chromosomes 4B, 6B, 2D, and 3D in some drought-resilient lines which may be linked to drought resilience. Therefore, we recommend these lines for further breeding to develop climate-resilient wheat varieties.

Stage-Specific Characterization of Physiological Response to Heat Stress in the Wheat Cultivar Norin 61

Bread wheat (Triticum aestivum) is less adaptable to high temperatures than other major cereals. Previous studies of the effects of high temperature on wheat focused on the reproductive stage. There are few reports on yield after high temperatures at other growth stages. Understanding growth-stage-specific responses to heat stress will contribute to the development of tolerant lines suited to high temperatures at various stages. We exposed wheat cultivar "Norin 61" to high temperature at three growth stages: seedling-tillering (GS1), tillering-flowering (GS2), and flowering-maturity (GS3). We compared each condition based on agronomical traits, seed maturity, and photosynthesis results. Heat at GS2 reduced plant height and number of grains, and heat at GS3 reduced the grain formation period and grain weight. However, heat at GS1 reduced senescence and prolonged grain formation, increasing grain weight without reducing yield. These data provide fundamental insights into the biochemical and molecular adaptations of bread wheat to high-temperature stresses and have implications for the development of wheat lines that can respond to high temperatures at various times of the year.

Predominant wheat-alien chromosome translocations in newly developed wheat of China

Founder wheat lines have played key role in Chinese wheat improvement. Wheat-Dasypyrum villosum translocation T6VS·6AL has been widely used in wheat breeding in recent years due to its high level of powdery mildew resistance and other beneficial genes. Reference oligo-nucleotide multiplex probe (ONMP)-FISH karyotypes of six T6VS·6AL donor lines were developed and used for characterizing 32 derivative cultivars and lines. T6VS·6AL was present in 27 cultivar/lines with 20 from southern China. Next, ONMP-FISH was used to study chromosome constitution of randomly collected wheat cultivars and advanced breeding lines from southern and northern regions of China: 123 lines from the regional test plots of southern China and 110 from northern China. In southern China, T6VS·6AL (35.8%) was the most predominant variation, while T1RS·1BL (27.3%) was the most predominant in northern China. The pericentric inversion perInv 6B derived from its founder wheat Funo and Abbondaza was the second most predominant chromosome variant in both regions. Other chromosome variants were present in very low frequencies. Additionally, 167 polymorphic chromosome types were identified. Based on these variations, 271 cultivars and lines were clustered into three groups, including southern, northern, and mixed groups that contained wheat from both regions. Different dominant chromosome variations were seen, indicating chromosome differentiation in the three groups of wheat. The clearly identified wheat lines with T6VS·6AL in different backgrounds and oligonucleotide probe set will facilitate their utilization in wheat breeding and in identifying other beneficial traits that may be linked to this translocation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01206-3.

Exploitation of Tolerance of Wheat Kernel Weight and Shape-Related Traits from Aegilops tauschii under Heat and Combined Heat-Drought Stresses

Kernel weight and shape-related traits are inherited stably and increase wheat yield. Narrow genetic diversity limits the progress of wheat breeding. Here, we evaluated kernel weight and shape-related traits and applied genome-wide association analysis to a panel of wheat multiple synthetic derivative (MSD) lines. The MSD lines harbored genomic fragments from Aegilops tauschii. These materials were grown under optimum conditions in Japan, as well as under heat and combined heat-drought conditions in Sudan. We aimed to explore useful QTLs for kernel weight and shape-related traits under stress conditions. These can be useful for enhancing yield under stress conditions. MSD lines possessed remarkable genetic variation for all traits under all conditions, and some lines showed better performance than the background parent Norin 61. We identified 82 marker trait associations (MTAs) under the three conditions; most of them originated from the D genome. All of the favorable alleles originated from Ae. tauschii. For the first time, we identified markers on chromosome 5D associated with a candidate gene encoding a RING-type E3 ubiquitin-protein ligase and expected to have a role in regulating wheat seed size. Our study provides important knowledge for the improvement of wheat yield under optimum and stress conditions. The results emphasize the importance of Ae. tauschii as a gene reservoir for wheat breeding.

Genome-Wide Association Study of Morpho-Physiological Traits in Aegilops tauschii to Broaden Wheat Genetic Diversity

Aegilops tauschii, the D-genome donor of bread wheat, is a storehouse of genetic diversity that can be used for wheat improvement. This species consists of two main lineages (TauL1 and TauL2) and one minor lineage (TauL3). Its morpho-physiological diversity is large, with adaptations to a wide ecological range. Identification of allelic diversity in Ae. tauschii is of utmost importance for efficient breeding and widening of the genetic base of wheat. This study aimed at identifying markers or genes associated with morpho-physiological traits in Ae. tauschii, and at understanding the difference in genetic diversity between the two main lineages. We performed genome-wide association studies of 11 morpho-physiological traits of 343 Ae. tauschii accessions representing the entire range of habitats using 34,829 DArTseq markers. We observed a wide range of morpho-physiological variation among all accessions. We identified 23 marker-trait associations (MTAs) in all accessions, 15 specific to TauL1 and eight specific to TauL2, suggesting independent evolution in each lineage. Some of the MTAs could be novel and have not been reported in bread wheat. The markers or genes identified in this study will help reveal the genes controlling the morpho-physiological traits in Ae. tauschii, and thus in bread wheat even if the plant morphology is different.

Metabolic and physiological responses to progressive drought stress in bread wheat

Wheat (Tritium aestivum) is vulnerable to future climate change because it is predominantly grown under rain-fed conditions in drought-prone areas. Thus, in-depth understanding of drought effect on wheat metabolism is essential for developing drought-tolerant wheat varieties. Here, we exposed wheat 'Norin 61' plants to progressive drought stress [0 (before drought), 2, 4, 6, 8, and 10 days after withholding water] during the flowering stage to investigate physiological and metabolomic responses. Transcriptional analyses of key abscisic acid-responsive genes indicated that abscisic acid signalling played a major role in the adaptation of wheat to water deficit. Carbon isotope composition had a higher value than the control while canopy temperature (CT) increased under drought stress. The CT depression was tightly correlated with soil water potential (SWP). Additionally, SWP at - 517 kPa was identified as the critical point for increasing CT and inducing reactive oxygen species. Metabolome analysis identified four potential drought-responsive biomarkers, the enhancement of nitrogen recycling through purine and pyrimidine metabolism, drought-induced senescence based on 1-aminocyclopropane-1-carboxylic acid and Asn accumulation, and an anti-senescence response through serotonin accumulation under severe drought stress. Our findings provide in-depth insight into molecular, physiological and metabolite changes involved in drought response which are useful for wheat breeding programs to develop drought-tolerant wheat varieties.

Appraisal of wheat genomics for gene discovery and breeding applications: a special emphasis on advances in Asia

We discussed the most recent efforts in wheat functional genomics to discover new genes and their deployment in breeding with special emphasis on advances in Asian countries. Wheat research community is making significant progress to bridge genotype-to-phenotype gap and then applying this knowledge in genetic improvement. The advances in genomics and phenomics have intrigued wheat researchers in Asia to make best use of this knowledge in gene and trait discovery. These advancements include, but not limited to, map-based gene cloning, translational genomics, gene mapping, association genetics, gene editing and genomic selection. We reviewed more than 57 homeologous genes discovered underpinning important traits and multiple strategies used for their discovery. Further, the complementary advancements in wheat phenomics and analytical approaches to understand the genetics of wheat adaptability, resilience to climate extremes and resistance to pest and diseases were discussed. The challenge to build a gold standard reference genome sequence of bread wheat is now achieved and several de novo reference sequences from the cultivars representing different gene pools will be available soon. New pan-genome sequencing resources of wheat will strengthen the foundation required for accelerated gene discovery and provide more opportunities to practice the knowledge-based breeding.

Phenotypic effects of the U-genome variation in nascent synthetic hexaploids derived from interspecific crosses between durum wheat and its diploid relative Aegilops umbellulata

Aegilops umbellulata is a wild diploid wheat species with the UU genome that is an important genetic resource for wheat breeding. To exploit new synthetic allohexaploid lines available as bridges for wheat breeding, a total of 26 synthetic hexaploid lines were generated through crossing between the durum wheat cultivar Langdon and 26 accessions of Ae. umbellulata. In nascent synthetic hexaploids with the AABBUU genome, the presence of the set of seven U-genome chromosomes was confirmed with U-genome chromosome-specific markers developed based on RNA-seq-derived data from Ae. umbellulata. The AABBUU synthetic hexaploids showed large variations in flowering- and morphology-related traits, and these large variations transmitted well from the parental Ae. umbellulata accessions. However, the variation ranges in most traits examined were reduced under the AABBUU hexaploid background compared with under the diploid parents. The AABBUU and AABBDD synthetic hexaploids were clearly discriminated by several morphological traits, and an increase of plant height and in the number of spikes and a decrease of spike length were commonly observed in the AABBUU synthetics. Thus, interspecific differences in several morphological traits between Ae. umbellulata and A. tauschii largely affected the basic plant architecture of the synthetic hexaploids. In conclusion, the AABBUU synthetic hexaploid lines produced in the present study are useful resources for the introgression of desirable genes from Ae. umbellulata to common wheat.

Introgression of chromosomal segments conferring early heading date from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars

The breeding of agriculturally useful genes from wild crop relatives must take into account recent and future climate change. In Japan, the development of early heading wheat cultivars without the use of any major gene controlling the heading date is desired to avoid overlap of the harvesting time before the rainy season. Here, we backcrossed two early heading lines of a synthetic hexaploid wheat, derived from a crossing between durum wheat and the wild wheat progenitor Aegilops tauschii, with four Japanese elite cultivars to develop early heading lines of bread wheat. In total, nine early heading lines that showed a heading date two to eight days earlier than their parental cultivars in field conditions were selected and established from the selfed progenies of the two- or three-times backcrossed populations. The whole appearance and spike shape of the selected early heading lines looked like their parental wheat cultivars. The mature grains of the selected lines had the parental cultivars’ characteristics, although the grains exhibited longer and narrower shapes. RNA sequencing-based genotyping was performed to detect single nucleotide polymorphisms between the selected lines and their parental wheat cultivars, which revealed the chromosomal regions transmitted from the parental synthetic wheat to the selected lines. The introgression regions could shorten wheat heading date, and their chromosomal positions were dependent on the backcrossed wheat cultivars. Therefore, early heading synthetic hexaploid wheat is useful for fine-tuning of the heading date through introgression of Ae. tauschii chromosomal regions.

Genetic analysis of Aegilops tauschii-derived seedling resistance to leaf rust in synthetic hexaploid wheat

Seedling resistance to leaf rust available in the synthetic hexaploid wheat line Syn137 was characterised by means of cytogenetic and linkage mapping. Monosomic analysis located a single dominant gene for leaf rust resistance on chromosome 5D. Molecular mapping not only confirmed this location but also positioned the gene to the distal part of the long arm of chromosome 5D. A test of allelism showed that the gene, tentatively named LrSyn137, is independent but closely linked to Lr1. It appears that Syn137 is occasionally heterogeneous for Lr1 since the analysis of the Lr1-specific marker RGA567-5 in the genetic mapping population indicated the presence of Lr1. Syn137 represents another source of genetic variation that can be useful for the diversification of leaf rust resistance in wheat cultivars.

Population-dependent reproducible deviation from natural bread wheat genome in synthetic hexaploid wheat

Sequence elimination is one of the main mechanisms that increases the divergence among homoeologous chromosomes after allopolyploidization to enhance the stability of recently established lineages, but it can cause a loss of some economically important genes. Synthetic hexaploid wheat (SHW) is an important source of genetic variation to the natural hexaploid wheat (NHW) genepool that has low genetic diversity. Here, we investigated the change between SHW and NHW genomes by utilizing a large germplasm set of primary synthetics and synthetic derivatives. Reproducible segment elimination (RSE) was declared if a large chromosomal chunk (>5 cM) produced no aligned reads in more than five SHWs. RSE in five genomic regions was the major source of variation between SHW and NHW. One RSE eliminated almost the complete short arm of chromosome 1B, which contains major genes for flour quality, disease resistance and different enzymes. The occurrence of RSE was highly dependent on the choice of diploid and tetraploid parental lines, their ancestral subpopulation and admixture, e.g. SHWs derived from Triticum dicoccon or from one of two Aegilops tauschii subpopulations were almost free of RSE, while highly admixed parents had higher RSE rates. The rate of RSE in synthetic derivatives was almost double that in primary synthetics. Genome-wide association analysis detected four loci with minor effects on the occurrence of RSE, indicating that both parental lines and genetic factors were affecting the occurrence of RSE. Therefore, pre-pre-breeding strategies should be applied before introducing SHW into pre-breeding programs to ensure genomic stability and avoid undesirable gene loss.

Ozone Tolerance Found in Aegilops tauschii and Primary Synthetic Hexaploid Wheat

Modern wheat cultivars are increasingly sensitive to ground level ozone, with 7-10% mean yield reductions in the northern hemisphere. In this study, three of the genome donors of bread wheat, Triticum urartu (AA), T. dicoccoides (AABB), and Aegilops tauschii (DD) along with a modern wheat cultivar (T. aestivum 'Skyfall'), a 1970s cultivar (T. aestivum 'Maris Dove'), and a line of primary Synthetic Hexaploid Wheat were grown in 6 L pots of sandy loam soil in solardomes (Bangor, North Wales) and exposed to low (30 ppb), medium (55 ppb), and high (110 ppb) levels of ozone over 3 months. Measurements were made at harvest of shoot biomass and grain yield. Ae. tauschii appeared ozone tolerant with no significant effects of ozone on shoot biomass, seed head biomass, or 1000 grain + husk weight even under high ozone levels. In comparison, T. urartu had a significant reduction in 1000 grain + husk weight, especially under high ozone (-26%). The older cultivar, 'Maris Dove', had a significant reduction in seed head biomass (-9%) and 1000 grain weight (-11%) but was less sensitive than the more recent cultivar 'Skyfall', which had a highly significant reduction in its seed head biomass (-21%) and 1000 grain weight (-27%) under high ozone. Notably, the line of primary Synthetic Hexaploid Wheat was ozone tolerant, with no effect on total seed head biomass (-1%) and only a 5% reduction in 1000 grain weight under high ozone levels. The potential use of synthetic wheat in breeding ozone tolerant wheat is discussed.

Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions

Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms. Knowledge about the geographical origins of these crops and the genes responsible for domestication traits largely pre-dates the era of next-generation sequencing, although sequencing will lead to new insights. Molecular markers were initially used to calculate distance (relatedness), genetic diversity and to generate genetic maps which were useful in cloning major domestication genes. Both crops are characterized by large, complex genomes which were long thought to be beyond the scope of whole-genome sequencing. However, advances in sequencing technologies have improved the state of genomic resources for both wheat and barley. The availability of reference genomes for wheat and some of its progenitors, as well as for barley, sets the stage for answering unresolved questions in domestication genomics of wheat and barley.

RNA Sequencing-Based Bulked Segregant Analysis Facilitates Efficient D-genome Marker Development for a Specific Chromosomal Region of Synthetic Hexaploid Wheat

Common wheat originated from interspecific hybridization between cultivated tetraploid wheat and its wild diploid relative Aegilops tauschii followed by amphidiploidization. This evolutionary process can be reproduced artificially, resulting in synthetic hexaploid wheat lines. Here we performed RNA sequencing (RNA-seq)-based bulked segregant analysis (BSA) using a bi-parental mapping population of two synthetic hexaploid wheat lines that shared identical A and B genomes but included with D-genomes of distinct origins. This analysis permitted identification of D-genome-specific polymorphisms around the Net2 gene, a causative locus to hybrid necrosis. The resulting single nucleotide polymorphisms (SNPs) were classified into homoeologous polymorphisms and D-genome allelic variations, based on the RNA-seq results of a parental tetraploid and two Ae. tauschii accessions. The difference in allele frequency at the D-genome-specific SNP sites between the contrasting bulks (ΔSNP-index) was higher on the target chromosome than on the other chromosomes. Several SNPs with the highest ΔSNP-indices were converted into molecular markers and assigned to the Net2 chromosomal region. These results indicated that RNA-seq-based BSA can be applied efficiently to a synthetic hexaploid wheat population to permit molecular marker development in a specific chromosomal region of the D genome.