Genome plasticity a key factor in the success of polyploid wheat under domestication

Transposable elements drive the subgenomic divergence of homoeologous genes to shape wheat domestication and improvement

Polyploidization is a fundamental evolutionary process in plants, including bread wheat. In the present study, we performed a comprehensive genome-wide analysis of dynamic homoeologous gene divergence in Aikang58 (AK58), a modern elite polyploid wheat cultivar with a recently released reference genome, and in other wheat genomes, including landraces, synthetic wheat, and several breeding lines. Over 40% of transposable element (TE) families exhibit biased distribution across the three wheat subgenomes. Approximately 95.0% (113 421) of genes are co-located with TEs, and these variable TEs significantly contribute to homoeologous divergence. We found that about 80% of triad homoeologs are divergent due to differences in expression or sub-functionalization. In addition, subgenome divergence potentially promote polyploid wheat domestication and improvement by increasing favorable homoeoallele combinations. Our findings suggest that homoeolog divergence contributes to the adaptation, domestication, and improvement of hexaploid wheat. The contribution of subgenomic divergence to polyploid heterosis is also discussed. This study provides a valuable resource for the investigation of how TEs drive homoeologous divergence during wheat domestication and improvement.

Salinity Tolerance in Wheat: Mechanisms and Breeding Approaches

High salinity and other abiotic stressors severely limit the productivity of wheat (Triticum aestivum L.). Wheat is a moderately salt-tolerant crop, and its salinity tolerance has been extensively studied due to the fact that it is one of the most essential food crops. It is essential to comprehend the mechanisms underlying salinity tolerance and create adaptable wheat types. In this paper, the morphological adaptations in wheat were first introduced under salinity stress, then the main physiological, biochemical and molecular reactions of wheat to salinity stress were summarized in detail. In addition, the advances in breeding approaches to salinity tolerance in wheat through germplasm evaluation, screening and gene editing were generally reviewed. Finally, proposals for further research or possible challenges in this process were also discussed. Our review will provide references for improving salt tolerance of wheat and for breeding salt-tolerant varieties.

Aegilops tauschii genome assembly v6.0 with improved sequence contiguity differentiates assembly errors from genuine differences with the D subgenome of Chinese Spring wheat assembly IWGSC RefSeq v2.1

Aegilops tauschii is the donor of the D subgenome of hexaploid wheat and a valuable genetic resource for wheat improvement. Several reference-quality genome sequences have been reported for A. tauschii accession AL8/78. A new genome sequence assembly (Aet v6.0) built from long Pacific Biosciences HiFi reads and employing an optical genome map constructed with a new technology is reported here for this accession. The N50 contig length of 31.81 Mb greatly exceeded that of the previous AL8/78 genome sequence assembly (Aet v5.0). Of 1,254 super-scaffolds, 92, comprising 98% of the total super-scaffold length, were anchored on a high-resolution genetic map, and pseudomolecules were assembled. The number of gaps in the pseudomolecules was reduced from 52,910 in Aet v5.0 to 351 in Aet v6.0. Gene models were transferred from the Aet v5.0 assembly into the Aet v6.0 assembly. A total of 40,447 putative orthologous gene pairs were identified between the Aet v6.0 and Chinese Spring wheat IWGSC RefSer v2.1 D-subgenome pseudomolecules. Orthologous gene pairs were used to compare the structure of the A. tauschii and wheat D-subgenome pseudomolecules. A total of 223 structural differences were identified. They included 44 large differences in sequence orientation and 25 differences in sequence location. A technique for discriminating between assembly errors and real structural variation between closely related genomes is suggested.

A Bread Wheat Line with the Substituted Wild Emmer Chromosome 4A Results in Fragment Deletions of Chromosome 4B and Weak Plants

In response to the growing genetic uniformity within wheat populations, developing efficient wheat-alien translocation strategies has become critically important. We observed that several offspring of the common wheat (Triticum aestivum L.)-wild emmer (Triticum turgidum L. var. dicoccoides) chromosome arm substitution line (CASL4AL) exhibited stunted growth, including significantly reduced plant height, spike length, spikelet number, and stem width compared to normal plants. Integrative transcriptomic analyses (RNA-Seq and BSR-Seq) revealed a statistically significant depletion (p < 0.01) of single nucleotide polymorphisms (SNPs) on chromosome 4B in compromised plants. Chromosome association analysis of differentially expressed genes (DEGs, up- or downregulated) revealed that downregulated genes were predominantly located on chromosome 4B. The 1244 downregulated DEGs on Chr4B were employed for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, and RNA metabolic processes, DNA repair, and transport systems were significantly enriched by GO analysis; however, only the mRNA surveillance pathway was enriched by KEGG enrichment. Molecular marker profiling showed a complete absence of target amplification in the critical 0-155 Mb region of chromosome 4B in all weak plants. Pearson's correlation coefficients confirmed significant associations (p < 0.01) between 4B-specific amplification and weak phenotypes. These results demonstrate that 4B segmental deletions drive weak phenotypes in CASL4AL progeny, and provide experimental evidence for chromosome deletions induced in wild emmer chromosome substitution lines. This study highlights the potential of wild emmer as a valuable tool for generating chromosomal variations in wheat breeding programs.

The Q-interacted protein QIP3 recruits TaTPL to regulate spike architecture in wheat

Spike architecture is a critical determinant of grain yield in wheat; yet the regulatory mechanisms remain poorly understood. Here, we demonstrate that the AP2 transcription factor Q directly represses the expression of TaMYB30-6A, a gene associated with spike length in wheat. We further identify QIP3 as a Q-interacting protein harboring an N-terminal EAR motif. Simultaneously, we reveal that QIP3 exhibits transcriptional repression activity, dependent on the EAR motif, and physically interacts with the transcriptional corepressor TaTPL. Importantly, the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-generated qip3-aabbdd mutants exhibit reduced plant height and increased spike length phenotypes. Furthermore, RNA-seq and RT-qPCR assays show that QIP3 negatively regulates the expression of the Q target gene TaMYB30-6A in wheat. Collectively, we propose that the EAR motif-containing QIP3 interacts with Q to regulate spike architecture by recruiting the transcriptional corepressor TaTPL in wheat.

Horizontally acquired CSP genes contribute to wheat adaptation and improvement

Although horizontal gene transfer (HGT) often facilitates environmental adaptation of recipient organisms, whether and how they might affect crop evolution and domestication is unclear. Here we show that three genes encoding cold-shock proteins (CSPs) were transferred from bacteria to Triticeae, a tribe of the grass family that includes several major staple crops such as wheat, barley and rye. The acquired CSP genes in wheat (TaCSPs) are functionally conserved in their bacterial homologues by encoding a nucleic acid-binding protein. Experimental evidence indicates that TaCSP genes positively regulate drought response and improve photosynthetic efficiency under water-deficient conditions by directly targeting a type 1 metallothionein gene to increase reactive oxygen species scavenging, which in turn contributed to the geographic expansion of wheat. We identified an elite CSP haplotype in Aegilops tauschii, introduction of which to wheat significantly increased drought tolerance, photosynthetic efficiency and grain yields. These findings not only provide major insights into the role of HGT in crop adaptation and domestication, but also demonstrate that novel microbial genes introduced through HGT offer a stable and naturally optimized resource for transgenic crop breeding and improvement.

Fine-tuning of heading time by earliness per se effect due to multi-allelic variants in VRN-B3 locus of hexaploid wheat

MAIN CONCLUSION

Wheat VRN-B3 contains multi-allelic variants conferring earliness per se effects and can generate a new allele by recombining multiple alleles, highlighting its importance for the fine-tuning of heading time. Fine-tuning of heading time is required for breeding well-adapted varieties of wheat in regional environments. The VRN-B3 locus, which encodes the FT-B1 gene, is known as a vernalization gene. In this study, we analyzed two alleles in the VRN-B3 region: QHt-7B_Zen of a Japanese variety (Zenkouji-komugi) and QHt-7B_spelt of a spelt wheat strain (st. Rumania). Phenotypic evaluation of near-isogeneic lines (NILs) of 'Chinese Spring' (CS) under long-day (16 h) conditions showed that QHt-7B_Zen and QHt-7B_spelt conferred approximately 3.9 d earlier and 3.0 d later heading time compared with CS, respectively. Differences in heading times among NILs were also observed for fully vernalized plants under long-day conditions, indicating their earliness per se effect. Both QTLs behaved as single genes with incomplete dominant effects, and fine-mapping showed that FT-B1 was responsible for heading time. Droplet digital PCR analysis revealed that QHt-7B_Zen contained three copies of FT-B1, similar to the CS. QHt-7B_spelt had one FT-B1 copy with 14 substitutions, a 15 bp insertion in the 4.8 kb promoter region, and one amino acid substitution in the third exon, which could be designated as a novel allele, Vrn-B3f. Furthermore, a new allele with two FT-B1 copies conferring an intermediate heading time between the parents was created by the recombination of FT-B1 copies of CS and NIL for QHt-7B_spelt. Our findings indicate that fine-tuning heading time is possible through the versatility of the VRN-B3 locus, which can generate multi-allelic variants that have both vernalization and earliness per se effects in wheat.

Transcriptome reveals Gafmt-1 and Gadlc-1-5 play positive roles in cotton resistance to Verticillium wilt

KEY MESSAGE

Both Gafmt-1 and Gadlc-1-5 from Gossypium arboreum respond to Verticillium dahilae infection in Gossypium hirsutum and may play positive roles in Verticillium wilt resistance via the salicylic acid pathway. Verticillium wilt (VW) caused by Verticillium dahliae is one of the most destructive diseases affecting cotton production and quality worldwide. Numerous resistance genes against the disease from tetraploid cultivated cotton (2n = 4x = AADD = 52) have been cloned and functionally analyzed to attempt to develop resistant varieties. However, VW continues to pose a significant threat to global cotton production due to the lack of cost-effective resistance genes to balance resistance and yield. Resistance genes from diploid cotton species such as Gossypium arboreum (2n = 2x = AA = 26) remain largely untapped, and their functions are unknown. Here, a resistant G. hirsutum-G. arboreum introgression line, DM10781, was employed to mine new resistance genes against V. dahliae from the diploid cotton species. We performed time-course transcriptome analysis on the RNA-seq data at 0, 4, 12, 24, 48, and 96 h post-inoculation. Weighted gene co-expression network analysis showed that nine differentially expressed genes (DEGs) caused by disease resistance have been identified. Among them, seven genes were found on the introgression segments from G. arboreum and suffered from virus-induced gene silencing in DM10781. Out of them, two genes were further overexpressing in Arabidopsis. The results indicated the two genes of Gafmt-1 and Gadlc-1-5 played positive roles in both cotton and Arabidopsis. Our study demonstrates that G. arboreum has the resistance genes to VW and can be used in future disease-resistance breeding, providing insights into the resistance of Gafmt-1 and Gadlc-1-5 against VW in cotton.

Phenotypic advantages and improved genomic stability following selection in advanced selfing-generations of Brassica allohexaploids

Allopolyploids often exhibit advantages in vigor and adaptability compared to diploids. A long-term goal in the economically important Brassica genus has been to develop a new allohexaploid crop type (AABBCC) by combining different diploid and allotetraploid crop species. However, early-generation allohexaploids often face challenges like unstable meiosis and low fertility, and the phenotypic performance of these synthetic lines has rarely been assessed. This study analyzes agronomic traits, fertility, and genome stability in ArArBcBcCcCc lines derived from four crosses between B. carinata and B. rapa after 9-11 selfing generations. Our results demonstrate polyploid advantage in vigor and seed traits, considerable phenotypic variation, and high fertility and genome stability. Meanwhile, parental genotypes significantly influence outcomes in advanced allohexaploids. Structural variants, largely resulting from A-C homoeologous exchanges, contribute to genomic variation and influence hexaploid genome stability, with the A sub-genome showing the highest variability. Both positive and negative impacts of SVs on fertility and seed weight are observed. Pseudo-euploids, frequently appearing, do not significantly affect fertility or other agronomic traits compared to euploids, indicating a potential pathway toward a stable allohexaploid species. These findings provide insights into the challenge and potential for developing an adaptable and stable Brassica hexaploid through selection.

Molecular genetic regulation of the vegetative-generative transition in wheat from an environmental perspective

The key to the wide geographical distribution of wheat is its high adaptability. One of the most commonly used methods for studying adaptation is investigation of the transition between the vegetative-generative phase and the subsequent intensive stem elongation process. These processes are determined largely by changes in ambient temperature, the diurnal and annual periodicity of daylength, and the composition of the light spectrum. Many genes are involved in the perception of external environmental signals, forming a complex network of interconnections that are then integrated by a few integrator genes. This hierarchical cascade system ensures the precise occurrence of the developmental stages that enable maximum productivity. This review presents the interrelationship of molecular-genetic pathways (Earliness per se, circadian/photoperiod length, vernalization - cold requirement, phytohormonal - gibberellic acid, light perception, ambient temperature perception and ageing - miRNA) responsible for environmental adaptation in wheat. Detailed molecular genetic mapping of wheat adaptability will allow breeders to incorporate new alleles that will create varieties best adapted to local environmental conditions.

Natural variation in TaERF-A1 confers semi-dwarf and lodging-resistant plant architecture in wheat

The introduction of Reduced height (Rht) genes into wheat varieties has been pivotal in developing semi-dwarf plant architectures, significantly improving lodging resistance and harvest indices. Therefore, identifying new Rht gene resources for breeding semi-dwarf wheat cultivars has been a key strategy for ensuring high and stable grain yields since the 1960s. In this study, we report the map-based cloning of TaERF-A1, which encodes an AP2/ERF (APETALA2/ethylene responsive factor) transcription factor that acts as a positive regulator of wheat stem elongation, as a novel gene that regulates plant height and spike length. The natural variant, TaERF-A1JD6, features a Phe (derived from 'Nongda3338') to Ser (derived from 'Jingdong6') substitution at position 178, which significantly reduces the stability of the TaERF-A1 protein. This substitution leads to partially attenuated transcriptional activation of downstream target genes, including TaPIF4 (Triticum aestivum Phytochrome Interacting Factor 4), thereby restricting stem and spike elongation. Importantly, the introgression of the semi-dwarfing allele TaERF-A1JD6 into wheat can significantly enhance lodging resistance, particularly in dense cropping systems. Therefore, our study identifies TaERF-A1JD6 as a new Rht gene resource for breeding semi-dwarf wheat varieties with increased yield stability.

Future of durum wheat research and breeding: Insights from early career researchers

Durum wheat (Triticum turgidum ssp. durum) is globally cultivated for pasta, couscous, and bulgur production. With the changing climate and growing world population, the need to significantly increase durum production to meet the anticipated demand is paramount. This review summarizes recent advancements in durum research, encompassing the exploitation of existing and novel genetic diversity, exploration of potential new diversity sources, breeding for climate-resilient varieties, enhancements in production and management practices, and the utilization of modern technologies in breeding and cultivar development. In comparison to bread wheat (T. aestivum), the durum wheat community and production area are considerably smaller, often comprising many small-family farmers, notably in African and Asian countries. Public breeding programs such as the International Maize and Wheat Improvement Center (CIMMYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA) play a pivotal role in providing new and adapted cultivars for these small-scale growers. We spotlight the contributions of these and others in this review. Additionally, we offer our recommendations on key areas for the durum research community to explore in addressing the challenges posed by climate change while striving to enhance durum production and sustainability. As part of the Wheat Initiative, the Expert Working Group on Durum Wheat Genomics and Breeding recognizes the significance of collaborative efforts in advancing toward a shared objective. We hope the insights presented in this review stimulate future research and deliberations on the trajectory for durum wheat genomics and breeding.

Development and characterization of small translocations between the Pm13 introgression from Aegilops longissima and wheat homoeologous A, B and D chromosomes

BACKGROUND

Wild relatives have substantial impacts on the resistance of wheat to biotic and abiotic stresses. The genetic diversity of these wild varieties can be employed to widen the wheat gene pool by introducing wild allele introgression and genome structure variations. The powdery mildew resistance gene Pm13 was derived from the wheat wild relative species Aegilops longissima (S1S1, 2n = 2x = 14) and was transferred into wheat chromosome 3BS over 30 years. Until recently, it has not been widely used in wheat breeding, possibly because of the linkage drag associated with Pm13 introgression or poor alien segment compensation to 3BS.

RESULTS

In this study, translocations between the Pm13 introgression and wheat homoeologous A, B and D chromosomes were developed by using a wheat ph1b mutant. The 3Sl (3B) substitution line was hybridized with the CS nullisomic-tetrasomic line N3AT3B, and then F1 was hybridized with the CSph1b mutant. Individuals homozygous for the ph1b mutant carrying the alien chromosome 3Sl were identified from the segregating populations via molecular markers and cytological analysis. Whole-arm recombinant translocations T3SlS.3AL and T3SlS.3BL and small recombinant translocations T3SlS-3AS.3AL, T3SlS-3BS.3BL and T3DS-3SlS-3DS.3DL carrying Pm13 introgression were subsequently identified via molecular cytological analysis. Furthermore, 4 disomic T3SlS-3BS.3BL recombinants carrying the homozygous Pm13 introgression were identified. All the translocations were nearly immune to powdery mildew.

CONCLUSIONS

Our results provide novel alien homoeologous Pm13 translocations for improving powdery mildew resistance in wheat and insights into the interactions between different wheat genomes and alien chromosome segments.

Refining polyploid breeding in sweet potato through allele dosage enhancement

Allele dosage plays a key role in the phenotypic variation of polyploids. Here we present a genome-wide variation map of hexaploid sweet potato that captures allele dosage information, constructed from deep sequencing of 294 hexaploid accessions. Genome-wide association studies identified quantitative trait loci with dosage effects on 23 agronomic traits. Our analyses reveal that sweet potato breeding has progressively increased the dosage of favourable alleles to enhance trait performance. Notably, the Mesoamerican gene pool has evolved towards higher dosages of favourable alleles at multiple loci, which have been increasingly introgressed into modern Chinese cultivars. We substantiated the breeding-driven dosage accumulation through transgenic validation of IbEXPA4, an expansin gene influencing tuberous root weight. In addition, we explored causative sequence variations that alter the expression of the Orange gene, which regulates flesh colour. Our findings illuminate the breeding history of sweet potato and establish a foundation for leveraging allele dosages in polyploid breeding practices.

A gain-of-function mutation at the C-terminus of FT-D1 promotes heading by interacting with 14-3-3A and FDL6 in wheat

Vernalization and photoperiod pathways converging at FT1 control the transition to flowering in wheat. Here, we identified a gain-of-function mutation in FT-D1 that results in earlier heading date (HD), and shorter plant height and spike length in the gamma ray-induced eh1 wheat mutant. Knockout of the wild-type and overexpression of the mutated FT-D1 indicate that both alleles are functional to affect HD and plant height. Protein interaction assays demonstrated that the frameshift mutation in FT-D1eh1 exon 3 led to gain-of-function interactions with 14-3-3A and FDL6, thereby enabling the formation of florigen activation complex (FAC) and consequently activating a flowering-related transcriptomic programme. This mutation did not affect FT-D1eh1 interactions with TaNaKR5 or TaFTIP7, both of which could modulate HD, potentially via mediating FT-D1 translocation to the shoot apical meristem. Furthermore, the 'Segment B' external loop is essential for FT-D1 interaction with FDL6, while residue Y85 is required for interactions with TaNaKR5 and TaFTIP7. Finally, the flowering regulatory hub gene, ELF5, was identified as the FT-D1 regulatory target. This study illustrates FT-D1 function in determining wheat HD with a suite of interaction partners and provides genetic resources for tuning HD in elite wheat lines.

On the evolution and genetic diversity of the bread wheat D genome

Bread wheat (Triticum aestivum) became a globally dominant crop after incorporating the D genome from the donor species Aegilops tauschii, but the evolutionary history that shaped the D genome during this process remains to be clarified. Here, we propose a renewed evolutionary model linking Ae. tauschii and the hexaploid wheat D genome by constructing an ancestral haplotype map covering 762 Ae. tauschii and hexaploid wheat accessions. We dissected the evolutionary trajectories of Ae. tauschii lineages and reported a few independent intermediate accessions, demonstrating that low-frequency inter-sublineage gene flow had enriched the diversity of Ae. tauschii. We discovered that the D genome of hexaploid wheat was inherited from a unified ancestral template, but with a mosaic composition that was highly mixed and derived mainly from three Ae. tauschii L2 sublineages located in the Caspian coastal region. This result suggests that early agricultural activities facilitated innovations in D-genome composition and finalized the success of hexaploidization. We found that the majority (51.4%) of genetic diversity was attributed to novel mutations absent in Ae. tauschii, and we identified large Ae. tauschii introgressions from various lineages, which expanded the diversity of the wheat D genome and introduced beneficial alleles. This work sheds light on the process of wheat hexaploidization and highlights the evolutionary significance of the multi-layered genetic diversity of the bread wheat D genome.

Decrease in purifying selection pressures on wheat homoeologous genes: tetraploidization versus hexaploidization

A series of polyploidizations in higher-order polyploids is the main event affecting gene content in a genome. Each polyploidization event can lead to massive functional divergence because of the subsequent decrease in selection pressure on duplicated genes; however, the causal relationship between multiple rounds of polyploidization and the functional divergence of duplicated genes is poorly understood. We focused on the Triticum-Aegilops complex lineage and compared selection pressure before and after tetraploidization and hexaploidization events. Although both events led to decreased selection pressure on homoeologous gene pairs (compared with diploids and tetraploids), the initial tetraploidization had a greater impact on selection pressure on homoeologous gene pairs than did subsequent hexaploidization. Consistent with this, selection pressure on expression patterns for the initial event relaxed more than those for the subsequent event. Surprisingly, the decreased selection pressure on these homoeologous genes was independent of the existence of in-paralogs within the same subgenome. Wheat homoeologous pairs had different evolutionary consequences compared with orthologs related to other mechanisms (ancient allopolyploidization, ancient autopolyploidization, and small-scale duplication). Furthermore, tetraploidization and hexaploidization also seemed to have different evolutionary consequences. This suggests that homoeologous genes retain unique functions, including functions that are unlikely to be preserved in genes generated by the other duplication mechanisms. We found that their unique functions differed between tetraploidization and hexaploidization (e.g., reproductive and chromosome segregation processes). These findings imply that the substantial number of gene pairs resulting from multiple allopolyploidization events, especially initial tetraploidization, may have been a unique source of functional divergence.

Cytogenetic features of intergeneric amphydiploids and genome-substituted forms of wheat

Synthetic intergeneric amphydiploids and genome-substituted wheat forms are an important source for transferring agronomically valuable genes from wild species into the common wheat (Triticum aestivum L.) genome. They can be used both in academic research and for breeding purposes as an original material for developing wheat-alien addition and substitution lines followed by translocation induction with the aid of irradiation or nonhomologous chromosome pairing. The chromosome sets and genome constitutions of allopolyploids are usually verified in early hybrid generations, whereas the subsequent fate of these hybrids remains unknown in most cases. Here we analyze karyotypes of five hexa- (2n = 6x = 42) and octoploid (2n = 8x = 56) amphydiploids of wheat with several species of the Aegilops, Haynaldia, and Hordeum genera, and six genome-substituted wheat-Aegilops forms, which were developed over 40 years ago and have been maintained in different gene banks. The analyses involve C-banding and fluorescence in situ hybridization (FISH) with pAs1 and pSc119.2 probes. We have found that most accessions are cytologically stable except for Avrodes (genome BBAASS, a hexaploid genome-substituted hybrid of wheat and Aegilops speltoides), which segregated with respect to chromosome composition after numerous reproductions. Chromosome analysis has not confirmed the presence of the N genome from Ae. uniaristata Vis. in the genome-substituted hybrid Avrotata. Instead, Avrotata carries the D genome. Our study shows that octoploid hybrids, namely AD 7, AD 7147 undergo more complex genome reorganizations as compared to hexaploids: the chromosome number of two presumably octoploid wheat-Aegilops hybrids were reduced to the hexaploid level. Genomes of both forms lost seven chromosome pairs, which represented seven homoeologous groups and derived from different parental subgenomes. Thus, each of the resulting hexaploids carries a synthetic/hybrid genome consisting of a unique combination of chromosomes belonging to different parental subgenomes.

Natural alleles of LEAFY and WAPO1 interact to regulate spikelet number per spike in wheat

KEY MESSAGE

Specific combinations of LFY and WAPO1 natural alleles maximize spikelet number per spike in wheat. Spikelet number per spike (SNS) is an important yield component in wheat that determines the maximum number of grains that can be formed in a wheat spike. In wheat, loss-of-function mutations in LEAFY (LFY) or its interacting protein WHEAT ORTHOLOG OF APO1 (WAPO1) significantly reduce SNS by reducing the rate of formation of spikelet meristems. In previous studies, we identified a natural amino acid change in WAPO1 (C47F) that significantly increases SNS in hexaploid wheat. In this study, we searched for natural variants in LFY that were associated with differences in SNS and detected significant effects in the LFY-B region in a nested association mapping population. We generated a large mapping population and confirmed that the LFY-B polymorphism R80S is linked with the differences in SNS, suggesting that LFY-B is the likely causal gene. A haplotype analysis revealed two amino acid changes P34L and R80S, which were both enriched during wheat domestication and breeding suggesting positive selection. We also explored the interactions between the LFY and WAPO1 natural variants for SNS using biparental populations and identified significant interaction, in which the positive effect of the 80S and 34L alleles from LFY-B was only detected in the WAPO-A1 47F background but not in the 47C background. Based on these results, we propose that the allele combination WAPO-A1-47F/LFY-B 34L 80S can be used in wheat breeding programs to maximize SNS and increase grain yield potential in wheat.

Aphidicidal activity of nano-emulsions of spearmint oil and carvone against Rhopalosiphum maidis and Sitobion avenae

Different species of aphids, responsible for severe yield losses of cereal crops including wheat, (Triticum aestivum L.) are managed by insecticides, which are harmful to organisms and the environment under field conditions. Therefore, an environment friendly aphidicidal product of plant origin is required. Mentha spicata oil was found to be rich in carvone (81.88%), but the use of its oil and carvone in crop protection is lacking due to their volatility, poor solubility, and stability. A nanoformulaton not only solves these problems but also improve the efficacy and dose of the bioactive compounds. Thus, nano-emulsions of the oil and carvone prepared were characterized, and evaluated against Rhopalosiphum maidis (corn aphid) and Sitobion avenae (wheat aphid) The average droplet size of nano-emulsions of the oil and carvone was found to be 22.1 and 41.21 nm. Nano-emulsion of carvone exhibited higher aphid mortality (LC50 = 0.87-1.94 mg/mL) at 24 h and acetylcholinesterase inhibitory activity (IC50 = 0.07-3.83 mg/mL) compared to the nano-emulsion of the oil (LC50 = 2.87-2.81 mg/mL; IC50 = 1.66-5.34 mg/mL). The repellence index (RI) in nano-emulsion of essential oil was found to be higher (84.73 and 81.72%) at the highest concentration (0.05 µL/cm2) than that of carvone (77.59 and 80.98%) for R. maidis and S. avenae. Further, in silico studies also revealed the favourable binding energy (- 6.6 to - 8.5 kcal/mol) of the main compounds in the oil with acetylcholinesterase, facilitated by hydrophobic interactions and hydrogen bonding. This study suggests that the nano-emulsions of the essential oil and carvone can be explored under field conditions to establish efficacy for their utilization as aphidicidal and repellent products against aphids. In the present study, aphidicial and repellent activities of its essential oil and carvone were reported for the first time against R.maidis and S.avenae.

The first assessment of grain yield and associated traits in durum wheat across a decade in Nepal

Rapid urbanization and evolving dietary preferences have heightened the demand for durum wheat and its derivatives in developing nations like Nepal. This study represents the first comprehensive exploration and evaluation of durum wheat genotypes in Nepal, addressing the escalating need for high-yielding varieties. The primary objective was to identify stable and prolific durum wheat lines for release, enhancing Nepal's durum wheat breeding program. Utilizing genotypes from CIMMYT's disease screening and yield nurseries from 2011/12 to 2020/21, a total of 132 genotypes, including international checks, underwent evaluation over ten years under the Alpha Lattice design. Results revealed significant variation among genotypes for grain yield and other traits, identifying high-yielding and stable lines suitable for Nepal. Heritability analysis highlighted moderate heritability for grain number per spike, thousand-grain weight, and grain yield. Cluster analysis identified distinct clusters with high grain yield and desirable agronomic traits. Disease incidence facilitated the selection of resistant lines, with DWK38 emerging as the highest grain yielder (4416.04 kg/ha). Overall, durum wheat lines from CIMMYT exhibited robust performance in Nepal, enabling the identification of superior lines with potential benefits for farmers and consumers. The study's implications include developing and releasing superior durum lines in Nepal, providing farmers with profitable alternatives amidst evolving food habits. In conclusion, the findings from this study provide a valuable foundation for future durum wheat breeding efforts in Nepal, guiding the selection of genotypes that are well-suited to the diverse environmental challenges of the region.

One Hundred Years of Progress and Pitfalls: Maximising Heterosis through Increasing Multi-Locus Nuclear Heterozygosity

The improvement in quantitative traits (e.g., yield, size) in F1 offspring over parent lines is described as hybrid vigour, or heterosis. There exists a fascinating relationship between parental genetic distance and genome dosage (polyploidy), and heterosis effects. The contribution of nuclear heterozygosity to heterosis is not uniform across diploid and polyploid crops, even within same species, thus demonstrating that polyploid crops should be part of any discussion on the mechanisms of heterosis. This review examines the records of correlating heterosis with parental genetic distance and the influence of adding supplementary genomes in wide crosses. Increasing nuclear heterozygosity through parental genetic distance has been shown to be an imperfect predictor for heterosis in a variety of commercial crops such as maize, rice, and pepper. However, increasing the ploidy level raises the maximum number of alleles that can be harboured at any one locus, and studies on crops such as oilseed rape, potato, alfalfa, maize, and rice have demonstrated that heterosis may be maximised upon increasing multi-locus nuclear heterozygosity. The novel heterotic phenotypes observed above the diploid level will contribute to our understanding on the mechanisms of heterosis and aid plant breeders in achieving the righteous goal of producing more food with fewer inputs.

Genome-wide identification of the E-class gene family in wheat: evolution, expression, and interaction

Introduction

Wheat (Triticum aestivum L.) is among themost important crop worldwide. Given a growing population and changing climate, enhancing wheat yield is of great importance. Yield is closely associated with flower and spike development, and E-class genes play important roles in the flower and kernel development of plants. Currently, the absence of systematic analysis on the E gene family hinders our comprehension of their roles in plant growth and development.

Methods

Identify E-class genes based on homologous sequence searches. Analyze the identified E-class genes through a series of gene family analyses. Determine the expression levels of wheat E-class genes by searching public databases. Validate the functions of these genes by transforming them into Arabidopsis. Finally, determine the interactions between the genes through yeast two-hybrid experiments.

Results

Fifteen E-class genes (TaEs) were identified in common wheat. Nine E-class genes were detected in five ancestral/closely related species, including one in Aegilops tauschii (AtE), one in T. Urartu (TuEs), two in T. turgidum (TtEs), two in T. dicoccoides (TdEs), and three in T. spelta (TsEs). The 24 E-class genes were classified into three subgroups using a phylogenetic approach. All genes were highly expressed in spikes, and most were only highly expressed at the floret meristem stage. The effects of TaSEP5-A on flowering and growth cycles were confirmed in homologous mutants and transgenic Arabidopsis thaliana. The E-class genes were able to regulate the growth cycle of Arabidopsis. Finally, we confirmed the interactions between TaSEP5-A and other wheat E-class genes based on yeast two-hybrid assays.

Discussion

Our findings provide information regarding the E-class genes in wheat and will potentially promote the application of these genes in wheat improvement.

Potential of tetraploid wheats in plant breeding: A review

Domestication syndrome, selection pressure, and modern plant breeding programs have reduced the genetic diversity of the wheat germplasm. For the genetic gains of breeding programs to be sustainable, plant breeders require a diverse gene pool to select genes for resistance to biotic stress factors, tolerance to abiotic stress factors, and improved quality and yield components. Thus, old landraces, subspecies and wild ancestors are rich sources of genetic diversity that have not yet been fully exploited, and it is possible to utilize this diversity. Compared with durum wheat, tetraploid wheat subspecies have retained much greater genetic diversity despite genetic drift and various environmental influences, and the identification and utilization of this diversity can make a greater contribution to the genetic enrichment of wheat. In addition, using the pre-breeding method, the valuable left-behind alleles in the wheat gene pool can be re-introduced through hybridization and introgressive gene flow to create a sustainable opportunity for the genetic gain of wheat. This review provides some insights about the potential of tetraploid wheats in plant breeding and the genetic gains made by them in plant breeding across past decades, and gathers the known functional information on genes/QTLs, metabolites, traits and their direct involvement in wheat resistance/tolerance to biotic/abiotic stresses.

Origin and evolution of the bread wheat D genome

Bread wheat (Triticum aestivum) is a globally dominant crop and major source of calories and proteins for the human diet. Compared with its wild ancestors, modern bread wheat shows lower genetic diversity, caused by polyploidisation, domestication and breeding bottlenecks1,2. Wild wheat relatives represent genetic reservoirs, and harbour diversity and beneficial alleles that have not been incorporated into bread wheat. Here we establish and analyse extensive genome resources for Tausch's goatgrass (Aegilops tauschii), the donor of the bread wheat D genome. Our analysis of 46 Ae. tauschii genomes enabled us to clone a disease resistance gene and perform haplotype analysis across a complex disease resistance locus, allowing us to discern alleles from paralogous gene copies. We also reveal the complex genetic composition and history of the bread wheat D genome, which involves contributions from genetically and geographically discrete Ae. tauschii subpopulations. Together, our results reveal the complex history of the bread wheat D genome and demonstrate the potential of wild relatives in crop improvement.

Quantitative Trait Loci Mapping of Heading Date in Wheat under Phosphorus Stress Conditions

Wheat (Triticum aestivum L.) is a crucial cereal crop, contributing around 20% of global caloric intake. However, challenges such as diminishing arable land, water shortages, and climate change threaten wheat production, making yield enhancement crucial for global food security. The heading date (HD) is a critical factor influencing wheat's growth cycle, harvest timing, climate adaptability, and yield. Understanding the genetic determinants of HD is essential for developing high-yield and stable wheat varieties. This study used a doubled haploid (DH) population from a cross between Jinmai 47 and Jinmai 84. QTL analysis of HD was performed under three phosphorus (P) treatments (low, medium, and normal) across six environments, using Wheat15K high-density SNP technology. The study identified 39 QTLs for HD, distributed across ten chromosomes, accounting for 2.39% to 29.52% of the phenotypic variance. Notably, five stable and major QTLs (Qhd.saw-3A.7, Qhd.saw-3A.8, Qhd.saw-3A.9, Qhd.saw-4A.4, and Qhd.saw-4D.3) were consistently detected across varying P conditions. The additive effects of these major QTLs showed that favorable alleles significantly delayed HD. There was a clear trend of increasing HD delay as the number of favorable alleles increased. Among them, Qhd.saw-3A.8, Qhd.saw-3A.9, and Qhd.saw-4D.3 were identified as novel QTLs with no prior reports of HD QTLs/genes in their respective intervals. Candidate gene analysis highlighted seven highly expressed genes related to Ca2+ transport, hormone signaling, glycosylation, and zinc finger proteins, likely involved in HD regulation. This research elucidates the genetic basis of wheat HD under P stress, providing critical insights for breeding high-yield, stable wheat varieties suited to low-P environments.

Genome-wide characterization and expression analysis of the CINNAMYL ALCOHOL DEHYDROGENASE gene family in Triticum aestivum

BACKGROUND

CINNAMYL ALCOHOL DEHYDROGENASE (CAD) catalyzes the NADPH-dependent reduction of cinnamaldehydes into cinnamyl alcohols and is a key enzyme found at the final step of the monolignol pathway. Cinnamyl alcohols and their conjugates are subsequently polymerized in the secondary cell wall to form lignin. CAD genes are typically encoded by multi-gene families and thus traditionally organized into general classifications of functional relevance.

RESULTS

In silico analysis of the hexaploid Triticum aestivum genome revealed 47 high confidence TaCAD copies, of which three were determined to be the most significant isoforms (class I) considered bone fide CADs. Class I CADs were expressed throughout development both in RNAseq data sets as well as via qRT-PCR analysis. Of the 37 class II TaCADs identified, two groups were observed to be significantly co-expressed with class I TaCADs in developing tissue and under chitin elicitation in RNAseq data sets. These co-expressed class II TaCADs were also found to be phylogenetically unrelated to a separate clade of class II TaCADs previously reported to be an influential resistance factor to pathogenic fungal infection. Lastly, two groups were phylogenetically identified as class III TaCADs, which possess distinct conserved gene structures. However, the lack of data supporting their catalytic activity for cinnamaldehydes and their bereft transcriptional presence in lignifying tissues challenges their designation and function as CADs.

CONCLUSIONS

Taken together, our comprehensive transcriptomic analyses suggest that TaCAD genes contribute to overlapping but nonredundant functions during T. aestivum growth and development across a wide variety of agroecosystems and provide tolerance to various stressors.

Genome Resequencing for Autotetraploid Rice and Its Closest Relatives Reveals Abundant Variation and High Potential in Rice Breeding

Polyploid rice and its reverted diploid show rich phenotypic variation and strong heterosis, showing great breeding value. However, the genomic differences among tetraploids, counterpart common diploids, tetraploid-revertant diploids, and hybrid descendants are unclear. In this work, we bred a new excellent two-line hybrid rice variety, Y Liang You Duo Hui 14 (HTRM12), using Haitian tetraploid self-reverted diploid (HTRM2). Furthermore, we comparatively analyzed the important agronomic traits and genome-wide variations of those closest relatives, Haitian diploid (HT2), Haitian tetraploid (HT4), HTRM2, and HTRM12 in detail, based on multiple phenotypic investigations, genome resequencing, and bioinformatics analysis. The results of agronomic traits analysis and genome-wide variation analysis of single nucleotide polymorphism (SNP), insertion-deletion (InDel), and copy number variation (CNV) show that HT4 and HTRM2 had abundant phenotypic and genomic variations compared to HT2. HTRM2 can inherit important traits and variations from HT4. This implies that tetraploid self-reverted diploid has high potential in creating excellent breeding materials and in breeding breakthrough hybrid rice varieties. Our study verifies the feasibility that polyploid rice could be used as a mutation carrier for creating variations and provides genomic information, new breeding materials, and a new way of application for tetraploid rice breeding.

Chromosome-level genome assemblies reveal genome evolution of an invasive plant Phragmites australis

Biological invasions pose a significant threat to ecosystems, disrupting local biodiversity and ecosystem functions. The genomic underpinnings of invasiveness, however, are still largely unknown, making it difficult to predict and manage invasive species effectively. The common reed (Phragmites australis) is a dominant grass species in wetland ecosystems and has become particularly invasive when transferred from Europe to North America. Here, we present a high-quality gap-free, telomere-to-telomere genome assembly of Phragmites australis consisting of 24 pseudochromosomes and a B chromosome. Fully phased subgenomes demonstrated considerable subgenome dominance and revealed the divergence of diploid progenitors approximately 30.9 million years ago. Comparative genomics using chromosome-level scaffolds for three other lineages and a previously published draft genome assembly of an invasive lineage revealed that gene family expansions in the form of tandem duplications may have contributed to the invasiveness of the lineage. This study sheds light on the genome evolution of Arundinoideae grasses and suggests that genetic drivers, such as gene family expansions and tandem duplications, may underly the processes of biological invasion in plants. These findings provide a crucial step toward understanding and managing the genetic basis of invasiveness in plant species.

Wild grass-derived alleles represent a genetic architecture for the resilience of modern common wheat to stresses

This review explores the integration of wild grass-derived alleles into modern bread wheat breeding to tackle the challenges of climate change and increasing food demand. With a focus on synthetic hexaploid wheat, this review highlights the potential of genetic variability in wheat wild relatives, particularly Aegilops tauschii, for improving resilience to multifactorial stresses like drought, heat, and salinity. The evolutionary journey of wheat (Triticum spp.) from diploid to hexaploid species is examined, revealing significant genetic contributions from wild grasses. We also emphasize the importance of understanding incomplete lineage sorting in the genomic evolution of wheat. Grasping this information is crucial as it can guide breeders in selecting the appropriate alleles from the gene pool of wild relatives to incorporate into modern wheat varieties. This approach improves the precision of phylogenetic relationships and increases the overall effectiveness of breeding strategies. This review also addresses the challenges in utilizing the wheat wild genetic resources, such as the linkage drag and cross-compatibility issues. Finally, we culminate the review with future perspectives, advocating for a combined approach of high-throughput phenotyping tools and advanced genomic techniques to comprehensively understand the genetic and regulatory architectures of wheat under stress conditions, paving the way for more precise and efficient breeding strategies.

Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge-A Transcriptomics Perspective

Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, a significant evolutionary process in the plant kingdom. Transcriptomic analysis provides invaluable insights into allopolyploid plants by elucidating the fate of duplicated genes, revealing evolutionary novelties and uncovering their environmental adaptations. By examining gene expression profiles, scientists can discern how duplicated genes have evolved to acquire new functions or regulatory roles. This process often leads to the development of novel traits and adaptive strategies that allopolyploid plants leverage to thrive in diverse ecological niches. Understanding these molecular mechanisms not only enhances our appreciation of the genetic complexity underlying allopolyploidy but also underscores their importance in agriculture and ecosystem resilience. However, transcriptome profiling is challenging due to genomic redundancy, which is further complicated by the presence of multiple chromosomes sets and the variations among homoeologs and allelic genes. Prior to transcriptome analysis, sub-genome phasing and homoeology inference are essential for obtaining a comprehensive view of gene expression. This review aims to clarify the terminology in this field, identify the most challenging aspects of transcriptome analysis, explain their inherent difficulties, and suggest reliable analytic strategies. Furthermore, bulk RNA-seq is highlighted as a primary method for studying allopolyploid gene expression, focusing on critical steps like read mapping and normalization in differential gene expression analysis. This approach effectively captures gene expression from both parental genomes, facilitating a comprehensive analysis of their combined profiles. Its sensitivity in detecting low-abundance transcripts allows for subtle differences between parental genomes to be identified, crucial for understanding regulatory dynamics and gene expression balance in allopolyploids.

Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing

BACKGROUND

The massive structural variations and frequent introgression highly contribute to the genetic diversity of wheat, while the huge and complex genome of polyploid wheat hinders efficient genotyping of abundant varieties towards accurate identification, management, and exploitation of germplasm resources.

RESULTS

We develop a novel workflow that identifies 1240 high-quality large copy number variation blocks (CNVb) in wheat at the pan-genome level, demonstrating that CNVb can serve as an ideal DNA fingerprinting marker for discriminating massive varieties, with the accuracy validated by PCR assay. We then construct a digitalized genotyping CNVb map across 1599 global wheat accessions. Key CNVb markers are linked with trait-associated introgressions, such as the 1RS·1BL translocation and 2NvS translocation, and the beneficial alleles, such as the end-use quality allele Glu-D1d (Dx5 + Dy10) and the semi-dwarf r-e-z allele. Furthermore, we demonstrate that these tagged CNVb markers promote a stable and cost-effective strategy for evaluating wheat germplasm resources with ultra-low-coverage sequencing data, competing with SNP array for applications such as evaluating new varieties, efficient management of collections in gene banks, and describing wheat germplasm resources in a digitalized manner. We also develop a user-friendly interactive platform, WheatCNVb ( http://wheat.cau.edu.cn/WheatCNVb/ ), for exploring the CNVb profiles over ever-increasing wheat accessions, and also propose a QR-code-like representation of individual digital CNVb fingerprint. This platform also allows uploading new CNVb profiles for comparison with stored varieties.

CONCLUSIONS

The CNVb-based approach provides a low-cost and high-throughput genotyping strategy for enabling digitalized wheat germplasm management and modern breeding with precise and practical decision-making.

Q negatively regulates wheat salt tolerance through directly repressing the expression of TaSOS1 and reactive oxygen species scavenging genes

The Q transcription factor plays important roles in improving multiple wheat domestication traits such as spike architecture, threshability and rachis fragility. However, whether and how it regulates abiotic stress adaptation remain unclear. We found that the transcriptional expression of Q can be induced by NaCl and abscisic acid treatments. Using the q mutants generated by CRISPR/Cas9 and Q overexpression transgenic lines, we showed that the domesticated Q gene causes a penalty in wheat salt tolerance. Then, we demonstrated that Q directly represses the transcription of TaSOS1-3B and reactive oxygen species (ROS) scavenging genes to regulate Na+ and ROS homeostasis in wheat. Furthermore, we showed that wheat salt tolerance protein TaWD40 interacts with Q to competitively interfere with the interaction between Q and the transcriptional co-repressor TaTPL. Taken together, our findings reveal that Q directly represses the expression of TaSOS1 and some ROS scavenging genes, thus causing a harmful effect on wheat salt tolerance.

Molecular genetic diversity and linkage disequilibrium structure of the Egyptian faba bean using Single Primer Enrichment Technology (SPET)

Faba bean is an important legume crop. The genetic diversity among faba bean genotypes is very important for the genetic improvement of target traits. A set of 128 fab bean genotypes that are originally from Egypt were used in this study to investigate the genetic diversity and population structure. The 128 genotypes were genotyped using the Single Primer Enrichment Technology (SPET) by which a set of 6759 SNP markers were generated after filtration. The SNP markers were distributed on all chromosomes with a range extending from 822 (Chr. 6) to 1872 (Chr.1). The SNP markers had wide ranges of polymorphic information content (PIC), gene diversity (GD), and minor allele frequency. The analysis of population structure divided the Egyptian faba bean population into five subpopulations. Considerable genetic distance was found among all genotypes, ranging from 0.1 to 0.4. The highly divergent genotype was highlighted in this study and the genetic distance among genotypes ranged from 0.1 and 0.6. Moreover, the structure of linkage disequilibrium was studied, and the analysis revealed a low level of LD in the Egyptian faba bean population. A slow LD decay at the genomic and chromosomal levels was observed. Interestingly, the distribution of haplotype blocks was presented in each chromosome and the number of haplotype block ranged from 65 (Chr. 4) to 156 (Chr. 1). Migration and genetic drift are the main reasons for the low LD in the Egyptian faba bean population. The results of this study shed light on the possibility of the genetic improvement of faba bean crop in Egypt and conducting genetic association analyses to identify candidate genes associated with target traits (e.g. protein content, grain yield, etc.) in this panel.

Response of winter wheat genotypes to salinity stress under controlled environments

This study was conducted in controlled environmental conditions to systematically evaluate multi-traits responses of winter wheat (Triticum aestivum L.) genotypes to different salinity levels. Responses were assessed at the germination to early seedling stage (Experiment 1). Seeds of different genotypes (n=292) were subjected to three salinity levels (0 [control], 60, and 120 mM NaCl). Principal Component Analysis (PCA) revealed that among studied traits seedling vigor index (SVI) contributed more towards the diverse response of genotypes to salinity stress. Based on SVI, eight contrasting genotypes assumed to be tolerant (Gage, Guymon, MTS0531, and Tascosa) and susceptible (CO04W320, Carson, TX04M410211) were selected for further physio-biochemical evaluation at the booting stage (Experiment 2) and to monitor grain yield. Higher level of salinity (120 mM NaCl) exposure at the booting stage increased thylakoid membrane damage, lipid peroxidation, sugars, proline, and protein while decreasing photosynthesis, chlorophyll index, starch, and grain yield. Based on grain yield, the assumed magnitude of the genotypic response shown in Experiment 1 was not analogous in Experiment 2. This indicates the necessity of individual screening of genotypes at different sensitive growth stages for identifying true salinity-tolerant and susceptible genotypes at a particular growth stage. However, based on higher grain yield and its least percentage reduction under higher salinity, Guymon and TX04M410211 were identified as tolerant, and Gage and CO04W320 as susceptible at the booting stage, and their biparental population can be used to identify genomic regions for booting stage-specific salinity response.

Genomic prediction of synthetic hexaploid wheat upon tetraploid durum and diploid Aegilops parental pools

Bread wheat (Triticum aestivum L.) is a globally important food crop, which was domesticated about 8-10,000 years ago. Bread wheat is an allopolyploid, and it evolved from two hybridization events of three species. To widen the genetic base in breeding, bread wheat has been re-synthesized by crossing durum wheat (Triticum turgidum ssp. durum) and goat grass (Aegilops tauschii Coss), leading to so-called synthetic hexaploid wheat (SHW). We applied the quantitative genetics tools of "hybrid prediction"-originally developed for the prediction of wheat hybrids generated from different heterotic groups - to a situation of allopolyploidization. Our use-case predicts the phenotypes of SHW for three quantitatively inherited global wheat diseases, namely tan spot (TS), septoria nodorum blotch (SNB), and spot blotch (SB). Our results revealed prediction abilities comparable to studies in 'traditional' elite or hybrid wheat. Prediction abilities were highest using a marker model and performing random cross-validation, predicting the performance of untested SHW (0.483 for SB to 0.730 for TS). When testing parents not necessarily used in SHW, combination prediction abilities were slightly lower (0.378 for SB to 0.718 for TS), yet still promising. Despite the limited phenotypic data, our results provide a general example for predictive models targeting an allopolyploidization event and a method that can guide the use of genetic resources available in gene banks.

Variation in TaSPL6-D confers salinity tolerance in bread wheat by activating TaHKT1;5-D while preserving yield-related traits

Na+ exclusion from above-ground tissues via the Na+-selective transporter HKT1;5 is a major salt-tolerance mechanism in crops. Using the expression genome-wide association study and yeast-one-hybrid screening, we identified TaSPL6-D, a transcriptional suppressor of TaHKT1;5-D in bread wheat. SPL6 also targeted HKT1;5 in rice and Brachypodium. A 47-bp insertion in the first exon of TaSPL6-D resulted in a truncated peptide, TaSPL6-DIn, disrupting TaHKT1;5-D repression exhibited by TaSPL6-DDel. Overexpressing TaSPL6-DDel, but not TaSPL6-DIn, led to inhibited TaHKT1;5-D expression and increased salt sensitivity. Knockout of TaSPL6-DDel in two wheat genotypes enhanced salinity tolerance, which was attenuated by a further TaHKT1;5-D knockdown. Spike development was preserved in Taspl6-dd mutants but not in Taspl6-aabbdd mutants. TaSPL6-DIn was mainly present in landraces, and molecular-assisted introduction of TaSPL6-DIn from a landrace into a leading wheat cultivar successfully improved yield on saline soils. The SPL6-HKT1;5 module offers a target for the molecular breeding of salt-tolerant crops.

Evaluation and Identification of Powdery Mildew Resistance Genes in Aegilops tauschii and Emmer Wheat Accessions

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a serious threat to wheat (Triticum aestivum L.) production. Narrow genetic basis of common wheat boosted the demand for diversified donors against powdery mildew. Aegilops tauschii Coss (2n = 2x = DD) and emmer wheat (2n = 4x = AABB), as the ancestor species of common wheat, are important gene donors for genetic improvement of common wheat. In this study, a total of 71 Ae. tauschii and 161 emmer wheat accessions were first evaluated for their powdery mildew resistance using the Bgt isolate E09. Thirty-three Ae. tauschii (46.5%) and 108 emmer wheat accessions (67.1%) were resistant. Then, all these accessions were tested by the diagnostic markers for 21 known Pm genes. The results showed that Pm2 alleles were detected in all the 71 Ae. tauschii and only Pm4 alleles were detected in 20 of 161 emmer wheat accessions. After haplotype analysis, we identified four Pm4 alleles (Pm4a, Pm4b, Pm4d, and Pm4f) in the emmer wheat accessions and three Pm2 alleles (Pm2d, Pm2e, and Pm2g) in the Ae. tauschii. Further resistance spectrum analysis indicated that these resistance accessions displayed different resistance reactions to different Bgt isolates, implying they may have other Pm genes apart from Pm2 and/or Pm4 alleles. Notably, a new Pm2 allele, Pm2S, was identified in Ae. tauschii, which contained a 64-bp deletion in the first exon and formed a new termination site at the 513th triplet of the shifted reading frame compared with reported Pm2 alleles. The phylogenetic tree of Pm2S showed that the kinship of Pm2S was close to Pm2h. To efficiently and accurately detect Pm2S and distinguish with other Pm2 alleles in Ae. tauschii background, a diagnostic marker, YTU-QS-3, was developed, and its effectiveness was verified. This study provided valuable Pm alleles and enriched the genetic diversity of the powdery mildew resistance in wheat improvement.

Genome-wide scanning to identify and validate single nucleotide polymorphism markers associated with drought tolerance in spring wheat seedlings

Unlike other growth stages of wheat, very few studies on drought tolerance have been done at the seedling stage, and this is due to the complexity and sensitivity of this stage to drought stress resulting from climate change. As a result, the drought tolerance of wheat seedlings is poorly understood and very few genes associated with drought tolerance at this stage were identified. To address this challenge, a set of 172 spring wheat genotypes representing 20 different countries was evaluated under drought stress at the seedling stage. Drought stress was applied on all tested genotypes by water withholding for 13 days. Two types of traits, namely morphological and physiological traits were scored on the leaves of all tested genotypes. Genome-wide association study (GWAS) is one of the effective genetic analysis methods that was used to identify target single nucleotide polymorphism (SNP) markers and candidate genes for later use in marker-assisted selection. The tested plant materials were genotyped using 25k Infinium iSelect array (25K) (herein after it will be identified as 25K) (for 172 genotypes) and genotyping-by-sequencing (GBS) (for 103 genotypes), respectively. The results of genotyping revealed 21,093 25K and 11,362 GBS-SNPs, which were used to perform GWAS analysis for all scored traits. The results of GWAS revealed that 131 and 55 significant SNPs were controlling morphological and physiological traits, respectively. Moreover, a total of eight and seven SNP markers were found to be associated with more than one morphological and physiological trait under drought stress, respectively. Remarkably, 10 significant SNPs found in this study were previously reported for their association with drought tolerance in wheat. Out of the 10 validated SNP markers, four SNPs were associated with drought at the seedling stage, while the remaining six SNPs were associated with drought stress at the reproductive stage. Moreover, the results of gene enrichment revealed 18 and six pathways as highly significant biological and molecular pathways, respectively. The selection based on drought-tolerant alleles revealed 15 genotypes with the highest number of different drought-tolerant alleles. These genotypes can be used as candidate parents in future breeding programs to produce highly drought-tolerant genotypes with high genetic diversity. Our findings in this study provide novel markers and useful information on the genetic basis of drought tolerance at early growth stages.

Are cereal grasses a single genetic system?

In 1993, a passionate and provocative call to arms urged cereal researchers to consider the taxon they study as a single genetic system and collaborate with each other. Since then, that group of scientists has seen their discipline blossom. In an attempt to understand what unity of genetic systems means and how the notion was borne out by later research, we survey the progress and prospects of cereal genomics: sequence assemblies, population-scale sequencing, resistance gene cloning and domestication genetics. Gene order may not be as extraordinarily well conserved in the grasses as once thought. Still, several recurring themes have emerged. The same ancestral molecular pathways defining plant architecture have been co-opted in the evolution of different cereal crops. Such genetic convergence as much as cross-fertilization of ideas between cereal geneticists has led to a rich harvest of genes that, it is hoped, will lead to improved varieties.

Generation of selenium-rich wheat mutants and exploration of responsive genes for selenium accumulation

KEY MESSAGE

Salt tolerance, selenium accumulation and expression of the responsive genes were analyzed in the wheat high selenium mutants. Selenium is an essential trace element for the human body, and its deficiency can lead to various diseases such as Keshan disease and large bone disease. Wheat, being a major staple crop, plays a crucial role in providing dietary selenium supplementation to combat this deficiency. Despite progress in understanding the molecular regulation of selenium accumulation in certain crops, the molecular mechanisms governing selenium accumulation-related gene expression in wheat plants remain poorly understood. In this study, three mutant wheat lines with elevated selenium content were identified. Under the treatment of Na2SeO3 or NaCl, the selenium-rich wheat mutants exhibited decreased sensitivity to both selenium and NaCl compared to the wild type. Additionally, there was an increase in the activities of SOD and POD, while the content of MDA decreased. Through qRT-PCR analysis, the expression of selenium-related genes was affected, revealing that some of these genes not only regulate the response of wheat to salt stress, but also play a role in the process of selenium accumulation. The transcriptome results revealed that the important genes encoding glutathione S-transferases, peroxidases, superoxide dismutases, and UDP-glucosyltransferases may function in the regulation of salt tolerance and selenium accumulation in wheat. These findings significantly contribute to the current understanding of the molecular regulation of selenium accumulation in wheat crops, while also offering novel germplasm resources for cultivating selenium-rich and salt-tolerant wheat lines.

Regulation of Root Exudation in Wheat Plants in Response to Alkali Stress

Soil alkalization is an important environmental factor limiting crop production. Despite the importance of root secretion in the response of plants to alkali stress, the regulatory mechanism is unclear. In this study, we applied a widely targeted metabolomics approach using a local MS/MS data library constructed with authentic standards to identify and quantify root exudates of wheat under salt and alkali stresses. The regulatory mechanism of root secretion in alkali-stressed wheat plants was analyzed by determining transcriptional and metabolic responses. Our primary focus was alkali stress-induced secreted metabolites (AISMs) that showed a higher secretion rate in alkali-stressed plants than in control and salt-stressed plants. This secretion was mainly induced by high-pH stress. We discovered 55 AISMs containing -COOH groups, including 23 fatty acids, 4 amino acids, 1 amino acid derivative, 7 dipeptides, 5 organic acids, 9 phenolic acids, and 6 others. In the roots, we also discovered 29 metabolites with higher levels under alkali stress than under control and salt stress conditions, including 2 fatty acids, 3 amino acid derivatives, 1 dipeptide, 2 organic acids, and 11 phenolic acids. These alkali stress-induced accumulated carboxylic acids may support continuous root secretion during the response of wheat plants to alkali stress. In the roots, RNAseq analysis indicated that 5 6-phosphofructokinase (glycolysis rate-limiting enzyme) genes, 16 key fatty acid synthesis genes, and 122 phenolic acid synthesis genes have higher expression levels under alkali stress than under control and salt stress conditions. We propose that the secretion of multiple types of metabolites with a -COOH group is an important pH regulation strategy for alkali-stressed wheat plants. Enhanced glycolysis, fatty acid synthesis, and phenolic acid synthesis will provide more energy and substrates for root secretion during the response of wheat to alkali stress.

Deciphering the differential expression patterns of yield-related negative regulators in hexaploid wheat cultivars and hybrids at different growth stages

BACKGROUND

Hexaploid bread wheat underwent a series of polyploidization events through interspecific hybridizations that conferred adaptive plasticity and resulted in duplication and neofunctionalization of major agronomic genes. The genetic architecture of polyploid wheat not only confers adaptive plasticity but also offers huge genetic diversity. However, the contribution of different gene copies (homeologs) encoded from different subgenomes (A, B, D) at different growth stages remained unexplored.

METHODS

In this study, hybrid of elite cultivars of wheat were developed via reciprocal crosses (cytoplasm swapping) and phenotypically evaluated. We assessed differential expression profiles of yield-related negative regulators in these cultivars and their F1 hybrids and identified various cis-regulatory signatures by employing bioinformatics tools. Furthermore, the preferential expression patterns of the syntenic triads encoded from A, B, and D subgenomes were assessed to decipher their functional redundancy at six different growth stages.

RESULTS

Hybrid progenies showed better heterosis such as up to 17% increase in the average number of grains and up to 50% increase in average thousand grains weight as compared to mid-parents. Based on the expression profiling, our results indicated significant dynamic transcriptional expression patterns, portraying the different homeolog-dominance at the same stage in the different cultivars and their hybrids. Albeit belonging to same syntenic triads, a dynamic trend was observed in the regulatory signatures of these genes that might be influencing their expression profiles.

CONCLUSION

These findings can substantially contribute and provide insights for the selective introduction of better cultivars into traditional and hybrid breeding programs which can be harnessed for the improvement of future wheat.

Diversification of quantitative morphological traits in wheat

BACKGROUND AND AIMS

The development and morphology of crop plants have been profoundly altered by evolution under cultivation, initially through unconscious selection, without deliberate foresight, and later by directed breeding. Wild wheats remain an important potential source of variation for modern breeders; however, the sequence and timing of morphological changes during domestication are not fully resolved.

METHODS

We grew and measured 142 wheat accessions representing different stages in wheat evolution, including three independent domestication events, and compared their morphological traits to define the morphospace of each group.

KEY RESULTS

The results show that wild and domesticated wheats have overlapping morphospaces, but each also occupies a distinct area of morphospace from one another. Polyploid formation in wheat increased leaf biomass and seed weight but had its largest effects on tiller loss. Domestication continued to increase the sizes of wheat leaves and seeds and made wheat grow taller, with more erect architecture. Associated changes to the biomass of domesticated wheats generated more grains and achieved higher yields. Landrace improvement subsequently decreased the numbers of tillers and spikes, to focus resource allocation to the main stem, accompanied by a thicker main stem and larger flag leaves. During the Green Revolution, wheat height was reduced to increase the harvest index and therefore yield. Modern wheats also have more erect leaves and larger flower biomass proportions than landraces.

CONCLUSIONS

Quantitative trait history in wheat differs by trait. Some trait values show progressive changes in the same direction (e.g. leaf size, grain weight), whereas others change in a punctuated way at particular stages (e.g. canopy architecture), and other trait values switch directions during wheat evolution (e.g. plant height, flower biomass proportion). Agronomically valued domestication traits arose during different stages of wheat history, such that modern wheats are the product of >10 000 years of morphological evolution.

Appropriate reduction of importin-α gene expression enhances yellow dwarf disease resistance in common wheat

Barley yellow dwarf viruses (BYDVs) cause widespread damage to global cereal crops. Here we report a novel strategy for elevating resistance to BYDV infection. The 17K protein, a potent virulence factor conserved in BYDVs, interacted with barley IMP-α1 and -α2 proteins that are nuclear transport receptors. Consistently, a nuclear localization signal was predicted in 17K, which was found essential for 17K to be transported into the nucleus and to interact with IMP-α1 and -α2. Reducing HvIMP-α1 and -α2 expression by gene silencing attenuated BYDV-elicited dwarfism, accompanied by a lowered nuclear accumulation of 17K. Among the eight common wheat CRISPR mutants with two to four TaIMP-α1 and -α2 genes mutated, the triple mutant α1aaBBDD /α2AAbbdd and the tetra-mutant α1aabbdd /α2AAbbDD displayed strong BYDV resistance without negative effects on plant growth under field conditions. The BYDV resistance exhibited by α1aaBBDD /α2AAbbdd and α1aabbdd /α2AAbbDD was correlated with decreased nuclear accumulation of 17K and lowered viral proliferation in infected plants. Our work uncovers the function of host IMP-α proteins in BYDV pathogenesis and generates the germplasm valuable for breeding BYDV-resistant wheat. Appropriate reduction of IMP-α gene expression may be broadly useful for enhancing antiviral resistance in agricultural crops and other economically important organisms.

Genomic approaches to enhance adaptive plasticity to cope with soil constraints amidst climate change in wheat

Climate change is varying the availability of resources, soil physicochemical properties, and rainfall events, which collectively determines soil physical and chemical properties. Soil constraints-acidity (pH < 6), salinity (pH ≤ 8.5), sodicity, and dispersion (pH > 8.5)-are major causes of wheat yield loss in arid and semiarid cropping systems. To cope with changing environments, plants employ adaptive strategies such as phenotypic plasticity, a key multifaceted trait, to promote shifts in phenotypes. Adaptive strategies for constrained soils are complex, determined by key functional traits and genotype × environment × management interactions. The understanding of the molecular basis of stress tolerance is particularly challenging for plasticity traits. Advances in sequencing and high-throughput genomics technologies have identified functional alleles in gene-rich regions, haplotypes, candidate genes, mechanisms, and in silico gene expression profiles at various growth developmental stages. Our review focuses on favorable alleles for enhanced gene expression, quantitative trait loci, and epigenetic regulation of plant responses to soil constraints, including heavy metal stress and nutrient limitations. A strategy is then described for quantitative traits in wheat by investigating significant alleles and functional characterization of variants, followed by gene validation using advanced genomic tools, and marker development for molecular breeding and genome editing. Moreover, the review highlights the progress of gene editing in wheat, multiplex gene editing, and novel alleles for smart control of gene expression. Application of these advanced genomic technologies to enhance plasticity traits along with soil management practices will be an effective tool to build yield, stability, and sustainability on constrained soils in the face of climate change.

Innovative computational tools provide new insights into the polyploid wheat genome

Bread wheat (Triticum aestivum) is an important crop and serves as a significant source of protein and calories for humans, worldwide. Nevertheless, its large and allopolyploid genome poses constraints on genetic improvement. The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging. Recently, we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome. Here, we summarize the methodological innovations and applications of these tools and databases. A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits. Furthermore, we outline future perspectives on new advanced tools and databases, taking into consideration the unique features of bread wheat, to accelerate genomic-assisted wheat breeding.

Allelic Variations in Vernalization (Vrn) Genes in Triticum spp

Rapid climate changes, with higher warming rates during winter and spring seasons, dramatically affect the vernalization requirements, one of the most critical processes for the induction of wheat reproductive growth, with severe consequences on flowering time, grain filling, and grain yield. Specifically, the Vrn genes play a major role in the transition from vegetative to reproductive growth in wheat. Recent advances in wheat genomics have significantly improved the understanding of the molecular mechanisms of Vrn genes (Vrn-1, Vrn-2, Vrn-3, and Vrn-4), unveiling a diverse array of natural allelic variations. In this review, we have examined the current knowledge of Vrn genes from a functional and structural point of view, considering the studies conducted on Vrn alleles at different ploidy levels (diploid, tetraploid, and hexaploid). The molecular characterization of Vrn-1 alleles has been a focal point, revealing a diverse array of allelic forms with implications for flowering time. We have highlighted the structural complexity of the different allelic forms and the problems linked to the different nomenclature of some Vrn alleles. Addressing these issues will be crucial for harmonizing research efforts and enhancing our understanding of Vrn gene function and evolution. The increasing availability of genome and transcriptome sequences, along with the improvements in bioinformatics and computational biology, offers a versatile range of possibilities for enriching genomic regions surrounding the target sites of Vrn genes, paving the way for innovative approaches to manipulate flowering time and improve wheat productivity.

Molecular evolution and phylogeographic analysis of wheat dwarf virus

Wheat dwarf virus (WDV) has caused considerable economic loss in the global production of grain crops. Knowledge of the evolutionary biology and population history of the pathogen remain poorly understood. We performed molecular evolution and worldwide phylodynamic analyses of the virus based on the genes in the protein-coding region of the entire viral genome. Our results showed that host-driven and geography-driven adaptation are major factors that affects the evolution of WDV. Bayesian phylogenetic analysis estimates that the average WDV substitution rate was 4.240 × 10-4 substitutions/site/year (95% credibility interval, 2.828 × 10-4-5.723 × 10-4), and the evolutionary rates of genes encoding proteins with virion-sense transcripts and genes encoding proteins with complementary-sense transcripts were different. The positively selected sites were detected in only two genes encoding proteins with complementary-sense, and WDV-barley are subject to stronger purifying selection than WDV-wheat. The time since the most recent common WDV ancestor was 1746 (95% credibility interval, 1517-1893) CE. Further analyses identified that the WDV-barley population and WDV-wheat population experienced dramatic expansion-decline episodes, and the expansion time of the WDV-barley population was earlier than that of the WDV-wheat population. Our phylogeographic analysis showed that the WDV population originating in Iran was subsequently introduced to Europe, and then spread from Eastern Europe to China.