Myb10-D confers PHS-3D resistance to pre-harvest sprouting by regulating NCED in ABA biosynthesis pathway of wheat

Evolution and Domestication of a Novel Biosynthetic Gene Cluster Contributing to the Flavonoid Metabolism and High-Altitude Adaptability of Plants in the Fagopyrum Genus

The diversity of secondary metabolites is an important means for plants to cope with the complex and ever-changing terrestrial environment. Plant biosynthetic gene clusters (BGCs) are crucial for the biosynthesis of secondary metabolites. The domestication and evolution of BGCs and how they affect plant secondary metabolites biosynthesis and environmental adaptation are still not fully understood. Buckwheat exhibits strong resistance and abundant secondary metabolites, especially flavonoids, allowing it to thrive in harsh environments. A non-canonical BGC named UFGT3 cluster is identified, which comprises a phosphorylase kinase (PAK), two transcription factors (MADS1/2), and a glycosyltransferase (UFGT3), forming a complete molecular regulatory module involved in flavonoid biosynthesis. This cluster is selected during Tartary buckwheat domestication and is widely present in species of the Fagopyrum genus. In wild relatives of cultivated buckwheat, a gene encoding anthocyanin glycosyltransferase (AGT), which glycosylates pelargonidin into pelargonidin-3-O-glucoside, is found inserted into this cluster. The pelargonidin-3-O-glucoside can help plants resist UV stress, endowing wild relatives with stronger high-altitude adaptability. This study provides a new research paradigm for the evolutionary dynamics of plant BGCs, and offers new perspectives for exploring the mechanism of plant ecological adaptability driven by environmental stress through the synthesis of secondary metabolites.

Current Insights into Weak Seed Dormancy and Pre-Harvest Sprouting in Crop Species

During the domestication of crops, seed dormancy has been reduced or eliminated to encourage faster and more consistent germination. This alteration makes cultivated crops particularly vulnerable to pre-harvest sprouting, which occurs when mature crops are subjected to adverse environmental conditions, such as excessive rainfall or high humidity. Consequently, some seeds may bypass the normal dormancy period and begin to germinate while still attached to the mother plant before harvest. Grains affected by pre-harvest sprouting are characterized by increased levels of α-amylase activity, resulting in poor processing quality and immediate grain downgrading. In the agriculture industry, pre-harvest sprouting causes annual economic losses exceeding USD 1 billion worldwide. This premature germination is influenced by a complex interplay of genetic, biochemical, and molecular factors closely linked to environmental conditions like rainfall. However, the exact mechanism behind this process is still unclear. Unlike pre-harvest sprouting, vivipary refers to the germination process and the activation of α-amylase during the soft dough stage, when the grains are still immature. Mature seeds with reduced levels of ABA or impaired ABA signaling (weak dormancy) are more susceptible to pre-harvest sprouting. While high seed dormancy can enhance resistance to pre-harvest sprouting, it can lead to undesirable outcomes for most crops, such as non-uniform seedling establishment after sowing. Thus, resistance to pre-harvest sprouting is crucial to ensuring productivity and sustainability and is an agronomically important trait affecting yield and grain quality. On the other hand, seed color is linked to sprouting resistance; however, the genetic relationship between both characteristics remains unresolved. The identification of mitogen-activated protein kinase kinase-3 (MKK3) as the gene responsible for pre-harvest sprouting-1 (Phs-1) represents a significant advancement in our understanding of how sprouting in wheat is controlled at the molecular and genetic levels. In seed maturation, Viviparous-1 (Vp-1) plays a crucial role in managing pre-harvest sprouting by regulating seed maturation and inhibiting germination through the suppression of α-amylase and proteases. Vp-1 is a key player in ABA signaling and is essential for the activation of the seed maturation program. Mutants of Vp-1 exhibit an unpigmented aleurone cell layer and exhibit precocious germination due to decreased sensitivity to ABA. Recent research has also revealed that TaSRO-1 interacts with TaVp-1, contributing to the regulation of seed dormancy and resistance to pre-harvest sprouting in wheat. The goal of this review is to emphasize the latest research on pre-harvest sprouting in crops and to suggest possible directions for future studies.

Genome-wide analysis and identification of Carotenoid Cleavage Oxygenase (CCO) gene family in coffee (coffee arabica) under abiotic stress

The coffee industry holds importance, providing livelihoods for millions of farmers globally and playing a vital role in the economies of coffee-producing countries. Environmental conditions such as drought and temperature fluctuations can adversely affect the quality and yield of coffee crops.Carotenoid cleavage oxygenases (CCO) enzymes are essential for coffee plants as they help break down carotenoids contributing to growth and stress resistance. However, knowledge about the CCO gene family in Coffee arabica was limited. In this study identified 21 CCO genes in Coffee arabica (C. arabica) revealing two subfamilies carotenoid cleavage dioxygenases (CCDs) and 9-cis-epoxy carotenoid dioxygenases (NCED) through phylogenic analysis. These subfamilies exhibited distribution patterns in terms of gene structure, domains, and motifs. The 21 CaCCO genes, comprising 5 NCED and 16 CCD genes were found across chromosomes. Promoter sequencing analysis revealed cis-elements that likely interact with plant stress-responsive, growth-related, and phytohormones, like auxin and abscisic acid. A comprehensive genome-wide comparison, between C. arabica and A. thaliana was conducted to understand the characteristics of CCO genes. RTqPCR data indicated that CaNCED5, CaNCED6, CaNCED12, and CaNCED20 are target genes involved in the growth of drought coffee plants leading to increased crop yield, in a conditions, with limited water availability. This reveals the role of coffee CCOs in responding to abiotic stress and identifies potential genes useful for breeding stress-resistant coffee varieties.

Beyond pathways: Accelerated flavonoids candidate identification and novel exploration of enzymatic properties using combined mapping populations of wheat

Although forward-genetics-metabolomics methods such as mGWAS and mQTL have proven effective in providing myriad loci affecting metabolite contents, they are somehow constrained by their respective constitutional flaws such as the hidden population structure for GWAS and insufficient recombinant rate for QTL. Here, the combination of mGWAS and mQTL was performed, conveying an improved statistical power to investigate the flavonoid pathways in common wheat. A total of 941 and 289 loci were, respectively, generated from mGWAS and mQTL, within which 13 of them were co-mapped using both approaches. Subsequently, the mGWAS or mQTL outputs alone and their combination were, respectively, utilized to delineate the metabolic routes. Using this approach, we identified two MYB transcription factor encoding genes and five structural genes, and the flavonoid pathway in wheat was accordingly updated. Moreover, we have discovered some rare-activity-exhibiting flavonoid glycosyl- and methyl-transferases, which may possess unique biological significance, and harnessing these novel catalytic capabilities provides potentially new breeding directions. Collectively, we propose our survey illustrates that the forward-genetics-metabolomics approaches including multiple populations with high density markers could be more frequently applied for delineating metabolic pathways in common wheat, which will ultimately contribute to metabolomics-assisted wheat crop improvement.

Abscisic acid activates transcription factor module MdABI5-MdMYBS1 during carotenoid-derived apple fruit coloration

Carotenoids are major pigments contributing to fruit coloration. We previously reported that the apple (Malus domestica Borkh.) mutant fruits of "Beni Shogun" and "Yanfu 3" show a marked difference in fruit coloration. However, the regulatory mechanism underlying this phenomenon remains unclear. In this study, we determined that carotenoid is the main factor influencing fruit flesh color. We identified an R1-type MYB transcription factor (TF), MdMYBS1, which was found to be highly associated with carotenoids and abscisic acid (ABA) contents of apple fruits. Overexpression of MdMYBS1 promoted, and silencing of MdMYBS1 repressed, β-branch carotenoids synthesis and ABA accumulation. MdMYBS1 regulates carotenoid biosynthesis by directly activating the major carotenoid biosynthetic genes encoding phytoene synthase (MdPSY2-1) and lycopene β-cyclase (MdLCYb). 9-cis-epoxycarotenoid dioxygenase 1 (MdNCED1) contributes to ABA biosynthesis, and MdMYBS1 enhances endogenous ABA accumulation by activating the MdNCED1 promoter. In addition, the basic leucine zipper domain TF ABSCISIC ACID-INSENSITIVE5 (MdABI5) was identified as an upstream activator of MdMYBS1, which promotes carotenoid and ABA accumulation. Furthermore, ABA promotes carotenoid biosynthesis and enhances MdMYBS1 and MdABI5 promoter activities. Our findings demonstrate that the MdABI5-MdMYBS1 cascade activated by ABA regulates carotenoid-derived fruit coloration and ABA accumulation in apple, providing avenues in breeding and planting for improvement of fruit coloration and quality.

Integrative Analysis of Metabolome and Transcriptome of Carotenoid Biosynthesis Reveals the Mechanism of Fruit Color Change in Tomato (Solanum lycopersicum)

Tomato fruit ripening is accompanied by carotenoid accumulation and color changes. To elucidate the regulatory mechanisms underlying carotenoid synthesis during fruit ripening, a combined transcriptomic and metabolomic analysis was conducted on red-fruited tomato (WP190) and orange-fruited tomato (ZH108). A total of twenty-nine (29) different carotenoid compounds were identified in tomato fruits at six different stages. The abundance of the majority of the carotenoids was enhanced significantly with fruit ripening, with higher levels of lycopene; (E/Z)-lycopene; and α-, β- and γ-carotenoids detected in the fruits of WP190 at 50 and 60 days post anthesis (DPA). Transcriptome analysis revealed that the fruits of two varieties exhibited the highest number of differentially expressed genes (DEGs) at 50 DPA, and a module of co-expressed genes related to the fruit carotenoid content was established by WGCNA. qRT-PCR analysis validated the transcriptome result with a significantly elevated transcript level of lycopene biosynthesis genes (including SlPSY2, SlZCIS, SlPDS, SlZDS and SlCRTSO2) observed in WP190 at 50 DPA in comparison to ZH108. In addition, during the ripening process, the expression of ethylene biosynthesis (SlACSs and SlACOs) and signaling (SlEIN3 and SlERF1) genes was also increased, and these mechanisms may regulate carotenoid accumulation and fruit ripening in tomato. Differential expression of several key genes in the fruit of two tomato varieties at different stages regulates the accumulation of carotenoids and leads to differences in color between the two varieties of tomato. The results of this study provide a comprehensive understanding of carotenoid accumulation and ethylene biosynthesis and signal transduction pathway regulatory mechanisms during tomato fruit development.

Variation of TaMyb10 and their function on grain color and pre-harvest sprouting resistance of wheat

Pre-harvest sprouting (PHS) is a significant threat to global food security due to its association with losses in both yield and quality. Among the genes involved in PHS resistance in wheat, PHS-3D (TaMyb10-D) plays a crucial role. Here, we characterized the sequence variations of TaMyb10 genes in 416 bread wheat and 302 Aegilops tauschii accessions. Within TaMyb10-A sequences, we identified a deletion ranging from 214 to 305 bp in the signal and amino acid coding region, present in 61.3% of the accessions. Similarly, 79.3% of the TaMyb10-B sequences within the third exon region exhibited a 19 bp deletion. Additionally, 40.8% of the accessions lacked the 2.4 Mb fragment (in/del mutations) on Chr3D, where TaMyb10-D/PHS-3D was located. Interestingly, the geographical distribution of accessions showed little correlation with the divergence of TaMyb10. TaMyb10-A-IIIDele, TaMyb10-B-IVDele, and TaMyb10-D-VDele genotypes were prevalent in wheat populations across continents. Despite their structural variations, the five distinct protein types exhibited comparable ability to bind the promoters of downstream genes in the flavonoid and ABA pathways, such as CHS, DFR, and NCED. Furthermore, the combination of TaMyb10 homologs was significantly associated with grain color and germination percentages. Accessions exclusively harboring TaMyb10-D displayed red seed color and reduced germination percentages, indicating the predominant role of TaMyb10-D compared to TaMyb10-A and TaMyb10-B. This comprehensive investigation enhances our understanding of the structural variations and functional divergence of TaMyb10, providing valuable insights and resources for improving PHS resistance in wheat.

Identification of Novel Loci Precisely Modulating Pre-Harvest Sprouting Resistance and Red Color Components of the Seed Coat in T. aestivum L

The association between pre-harvest sprouting (PHS) and seed coat color has long been recognized. Red-grained wheats generally exhibit greater PHS resistance compared to white-grained wheat, although variability in PHS resistance exists within red-grained varieties. Here, we conducted a genome-wide association study on a panel consisting of red-grained wheat varieties, aimed at uncovering genes that modulate PHS resistance and red color components of seed coat using digital image processing. Twelve loci associated with PHS traits were identified, nine of which were described for the first time. Genetic loci marked by SNPs AX-95172164 (chromosome 1B) and AX-158544327 (chromosome 7D) explained approximately 25% of germination index variance, highlighting their value for breeding PHS-resistant varieties. The most promising candidate gene for PHS resistance was TraesCS6B02G147900, encoding a protein involved in aleurone layer morphogenesis. Twenty-six SNPs were significantly associated with grain color, independently of the known Tamyb10 gene. Most of them were related to multiple color characteristics. Prioritization of genes within the revealed loci identified TraesCS1D03G0758600 and TraesCS7B03G1296800, involved in the regulation of pigment biosynthesis and in controlling pigment accumulation. In conclusion, our study identifies new loci associated with grain color and germination index, providing insights into the genetic mechanisms underlying these traits.

Transcriptional convergence after repeated duplication of an amino acid transporter gene leads to the independent emergence of the black husk/pericarp trait in barley and rice

The repeated emergence of the same trait (convergent evolution) in distinct species is an interesting phenomenon and manifests visibly the power of natural selection. The underlying genetic mechanisms have important implications to understand how the genome evolves under environmental challenges. In cereal crops, both rice and barley can develop black-coloured husk/pericarp due to melanin accumulation. However, it is unclear if this trait shares a common origin. Here, we fine-mapped the barley HvBlp gene controlling the black husk/pericarp trait and confirmed its function by gene silencing. The result was further supported by a yellow husk/pericarp mutant with deletion of the HvBlp gene, derived from gamma ray radiation of the wild-type W1. HvBlp encodes a putative tyrosine transporter homologous to the black husk gene OsBh4 in rice. Surprisingly, synteny and phylogenetic analyses showed that HvBlp and OsBh4 belonged to different lineages resulted from dispersed and tandem duplications, respectively, suggesting that the black husk/pericarp trait has emerged independently. The dispersed duplication (dated at 21.23 MYA) yielding HvBlp occurred exclusively in the common ancestor of Triticeae. HvBlp and OsBh4 displayed converged transcription in husk/pericarp tissues, contributing to the black husk/pericarp trait. Further transcriptome and metabolome data identified critical candidate genes and metabolites related to melanin production in barley. Taken together, our study described a compelling case of convergent evolution resulted from transcriptional convergence after repeated gene duplication, providing valuable genetic insights into phenotypic evolution. The identification of the black husk/pericarp genes in barley also has great potential in breeding for stress-resilient varieties with higher nutritional values.

A wheat heat shock transcription factor gene, TaHsf-7A, regulates seed dormancy and germination

Heat shock transcription factors (Hsfs) play multifaceted roles in plant growth, development, and responses to environmental factors. However, their involvement in seed dormancy and germination processes has remained elusive. In this study, we identified a wheat class B Hsf gene, TaHsf-7A, with higher expression in strong-dormancy varieties compared to weak-dormancy varieties during seed imbibition. Specifically, TaHsf-7A expression increased during seed dormancy establishment and subsequently declined during dormancy release. Through the identification of a 1-bp insertion (ins)/deletion (del) variation in the coding region of TaHsf-7A among wheat varieties with different dormancy levels, we developed a CAPS marker, Hsf-7A-1319, resulting in two allelic variations: Hsf-7A-1319-ins and Hsf-7A-1319-del. Notably, the allele Hsf-7A-1319-ins correlated with a reduced seed germination rate and elevated dormancy levels, while Hsf-7A-1319-del exhibited the opposite trend across 175 wheat varieties. The association of TaHsf-7A allelic status with seed dormancy and germination levels was confirmed in various genetically modified species, including Arabidopsis, rice, and wheat. Results from the dual luciferase assay demonstrated notable variations in transcriptional activity among transformants harboring distinct TaHsf-7A alleles. Furthermore, the levels of abscisic acid (ABA) and gibberellin (GA), along with the expression levels of ABA and GA biosynthesis genes, showed significant differences between transgenic rice lines carrying different alleles of TaHsf-7A. These findings represent a significant step towards a comprehensive understanding of TaHsf-7A's involvement in the dormancy and germination processes of wheat seeds.

Functional analysis of a wheat class III peroxidase gene, TaPer12-3A, in seed dormancy and germination

BACKGROUND

Class III peroxidases (PODs) perform crucial functions in various developmental processes and responses to biotic and abiotic stresses. However, their roles in wheat seed dormancy (SD) and germination remain elusive.

RESULTS

Here, we identified a wheat class III POD gene, named TaPer12-3A, based on transcriptome data and expression analysis. TaPer12-3A showed decreasing and increasing expression trends with SD acquisition and release, respectively. It was highly expressed in wheat seeds and localized in the endoplasmic reticulum and cytoplasm. Germination tests were performed using the transgenic Arabidopsis and rice lines as well as wheat mutant mutagenized with ethyl methane sulfonate (EMS) in Jing 411 (J411) background. These results indicated that TaPer12-3A negatively regulated SD and positively mediated germination. Further studies showed that TaPer12-3A maintained H2O2 homeostasis by scavenging excess H2O2 and participated in the biosynthesis and catabolism pathways of gibberellic acid and abscisic acid to regulate SD and germination.

CONCLUSION

These findings not only provide new insights for future functional analysis of TaPer12-3A in regulating wheat SD and germination but also provide a target gene for breeding wheat varieties with high pre-harvest sprouting resistance by gene editing technology.

Genome-Wide Identification and Expression Profiling of Velvet Complex Transcription Factors in Populus alba × Populus glandulosa

The discovery of new genes with novel functions is a major driver of adaptive evolutionary innovation in plants. Especially in woody plants, due to genome expansion, new genes evolve to regulate the processes of growth and development. In this study, we characterized the unique VeA transcription factor family in Populus alba × Populus glandulosa, which is associated with secondary metabolism. Twenty VeA genes were characterized systematically on their phylogeny, genomic distribution, gene structure and conserved motif, promoter binding site, and expression profiling. Furthermore, through ChIP-qPCR, Y1H, and effector-reporter assays, it was demonstrated that PagMYB128 directly regulated PagVeA3 to influence the biosynthesis of secondary metabolites. These results provide a basis for further elucidating the function of VeAs gene in poplar and its genetic regulation mechanism.

Mapping of a Major-Effect Quantitative Trait Locus for Seed Dormancy in Wheat

The excavation and utilization of dormancy loci in breeding are effective endeavors for enhancing the resistance to pre-harvest sprouting (PHS) of wheat varieties. CH1539 is a wheat breeding line with high-level seed dormancy. To clarify the dormant loci carried by CH1539 and obtain linked molecular markers, in this study, a recombinant inbred line (RIL) population derived from the cross of weak dormant SY95-71 and strong dormant CH1539 was genotyped using the Wheat17K single-nucleotide polymorphism (SNP) array, and a high-density genetic map covering 21 chromosomes and consisting of 2437 SNP markers was constructed. Then, the germination percentage (GP) and germination index (GI) of the seeds from each RIL were estimated. Two QTLs for GP on chromosomes 5A and 6B, and four QTLs for GI on chromosomes 5A, 6B, 6D and 7A were identified. Among them, the QTL on chromosomes 6B controlling both GP and GI, temporarily named QGp/Gi.sxau-6B, is a major QTL for seed dormancy with the maximum phenotypic variance explained of 17.66~34.11%. One PCR-based diagnostic marker Ger6B-3 for QGp/Gi.sxau-6B was developed, and the genetic effect of QGp/Gi.sxau-6B on the RIL population and a set of wheat germplasm comprising 97 accessions was successfully confirmed. QGp/Gi.sxau-6B located in the 28.7~30.9 Mbp physical position is different from all the known dormancy loci on chromosomes 6B, and within the interval, there are 30 high-confidence annotated genes. Our results revealed a novel QTL QGp/Gi.sxau-6B whose CH1539 allele had a strong and broad effect on seed dormancy, which will be useful in further PHS-resistant wheat breeding.

Fine mapping of powdery mildew resistance gene PmXNM in a Chinese wheat landrace Xiaonanmai

KEY MESSAGE

Powdery mildew resistance gene PmXNM, originated from the Chinese wheat landrace Xiaonanmai, was delimited to a 300.7-kb interval enriched with resistance genes. Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a globally devastating disease threatening the yield and quality of wheat worldwide. The use of broad-spectrum disease resistance genes from wheat landraces is an effective strategy to prevent this pathogen. Chinese wheat landrace Xiaonanmai (XNM) was immune to 23 tested Bgt isolates at the seedling stage. The F1, F2, and F2:4 progenies derived from the cross between XNM and Chinese Spring (CS) were used in this study. Genetic analysis revealed that powdery mildew resistance in XNM was controlled by a single dominant gene, temporarily designated PmXNM. Bulked segregant analysis and molecular mapping delimited PmXNM to the distal terminal region of chromosome 4AL flanked by markers caps213923 and kasp511718. The region carrying the PmXNM locus was approximately 300.7 kb and contained nine high-confidence genes according to the reference genome sequence of CS. Five of these genes, annotated as disease resistance RPP13-like proteins 1, were clustered in the target region. Haplotype analysis using the candidate gene-specific markers indicated that the majority of 267 common wheat accessions (75.3%) exhibited extensive gene losses at the PmXNM locus, as confirmed by aligning the targeted genome sequences of CS with those of other sequenced wheat cultivars. Seven candidate gene-specific markers have proven effective for marker-assisted introgression of PmXNM into modern elite cultivars.

Genome-Wide Association Study of Preharvest Sprouting in Wheat

Genome-wide association study (GWAS) is widely used to characterize genes or quantitative trait loci (QTLs) associated with preharvest sprouting and seed dormancy. GWAS can identify both previously discovered and novel QTLs across diverse genetic panels. The high-throughput SNP arrays or next-generation sequencing technologies have facilitated the identification of numerous genetic markers, thereby significantly enhancing the resolution of GWAS. Although various methods have been developed, the fundamental principles underlying these techniques remain constant. Here, we provide a basic technological flow to perform seed dormancy assay, followed by GWAS using population structure control, and compared it with previous identified QTLs and genes.

TaSRO1 interacts with TaVP1 to modulate seed dormancy and pre-harvest sprouting resistance in wheat

Dormancy is an adaptive trait which prevents seeds from germinating under unfavorable environmental conditions. Seeds with weak dormancy undergo pre-harvest sprouting (PHS) which decreases grain yield and quality. Understanding the genetic mechanisms that regulate seed dormancy and resistance to PHS is crucial for ensuring global food security. In this study, we illustrated the function and molecular mechanism of TaSRO1 in the regulation of seed dormancy and PHS resistance by suppressing TaVP1. The tasro1 mutants exhibited strong seed dormancy and enhanced resistance to PHS, whereas the mutants of tavp1 displayed weak dormancy. Genetic evidence has shown that TaVP1 is epistatic to TaSRO1. Biochemical evidence has shown that TaSRO1 interacts with TaVP1 and represses the transcriptional activation of the PHS resistance genes TaPHS1 and TaSdr. Furthermore, TaSRO1 undermines the synergistic activation of TaVP1 and TaABI5 in PHS resistance genes. Finally, we highlight the great potential of tasro1 alleles for breeding elite wheat cultivars that are resistant to PHS.

Advance Research on the Pre-Harvest Sprouting Trait in Vegetable Crop Seeds

Pre-harvest sprouting (PHS), the germination of seeds on the plant prior to harvest, poses significant challenges to agriculture. It not only reduces seed and grain yield, but also impairs the commodity quality of the fruit, ultimately affecting the success of the subsequent crop cycle. A deeper understanding of PHS is essential for guiding future breeding strategies, mitigating its impact on seed production rates and the commercial quality of fruits. PHS is a complex phenomenon influenced by genetic, physiological, and environmental factors. Many of these factors exert their influence on PHS through the intricate regulation of plant hormones responsible for seed germination. While numerous genes related to PHS have been identified in food crops, the study of PHS in vegetable crops is still in its early stages. This review delves into the regulatory elements, functional genes, and recent research developments related to PHS in vegetable crops. Meanwhile, this paper presents a novel understanding of PHS, aiming to serve as a reference for the study of this trait in vegetable crops.

Research on the evolutionary history of the morphological structure of cotton seeds: a new perspective based on high-resolution micro-CT technology

Cotton (Gossypium hirsutum L.) seed morphological structure has a significant impact on the germination, growth and quality formation. However, the wide variation of cotton seed morphology makes it difficult to achieve quantitative analysis using traditional phenotype acquisition methods. In recent years, the application of micro-CT technology has made it possible to analyze the three-dimensional morphological structure of seeds, and has shown technical advantages in accurate identification of seed phenotypes. In this study, we reconstructed the seed morphological structure based on micro-CT technology, deep neural network Unet-3D model, and threshold segmentation methods, extracted 11 basics phenotypes traits, and constructed three new phenotype traits of seed coat specific surface area, seed coat thickness ratio and seed density ratio, using 102 cotton germplasm resources with clear year characteristics. Our results show that there is a significant positive correlation (P< 0.001) between the cotton seed size and that of the seed kernel and seed coat volume, with correlation coefficients ranging from 0.51 to 0.92, while the cavity volume has a lower correlation with other phenotype indicators (r<0.37, P< 0.001). Comparison of changes in Chinese self-bred varieties showed that seed volume, seed surface area, seed coat volume, cavity volume and seed coat thickness increased by 11.39%, 10.10%, 18.67%, 115.76% and 7.95%, respectively, while seed kernel volume, seed kernel surface area and seed fullness decreased by 7.01%, 0.72% and 16.25%. Combining with the results of cluster analysis, during the hundred-year cultivation history of cotton in China, it showed that the specific surface area of seed structure decreased by 1.27%, the relative thickness of seed coat increased by 8.70%, and the compactness of seed structure increased by 50.17%. Furthermore, the new indicators developed based on micro-CT technology can fully consider the three-dimensional morphological structure and cross-sectional characteristics among the indicators and reflect technical advantages. In this study, we constructed a microscopic phenotype research system for cotton seeds, revealing the morphological changes of cotton seeds with the year in China and providing a theoretical basis for the quantitative analysis and evaluation of seed morphology.

Overexpression of 9-cis-Epoxycarotenoid Dioxygenase Gene, IbNCED1, Negatively Regulates Plant Height in Transgenic Sweet Potato

Plant height is one of the key agronomic traits for improving the yield of sweet potato. Phytohormones, especially gibberellins (GAs), are crucial to regulate plant height. The enzyme 9-cis-epoxycarotenoid dioxygenase (NCED) is the key enzyme for abscisic acid (ABA) biosynthesis signalling in higher plants. However, its role in regulating plant height has not been reported to date. Here, we cloned a new NCED gene, IbNCED1, from the sweet potato cultivar Jishu26. This gene encoded the 587-amino acid polypeptide containing an NCED superfamily domain. The expression level of IbNCED1 was highest in the stem and the old tissues in the in vitro-grown and field-grown Jishu26, respectively. The expression of IbNCED1 was induced by ABA and GA3. Overexpression of IbNCED1 promoted the accumulation of ABA and inhibited the content of active GA3 and plant height and affected the expression levels of genes involved in the GA metabolic pathway. Exogenous application of GA3 could rescue the dwarf phenotype. In conclusion, we suggest that IbNCED1 regulates plant height and development by controlling the ABA and GA signalling pathways in transgenic sweet potato.

Comprehensive Transcriptomic and Metabolic Profiling of Agrobacterium-tumefaciens-Infected Immature Wheat Embryos

The transformation efficiency (TE) was improved by a series of special chemical and physical methods using immature embryos from the cultivar Fielder, with the PureWheat technique. To analyze the reaction of immature embryos infected, which seemed to provide the necessary by Agrobacterium tumefaciens in PureWheat, a combination of scanning electron microscopy (SEM), complete transcriptome analysis, and metabolome analysis was conducted to understand the progress. The results of the SEM analysis revealed that Agrobacterium tumefaciens were deposited under the damaged cortex of immature embryos as a result of pretreatment and contacted the receptor cells to improve the TE. Transcriptome analysis indicated that the differentially expressed genes were mainly enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, plant-pathogen interaction, plant hormone signal transduction, and the MAPK (Mitogen-activated protein kinase) signaling pathway. By analyzing the correlation between differentially expressed genes and metabolites, the expression of many genes and the accumulation of metabolites were changed in glucose metabolism and the TCA cycle (Citrate cycle), as well as the amino acid metabolism; this suggests that the infection of wheat embryos with Agrobacterium is an energy-demanding process. The shikimate pathway may act as a hub between glucose metabolism and phenylpropanoid metabolism during Agrobacterium infection. The downregulation of the F5H gene and upregulation of the CCR gene led to the accumulation of lignin precursors through phenylpropanoid metabolism. In addition, several metabolic pathways and oxidases were found to be involved in the infection treatment, including melatonin biosynthesis, benzoxazinoid biosynthesis, betaine biosynthesis, superoxide dismutase, and peroxidase, suggesting that wheat embryos may be under the stress of Agrobacterium and, thus, undergo an oxidative stress response. These findings explore the physiological and molecular changes of immature embryos during the co-culture stage of the PureWheat technique and provide insights for Agrobacterium-mediated transgenic wheat experiments.

OsNF-YA3 regulates plant growth and osmotic stress tolerance by interacting with SLR1 and SAPK9 in rice

The antagonism between gibberellin (GA) and abscisic acid (ABA) signaling pathways is vital to balance plant growth and stress response. Nevertheless, the mechanism by which plants determine the balance remains to be elucidated. Here, we report that rice NUCLEAR FACTOR-Y A3 (OsNF-YA3) modulates GA- and ABA-mediated balance between plant growth and osmotic stress tolerance. OsNF-YA3 loss-of-function mutants exhibit stunted growth, compromised GA biosynthetic gene expression, and decreased GA levels, while its overexpression lines have promoted growth and enhanced GA content. Chromatin immunoprecipitation-quantitative polymerase chain reaction analysis and transient transcriptional regulation assays demonstrate that OsNF-YA3 activates GA biosynthetic gene OsGA20ox1 expression. Furthermore, the DELLA protein SLENDER RICE1 (SLR1) physically interacts with OsNF-YA3 and thus inhibits its transcriptional activity. On the other side, OsNF-YA3 negatively regulates plant osmotic stress tolerance by repressing ABA response. OsNF-YA3 reduces ABA levels by transcriptionally regulating ABA catabolic genes OsABA8ox1 and OsABA8ox3 by binding to their promoters. Furthermore, OSMOTIC STRESS/ABA-ACTIVATED PROTEIN KINASE 9 (SAPK9), the positive component in ABA signaling, interacts with OsNF-YA3 and mediates OsNF-YA3 phosphorylation, resulting in its degradation in plants. Collectively, our findings establish OsNF-YA3 as an important transcription factor that positively modulates GA-regulated plant growth and negatively controls ABA-mediated water-deficit and salt tolerance. These findings shed light on the molecular mechanism underlying the balance between the growth and stress response of the plant.

The GATA transcription factor TaGATA1 recruits demethylase TaELF6-A1 and enhances seed dormancy in wheat by directly regulating TaABI5

Seed dormancy is an important agronomic trait in crops, and plants with low dormancy are prone to preharvest sprouting (PHS) under high-temperature and humid conditions. In this study, we report that the GATA transcription factor TaGATA1 is a positive regulator of seed dormancy by regulating TaABI5 expression in wheat. Our results demonstrate that TaGATA1 overexpression significantly enhances seed dormancy and increases resistance to PHS in wheat. Gene expression patterns, abscisic acid (ABA) response assay, and transcriptome analysis all indicate that TaGATA1 functions through the ABA signaling pathway. The transcript abundance of TaABI5, an essential regulator in the ABA signaling pathway, is significantly elevated in plants overexpressing TaGATA1. Chromatin immunoprecipitation assay (ChIP) and transient expression analysis showed that TaGATA1 binds to the GATA motifs at the promoter of TaABI5 and induces its expression. We also demonstrate that TaGATA1 physically interacts with the putative demethylase TaELF6-A1, the wheat orthologue of Arabidopsis ELF6. ChIP-qPCR analysis showed that H3K27me3 levels significantly decline at the TaABI5 promoter in the TaGATA1-overexpression wheat line and that transient expression of TaELF6-A1 reduces methylation levels at the TaABI5 promoter, increasing TaABI5 expression. These findings reveal a new transcription module, including TaGATA1-TaELF6-A1-TaABI5, which contributes to seed dormancy through the ABA signaling pathway and epigenetic reprogramming at the target site. TaGATA1 could be a candidate gene for improving PHS resistance.

Cytological and genetic effects of rye chromosomes 1RS and 3R on the wheat-breeding founder parent Chuanmai 42 from southwestern China

Rye (Secale cereale L.) is an important genetic resource for improving the disease resistance of wheat. An increasing number of rye chromosome segments have been transferred into modern wheat cultivars via chromatin insertions. In this study, 185 recombinant inbred lines (RILs) derived from a cross between a wheat accession containing rye chromosomes 1RS and 3R and a wheat-breeding founder parent Chuanmai 42 from southwestern China were used to decipher the cytological and genetic effects of 1RS and 3R via fluorescence/genomic in situ hybridization and quantitative trait locus (QTL) analyses. Chromosome centromere breakage and fusion were detected in the RIL population. Additionally, the recombination of chromosomes 1BS and 3D from Chuanmai 42 was completely suppressed by 1RS and 3R in the RIL population. In contrast to chromosome 3D of Chuanmai 42, rye chromosome 3R was significantly associated with white seed coats and decreased yield-related traits, as revealed by QTL and single marker analyses, whereas it had no effect on stripe rust resistance. Rye chromosome 1RS did not affect yield-related traits and it increased the susceptibility of plants to stripe rust. Most of the detected QTLs that positively affected yield-related traits were from Chuanmai 42. The findings of this study suggest that the negative effects of rye-wheat substitutions or translocations, including the suppression of the pyramiding of favorable QTLs on paired wheat chromosomes from different parents and the transfer of disadvantageous alleles to filial generations, should be considered when selecting alien germplasm to enhance wheat-breeding founder parents or to breed new varieties.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01386-0.

Genetic Improvement of Wheat with Pre-Harvest Sprouting Resistance in China

Wheat pre-harvest sprouting (PHS) refers to the germination of seeds directly on the spike due to rainy weather before harvest, which often results in yield reduction, quality deterioration, and seed value loss. In this study, we reviewed the research progress in the quantitative trait loci (QTL) detection and gene excavation related to PHS resistance in wheat. Simultaneously, the identification and creation of germplasm resources and the breeding of wheat with PHS resistance were expounded in this study. Furthermore, we also discussed the prospect of molecular breeding during genetic improvement of PHS-resistant wheat.

Exogenous abscisic acid and sodium nitroprusside regulate flavonoid biosynthesis and photosynthesis of Nitraria tangutorum Bobr in alkali stress

Abscisic acid (ABA) and nitric oxide (NO) are involved in mediating abiotic stress-induced plant physiological responses. Nitraria tangutorum Bobr is a typical salinized desert plant growing in an arid environment. In this study, we investigated the effects of ABA and NO on N.tangutorum seedlings under alkaline stress. Alkali stress treatment caused cell membrane damage, increased electrolyte leakage, and induced higher production of reactive oxygen species (ROS), which caused growth inhibition and oxidative stress in N.tangutorum seedlings. Exogenous application of ABA (15μm) and Sodium nitroprusside (50μm) significantly increased the plant height, fresh weight, relative water content, and degree of succulency in N.tangutorum seedlings under alkali stress. Meanwhile, the contents of ABA and NO in plant leaves were significantly increased. ABA and SNP can promote stomatal closure, decrease the water loss rate, increase leaf surface temperature and the contents of osmotic regulator proline, soluble protein, and betaine under alkali stress. Meanwhile, SNP more significantly promoted the accumulation of chlorophyll a/b and carotenoids, increased quantum yield of photosystem II (φPSII) and electron transport rate (ETRII) than ABA, and decreased photochemical quenching (qP), which improved photosynthetic efficiency and accelerated the accumulation of soluble sugar, glucose, fructose, sucrose, starch, and total sugar. However, compared with exogenous application of SNP in the alkaline stress, ABA significantly promoted the transcription of NtFLS/NtF3H/NtF3H/NtANR genes and the accumulation of naringin, quercetin, isorhamnetin, kaempferol, and catechin in the synthesis pathway of flavonoid metabolites, and isorhamnetin content was the highest. These results indicate that both ABA and SNP can reduce the growth inhibition and physiological damage caused by alkali stress. Among them, SNP has a better effect on the improvement of photosynthetic efficiency and the regulation of carbohydrate accumulation than ABA, while ABA has a more significant effect on the regulation of flavonoid and anthocyanin secondary metabolite accumulation. Exogenous application of ABA and SNP also improved the antioxidant capacity and the ability to maintain Na⁺/K⁺ balance of N. tangutorum seedlings under alkali stress. These results demonstrate the beneficial effects of ABA and NO as stress hormones and signaling molecules that positively regulate the defensive response of N. tangutorum to alkaline stress.

SiNCED1, a 9-cis-epoxycarotenoid dioxygenase gene in Setaria italica, is involved in drought tolerance and seed germination in transgenic Arabidopsis

Foxtail millet (Setaria italica L.) is a vital cereal food crop with promising development and utilization potential because of its outstanding ability to resist drought stress. However, the molecular mechanisms underlying its drought stress resistance remain unclear. In this study, we aimed to elucidate the molecular function of a 9-cis-epoxycarotenoid dioxygenase gene, SiNCED1, in the drought stress response of foxtail millet. Expression pattern analysis showed that SiNCED1 expression was significantly induced by abscisic acid (ABA), osmotic stress, and salt stress. Furthermore, ectopic overexpression of SiNCED1 could enhance drought stress resistance by elevating endogenous ABA levels and promoting stomatal closure. Transcript analysis indicated that SiNCED1 modulated ABA-related stress responsive gene expression. In addition, we found that ectopic expression of SiNCED1 delayed seed germination under normal and abiotic stress conditions. Taken together, our results show that SiNCED1 plays a positive role in the drought tolerance and seed dormancy of foxtail millet by modulating ABA biosynthesis. In conclusion, this study revealed that SiNCED1 is an important candidate gene for the improvement of drought stress tolerance in foxtail millet and could be beneficial in the breeding and investigation of drought tolerance in other agronomic crops.

GWAS and genomic prediction for pre-harvest sprouting tolerance involving sprouting score and two other related traits in spring wheat

In wheat, a genome-wide association study (GWAS) and genomic prediction (GP) analysis were conducted for pre-harvest sprouting (PHS) tolerance and two of its related traits. For this purpose, an association panel of 190 accessions was phenotyped for PHS (using sprouting score), falling number, and grain color over two years and genotyped with 9904 DArTseq based SNP markers. GWAS for main-effect quantitative trait nucleotides (M-QTNs) using three different models (CMLM, SUPER, and FarmCPU) and epistatic QTNs (E-QTNs) using PLINK were performed. A total of 171 M-QTNs (CMLM, 47; SUPER, 70; FarmCPU, 54) for all three traits, and 15 E-QTNs involved in 20 first-order epistatic interactions were identified. Some of the above QTNs overlapped the previously reported QTLs, MTAs, and cloned genes, allowing delineating 26 PHS-responsive genomic regions that spread over 16 wheat chromosomes. As many as 20 definitive and stable QTNs were considered important for use in marker-assisted recurrent selection (MARS). The gene, TaPHS1, for PHS tolerance (PHST) associated with one of the QTNs was also validated using the KASP assay. Some of the M-QTNs were shown to have a key role in the abscisic acid pathway involved in PHST. Genomic prediction accuracies (based on the cross-validation approach) using three different models ranged from 0.41 to 0.55, which are comparable to the results of previous studies. In summary, the results of the present study improved our understanding of the genetic architecture of PHST and its related traits in wheat and provided novel genomic resources for wheat breeding based on MARS and GP.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01357-5.

QTL Mapping for Wheat Seed Dormancy in a Yangmai16/Zhongmai895 Double Haploid Population

Pre-harvest sprouting (PHS) of wheat reduces grain yield and quality, and it is strongly affected by seed dormancy. Therefore, identification of quantitative trait loci (QTL) for seed dormancy is essential for PHS resistance breeding. A doubled haploid (DH) population, consisting of 174 lines from the cross between Yangmai16 (YM16) and Zhongmai895 (ZM895) was used to detect QTLs for seed dormancy and grain color. For seed dormancy, a total of seven QTLs were detected on chromosomes 2A, 3A, 3D, 4D, 5B and 5D over four environments, among which Qdor.hzau-3A, Qdor.hzau-3D.1 and Qdor.hzau-3D.2 were stably detected in more than two environments. For grain color, only two QTLs, Qgc.hzau-3A and Qgc.hzau-3D were detected on chromosomes 3A and 3D, which physically overlapped with Qdor.hzau-3A and Qdor.hzau-3D.1, respectively. Qdor.hzau-3D.2 has never been reported elsewhere and is probably a novel locus with allelic effect of seed dormancy contributed by weakly dormant parent ZM895, and a KASP marker was developed and validated in a wheat natural population. This study provides new information on the genetic dissection of seed dormancy, which may aid in further improvement for marker-assisted wheat breeding for PHS resistance.

Mapping quantitative trait loci and developing their KASP markers for pre-harvest sprouting resistance of Henan wheat varieties in China

INTRODUCTION

Pre-harvest Sprouting (PHS) seriously affects wheat quality and yield. However, to date there have been limited reports. It is of great urgency to breed resistance varieties via quantitative trait nucleotides (QTNs) or genes for PHS resistance in white-grained wheat.

METHODS

629 Chinese wheat varieties, including 373 local wheat varieties from 70 years ago and 256 improved wheat varieties were phenotyped for spike sprouting (SS) in two environments and genotyped by wheat 660K microarray. These phenotypes were used to associate with 314,548 SNP markers for identifying QTNs for PHS resistance using several multi-locus genome-wide association study (GWAS) methods. Their candidate genes were verified by RNA-seq, and the validated candidate genes were further exploited in wheat breeding.

RESULTS

As a result, variation coefficients of 50% and 47% for PHS in 629 wheat varieties, respectively, in 2020-2021 and 2021-2022 indicated large phenotypic variation, in particular, 38 white grain varieties appeared at least medium resistance, such as Baipimai, Fengchan 3, and Jimai 20. In GWAS, 22 significant QTNs, with the sizes of 0.06% ~ 38.11%, for PHS resistance were stably identified by multiple multi-locus methods in two environments, e.g., AX-95124645 (chr3D:571.35Mb), with the sizes of 36.390% and 45.850% in 2020-2021 and 2021-2022, respectively, was detected by several multi-locus methods in two environments. As compared with previous studies, the AX-95124645 was used to develop Kompetitive Allele-Specific PCR marker QSS.TAF9-3D (chr3D:569.17Mb~573.55Mb) for the first time, especially, it is available in white-grain wheat varieties. Around this locus, nine genes were significantly differentially expressed, and two of them (TraesCS3D01G466100 and TraesCS3D01G468500) were found by GO annotation to be related to PHS resistance and determined as candidate genes.

DISCUSSION

The QTN and two new candidate genes related to PHS resistance were identified in this study. The QTN can be used to effectively identify the PHS resistance materials, especially, all the white-grained varieties with QSS.TAF9-3D-TT haplotype are resistant to spike sprouting. Thus, this study provides candidate genes, materials, and methodological basis for breeding wheat PHS resistance in the future.

Identification and validation of coding and non-coding RNAs involved in high-temperature-mediated seed dormancy in common wheat

INTRODUCTION

Seed dormancy (SD) significantly decreases under high temperature (HT) environment during seed maturation, resulting in pre-harvest sprouting (PHS) damage under prolonged rainfall and wet weather during wheat harvest. However, the molecular mechanism underlying HT-mediated SD remains elusiveSeed dormancy (SD) significantly decreases under high temperature (HT) environment during seed maturation, resulting in pre-harvest sprouting (PHS) damage under prolonged rainfall and wet weather during wheat harvest. However, the molecular mechanism underlying HT-mediated SD remains elusive.

METHODS

Here, the wheat landrace 'Waitoubai' with strong SD and PHS resistance was treated with HT from 21 to 35 days post anthesis (DPA). Then, the seeds under HT and normal temperature (NT) environments were collected at 21 DPA, 28 DPA, and 35 DPA and subjected to whole-transcriptome sequencing.

RESULTS

The phenotypic data showed that the seed germination percentage significantly increased, whereas SD decreased after HT treatment compared with NT, consistent with the results of previous studies. In total, 5128 mRNAs, 136 microRNAs (miRNAs), 273 long non-coding RNAs (lncRNAs), and 21 circularRNAs were found to be responsive to HT, and some of them were further verified through qRT-PCR. In particular, the known gibberellin (GA) biosynthesis gene TaGA20ox1 (TraesCS3D02G393900) was proved to be involved in HT-mediated dormancy by using the EMS-mutagenized wheat cultivar Jimai 22. Similarly, a novel gene TaCDPK21 (TraesCS7A02G267000) involved in the calcium signaling pathway was validated to be associated with HT-mediated dormancy by using the EMS mutant. Moreover, TaCDPK21 overexpression in Arabidopsis and functional complementarity tests supported the negative role of TaCDPK21 in SD. We also constructed a co-expression regulatory network based on differentially expressed mRNAs, miRNAs, and lncRNAs and found that a novel miR27319 was located at a key node of this regulatory network. Subsequently, using Arabidopsis and rice lines overexpressing miR27319 precursor or lacking miR27319 expression, we validated the positive role of miR27319 in SD and further preliminarily dissected the molecular mechanism of miR27319 underlying SD regulation through phytohormone abscisic acid and GA biosynthesis, catabolism, and signaling pathways.

DISCUSSION

These findings not only broaden our understanding of the complex regulatory network of HT-mediated dormancy but also provide new gene resources for improving wheat PHS resistance to minimize PHS damage by using the molecular pyramiding approach.

Low red/far-red ratio can induce cytokinin degradation resulting in the inhibition of tillering in wheat (Triticum aestivum L.)

Shoot branching is inhibited by a low red/far-red ratio (R/FR). Prior studies have shown that the R/FR suppressed Arabidopsis thaliana branching by promotes bud abscisic acid (ABA) accumulation directly. Given that wheat tiller buds are wrapped in leaf sheaths and may not respond rapidly to a R/FR, systemic cytokinin (CTK) may be more critical. Here, systemic hormonal signals including indole-3-acetic acid (IAA), gibberellins (GA) and CTK and bud ABA signals in wheat were tested under a low R/FR. The results showed that a low R/FR reduced the percentage of tiller occurrence of tiller IV and the tiller number per plant. The low R/FR did not rapidly induced ABA accumulation in the tiller IV because of the protection of the leaf sheath and had little effect on IAA content and signaling in the tiller nodes. The significant change in the CTK levels was observed earlier than those of other hormone (ABA, IAA and GA) and exogenous cytokinin restored the CTK levels and tiller number per plant under low R/FR conditions. Further analysis revealed that the decrease in cytokinin levels was mainly associated with upregulation of cytokinin degradation genes (TaCKX5, TaCKX11) in tiller nodes. In addition, exposure to a decreased R/FR upregulated the expression of GA biosynthesis genes (TaGA20ox1, TaGA3ox2), resulting in elevated GA levels, which might further promote CTK degradation in tiller nodes and inhibit tillering. Therefore, our results provide evidence that the enhancement of cytokinin degradation is a novel mechanism underlying the wheat tillering response to a low R/FR.

Identification of a stable major-effect quantitative trait locus for pre-harvest sprouting in common wheat (Triticum aestivum L.) via high-density SNP-based genotyping

A major and stable QTL cQSGR.sau.3D, which can explain 33.25% of the phenotypic variation in SGR, was mapped and validated, and cQSGR.sau.3D was found to be independent of GI. In this study, a recombinant inbred line (RIL) population containing 304 lines derived from the cross of Chuan-nong17 (CN17) and Chuan-nong11 (CN11) was genotyped using the Wheat55K single-nucleotide polymorphism array. A high-density genetic map consisting of 8329 markers spanning 4131.54 cM and distributed across 21 wheat chromosomes was constructed. QTLs for whole spike germination rate (SGR) were identified in multiple years. Six and fourteen QTLs were identified using the Inclusive Composite Interval Mapping-Biparental Populations and Multi-Environment Trial methods, respectively. A total of 106 digenic epistatic QTLs were also detected in this study. One of the additive QTLs, cQSGR.sau.3D, which was mapped in the region from 3.5 to 4.5 cM from linkage group 3D-2 on chromosome 3D, can explain 33.25% of the phenotypic variation in SGR and be considered a major and stable QTL for SGR. This QTL was independent of the seeds' germination traits, such as germination index. One Kompetitive Allele-Specific PCR (KASP) marker, KASP-AX-110772653, which is tightly linked to cQSGR.sau.3D, was developed. The genetic effect of cQSGR.sau.3D on SGR in the RIL and natural populations was successfully confirmed. Furthermore, within the interval in which cQSGR.sau.3D is located in Chinese Spring reference genomes, thirty-seven genes were found. cQSGR.sau.3D may provide new resources for pre-harvest sprouting resistance breeding of wheat in the future.

Improvement of preharvest sprouting resistance with MOTHER OF FT AND TFL 1 + mutated ABA 8'-hydroxylase in white-seeded durum wheat

Improvement of preharvest sprouting (PHS) resistance is an important objective in the breeding of durum wheat (Triticum turgidum ssp. durum (Desf.) Husn.) in Japan, where the harvest timing overlaps with the rainy season. In a previous study, we showed that an R-gene associated with red seed color was the most effective at promoting PHS resistance in durum wheat. However, red-seeded durum wheat is not popular because it discolors pasta. Here, to improve PHS resistance without the R-gene, we introduced a PHS resistance allele of MOTHER OF FT AND TFL 1 (MFT) and a mutated ABA 8'-hydroxylase (ABA8'OH1-A), which is involved in abscisic acid (ABA) catabolism, singly or together into white-seeded durum wheat. The introduction of both genes reliably and stably improved PHS resistance under all tested conditions. Modification of ABA catabolism might be an effective way to improve PHS resistance in durum wheat. Our findings will contribute to improved PHS resistance in breeding for white-seeded durum wheat.

Genetic variation of seed dormancy in wheat (Triticum aestivum L.) is mediated by transcriptional regulation of abscisic acid metabolism and signaling

Abscisic acid (ABA) regulates seed dormancy and therefore preharvest sprouting (PHS) in wheat. This study investigated the contribution of transcriptional regulation of ABA metabolism and signaling genes to genetic variation in dormancy of wheat seeds. Our results showed that genetic variation in seed dormancy is highly correlated with ABA content (r > 0.86), which, in turn, was closely associated with the expression levels of ABA biosynthesis genes, TaNCED1 (r = 0.78) and TaNCED2 (r = 0.67). A relatively lower correlation was observed between ABA content and the expression levels of ABA catabolism genes, TaCYP707A1 (r = 0.51) and TaCYP707A2 (r = 0.57). The expression level of TaABI5 exhibited strong associations with the levels of ABA (r = 0.8) and seed dormancy (r > 0.9), indicating the importance of seed ABA sensitivity in mediating genetic variation in dormancy. Furthermore, high positive correlations were prevalent between the expression patterns of TaABI5 and TaNCED1 (r = 0.91) or TaNCED2 (r = 0.82). Overall, our results implicated the significance of TaNCEDs and TaABI5 in regulating genetic variation in ABA level and sensitivity and thereby seed dormancy, highlighting the potential use of these genes to develop molecular markers for incorporating PHS resistance in wheat.

TaFDL2-1A confers drought stress tolerance by promoting ABA biosynthesis, ABA responses, and ROS scavenging in transgenic wheat

Plants have developed various protective mechanisms to survive drought stress. Previously, it was shown that a wheat bZIP transcription factor gene TaFD-Like2-1A (TaFDL2-1A) can confer drought tolerance in Arabidopsis. However, the biological functions related to drought stress tolerance of TaFDL2-1A in wheat (Triticum aestivum L.) remain unclear. In the present study, overexpression of TaFDL2-1A in the wheat cultivar Fielder improved drought resistance and conferred abscisic acid (ABA) hypersensitivity. Further analysis showed that overexpression of TaFDL2-1A increased the hypersensitivity of stomata to drought stress and endogenous ABA content under drought conditions. Genetic analysis and transcriptional regulation analysis indicated that TaFDL2-1A binds directly to the promoter fragments of TaRAB21s and TaNCED2s via ACGT core cis-elements, thereby activating their expression, leading to enhanced ABA responses and endogenous ABA accumulation. In addition, our results demonstrate that overexpression of TaFDL2-1A results in higher SOD and GPX activities in wheat under drought conditions by promoting the expression of TaSOD1 and TaGPx1-D, indicating enhanced reactive oxygen species (ROS) scavenging. These results imply that TaFDL2-1A positively regulates ABA biosynthesis, ABA responses, and ROS scavenging to improve drought stress tolerance in transgenic wheat. Our findings improve our understanding of the mechanisms that allow the wheat bZIP transcription factor to improve drought resistance and provide a useful reference gene for breeding programs to enhance drought resistance.

Folate (vitamin B9) content analysis in bread wheat (Triticum aestivum L.)

Vitamin B9, particularly folic acid, is an essential molecule for human health. Wheat flour is one of the major sources of calorie intake by humans. The selection of folate-rich genotypes in wheat breeding can enhance the natural folate value in the daily diet. This study used a precise, high-performance liquid chromatography (HPLC) assay to analyze folate content in a 262-accession Chinese wheat mini-core collection (MCC) grown under three environments. Four folate derivatives in grains including tetrahydrofolate (THF), 5-methyltetrahydrofolate (5-CH₃-THF), 5-formyltetrahydrofolate (5-CHO-THF), and 5,10-methenyltetrahydrofolate (5,10-CH⁺THF) were considered. An association analysis of water regimes, accession types, released years, geographical origin, and agronomic traits with folate content was conducted for the first time. There was a large amount of variation in folate content in the analyzed accessions, with genotype identified as the main influencing factor. Total folate content was significantly correlated with the content of the four MCC derivatives under the three environments. 5-CH₃-THF and 5-CHO-THF were the most abundant among the four folate derivatives and were positively correlated with high folate content. The 12 accessions with the highest folate content showed an average of more than 80 μg/100 g. The analysis demonstrated that this Chinese wheat had not undergone extensive selection for folate content during breeding, which is unrelated to the geographical origin, accession types, winter/spring types, and grain colors of wheat. The content of THF, 5-CH₃-THF, and 5,10-CH⁺THF was significantly negatively correlated with grain width, grain thickness, and thousand kernel weight. A relatively weak negative relationship manifested between folate contents and flowering date, whereas no significant correlation with tiller number, grain number per spike, maturity date, height, and spike length was detected. The investigation benefits wheat breeders for folate enhancement.

QTL mapping and KASP marker development for seed vigor related traits in common wheat

Seed vigor is an important parameter of seed quality, and identification of seed vigor related genes can provide an important basis for highly efficient molecular breeding in wheat. In the present study, a doubled haploid (DH) population with 174 lines derived from a cross between Yangmai16 and Zhongmai 895 was used to evaluate 10 seed vigor related traits in Luoyang during the 2018-2019 cropping season and in Mengjin and Luoning Counties during 2019-2020 cropping season for three environments. Quantitative trait locus (QTL) mapping of 10 seed vigor related traits in the DH population resulted in the discovery/identification of 28 QTLs on chromosomes 2B, 3D, 4B, 4D, 5A, 5B, 6A, 6B, 6D, 7A and 7D, explaining 3.6-23.7% of the phenotypic variances. Among them, one QTL cluster for shoot length, root length and vigor index was mapped between AX-89421921 and Rht-D1_SNP on chromosome 4D in the physical intervals of 18.78-19.29 Mb (0.51 Mb), explaining 9.2-20.5% of the phenotypic variances. Another QTL for these traits was identified at the physical position 185.74 Mb on chromosome 5B, which was flanked by AX-111465230 and AX-109519938 and accounted for 8.0-13.3% of the phenotypic variances. Two QTLs for shoot length, shoot fresh weight and shoot dry weight were identified in the marker intervals of AX-109384026-AX-111120402 and AX-111651800-AX-94443918 on chromosomes 6A and 6B, explaining 8.2-11.7% and 3.6-10.3% of the phenotypic variance, respectively; both alleles for increasing phenotypic values were derived from Yangmai 16. We also developed the KASP markers for the QTL cluster QVI.haust-4D.1/QSL.haust-4D/QRL.haust-4D, and validated in an international panel of 135 wheat accessions. The germplasm, genes and KASP markers were developed for breeders to improve wheat varieties with seed vigor related traits.

Fine mapping of the Hairy glume (Hg) gene in a chromosome variation region at the distal terminus of 1AS

Trichomes are differentiated epidermal cells and exist on above-ground organs of nearly all land plants with important roles in resistance to a wide range of biotic and abiotic stresses. We attempted to obtain candidate gene (s) for Hairy glume (Hg), responsible for the trichome on wheat glume, by using bulked segregant exome capture sequencing (BSE-Seq), while Hg was only mapped in 0.52-3.26 Mb of 1AS. To further fine map this gene and identify candidate genes in this region, a near isogenic line-derived population consisting of 2,050 F2 lines was generated in the present study. By analyzing this population, Hg was fine mapped into a 0.90 cM region covering a physical distance of ~825.03 Kb encompassing 6 high- and 23 low-confidence genes in the reference genome of Chinese Spring. A presence-absence variation was identified in the fine mapping region through analyses of sequence-tagged sites markers and genome sequences of the hairy glume parent of the near isogenic lines. The results presented here will be useful for further cloning Hg in wheat.

QTL Analysis for Bread Wheat Seed Size, Shape and Color Characteristics Estimated by Digital Image Processing

The size, shape, and color of wheat seeds are important traits that are associated with yield and flour quality (size, shape), nutritional value, and pre-harvest sprouting (coat color). These traits are under multigenic control, and to dissect their molecular and genetic basis, quantitative trait loci (QTL) analysis is used. We evaluated 114 recombinant inbred lines (RILs) in a bi-parental RIL mapping population (the International Triticeae Mapping Initiative, ITMI/MP) grown in 2014 season. We used digital image analysis for seed phenotyping and obtained data for seven traits describing seed size and shape and 48 traits of seed coat color. We identified 212 additive and 34 pairs of epistatic QTLs on all the chromosomes of wheat genome except chromosomes 1A and 5D. Many QTLs were overlapping. We demonstrated that the overlap between QTL regions was low for seed size/shape traits and high for coat color traits. Using the literature and KEGG data, we identified sets of genes in Arabidopsis and rice from the networks controlling seed size and color. Further, we identified 29 and 14 candidate genes for seed size-related loci and for loci associated with seed coat color, respectively.

Identification of effective alleles and haplotypes conferring pre-harvest sprouting resistance in winter wheat cultivars

BACKGROUND

Pre-harvest sprouting (PHS) is a serious limiting factor for wheat (Triticum aestivum L.) grain yield and end-use quality. Identification of reliable molecular markers and PHS-resistant germplasms is vital to improve PHS resistance by molecular marker-assisted selection (MAS), but the effects of allelic variation and haplotypes in genes conferring PHS resistance in winter wheat cultivars are less understood.

RESULTS

Resistance to PHS was tested in 326 commercial winter wheat cultivars for three consecutive growing seasons from 2018-2020. The effects of alleles and haplotypes of 10 genes associated with PHS resistance were determined for all cultivars and were validated by introgressing the PHS-resistance allele and haplotype into a susceptible wheat cultivar. High level of phenotypic variation in PHS resistance was observed in this set of cultivars and 8 of them were highly resistant to PHS with stable germination index (GI) of less than 25% in each individual year. Allelic effects of nine genes and TaMFT haplotype analysis demonstrated that the haplotype Hap1 with low-GI alleles at five positions had the best PHS resistance. This haplotype has the priority to use in improving PHS resistance because of its high effectiveness and rare present in the current commercial cultivars. Among 14 main allelic combinations (ACs) identified, the AC1 carrying the haplotype Hap1 and the TaSdr-B1a allele had better PHS resistance than the other classes. The introgression of Hap1 and TaSdr-B1a is able to significantly improve the PHS resistance in the susceptible cultivar Lunxuan 13.

CONCLUSIONS

The effectiveness of alleles conferring PHS resistance in winter wheat cultivars was determined and the useful alleles and haplotypes were identified, providing valuable information for parental selection and MAS aiming at improving PHS-resistance in winter wheat. The identification of the PHS-resistant cultivars without known resistance alleles offers an opportunity to explore new PHS-resistant genes.

Genome-wide association mapping and genomic prediction for pre‑harvest sprouting resistance, low α-amylase and seed color in Iranian bread wheat

BACKGROUND

Pre-harvest sprouting (PHS) refers to a phenomenon, in which the physiologically mature seeds are germinated on the spike before or during the harvesting practice owing to high humidity or prolonged period of rainfall. Pre-harvest sprouting (PHS) remarkably decreases seed quality and yield in wheat; hence it is imperative to uncover genomic regions responsible for PHS tolerance to be used in wheat breeding. A genome-wide association study (GWAS) was carried out using 298 bread wheat landraces and varieties from Iran to dissect the genomic regions of PHS tolerance in a well-irrigated environment. Three different approaches (RRBLUP, GBLUP and BRR) were followed to estimate prediction accuracies in wheat genomic selection.

RESULTS

Genomes B, A, and D harbored the largest number of significant marker pairs (MPs) in both landraces (427,017, 328,006, 92,702 MPs) and varieties (370,359, 266,708, 63,924 MPs), respectively. However, the LD levels were found the opposite, i.e., genomes D, A, and B have the highest LD, respectively. Association mapping by using GLM and MLM models resulted in 572 and 598 marker-trait associations (MTAs) for imputed SNPs (- log10 P > 3), respectively. Gene ontology exhibited that the pleitropic MPs located on 1A control seed color, α-Amy activity, and PHS. RRBLUP model indicated genetic effects better than GBLUP and BRR, offering a favorable tool for wheat genomic selection.

CONCLUSIONS

Gene ontology exhibited that the pleitropic MPs located on 1A can control seed color, α-Amy activity, and PHS. The verified markers in the current work can provide an opportunity to clone the underlying QTLs/genes, fine mapping, and genome-assisted selection.Our observations uncovered key MTAs related to seed color, α-Amy activity, and PHS that can be exploited in the genome-mediated development of novel varieties in wheat.

Fine mapping of Pm58 from Aegilops tauschii conferring powdery mildew resistance

The powdery mildew resistance gene Pm58 was traced to a 141.3-kb interval with the co-segregating marker Xkasp68500 in wheat breeding. Pm58 is a powdery mildew resistance gene identified in Aegilops tauschii accession TA1662 and effective in a common wheat background. To finely map Pm58, an F₂ population of 676 plants derived from the cross T093 × TA1662 was used for recombinant screening. We obtained 13 recombinants that occurred between the flanking markers Xhnu670 and Xhnu186. Genotyping and phenotyping these recombinant F_2:3 families delimited Pm58 to a 0.22-cM interval (Xsts20220-Xkasp61553) on chromosome arm 2DS. The region carrying the Pm58 locus was approximately 141.3-kb, which contained eight annotated genes according to the reference genome sequence of Ae. tauschii AL8/78. Haplotype analysis of 178 Ae. tauschii accessions using the candidate gene-specific markers identified a disease resistance gene AET2Gv20068500 as a candidate for Pm58. Comparative mapping of the Pm58-containing interval revealed two presence/absence variations (PAVs) between AL8/78 and common wheat Chinese Spring. PAV-1 resides in the 3'-end of AET2Gv20068500. The majority of 158 common wheat cultivars (84.8%) displayed the absence of a 14.1-kb fragment in the PAV-1 region, which was confirmed by aligning the targeted genome sequences of the other sequenced Ae. tauschii accessions and common wheat cultivars. A co-segregating marker Xkasp68500 developed from AET2Gv20068500 can distinguish TA1662 from all randomly selected common wheat cultivars and will be instrumental for tracking Pm58 in breeding programs.

Genome-Wide Linkage Mapping for Preharvest Sprouting Resistance in Wheat Using 15K Single-Nucleotide Polymorphism Arrays

Preharvest sprouting (PHS) significantly reduces grain yield and quality. Identification of genetic loci for PHS resistance will facilitate breeding sprouting-resistant wheat cultivars. In this study, we constructed a genetic map comprising 1,702 non-redundant markers in a recombinant inbred line (RIL) population derived from cross Yangxiaomai/Zhongyou9507 using the wheat 15K single-nucleotide polymorphism (SNP) assay. Four quantitative trait loci (QTL) for germination index (GI), a major indicator of PHS, were identified, explaining 4.6-18.5% of the phenotypic variances. Resistance alleles of Qphs.caas-3AL, Qphs.caas-3DL, and Qphs.caas-7BL were from Yangxiaomai, and Zhongyou9507 contributed a resistance allele in Qphs.caas-4AL. No epistatic effects were detected among the QTL, and combined resistance alleles significantly increased PHS resistance. Sequencing and linkage mapping showed that Qphs.caas-3AL and Qphs.caas-3DL corresponded to grain color genes Tamyb10-A and Tamyb10-D, respectively, whereas Qphs.caas-4AL and Qphs.caas-7BL were probably new QTL for PHS. We further developed cost-effective, high-throughput kompetitive allele-specific PCR (KASP) markers tightly linked to Qphs.caas-4AL and Qphs.caas-7BL and validated their association with GI in a test panel of cultivars. The resistance alleles at the Qphs.caas-4AL and Qphs.caas-7BL loci were present in 72.2 and 16.5% cultivars, respectively, suggesting that the former might be subjected to positive selection in wheat breeding. The findings provide not only genetic resources for PHS resistance but also breeding tools for marker-assisted selection.

Exploring the genic resources underlying metabolites through mGWAS and mQTL in wheat: From large-scale gene identification and pathway elucidation to crop improvement

Common wheat (Triticum aestivum L.) is a leading cereal crop, but has lagged behind with respect to the interpretation of the molecular mechanisms of phenotypes compared with other major cereal crops such as rice and maize. The recently available genome sequence of wheat affords the pre-requisite information for efficiently exploiting the potential molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets. Meanwhile, the successful application of metabolomics as an emergent large-scale profiling methodology in several species has demonstrated this approach to be accessible for reaching the above goals. One such productive avenue is combining metabolomics approaches with genetic designs. However, this trial is not as widespread as that for sequencing technologies, especially when the acquisition, understanding, and application of metabolic approaches in wheat populations remain more difficult and even arguably underutilized. In this review, we briefly introduce the techniques used in the acquisition of metabolomics data and their utility in large-scale identification of functional candidate genes. Considerable progress has been made in delivering improved varieties, suggesting that the inclusion of information concerning these metabolites and genes and metabolic pathways enables a more explicit understanding of phenotypic traits and, as such, this procedure could serve as an -omics-informed roadmap for executing similar improvement strategies in wheat and other species.

Transcriptome Reveals Roles of Lignin-Modifying Enzymes and Abscisic Acid in the Symbiosis of Mycena and Gastrodia elata

Gastrodia elata is a well-known medicinal and heterotrophic orchid. Its germination, limited by the impermeability of seed coat lignin and inhibition by abscisic acid (ABA), is triggered by symbiosis with fungi such as Mycena spp. However, the molecular mechanisms of lignin degradation by Mycena and ABA biosynthesis and signaling in G. elata remain unclear. In order to gain insights into these two processes, this study analyzed the transcriptomes of these organisms during their dynamic symbiosis. Among the 25 lignin-modifying enzyme genes in Mycena, two ligninolytic class II peroxidases and two laccases were significantly upregulated, most likely enabling Mycena hyphae to break through the lignin seed coats of G. elata. Genes related to reduced virulence and loss of pathogenicity in Mycena accounted for more than half of annotated genes, presumably contributing to symbiosis. After coculture, upregulated genes outnumbered downregulated genes in G. elata seeds, suggesting slightly increased biological activity, while Mycena hyphae had fewer upregulated than downregulated genes, indicating decreased biological activity. ABA biosynthesis in G. elata was reduced by the downregulated expression of 9-cis-epoxycarotenoid dioxygenase (NCED-2), and ABA signaling was blocked by the downregulated expression of a receptor protein (PYL12-like). This is the first report to describe the role of NCED-2 and PYL12-like in breaking G. elata seed dormancy by reducing the synthesis and blocking the signaling of the germination inhibitor ABA. This study provides a theoretical basis for screening germination fungi to identify effective symbionts and for reducing ABA inhibition of G. elata seed germination.

Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement

Increasing crop production is necessary to feed the world's expanding population, and crop breeders often utilize genetic variations to improve crop yield and quality. However, the narrow diversity of the wheat D genome seriously restricts its selective breeding. A practical solution is to exploit the genomic variations of Aegilops tauschii via introgression. Here, we established a rapid introgression platform for transferring the overall genetic variations of A. tauschii to elite wheats, thereby enriching the wheat germplasm pool. To accelerate the process, we assembled four new reference genomes, resequenced 278 accessions of A. tauschii and constructed the variation landscape of this wheat progenitor species. Genome comparisons highlighted diverse functional genes or novel haplotypes with potential applications in wheat improvement. We constructed the core germplasm of A. tauschii, including 85 accessions covering more than 99% of the species' overall genetic variations. This was crossed with elite wheat cultivars to generate an A. tauschii-wheat synthetic octoploid wheat (A-WSOW) pool. Laboratory and field analysis with two examples of the introgression lines confirmed its great potential for wheat breeding. Our high-quality reference genomes, genomic variation landscape of A. tauschii and the A-WSOW pool provide valuable resources to facilitate gene discovery and breeding in wheat.

Genetic Mapping and Identification of the Candidate Gene for White Seed Coat in Cucurbita maxima

Seed coat color is an important agronomic trait of edible seed pumpkin in Cucurbita maxima. In this study, the development pattern of seed coat was detected in yellow and white seed coat accessions Wuminglv and Agol. Genetic analysis suggested that a single recessive gene white seed coat (wsc) is involved in seed coat color regulation in Cucurbita maxima. An F₂ segregating population including 2798 plants was used for fine mapping and a candidate region containing nine genes was identified. Analysis of 54 inbred accessions revealed four main Insertion/Deletion sites in the promoter of CmaCh15G005270 encoding an MYB transcription factor were co-segregated with the phenotype of seed coat color. RNA-seq analysis and qRT-PCR revealed that some genes involved in phenylpropanoid/flavonoid metabolism pathway displayed remarkable distinction in Wuminglv and Agol during the seed coat development. The flanking InDel marker S1548 was developed to predict the seed coat color in the MAS breeding with an accuracy of 100%. The results may provide valuable information for further studies in seed coat color formation and structure development in Cucurbitaceae crops and help the molecular breeding of Cucurbita maxima.