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

Identification and molecular marker analysis of PHS resistance of high generation wheat materials

Pre-harvest sprouting (PHS) of wheat will significantly reduce the yield and quality of wheat and threaten the safety of wheat production in China. Screening and utilization of resistant germplasm and functional molecular markers is the fundamental way to reduce the harm of PHS. In this study, 238 high generation lines were used to identify and evaluate PHS resistance by grain germination method, and the distribution of PHS function markers Vp1B3, myb10-D, PM19-A1 and MFT-A2 in resistant germplasm was determined and their breeding effects were evaluated. Phenotypic identification showed that there were significant differences in the relative seed germination index (RSGI) of 238 wheat germplasm resources. The RSGI ranged from 0.03 to 1, and the average RSGI was 0.31. The difference significance analysis showed that the RSGI of the alleles of functional markers Vp1B3, PM19-A1 and MFT-A2 were significantly different, suggesting that Vp1B3, PM19-A1 and MFT-A2 could be used for detection of PHS resistance genotypes and marker-assisted breeding. Based on the phenotype and genotype results, three red wheat materials with high PHS resistance (23JD392, 23JD393 and 23JD481) and four white wheat materials with high PHS resistance (23JD025, 23JD085, 23JD541 and 23JD655) were selected. At the same time, the high resistance materials 23JD392 and 23JD393 which amplified TaVp-1Bc/TaPM19-A1a/TaMFT-A2a had the lowest RSGI. These results can be used for genetic breeding and layout of wheat varieties resistant to PHS, indicating that resistance can be significantly improved by using functional markers. This study combined molecular markers and phenotypic identification to screen anti-PHS materials, which is expected to improve the level of wheat PHS resistance.

Comparative miRNAome combined with transcriptome and degradome analysis reveals a novel miRNA-mRNA regulatory network associated with starch metabolism affecting pre-harvest sprouting resistance in wheat

BACKGROUND

Pre-harvest sprouting (PHS) is one of the most important problems associated with the severe decrease of yield and quality under disaster weather of continuous rain in wheat harvesting stage. At present, the functions and mechanisms related to the involvement of post-transcriptional regulation has not been studied very clearly in PHS resistance.

RESULTS

This study compared the differences of germinated seeds in miRNAome between the PHS-tolerant and PHS-susceptible white wheat varieties. A total of 1879 miRNAs were identified from three different stages during seed germination. In order to further obtain candidate miRNAs, the different datasets of differentially expressed miRNAs were excavated by using differential-expression and time-series analysis. Combined with degradome data, the miRNA-mRNA networks analysis was performed after genome-wide screening of target genes, and then KEGG enrichment highlighted that the starch and sucrose metabolism pathway related to PHS was specifically enriched in an especial target-gene dataset derived from R12R18-HE miRNAs. Based on transcriptome data, a network associated with starch metabolism was systematically and completely reconstructed in wheat. Then, the starch degradation pathway controlled by seven miRNA-RNA pairs were supposed to be the essential regulation center for seed germination in wheat, which also could play a critical role on the PHS resistance.

CONCLUSION

Our findings revealed the complex impact of the miRNA-mediated mechanism for forming intrinsic and inherent differences, which resulting in significant difference on PHS performance between white wheat varieties.

ABA and Pre-Harvest Sprouting Differences in Knockout Lines of OsPHS3 Encoding Carotenoid Isomerase via CRISPR/Cas9 in Rice

We generated and characterized knockout mutant lines of the OsPHS3 gene using the CRISPR/Cas9 system. The knockout lines of the OsPHS3 gene showed that 1 bp and 7 bp deletion, early termination codons were used for protein production. Agronomic characteristics of knock-out lines were reduced in plant height, culm diameter, panicle length, seed size and weight, except for the number of tillers. In addition, we analyzed the expression levels of carotenoid biosynthesis genes by qRT-PCR. Among the genes encoding carotenoid metabolic pathway enzymes, the level of transcripts of PSY1, PSY2, PSY3, PDS and ZDS were higher in the KO lines than in the WT line. In contrast, transcription of the ε-LCY, β-LCY and ZEP1 genes were downregulated in the KO lines compared to the WT line. Also, the KO lines decreased carotenoid content and ABA amount compared to WT, while preharvest sprouts increased. These results suggested that they would certainly help explain the molecular mechanisms of PHS in other crops, such as wheat and barley, which are susceptible to PHS.

Comparative transcriptomes and WGCNA reveal hub genes for spike germination in different quinoa lines

BACKGROUND

Quinoa, as a new food crop, has attracted extensive attention at home and abroad. However, the natural disaster of spike germination seriously threatens the quality and yield of quinoa. Currently, there are limited reports on the molecular mechanisms associated with spike germination in quinoa.

RESULTS

In this study, we utilized transcriptome sequencing technology and successfully obtained 154.51 Gb of high-quality data with a comparison efficiency of more than 88%, which fully demonstrates the extremely high reliability of the sequencing results and lays a solid foundation for subsequent analysis. Using these data, we constructed a weighted gene co-expression network (WGCNA) related to starch, sucrose, α-amylase, and phenolic acid metabolites, and screened six co-expression modules closely related to spike germination traits. Two of the modules associated with physiological indicators were analyzed in depth, and nine core genes were finally predicted. Further functional annotation revealed four key transcription factors involved in the regulation of dormancy and germination processes: gene LOC110698065, gene LOC110696037, gene LOC110736224, and gene LOC110705759, belonging to the bHLH, NF-YA, MYB, and FAR1 gene families, respectively.

CONCLUSIONS

These results provide clues to identify the core genes involved in quinoa spike germination. This will ultimately provide a theoretical basis for breeding new quinoa varieties with resistance.

Utilizing Short Interspersed Nuclear Element as a Genetic Marker for Pre-Harvest Sprouting in Wheat

Pre-harvest sprouting (PHS) is a complex abiotic stress caused by multiple exogenous and endogenous variables that results in random but significant quality and yield loss at the terminal crop stage in more than half of the wheat-producing areas of the world. Systematic research over more than five decades suggests that addressing this challenge requires tools beyond the traditional genetic manipulation approach. Previous molecular studies indicate a possible role of epigenetics in the regulation of seed dormancy and PHS in crops, especially through RNA-directed DNA methylation (RdDM) pathways mediated by Argonaute (AGO) proteins. In this study, we explore the role of the AGO802B gene associated with PHS resistance in wheat, through the presence of a SINE retrotransposon insertion. The current study found the SINE insertion at 3'UTR of the TaAGO802B present in 73.2% of 41 cultivars analyzed and in 92.6% of the resistant cultivar subset. The average expression of TaAGO802B in cultivars with the SINE insertion was 73.3% lower than in cultivars without insertion. This study also indicated a significant positive correlation between the PHS score and methylation levels in the cultivars. The resistant cultivars with the SINE insertion recorded 54.7% lower methylation levels than susceptible cultivars. Further analysis of a DH population (Sadash × P2711) reveals that SINE insertion co-segregates with PHS resistance. This sets forth the SINE insertion in TaAGO802B as a genetic marker for screening wheat germplasm and as an efficient tool for breeding PHS-resistant wheat cultivars.

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.

Development of Novel Monoclonal Antibodies to Wheat Alpha-Amylases Associated with Grain Quality Problems That Are Increasing with Climate Change

Accurate, rapid testing platforms are essential for early detection and mitigation of late maturity α-amylase (LMA) and preharvest sprouting (PHS) in wheat. These conditions are characterized by elevated α-amylase levels and negatively impact flour quality, resulting in substantial economic losses. The Hagberg-Perten Falling Number (FN) method is the industry standard for measuring α-amylase activity in wheatmeal. However, FN does not directly detect α-amylase and has major limitations. Developing α-amylase immunoassays would potentially enable early, accurate detection regardless of testing environment. With this goal, we assessed an expression of α-amylase isoforms during seed development. Transcripts of three of the four isoforms were detected in developing and mature grain. These were cloned and used to develop E. coli expression lines expressing single isoforms. After assessing amino acid conservation between isoforms, we identified peptide sequences specific to a single isoform (TaAMY1) or that were conserved in all isoforms, to develop monoclonal antibodies with targeted specificities. Three monoclonal antibodies were developed, anti-TaAMY1-A, anti-TaAMY1-B, and anti-TaAMY1-C. All three detected endogenous α-amylase(s). Anti-TaAMY1-A was specific for TaAMY1, whereas anti-TaAMY1-C detected TaAMY1, 2, and 4. Thus, confirming that they possessed the intended specificities. All three antibodies were shown to be compatible for use with immuno-pulldown and immuno-assay applications.

CRISPR-mediated acceleration of wheat improvement: advances and perspectives

Common wheat (Triticum aestivum) is one of the most widely cultivated and consumed crops globally. In the face of limited arable land and climate changes, it is a great challenge to maintain current and increase future wheat production. Enhancing agronomic traits in wheat by introducing mutations across all three homoeologous copies of each gene has proven to be a difficult task due to its large genome with high repetition. However, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease (Cas) genome editing technologies offer a powerful means of precisely manipulating the genomes of crop species, thereby opening up new possibilities for biotechnology and breeding. In this review, we first focus on the development and optimization of the current CRISPR-based genome editing tools in wheat, emphasizing recent breakthroughs in precise and multiplex genome editing. We then describe the general procedure of wheat genome editing and highlight different methods to deliver the genome editing reagents into wheat cells. Furthermore, we summarize the recent applications and advancements of CRISPR/Cas technologies for wheat improvement. Lastly, we discuss the remaining challenges specific to wheat genome editing and its future prospects.

Editorial for the Special Issue "Genetics Studies on Wheat"

Wheat (Triticum aestivum L [...].