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.

A plasma membrane-localized transporter remobilizes aleurone layer magnesium for seed germination in rice.

The aleurone layer in cereal grains acts as a major reservoir of essential mineral nutrients, significantly influencing seed germination. However, the molecular mechanism underlying the redistribution of nutrients from the aleurone layer in the germinating seed is still not well understood. Here, in rice, we identified a plasma membrane (PM) localized magnesium transporter, MAGNESIUM RELEASE TRANSPORTER 3 (MGR3), is critical for seed germination. OsMGR3 is predominantly expressed in the aleurone layer cells of endosperm, facilitating magnesium remobilization during germination. Non-invasive Micro-test Technology assay data demonstrated that the loss-of-function of OsMGR3 restrained magnesium efflux from the aleurone layer. In the embryo/endosperm grafting experiment, we observed that the mutation of OsMGR3 in the aleurone layer suppressed the growth and differentiation of the embryo during germination. Furthermore, magnesium fluorescence imaging revealed the osmgr3 mutant seeds showed impaired exportation of aleurone layer-stored magnesium to the embryo, consequently delaying germination. Importantly, we discovered that disrupting OsMGR3 could inhibit pre-harvest sprouting without affecting rice yield and quality. Therefore, the magnesium efflux transporter OsMGR3 in the aleurone layer represents a promising genetic target for future agronomic trait improvement.

In silico analysis of the wheat BBX gene family and identification of candidate genes for seed dormancy and germination.

BACKGROUND: B-box (BBX) proteins are a type of zinc finger proteins containing one or two B-box domains. They play important roles in development and diverse stress responses of plants, yet their roles in wheat remain unclear. RESULTS: In this study, 96 BBX genes were identified in the wheat genome and classified into five subfamilies. Subcellular localization prediction results showed that 68 TaBBXs were localized in the nucleus. Protein interaction prediction analysis indicated that interaction was one way that these proteins exerted their functions. Promoter analysis indicated that TaBBXs may play important roles in light signal, hormone, and stress responses. qRT-PCR analysis revealed that 14 TaBBXs were highly expressed in seeds compared with other tissues. These were probably involved in seed dormancy and germination, and their expression patterns were investigated during dormancy acquisition and release in the seeds of wheat varieties Jing 411 and Hongmangchun 21, showing significant differences in seed dormancy and germination phenotypes. Subcellular localization analysis confirmed that the three candidates TaBBX2-2 A, TaBBX4-2 A, and TaBBX11-2D were nuclear proteins. Transcriptional self-activation experiments further demonstrated that TaBBX4-2A was transcriptionally active, but TaBBX2-2A and TaBBX11-2D were not. Protein interaction analysis revealed that TaBBX2-2A, TaBBX4-2A, and TaBBX11-2D had no interaction with each other, while TaBBX2-2A and TaBBX11-2D interacted with each other, indicating that TaBBX4-2A may regulate seed dormancy and germination by transcriptional regulation, and TaBBX2-2A and TaBBX11-2D may regulate seed dormancy and germination by forming a homologous complex. CONCLUSIONS: In this study, the wheat BBX gene family was identified and characterized at the genomic level by bioinformatics analysis. These observations provide a theoretical basis for future studies on the functions of BBXs in wheat and other species.

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 characterization of SDR gene family and its potential role in seed dormancy of Brassica napus L.

Rapeseed (Brassica napus L.) with short or no dormancy period are easy to germinate before harvest (pre-harvest sprouting, PHS). PHS has seriously decreased seed weight and oil content in B. napus. Short-chain dehydrogenase/ reductase (SDR) genes have been found to related to seed dormancy by promoting ABA biosynthesis in rice and Arabidopsis. In order to clarify whether SDR genes are the key factor of seed dormancy in B. napus, homology sequence blast, protein physicochemical properties, conserved motif, gene structure, cis-acting element, gene expression and variation analysis were conducted in present study. Results shown that 142 BnaSDR genes, unevenly distributed on 19 chromosomes, have been identified in B. napus genome. Among them, four BnaSDR gene clusters present in chromosome A04、A05、C03、C04 were also identified. These 142 BnaSDR genes were divided into four subfamilies on phylogenetic tree. Members of the same subgroup have similar protein characters, conserved motifs, gene structure, cis-acting elements and tissue expression profiles. Specially, the expression levels of genes in subgroup A, B and C were gradually decreased, but increased in subgroup D with the development of seeds. Among seven higher expressed genes in group D, six BnaSDR genes were significantly higher expressed in weak dormancy line than that in nondormancy line. And the significant effects of BnaC01T0313900ZS and BnaC03T0300500ZS variation on seed dormancy were also demonstrated in present study. These findings provide a key information for investigating the function of BnaSDRs on seed dormancy in B. napus.

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.

A rice seed-specific glycine-rich protein OsDOR1 interacts with GID1 to repress GA signaling and regulates seed dormancy.

Seed dormancy is an important agronomic trait under the control of complex genetic and environmental interactions, which have not been yet comprehensively understood. From the field screening of rice mutant library generated by a Ds transposable element, we identified a pre-harvest sprouting (PHS) mutant dor1. This mutant has a single insertion of Ds element at the second exon of OsDOR1 (LOC_Os03g20770), which encodes a novel seed-specific glycine-rich protein. This gene successfully complemented the PHS phenotype of dor1 mutant and its ectopic expression enhanced seed dormancy. Here, we demonstrated that OsDOR1 protein binds to the GA receptor protein, OsGID1 in rice protoplasts, and interrupts with the formation OsGID1-OsSLR1 complex in yeast cells. Co-expression of OsDOR1 with OsGID1 in rice protoplasts attenuated the GA-dependent degradation of OsSLR1, the key repressor of GA signaling. We showed the endogenous OsSLR1 protein level in the dor1 mutant seeds is significantly lower than that of wild type. The dor1 mutant featured a hypersensitive GA-response of α-amylase gene expression during seed germination. Based on these findings, we suggest that OsDOR1 is a novel negative player of GA signaling operated in the maintenance of seed dormancy. Our findings provide a novel source of PHS resistance.

Overexpression of Taetr1-1 promotes enhanced seed dormancy and ethylene insensitivity in wheat.

MAIN CONCLUSION: Taetr1-1 can promote enhanced seed dormancy and ethylene insensitivity in wheat, indicating a conserved function of ETR1 in regulating seed dormancy. Lots of wheat cultivars have weak dormant seed. Weak seed dormancy can cause pre-harvest sprouting (PHS) in grain which significantly reduces grain yield and quality. The mining of causal genes of PHS resistance will serve to enhance breeding selection and cultivar development. In a previous study in Arabidopsis, we identified reduced dormancy 3 as a loss-of-function mutant of the ethylene receptor 1 (ETR1), which can control seed dormancy through the ERF12-TPL-DOG1 pathway. However, it is unknown whether ETR1 also functions in the regulation of wheat seed dormancy. To identify the regulatory role of ETR1 in wheat, we cloned TaETR1 and overexpressed the gain-of-function mutant Taetr1-1. The result indicated that overexpression of Taetr1-1 can promote enhanced seed dormancy and ethylene insensitivity in wheat. This study contributed to our understanding of the molecular basis for the regulation of wheat PHS resistance.

The molybdenum cofactor biosynthesis gene, OsCNX1, is essential for seedling development and seed germination in rice.

Pre-harvest sprouting (PHS) frequently occurs in rice due to the long spells of rainy weather, and causes severe yield loss and grain quality decrease. Here, we identified one PHS-related gene OsCNX1 cloned from rice PHS mutant, which encoded a molybdenum cofactor (MoCo) biosynthesis enzyme. Genetic complementation indicated OsCNX1 could rescue the PHS and seedling lethal phenotype of the mutant. Expression pattern showed that OsCNX1 was expressed in rice tissue including seedling shoot, culm, blade, and sheath of flag leaf, young panicle, and the seeds at different development stages. Overexpression of OsCNX1 significantly decreased the plant height, and the seed germination of the dormant seeds harvested from fresh panicles, comparing to the wild type (WT). In addition, 1492 differentially expressed genes (DEGs) were identified between OsCNX1-overexpressed line and WT by RNA-sequencing, which were mainly classified in plant-pathogen interaction, plant hormone signal transduction, and starch/sucrose metabolism. These results showed that OsCNX1 was not only necessary for rice seed germination, but also participated in plant development, indicating that OsCNX1 may be useful in rice breeding of PHS resistance and plant height. Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01424-x.

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.

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.

Grain Germination Changes the Profile of Phenolic Compounds and Benzoxazinoids in Wheat: A Study on Hard and Soft Cultivars.

Pre-harvest sprouting is a frequent problem for wheat culture that can be simulated by laboratory-based germination. Despite reducing baking properties, wheat sprouting has been shown to increase the bioavailability of some nutrients. It was investigated whether wheat cultivars bearing distinct grain texture characteristics (BRS Guaraim, soft vs. BRS Marcante, hard texture) would have different behavior in terms of the changes in phytochemical compounds during germination. Using LC-Q-TOF-MS, higher contents of benzoxazinoids and flavonoids were found in the hard cultivar than in the soft one. Free phytochemicals, mainly benzoxazinoids, increased during germination in both cultivars. Before germination, soft and hard cultivars had a similar profile of matrix-bound phytochemicals, but during germination, these compounds have been shown to decrease only in the hard-texture cultivar, due to decreased levels of phenolic acids (trans-ferulic acid) and flavonoids (apigenin) that were bound to the cell wall through ester-type bonds. These findings confirm the hypothesis that hard and soft wheat cultivars have distinct behavior during germination concerning the changes in phytochemical compounds, namely the matrix-bound compounds. In addition, germination has been shown to remarkably increase the content of benzoxazinoids and the antioxidant capacity, which could bring a health-beneficial appeal for pre-harvested sprouted grains.

Comparative transcriptomic analysis provides insights into the molecular basis underlying pre-harvest sprouting in rice.

BACKGROUND: Pre-harvest sprouting (PHS) is one of the most serious rice production constraints in areas where prolonged rainfall occurs during harvest. However, the molecular mechanisms of transcriptional regulation underlying PHS remain largely unknown. RESULTS: In the current study, comparative transcriptome analyses were performed to characterize the similarities and differences between two rice varieties: PHS-sensitive Jiuxiangzhan (JXZ) and PHS-resistant Meixiangxinzhan (MXXZ). The physiological experimental results indicated that PHS causes a significant decrease in starch content and, in contrast, a significant increase in soluble sugar content and amylase activity. The extent of change in these physiological parameters in the sensitive variety JXZ was greater than that in the resistant variety MXXZ. A total of 9,602 DEGs were obtained from the transcriptome sequencing data, and 5,581 and 4,021 DEGs were identified in JXZ and MXXZ under high humidity conditions, respectively. The KEGG pathway enrichment analysis indicated that many DEGs under high humidity treatment were mainly linked to plant hormone signal transduction, carbon metabolism, starch and sucrose metabolism, and phenylpropanoid biosynthesis. Furthermore, the number of upregulated genes involved in these pathways was much higher in JXZ than in MXXZ, while the number of downregulated genes was higher in MXXZ than in JXZ. These results suggest that the physiological and biochemical processes of these pathways are more active in the PHS-sensitive JXZ than in the PHS-resistant MXXZ. CONCLUSION: Based on these results, we inferred that PHS in rice results from altered phytohormone regulation, more active carbon metabolism and energy production, and enhanced phenylpropanoid biosynthesis. Our study provides a theoretical foundation for further elucidation of the complex regulatory mechanism of PHS in rice and the molecular breeding of PHS-resistant rice varieties.

Genome sequencing-based coverage analyses facilitate high-resolution detection of deletions linked to phenotypes of gamma-irradiated wheat mutants.

BACKGROUND: Gamma-irradiated mutants of Triticum aestivum L., hexaploid wheat, provide novel and agriculturally important traits and are used as breeding materials. However, the identification of causative genomic regions of mutant phenotypes is challenging because of the large and complicated genome of hexaploid wheat. Recently, the combined use of high-quality reference genome sequences of common wheat and cost-effective resequencing technologies has made it possible to evaluate genome-wide polymorphisms, even in complex genomes. RESULTS: To investigate whether the genome sequencing approach can effectively detect structural variations, such as deletions, frequently caused by gamma irradiation, we selected a grain-hardness mutant from the gamma-irradiated population of Japanese elite wheat cultivar "Kitahonami." The Hardness (Ha) locus, including the puroindoline protein-encoding genes Pina-D1 and Pinb-D1 on the short arm of chromosome 5D, primarily regulates the grain hardness variation in common wheat. We performed short-read genome sequencing of wild-type and grain-hardness mutant plants, and subsequently aligned their short reads to the reference genome of the wheat cultivar "Chinese Spring." Genome-wide comparisons of depth-of-coverage between wild-type and mutant strains detected ~ 130 Mbp deletion on the short arm of chromosome 5D in the mutant genome. Molecular markers for this deletion were applied to the progeny populations generated by a cross between the wild-type and the mutant. A large deletion in the region including the Ha locus was associated with the mutant phenotype, indicating that the genome sequencing is a powerful and efficient approach for detecting a deletion marker of a gamma-irradiated mutant phenotype. In addition, we investigated a pre-harvest sprouting tolerance mutant and identified a 67.8 Mbp deletion on chromosome 3B where Viviparous-B1 and GRAS family transcription factors are located. Co-dominant markers designed to detect the deletion-polymorphism confirmed the association with low germination rate, leading to pre-harvest sprouting tolerance. CONCLUSIONS: Short read-based genome sequencing of gamma-irradiated mutants facilitates the identification of large deletions linked to mutant phenotypes when combined with segregation analyses in progeny populations. This method allows effective application of mutants with agriculturally important traits in breeding using marker-assisted selection.

Genome-wide association mapping and genomic prediction for pre­harvest 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.

Combining QTL mapping and gene co-expression network analysis for prediction of candidate genes and molecular network related to yield in wheat.

BACKGROUND: Wheat (Triticum aestivum L.) is an important cereal crop. Increasing grain yield for wheat is always a priority. Due to the complex genome of hexaploid wheat with 21 chromosomes, it is difficult to identify underlying genes by traditional genetic approach. The combination of genetics and omics analysis has displayed the powerful capability to identify candidate genes for major quantitative trait loci (QTLs), but such studies have rarely been carried out in wheat. In this study, candidate genes related to yield were predicted by a combined use of linkage mapping and weighted gene co-expression network analysis (WGCNA) in a recombinant inbred line population. RESULTS: QTL mapping was performed for plant height (PH), spike length (SL) and seed traits. A total of 68 QTLs were identified for them, among which, 12 QTLs were stably identified across different environments. Using RNA sequencing, we scanned the 99,168 genes expression patterns of the whole spike for the recombinant inbred line population. By the combined use of QTL mapping and WGCNA, 29, 47, 20, 26, 54, 46 and 22 candidate genes were predicted for PH, SL, kernel length (KL), kernel width, thousand kernel weight, seed dormancy, and seed vigor, respectively. Candidate genes for different traits had distinct preferences. The known PH regulation genes Rht-B and Rht-D, and the known seed dormancy regulation genes TaMFT can be selected as candidate gene. Moreover, further experiment revealed that there was a SL regulatory QTL located in an interval of about 7 Mbp on chromosome 7A, named TaSL1, which also involved in the regulation of KL. CONCLUSIONS: A combination of QTL mapping and WGCNA was applied to predicted wheat candidate genes for PH, SL and seed traits. This strategy will facilitate the identification of candidate genes for related QTLs in wheat. In addition, the QTL TaSL1 that had multi-effect regulation of KL and SL was identified, which can be used for wheat improvement. These results provided valuable molecular marker and gene information for fine mapping and cloning of the yield-related trait loci in the future.

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.

Regulation of germination by targeted mutagenesis of grain dormancy genes in barley.

High humidity during harvest season often causes pre-harvest sprouting in barley (Hordeum vulgare). Prolonged grain dormancy prevents pre-harvest sprouting; however, extended dormancy can interfere with malt production and uniform germination upon sowing. In this study, we used Cas9-induced targeted mutagenesis to create single and double mutants in QTL FOR SEED DORMANCY 1 (Qsd1) and Qsd2 in the same genetic background. We performed germination assays in independent qsd1 and qsd2 single mutants, as well as in two double mutants, which revealed a strong repression of germination in the mutants. These results demonstrated that normal early grain germination requires both Qsd1 and Qsd2 function. However, germination of qsd1 was promoted by treatment with 3% hydrogen peroxide, supporting the notion that the mutants exhibit delayed germination. Likewise, exposure to cold temperatures largely alleviated the block of germination in the single and double mutants. Notably, qsd1 mutants partially suppress the long dormancy phenotype of qsd2, while qsd2 mutant grains failed to germinate in the light, but not in the dark. Consistent with the delay in germination, abscisic acid accumulated in all mutants relative to the wild type, but abscisic acid levels cannot maintain long-term dormancy and only delay germination. Elucidation of mutant allele interactions, such as those shown in this study, are important for fine-tuning traits that will lead to the design of grain dormancy through combinations of mutant alleles. Thus, these mutants will provide the necessary germplasm to study grain dormancy and germination in barley.

Pyramiding wheat pre-harvest sprouting resistance genes in triticale breeding.

Pre -harvest sprouting (PHS) is an important problem in cereal production reducing yield and grain quality. After decades of improvement, triticale remains particularly susceptible to PHS but no resistance genes or QTLs were identified so far in this species. As wheat shares the A and B genomes with triticale, wheat PHS resistance genes can be introgressed into triticale genome by recombination after interspecific crosses. In this project, three PHS resistance genes have been transferred from wheat to triticale by marker-assisted interspecific crosses, followed by four backcrosses. The gene TaPHS1 from the 3AS chromosome of cultivar Zenkoujikomugi (Zen) and the TaMKK3 and TaQsd1, respectively located on the 4AL and 5BL chromosomes derived both from cultivar Aus1408, were pyramided in the triticale cultivar Cosinus. Only the TaPHS1 gene increases consistently the PHS resistance in triticale. The lack of efficacy of the other two genes, especially TaQsd1, could be the result of an imperfect linkage between the marker and the gene of interest. The introduction of PHS resistance genes did not alter agronomic nor disease resistance performances of triticale. This approach leads to two new, agronomically performant and PHS-resistant triticale cultivars. Today, two breeding triticale lines are ready to enter the official registration process.

Sdr4 dominates pre-harvest sprouting and facilitates adaptation to local climatic condition in Asian cultivated rice.

Pre-harvest sprouting (PHS), which reduces grain yield and quality, is controlled by seed dormancy genes. Because few dormancy-related genes have been cloned, the genetic basis of seed dormancy in rice (Oryza sativa L.) remains unclear. Here, we performed a genome-wide association study and linkage mapping to dissect the genetic basis of seed dormancy in rice. Our findings suggest that Seed Dormancy4 (Sdr4), a central modulator of seed dormancy, integrates the abscisic acid and gibberellic acid signaling pathways at the transcriptional level. Haplotype analysis revealed that three Sdr4 alleles in rice cultivars already existed in ancestral Oryza rufipogon accessions. Furthermore, like the semi-dwarf 1 (SD1) and Rc loci, Sdr4 underwent selection during the domestication and improvement of Asian cultivated rice. The distribution frequency of the Sdr4-n allele in different locations in Asia is negatively associated with local annual temperature and precipitation. Finally, we developed functional molecular markers for Sdr4, SD1, and Rc for use in molecular breeding. Our results provide clues about the molecular basis of Sdr4-regulated seed dormancy. Moreover, these findings provide guidance for utilizing the favorable alleles of Sdr4 and Rc to synergistically boost PHS resistance, yield, and quality in modern rice varieties.