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• Pre-harvest sprouting (PHS), the germination of grain before harvest, is a serious problem resulting in wheat yield and quality losses. • Here, we mapped the PHS resistance gene PHS-3D from synthetic hexaploid wheat to a 2.4 Mb presence–absence variation (PAV) region and found that its resistance effect was attributed to the pleiotropic Myb10-D by integrated omics and functional analyses. • Three haplotypes were detected in this PAV region among 262 worldwide wheat lines and 16 Aegilops tauschii, and the germination percentages of wheat lines containing Myb10-D was approximately 40% lower than that of the other lines. Transcriptome and metabolome profiling indicated that Myb10-D affected the transcription of genes in both the flavonoid and abscisic acid (ABA) biosynthesis pathways, which resulted in increases in flavonoids and ABA in transgenic wheat lines. Myb10-D activates 9-cis-epoxycarotenoid dioxygenase (NCED) by biding the secondary wall MYB-responsive element (SMRE) to promote ABA biosynthesis in early wheat seed development stages. • We revealed that the newly discovered function of Myb10-D confers PHS resistance by enhancing ABA biosynthesis to delay germination in wheat. The PAV harboring Myb10-D associated with grain color and PHS will be useful for understanding and selecting white grained PHS resistant wheat cultivars.

Identification of high carotenoid germplasm is crucial to assist breeders in provitamin-A biofortification of sorghum ( Sorghum bicolor [L.] Moench). High-performance liquid chromatography is the gold standard for carotenoid quantification, however, it is not feasible for large scale phenotyping due to its high cost and low throughput. In this study, we tested the feasibility of using grain color as a high-throughput method of carotenoid biofortification breeding. We hypothesized that visual, color-based selection can be an effective strategy to identify high-carotenoid accessions. Yellow grain had significantly higher carotenoid content than red, brown, and white grain. The degree of yellowness could distinguish the presence or absence of carotenoids, but could not distinguish carotenoid concentrations within yellow-only accessions. The degree of luminosity of the grain, however, was able to better predict carotenoid concentrations within yellow-only accessions. Genome-wide association studies identified significant marker-trait associations for qualitative and quantitative grain color traits and carotenoid concentrations near carotenoid pathway genes— ZEP , PDS , CYP97A , NCED, CCD , and LycE —three of which were common between grain color and carotenoid traits. These findings suggest that using grain color as a method for screening germplasm may be an effective high-throughput selection tool for prebreeding and early-stage breeding in carotenoid biofortification.

Polyphenols in whole grain wheat have potential health benefits, but little is known about the expression patterns of phenolic acid biosynthesis genes and the accumulation of phenolic acid compounds in different-colored wheat grains. We found that purple wheat varieties had the highest total phenolic content (TPC) and antioxidant activity. Among phenolic acid compounds, bound ferulic acid, vanillic, and caffeic acid levels were significantly higher in purple wheat than in white and red wheat, while total soluble phenolic acid, soluble ferulic acid, and vanillic acid levels were significantly higher in purple and red wheat than in white wheat. Ferulic acid and syringic acid levels peaked at 14 days after anthesis (DAA), whereas p-coumaric acid and caffeic acid levels peaked at 7 DAA, and vanillic acid levels gradually increased during grain filling and peaked near ripeness (35 DAA). Nine phenolic acid biosynthesis pathway genes (TaPAL1, TaPAL2, TaC3H1, TaC3H2, TaC4H, Ta4CL1, Ta4CL2, TaCOMT1, and TaCOMT2) exhibited three distinct expression patterns during grain filling, which may be related to the different phenolic acids levels. White wheat had higher phenolic acid contents and relatively high gene expression at the early stage, while purple wheat had the highest phenolic acid contents and gene expression levels at later stages. These results suggest that the expression of phenolic acid biosynthesis genes may be closely related to phenolic acids accumulation.

Background Pre-harvest sprouting (PHS) is a serious problem in wheat production globally. Grain color (GC) has a notable impact on PHS resistance, red grains typically show higher resistance compared to white grains. To understand the genetic factors influencing PHS and GC, a genome-wide association study (GWAS) was conducted on a natural population of 235 wheat cultivars using a 90 K single nucleotide polymorphism (SNP) arrays. Results A strong correlation between PHS and GC was observed, with the highest correlation coefficient of 0.85 ( P  < 0.0001). Association mapping was performed using four different models (BLINK, FarmCPU, MMLM and MLM) in the GAPIT along with MLM model in the Tassel. The study identified twelve stable quantitative trait loci (QTLs) related to PHS resistance and another twelve stable QTLs associated with GC. Notably, six QTLs for PHS resistance were newly discovered, explaining 5.8–10.0% of the phenotypic variation. Additionally, four common QTLs were identified that are linked to both PHS resistance and GC. Among these, Qphs.hbaas-3B.2 / Qgc.hbaas-3B.2 and Qphs.hbaas-3D / Qgc.hbaas-3D were recognized as major loci significantly affecting both traits, likely associated with the genes Tamyb-B1 and Tamyb-D1 , respectively. The other two new QTLs on chromosome 2B explained 7.0–10.0% of phenotypic variation in PHS resistance and 4.7–7.4% of phenotypic variation in GC. Furthermore, six candidate genes associated with PHS resistance were predicted, warranting further investigation. Three KASP markers IACX5850 , Tdurum_contig11028_236 and wsnp_Ex_c269_518324 linked to three QTLs ( Qphs.hbaas-2B.2 , Qphs.hbaas-2B.4 , and Qphs.hbaas-7B.2 ) are applicable for marker-assisted selection in wheat breeding to enhance PHS resistance. Conclusions This study provides valuable genetic loci and KASP markers that can enhance PHS resistance in wheat breeding programs and offers insights for discovering PHS resistance genes.

Sediment has been shown to be a major stressor to coral reefs globally. Although many researchers have tested the impact of sedimentation on coral reef ecosystems in both the laboratory and the field and some have measured the impact of suspended sediment on the photosynthetic response of corals, there has yet to be a detailed investigation on how properties of the sediment itself can affect light availability for photosynthesis. We show that finer-grained and darker-colored sediment at higher suspended-sediment concentrations attenuates photosynthetically active radiation (PAR) significantly more than coarser, lighter-colored sediment at lower concentrations and provide PAR attenuation coefficients for various grain sizes, colors, and suspended-sediment concentrations that are needed for biophysical modeling. Because finer-grained sediment particles settle more slowly and are more susceptible to resuspension, they remain in the water column longer, thus causing greater net impact by reducing light essential for photosynthesis over a greater duration. This indicates that coral reef monitoring studies investigating sediment impacts should concentrate on measuring fine-grained lateritic and volcanic soils, as opposed to coarser-grained siliceous and carbonate sediment. Similarly, coastal restoration efforts and engineering solutions addressing long-term coral reef ecosystem health should focus on preferentially retaining those fine-grained soils rather than coarse silt and sand particles.

Background Pre-harvest sprouting (PHS) in wheat can cause substantial reduction in grain yield and end-use quality. Grain color (GC) together with other components affect PHS resistance. Several quantitative trait loci (QTL) have been reported for PHS resistance, and two of them on chromosome 3AS ( TaPHS1 ) and 4A have been cloned. Methods To determine genetic architecture of PHS and GC and genetic relationships of the two traits, a genome-wide association study (GWAS) was conducted by evaluating a panel of 185 U.S. elite breeding lines and cultivars for sprouting rates of wheat spikes and GC in both greenhouse and field experiments. The panel was genotyped using the wheat 9K and 90K single nucleotide polymorphism (SNP) arrays. Results Four QTL for GC on four chromosomes and 12 QTL for PHS resistance on 10 chromosomes were identified in at least two experiments. QTL for PHS resistance showed varied effects under different environments, and those on chromosomes 3AS, 3AL, 3B, 4AL and 7A were the more frequently identified QTL. The common QTL for GC and PHS resistance were identified on the long arms of the chromosome 3A and 3D. Conclusions Wheat grain color is regulated by the three known genes on group 3 chromosomes and additional genes from other chromosomes. These grain color genes showed significant effects on PHS resistance in some environments. However, several other QTL that did not affect grain color also played a significant role on PHS resistance. Therefore, it is possible to breed PHS-resistant white wheat by pyramiding these non-color related QTL.

The color of grain in cereals is determined mainly by anthocyanin pigments. A large level of genetic diversity for anthocyanin content and composition in the grain of different species was observed. In rye, recessive mutations in six genes (vi1...vi6) lead to the absence of anthocyanins in all parts of the plant. Moreover, dominant genes of anthocyanin synthesis in aleurone (gene C) and pericarp (gene Vs) also affect the color of the grain. Reverse phase high-performance liquid chromatography and mass spectrometry were used to study anthocyanins in 24 rye samples. A lack of anthocyanins in the lines with yellow and brown grain was determined. Delphinidin rutinoside and cyanidin rutinoside were found in the green-seeded lines. Six samples with violet grains significantly varied in terms of anthocyanin composition and content. However, the main aglycone was cyanidin or peonidin in all of them. Monosaccharide glucose and disaccharide rutinose served as the glycoside units. Violet-seeded accession forms differ in the ratio of the main anthocyanins and the range of their acylated derivatives. The acyl groups were presented mainly by radicals of malonic and sinapic acids. For the colored forms, a profile of the revealed anthocyanins with the indication of their contents was given. The obtained results are discussed in connection to similar data in rice, barley, and wheat, which will provide a perspective for future investigations.

Blue barley grain pigmentation results from anthocyanin accumulation in the aleurone layer. Anthocyanins are known for their beneficial effects on human health. The gene encoding the MYELOCYTOMATOSIS 2 (MYC2) transcription factor is potentially responsible for the blue coloration of the aleurone. In non-pigmented barley, a single nucleotide insertion in this gene causes a frameshift mutation with a premature stop codon. It was hypothesized that restoring the MYC2 reading frame could activate anthocyanin accumulation in the aleurone. Using a targeted mutagenesis approach in the present study, the reading frame of MYC2 was restored in the non-pigmented cultivar Golden Promise. Genetic constructs harboring cas9 and gRNA expression units were developed, pre-validated in protoplasts, and then functional MYC2 alleles were generated at the plant level via Agrobacterium-mediated transformation. Anthocyanin accumulation in the aleurone layer of grains from these mutants was confirmed through microscopy and chemical analysis. The expression of anthocyanin biosynthesis genes was analyzed, revealing that the restoration of MYC2 led to increased transcript levels of F3H and ANS genes. These results confirm the critical role of the MYC2 transcription factor in the blue aleurone trait and provide a biotechnological solution for enriching barley grain with anthocyanins.

Sorghum is a major staple crop in semi-arid regions; however, its generally low grain carotenoid content limits its potential contribution to alleviating vitamin A deficiency. Elucidating the regulatory mechanisms underlying carotenoid accumulation is therefore essential for the nutritional improvement of sorghum. Five sorghum varieties with distinct grain colors (white, gray, yellow, red, and black) were analyzed using integrated targeted carotenoid metabolomic and transcriptomic approaches to characterize carotenoid composition and its molecular regulation. A total of 37 carotenoid compounds were identified across the five sorghum varieties, with lutein as the predominant component. The yellow-grained variety exhibited the highest total carotenoid content (16.79 ± 0.61 mg/g), whereas the red-grained variety showed the lowest overall content but accumulated several unique carotenoids. Transcriptomic analysis identified nine key differentially expressed genes involved in carotenoid metabolism, including genes associated with precursor supply (geranylgeranyl pyrophosphate synthase, GGPPS), core carotenoid biosynthesis (15-cis-phytoene desaturase, PDS), xanthophyll modification (cytochrome P450 716A1, CYP716A1), and carotenoid catabolism (9-cis-epoxycarotenoid cleavage dioxygenase 5, NCED5). These genes displayed distinct expression patterns among varieties, indicating coordinated regulation of carotenoid biosynthesis and degradation. Correlation analysis further revealed that PDS and CYP716A1 were significantly associated with the accumulation of β-carotene, lutein, and zeaxanthin. Collectively, these findings demonstrate a transcriptionally regulated carotenoid metabolic network in sorghum and indicate that grain color alone does not reliably predict carotenoid composition, as other pigments such as anthocyanins and tannins also contribute to grain coloration. PDS and CYP716A1 are therefore identified as promising targets for carotenoid biofortification and for the development of nutritionally enhanced sorghum varieties.

Resistance to pre-harvest sprouting (PHS) is an agronomically important trait affecting the yield and grain quality of bread wheat. PHS resistance depends both on environmental factors and the genotypic and phenotypic properties of wheat varieties. It is known that wheat varieties with red-grain are more resistant to PHS than white-grain varieties. However, at present there are no methodological approaches that allow to unambiguously distinguish red-grain varieties according to the level of PHS resistance. The purpose of the study was to compare different methods for efficient differentiation of soft winter wheat ( Triticum aestivum L.) varieties for resistance to PHS. The germination index (GI), α-amylase activity (AAA), a digital grade of the grain color and genetic bases of the wheat varieties the grain was determined in 164 winter wheat, among them 156 were red-grain. The studies were carried out at the late milk/hard dough (LM/HD; GS77-GS87) stage and the hard grain (HG; GS92-GS93) stage. Based on the dynamics of GI it was found that late LM/HD stage is the most suitable for GI evaluation. AAA was performed using the Ceralpha method and falling number (FN) evaluation. An increase in the level of AAA during grain ripening of wheat varieties was shown. A negative correlation was found between GI and FN, FN and AAA. Using the Lab color model to assess the color variation of the grain coat allow to identify 3 variants of grain color. Genetic base of wheat varieties was analyzed by means of allelic composition of the Tamyb10 gene, which participate in the formation of the red color of grain. The results indicated that digital analysis and allelic composition of the Tamyb10 cannot be used as additional criterion for separation of red-grain wheat varieties for resistance to PHS. This is despite the fact that the numerous group of the varieties contain two or more dominant Tamyb10 gene. In general, a comparison of varieties by all three parameters allow to identify a group of varieties that are most PHS resistant. This group consist of 73 red-grain varieties out of 156, while no white-grain PHS-resistant varieties were identified.