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.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.17312

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

Abstract 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 &gt; 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. 

/pdf/genome-wide-association-mapping-and-genomic-prediction-for-26xg6ju4.pdf

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

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.

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.

/pdf/qtl-mapping-for-wheat-seed-dormancy-in-a-yangmai16-2nleuuga.pdf

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

Pre-harvest sprouting (PHS) induced by the absence of seed dormancy causes a severe reduction in crop yield and flour quality. In this study, we isolated and characterized TaABI4, an ABA-responsive transcription factor that participates in regulating seed germination in wheat. Sequence analysis revealed that TaABI4 has three homologues, located on chromosomes 1A/1B/1D. TaABI4 contains a conserved AP2 domain, and AP2-associated, LRP and potential PEST motifs. Putative cis-acting regulatory elements (CE1-like box, W-box, ABRE elements and RY elements) were identified in the TaABI4 promoter region that showed high conservation in 17 wheat cultivars and wheat-related species. Expression profiling of TaABI4 indicated that it is a seed-specific gene accumulating during the middle stages of seed development. Transcript accumulation of TaABI4 in wheat cultivar Chuanmai 32 (CM32, PHS susceptible) was 5.07-fold and 1.39-fold higher than that in synthetic hexaploidy wheat SHW-L1 (PHS resistant) at 15 and 20 DPA, respectively. Six expression quantitative trait loci (eQTL) of TaABI4 on chromosomes 2A, 2D, 3B and 4A were characterized based on the accumulated transcripts of TaABI4 in SHW-L1 and CM32-derived recombinant inbred lines. These QTLs explained 10.7 to 46.1% of the trait variation with 4.53–10.59 of LOD scores, which contain genes that may affect the expression of TaABI4.

/pdf/characterization-and-expression-quantitative-trait-loci-34wa7rfojb.pdf

Characterization and expression quantitative trait loci analysis of TaABI4, a pre-harvest sprouting related gene in wheat

Pre-harvest sprouting (PHS) causes serious damage that leads to deterioration in overall quality and decreased yield and reduction of grain yield in cereal. In this study, two major quantitative trait loci (QTLs), qPHS.sicau-3D and qPHS.sicau-1B, were detected in synthetic wheat (SHW-L1) and were derived from Aegilops tauschii AS60 (deep dormant) and Triticum turgidum AS2255 (medium PHS-resistant). qPHS.sicau-1B is located in the region near the telomere of 1BS, and qPHS.sicau-3D is located on the end of 3DL; these QTLs explain approximately 20.99% and 42.47% of the phenotypic variation. Pyramiding of both QTLs showed superior PHS resistance in recombinant inbred lines (RILs). The array-based SNP markers AX-94924265 for qPHS.sicau-1B and AX-94415259 for qPHS.sicau-3D were successfully converted to Kompetitive Allele Specific Polymerase Chain Reaction (KASP) and STS markers. L10-1580 is a light red breeding materials selected from SHW-L1-derived breeding lines that harbors the PHS-tolerant elite alleles which showed similar germination level with SHW-L1 and better resistance than other common wheat parents. L10-1580 harbors the elite alleles AX-94924265_GG/AX-94415259_B which showed similar PHS resistance as SHW-L1 and better resistance than other common wheat parents. Therefore, these QTLs for PHS resistance obtained from synthetic wheat could combine or coexist with other elite agronomic traits in high-yield wheat cultivars.

Identification of qPHS.sicau-1B and qPHS.sicau-3D from synthetic wheat for pre-harvest sprouting resistance wheat improvement

Ilex verticillata (L.) A. Gray (Winter Red) is a deciduous shrub and native to North America with high ornamental value, which was introduced into China in 2006. In Oct. 2020, leaf spots occurred on I. verticillata at the nursery of Baima Base for Teaching and Scientific Research of Nanjing Forestry University (31°36'51"N, 119°11'8"E). In the early stage, there were small black spots occurred on the leaves. Then, these spots enlarged and coalesced into regular or irregular gray necrotic lesions with dark margins (Fig. S1A). The incidence of this disease was ca. 93%. Infected leaves were collected and surface-sterilized with 75% ethanol. Pieces cut from the margin of the lesions of ca. 5×5 mm were placed on potato dextrose agar (PDA) Petri plates and incubated at 25±2°C for 7 days. Ten Alternaria fungal isolates were single-spore isolated. Since these isolates shared similar morphological characters, isolates 9-1 and 15-2-2 were randomly chosen for further experiments. 2-yr-old potted I. verticillata were used for pathogenicity test in vivo. Leaves were surface-sterilized using 75% ethanol and wounded using a sterilized needle and inoculated with mycelial plugs or 10 μL of conidial suspensions (105 spores mL-1), respectively. The inoculated plants were kept in a growth chamber at 25°C and 85% RH under a 12-h photoperiod. PDA plugs without fungus or sterilized H2O were used as controls, respectively. The experiment was repeated 2 times. Each treatment had 3 replicates. By day 7, necrotic lesions were observed on the leaves inoculated with the fungal isolates 9-1 or 15-2-2. No lesions were found on the plants inoculated with PDA discs or dH2O (Fig. S1). To complete Koch's postulates, the pathogen was re-isolated from the infected leaves and shared similar morphological characteristics of colonies and conidia with the original inoculated isolates. Conidiophores of the 2 isolates were pale brown, erect or curved, (20.1-)21.4-29.9(-39.9) × (8.4-)10.6-14.9(-18.3) μm, (n = 30). Conidia were dictyospores, nearly ovoid or clubbed, brown or grayish brown, (25.2-)27.5-42.8(-47.9) × (5.7-)6-7.7(-8.7) μm, (n = 30), in branched or unbranched chains (Fig. S1). These morphological characteristics matched A. alternata (Woudenberg et al. 2013). The internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH), endopolygalacturonase gene (endoPG), anonymous noncoding region (OPA10-2), small subunit gene (SSU), and large subunit gene (LSU) of isolates 9-1 and 15-2-2 were amplified using primer sets of Woudenberg et al. (2013). The SSU (OK428540, OK428541), LSU (OK428538, OK428539), ITS (OK316966, OK316967), GAPDH (OK428542, OK428543), endoPG (OK428544, OK428545), and OPA10-2 (OK428536, OK428537) of isolates 9-1 and 15-2-2 showed 99, 99, 99, 99, 100, and 100% similarity to the sequences of A. alternata ex-type CBS 916.96, respectively. Phylogenetic analyses using concatenated sequences of ITS, GAPDH, OPA10-2, LSU, SSU, and endOPG also showed that the isolates of 9-1 and 15-2-2 clustered with A. alternata ex-type and was supported with a 100% bootstrap value (Fig. S2). Based on the morphological and phylogenetic results, these fungal isolates were identified as A. alternata. A. alternata was reported as the pathogen of leaf spot and other diseases on more than 380 hosts (Farr & Rossman, 2022). To our knowledge, this was the first report of A. alternata causing leaf spot on I. verticillata in China. This report is important because the discovery is related to the management strategies of the new pathogen on I. verticillata. The monitoring and control of the disease needs to be emphasized in the future.

First report of leaf spot on Ilex verticillata caused by Alternaria alternata in China.

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Identification of qPHS.sicau-1B and qPHS.sicau-3D from synthetic wheat for pre-harvest sprouting resistance wheat improvement

First report of leaf spot on Ilex verticillata caused by Alternaria alternata in China.