The TaqW-6BL gene, which encodes a TAXI-type inhibitor, influences the water-extractable arabinoxylan content in wheat grains. Water-extractable arabinoxylans (WE-AX) are major dietary fiber components and play a crucial role in wheat end-use quality, especially its nutritional quality. In this study, TaqW-6BL was cloned from parental varieties of a recombinant inbred line (RIL) population, in which a missense mutation (+ 296 bp, T/C) was detected and found to cause a methionine (Met) to threonine (Thr) substitution. Overexpression of TaqW-6BL positively regulated grain WE-AX content, thousand kernel weight (TKW) and mean grain perimeter (MP), with increases of 30.80
This study confirms that ZmHY5L positively regulates the transcription ofwaxy gene through specifically binding to G-box elements on its promoter, and can simultaneously affect starch quality and grain morphology of maize endosperm. The waxy gene in maize encodes granule-bound starch synthase (GBSSI) protein, which controls the synthesis of amylose and is one of the key genes affecting grain quality and yield, but its regulatory mechanism remains not fully understood. Taking two characteristic Yunnan waxy maize landraces as materials, this study through DNA pull-down combined with mass spectrometry screened the upstream regulatory factor of waxy gene, and identified ZmHY5L, a basic leucine zipper (bZIP) family transcription factor that is one of the homologous genes of Arabidopsis HY5. Numerous previous studies have shown that HY5 is a core transcription factor in the light signaling pathway. This study subcellular localization verified that ZmHY5L protein is localized in the nucleus; EMSA and yeast one-hybrid assays further confirmed the direct interaction between ZmHY5L and the regulatory region of waxy gene. By constructing ZmHY5L gene editing mutants for phenotype comparison, it was found that the mutation of ZmHY5L gene significantly reduced the GBSSI protein content in maize kernels, while the amylopectin proportion, grain volume, hundred-grain weight of the mutants were remarkably increased, the gelatinization characteristics of starch also changed obviously, without altering the total starch content of kernels. This study confirms that ZmHY5L positively regulates the transcription of waxy gene through specifically binding to G-box elements on its promoter, and can simultaneously affect starch quality and grain morphology of maize endosperm.
Cold stress severely restricts pepper (Capsicum annuum L.) growth and productivity by disrupting cellular homeostasis and inducing oxidative damage. Although HD-ZIP transcription factors play important roles in plant abiotic stress responses, the molecular mechanisms regulating their function during cold stress remain largely unknown. Here, we characterized the pepper HD-ZIP transcription factor CaHD-ZIP and demonstrated that it is a nuclear-localized, cold-responsive protein that positively contributes to cold stress tolerance. To further investigate the regulatory mechanism underlying CaHD-ZIP function, a yeast two-hybrid (Y2H) screen identified the sucrose non-fermenting 1-related protein kinase CaSNF1 as a previously unrecognized interacting partner of CaHD-ZIP. Their interaction was confirmed by yeast two-hybrid, luciferase complementation imaging, and bimolecular fluorescence complementation assays, with BiFC indicating that the interaction occurs predominantly in the nucleus. In vitro phosphorylation analysis further demonstrated that CaSNF1 directly phosphorylates CaHD-ZIP, providing biochemical evidence for a functional regulatory relationship between these proteins. Complementary loss- and gain-of-function analyses, including virus-induced gene silencing and transient overexpression in pepper together with stable overexpression in Arabidopsis, demonstrated that CaSNF1 positively regulates cold tolerance. Silencing of CaSNF1 increased oxidative damage, impaired antioxidant enzyme activities, and suppressed the expression of antioxidant and cold-responsive genes, whereas overexpression produced the opposite effects and significantly enhanced cold tolerance. Together, these findings identify CaSNF1 as a CaHD-ZIP-interacting kinase and reveal a potential CaSNF1–CaHD-ZIP regulatory module involved in pepper cold stress adaptation. This study advances our understanding of the molecular mechanisms underlying pepper cold tolerance and provides potential genetic targets for improving cold resilience in pepper and other Solanaceae crops.
A standardized superior haplotype framework, validated across cereals, oilseeds and legumes, resolves genetic architecture overlooked by the SNP-based approach and guides targeted breeding for developing climate-resilient crops. Climate change and the rapid rise in the global population are exerting immense pressure on limited natural and genetic resources. Meeting future food demands requires accelerated genetic gain under rapidly changing environmental conditions. Advances in genomics, supported by large-scale sequencing of diverse crop germplasm, have enabled the mapping of key genes and the development of climate-resilient varieties. However, the utility of these genes and their associated haplotypes is often limited, as they are specific to particular ecologies and populations, restricting their broader introgression into various breeding programmes. The concept of superior haplotypes can help us address these limitations by identifying the allelic combination that confers a desirable trait with stable, consistent and significant performance across diverse panels and environments. For instance, in rice, the GS3-H1 haplotype is associated with improved grain size and yield potential, while Sub1A-1 confers superior submergence tolerance compared to Sub1A-2. Similarly, in rapeseed, Hap1 of qOCA3 and qOCC6 is associated with higher oil content. Building on such examples, this review systematically catalogues superior haplotypes identified across major crops, highlights key research gaps, and outlines a roadmap for their deployment in genomic-assisted breeding to enhance crop productivity, adaptability, and resilience.
Synthetic hexaploid wheat harbours STB resistance-associated loci with multi-isolate and isolate-specific effects, with partly independent genetic control of pycnidia suppression and necrosis. Septoria tritici blotch (STB), caused by Zymoseptoria tritici, is a major constraint on wheat production. Erosion of host resistance and declining fungicide efficacy highlight the need to exploit new resistance sources, including synthetic hexaploid wheat (SHW). We used a three-family nested association mapping (NAM) population derived from Niab SHW donors (SHW.035, SHW.054, and SHW.075) crossed with the UK variety Robigus to dissect the genetic basis of STB resistance under controlled conditions. Seedlings were challenged with five UK Z. tritici isolates differing in virulence, and disease progress was quantified separately as necrosis (AUDPC_N) and pycnidia coverage (AUDPC_P). Many SHW-derived lines showed strong suppression of pycnidia despite visible necrosis, consistent with partial genetic decoupling of pathogen reproduction and host tissue damage. GWAS identified a major multi-isolate association on chromosome 3D (qSTB-3D.1), contributed by SHW.035 and detected in response to four of the five isolates, defining a 23.7 Mb candidate resistance-associated interval. This interval encompasses the Stb16q region but also contains other plausible resistance candidates, including a WAK close to the strongest association at 609.21 Mb; the causal basis therefore remains unresolved. Additional isolate-specific resistance-associated intervals were detected on chromosomes 1B, 2D, 3A, and 6D. In a BC2F2 population derived from a resistant SHW.035-derived NAM line, pycnidia suppression segregated in a 3:1 ratio consistent with a single dominant factor, whereas necrosis showed more complex inheritance. These findings show that Niab SHWs are a valuable source of STB resistance and highlight the potential to select for reduced pathogen reproduction independently of visible leaf damage.
