Jul 2026· Plant, Cell and Environment· 0 citations· 42 references
Medicine
TL;DR
A B3-domain transcription factor (B3TF) is identified as a key regulator of seed growth and metabolic partitioning in wheat, providing a framework for exploiting regulatory alleles to enhance yield and nutritional quality in modern wheat.
Abstract
Seed weight (SW) and nutrient allocation are key determinants of yield and grain quality in wheat, yet the regulatory basis of naturally occurring variation in these traits remains poorly resolved. Wild emmer wheat (Triticum dicoccoides), the progenitor of modern wheat, retains extensive eco-geographically structured genetic diversity that was largely eroded during domestication. Here, we identify a B3-domain transcription factor (B3TF) as a key regulator of seed growth and metabolic partitioning in wheat. Genome-wide association analysis of ~460 wild emmer accessions reveals a major locus on chromosome 2BL associated with SW, seed area and nitrogen (N) content, displaying pronounced climatic differentiation across environmental gradients. Introgression of the 2BL wild segment into the hexaploid wheat cultivars Chinese Spring and Bethlehem increases SW in cultivated backgrounds. Independent loss-of-function alleles generated by EMS mutagenesis in the tetraploid wheat cultivar Kronos produce larger seeds. Further, RNA-seq of EMS mutants revealed metabolic reprogramming with upregulated fatty acid, nitrogen and phenylpropanoid pathways and downregulated carbohydrate metabolism and sugar transport. Metabolomic, lipidomic and ICP-MS data showed increased essential amino acids, sugars, lipids, N content and minerals (Zn, Fe, Mo). Furthermore, CRISPR/Cas9-mediated editing in the hexaploid wheat cultivar Fielder produced similar increases in SW and N content as observed in the EMS mutants, establishing this gene as a negative regulator of seed growth across ploidy levels. In addition, natural haplotypes show reciprocal climatic distributions, linking regulatory variation to environmental adaptation. Our findings uncover a TF underlying natural seed trait variation in wild wheat, providing a framework for exploiting regulatory alleles to enhance yield and nutritional quality in modern wheat.
The genetic architecture and core candidate genes for shoot length (SL) and root length (RL) at the germination stage are dissected and seven core candidate genes for SL and 13 for RL are identified, including three pleiotropic genes regulating both traits.
Synthetic nitrogen fertilizers have greatly increased crop yields, yet much of the applied nitrogen is lost from agroecosystems and contributes to environmental pollution and higher economic costs. Improving nitrogen uptake efficiency (NUpE) benefits from understanding how root system architecture (RSA) governs soil nitrogen capture. Although root traits have seldom been explicit breeding targets, selection for variation in above-ground nitrogen accumulation has also likely shaped differences in RSA. The Illinois Protein Strain Recombinant Inbred population, derived from more than a century of divergent selection for seed protein concentration, offers a powerful resource for dissecting RSA variation. Using multi-year field phenotyping of excavated root crowns and genome-wide association analysis, we identified a quantitative trait locus on chromosome 10 containing E1OGDH1, which encodes the E1 subunit of the 2-oxoglutarate dehydrogenase (OGDH) complex. OGDH performs a key step in the tricarboxylic acid cycle that also modulates 2-oxoglutarate, an important entry point into nitrogen metabolism and a co-factor for enzymes involved in hormone and secondary product synthesis. Long-read sequencing of inbreds derived from the divergent IHP and ILP parental populations revealed promoter polymorphisms defining E1OGDH1 alleles and differed in E1OGDH1 expression in root tissue. Field experiments in IPSRI lines carrying IHP- or ILP-associated E1OGDH1 alleles showed differences in root architectural traits over two years. CRISPR-Cas9 knockout mutants confirmed a functional role for E1OGDH1 in whole-plant performance and nitrogen-responsive root development. Mutants were shorter, had reduced biomass, and exhibited altered architectural responses to soil nitrogen levels. Transcriptome analysis further showed that loss of E1OGDH1 altered basal and nitrogen-responsive expression of genes associated with root development and nitrogen uptake and metabolism. Together, these findings identify E1OGDH1 as a strong candidate quantitative regulator of maize RSA and nitrogen plasticity, suggesting that central carbon–nitrogen metabolic genes can contribute to root developmental responses relevant to NUpE.
Michelle S. Cho, Zhengbin Liu, Collin Luebbert et al.· bioRxiv· 0 citations
A pangenome of tetraploid wheat constructed from 12 de novo genome assemblies spanning all 10 recognized tetraploid wheat subspecies, integrating with whole-genome sequencing data, highlights genetic variation associated with agricultural traits.
A key domestication-selected regulatory module that coordinates resource allocation is elucidate, promoting source-to-sink allocation to increase harvest index and grain yield even under nitrogen-limiting conditions.
Li Guo, Jinliang Xia, Junxiang Tang et al.· Cell· 1 citation
The validated hub genes may serve as promising candidate targets for the development of functional markers in marker-assisted selection (MAS), potentially facilitating early-stage screening and pyramiding of drought-tolerant alleles in barley breeding programs, pending experimental validation.
Hossein Sabouri, B. Kazerani, Fakhtak Taliei et al.· Euphytica· 0 citations
Analysis of natural variation in SlGRF10 in over 1,000 tomato accessions revealed that increased single-nucleotide polymorphism diversity in SlGRF10 is associated with lower fruit weight, which suggests that putative impaired activity contributes to reduced fruit weight, while breeding-induced reduction of genetic variation may have promoted increased fruit weight.
Julia von Steimker, M. Macho, Regina Wendenburg et al.· Plant Physiology· 0 citations
