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.
Abstract
Crop yield is fundamentally determined by the harvest index, the proportion of photosynthates allocated to grain. However, its genetic and evolutionary basis remains elusive. Here, we show that the maize harvest index increased by 81% during domestication. A major locus, Harvest Index1 (HI1), contributes to this divergence and is controlled by a 9.1-kb presence/absence variation. This insertion acts as a distant enhancer to boost the expression of the downstream B-type response regulator BRR1 and was fixed by selection. Mechanistically, the transcription factor CONZ1 binds to both the HI1 enhancer and the BRR1 promoter, recruiting the acetyltransferase General Control Nonrepressed 5 (GCN5) to form a chromatin loop that enhances BRR1 expression. BRR1 directly activates genes involved in carbon and nitrogen metabolism and transport, promoting source-to-sink allocation to increase harvest index and grain yield even under nitrogen-limiting conditions. Our findings elucidate a key domestication-selected regulatory module that coordinates resource allocation, providing a strategic target for sustainable crop improvement.
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
Improving protein accumulation in maize is essential for sustainable agriculture, yet the regulatory mechanisms governing the intermediate "flow" of organic nitrogen remain elusive. Here, we reveal that the maize stem acts as a critical regulatory node for nitrogen allocation. By integrating spatial transcriptomics and metabolomics with quantitative genetics, we demonstrate that the high-protein phenotype of the wild maize accession Ames21814 is orchestrated by a transport-oriented stem program. We identified a major locus, Whole-plant High Protein 10 (WHP10), which encodes a tandemly duplicated cluster of amino-acid transporter genes. WHP10 exhibits strong vascular-biased expression, driven by promoter divergence that enhances the wild allele's activity. Functional assays and genetic validation support a model in which the WHP10 cluster facilitates the transport of multiple key nitrogen-rich amino acids, thereby contributing to vascular-associated amino-acid transport and post-uptake organic-nitrogen partitioning. Our findings establish stem flow as a pivotal regulatory layer for protein accumulation and identify WHP10 as a high-value target for precision breeding to enhance whole-plant protein accumulation without compromising grain yield.
Wenhao Li, Youliang Li, Xiang Lin et al.· Molecular Plant· 0 citations
Cannabis sativa is a multi-purpose crop with a wide range of industrial and medicinal end uses. Despite its long history of cultivation, it has not received the same breeding efforts as many other crops due to regulatory barriers. In particular, it bypassed the Green Revolution, which improved harvest indices of crops via developing semi-dwarf varieties by manipulating endogenous gibberellin signalling pathways. We chemically manipulated gibberellin signalling through the exogenous application of gibberellic acid and the gibberellin biosynthesis inhibitor paclobutrazol. We used multi-omic analysis to determine the effect of these applications on the proteome, transcriptome and secondary metabolite accumulation to assess the potential of gibberellin modulation for improved C. sativa end uses. Paclobutrazol treatments resulted in a semi-dwarf phenotype with an improved high harvest index and enhanced cannabinoid accumulation. Differentially expressed gene and weighted gene co-expression network analysis revealed the importance of source/sink dynamics for harvest index, with the increased expression of sucrose synthases and sugar transporters key to the phenotypic changes induced by gibberellin modulation. At the same time, the availability of hexanoate precursors via the degradation of long-chain fatty acids emerged as a likely constraint on cannabinoid accumulation. This study provides a basis for exploring the manipulation of gibberellin pathways in C. sativa varieties and their relevance to cannabinoid production.
Lennard Garcia-de Heer, Matthew Nolan, J. Mieog et al.· Plant and Cell Physiology· 0 citations
The uncharacterized gene, GhFIR_A08 is revealed to positively regulate fiber initiation to increase LP, and provides valuable genetic resources for molecular breeding aimed at improving cotton yield.
Yuanxue Li, Chao Fu, Yuhuan Xiao et al.· Journal of Advanced Research· 0 citations
Nitrogen (N) is a major determinant of plant growth and productivity. Because soil N availability and internal N demand fluctuate, plants have evolved sophisticated mechanisms to coordinate N acquisition and utilization at the whole-plant level. However, how this coordination is achieved remains poorly understood. Here, we show that N-inducible LATERAL ORGAN BOUNDARIES DOMAIN transcription factors LBD37, LBD38, and LBD39 (LBDs) function as repressors of local N uptake and assimilation and systemic N-demand signaling in Arabidopsis. Triple mutants lacking these three LBDs displayed enhanced nitrate influx and increased accumulation of nitrate, amino acids, and total N. Transcriptome analysis identified an array of N-starvation- and nitrate-inducible genes derepressed in shoots and roots, including C-TERMINALLY ENCODED PEPTIDE (CEP) and CEP DOWNSTREAM (CEPD) genes, as well as genes involved in N uptake and assimilation. Grafting and genetic analyses revealed that LBDs gate the systemic N-demand signaling relay by repressing CEP and CEPD expression organ-autonomously. We also found that LBDs locally repress genes involved in N uptake and assimilation through a distinct regulatory mechanism. We propose that LBDs are key transcriptional repressors in a regulatory framework for optimizing N acquisition and utilization under fluctuating N conditions at the whole-plant level.
Takatoshi Kiba, Hana Takahashi, Kota Monden et al.· bioRxiv· 0 citations
Flag leaf angle (FLA) critically determines rice yield potential under dense planting conditions. As two pivotal phytohormones determine rice FLA, the antagonistic interaction between brassinosteroid (BR) and auxin remains largely uncharacterized. We here demonstrate that BR signaling reduces auxin biosynthesis to control FLA via regulating the biosynthesis of secondary cell wall (SCW). Genetic evidence demonstrates OsYUC8 mutants disrupt SCW formation, leading to increased FLA. At the molecular level, the BR-related transcription factor OsBZR1 directly binds to and represses OsYUC8 promoter activity, thereby fine-tuning auxin-mediated SCW biosynthesis. Field evaluations reveal that osbzr1 mutants display optimized flag leaf architecture and improved yield performance under high-density cultivation. Our study not only delineates the antagonistic BR-auxin interaction governing FLA but also establishes a genetic strategy for manipulating crop architecture to maximize yield in dense planting conditions. One-sentence summary OsBZR1-mediated repression of OsYUC8-driven auxin biosynthesis modulates secondary cell wall formation to optimize flag leaf architecture, providing a genetic strategy for maximizing yield under high-density cultivation.