A Wild Emmer Wheat B3 Transcription Factor Regulates Seed Growth and Nutrient Allocation.

Genome-Wide Association Study and Identification of Core Candidate Genes for Shoot and Root Length in Wheat During Germination

To address the core breeding demand for greater seedling vigor in bread wheat (Triticum aestivum L.) varieties adapted to the uniform sowing system in China’s Huang-Huai Wheat Region, we aimed to dissect the genetic architecture and identify core candidate genes for shoot length (SL) and root length (RL) at the germination stage. A natural population consisting of 204 wheat accessions was genotyped using the 660K SNP array, and a genome-wide association study (GWAS) integrated with transcriptomic, metabolomic, and proteomic analyses of extreme phenotypic accessions was performed. Both SL and RL were typical quantitative traits with an extremely significant positive correlation. A total of 111 and 176 significant SNPs were associated with SL and RL, respectively, including 56 shared loci. Glutathione metabolism was identified as the conserved core pathway for both tissues, while photosynthesis–antenna proteins and phenylpropanoid biosynthesis were identified as tissue-specific pathways in shoots and roots, respectively. Finally, we identified 7 core candidate genes for SL and 13 for RL, including three pleiotropic genes regulating both traits. This study provides valuable genetic resources and key targets for the molecular breeding of wheat varieties specialized for uniform sowing.

The carbon-nitrogen metabolism gene E1OGDH1 influences maize root system architecture and nitrogen plasticity

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.

A pangenome of tetraploid wheat reveals the genetic architecture underlying domestication and genomic diversity for breeding

Tetraploid wheat (Triticum turgidum L., BBAA), a key pasta crop, serves as an untapped genetic resource with rich genomic diversity for hexaploid bread wheat improvement. Here we de novo assembled 12 genomes spanning all 10 recognized tetraploid wheat (genome BBAA) subspecies, and a graph-based pangenome was constructed. Chromosome rearrangements drove subgenome asymmetry and shaped genomic divergence, with an average of 0.25 million structural variations per accession, predominantly attributable to transposon activity. Using 736 globally distributed tetraploid wheat accessions, we identified locally adapted subgroups with untapped breeding potential and discovered a novel retrotransposon‑induced loss‑of‑function Btr1-A allele responsible for convergent adaptation of non-brittle rachis. Genome-wide association studies identified 287 loci associated with 32 traits. A homeodomain-leucine zipper transcription factor HAT14-B that enhances both spikelet number and grain size was identified. This subspecies-wide pangenome enriches Triticeae AB subgenome resources and facilitates the discovery and application of agronomically important genetic variations. A pangenome of tetraploid wheat constructed from 12 de novo genome assemblies spanning 10 subspecies, integrating with whole-genome sequencing data, highlights genetic variation associated with agricultural traits.

A domestication-selected enhancer coordinates source-sink balance to improve harvest index and yield in maize.

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.

Emerging molecular strategies to improve drought tolerance in barley Hordeum vulgare L.)

Natural variation in SlGRF10 reveals a role in regulating tomato fruit weight

Abstract Fruit weight is a key determinant of yield in high-value vegetable crops such as tomato. Despite extensive research, the molecular mechanisms underlying this complex trait remain largely elusive, with only a few genes cloned to date based on quantitative trait loci (QTL). Here, we analyzed 2 populations and reanalyzed 3 previously published populations and identified 945 QTL associated with agro-morphological traits, including both previously reported and unidentified loci. We focused on SlGRF10 (GROWTH-REGULATING FACTOR 10) underlying a fruit weight QTL, fw1.2. Loss of SlGRF10 reduced fruit weight by decreasing cell size, without affecting cell number. 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. This suggests that putative impaired activity contributes to reduced fruit weight, while breeding-induced reduction of genetic variation may have promoted increased fruit weight. Transcriptome profiling of SlGRF10 knockout lines 7 and 20 days postanthesis identified several differentially expressed genes involved in cell cycle progression. Our findings not only confirm the role of SlGRF10 in regulating tomato fruit weight but also highlight a set of candidate genes associated with key morpho-physiological traits. With fw11.3, named as CELL SIZE REGULATOR, being the only QTL related to cell size determination in tomato fruits so far, SlGRF10 offers a valuable target for precision breeding and enhances our understanding of fruit weight in tomato and related fruit-bearing species.