Journal of Genetics and Genomics

Dissecting the genetic basis of reproductive transition and reproductive growth in wheat by considering accumulated temperature

Liujie Jin, Kening Duo, et al.

doi: 10.1016/j.jgg.2025.09.012

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Maize Chlorotic Leaf Spot1 encodes a fumarylacetoacetate hydrolase essential for carbohydrate partitioning

Ruchang Ren, Sihang Zhao, et al.

doi: 10.1016/j.jgg.2025.10.002

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Abstract:
Carbohydrate partitioning from photosynthetic sources to non-photosynthetic sinks is essential for plant development and crop yield. Using a maize-teosinte BC₂S₃ population, we identify Chlorotic Leaf Spot1 (CLS1), a fumarylacetoacetate hydrolase (FAH) in the tyrosine degradation pathway that plays an essential role in carbohydrate partitioning in maize. CLS1 localizes to the plasma membrane, cytoplasm, and nucleus. Allelic tests and sequence analysis reveal that the teosinte parent CIMMYT8759 carries a weak allele of CLS1, likely due to rare amino acid substitutions at residues 175 and 355. Loss-of-function mutants of CLS1 develop chlorotic leaf spots accompanied by carbohydrate hyperaccumulation, reduced photosynthetic efficiency, chloroplast damage, and impaired transient starch conversion. Critically, cls1 mutants exhibit ectopic callose accumulation and aberrant plasmodesmata ultrastructure at the mesophyll-bundle sheath and bundle sheath-vascular parenchyma interfaces. This defect causes starch granule and soluble sugar accumulation in chlorotic leaf tissues, indicating a disruption of the symplastic transport pathway. Collectively, our results uncover an important role for FAH in plant development and identify CLS1 as a key regulator of symplastic carbohydrate partitioning.

circRNAs derived from a nuclear hormone receptor act differentially on insect metamorphosis and reproduction

Lulu Gao, Qiang Yan, et al.

doi: 10.1016/j.jgg.2025.10.001

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Abstract:
Insects are the most diverse group on earth, partially owing to their metamorphosis and strong fecundity. Circular RNAs (circRNAs) are stable molecules implicated in a broad range of biological processes. However, the regulatory roles of circRNAs in insect metamorphosis and reproduction are unclear. Methoprene-tolerant (Met) is the nuclear receptor of juvenile hormone (JH) that plays dual roles of inhibiting precocious metamorphosis and promoting reproduction. Here, we report that locust Met generates two circRNAs, circMet1 and circMet2, respectively. While circMet1 is highly expressed in the cuticle of late final instar, circMet2 is more abundant in the corpora allata, brain, and fat body of early vitellogenic adults. Interestingly, circMet2 is generated by complementary pairing of Penelope-like remnants across the introns of Met. Moreover, circMet2 functions as a miRNA sponge of four species-specific miRNAs that downregulate Met translation. siRNA-mediated knockdown of circMet1 causes the delay of metamorphosis and retarded vitellogenesis. Loss of circMet2 results in significantly decreased vitellogenin synthesis, along with blocked ovarian growth. These results reveal the differential roles of circMet1 and circMet2 in modulating insect metamorphosis and female reproduction. This study advances our understanding of how circRNAs derived from a single gene exert distinct roles in insect life history.

Single-molecule chromatin profiling reveals cell type-specific A/B compartment alteration and multi-enhancer transcriptional coordination

Luo-Ran Liu, Jia-Yong Zhong, et al.

doi: 10.1016/j.jgg.2025.09.011

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In eukaryotic organisms, the three-dimensional organization and epigenomic landscape of chromatin are fundamental to the regulation of gene expression. Previous studies have provided significant insights into CpG methylation, chromatin accessibility, and the dynamics of 3D architecture. However, a systematic delineation of how these epigenomic features regulate transcriptional activity remains limited. In this study, we develop nanoCAM-seq, a single-molecule sequencing technique designed to simultaneously profile higher-order chromatin interactions, chromatin accessibility, and endogenous CpG methylation. This approach provides an integrative view of chromatin features associated with cis-regulatory elements and reveals their coordinated dynamics during transitions of A/B compartments. Single-molecule analyses using nanoCAM-seq further reveal that promoters characterized by low CpG methylation and high chromatin accessibility more frequently interact with multiple enhancers. Collectively, our findings establish nanoCAM-seq as a powerful approach for resolving the coordinated dynamics of chromatin architecture and epigenetic modifications, offering critical insights into the regulatory mechanisms underlying gene expression.

Genomic insights into population structure, adaptation, and archaic introgression at the Himalayan–East Asian crossroads

Mengge Wang, Shuhan Duan, et al.

doi: 10.1016/j.jgg.2025.09.010

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Tibetan-Yi Corridor (TYC) is a crucial agro-pastoral region in the eastern Himalayas, linking Qinghai‒Xizang Plateau with the lowlands of East Asia and facilitating human migration for millennia. However, genomic research on TYC populations remains limited, which limits the understanding of their origins and health. We provide genomic data from 1031 individuals belonging to Austroasiatic and Sino-Tibetan groups, including 147 whole-genome sequences from 13 underrepresented Tibeto-Burman and Austroasiatic communities. Our analysis reveals approximately 3.3 million new genetic variants and 4 distinct genetic backgrounds within TYC populations. Demographic reconstructions reveal strong genetic connections among Tibeto-Burman groups, Central Plain Sinitic populations, and Yangshao farmers, supporting a common origin for Sino-Tibetan speakers. We identify signatures of high-altitude adaptations typical of Tibetans and TYC-specific variants linked to pigmentation and hypoxia responses. Differentiation involves mechanisms such as HLA-DQB1, which are related to immune function. Several rare pathogenic variants, like CYP21A2 and PRX, are notably frequent. Variants influencing warfarin sensitivity show significant variation. Archaic human introgression further promotes genomic complexity, impacting cardiovascular and immune-related genes, which suggests adaptation through ancient human interactions. These findings refine the evolutionary history of TYC populations and underscore the need for broader genomic research to capture regional diversity and inform precision medicine.

A SABRE family protein DITA1 regulates plant height and tiller angle in rice

Ting Zou, Jing Liang, et al.

doi: 10.1016/j.jgg.2025.09.009

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Rice plant architecture is shaped by complex agronomic traits, such as plant height and tiller angle, which collectively determine yield potential. Although SABRE family proteins are conserved across eukaryotes, their roles in regulating plant architecture remain poorly understood. Here, we characterize the rice dwarf and increased tiller angle1 (dita1) mutant, which exhibits reduced plant height and spreading tillers due to abnormal cell morphology. Physiological analyses reveal that the dita1 mutant displays attenuated gravitropic responses, disrupted cytoskeleton organization, and impaired amyloplast sedimentation. DITA1 encodes a rice SABRE family member that likely localizes to the endoplasmic reticulum. Expression profiling shows that DITA1 is upregulated following gravistimulation and is enriched in the tiller base during the tillering stage. Mutation in DITA1 alters the transcript levels of genes involved in auxin biosynthesis and asymmetric distribution. Furthermore, analysis of natural variation within the DITA1 coding region identifies associations between haplotypes and tiller angles. Collectively, our findings suggest that DITA1 contributes to the regulation of plant architecture through potentially influencing on cytoskeletal dynamics, statolith-mediated gravitropism, and asymmetric auxin distribution, providing a genetic target for optimizing plant architecture in breeding programs.