Comprehensive dissection of meiotic DNA double-strand breaks and crossovers in cucumber.

Meiotic recombination drives genetic diversity and crop genome optimization. In plant breeding, parents with favorable traits are crossed to create elite varieties. Different hybridizations produce diverse types of segment reshuffling between homologous chromosomes. However, little is known about the factors that cause hybrid-specific changes in crossovers (COs). Here, we constructed 2 F2 populations from crosses between a semiwild and 2 domesticated cucumber (Cucumis sativus) accessions and examined CO events. COs mainly occurred around genes and differed unevenly along chromosomes between the 2 hybrids. Fine-scale CO distributions were suppressed in regions of heterozygous structural variations (SVs) and were accelerated by high sequence polymorphism. C. sativus RADiation sensitive 51A (CsRAD51A) binding, histone H3 lysine 4 trimethylation (H3K4me3) modification, chromatin accessibility, and hypomethylation were positively associated with global CO landscapes and in local DNA double-strand break (DSB) hotspots and genes. The frequency and suppression of COs could be roughly predicted based on multiomic information. Differences in CO events between hybrids could be partially traced to distinct genetic and epigenetic features and were significantly associated with specific DSB hotspots and heterozygous SVs. Our findings identify the genomic and epigenetic features that contribute to CO formation and hybrid-specific divergence in cucumber and provide theoretical support for selecting parental combinations and manipulating recombination events at target genomic regions during plant breeding.

Genome-Scale Analysis of Homologous Genes among Subgenomes of Bread Wheat (Triticum aestivum L.).

Determining the distribution and correspondence of genome-scale homologous genes in wheat are effective ways to uncover chromosome rearrangement that has occurred during crop evolution and domestication, which can contribute to improvements in crop breeding. High-resolution and comprehensive analysis of the wheat genome by the International Wheat Genome Sequencing Consortium (IWGSC) revealed a total of 88,733 high-confidence homologous genes of four major types (1:1:1, 1:1:0, 0:1:1 and 1:0:1) among the A, B and D subgenomes of wheat. This data was used to compare homologous gene densities among chromosomes, clarify their distribution and correspondence relationship, and compare their functional enrichment. The average density of 1:1:1 homologous genes was about 10 times more than the density of the other three types of homologous genes, although the homologous gene densities of the various chromosomes were similar within each homologous type. Three regions of exceptional density were detected in 1:1:1 homologous genes, the isolate peak on the tail of chromosome 4A, and the desert regions at the start of chromosome 7A and 7D. The correspondence between homologous genes of the wheat subgenomes demonstrated translocation between the tail segments of chromosome 4A and 5A, and the inversion of the segment of original 5A and 7B into the tail of 4A. The homologous genes on the inserting segments of 5A and 7B to 4A were highly enriched in nitrogen, primary metabolite and small molecular metabolism processes, compared with genes on other regions of the original 4A chromosome. This study provides a refined genome-scale reference of homologous genes for wheat molecular research and breeding, which will help to broaden the application of the wheat genome and can be used as a template for research on other polyploid plants.

Integrated Pleiotropic Gene Set Unveils Comorbidity Insights across Digestive Cancers and Other Diseases.

Comorbidities are prevalent in digestive cancers, intensifying patient discomfort and complicating prognosis. Identifying potential comorbidities and investigating their genetic connections in a systemic manner prove to be instrumental in averting additional health challenges during digestive cancer management. Here, we investigated 150 diseases across 18 categories by collecting and integrating various factors related to disease comorbidity, such as disease-associated SNPs or genes from sources like MalaCards, GWAS Catalog and UK Biobank. Through this extensive analysis, we have established an integrated pleiotropic gene set comprising 548 genes in total. Particularly, there enclosed the genes encoding major histocompatibility complex or related to antigen presentation. Additionally, we have unveiled patterns in protein-protein interactions and key hub genes/proteins including TP53, KRAS, CTNNB1 and PIK3CA, which may elucidate the co-occurrence of digestive cancers with certain diseases. These findings provide valuable insights into the molecular origins of comorbidity, offering potential avenues for patient stratification and the development of targeted therapies in clinical trials.