Abstract Drought‐yield quantitative trait loci (QTLs) qDTY 2.2 and qDTY 4.1 improve grain yield under reproductive‐stage drought in rice ( Oryza sativa L.), yet their genomic architecture remains poorly resolved in elite indica breeding backgrounds. We generated a chromosome‐level assembly of IR87707‐446‐B‐B‐B (IR64‐qDTY 2.2 + qDTY 4.1 ), which carries both QTLs in the IR64 background, and delineated donor‐derived introgressions using informative parental single‐nucleotide polymorphisms (SNPs). The 395.5‐Mb assembly comprised 12 chromosomes, showed 99.2% BUSCO completeness, and contained 40,189 predicted protein‐coding genes. Informative‐SNP analysis, supported by read‐depth assessment of low‐information regions, resolved qDTY 2.2 and qDTY 4.1 as continuous donor‐derived introgressions containing 194 and 97 genes, respectively. Comparative genome analysis showed that qDTY 2.2 was largely macrostructurally collinear with IRGSP‐1.0, whereas qDTY 4.1 showed pronounced structural divergence and contained a 15.6‐kb inversion relative to IR64sj. Comparative gene‐content analysis further showed that 37.1% and 55.7% of genes in qDTY 2.2 and qDTY 4.1 , respectively, lacked collinear orthologs in IRGSP‐1.0. Multi‐accession allele analysis revealed contrasting candidate‐gene profiles between the two loci. Six of eight qDTY 2.2 candidates had coding sequences identical to IR64sj, whereas all four qDTY 4.1 candidates showed coding differences from IR64sj. Coordinate‐based SNP markers were also developed for donor‐haplotype tracking across both QTL intervals. These results provide a genome‐resolved framework for characterizing drought‐yield QTLs and developing breeding‐background‐specific markers for recombination‐aware rice breeding.
Abstract Citrus production has declined substantially due to Huanglongbing (HLB), a bacterial disease that has caused severe economic losses worldwide. Long‐term field studies indicate that citrus species differ in their tolerance to HLB, underscoring the importance of incorporating disease‐tolerant traits to sustain the citrus industry. This study investigates phylogenetic relationships and genetic diversity among citrus accessions to support their effective use in breeding programs. Thirty‐two citrus accessions representing diverse groups were analyzed using phylogenetic analysis, homozygosity‐by‐descent analysis, and principal component analysis (PCA). PCA separated the cultivars into two distinct groups, explaining 73.3% of the total genetic variation. This clustering revealed unique genetic diversity within Australasian citrus, underscoring its value for conservation and future research. Australasian accessions, classified as HLB‐resistant or HLB‐tolerant, were further compared with the susceptible cultivar Citrus sinensis L. Osbeck (Hamlin 1‐4‐1) to identify potential defense mechanisms using diagnostic variants (DVs). Annotation of transposable elements in these DVs revealed insertions within genes, suggesting potential effects on gene regulation during defense responses. Functional annotation of DVs, based on sequence comparisons shared between resistant and tolerant groups, identified an amino acid substitution present only in susceptible cultivars that may compromise HLB defense. No such substitutions occurred in the Australasian citrus species. The affected genes are associated with key components of plant defense, including signaling pathways, phytohormone regulation, and secondary metabolite biosynthesis. Overall, this study highlights valuable genetic diversity in citrus germplasm for combating HLB.
Abstract Rice blast, caused by Magnaporthe oryzae , remains a major constraint to rice ( Oryza sativa L.) production, and durable resistance will require broader use of genetic diversity beyond commonly studied elite cultivars. We present chromosome‐scale genome assemblies of two agronomically significant but genetically divergent rice cultivars: CT21375‐F4‐4 (hereafter, CT21) and Moroberekan. Despite their genetic divergence, both cultivars show consistently strong resistance to blast under multiyear field conditions. We combined field phenotyping with genome‐wide protein‐to‐genome alignment, predicted proteome comparisons, nucleotide‐binding leucine‐rich repeat (NLR) annotation, and locus‐specific analyses of cloned blast resistance genes to examine resistance‐associated genomic variation in these cultivars. The cultivars contained similar numbers and overall subtype compositions of NLR loci, but differed markedly in their correspondence to characterized blast resistance genes. CT21 contained multiple exact or near‐exact matches to cloned blast resistance genes and alleles, whereas Moroberekan contained fewer exact matches and was characterized predominantly by high‐identity but divergent homologs, suggesting the presence of divergent alleles or resistance architectures that are not well represented by the cloned gene repertoire. Locus‐specific analyses further confirmed that high sequence similarity alone does not reliably predict resistance function, and revealed structural variation, including duplication within the Pish NLR cluster in CT21. These results demonstrate that comparable blast resistance phenotypes can occur in cultivars with distinct allelic and structural architectures at known resistance loci. The assemblies and comparative framework developed here provide resources for identifying resistance diversity that may be overlooked by reference gene or marker‐based analyses and for prioritizing candidate loci for functional validation and rice improvement.
Abstract A nonautonomous DNA transposon was identified within the dehydration responsive factor 1 ( DRF1 ) gene, a member of the DREB (dehydration responsive element binding) family involved in abiotic stress responses. The element was first detected in the Triticum durum TdDRF1 locus and subsequently in homologous genes from T. aestivum and its progenitors, T. urartu , Aegilops speltoides , and A. tauschii . The DRF1 gene consists of four exons and three introns, with the transposon inserted between Intron 1 and Intron 3. The element exhibits characteristic signatures of DNA transposons, including terminal inverted repeats (TIRs), target site duplications, and multiple internal direct and inverted repeats. Based on TIR organization, we propose a putative mechanism for its integration. Because no transposase‑coding region was detected, the element is classified as nonautonomous. We hypothesized—as a working model and a plausible evolutionary scenario—that transposable‐element activity contributed to the reconstruction of DRF1 architecture, together with the potential involvement of nonsense‐mediated decay/RNA interference pathways. The transposon carries a conserved core element composed of Exon 2, Intron 2, and Exon 3, which participate in alternative splicing of DRF1 . Comparative and phylogenomic analyses reveal that an intact transposon is restricted to Triticeae, whereas earlier diverging Poaceae retain only degraded remnants of the core element. No comparable insertion or splice variants were detected in dicots such as Arabidopsis thaliana , indicating a monocot‑specific evolutionary event. These results suggest that a recently evolved nonautonomous transposon contributed to structural diversification and alternative splicing of DRF1 in grasses, highlighting the broader role of transposable elements in shaping gene regulation and genome evolution in Triticeae.
Abstract The olive tree ( Olea europaea L. subsp. europaea ) is one of the most representative perennial crops of the Mediterranean Basin, yet the genomic processes underlying its domestication and diversification remain poorly understood. Here, we investigated repeatome variation across 20 accessions, including 11 wild oleasters and nine cultivated varieties, using comparative clustering of high‐throughput sequencing data, complemented by structural analyses of transposable elements (TEs) and tandem repeats (TRs). Repetitive DNA accounts for about 54% of the olive genomes and is composed primarily of long terminal repeat retrotransposons (LTR‐REs) and TRs. Comparative analyses revealed lineage‐specific differences in LTR‐REs between wild and cultivated genotypes, while TRs exhibited higher abundances and greater variability in oleasters for some families (e.g., Oe‐80 and Oe‐178), reinforcing the view that TRs evolve rapidly and largely independently in olive. We also identified a new TR (Oe‐155) and confirmed its distinct monomer sequence and chromosomal organization, suggesting that this subfamily is differentiating from TRs Oe‐218 and Oe‐80. To refine TE dynamics, we surveyed full‐length elements in two reference assemblies (cv. Leccino and a wild sylvestris genotype). Leccino is enriched in intact LTR‐REs, whereas sylvestris harbored more full‐length Class II DNA transposons. Additionally, the patterns of TE‐gene proximity vary significantly between them. Dating of full‐length LTR‐RE insertions revealed that most RE activity predates domestication, with only a small fraction of very recent insertions. These results highlight repetitive DNA as a major contributor to genome diversification in olive and provide a foundation for integrating repeatome variation with demographic history, introgression, and clonal propagation.
