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Background Rice aleurone layer develops different colours with various chemical tests that may help to develop some rapid tests for identification/grouping of rice varieties. Understanding the colour inheritance pattern could enable to develop chemical clues that may help for genetic purity analysis along with grow-out-test. Results In this study, inheritance pattern of aleurone layer colour was studied in parents, F 1 and F 2 progenies derived from the crosses IR 36  ×  Acc. No. 2693 and IR 64  ×  Acc. No. 2693. The parent IR 36 showed light yellow (NaOH/KOH) and brown (phenol/modified phenol test) colour; whereas, Acc. No. 2693 revealed wine red/dark wine red (NaOH/KOH) and light brown colour/no reaction (phenol/modified phenol test). In contrary, another parent IR 64 exhibited light yellow (KOH/NaOH) and dark brown (phenol, modified phenol) colour. Both the F 1 showed an intermediate light wine red colour (NaOH/KOH) and dark brown (phenol and modified phenol) colour, which is dominant over their one of the parents. The colour pattern with standard phenol/modified phenol, NaOH and KOH tests in F 2 progenies of both the crosses showed 9:7 (complementary gene interaction) and 11:5 ratios (reciprocal dominance modification of recessive alleles), respectively. Conclusions Our findings clearly elucidate the colour inheritance pattern in rice that may facilitate to develop rapid chemical tests to identify/ group the varieties for genetic purity analysis.

A survey of bacterial and archaeal genomes shows that many Tn7-like transposons contain minimal type I-F CRISPR-Cas systems that consist of fused cas8f and cas5f, cas7f, and cas6f genes and a short CRISPR array. Several small groups of Tn7-like transposons encompass similarly truncated type I-B CRISPR-Cas. This minimal gene complement of the transposon-associated CRISPR-Cas systems implies that they are competent for pre-CRISPR RNA (precrRNA) processing yielding mature crRNAs and target binding but not target cleavage that is required for interference. Phylogenetic analysis demonstrates that evolution of the CRISPR-Cas–containing transposons included a single, ancestral capture of a type I-F locus and two independent instances of type I-B loci capture. We show that the transposon-associated CRISPR arrays contain spacers homologous to plasmid and temperate phage sequences and, in some cases, chromosomal sequences adjacent to the transposon. We hypothesize that the transposon-encoded CRISPR-Cas systems generate displacement (R-loops) in the cognate DNA sites, targeting the transposon to these sites and thus facilitating their spread via plasmids and phages. These findings suggest the existence of RNA-guided transposition and fit the guns-for-hire concept whereby mobile genetic elements capture host defense systems and repurpose them for different stages in the life cycle of the element.

The major histocompatibility complex (MHC) is a core part of the adaptive immune system. As in other vertebrate taxa, it may also affect human chemical communication via odour-based mate preferences, with greater attraction towards MHC-dissimilar partners. However, despite some well-known findings, the available evidence is equivocal and made complicated by varied approaches to quantifying human mate choice. To address this, we here conduct comprehensive meta-analyses focusing on studies assessing: (i) genomic mate selection, (ii) relationship satisfaction, (iii) odour preference, and (iv) all studies combined. Analysis of genomic studies reveals no association between MHC-dissimilarity and mate choice in actual couples; however, MHC effects appear to be independent of the genomic background. The effect of MHC-dissimilarity on relationship satisfaction was not significant, and we found evidence for publication bias in studies on this area. There was also no significant association between MHC-dissimilarity and odour preferences. Finally, combining effect sizes from all genomic, relationship satisfaction, odour preference and previous mate choice studies into an overall estimate showed no overall significant effect of MHC-similarity on human mate selection. Based on these findings, we make a set of recommendations for future studies, focusing both on aspects that should be implemented immediately and those that lurk on the far horizon. We need larger samples with greater geographical and cultural diversity that control for genome-wide similarity. We also need more focus on mechanisms of MHC-associated odour preferences and on MHC-associated pregnancy loss. This article is part of the Theo Murphy meeting issue ‘Olfactory communication in humans’.

Anthocyanin regulation can be fruitfully explored from a diverse perspective by studying distantly related model organisms. Land plants pioneers faced a huge evolutionary leap, involving substantial physiological and genetic changes. Anthocyanins have evolved alongside these changes, becoming versatile compounds capable of mitigating terrestrial challenges such as drought, salinity, extreme temperatures and high radiation. With the accessibility of whole-genome sequences from ancient plant lineages, deeper insights into the evolution of key metabolic pathways like phenylpropanoids have emerged. Despite understanding the function of anthocyanins under stress, gaps remain in uncovering the precise metabolic and regulatory mechanisms driving their overproduction under stressful conditions. For example, the regulatory effect of reactive oxygen species (ROS) on well-known transcription factors like MYBs is not fully elucidated. This manuscript presents an evolutionary analysis of the anthocyanin biosynthetic pathway to elucidate key genes. CINNAMATE 4-HYDROXYLASE ( C4H ) and CHALCONE ISOMERASE ( CHI2 ) received particular attention. C4H exposes remarkable differences between aquatic and land plants, while CHI2 demonstrates substantial variation in gene copy number and sequence similarity across species. The role of transcription factors, such as MYB, and the involvement of ROS in the regulation of anthocyanin biosynthesis are discussed. Complementary gene expression analyses under abiotic stress in Arabidopsis thaliana , Selaginella moellendorffii , and Marchantia polymorpha reveal intriguing gene-stress relationships. This study highlights evolutionary trends and the regulatory complexity of anthocyanin production under abiotic stress, providing insights and opening avenues for future research. Key message We propose that CHI2 is a distinctive gene in the anthocyanin biosynthetic pathway, with an unusual evolutionary pattern and a significant role in abiotic stress adaptation via bioinformatics analysis and reviewing current literature.

• Parastagonospora nodorum is a fungal pathogen of wheat. As a necrotrophic specialist, it deploys effector proteins that target dominant host susceptibility genes to elicit programmed cell death (PCD). Here we identify and functionally validate the effector targeting the host susceptibility genes Snn2, Snn6 and Snn7. • We utilized whole-genome sequencing, association mapping, gene-disrupted mutants, gain-of-function transformants, virulence assays, bioinformatics and quantitative PCR to characterize these interactions. • A single proteinaceous effector, SnTox267, targeted Snn2, Snn6 and Snn7 to trigger PCD. Snn2 and Snn6 functioned cooperatively to trigger PCD in a light-dependent pathway, whereas Snn7-mediated PCD functioned in a light-independent pathway. Isolates harboring 20 SnTox267 protein isoforms quantitatively varied in virulence. The diversity and distribution of isoforms varied between populations, indicating adaptation to local selection pressures. SnTox267 deletion resulted in the upregulation of effector genes SnToxA, SnTox1 and SnTox3. • We validated a novel effector operating in an inverse-gene-for-gene manner to target three genetically distinct host susceptibility genes and elicit PCD. The discovery of the complementary gene action of Snn2 and Snn6 indicates their potential function in a guard or decoy model. Additionally, differences in light dependency in the elicited pathways and upregulation of unlinked effectors sheds new light onto a complex fungal necrotroph–host interaction.

Two genes controlling the purple pericarp trait in wheat, TaPpm1 and TaPpb1, are identified and the mechanism by which they co-regulate anthocyanin synthesis is proposed. Abstract Purple pericarps of bread wheat (Triticum aestivum L.) are a useful source of dietary anthocyanins. Previous mapping results indicated that the purple pericarp trait is controlled by two complementary genes located on chromosomes 7D and 2A. However, the identity of the genes and the mechanisms by which they regulate the trait are unknown. In this study, two transcription factors were characterised as anthocyanin activators in purple pericarps: TaPpm1 (purple pericarp-MYB 1) and TaPpb1 (purple pericarp-bHLH 1). Three non-functional variants were detected in the coding sequence of TaPpm1 from non-purple seed lines, in which the function of TaPpm1 was destroyed either by insertion-induced frame shifts or truncated peptides. There were six 261-bp tandem repeats in the promoter region of TaPpb1 in the purple-grained varieties, while there was only one repeat unit present in the non-purple varieties. Furthermore, using yeast two-hybrid, dual luciferase, yeast one-hybrid, and transient assays, we were able to demonstrate that the interaction of TaPpm1 and TaPpb1 co-regulates the synthesis of anthocyanin. Overall, our results provide a better understanding of the molecular basis of anthocyanin synthesis in the wheat pericarp and indicate the existence of an integrated regulatory mechanism that controls production.

Background The availability of draft crop plant genomes allows the prediction of the full complement of genes that encode NB-LRR resistance gene homologs, enabling a more targeted breeding for disease resistance. Recently, we developed the RenSeq method to reannotate the full NB-LRR gene complement in potato and to identify novel sequences that were not picked up by the automated gene prediction software. Here, we established RenSeq on the reference genome of tomato ( Solanum lycopersicum ) Heinz 1706, using 260 previously identified NB-LRR genes in an updated Solanaceae RenSeq bait library. Result Using 250-bp MiSeq reads after RenSeq on genomic DNA of Heinz 1706, we identified 105 novel NB-LRR sequences. Reannotation included the splitting of gene models, combination of partial genes to a longer sequence and closing of assembly gaps. Within the draft S. pimpinellifolium LA1589 genome, RenSeq enabled the annotation of 355 NB-LRR genes. The majority of these are however fragmented, with 5′- and 3′-end located on the edges of separate contigs. Phylogenetic analyses show a high conservation of all NB-LRR classes between Heinz 1706, LA1589 and the potato clone DM, suggesting that all sub-families were already present in the last common ancestor. A phylogenetic comparison to the Arabidopsis thaliana NB-LRR complement verifies the high conservation of the more ancient CC RPW8 -type NB-LRRs. Use of RenSeq on cDNA from uninfected and late blight-infected tomato leaves allows the avoidance of sequence analysis of non-expressed paralogues. Conclusion RenSeq is a promising method to facilitate analysis of plant resistance gene complements. The reannotated tomato NB-LRR complements, phylogenetic relationships and chromosomal locations provided in this paper will provide breeders and scientists with a useful tool to identify novel disease resistance traits. cDNA RenSeq enables for the first time next-gen sequencing approaches targeted to this very low-expressed gene family without the need for normalization.

Invertebrates represent a large proportion of the biomass in aquatic ecosystems, particularly in the ocean. In recent years, invertebrates have been well-consolidated models in evolutionary developmental biology research and, consequently, genomic and transcriptomic sequence databases from a plethora of species across the animal kingdom have become available. This has provided an excellent source of evidence confirming that invertebrates operate endogenous mechanisms for PUFA production. The present paper reviews the current knowledge of gene complement and, where possible, the function of desaturases and elongases with pivotal roles in PUFA biosynthesis of aquatic invertebrates. More specifically, this review covers three major enzyme types, namely ωx desaturases, front-end desaturases and elongases, that have been characterised from species of sponges, cnidarians, molluscs, annelids, crustaceans, rotifers, echinoderms and non-vertebrate chordates (amphioxus and sea squirt). These studies have shown that invertebrates operate alternative and unusual pathways of PUFA biosynthesis involving gene families with complex phylogeny and functional diversity. Consequently, research in this area provides potentially valuable molecular tools in the form of genes that can be used in the biotechnological production of n-3 products.

Investigating the features and implications of epigenetic mechanisms across the breadth of organisms and ecosystems is important for understanding the ecological relevance of epigenetics. Several cost-effective reduced representation bisulfite sequencing approaches (RRBS) have been recently developed and applied to different organisms that lack a well annotated reference genome. These new approaches improve the assessment of epigenetic diversity in ecological settings and may provide functional insights. We assess here the opportunities and limitations of RRBS in nonmodel plant species. Well thought out experimental designs that include complementary gene expression studies, and the improvement of genomics resources for the target group, promise to maximize the effect of future RRBS studies.

Hybrid breakdown (HB), a phenomenon of reduced viability or fertility accompanied with retarded growth in hybrid progenies, often arises in the offspring of intersubspecific hybrids between indica and japonica in rice. We detected HB plants in F₈ recombinant inbred lines derived from the cross between an indica variety, Milyang 23, and a japonica variety, Tong 88-7. HB plants showed retarded growth, with fewer tillers and spikelets. Genetic analysis revealed that HB was controlled by the complementary action of two recessive genes, hwh1 and hwh2, originating from each of both parents, which were fine-mapped on the short arm of chromosome 2 and on the near centromere region of the long arm of chromosome 11, respectively. A comparison of the sequences of candidate genes among both parents and HB plants revealed that hwh1 encoded a putative glucose-methanol-choline oxidoreductase with one amino acid change compared to Hwh1 and that hwh2 probably encoded a putative hexose transporter with a six amino acid insertion compared to Hwh2. Investigation of the distribution of these alleles among 54 japonica and indica cultivars using candidate gene-based markers suggested that the two loci might be involved in developing reproductive barriers between two subspecies.