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Sorghum (Sorghum bicolor L.) ranks fifth as the most crucial cereal crop globally, yet its seed morphology remains relatively unexplored. This study investigated seed morphology in sorghum based on 115 mini-core and 130 Senegalese germplasms. Eight seed morphology traits encompassing size, shape, and color parameters were assessed. Statistical analyses explored potential associations between these traits and resistance to three major sorghum diseases: anthracnose, head smut, and downy mildew. Furthermore, genome-wide association studies (GWAS) were conducted using phenotypic data from over 24,000 seeds and over 290,000 publicly available single nucleotide polymorphisms (SNPs) through the Genome Association and Prediction Integrated Tool (GAPIT) R package. Significant SNPs associated with various seed morphology traits were identified and mapped onto the reference sorghum genome to identify novel candidate defense genes. [ABSTRACT FROM AUTHOR]

A newly documented pathotype 5 of the soil-borne fungus Sporisorium reilianum, causing head smut in sorghum, was tested against 153 unexplored Senegalese sorghum accessions. Among the 153 sorghum accessions tested, 63 (41%) exhibited complete resistance, showing no signs of infection by the fungus. The remaining 90 accessions (59%) displayed varying degrees of susceptibility. Sorghum responses against S. reilianum were explored to analyze the potential link with previously known seed morphology-related traits and new phenotype data from 59 lines for seed weight. A genome-wide association study (GWAS) screened 297,876 SNPs and identified highly significant associations (p < 1 × 10−5) with head smut resistance in sorghum. By mapping these significant SNPs to the reference genome, this study revealed 35 novel candidate defense genes potentially involved in disease resistance. [ABSTRACT FROM AUTHOR]

The World Collection of Sugarcane and Related Grasses, maintained at the USDA-ARS in Miami, FL, is one of the largest sugarcane germplasm repositories in the world. However, the genetic integrity of the Saccharum spp. germplasm in this collection has not been fully analyzed. In this study, we employed a single-dose SNP panel to genotype 901 sugarcane accessions, representing six Saccharum species and various hybrids. Our analysis uncovered a high rate of clone mislabeling in the collection. Specifically, we identified 86 groups of duplicates, characterized by identical SNP genotypes, which encompassed 211 accessions (23% of the total clones), while 135 groups, constituting 471 clones (52% of the total), exhibited near-identical genotypes. In addition, twenty-seven homonymous groups were detected, which shared the same clone name but differed in SNP genotypes. Hierarchical analysis of population structure partitioned the Saccharum germplasm into five clusters, corresponding to S. barberi, S. sinense, S. officinarum, S. spontaneum and S. robustum/S. edule. An assignment test, based on the five Saccharum species, enabled correcting 141 instances of mislabeled species memberships and inaccuracies. Moreover, we clarified the species membership and parentage of 298 clones that had ambiguous passport records (e.g., ‘Saccharum spp’, ‘unknown’, and ‘hybrid’). Population structure and genetic diversity in these five species were further supported by Principal Coordinate Analysis and neighbor- joining clustering analysis. Analysis of Molecular Variance revealed that within- species genetic variations accounted for 85% of the total molecular variance, with the remaining 15% attributed to among-species genetic variations. The single-dose SNP markers developed in this study offer a robust tool for characterizing sugarcane germplasm worldwide. These findings have important implications for sugarcane genebank management, germplasm exchange, and crop genetic improvement. [ABSTRACT FROM AUTHOR]

Since the early 19th century, a substantial amount of jujube (Ziziphus spp.) germplasm has been introduced from China and Europe into the United States. However, due to a lack of passport data, cultivar mislabeling is common and the genetic background of the introduced germplasm remains unknown. In the present study, a low-density SNP array was employed to genotype 204 jujube trees sampled from multiple locations in New Mexico, Texas, Missouri, and Kentucky. Multilocus matching of SNP profiles revealed a significant rate of genetic redundancy among these jujube samples. A total of 14 synonymous groups were detected, comprising 48 accessions. Bayesian clustering analysis and neighbor-joining tree partitioned the US jujube germplasm into two major clusters. The first cluster included cultivated genotypes (Ziziphus jujuba Mill.), whereas the other major cluster comprised the wild/sour jujube (Ziziphus spinosa Hu.). The results also revealed a unique jujube population at Fabens/Tornillo, Texas, and a semi-naturalized population at Tucumcari, NM. These findings will provide valuable guidance to jujube growers and researchers on the effective utilization of jujube germplasm in the horticultural industry. [ABSTRACT FROM AUTHOR]

Premise: Despite myriad examples of local adaptation, the phenotypes and genetic variants underlying such adaptive differentiation are seldom known. Recent work on freezing tolerance and local adaptation in ecotypes of Arabidopsis thaliana from Italy and Sweden provides an essential foundation for uncovering the genotype–phenotype–fitness map for an adaptive response to a key environmental stress. Methods: We examined the consequences of a naturally occurring loss‐of‐function (LOF) mutation in an Italian allele of the gene that encodes the transcription factor CBF2, which underlies a major freezing‐tolerance locus. We used four lines with a Swedish genetic background, each containing a LOF CBF2 allele. Two lines had introgression segments containing the Italian CBF2 allele, and two contained deletions created using CRISPR‐Cas9. We used a growth chamber experiment to quantify freezing tolerance and gene expression before and after cold acclimation. Results: Freezing tolerance was lower in the Italian (11%) compared to the Swedish (72%) ecotype, and all four experimental CBF2 LOF lines had reduced freezing tolerance compared to the Swedish ecotype. Differential expression analyses identified 10 genes for which all CBF2 LOF lines, and the IT ecotype had similar patterns of reduced cold responsive expression compared to the SW ecotype. Conclusions: We identified 10 genes that are at least partially regulated by CBF2 that may contribute to the differences in cold‐acclimated freezing tolerance between the Italian and Swedish ecotypes. These results provide novel insight into the molecular and physiological mechanisms connecting a naturally occurring sequence polymorphism to an adaptive response to freezing conditions. [ABSTRACT FROM AUTHOR]

The Arabidopsis thaliana Calmodulin-binding Transcription Activator (CAMTA) transcription factors CAMTA1, CAMTA2, and CAMTA3 (CAMTA123) serve as master regulators of salicylic acid (SA)-mediated immunity, repressing the biosynthesis of SA in healthy plants. Here, we show that CAMTA123 also repress the biosynthesis of pipecolic acid (Pip) in healthy plants. Loss of CAMTA123 function resulted in the induction of AGD2-like defense response protein 1 (ALD1), which encodes an enzyme involved in Pip biosynthesis. Induction of ALD1 resulted in the accumulation of high levels of Pip, which brought about increased levels of the SA receptor protein NPR1 without induction of NPR1 expression or requirement for an increase in SA levels. Pip-mediated induction of ALD1 and genes regulating the biosynthesis of SA— CBP60g , SARD1 , PAD4 , and EDS1 —was largely dependent on NPR1. Furthermore, Pip-mediated increase in NPR1 protein levels was associated with priming of Pip and SA biosynthesis genes to induction by low levels of SA. Taken together, our findings expand the role for CAMTA123 in regulating key immunity genes and suggest a working model whereby loss of CAMTA123 repression leads to the induction of plant defense genes and initiation of SAR. CAMTA123 transcription factors play a key role in repressing the expression of immunity genes in Arabidopsis. This study finds that loss of CAMTA123 repression activity, without an increase in salicylic acid (SA), resulted in the biosynthesis of pipecolic acid (Pip), Pip-mediated increase in NPR1 protein levels, and the priming of Pip and SA biosynthesis genes to induction by low levels of SA. [ABSTRACT FROM AUTHOR]

Arabidopsis thaliana (Arabidopsis) increases in freezing tolerance in response to low nonfreezing temperatures, a phenomenon known as cold acclimation. The CBF regulatory pathway, which contributes to cold acclimation, includes three genes—CBF1, CBF2 and CBF3—encoding closely-related transcription factors that regulate the expression of more than 100 genes—the CBF regulon—that impart freezing tolerance. Here we compare the CBF pathways of two Arabidopsis ecotypes collected from sites in Sweden (SW) and Italy (IT). Previous studies showed that the SW ecotype was more freezing tolerant than the IT ecotype and that the IT ecotype had a nonfunctional CBF2 gene. Here we present results establishing that the difference in CBF2 alleles contributes to the difference in freezing tolerance between the two ecotypes. However, other differences in the CBF pathway as well as CBF-independent pathways contribute the large majority of the difference in freezing tolerance between the two ecotypes. The results also provided evidence that most cold-induced CBF regulon genes in both the SW and IT ecotypes are coregulated by CBF-independent pathways. Additional analysis comparing our results with those published by others examining the Col-0 accession resulted in the identification of 44 CBF regulon genes that were conserved among the three accessions suggesting that they likely have important functions in life at low temperature. The comparison further supported the conclusion that the CBF pathway can account for a large portion of the increase in freezing tolerance that occurs with cold acclimation in a given accession, but that CBF-independent pathways can also make a major contribution. [ABSTRACT FROM AUTHOR]

Histone lysine methylation patterns underlie much of the functional diversity of nucleosomes in eukaryotes, and an interesting aspect of histone methylation is the potential functional specificity for different methylation states on a given lysine. Trimethylation of histone H3 (H3K27me3) is intimately related to developmental gene silencing through the so-called Polycomb Group (PcG) mechanism. How this modification becomes established at PcG-repressed loci is generally not known, but it has been suggested that it may be facilitated by prior occupancy by H3K27me2. In this study we mapped the genomic and gene-level distribution of H3K27me2 in Arabidopsis thaliana using ChIP and a high-density tiling microarray, and integrated this with previous maps of other chromatin features and gene expression data. At the genome level, H3K27me2 enrichment sites were sparsely distributed across chromosomes, within an average size expected for a single nucleosome, and contrasted with the longer domains seen for H3K27me3. In both heterochromatic and euchromatic segments of the genome, H3K27me2 enrichment was often localized within transposon-related genes, with the longest genomic stretches of this modification corresponding to retroelements. However, H3K27me2 was more frequently found within protein-coding genes. These genes generally also showed moderate enrichment for H3K27me3, but H3K27me2 was strongly depleted within those genes most enriched in H3K27me3. H3K27me2 within highly transcribed genes was at highest levels at transcriptional starts and was strongly depleted throughout the transcribed regions, and reached higher levels at active than at silent promoters. [ABSTRACT FROM AUTHOR]

Paf1C is a transcriptional cofactor that has been implicated in various transcription-associated mechanisms spanning initiation, elongation and RNA processing, and is important for multiple aspects of development in Arabidopsis. Our recent studies suggest Arabidopsis Paf1C is crucial for proper regulation of genes within H3K27me3-enriched chromatin, and that a protein named PHP may act as an accessory subunit of Paf1C that promotes this function.

In budding yeast, intragenic histone modification is linked with transcriptional elongation through the conserved regulator Paf1C. To investigate Paf1C-related function in higher eukaryotes, we analyzed the effects of loss of Paf1C on histone H3 density and patterns of H3 methylated at K4, K27, and K36 in Arabidopsis genes, and integrated this with existing gene expression data. Loss of Paf1C did not change global abundance of H3K4me3 or H3K36me2 within chromatin, but instead led to a 3' shift in the distribution of H3K4me3 and a 5' shift in the distribution of H3K36me2 within genes. We found that genes regulated by plant Paf1C showed strong enrichment for both H3K4me3 and H3K27me3 and also showed a high degree of tissue-specific expression. At the Paf1C- and PcG-regulated gene FLC, transcriptional silencing and loss of H3K4me3 and H3K36me2 were accompanied by expansion of H3K27me3 into the promoter and transcriptional start regions and further enrichment of H3K27me3 within the transcribed region. These results highlight both genic and global functions for plant Paf1C in histone modification and gene expression, and link transcriptional activity with cellular memory., Competing Interests: The authors have declared that no competing interests exist.

Cycling between vegetative growth and dormancy is an important adaptive mechanism in temperate woody plants. To gain insights into the underlying molecular mechanisms, we carried out global transcription analyses on stem samples from poplar (Populus deltoides Bartr. ex Marsh.) trees grown in the field and in controlled environments. Among seasonal changes in the transcriptome, up-regulation of defense-related genes predominated in early winter, whereas signaling-related genes were up-regulated during late winter. Cluster analysis of the differentially expressed genes showed that plants regulated seasonal growth by integrating environmental factors with development. Short day lengths induced some cold-associated genes without concomitant low temperature exposure, and enhanced the expression of some genes when combined with low temperature exposure. These mechanisms appear to maintain closer synchrony between cold hardiness and climate than would be achieved through responses to temperature alone.

The plant hormone auxin regulates various growth and developmental processes by controlling the expression of auxin-response genes. While many genes up-regulated by auxin have been characterized, less is known about the genes that are down-regulated by auxin. We isolated and characterized an auxin-repressed gene (RpARP) from the tree legume, Robinia pseudoacacia L. A sequence similarity search in public databases showed that the RpARP gene has homologs in various higher plants including monocots and dicots. The deduced amino acid sequences are highly conserved among these homologs (up to 85% identity). Northern blot analysis showed that auxin repressed RpARP gene expression and that repression was dependent on the presence of metabolizable sugar and on protein synthesis. In addition, cold treatment abolished the auxin-mediated repression of RpARP gene expression. Results from transgenic plant analyses suggest that RpARP gene expression is posttranscriptionally regulated by auxin and by the untranslated regions. Sequence analysis of the promoter region (-70 and -500 bp upstream of the putative transcription initiation site) of the RpARP gene identified four sucrose-repressible response elements (TATCCAT-motifs; Huang et al. 1990), suggesting that the cis-elements responsible for regulation by sucrose are located in the promoter region. In fact, the expression of the transgenic RpARP gene was unaffected by sucrose when driven by a CaMV 35S promoter. We present evidence that RpARP gene expression is negatively associated with hypocotyl elongation.