Phytochrome-interacting factors (PIFs) are essential for plant growth, development, and defense responses. However, research on the PIFs in sweet potato has been insufficient to date. In this study, we identified PIF genes in the cultivated hexaploid sweet potato (Ipomoea batatas) and its two wild relatives, Ipomoea triloba, and Ipomoea trifida. Phylogenetic analysis revealed that IbPIFs could be divided into four groups, showing the closest relationship with tomato and potato. Subsequently, the PIFs protein properties, chromosome location, gene structure, and protein interaction network were systematically analyzed. RNA-Seq and qRT-PCR analyses showed that IbPIFs were mainly expressed in stem, as well as had different gene expression patterns in response to various stresses. Among them, the expression of IbPIF3.1 was strongly induced by salt, drought, H₂O₂, cold, heat, Fusarium oxysporum f. sp. batatas (Fob), and stem nematodes, indicating that IbPIF3.1 might play an important role in response to abiotic and biotic stresses in sweet potato. Further research revealed that overexpression of IbPIF3.1 significantly enhanced drought and Fusarium wilt tolerance in transgenic tobacco plants. This study provides new insights for understanding PIF-mediated stress responses and lays a foundation for future investigation of sweet potato PIFs.

Leaf length is an important component of barley plant architecture, but its genetic basis remains incompletely understood. Here, we integrated genome-wide association study (GWAS), RNA sequencing (RNA-seq), and sequence variation analyses to investigate the genetic and transcriptional basis of barley leaf-length variation. A panel of 198 barley accessions was evaluated across two growing seasons, and contrasting long- and short-leaf accessions were subjected to RNA-seq. GWAS identified a major association signal on chromosome 4H, with a core interval of approximately 941.73 kb defined by local linkage disequilibrium analysis. RNA-seq identified 3507 and 3878 differentially expressed genes (DEGs) in flag leaves and second leaves below the flag leaf, respectively, including 2648 shared DEGs. Functional enrichment and gene set enrichment analyses indicated differences in developmental, signaling, metabolic, and temperature-responsive processes. Integration of GWAS and RNA-seq data prioritized three candidate genes, LOC123447426, LOC123449930, and LOC123450878, with different levels of supporting evidence. LOC123447426 and LOC123450878 were located within the core association interval, whereas LOC123449930 was located in the extended candidate-screening region, approximately 2.2 Mb from the lead SNP. LOC123447426 showed the strongest integrated support, with evidence from GWAS and differential expression in both leaf positions. Sequence variation, and qRT-PCR analyses provided further support for these candidates. Overall, this study prioritizes a major chromosome 4H region and three candidate genes associated with barley leaf-length variation, providing a basis for further investigation of their potential roles in leaf development. However, the current evidence does not establish causal relationships between these genes and leaf-length variation, and their biological functions remain to be experimentally verified.

Background: Grain length is a key determinant of yield and quality in barley (Hordeum vulgare L.) and is typically governed by complex quantitative traits. Methods: In this study, a diverse natural population comprising 198 barley accessions was evaluated across two years to investigate the genetic basis of grain length. Results: Phenotypic analysis revealed continuous variation with near-normal distribution, indicating polygenic control. Genome-wide association study (GWAS) identified 84 stable single nucleotide polymorphism (SNP) loci significantly associated with grain length, predominantly enriched on chromosome 7. RNA sequencing (RNA-seq) was conducted using two contrasting genotypes at four developmental stages. Differentially expressed genes (DEGs) were mainly enriched in structural constituent of chromatin, protein heterodimerization activity, and the starch and sucrose metabolism. Integration of GWAS and RNA-seq identified 7 key candidate genes seven key candidate genes, including LOC123412467, LOC123408579, LOC123407599, LOC123410619, LOC123410954, LOC123411868, and LOC123426274. Sequence variation analysis further revealed functional polymorphisms, including non-synonymous mutations. The sequencing results show that LOC123412467 and LOC123410619 exhibited consistent allelic variation between long-grain and short-grain accessions, while LOC123426274 displayed stable differential expression across developmental stages, indicating their potential roles as key genes controlling grain length. Conclusions: Collectively, these findings suggest that chromosome 7 contains major regulatory loci controlling barley grain length and demonstrate that integrative multi-omics analysis is an effective strategy for identifying high-confidence candidate genes associated with complex agronomic traits. This study provides valuable insights into the genetic basis of grain length and offers key candidate genes for barley molecular breeding.

Background/Objectives: Stay-green proteins (SGRs) play a vital role in regulating plant chlorophyll degradation and senescence. However, this gene family has not been explored in Ipomoea species and sweet potato. Methods: A total of 19 SGR family genes (SGRs) were identified using Basic Local Alignment Search Tool (BLAST) methods. The proteins’ physiological properties, evolutionary and phylogenetic relationships, conserved domain and motifs, gene structures, collinearity, and promoter cis-elements were systematically analyzed. Moreover, expression patterns and protein interaction network analyses were performed for sweet potato. Results: In this study, we identified 19 SGRs in six Ipomoea species. These SGRs were divided into four subgroups according to their phylogenetic relationships. Domian analysis revealed that SGRs had the conserved “stay-green” domain. Gene structure analysis showed that SGRs had similar structures. The collinearity analysis revealed that the SGRs originated from two genes, with one gene undergoing duplication during evolution history; moreover, the SGRs experienced rearrangement throughout the evolutionary process in the Ipomoea species. Cis-elements related to pigment biosynthesis and hormone and stress responses were found. In addition, expression pattern analysis showed that IbSGRs, especially IbSGR1, IbSGR2, and IbSGR3, might play an important role in pigment accumulation. The SGRs could also respond to stress responses (i.e., cold, drought, and salt) and take part in hormone crosstalk (i.e., abscisic acid (ABA), methyl jasmonate (MeJA), salicylic acid (SA)). Conclusions: Taken together, the findings of this study provide new insights for further understanding the functions of SGRs and candidate genes for pigment accumulation and stress tolerance in sweet potatoes.