Tetraploid cotton contains two sets of homologous chromosomes, the At- and Dt-subgenomes. Consequently, many markers in cotton were mapped to multiple positions during linkage genetic map construction, posing a challenge to anchoring linkage groups and mapping economically-important genes to particular chromosomes. Chromosome-specific markers could solve this problem. Recently, the genomes of two diploid species were sequenced whose progenitors were putative contributors of the At- and Dt-subgenomes to tetraploid cotton. These sequences provide a powerful tool for developing chromosome-specific markers given the high level of synteny among tetraploid and diploid cotton genomes. In this study, simple sequence repeats (SSRs) on each chromosome in the two diploid genomes were characterized. Chromosome-specific SSRs were developed by comparative analysis and proved to distinguish chromosomes. A total of 200,744 and 142,409 SSRs were detected on the 13 chromosomes of Gossypium arboreum L. and Gossypium raimondii Ulbrich, respectively. Chromosome-specific SSRs were obtained by comparing SSR flanking sequences from each chromosome with those from the other 25 chromosomes. The average was 7,996 per chromosome. To confirm their chromosome specificity, these SSRs were used to distinguish two homologous chromosomes in tetraploid cotton through linkage group construction. The chromosome-specific SSRs and previously-reported chromosome markers were grouped together, and no marker mapped to another homologous chromosome, proving that the chromosome-specific SSRs were unique and could distinguish homologous chromosomes in tetraploid cotton. Because longer dinucleotide AT-rich repeats were the most polymorphic in previous reports, the SSRs on each chromosome were sorted by motif type and repeat length for convenient selection. The primer sequences of all chromosome-specific SSRs were also made publicly available. Chromosome-specific SSRs are efficient tools for chromosome identification by anchoring linkage groups to particular chromosomes during genetic mapping and are especially useful in mapping of qualitative-trait genes or quantitative trait loci with just a few markers. The SSRs reported here will facilitate a number of genetic and genomic studies in cotton, including construction of high-density genetic maps, positional gene cloning, fingerprinting, and genetic diversity and comparative evolutionary analyses among Gossypium species.

Plant NAC (NAM, ATAF1/2, and CUC2) family is involved in various development processes including Programmed Cell Death (PCD) associated development. However, the relationship between NAC family and PCD-associated cotton pigment gland development is largely unknown. In this study, we identified 150, 153 and 299 NAC genes in newly updated genome sequences of G. arboreum, G. raimondii and G. hirsutum, respectively. All NAC genes were divided into 8 groups by the phylogenetic analysis and most of them were conserved during cotton evolution. Using the vital regulator of gland formation GhMYC2-like as bait, expression correlation analysis screened out 6 NAC genes which were low-expressed in glandless cotton and high-expressed in glanded cotton. These 6 NAC genes acted downstream of GhMYC2-like and were induced by MeJA. Silencing CGF1(Cotton Gland Formation1), another MYC-coding gene, caused almost glandless phenotype and down-regulated expression of GhMYC2-like and the 6 NAC genes, indicating a MYC-NAC regulatory network in gland development. In addition, predicted regulatory mechanism showed that the 6 NAC genes were possibly regulated by light, various phytohormones and transcription factors as well as miRNAs. The interaction network and DNA binding sites of the 6 NAC transcription factors were also predicted. These results laid the foundation for further study of gland-related genes and gland development regulatory network.

Fuzzless mutants are ideal materials to decipher the regulatory network and mechanism underlying fuzz initiation and formation. In this study, we utilized two Gossypium arboreum accessions differing in fuzz characteristics to explore expression pattern differences and discriminate genes involved in fuzz development using RNA sequencing. Gene ontology (GO) analysis was conducted and found that DEGs were mainly enriched in the regulation of transcription, metabolic processes and oxidation–reduction-related processes. Weighted gene co-expression network analysis discerned the MEmagenta module highly associated with a fuzz/fuzzless trait, which included a total of 50 hub genes differentially expressed between two materials. GaFZ, which negatively regulates trichome and fuzz formation, was found involved in MEmagenta cluster1. In addition, twenty-eight hub genes in MEmagenta cluster1 were significantly up-regulated and expressed in fuzzless mutant DPL972. It is noteworthy that Ga04G1219 and Ga04G1240, which, respectively, encode Fasciclin-like arabinogalactan protein 18(FLA18) and transport protein, showed remarkable differences of expression level and implied that they may be involved in protein glycosylation to regulate fuzz formation and development. This module and hub genes identified in this study will provide new insights on fiber and fuzz formation and be useful for the molecular design breeding of cotton genetic improvement.

Cotton is one of the major industrial crops that supply natural fibers and oil for industries. This study was conducted to understand the mechanism of delayed gland morphogenesis in seeds of Gossypium bickii. In this study, we compared glandless seeds of G. bickii with glanded seeds of Gossypium arboreum. High-throughput sequencing technology was used to explore and classify the expression patterns of gland-related genes in seeds and seedlings of cotton plants. Approximately 131.33 Gigabases of raw data from 12 RNA sequencing samples with three biological replicates were generated. A total of 7196 differentially-expressed genes (DEGs) were identified in all transcriptome data. Among them, 3396 genes were found up-regulated and 3480 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were performed to identify different functions between genes unique to glandless imbibed seeds and glanded seedlings. Co-expression network analysis revealed four modules that were identified as highly associated with the development of glandless seeds. Here the hub genes in each module were identified by weighted gene co-expression network analysis (WGCNA). In total, we have selected 13 genes involved in transcription factors, protein and MYB-related functions, that were differentially expressed in transcriptomic data and validated by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). These selected genes may play an important role for delayed gland morphogenesis. Our study provides comprehensive insight into the key genes related to glandless traits of seeds and plants, and can be further exploited by functional and molecular studies.

Phospholipids function as dynamic regulators of plant growth and environmental adaptation, extending well beyond their structural roles in biological membranes. This review synthesizes the phospholipid metabolic network and its regulatory functions in plant physiology. We first describe enzymatic reactions and acyl-chain remodeling in phospholipid biosynthesis, and then examine the interaction between phospholipid metabolism and auxin signaling, focusing on phosphatidic acid (PA) and phosphoinositide phosphate (PIP). These lipid molecules regulate the polarization and vesicular trafficking of PIN-FORMED proteins via endocytosis and phosphorylation-dependent mechanisms, thereby controlling auxin distribution during development and stress adaptation. Particular emphasis is placed on PA, a multifunctional signaling lipid that serves as a central molecular hub. PA coordinates hormonal, stress, and circadian signals by engaging and modulating a broad spectrum of protein targets, including kinases, phosphatases, and transcription factors. We also discuss the emerging and evolutionarily conserved functions of phospholipid signaling in cell fate determination, drawing parallels from mammalian cell reprogramming to the regulation of plant cell totipotency and root patterning. Collectively, these findings underscore the critical role of phospholipid-mediated signaling in converting metabolic and environmental cues into developmental reprogramming, providing novel theoretical and functional frameworks for future research in plant lipid biology.

Flower and inflorescence architecture play fundamental roles in crop seed formation and final yield. Sesame is an ancient oilseed crop. Exploring the genetic mechanisms of inflorescence architecture and developmental characteristics is necessary for high-yield breeding improvements for sesame and other crops. In this study, we performed a genetic analysis of the sesame mutant css1 with a malformed corolla and small seed size that was mutagenized by ethyl methanesulfonate (EMS) from the cultivar Yuzhi 11. Inheritance analysis of the cross derived from css1 mutant × Yuzhi 11 indicated that the mutant traits were controlled by a single recessive gene. Based on the genome resequencing of 48 F₂ individuals and a genome-wide association study, we determined SNP9_15914090 with the lowest p value was associated with the split corolla and small seed size traits, which target gene Sigif1 (GRF-Interacting Factor 1). SiGIF1 contains four exons and encodes a coactivating transcription factor. Compared to the wild-type allelic gene SiGIF1, Sigif1 in the mutant css1 has a splice donor variant at the exon2 and intron2 junction, which results in incorrect transcript splicing with a 13 bp deletion in exon2. The expression profile indicated that SiGIF1 was highly expressed in the flower, ovary, and capsule but lowly expressed in the root, stem, and leaf tissues of the control. In summary, we identified a gene, SiGIF1, that regulates flower organs and seed size in sesame, which provides a molecular and genetic foundation for the high-yield breeding of sesame and other crops.