Duplication, divergence and persistence in the Phytochrome photoreceptor gene family of cottons (Gossypium spp.)

<p>Abstract</p> <p>Background</p> <p>Phytochromes are a family of red/far-red photoreceptors that regulate a number of important developmental traits in cotton (<it>Gossypium </it>spp.), including plant architecture, fiber development, and photoperiodic flowering. Little is known about the composition and evolution of the phytochrome gene family in diploid (<it>G. herbaceum</it>, <it>G. raimondii</it>) or allotetraploid (<it>G. hirsutum</it>, <it>G. barbadense</it>) cotton species. The objective of this study was to obtain a preliminary inventory and molecular-evolutionary characterization of the phytochrome gene family in cotton.</p> <p>Results</p> <p>We used comparative sequence resources to design low-degeneracy PCR primers that amplify genomic sequence tags (GSTs) for members of the <it>PHYA</it>, <it>PHYB/D</it>, <it>PHYC </it>and <it>PHYE </it>gene sub-families from A- and D-genome diploid and AD-genome allotetraploid <it>Gossypium </it>species. We identified two paralogous <it>PHYA </it>genes (designated <it>PHYA1 </it>and <it>PHYA2</it>) in diploid cottons, the result of a Malvaceae-specific <it>PHYA </it>gene duplication that occurred approximately 14 million years ago (MYA), before the divergence of the A- and D-genome ancestors. We identified a single gene copy of <it>PHYB</it>, <it>PHYC</it>, and <it>PHYE </it>in diploid cottons. The allotetraploid genomes have largely retained the complete gene complements inherited from both of the diploid genome ancestors, with at least four <it>PHYA </it>genes and two genes encoding <it>PHYB</it>, <it>PHYC </it>and <it>PHYE </it>in the AD-genomes. We did not identify a <it>PHYD </it>gene in any cotton genomes examined.</p> <p>Conclusions</p> <p>Detailed sequence analysis suggests that phytochrome genes retained after duplication by segmental duplication and allopolyploidy appear to be evolving independently under a birth-and-death-process with strong purifying selection. Our study provides a preliminary phytochrome gene inventory that is necessary and sufficient for further characterization of the biological functions of each of the cotton phytochrome genes, and for the development of 'candidate gene' markers that are potentially useful for cotton improvement via modern marker-assisted selection strategies.</p

Cotton as a Model for Polyploidy and Fiber Development Study

Cotton is one of the most important crops in the world. The Gossypium genus is represented by 50 species, divided into two levels of ploidy: diploid (2n = 26) and tetraploid (2n = 52). This diversity of Gossypium species provides an ideal model for studying the evolution and domestication of polyploids. In this regard, studies of the origin and evolution of polyploid cotton species are crucial for understanding the ways and mechanisms of gene and genome evolution. In addition, studies of polyploidization of the cotton genome will allow to more accurately determine the localization of QTLs that determine fiber quality. In addition, due to the fact that cotton fibers are single trichomes originating from epidermal cells, they are one of the most favorable model systems for studying the molecular mechanisms of regulation of cell and cell wall elongation, as well as cellulose biosynthesis

Chemical Interventions to Alleviate Salt Stress in Cotton Plants: A Review

The alleviation of salt stress in cotton plants through the application of exogenous chemicals has emerged as a viable strategy to mitigate the adverse effects on various plant attributes, including growth, development, yield, and flowering. Plant hormones, known for their efficacy at low doses, have garnered significant attention in this context. Despite being inherently susceptible to salt stress, cotton plants experience severe impediments in water absorption from the soil, leading to delayed growth and development. Several phytohormones, including jasmonic acid, salicylic acid, and glycine betaine, have been extensively investigated in numerous studies for their potential to ameliorate salt stress in cotton plants. Promising results have been obtained with both foliar and seed treatments employing these substances. This foundational knowledge has paved the way for the development of alternative strategies to mitigate salt stress. However, the practical utilization of these chemicals is hindered by their elevated cost. Plant growth regulators, such as nitric oxide and melatonin, have also garnered interest for their ability to alleviate salt stress in cotton plants. Numerous studies have corroborated their effectiveness in this regard. This review comprehensively examines the aforementioned substances and extracts that have been investigated for their potential to mitigate the detrimental effects of salt stress on cotton plants

Effects of plant growth regulators on callogenesis and embryogenesis in sarnav and desiree potato (Solanum tuberosum L.) varieties

Somatic embryos play a pivotal role in the production of high-quality potatoes and seed breeding. This study focused on determining the concentrations of 1-naphthaleneacetic acid (NAA) and 6-benzyl amino purine (BAP) in the formation of callus tissue and callus induction. Our goal was to assess the efficiency of potato explants with the highest potential for somatic embryo production. To achieve this, we cultivated Sarnav and Desiree potato varieties under in vitro tissue culture conditions, utilizing the obtained tissue cultures for subsequent experiments. The MS nutrient media were enriched with NAA and BAP at ratios of 1.5: 1, 1: 1.5, and 1: 1 mg/L, along with NAA concentrations of 1.5, 1, or 2 mg/L. Somatic embryogenesis experiments were conducted using various MS nutrient media, enriched with BAP and GA3 at concentrations of 1: 0.5, 0.4: 0.1, 0.5: 0.2, and 0.1: 0.1 mg/L of plant growth regulators. During the course of the study, diverse callus formations were observed in both leaf and internodal stem explants. Among the nutrient media, the M2 medium enriched with 1: 1.5 mg/L of NAA and BAP yielded the highest callus formation rates: 92% for the Desiree variety and 100% for the Sarnav variety, specifically in internodal stem explants. Notably, the index of embryo formation in leaf explants selected for somatic embryogenesis within the SE4 medium was 70% for the Sarnav variety and 65% for the Desiree variety. The inclusion of BAP and GA3 at a ratio of 0.1: 0.1 mg/l in the SE4 nutrient medium resulted in somatic embryogenesis in 80% of calli for the Sarnav variety and 78% for the Desiree variety. These findings underscore the potential for regenerating plants through somatic embryogenesis in the Sarnav potato variety, a significant development with implications for genetic transformation studies involving this particular variety

Genome Editing in Plants: An Overview of Tools and Applications

The emergence of genome manipulation methods promises a real revolution in biotechnology and genetic engineering. Targeted editing of the genomes of living organisms not only permits investigations into the understanding of the fundamental basis of biological systems but also allows addressing a wide range of goals towards improving productivity and quality of crops. This includes the creation of plants with valuable compositional properties and with traits that confer resistance to various biotic and abiotic stresses. During the past few years, several novel genome editing systems have been developed; these include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9). These exciting new methods, briefly reviewed herein, have proved themselves as effective and reliable tools for the genetic improvement of plants

Recent Developments in Fiber Genomics of Tetraploid Cotton Species

Cotton (Gossypium spp.) produces naturally soft, single-celled trichomes as fiber on the seed coat supplying the main source of natural raw material for the textile industry. It is economically considered as one of the most leading cash crops in the world and evolutionarily very important as a model system for detailed scientific investigations. Cotton production is going through a big transition stage such as losing the market share in competition with the synthetic fibers, high popularity of Bt and herbicide resistance genes in cotton cultivars, and the recent shift of fiber demands to meet the standard fiber quality due to change of textile technologies to produce high superior quality of fibers in the global market. Recently, next-generation sequencing technologies through high-throughput sequencing at greatly reduced costs provided opportunities to sequence the diploid and tetraploid cotton genomes. With the availability of large volume of literatures on molecular mapping, new genomic resources, characterization of cotton genomes, discoveries of many novel genes, regulatory elements including small and microRNAs and new genetic tools such as gene silencing or gene editing technique for genome manipulation, this report attempted to provide the readers a comprehensive review on the recent advances of cotton fiber genomics research