Allotetraploid Species Research Articles

Genome-Wide Identification and Expression Analysis Elucidates the Potential Role of PFK Gene Family in Drought Stress Tolerance and Sugar Metabolism in Cotton.

Drought has been identified as a major threat for global crop production worldwide. Phosphofructokinase (PFK) is vital for sugar metabolism. During phosphorylation, plants have two enzymes: ATP-dependent phosphofructokinase (PFK) and pyrophosphate-dependent fructose-6-phosphate phosphotransferase (PFP). Genome-wide identification led to the identification of 80 PFK genes, 26 genes in G. hirsutum and G. barbadense, and 14 genes in G. arboreum and G. raimondii. Phylogenetic, gene structure, and motif analyses showed that PFK genes were grouped into two main categories, namely, PFK and PFP, with 18 and 8 genes in the allotetraploid species and 10 PFK and 4 PFP genes in the diploid species, respectively. Using the RNA-seq expressions of 26 genes from GhPFK, a co-expression network analysis was performed to identify the hub genes. GhPFK04, GhPFK05, GhPFK09, GhPFK11, GhPFK13, GhPFK14, and GhPFK17 in leaves and GhPFK02, GhPFK09, GhPFK11, GhPFK15, GhPFK16, and GhPFK17 in root tissues were found as hub genes. RT-qPCR analysis validated the expressions of identified hub genes. Interestingly, GhPFK11 and GhPFK17 were identified as common hub genes, and these might be the true candidate genes involved in the drought stress tolerance. In the KEGG enrichment analysis, amino acids such as L-valine, L-histidine, L-glutamine, L-serine, L-homoserine, L-methionine, L-cysteine, and gluconic acid were significantly upregulated, whereas sugars, mainly fructose-1-phosphate, D-mannitol, D-sorbitol, dulcitol, and lactose, were significantly downregulated during drought stress. Genome-wide analysis paves the way for a deeper understanding of the PFK genes and establishes the groundwork for future research into PFK’s role in enhancing drought stress tolerance and sugar metabolism in cotton.

Immunoglobulin heavy-chain loci in ancient allotetraploid goldfish

As an ancient allotetraploid species, goldfish (Carassius auratus) have two sets of subgenomes. In this study, immunoglobulin heavy-chain (IGH) genes were cloned from the red crucian carp (Carassius auratus red var.), and the corresponding loci were identified in the gynogenetic diploid red crucian carp (GRCC) genome as well as the genomes of three other goldfish strains (Wakin, G-12, and CaTCV-1). Examination showed that each goldfish strain possessed two sets of parallel IGH loci: a complete IGHA locus and a degenerated IGHB locus that was nearly 40 × smaller. In the IGHA locus, multiple τ chain loci were arranged in tandem between the μ&δ chain locus and the variable genes, but no τ-like genes were found in the IGHB locus.

Tragopogon dubius: Multiple introductions to North America and the formation of the New World tetraploids

AbstractTragopogon (Asteraceae) is an evolutionary model for the study of whole‐genome duplication, with two recently and repeatedly formed allopolyploids, T. mirus and T. miscellus, and many additional polyploid species. Tragopogon mirus and T. miscellus formed in western North America following the introduction of three diploids from Europe: T. dubius, T. porrifolius, and T. pratensis. Of these diploids, T. dubius is a shared parent of both tetraploids and is broadly defined and widely distributed in Eurasia. Because human‐mediated intercontinental introductions may lead to hybridization with local species, and associated polyploidization, the introduction history of T. dubius from Europe to North America provides further opportunity to investigate both the extent and consequences of plant introductions. Using ITS sequence data, we show that the morphologically diverse, broadly defined T. dubius comprises a complex of at least 10 different ITS types in its native range, six of which have been introduced from Europe into North America. Significantly, although the two allotetraploid species have each formed multiple times on geographical scales from local to regional, recurrent formation is the result of repeated hybridization involving only one of these ITS subtypes. These results reinforce earlier data suggesting that not all diploid genotypes can form allopolyploids. Several entities traditionally considered part of T. dubius s.l. are now recognized as distinct species (e.g., T. lainzii), and it is likely that other distinct ITS genotypes identified here may also mark unique lineages that ultimately merit recognition as separate species. However, more intensive phylogenetic analyses involving many more samples from across the geographic range of T. dubius are required, as are detailed assessments of taxonomy, morphology, and cytology.

Allele segregation analysis of F1 hybrids between independent Brassica allohexaploid lineages

In the Brassica genus, we find both diploid species (one genome) and allotetraploid species (two different genomes) but no naturally occurring hexaploid species (three different genomes, AABBCC). Although hexaploids can be produced via human intervention, these neo-polyploids have quite unstable genomes and usually suffer from severe genome reshuffling. Whether these genome rearrangements continue in later generations and whether genomic arrangements follow similar, reproducible patterns between different lineages is still unknown. We crossed Brassica hexaploids resulting from different species combinations to produce five F1 hybrids and analyzed the karyotypes of the parents and the F1 hybrids, as well as allele segregation in a resulting test-cross population via molecular karyotyping using SNP array genotyping. Although some genomic regions were found to be more likely to be duplicated, deleted, or rearranged, a consensus pattern was not shared between genotypes. Brassica hexaploids had a high tolerance for fixed structural rearrangements, but which rearrangements occur and become fixed over many generations does not seem to show either strong reproducibility or to indicate selection for stability. On average, we observed 10 de novo chromosome rearrangements contributed almost equally from both parents to the F1 hybrids. At the same time, the F1 hybrid meiosis produced on average 8.6 new rearrangements. Hence, the increased heterozygosity in the F1 hybrid did not significantly improve genome stability in our hexaploid hybrids and might have had the opposite effect. However, hybridization between lineages was readily achieved and may be exploited for future genetics and breeding purposes.

Effect of secondary attack by Aeromonas hydrophila on the expression level of hif genes in common carp (Cyprinus carpio).

Hypoxia-inducible factors (hifs) are involved in infectious diseases inflammatory reactions, and immune regulation. Common carp, a representative allotetraploid species that has undergone genome-wide replication events, has important research value. In this study, common carp were infected twice with Aeromonas hydrophila. Liver tissues of common carp were collected at 4h, 12h, 24h, 48h, 3days, 7days post-first infection and 4h, 12h, 24h post-second infection. The mRNA levels of hif genes were determined at different time points. The hif2a-2, hif3a-2, hif3b-1 and hif3b-2 expression levels in the infected group were upregulated when compared with those in the control group, whereas the expression levels of other genes were downregulated after the second infection. This indicates that the effect of A.hydrophila infection on gene expression pattern is dependent on the host, pathogen, infected tissue and gene. Pressure analysis of the hif gene family revealed that the non-synonymous substitution to synonymous substitution ratio of 12 hif genes was <1, which indicated that they were in a state of purification and selection. Combined with the differences between copy genes, the polyclonal antibodies against Hif1b-1 and Hif1b-2 were successfully prepared in this study. Western blot analysis showed that the protein expression of Hif1b-1 and Hif1b-2 reached to the highest level 48h after the first infection. After the second A.hydrophila infection, the protein expression levels of Hif1b-1 and Hif1b-2 reached the highest levels at 4 and 48h, respectively. This may indicate that the Hif1b-1 and Hif1b-2 genes in common carp play an important role in the immune mechanism at the protein level. The findings of this study will lay the foundation for future studies on the immune regulatory function of common carp hif genes, which may aid in devising novel therapeutic strategies for common carp diseases, such as A.hydrophila infection.

Chromosome-scale genome assembly provides insights into speciation of allotetraploid and massive biomass accumulation of elephant grass (Pennisetum purpureum Schum.).

Elephant grass (Pennisetum purpureum Schum) is an important forage, biofuels and industrial plant widely distributed in tropical and subtropical areas globally. It is characterized with robust growth and high biomass. We sequenced its allopolyploid genome and assembled 2.07Gb into A' and B subgenomes of 14 chromosomes with scaffold N50 of 8.47Mb, yielding a total of 77,139genes. The allotetraploid speciation occurred approximately 15Ma after the divergence between Setaria italica and Pennisetum glaucum, according to a phylogenetic analysis of Pennisetum species. Double whole-genome duplication (WGD) and polyploidization events resulted in large-scale gene expansion, especially in the key steps of growth and biomass accumulation. Integrated transcriptome profiling revealed the functional divergence between subgenomes A' and B. A' subgenome mainly contributed to plant growth, development and photosynthesis, whereas the B subgenome was primarily responsible for effective transportation and resistance to stimulation. Some key gene families related to cellulose biosynthesis were expanded and highly expressed in stems, which could explain the high cellulose content in elephant grass. Our findings provide deep insights into genetic evolution of elephant grass and will aid future biological research and breeding, even for other grasses in the family Poaceae.

Application of CRISPR/Cas9 in Rapeseed for Gene Function Research and Genetic Improvement

Brassica napus L. provides high-quality edible oil and clean energy for humans. For a long time, rapeseed breeders have tried to breed improved varieties through traditional breeding strategies. However, B. napus is an allotetraploid species containing many repetitive sequences. It is very inefficient to change traits through traditional genetic methods such as hybridization and random mutagenesis due to gene redundancy. Today, the burgeoning CRISPR/Cas9 technology has been applied in polyploid rapeseed for gene function research and targeted genetic improvement because of its unique advantages of high efficiency and simplicity. This review summarizes current reports about the application of CRISPR/Cas9 system for gene function research and genetic improvement in rapeseed, involving important agronomic traits such as yield, oil content, and fatty acid composition. The application status of emerging precise genome editing technology in plants and several potential limitations and technical bottlenecks in rapeseed gene editing is discussed, which will provide confidence for researchers in rapeseed gene function research and genetic improvement through genome editing technology.

GISH Analysis of the Introgression of the B Subgenome Genetic Material of Wild Allotetraploid Species Solanum stoloniferum into Backcrossing Progenies with Potato

Wild relatives of cultivated potato are used in breeding to increase the genetic diversity of Solanum tuberosum (AAAA genome) varieties. Wild Mexican allotetraploid species Solanum stoloniferum (AABB genome) was used in breeding for extreme resistance to viruses and late blight. In this study, genomic in situ hybridization (GISH) was used for visualization of introgression of genetic material of the B subgenome of S. stoloniferum into the genome of backcross hybrids. The fertile hexaploid hybrid had 48 chromosomes of the A genome and 24 chromosomes of the B subgenome. Plants of the BC1 generation were pentaploid having the AAAAB genome constitution and three selected BC2 hybrids were aneuploid, containing one to six chromosomes of the B subgenome and 48 chromosomes of the A genome. The B subgenome of S. stoloniferum was inherited in the backcross generations as single chromosomes and in rare cases as recombinant chromosomes. GISH showed that chromosome pairing in the backcross hybrids was predominantly intragenomic. Most chromosomes of the B subgenome remained as univalents in backcross hybrids. Rare homeologous A/B chromosome pairing was detected in all analyzed hybrids. The obtained data indicate that the B subgenome of S. stoloniferum was able to recombine with the A genome.

Comprehensive identification and expression analysis of CRY gene family in Gossypium

BackgroundThe cryptochromes (CRY) are specific blue light receptors of plants and animals, which play crucial roles in physiological processes of plant growth, development, and stress tolerance.ResultsIn the present work, a systematic analysis of the CRY gene family was performed on twelve cotton species, resulting in 18, 17, 17, 17, and 17 CRYs identified in five alloteraploid cottons (Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum and G. darwinii), respectively, and five to nine CRY genes in the seven diploid species. Phylogenetic analysis of protein-coding sequences revealed that CRY genes from cottons and Arabidopsis thaliana could be classified into seven clades. Synteny analysis suggested that the homoeolog of G. hirsutum Gh_A02G0384 has undergone an evolutionary loss event in the other four allotetraploid cotton species. Cis-element analysis predicated the possible functions of CRY genes in G. hirsutum. RNA-seq data revealed that Gh_D09G2225, Gh_A09G2012 and Gh_A11G1040 had high expressions in fiber cells of different developmental states. In addition, the expression levels of one (Gh_A03G0120), 15 and nine GhCRY genes were down-regulated following the PEG, NaCl and high-temperature treatments, respectively. For the low-temperature treatment, five GhCRY genes were induced, and five were repressed. These results indicated that most GhCRY genes negatively regulate the abiotic stress treatments.ConclusionWe report the structures, domains, divergence, synteny, and cis-elements analyses systematically of G. hirsutum CRY genes. Possible biological functions of GhCRY genes in differential tissues as well as in response to abiotic stress during the cotton plant life cycle were predicted.

Overexpression of the Salix matsudana SmAP2-17 gene improves Arabidopsis salinity tolerance by enhancing the expression of SOS3 and ABI5

BackgroundSalix matsudana (Koidz.) is a widely planted ornamental allotetraploid tree species. Genetic engineering can be used to enhance the tolerance of this species to soil salinization, endowing varieties with the ability to grow along coastlines, thereby mitigating afforestation and protecting the environment. The AP2/ERF family of transcription factors (TFs) plays multidimensional roles in plant biotic/abiotic stress tolerance and plant development. In this study, we cloned the SmAP2-17 gene and performed functional analysis of its role in salt tolerance. This study aims to identify key genes for future breeding of stress-resistant varieties of Salix matsudana.ResultsSmAP2-17 was predicted to be a homolog of AP2-like ethylene-responsive transcription factor ANT isoform X2 from Arabidopsis, with a predicted ORF of 2058 bp encoding an estimated protein of 685 amino acids containing two conserved AP2 domains (PF00847.20). SmAP2-17 had a constitutive expression pattern and was localized to the nucleus. The overexpression of the native SmAP2-17 CDS sequence in Arabidopsis did not increase salt tolerance because of the reduced expression level of ectopic SmAP2-17, potentially caused by salt-induced RNAi. Transgenic lines with high expression of optimized SmAP2-17 CDS under salt stress showed enhanced tolerance to salt. Moreover, the expression of general stress marker genes and important salt stress signaling genes, including RD29A, ABI5, SOS3, AtHKT1, and RBohF, were upregulated in SmAP2-17-overexpressed lines, with expression levels consistent with that of SmAP2-17 or optimized SmAP2-17. Promoter activity analysis using dual luciferase analysis showed that SmAP2-17 could bind the promoters of SOS3 and ABI5 to activate their expression, which plays a key role in regulating salt tolerance.ConclusionsThe SmAP2-17 gene isolated from Salix matsudana (Koidz.) is a positive regulator that improves the resistance of transgenic plants to salt stress by upregulating SOS3 and ABI5 genes. This study provides a potential functional gene resource for future generation of salt-resistant Salix lines by genetic engineering.

Genome-Wide Identification of the TIFY Gene Family in Brassiceae and Its Potential Association with Heavy Metal Stress in Rapeseed.

The TIFY gene family plays important roles in various plant biological processes and responses to stress and hormones. The chromosome-level genome of the Brassiceae species has been released, but knowledge concerning the TIFY family is lacking in the Brassiceae species. The current study performed a bioinformatics analysis on the TIFY family comparing three diploid (B. rapa, B. nigra, and B. oleracea) and two derived allotetraploid species (B. juncea, and B. napus). A total of 237 putative TIFY proteins were identified from five Brassiceae species, and classified into ten subfamilies (six JAZ types, one PPD type, two TIFY types, and one ZML type) based on their phylogenetic relationships with TIFY proteins in A. thaliana and Brassiceae species. Duplication and synteny analysis revealed that segmental and tandem duplications led to the expansion of the TIFY family genes during the process of polyploidization, and most of these TIFY family genes (TIFYs) were subjected to purifying selection after duplication based on Ka/Ks values. The spatial and temporal expression patterns indicated that different groups of BnaTIFYs have distinct spatiotemporal expression patterns under normal conditions and heavy metal stresses. Most of the JAZIII subfamily members were highest in all tissues, but JAZ subfamily members were strongly induced by heavy metal stresses. BnaTIFY34, BnaTIFY59, BnaTIFY21 and BnaTIFY68 were significantly upregulated mostly under As3+ and Cd2+ treatment, indicating that they could be actively induced by heavy metal stress. Our results may contribute to further exploration of TIFYs, and provided valuable information for further studies of TIFYs in plant tolerance to heavy metal stress.

Genome-wide mining of gpx gene family provides new insights into cadmium stress responses in common carp (Cyprinus carpio)

Glutathione peroxidase (Gpx) is an important member of antioxidant enzymes, which can play a vital role in metabolizing reactive oxygen species (ROS) and in maintaining cell homeostasis. In order to study the evolutionary dynamics of gpx gene family in allotetraploid fish species, we identified a total of 14 gpx genes in common carp Cyprinus carpio, while 9 gpx genes were discovered in the diploid progenitor-like species Poropuntius huangchuchieni. Comparative genomic analysis and phylogenetic analysis revealed that the common carp gpx genes had significant expansion and were divided into five distinct subclades. Exon-intron distribution patterns and conserved motif analysis revealed highly conserved evolutionary patterns. Transcript profiles suggested that different gpx genes had specific patterns of regulation during early embryonic development. In adult tissues, gpx genes had a relatively broad expression distribution, most of which were highly expressed in the gills, intestines, and gonads. RT-qPCR studies showed that most gpx genes were downregulated during the initial cd2+ treatment stage. Dietary supplementation of Bacillus coagulans at different concentrations (Group 2 of 1.0 × 107 cfu/g, Group 3 of 1.0 × 108 cfu/g, and Group 4 of 1.0 × 109 cfu/g) induced different regulatory responses of gpx subclades. This result suggested that the appropriate concentration of B. coagulans can improve gpx gene expression when exposed to heavy metal cadmium treatment, which may play a vital role in the resistance to oxidative stress and immune responses. This study has expanded our understanding of the functional evolution of the gpx gene family in common carp.

Transcriptome shock in interspecific F1 allotriploid hybrids between Brassica species.

Interspecific hybridization drives the evolution of angiosperms and can be used to introduce novel alleles for important traits or to activate heterosis in crop breeding. Hybridization brings together gene expression networks from two different species, potentially causing global alterations of gene expression in the F1 plants which is called 'transcriptome shock'. Here, we explored such a transcriptome shock in allotriploid Brassica hybrids. We generated interspecific F1 allotriploid hybrids between the allotetraploid species Brassica napus and three accessions of the diploid species Brassica rapa. RNA-seq of the F1 hybrids and the parental plants revealed that 26.34-30.89% of genes were differentially expressed between the parents. We also analyzed expression level dominance and homoeolog expression bias between the parents and the F1 hybrids. The expression-level dominance biases of the Ar, An, and Cn subgenomes was genotype and stage dependent, whereas significant homoeolog expression bias was observed among three subgenomes from different parents. Furthermore, more genes were involved in trans regulation than in cis regulation in allotriploid F1 hybrids. Our findings provide new insights into the transcriptomic responses of cross-species hybrids and hybrids showing heterosis, as well as a new method for promoting the breeding of desirable traits in polyploid Brassica species.

Activation of DNA Transposons and Evolution of piRNA Genes Through Interspecific Hybridization in Xenopus Frogs.

Interspecific hybridization between two closely related species sometimes resulted in a new species with allotetraploid genomes. Many clawed frog species belonging to the Xenopus genus have diverged from the allotetraploid ancestor created by the hybridization of two closely related species with the predicted L and S genomes. There are species-specific repeated sequences including transposable elements in each genome of organisms that reproduce sexually. To understand what happened on and after the hybridization of the two distinct systems consisting of repeated sequences and their corresponding piRNAs, we isolated small RNAs from ovaries and testes of three Xenopus species consisting of allotetraploid X. laevis and X. borealis and diploid X. tropicalis as controls. After a comprehensive sequencing and selection of piRNAs, comparison of their sequences showed that most piRNA sequences were different between the ovaries and testes in all three species. We compared piRNA and genome sequences and specified gene clusters for piRNA expression in each genome. The synteny and homology analyses showed many distinct piRNA clusters among the three species and even between the two L and/or S subgenomes, indicating that most clusters of the two allotetraploid species changed after hybridization. Moreover, evolutionary analysis showed that DNA transposons including Kolobok superfamily might get activated just after hybridization and then gradually inactivated. These findings suggest that some DNA transposons and their piRNAs might greatly influence allotetraploid genome evolution after hybridization.

TIP41L, a putative candidate gene conferring both seed size and boll weight, was fine-mapped in an introgression line of Gossypium hirsutum-Gossypium arboreum

QTLs for yield-related traits in tetraploid cotton have been widely mapped, but QTLs introduced from diploid species into tetraploid cotton background remain uninvolved. Here, a stable introgression line with the traits of small boll and seed on Chr. A12, IL197 derived from Gossypium hirsutum (2n = AADD = 52) × Gossypium arboreum (2n = AA = 26), was employed to construct the F2 and F3 secondary populations for fine-mapping QTLs of yield-related traits. QTL analysis showed eight QTLs were detected for three traits, boll weight (BW), seed index (SI, one-hundred-seed weight in g), and lint percentage, with 3.94–28.13 % of the phenotypic variance explained. Of them, a stable major QTL, q(BW + SI)-A12-1 controlling both BW and SI and covering the shortest region in Chr. A12, was further narrowed into a 60.09 kb-interval through substitution mapping. Finally, five candidate genes were detected in the interval. The qRT-PCR analysis revealed only TIP41-like family protein (TIP41L) kept up-regulated expression and significantly lower in TM-1 than that in IL197 from -1 DPA to 15 DPA during cotton boll rapid developmental stage. Therefore, TIP41L gene is speculated as the most likely candidate gene. Comparative analysis with the other four allotetraploid species showed TIP41L gene was probably diverged after the formation of allotetraploid cotton, which may be selected and swept during domestication of modern upland cotton because small boll and seed are detrimental to fibre yield of cotton. This research would lay a solid foundation for further elucidating the molecular mechanism of cotton boll and seed development.

Enhanced Loss of Retinoic Acid Network Genes in Xenopus laevis Achieves a Tighter Signal Regulation.

Retinoic acid (RA) is a major regulatory signal during embryogenesis produced from vitamin A (retinol) by an extensive, autoregulating metabolic and signaling network to prevent fluctuations that result in developmental malformations. Xenopus laevis is an allotetraploid hybrid frog species whose genome includes L (long) and S (short) chromosomes from the originating species. Evolutionarily, the X. laevis subgenomes have been losing either L or S homoeologs in about 43% of genes to generate singletons. In the RA network, out of the 47 genes, about 47% have lost one of the homoeologs, like the genome average. Interestingly, RA metabolism genes from storage (retinyl esters) to retinaldehyde production exhibit enhanced gene loss with 75% singletons out of 28 genes. The effect of this gene loss on RA signaling autoregulation was studied. Employing transient RA manipulations, homoeolog gene pairs were identified in which one homoeolog exhibits enhanced responses or looser regulation than the other, while in other pairs both homoeologs exhibit similar RA responses. CRISPR/Cas9 targeting of individual homoeologs to reduce their activity supports the hypothesis where the RA metabolic network gene loss results in tighter network regulation and more efficient RA robustness responses to overcome complex regulation conditions.

Development and Genetic Characterization of Peanut Advanced Backcross Lines That Incorporate Root-Knot Nematode Resistance From Arachis stenosperma.

Crop wild species are increasingly important for crop improvement. Peanut (Arachis hypogaea L.) wild relatives comprise a diverse genetic pool that is being used to broaden its narrow genetic base. Peanut is an allotetraploid species extremely susceptible to peanut root-knot nematode (PRKN) Meloidogyne arenaria. Current resistant cultivars rely on a single introgression for PRKN resistance incorporated from the wild relative Arachis cardenasii, which could be overcome as a result of the emergence of virulent nematode populations. Therefore, new sources of resistance may be needed. Near-immunity has been found in the peanut wild relative Arachis stenosperma. The two loci controlling the resistance, present on chromosomes A02 and A09, have been validated in tetraploid lines and have been shown to reduce nematode reproduction by up to 98%. To incorporate these new resistance QTL into cultivated peanut, we used a marker-assisted backcrossing approach, using PRKN A. stenosperma-derived resistant lines as donor parents. Four cycles of backcrossing were completed, and SNP assays linked to the QTL were used for foreground selection. In each backcross generation seed weight, length, and width were measured, and based on a statistical analysis we observed that only one generation of backcrossing was required to recover the elite peanut’s seed size. A populating of 271 BC3F1 lines was genome-wide genotyped to characterize the introgressions across the genome. Phenotypic information for leaf spot incidence and domestication traits (seed size, fertility, plant architecture, and flower color) were recorded. Correlations between the wild introgressions in different chromosomes and the phenotypic data allowed us to identify candidate regions controlling these domestication traits. Finally, PRKN resistance was validated in BC3F3 lines. We observed that the QTL in A02 and/or large introgression in A09 are needed for resistance. This present work represents an important step toward the development of new high-yielding and nematode-resistant peanut cultivars.

In silico analysis of the regulatory gene families for proanthocyanidins biosynthesis in the genus Gossypium L.

The flavonoid pigments provide cotton cultivars with various shades of the naturally colored fiber. Despite of the deep knowledge about the flavonoids biosynthesis pathway in cotton, the genetic features underlying its control are not fully understood. Particularly, data on regulatory genes for the proanthocyanidins (PAs) branch are incomplete for the genus Gossypium L. Here we report results of comprehensive in silico analysis of the R2R3-Myb, bHLH-Myc and WD40 regulatory gene families, involved in the biosynthesis of flavonoid pigment PAs in cotton. For the first time, we identified regulatory genes R2R3-Myb, bHLH-Myc and WD40, including paralogous and homoeologous copies, among all sequenced diploid and allotetraploid cotton species: G. hirsutum L., G. barbadence L., G. raimondii L. and G. arboreum L. All duplication events occurred in the genome of the common diploid ancestor of the genus Gossypium and were supported by a negative evolution (Ka/Ks < 1). However, the GhTTG1/GhTTG3 genes are proved to be the most conservative and predominantly supported by selection, while GhTT2/GhMYB10 and GhTT8 are more variable and suitable for further analysis. The thorough study has suggested that all genes, with the exception of GhTT8-A2, possibly involved in the PAs biosynthesis. Therefore, information about structural organization and functionality of the all MBW genes in cotton genome is represented here. Revealing of the allelic diversities among identified genes, associating with contrast phenotype, may be useful for marker-assisted selection or genome editing for creation of naturally colored cotton cultivars with agriculturally valuable traits.

Subgenome Bias and Temporal Postponement of Gene Expression Contributes to the Distinctions of Fiber Quality in Gossypium Species.

As two cultivated widely allotetraploid cotton species, although Gossypium hirsutum and Gossypium barbadense evolved from the same ancestor, they differ in fiber quality; the molecular mechanism of that difference should be deeply studied. Here, we performed RNA-seq of fiber samples from four G. hirsutum and three G. barbadense cultivars to compare their gene expression patterns on multiple dimensions. We found that 15.90–37.96% of differentially expressed genes showed biased expression toward the A or D subgenome. In particular, interspecific biased expression was exhibited by a total of 330 and 486 gene pairs at 10 days post-anthesis (DPA) and 20 DPA, respectively. Moreover, 6791 genes demonstrated temporal differences in expression, including 346 genes predominantly expressed at 10 DPA in G. hirsutum (TM-1) but postponed to 20 DPA in G. barbadense (Hai7124), and 367 genes predominantly expressed at 20 DPA in TM-1 but postponed to 25 DPA in Hai7124. These postponed genes mainly participated in carbohydrate metabolism, lipid metabolism, plant hormone signal transduction, and starch and sucrose metabolism. In addition, most of the co-expression network and hub genes involved in fiber development showed asymmetric expression between TM-1 and Hai7124, like three hub genes detected at 10 DPA in TM-1 but not until 25 DPA in Hai7124. Our study provides new insights into interspecific expression bias and postponed expression of genes associated with fiber quality, which are mainly tied to asymmetric hub gene network. This work will facilitate further research aimed at understanding the mechanisms underlying cotton fiber improvement.

Wild rice research: Advancing plant science and food security

Wild rice research: Advancing plant science and food security