Transcriptome profiling and cataloging differential gene expression in floral buds of fertile and sterile lines of cotton (Gossypium hirsutum L.)

Dynamic roles of small RNAs and DNA methylation associated with heterosis in allotetraploid cotton (Gossypium hirsutum L.)

BACKGROUND

Heterosis is a complex phenomenon wherein the hybrids outperform their parents. Understanding the underlying molecular mechanism by which hybridization leads to higher yields in allopolyploid cotton is critical for effective breeding programs. Here, we integrated DNA methylation, transcriptomes, and small RNA profiles to comprehend the genetic and molecular basis of heterosis in allopolyploid cotton at three developmental stages.

RESULTS

Transcriptome analysis revealed that numerous DEGs responsive to phytohormones (auxin and salicylic acid) were drastically altered in F1 hybrid compared to the parental lines. DEGs involved in energy metabolism and plant growth were upregulated, whereas DEGs related to basal defense were downregulated. Differences in homoeologous gene expression in F1 hybrid were greatly reduced after hybridization, suggesting that higher levels of parental expression have a vital role in heterosis. Small RNAome and methylome studies showed that the degree of DNA methylation in hybrid is higher when compared to the parents. A substantial number of allele-specific expression genes were found to be strongly regulated by CG allele-specific methylation levels. The hybrid exhibited higher 24-nt-small RNA (siRNA) expression levels than the parents. The regions in the genome with increased levels of 24-nt-siRNA were chiefly related to genes and their flanking regulatory regions, demonstrating a possible effect of these molecules on gene expression. The transposable elements correlated with siRNA clusters in the F1 hybrid had higher methylation levels but lower expression levels, which suggest that these non-additively expressed siRNA clusters, reduced the activity of transposable elements through DNA methylation in the hybrid.

CONCLUSIONS

These multi-omics data provide insights into how changes in epigenetic mechanisms and gene expression patterns can lead to heterosis in allopolyploid cotton. This makes heterosis a viable tool in cotton breeding.

TaEXPB5 functions as a gene related to pollen development in thermo-sensitive male-sterility wheat with Aegilops kotschyi cytoplasm

The thermo-sensitive cytoplasmic male-sterility line with Aegilops kotschyi cytoplasm (K-TCMS) is completely male sterile under low temperature (< 18 ℃) during Zadoks growth stages 45-52, whereas its fertility can be restored under hot temperature (≥ 20 ℃). The K-TCMS line may facilitate hybrid breeding and hybrid wheat production. Therefore, to elucidate the molecular mechanisms of its male sterility/fertility conversion, we conducted the association analysis of proteins and transcript expression to screen fertility related genes using RNA-seq, iTRAQ, and PRM-based assay. A gene encoding expansin protein in wheat, TaEXPB5, was isolated in K-TCMS line KTM3315A, which upregulated expression in the fertility anthers. Subcellular localization analysis suggested that TaEXPB5 protein localized to nucleus and cell wall. The silencing of TaEXPB5 displayed pollen abortion and the declination of fertility. Further, cytological investigation indicated that the silencing of TaEXPB5 induced the early degradation of tapetum and abnormal development of pollen wall. These results implied that TaEXPB5 may be essential for anther or pollen development and male fertility of KTM3315A. These findings provide a novel insight into molecular mechanism of fertility conversion for thermo-sensitive cytoplasmic male-sterility wheat, and contribute to the molecular breeding of hybrid wheat in the future.

Unravelling the treasure trove of drought-responsive genes in wild-type peanut through transcriptomics and physiological analyses of root

Peanut is one of the most valuable legumes, grown mainly in arid and semi-arid regions, where its production may be hindered by the lack of water. Therefore, breeding drought tolerant varieties is of great importance for peanut breeding programs around the world. Unlike cultivated peanuts, wild peanuts have greater genetic diversity and are an important source of alleles conferring tolerance/resistance to abiotic and biotic stresses. To decipher the transcriptome changes under drought stress, transcriptomics of roots of highly tolerant Arachis duranensis (ADU) and moderately susceptible A. stenosperma (AST) genotypes were performed. Transcriptome analysis revealed an aggregate of 1465 differentially expressed genes (DEGs), and among the identified DEGs, there were 366 single nucleotide polymorphisms (SNPs). Gene ontology and Mapman analyses revealed that the ADU genotype had a higher number of transcripts related to DNA methylation or demethylation, phytohormone signal transduction and flavonoid production, transcription factors, and responses to ethylene. The transcriptome analysis was endorsed by qRT-PCR, which showed a strong correlation value (R² = 0.96). Physio-biochemical analysis showed that the drought-tolerant plants produced more osmolytes, ROS phagocytes, and sugars, but less MDA, thus attenuating the effects of drought stress. In addition, three SNPs of the gene encoding transcription factor NFAY (Aradu.YE2F8), expansin alpha (Aradu.78HGD), and cytokinin dehydrogenase 1-like (Aradu.U999X) exhibited polymorphism in selected different genotypes. Such SNPs could be useful for the selection of drought-tolerant genotypes.

Stage specific comparative transcriptomic analysis to reveal gene networks regulating iron and zinc content in pearl millet [Pennisetum glaucum (L.) R. Br.]

Pearl millet is an important staple food crop of poor people and excels all other cereals due to its unique features of resilience to adverse climatic conditions. It is rich in micronutrients like iron and zinc and amenable for focused breeding for these micronutrients along with high yield. Hence, this is a key to alleviate malnutrition and ensure nutritional security. This study was conducted to identify and validate candidate genes governing grain iron and zinc content enabling the desired modifications in the genotypes. Transcriptome sequencing using ION S5 Next Generation Sequencer generated 43.5 million sequence reads resulting in 83,721 transcripts with N₅₀ of 597 bp and 84.35% of transcripts matched with the pearl millet genome assembly. The genotypes having high iron and zinc showed differential gene expression during different stages. Of which, 155 were up-regulated and 251 were down-regulated while during flowering stage and milking stage 349 and 378 transcripts were differentially expressed, respectively. Gene annotation and GO term showed the presence of transcripts involved in metabolic activities associated with uptake and transport of iron and zinc. Information generated will help in gaining insights into iron and zinc metabolism and develop genotypes with high yield, grain iron and zinc content.

Genic microsatellite marker characterization and development in little millet (Panicum sumatrense) using transcriptome sequencing

Little millet is a climate-resilient and high-nutrient value plant. The lack of molecular markers severely limits the adoption of modern genomic approaches in millet breeding studies. Here the transcriptome of three samples were sequenced. A total of 4443 genic-SSR motifs were identified in 30,220 unigene sequences. SSRs were found at a rate of 12.25 percent, with an average of one SSR locus per 10 kb. Among different repeat motifs, tri-nucleotide repeat (66.67) was the most abundant one, followed by di- (27.39P), and tetra- (3.83P) repeats. CDS contained fewer motifs with the majority of tri-nucleotides, while 3' and 5' UTR carry more motifs but have shorter repeats. Functional annotation of unigenes containing microsatellites, revealed that most of them were linked to metabolism, gene expression regulation, and response to environmental stresses. Fifty primers were randomly chosen and validated in five little millet and 20 minor millet genotypes; 48% showed polymorphism, with a high transferability (70%) rate. Identified microsatellites can be a noteworthy resource for future research into QTL-based breeding, genetic resource conservation, MAS selection, and evolutionary genetics.

Transcriptome analysis of two Pogostemon cablin chemotypes reveals genes related to patchouli alcohol biosynthesis

Pogostemon cablin, a medicinally and economically important perennial herb, is cultivated around the world due to its medicinal and aromatic properties. Different P. cablin cultivars exhibit different morphological traits and patchouli oil components and contents (especially patchouli alcohol (PA) and pogostone (PO)). According to the signature constituent of the leaf, P. cablin was classified into two different chemotypes, including PA-type and PO-type. To better understand the molecular mechanisms of PA biosynthesis, the transcriptomes of Chinese-cultivated P. cablin cv. PA-type “Nanxiang” (NX) and PO-type “Paixiang” (PX) were analyzed and compared with ribonucleic acid sequencing (RNA-Seq) technology. We obtained a total of 36.83 G clean bases from the two chemotypes, compared them with seven databases and revealed 45,394 annotated unigenes. Thirty-six candidate unigenes participating in the biosynthesis of PA were found in the P. cablin transcriptomes. Overall, 8,390 differentially expressed unigenes were identified between the chemotypes, including 2,467 upregulated and 5,923 downregulated unigenes. Furthermore, six and nine differentially expressed genes (DEGs) were mapped to the terpenoid backbone biosynthetic and sesquiterpenoid and triterpenoid biosynthetic pathways, respectively. One key sesquiterpene synthase gene involved in the sesquiterpenoid and triterpenoid biosynthetic pathways, encoding patchoulol synthase variant 1, was significantly upregulated in NX. Additionally, GC-MS analysis of the two chemotypes in this study showed that the content of PA in NX was significantly higher than that of PX, while the content of PO showed the opposite phenotype. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the DEG expression tendency was consistent with the transcriptome sequencing results. Overall, 23 AP2/ERF, 13 bHLH, 11 MYB, 11 NAC, three Trihelix, 10 WRKY and three bZIP genes that were differentially expressed may act as regulators of terpenoid biosynthesis. Altogether, 8,314 SSRs were recognized within 6,825 unigenes, with a distribution frequency of 18.32%, among which 1,202 unigenes contained more than one SSR. The transcriptomic characteristics of the two P. cablin chemotypes are comprehensively reported in this study, and these results will contribute to a better understanding of the molecular mechanism of PA biosynthesis. Our transcriptome data also provide a valuable genetic resource for further studies on P. cablin.

Differentially Expressed Genes Shared by Two Distinct Cytoplasmic Male Sterility (CMS) Types of Silene vulgaris Suggest the Importance of Oxidative Stress in Pollen Abortion

Cytoplasmic male sterility (CMS), encoded by the interacting mitochondrial and nuclear genes, causes pollen abortion or non-viability. CMS is widely used in agriculture and extensively studied in crops. Much less is known about CMS in wild species. We performed a comparative transcriptomic analysis of male sterile and fertile individuals of Silene vulgaris, a model plant for the study of gynodioecy, to reveal the genes responsible for pollen abortion in this species. We used RNA-seq datasets previously employed for the analysis of mitochondrial and plastid transcriptomes of female and hermaphrodite flower buds, making it possible to compare the transcriptomes derived from three genomes in the same RNA specimen. We assembled de novo transcriptomes for two haplotypes of S. vulgaris and identified differentially expressed genes between the females and hermaphrodites, associated with stress response or pollen development. The gene for alternative oxidase was downregulated in females. The genetic pathways controlling CMS in S. vulgaris are similar to those in crops. The high number of the differentially expressed nuclear genes contrasts with the uniformity of organellar transcriptomes across genders, which suggests these pathways are evolutionarily conserved and that selective mechanisms may shield organellar transcription against changes in the cytoplasmic transcriptome.

Deficiencies in the formation and regulation of anther cuticle and tryphine contribute to male sterility in cotton PGMS line

BACKGROUND

Male sterility is a simple and efficient pollination control system that is widely exploited in hybrid breeding. In upland cotton, CCRI9106, a photosensitive genetic male sterile (PGMS) mutant isolated from CCRI040029, was reported of great advantages to cotton heterosis. However, little information concerning the male sterility of CCRI9106 is known. Here, comparative transcriptome analysis of CCRI9106 (the mutant, MT) and CCRI040029 (the wild type, WT) anthers in Anyang (long-day, male sterile condition to CCRI9106) was performed to reveal the potential male sterile mechanism of CCRI9106.

RESULTS

Light and electron microscopy revealed that the male sterility phenotype of MT was mainly attributed to irregularly exine, lacking tryphine and immature anther cuticle. Based on the cytological characteristics of MT anthers, anther RNA libraries (18 in total) of tetrad (TTP), late uninucleate (lUNP) and binucleate (BNP) stages in MT and WT were constructed for transcriptomic analysis, therefore revealing a total of 870,4 differentially expressed genes (DEGs). By performing gene expression pattern analysis and protein-protein interaction (PPI) networks construction, we found down-regulation of DEGs, which enriched by the lipid biosynthetic process and the synthesis pathways of several types of secondary metabolites such as terpenoids, flavonoids and steroids, may crucial to the male sterility phenotype of MT, and resulting in the defects of anther cuticle and tryphine, even the irregularly exine. Furthermore, several lipid-related genes together with ABA-related genes and MYB transcription factors were identified as hub genes via weighted gene co-expression network analysis (WGCNA). Additionally, the ABA content of MT anthers was reduced across all stages when compared with WT anthers. At last, genes related to the formation of anther cuticle and tryphine could activated in MT under short-day condition.

CONCLUSIONS

We propose that the down-regulation of genes related to the assembly of anther cuticle and tryphine may lead to the male sterile phenotype of MT, and MYB transcription factors together with ABA played key regulatory roles in these processes. The conversion of fertility in different photoperiods may closely relate to the functional expression of these genes. These findings contribute to elucidate the mechanism of male sterility in upland cotton.

Deficiencies in the formation and regulation of anther cuticle and tryphine contribute to male sterility in cotton PGMS line

Background

Male sterility is a simple and efficient pollination control system that is widely exploited in hybrid breeding. In upland cotton, CCRI9106, a photosensitive genetic male sterile (PGMS) mutant isolated from CCRI040029, was reported of great advantages to cotton heterosis. However, little information concerning the male sterility of CCRI9106 is known. Here, comparative transcriptome analysis of CCRI9106 (the mutant, MT) and CCRI040029 (the wild type, WT) anthers in Anyang (long-day, male sterile condition to CCRI9106) was performed to reveal the potential male sterile mechanism of CCRI9106.

Results

Light and electron microscopy revealed that the male sterility phenotype of MT was mainly attributed to irregularly exine, lacking tryphine and immature anther cuticle. Based on the cytological characteristics of MT anthers, anther RNA libraries (18 in total) of tetrad (TTP), late uninucleate (lUNP) and binucleate (BNP) stages in MT and WT were constructed for transcriptomic analysis, therefore revealing a total of 870,4 differentially expressed genes (DEGs). By performing gene expression pattern analysis and protein-protein interaction (PPI) networks construction, we found down-regulation of DEGs, which enriched by the lipid biosynthetic process and the synthesis pathways of several types of secondary metabolites such as terpenoids, flavonoids and steroids, may crucial to the male sterility phenotype of MT, and resulting in the defects of anther cuticle and tryphine, even the irregularly exine. Furthermore, several lipid-related genes together with ABA-related genes and MYB transcription factors were identified as hub genes via weighted gene co-expression network analysis (WGCNA). Additionally, the ABA content of MT anthers was reduced across all stages when compared with WT anthers. At last, genes related to the formation of anther cuticle and tryphine could activated in MT under short-day condition.

Conclusions

We propose that the down-regulation of genes related to the assembly of anther cuticle and tryphine may lead to the male sterile phenotype of MT, and MYB transcription factors together with ABA played key regulatory roles in these processes. The conversion of fertility in different photoperiods may closely relate to the functional expression of these genes. These findings contribute to elucidate the mechanism of male sterility in upland cotton.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07250-1.

Uncloaking lncRNA-meditated gene expression as a potential regulator of CMS in cotton (Gossypium hirsutum L.)

Cytoplasmic male sterility is a well-proven mechanism for cotton hybrid production. Long non-coding RNAs belong to a class of transcriptional regulators that function in multiple biological processes. The cDNA libraries from the flower buds of the cotton CGMS, it's restorer (Rf) and maintainer lines were sequenced using high throughput NGS technique. A total of 1531 lncRNAs showed significant differential expression patterns between these three lines. Functional analysis of the co-expression network of lncRNA-mRNA using gene ontology vouchsafes that, lncRNAs play a crucial role in cytoplasmic male sterility and fertility restoration through pollen development, INO80 complex, development of anther wall tapetum, chromatin remodeling, and histone modification. Additionally, 94 lncRNAs were identified as putative precursors of 49 miRNAs. qRT-PCR affirms the concordance of expression pattern to RNA-seq data. These findings divulge the lncRNA driven miRNA-mediated regulation of gene expression profiling superintended for a better understanding of the CMS mechanisms of cotton.

Comparative RNA-Seq profiling of a resistant and susceptible peanut (Arachis hypogaea) genotypes in response to leaf rust infection caused by Puccinia arachidis

The goal of this study was to identify differentially expressed genes (DEGs) responsible for peanut plant (Arachis hypogaea) defence against Puccinia arachidis (causative agent of rust disease). Genes were identified using a high-throughput RNA-sequencing strategy. In total, 86,380,930 reads were generated from RNA-Seq data of two peanut genotypes, JL-24 (susceptible), and GPBD-4 (resistant). Gene Ontology (GO) and KEGG analysis of DEGs revealed essential genes and their pathways responsible for defence response to P. arachidis. DEGs uniquely upregulated in resistant genotype included pathogenesis-related (PR) proteins, MLO such as protein, ethylene-responsive factor, thaumatin, and F-box, whereas, other genes down-regulated in susceptible genotype were Caffeate O-methyltransferase, beta-glucosidase, and transcription factors (WRKY, bZIP, MYB). Moreover, various genes, such as Chitinase, Cytochrome P450, Glutathione S-transferase, and R genes such as NBS-LRR were highly up-regulated in the resistant genotype, indicating their involvement in the plant defence mechanism. RNA-Seq analysis data were validated by RT-qPCR using 15 primer sets derived from DEGs producing high correlation value (R ² = 0.82). A total of 4511 EST-SSRs were identified from the unigenes, which can be useful in evaluating genetic diversity among genotypes, QTL mapping, and plant variety improvement through marker-assisted breeding. These findings will help to understand the molecular defence mechanisms of the peanut plant in response to P. arachidis infection.

Variation in plastid genomes in the gynodioecious species Silene vulgaris

BACKGROUND

Gynodioecious species exist in two sexes - male-sterile females and hermaphrodites. Male sterility in higher plants often results from mitonuclear interaction between the CMS (cytoplasmic male sterility) gene(s) encoded by mitochondrial genome and by nuclear-encoded restorer genes. Mitochondrial and nuclear-encoded transcriptomes in females and hermaphrodites are intensively studied, but little is known about sex-specific gene expression in plastids. We have compared plastid transcriptomes between females and hermaphrodites in two haplotypes of a gynodioecious species Silene vulgaris with known CMS candidate genes.

RESULTS

We generated complete plastid genome sequences from five haplotypes S. vulgaris including the haplotypes KRA and KOV, for which complete mitochondrial genome sequences were already published. We constructed a phylogenetic tree based on plastid sequences of S. vulgaris. Whereas lowland S. vulgaris haplotypes including KRA and KOV clustered together, the accessions from high European mountains diverged early in the phylogram. S. vulgaris belongs among Silene species with slowly evolving plastid genomes, but we still detected 212 substitutions and 112 indels between two accessions of this species. We estimated elevated Ka/Ks in the ndhF gene, which may reflect the adaptation of S. vulgaris to high altitudes, or relaxed selection. We compared depth of coverage and editing rates between female and hermaphrodite plastid transcriptomes and found no significant differences between the two sexes. We identified 51 unique C to U editing sites in the plastid genomes of S. vulgaris, 38 of them in protein coding regions, 2 in introns, and 11 in intergenic regions. The editing site in the psbZ gene was edited only in one of two plastid genomes under study.

CONCLUSIONS

We revealed no significant differences between the sexes in plastid transcriptomes of two haplotypes of S. vulgaris. It suggests that gene expression of plastid genes is not affected by CMS in flower buds of S. vulgaris, although both sexes may still differ in plastid gene expression in specific tissues. We revealed the difference between the plastid transcriptomes of two S. vulgaris haplotypes in editing rate and in the coverage of several antisense transcripts. Our results document the variation in plastid genomes and transcriptomes in S. vulgaris.

Comparative transcriptional analysis of Capsicum flower buds between a sterile flower pool and a restorer flower pool provides insight into the regulation of fertility restoration

BACKGROUND

Cytoplasmic male sterility (CMS) and its restoration of fertility (Rf) system is an important mechanism to produce F₁ hybrid seeds. Understanding the interaction that controls restoration at a molecular level will benefit plant breeders. The CMS is caused by the interaction between mitochondrial and nuclear genes, with the CMS phenotype failing to produce functional anthers, pollen, or male gametes. Thus, understanding the complex processes of anther and pollen development is a prerequisite for understanding the CMS system. Currently it is accepted that the Rf gene in the nucleus restores the fertility of CMS, however the Rf gene has not been cloned. In this study, CMS line 8A and the Rf line R1, as well as a sterile pool (SP) of accessions and a restorer pool (RP) of accessions analyzed the differentially expressed genes (DEGs) between CMS and its fertility restorer using the conjunction of RNA sequencing and bulk segregation analysis.

RESULTS

A total of 2274 genes were up-regulated in R1 as compared to 8A, and 1490 genes were up-regulated in RP as compared to SP. There were 891 genes up-regulated in both restorer accessions, R1 and RP, as compared to both sterile accessions, 8A and SP. Through annotation and expression analysis of co-up-regulated expressed genes, eight genes related to fertility restoration were selected. These genes encode putative fructokinase, phosphatidylinositol 4-phosphate 5-kinase, pectate lyase, exopolygalacturonase, pectinesterase, cellulose synthase, fasciclin-like arabinogalactan protein and phosphoinositide phospholipase C. In addition, a phosphatidylinositol signaling system and an inositol phosphate metabolism related to the fertility restorer of CMS were ranked as the most likely pathway for affecting the restoration of fertility in pepper.

CONCLUSIONS

Our study revealed that eight genes were related to the restoration of fertility, which provides new insight into understanding the molecular mechanism of fertility restoration of CMS in Capsicum.

Genome wide search to identify reference genes candidates for gene expression analysis in Gossypium hirsutum

BACKGROUND

Cotton is one of the most important commercial crops as the source of natural fiber, oil and fodder. To protect it from harmful pest populations number of newer transgenic lines have been developed. For quick expression checks in successful agriculture qPCR (quantitative polymerase chain reaction) have become extremely popular. The selection of appropriate reference genes plays a critical role in the outcome of such experiments as the method quantifies expression of the target gene in comparison with the reference. Traditionally most commonly used reference genes are the "house-keeping genes", involved in basic cellular processes. However, expression levels of such genes often vary in response to experimental conditions, forcing the researchers to validate the reference genes for every experimental platform. This study presents a data science driven unbiased genome-wide search for the selection of reference genes by assessing variation of > 50,000 genes in a publicly available RNA-seq dataset of cotton species Gossypium hirsutum.

RESULT

Five genes (TMN5, TBL6, UTR5B, AT1g65240 and CYP76B6) identified by data-science driven analysis, along with two commonly used reference genes found in literature (PP2A1 and UBQ14) were taken through qPCR in a set of 33 experimental samples consisting of different tissues (leaves, square, stem and root), different stages of leaf (young and mature) and square development (small, medium and large) in both transgenic and non-transgenic plants. Expression stability of the genes was evaluated using four algorithms - geNorm, BestKeeper, NormFinder and RefFinder.

CONCLUSION

Based on the results we recommend the usage of TMN5 and TBL6 as the optimal candidate reference genes in qPCR experiments with normal and transgenic cotton plant tissues. AT1g65240 and PP2A1 can also be used if expression study includes squares. This study, for the first time successfully displays a data science driven genome-wide search method followed by experimental validation as a method of choice for selection of stable reference genes over the selection based on function alone.

Transcriptome landscaping for gene mining and SSR marker development in Coriander (Coriandrum sativum L.)

Coriander (Coriandrum sativum L.) is an aromatic herb, widely used as a spice and is of great pharmaceutical interest. Despite high medicinal and economic value, there is a dearth of genomic information about profiling as well as the expressed sequence-based genic markers. In this study, transcriptome was sequenced from seeds, leaves, and flower for gene mining and identification of SSR markers. A total of 9746 SSR containing loci were identified, the most abundant type of SSR identified were the di-nucleotide repeat motifs (45.5%), followed by tri- (34.6%), tetra- (4.5%), penta- (1.5%) and hexanucleotide repeats (1%). A total of 3795 primers were designed, out of which 120 randomly selected were validated in 14 accessions of coriander cultivated in India. The current study provides useful information about preliminary transcriptome sketch and genic markers, which can be useful in breeding and genetic diversity estimation of coriander.

Transcriptome analysis identified aberrant gene expression in pollen developmental pathways leading to CGMS in cotton (Gossypium hirsutum L.)

Male sterility (induced or natural) is a potential tool for commercial hybrid seed production in different crops. Despite numerous endeavors to understand the physiological, hereditary, and molecular cascade of events governing CMS in cotton, the exact biological process controlling sterility and fertility reconstruction remains obscure. During current study, RNA-Seq using Ion Torrent S5 platform is carried out to identify 'molecular portraits' in floral buds among the Cytoplasmic Genic Male Sterility (CGMS) line, its near-isogenic maintainer, and restorer lines. A total of 300, 438 and 455 genes were differentially expressed in CGMS, Maintainer, and Restorer lines respectively. The functional analysis using AgriGo revealed suppression in the pathways involved in biogenesis and metabolism of secondary metabolites which play an important role in pollen and anther maturation. Enrichment analysis showed dearth related to pollen and anther's development in sterile line, including anomalous expression of genes and transcription factors that have a role in the development of the reproductive organ, abnormal cytoskeleton formation, defects in cell wall formation. The current study found aberrant expression of DYT1, AMS and cytochrome P450 genes involved in tapetum formation, pollen development, pollen exine and anther cuticle formation associated to male sterility as well as fertility restoration of CGMS. In the current study, more numbers of DEGs were found on Chromosome D05 and A05 as compared to other chromosomes. Expression pattern analysis of fourteen randomly selected genes using qRT-PCR showed high concurrence with gene expression profile of RNA-Seq analysis accompanied by a strong correlation of 0.82. The present study provides an important support for future studies in identifying interaction between cyto-nuclear molecular portraits, to accelerate functional genomics and molecular breeding related to cytoplasmic male sterility studies in cotton.

Mitochondrial genome and transcriptome analysis of five alloplasmic male-sterile lines in Brassica juncea

Background

Alloplasmic lines, in which the nuclear genome is combined with wild cytoplasm, are often characterized by cytoplasmic male sterility (CMS), regardless of whether it was derived from sexual or somatic hybridization with wild relatives. In this study, we sequenced and analyzed the mitochondrial genomes of five such alloplasmic lines in Brassica juncea.

Results

The assembled and annotated mitochondrial genomes of the five alloplasmic lines were found to have virtually identical gene contents. They preserved most of the ancestral mitochondrial segments, and the same candidate male sterility gene (orf108) was found harbored in mitotype-specific sequences. We also detected promiscuous sequences of chloroplast origin that were conserved among plants of the Brassicaceae, and found the RNA editing profiles to vary across the five mitochondrial genomes.

Conclusions

On the basis of our characterization of the genetic nature of five alloplasmic mitochondrial genomes, we speculated that the putative candidate male sterility gene orf108 may not be responsible for the CMS observed in Brassica oxyrrhina and Diplotaxis catholica. Furthermore, we propose the potential coincidence of CMS in alloplasmic lines. Our findings lay the foundation for further elucidation of male sterility gene.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5721-2) contains supplementary material, which is available to authorized users.

Transcriptome, cytological and biochemical analysis of cytoplasmic male sterility and maintainer line in CMS-D8 cotton

Key message This research based on RNA-seq, biochemical, and cytological analyses sheds that ROS may serve as important signaling molecules of cytoplasmic male sterility in CMS-D8 cotton. To understand the mechanism of cytoplasmic male sterility in cotton (Gossypium hirsutum), transcriptomic, cytological, and biochemical analysis were performed between the cytoplasmic male sterility CMS-D8 line, Zhong41A, and its maintainer line Zhong41B. A total of 2335 differentially expressed genes (DEGs) were identified in the CMS line at three different stages of anther development. Bioinformatics analysis of these DEGs indicated their relationship to reactive oxygen species (ROS) homeostasis, including reduction-oxidation reactions and the metabolism of glutathione and ascorbate. At the same time, DEGs associated with tapetum development, especially the transition to secretory tapetum, were down-regulated in the CMS line. Biochemical analysis indicated that the ability of the CMS line to eliminate ROS was decreased, which led to the rapid release of H₂O₂. Cytological analysis revealed that the most crucial defect in the CMS line was the abnormal tapetum. All these results are consistent with the RNA sequencing data. On the basis of our findings, we propose that ROS act as signal molecules, which are released from mitochondria and transferred to the nucleus, triggering the formation of abnormal tapetum.