Comparative transcriptome analysis of the petal degeneration mutant pdm in Chinese cabbage (Brassica campestris ssp. pekinensis) using RNA-Seq

Fine mapping and analysis of candidate genes for qFT7.1, a major quantitative trait locus controlling flowering time in Brassica rapa L

qFT7.1, a major QTL for flowering time in Brassica rapa was fine-mapped to chromosome A07 in a 56.4-kb interval, in which the most likely candidate gene is BraA07g018240.3C. In Brassica rapa, flowering time (FT) is an important agronomic trait that affects the yield, quality, and adaption. FT is a complicated trait that is regulated by many genes and is affected greatly by the environment. In this study, a chromosome segment substitution line (CSSL), CSSL16, was selected that showed later flowering than the recurrent parent, a rapid-cycling inbred line of B. rapa (RcBr). Using Bulked Segregant RNA sequencing, we identified a late flowering quantitative trait locus (QTL), designated as qFT7.1, on chromosome A07, based on a secondary-F₂ population derived from the cross between CSSL16 and RcBr. qFT7.1 was further validated by conventional QTL mapping. This QTL explained 39.9% (logarithm of odds = 32.2) of the phenotypic variations and was fine mapped to a 56.4-kb interval using recombinant analysis. Expression analysis suggested that BraA07g018240.3C, which is homologous to ATC (encoding Arabidopsis thaliana CENTRORADIALIS homologue), a gene for delayed flowering in Arabidopsis, as the most promising candidate gene. Sequence analysis demonstrated that two synonymous mutations existed in the coding region and numerous bases replacements existed in promoter region between BraA07g018240.3C from CSSL16 and RcBr. The results will increase our knowledge related to the molecular mechanism of late flowering in B. rapa and lays a solid foundation for the breeding of late bolting B. rapa.

Role of BrSDG8 on bolting in Chinese cabbage (Brassica rapa)

Mapping and resequencing of two allelic early bolting mutants ebm5-1 and ebm5-2 revealed that the BrSDG8 gene is related to bolting in Chinese cabbage (Brassica rapa ssp. pekinensis). Bolting influences the leafy head formation and seed yield of Chinese cabbage therefore being an important agronomic trait. Herein, two allelic early bolting mutants, ebm5-1 and ebm5-2, stably inherited in Chinese cabbage were obtained from wild-type 'FT' seeds by ethyl methane sulfonate mutagenesis. Both mutants flowered significantly earlier than 'FT,' and genetic analysis revealed that the early bolting of the two mutants was controlled by one recessive nuclear gene. With BSR-seq, the mutations originating lines ebm5-1 and ebm5-2 were located to the same region in chromosome A07. Using the 1741 F₂ individuals with the ebm5-1 phenotype as the mapping population, this region was narrowed to 56.24 kb between markers InDel18 and InDel45. A single-nucleotide polymorphism (SNP) was aligned to the BraA07g040740.3C (BrSDG8) region by whole-genome resequencing of ebm5-1 mutant and 'FT.' BrSDG8 is a homolog of Arabidopsis thaliana SDG8 encoding a histone methyltransferase affecting H3K4 trimethylation in FLOWERING LOCUS C chromatin. Comparative sequencing established that the SNP occurred on BrSDG8 17th exon in ebm5-1. Genotype analysis showed full co-segregation of the early bolting phenotype with this SNP. Cloning of allelic mutant ebm5-2 indicated that it harbors a deletion mutation on the 12th exon of BrSDG8. Quantitative real-time PCR analysis indicated that BrSDG8 expression level was observably lower in mutant ebm5-1 than in 'FT.' Overall, the present results provide strong evidence that BrSDG8 mutation leads to early bolting in Chinese cabbage, thereby providing a basis to understand the molecular mechanisms underlying this phenotype.

An Insertion Mutation in Bra032169 Encoding a Histone Methyltransferase Is Responsible for Early Bolting in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Bolting is an important agronomic character of the Chinese cabbage, but premature bolting can greatly reduce its commercial value, yield, and quality. Here, early-bolting mutant 1 (ebm1) was obtained from a Chinese cabbage doubled haploid (DH) line "FT," by using an isolated microspore culture and ethyl methanesulfonate (EMS) mutagenesis. The ebm1 was found to bolt extremely earlier than the wild type "FT." Genetic analysis indicated that the phenotype of the ebm1 was controlled by a single recessive nuclear gene. Using a mapping population of 1,502 recessive homozygous F2 individuals with the ebm1 phenotype, the ebm1 gene was mapped to between the markers SSRhl-53 and SSRhl-61 on chromosome A04 by using SSR markers, and its physical distance was 73.4 kb. Seven genes were predicted in the target region and then cloned and sequenced; the only difference in the sequences of the ebm1 and "FT" genes was with Bra032169. Unlike that in "FT," the Bra032169 in ebm1 had a novel 53 bp insertion that caused the termination of amino acid coding. The mutation was not consistent with EMS mutagenesis, and thus, may have been caused by spontaneous mutations during the microspore culture. Based on the gene annotation information, Bra032169 was found to encode the histone methyltransferase CURLY LEAF (CLF) in Arabidopsis thaliana. CLF regulates the expression of flowering-related genes. Further genotyping revealed that the early-bolting phenotype was fully co-segregated with the insertion mutation, suggesting that Bra032169 was the most likely candidate gene for ebm1. No significant differences were noted in the Bra032169 expression levels between the ebm1 and "FT." However, the expression levels of the flowering-related genes FLC, FT, AG, and SEP3 were significantly higher in the ebm1 than in the "FT." Thus, the mutation of Bra032169 is responsible for the early-bolting trait in Chinese cabbage. These results provide foundation information to help understand the molecular mechanisms of bolting in the Chinese cabbage.

Identification of two recessive etiolation genes (py1, py2) in pakchoi (Brassica rapa L. ssp. chinensis)

BACKGROUND

Leaf color is a major agronomic trait, which has a strong influence on crop yields. Isolating leaf color mutants can represent valuable materials for research in chlorophyll (Chl) biosynthesis and metabolism regulation.

RESULTS

In this study, we identified a stably inherited yellow leaf mutant derived from 'Huaguan' pakchoi variety via isolated microspore culture and designated as pylm. This mutant displayed yellow leaves after germination. Its etiolated phenotype was nonlethal and stable during the whole growth period. Its growth was weak and its hypocotyls were markedly elongated. Genetic analysis revealed that two recessive nuclear genes, named py1 and py2, are responsible for the etiolation phenotype. Bulked segregant RNA sequencing (BSR-Seq) showed that py1 and py2 were mapped on chromosomes A09 and A07, respectively. The genes were single Mendelian factors in F_3:4 populations based on a 3:1 phenotypic segregation ratio. The py1 was localized to a 258.3-kb interval on a 34-gene genome. The differentially expressed gene BraA09004189 was detected in the py1 mapping region and regulated heme catabolism. One single-nucleotide polymorphism (SNP) of BraA09004189 occurred in pylm. A candidate gene-specific SNP marker in 1520 F_3:4 yellow-colored individuals co-segregated with py1. For py2, 1860 recessive homozygous F_3:4 individuals were investigated and localized py2 to a 4.4-kb interval. Of the five genes in this region, BraA07001774 was predicted as a candidate for py2. It encoded an embryo defective 1187 and a phosphotransferase related to chlorophyll deficiency and hypocotyl elongation. One SNP of BraA07001774 occurred in pylm. It caused a single amino acid mutation from Asp to Asn. According to quantitative real-time polymerase chain reaction (qRT-PCR), BraA07001774 was downregulated in pylm.

CONCLUSIONS

Our study identified a Chl deficiency mutant pylm in pakchoi. Two recessive nuclear genes named py1 and py2 had a significant effect on etiolation. Candidate genes regulating etiolation were identified as BraA09004189 and BraA07001774, respectively. These findings will elucidate chlorophyll metabolism and the molecular mechanisms of the gene interactions controlling pakchoi etiolation.

Investigation of the genes associated with a male sterility mutant (msm) in Chinese cabbage (Brassica campestris ssp. pekinensis) using RNA-Seq

In Chinese cabbage, hybrid seed production is performed using male sterility lines, an important approach to heterosis utilization. In this study, a stably inherited male sterile mutant msm was obtained from the 'FT'-doubled haploid line of Chinese cabbage using isolated microspore culture combined with ⁶⁰Co γ-ray mutagenesis. The genetic backgrounds of 'FT' and msm were highly consistent; however, compared with wild-type 'FT', msm exhibited completely degenerated stamens and no pollen phenotype. Other characters showed no significant differences. Cytological observations revealed that stamen abortion in msm begins during the tetrad period and that tapetum cells were abnormally expanded and highly vacuolated, leading to microspore abortion. Genetic analysis indicated that the msm mutant phenotype is controlled by a single recessive nuclear gene. Comparative transcriptome analysis of 'FT' and msm flower buds using RNA-Seq technology revealed 1653 differentially expressed genes, among which, a large number associated with male sterility were detected, including 64 pollen development- and pollen tube growth-related genes, 94 pollen wall development-related genes, 11 phytohormone-related genes, and 16 transcription factor-related genes. An overwhelming majority of these genes were down-regulated in msm compared with 'FT'. Furthermore, KEGG pathway analysis indicated that a variety of carbohydrate metabolic and lipid metabolic pathways were significantly enriched, which may be related to pollen abortion. The expression patterns of 24 male sterility-related genes were analyzed using qRT-PCR. In addition, 24,476 single-nucleotide polymorphisms and 413,073 insertion-deletion events were specifically detected in msm. These results will facilitate elucidation of the regulatory mechanisms underlying male sterility in Chinese cabbage.

Mutation in EMB1923 gene promoter is associated with chlorophyll deficiency in Chinese cabbage (Brassica campestris ssp. pekinensis)

Leaf color mutants are widespread in higher plants and can be used as markers in crop breeding or as important material in understanding the regulatory mechanisms of chlorophyll biosynthesis and chloroplast development. A stably inherited plant etiolated mutation (pem) was obtained from its wild-type 'FT' (a doubled haploid line of the Chinese cabbage variety 'Fukuda 50') by combining ⁶⁰ Co-γ radiation and isolated microspore culture in Chinese cabbage. Compared to the wild-type 'FT', the chlorophyll content in the pem mutant was decreased, the photosynthetic capacity was reduced and the chloroplast development was retarded. These physiological changes may lead to a reduction in growth and yield in the pem mutant line. Genetic analysis showed that the mutant phenotype was controlled by the single recessive nuclear pem gene. The pem gene was mapped to a 25.88 kb region on the A03 chromosome. Cloning and sequencing results showed that there was only one DNA sequence variation in this region, which was a 30 bp deletion on the promoter of Bra024218. Its homologous gene encodes EMBRYO DEFECTIVE 1923 (EMB1923) in Arabidopsis thaliana. We therefore predicted that Bra024218 was the mutated gene associated with etiolated leaves in Chinese cabbage. The pem mutant is a useful line for researching chloroplast development and the mechanism of leaf color mutation in Chinese cabbage.

Transcriptome-based analysis of carotenoid accumulation-related gene expression in petals of Chinese cabbage (Brassica rapa L.)

To identify genes associated with carotenoid accumulation in petals of Chinese cabbage, the composition and content of carotenoids were analyzed, and comparative transcriptome sequencing was performed between the yellow flower line, 92S105, and the orange flower line, 94C9. High-performance liquid chromatography (HPLC) revealed that petals of 92S105 were high in violaxanthin as well as lutein, whereas petals of 94C9 showed considerable levels of lutein and β-carotene. Transcriptome analysis showed that 3534 and 3833 genes were up- and down-regulated in 94C9, respectively. Among these differentially expressed genes (DEGs), many related to carotenoid accumulation were identified, including 12 carotenoid biosynthesis pathway genes, 4 transcription factor genes, and 1028 specifically expressed genes. β-carotene hydroxylase 1 (BrBCH1), BrBCH2, zeaxanthin epoxidase (BrZEP), and MYB transcription factor gene (BrGAMYB) were down-regulated in petals of 94C9 when compared with petals of 92S105, which caused β-carotene accumulation and may lead to orange petal color in 94C9. Expression levels of 20 DEGs were verified by qPCR and the results were highly consistent with those of transcriptome sequencing. Moreover, Gene Ontology (GO) enrichment analysis revealed that membrane, binding, and metabolic processes were the most significantly enriched GO terms in cellular component, molecular function, and biological process ontologies, respectively. In conclusion, our study analyzed the differences in composition and content of carotenoids between 92S105 and 94C9 and identified potential candidate genes related to carotenoid accumulation in petals, thereby creating a solid foundation for future studies on the mechanism regulating carotenoid accumulation in petals of Chinese cabbage.

Mutation of ACX1, a Jasmonic Acid Biosynthetic Enzyme, Leads to Petal Degeneration in Chinese Cabbage (Brassica campestris ssp. pekinensis)

Petal color, size, and morphology play important roles in protecting other floral organs, attracting pollinators, and facilitating sexual reproduction in plants. In a previous study, we obtained a petal degeneration mutant (pdm) from the ‘FT’ doubled haploid line of Chinese cabbage and found that the candidate gene for pdm, Bra040093, encodes the enzyme acyl-CoA oxidase1. In this study, we sought to examine the gene networks regulating petal development in pdm plants. We show that the mRNA and protein expression of Bra040093, which is involved in the jasmonic acid (JA) biosynthetic pathway, were significantly lower in the petals of pdm plants than in those of ‘FT’ plants. Similarly, the JA and methyl jasmonate (MeJA) contents of petals were significantly lower in pdm plants than in ‘FT’ plants and we found that exogenous application of these hormones to the inflorescences of pdm plants restored the ‘FT’ phenotype. Comparative analyses of the transcriptomes of ‘FT’, pdm and pdm + JA (pJA) plants revealed 10,160 differentially expressed genes (DEGs) with consistent expression tendencies in ‘FT’ vs. pdm and pJA vs. pdm comparisons. Among these DEGs, we identified 69 DEGs related to floral organ development, 11 of which are involved in petal development regulated by JA. On the basis of qRT-PCR verification, we propose regulatory pathways whereby JA may mediate petal development in the pdm mutant. We demonstrate that mutation of Bra040093 in pdm plants leads to reduced JA levels and that this in turn promotes changes in the expression of genes that are expressed in response to JA, ultimately resulting in petal degeneration. These findings thus indicate that JA is associated with petal development in Chinese cabbage. These results enhance our knowledge on the molecular mechanisms underlying petal development and lay the foundations for further elucidation of the mechanisms associated with floral organ development in Chinese cabbage.

Comparative Transcriptome Analysis between Fertile and CMS Flower Buds in Wucai (Brassica campestris L.)

Background

Wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen) is a variant of nonheading Chinese cabbage (Brassica campestris L.), which is one of the major vegetables in China. Cytoplasmic male sterility (CMS) has been used for Wucai breeding in recent years. However, the underlying molecular mechanism of Wucai CMS remains unclear. In this study, the phenotypic and cytological features of Wucai CMS were observed by anatomical analysis, and a comparative transcriptome analysis was carried out to identify genes related to male sterility using Illumina RNA sequencing technology (RNA-Seq).

Results

Microscopic observation demonstrated that tapetum development was abnormal in the CMS line, which failed to produce fertile pollen. Bioinformatics analysis detected 4430 differentially expressed genes (DEGs) between the fertile and sterile flower buds. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to better understand the functions of these DEGs. Among the DEGs, 35 genes (53 DEGS) were implicated in anther and pollen development, and 11 genes were involved in pollen cell wall formation and modification; most of these showed downregulated expression in sterile buds. In addition, several genes related to tapetum development (A6, AMS, MS1, MYB39, and TSM1) and a few genes annotated to flowering (CO, AP3, VIN3, FLC, FT, and AGL) were detected and confirmed by qRT-PCR as being expressed at the meiosis, tetrad, and uninucleate microspore stages, thus implying possible roles in specifying or determining the fate and development of the tapetum, male gametophyte and stamen. Moreover, the top four largest transcription factor families (MYB, bHLH, NAC and WRKY) were analyzed, and most showed reduced expression in sterile buds. These differentially expressed transcription factors might result in abortion of pollen development in Wucai.

Conclusion

The present comparative transcriptome analysis suggested that many key genes and transcription factors involved in anther development show reduced gene expression patterns in the CMS line, which might contribute to male sterility in Wucai. This study provides valuable information for a better understanding of CMS molecular mechanisms and functional genome studies in Wucai.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5331-4) contains supplementary material, which is available to authorized users.

Transcriptome Analysis of a Female-sterile Mutant (fsm) in Chinese Cabbage (Brassica campestris ssp. pekinensis)

Female-sterile mutants are ideal materials for studying pistil development in plants. Here, we identified a female-sterile mutant fsm in Chinese cabbage. This mutant, which exhibited stable inheritance, was derived from Chinese cabbage DH line 'FT' using a combination of isolated microspore culture and ethyl methanesulfonate mutagenesis. Compared with the wild-type line 'FT,' the fsm plants exhibited pistil abortion, and floral organs were also relatively smaller. Genetic analysis indicated that the phenotype of fsm is controlled by a single recessive nuclear gene. Morphological observations revealed that the presence of abnormal ovules in fsm likely influenced normal fertilization process, ultimately leading to female sterility. Comparative transcriptome analysis on the flower buds of 'FT' and fsm using RNA-Seq revealed a total of 1,872 differentially expressed genes (DEGs). Of these, a number of genes involved in pistil development were identified, such as PRETTY FEW SEEDS 2 (PFS2), temperature-induced lipocalin (TIL), AGAMOUS-LIKE (AGL), and HECATE (HEC). Furthermore, GO and KEGG pathway enrichment analyses of the DEGs suggested that a variety of biological processes and metabolic pathways are significantly enriched during pistil development. In addition, the expression patterns of 16 DEGs, including four pistil development-related genes and 12 floral organ development-related genes, were analyzed using qRT-PCR. A total of 31,272 single nucleotide polymorphisms were specifically detected in fsm. These results contribute to shed light on the regulatory mechanisms underlying pistil development in Chinese cabbage.

Heat Stress Regulates the Expression of Genes at Transcriptional and Post-Transcriptional Levels, Revealed by RNA-seq in Brachypodium distachyon

Heat stress greatly affects plant growth/development and influences the output of crops. With the increased occurrence of extreme high temperature, the negative influence on cereal products from heat stress becomes severer and severer. It is urgent to reveal the molecular mechanism in response to heat stress in plants. In this research, we used RNA-seq technology to identify differentially expressed genes (DEGs) in leaves of seedlings, leaves and inflorescences at heading stage of Brachypodium distachyon, one model plant of grasses. Results showed many genes in responding to heat stress. Of them, the expression level of 656 DEGs were altered in three groups of samples treated with high temperature. Gene ontology (GO) analysis showed that the highly enriched DEGs were responsible for heat stress and protein folding. According to KEGG pathway analysis, the DEGs were related mainly to photosynthesis-antenna proteins, the endoplasmic reticulum, and the spliceosome. Additionally, the expression level of 454 transcription factors belonging to 49 gene families was altered, as well as 1,973 splicing events occurred after treatment with high temperature. This research lays a foundation for characterizing the molecular mechanism of heat stress response and identifying key genes for those responses in plants. These findings also clearly show that heat stress regulates the expression of genes not only at transcriptional level, but also at post-transcriptional level.