Morphology, carbohydrate composition and vernalization response in a genetically diverse collection of Asian and European turnips (Brassica rapa subsp. rapa)

Integrated metabolomic and transcriptomic analyses provide insights into regulation mechanisms during bulbous stem development in the Chinese medicinal herb plant, Stephania kwangsiensis

BACKGROUND

Stephania kwangsiensis Lo (Menispermaceae) is a well-known Chinese herbal medicine, and its bulbous stems are used medicinally. The storage stem of S. kwangsiensis originated from the hypocotyls. To date, there are no reports on the growth and development of S. kwangsiensis storage stems.

RESULTS

The bulbous stem of S. kwangsiensis, the starch diameter was larger at the stable expanding stage (S3T) than at the unexpanded stage (S1T) or the rapidly expanding stage (S2T) at the three different time points. We used ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and Illumina sequencing to identify key genes involved in bulbous stem development. A large number of differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) were identified. Based on the differential expression profiles of the metabolites, alkaloids, lipids, and phenolic acids were the top three differentially expressed classes. Compared with S2T, significant changes in plant signal transduction and isoquinoline alkaloid biosynthesis pathways occurred at both the transcriptional and metabolic levels in S1T. In S2T compared with S3T, several metabolites involved in tyrosine metabolism were decreased. Temporal analysis of S1T to S3T indicated the downregulation of phenylpropanoid biosynthesis, including lignin biosynthesis. The annotation of key pathways showed an up-down trend for genes and metabolites involved in isoquinoline alkaloid biosynthesis, whereas phenylpropanoid biosynthesis was not completely consistent.

CONCLUSIONS

Downregulation of the phenylpropanoid biosynthesis pathway may be the result of carbon flow into alkaloid synthesis and storage of lipids and starch during the development of S. kwangsiensis bulbous stems. A decrease in the number of metabolites involved in tyrosine metabolism may also lead to a decrease in the upstream substrates of phenylpropane biosynthesis. Downregulation of lignin synthesis during phenylpropanoid biosynthesis may loosen restrictions on bulbous stem expansion. This study provides the first comprehensive analysis of the metabolome and transcriptome profiles of S. kwangsiensis bulbous stems. These data provide guidance for the cultivation, breeding, and harvesting of S. kwangsiensis.

Differences in pseudogene evolution contributed to the contrasting flavors of turnip and Chiifu, two Brassica rapa subspecies

Pseudogenes are important resources for investigation of genome evolution and genomic diversity because they are nonfunctional but have regulatory effects that influence plant adaptation and diversification. However, few systematic comparative analyses of pseudogenes in closely related species have been conducted. Here, we present a turnip (Brassica rapa ssp. rapa) genome sequence and characterize pseudogenes among diploid Brassica species/subspecies. The results revealed that the number of pseudogenes was greatest in Brassica oleracea (CC genome), followed by B. rapa (AA genome) and then Brassica nigra (BB genome), implying that pseudogene differences emerged after species differentiation. In Brassica AA genomes, pseudogenes were distributed asymmetrically on chromosomes because of numerous chromosomal insertions/rearrangements, which contributed to the diversity among subspecies. Pseudogene differences among subspecies were reflected in the flavor-related glucosinolate (GSL) pathway. Specifically, turnip had the highest content of pungent substances, probably because of expansion of the methylthioalkylmalate synthase-encoding gene family in turnips; these genes were converted into pseudogenes in B. rapa ssp. pekinensis (Chiifu). RNA interference-based silencing of the gene encoding 2-oxoglutarate-dependent dioxygenase 2, which is also associated with flavor and anticancer substances in the GSL pathway, resulted in increased abundance of anticancer compounds and decreased pungency of turnip and Chiifu. These findings revealed that pseudogene differences between turnip and Chiifu influenced the evolution of flavor-associated GSL metabolism-related genes, ultimately resulting in the different flavors of turnip and Chiifu.

The clonal growth in Aconitum carmichaelii Debx

Aconitum carmichaelii Debx. is used as traditional herbal medicine in China, Japan, and other Asian countries. A. carmichaelii has two modes for reproduction: sexual reproduction with seed and vegetative reproduction with vegetative propagules. The vegetative propagules are belowground and invisible. To date, only a handful of studies for the clonal growth are available. In this study, we investigated the clonal growth by anatomical and morphological changes. Results revealed that the axillary bud appeared on the rhizome. Furthermore, the axillary meristem in the axillary bud differentiated a bud upwards and an adventitious root (AR) downwards. The AR expanded to a tuberous root in order to provide the bud nutrients for the new plant. The AR branched LRs. In addition, some lateral roots (LRs) on the AR also swelled. Both the AR and LR were found to follow a similar pattern of development. However, high lignification in the stele region of LRs inhibited further expansion. AR development was attributed to activities of the cambium and meristem cell, starch accumulation, stele lignification, and a polyarch stele. Our study not only provides a better understanding of clonal growth but also provides clues to explore the regulatory mechanisms underlying AR development in A. carmichaelii.

Measurement of reactive oxygen species production by luminol-based assay in Nicotiana benthamiana, Arabidopsis thaliana and Brassica rapa ssp. rapa

Reactive oxygen species (ROS) are critical for plant biological processes. As signaling molecules, ROS regulate plant growth and development through cell expansion, elongation, and programmed cell death. Furthermore, ROS production is induced by microbe-associated molecular patterns (MAMPs) treatment and biotic stresses, and contributes to plant resistance to pathogens. Thus, MAMP-induced ROS production has been an indicator for plant early immune responses or stress responses. One of widely used methods for the measurement is a luminol-based assay to measure extracellular ROS production with a bacterial flagellin epitope (flg22) as a MAMP elicitor. Nicotiana benthamiana is susceptible to a wide variety of plant pathogenic agents and therefore commonly used for ROS measurements. On the other hand, Arabidopsis thaliana, many of genetical lines of which are available, is also conducted to ROS measurements. Tests in an asterid N. benthamiana and a rosid A. thaliana can reveal conserved molecular mechanisms in ROS production. However, the small size of A. thaliana leaves requires many seedlings for experiments. This study examined flg22-induced ROS production in another member of the Brassicaceae family, Brassica rapa ssp. rapa (turnip), which has large and flat leaves. Our experiments indicated that 10 nM and 100 nM flg22 treatments induced high ROS levels in turnip. Turnip tended to have a lower standard deviation in multiple concentrations of flg22 treatment. Therefore, these results suggested that turnip can be a good material from the rosid clade for ROS measurement.

Transposable element insertion: a hidden major source of domesticated phenotypic variation in Brassica rapa

Transposable element (TE) is prevalent in plant genomes. However, studies on their impact on phenotypic evolution in crop plants are relatively rare, because systematically identifying TE insertions within a species has been a challenge. Here, we present a novel approach for uncovering TE insertion polymorphisms (TIPs) using pan-genome analysis combined with population-scale resequencing, and we adopt this pipeline to retrieve TIPs in a Brassica rapa germplasm collection. We found that 23% of genes within the reference Chiifu-401-42 genome harbored TIPs. TIPs tended to have large transcriptional effects, including modifying gene expression levels and altering gene structure by introducing new introns. Among 524 diverse accessions, TIPs broadly influenced genes related to traits and acted a crucial role in the domestication of B. rapa morphotypes. As examples, four specific TIP-containing genes were found to be candidates that potentially involved in various climatic conditions, promoting the formation of diverse vegetable crops in B. rapa. Our work reveals the hitherto hidden TIPs implicated in agronomic traits and highlights their widespread utility in studies of crop domestication.

Gibberellin inhibition of taproot formation by modulation of DELLA-NAC complex activity in turnip (Brassica rapa var. rapa)

Turnip is a member of the Brassica rapa species and is characterized by a swollen taproot that develops from the hypocotyl and part of the root. Gibberellins (GAs) are plant growth regulators involved in promoting cell elongation and play important roles in many aspects of plant growth and development. Interestingly, exogenous application of GA₃ was found to significantly inhibit taproot formation in turnip. Moreover, endogenous GA contents decreased during the early developmental stages of taproot formation, suggesting that GA plays a negative role in taproot formation. We examined the anatomical structure of the taproot and found that lignification of the xylem cell wall was enhanced after treatment with GA₃. Yeast two-hybrid assays suggested the occurrence of protein interactions between DELLAs and NACs in turnip. We also found that the expression of NAC-targeted genes involved in lignification of the secondary cell wall was significantly upregulated upon GA₃ treatment. Taken together, these results supported the hypothesis that GA induced DELLA proteins degradation to release NAC proteins and induced xylem lignification, therefore inhibiting taproot formation, providing new insight into the molecular mechanism underlying turnip taproot formation.

QTL Mapping and Candidate Gene Identification of Swollen Root Formation in Turnip

The swollen root is an important agronomic trait and is a determinant of yield for turnips, which are cultivated as both vegetables and fodder. However, the genetic mechanism of swollen root formation is poorly understood. In this study, we analyzed the F₂ and BC₁P₂ populations derived from a cross between “10601” (European turnip with swollen root, Brassica rapa ssp. rapifera, AA, 2n = 2× = 20) and “10603” (Chinese cabbage with normal root, Brassica rapa ssp. pekinensis, AA, 2n = 2× = 20), and suggested that the swollen root is a quantitative trait. Two major quantitative trait loci (QTLs), FR1.1 (Fleshy root 1.1) and FR7.1 (Fleshy root 7.1), were identified by QTL-seq analysis and further confirmed by QTL mapping in F₂ and BC₁P₂ populations. The QTL FR1.1 with a likelihood of odd (LOD) of 7.01 explained 17.2% of the total phenotypic variations for root diameter and the QTL FR7.1 explained 23.0% (LOD = 9.38) and 31.0% (LOD = 13.27) of the total phenotypic variations in root diameter and root weight, respectively. After a recombinant screening, the major QTL FR7.1 was further narrowed down to a 220 kb region containing 47 putative genes. A candidate gene, Bra003652, which is a homolog of AT1G78240 that plays an essential role in cell adhesion and disorganized tumor-like formation in Arabidopsis thaliana, was identified in this region. In addition, expression and parental allele analysis supported that Bra003652 was a possible candidate gene of QTL FR7.1 for swollen root formation in turnip. Our research may provide new insight into the molecular mechanism of swollen root formation in root crops.

Single-Molecule Real-Time Transcript Sequencing of Turnips Unveiling the Complexity of the Turnip Transcriptome

To generate the full-length transcriptome of Xinjiang green and purple turnips, Brassica rapa var. Rapa, using single-molecule real-time (SMRT) sequencing. The samples of two varieties of Brassica rapa var. Rapa at five developmental stages were collected and combined to perform SMRT sequencing. Meanwhile, next generation sequencing was performed to correct SMRT sequencing data. A series of analyses were performed to investigate the transcript structure. Finally, the obtained transcripts were mapped to the genome of Brassica rapa ssp. pekinesis Chiifu to identify potential novel transcripts. For green turnip (F01), a total of 19.54 Gb clean data were obtained from 8 cells. The number of reads of insert (ROI) and full-length non-chimeric (FLNC) reads were 510,137 and 267,666. In addition, 82,640 consensus isoforms were obtained in the isoform sequences clustering, of which 69,480 were high-quality, and 13,160 low-quality sequences were corrected using Illumina RNA seq data. For purple turnip (F02), there were 20.41 Gb clean data, 552,829 ROIs, and 274,915 FLNC sequences. A total of 93,775 consensus isoforms were obtained, of which 78,798 were high-quality, and the 14,977 low-quality sequences were corrected. Following the removal of redundant sequences, there were 46,516 and 49,429 non-redundant transcripts for F01 and F02, respectively; 7,774 and 9,385 alternative splicing events were predicted for F01 and F02; 63,890 simple sequence repeats, 59,460 complete coding sequences, and 535 long-non coding RNAs were predicted. Moreover, 5,194 and 5,369 novel transcripts were identified by mapping to Brassica rapa ssp. pekinesis Chiifu. The obtained transcriptome data may improve turnip genome annotation and facilitate further study of the Brassica rapa var. Rapa genome and transcriptome.

Glucosinolate variability between turnip organs during development

Turnip (Brassica rapa spp. rapa) is an important vegetable species, with a unique physiology. Several plant parts, including both the turnip tubers and leaves, are important for human consumption. During the development of turnip plants, the leaves function as metabolic source tissues, while the tuber first functions as a sink, while later the tuber turns into a source for development of flowers and seeds. In the present study, chemical changes were determined for two genotypes with different genetic background, and included seedling, young leaves, mature leaves, tuber surface, tuber core, stalk, flower and seed tissues, at seven different time points during plant development. As a basis for understanding changes in glucosinolates during plant development, the profile of glucosinolates was analysed using liquid chromatography (LC) coupled to mass spectrometry (MS). This analysis was complemented by a gene expression analysis, focussed on GLS biosynthesis, which could explain part of the observed variation, pointing to important roles of specific gene orthologues for defining the chemical differences. Substantial differences in glucosinolate profiles were observed between above-ground tissues and turnip tuber, reflecting the differences in physiological role. In addition, differences between the two genotypes and between tissues that were harvested early or late during the plant lifecycle. The importance of the observed differences in glucosinolate profile for the ecophysiology of the turnip and for breeding turnips with optimal chemical profiles is discussed.

What makes turnips: anatomy, physiology and transcriptome during early stages of its hypocotyl-tuber development

Brassica species are characterized by their tremendous intraspecific diversity, exemplified by leafy vegetables, oilseeds, and crops with enlarged inflorescences or above ground storage organs. In contrast to potato tubers that are edible storage organs storing energy as starch and are the vegetative propagation modules, the storage organs of turnips, grown from true seed, are swollen hypocotyls with varying degrees of root and stem that mainly store glucose and fructose. To highlight their anatomical origin, we use the term "hypocotyl-tuber" for these turnip vegetative storage organs. We combined cytological, physiological, genetic and transcriptomic approaches, aiming to identify the initial stages, molecular pathways and regulatory genes for hypocotyl-tuber induction in turnips (B. rapa subsp. rapa). We first studied the development of the hypocotyl zone of turnip and Pak choi and found that 16 days after sowing (DAS) morphological changes occurred in the xylem which indicated the early tuberization stage. Tissue culture experiments showed a clear effect of auxin on hypocotyl-tuber growth. Differentially expressed genes between 1 and 6 weeks after sowing in turnip hypocotyls, located in genomic regions involved in tuber initiation and/or tuber growth defined by QTL and selective sweeps for tuber formation, were identified as candidate genes that were studied in more detail for their role in hypocotyl-tuber formation. This included a Bra-FLOR1 paralogue with increased expression 16 DAS, when the hypocotyl starts swelling, suggesting dual roles for duplicated flowering time genes in flowering and hypocotyl-tuber induction. Bra-CYP735A2 was identified for its possible role in tuber growth via trans-zeatin. Weigthed Co-expression Network Analysis (WGCNA) identified 59 modules of co-expressed genes. Bra-FLOR1 and Bra-CYP735A2 were grouped in a module that included several genes involved in carbohydrate transport and metabolism, cell-wall growth, auxin regulation and secondary metabolism that serve as starting points to illuminate the transcriptional regulation of hypocotyl-tuber formation and development.

What makes turnips: anatomy, physiology and transcriptome during early stages of its hypocotyl-tuber development

Brassica species are characterized by their tremendous intraspecific diversity, exemplified by leafy vegetables, oilseeds, and crops with enlarged inflorescences or above ground storage organs. In contrast to potato tubers that are edible storage organs storing energy as starch and are the vegetative propagation modules, the storage organs of turnips, grown from true seed, are swollen hypocotyls with varying degrees of root and stem that mainly store glucose and fructose. To highlight their anatomical origin, we use the term "hypocotyl-tuber" for these turnip vegetative storage organs. We combined cytological, physiological, genetic and transcriptomic approaches, aiming to identify the initial stages, molecular pathways and regulatory genes for hypocotyl-tuber induction in turnips (B. rapa subsp. rapa). We first studied the development of the hypocotyl zone of turnip and Pak choi and found that 16 days after sowing (DAS) morphological changes occurred in the xylem which indicated the early tuberization stage. Tissue culture experiments showed a clear effect of auxin on hypocotyl-tuber growth. Differentially expressed genes between 1 and 6 weeks after sowing in turnip hypocotyls, located in genomic regions involved in tuber initiation and/or tuber growth defined by QTL and selective sweeps for tuber formation, were identified as candidate genes that were studied in more detail for their role in hypocotyl-tuber formation. This included a Bra-FLOR1 paralogue with increased expression 16 DAS, when the hypocotyl starts swelling, suggesting dual roles for duplicated flowering time genes in flowering and hypocotyl-tuber induction. Bra-CYP735A2 was identified for its possible role in tuber growth via trans-zeatin. Weigthed Co-expression Network Analysis (WGCNA) identified 59 modules of co-expressed genes. Bra-FLOR1 and Bra-CYP735A2 were grouped in a module that included several genes involved in carbohydrate transport and metabolism, cell-wall growth, auxin regulation and secondary metabolism that serve as starting points to illuminate the transcriptional regulation of hypocotyl-tuber formation and development.

Plant Vascular Tissues-Connecting Tissue Comes in All Shapes

For centuries, humans have grown and used structures based on vascular tissues in plants. One could imagine that life would have developed differently without wood as a resource for building material, paper, heating energy, or fuel and without edible tubers as a food source. In this review, we will summarise the status of research on Arabidopsis thaliana vascular development and subsequently focus on how this knowledge has been applied and expanded in research on the wood of trees and storage organs of crop plants. We will conclude with an outlook on interesting open questions and exciting new research opportunities in this growing and important field.

Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea

Brassica species, including crops such as cabbage, turnip and oilseed, display enormous phenotypic variation. Brassica genomes have all undergone a whole-genome triplication (WGT) event with unknown effects on phenotype diversification. We resequenced 199 Brassica rapa and 119 Brassica oleracea accessions representing various morphotypes and identified signals of selection at the mesohexaploid subgenome level. For cabbage morphotypes with their typical leaf-heading trait, we identified four subgenome loci that show signs of parallel selection among subgenomes within B. rapa, as well as four such loci within B. oleracea. Fifteen subgenome loci are under selection and are shared by these two species. We also detected strong subgenome parallel selection linked to the domestication of the tuberous morphotypes, turnip (B. rapa) and kohlrabi (B. oleracea). Overall, we demonstrated that the mesohexaploidization of the two Brassica genomes contributed to their diversification into heading and tuber-forming morphotypes through convergent subgenome parallel selection of paralogous genes.

SNP diversity within and among Brassica rapa accessions reveals no geographic differentiation

Genetic diversity was studied in a collection of 61 accessions of Brassica rapa, which were mostly oil-type turnip rapes but also included two oil-type subsp. dichotoma and five subsp. trilocularis accessions, as well as three leaf-type subspecies (subsp. japonica, pekinensis, and chinensis) and five turnip cultivars (subsp. rapa). Two-hundred and nine SNP markers, which had been discovered by amplicon resequencing, were used to genotype 893 plants from the B. rapa collection using Illumina BeadXpress. There was great variation in the diversity indices between accessions. With STRUCTURE analysis, the plant collection could be divided into three groups that seemed to correspond to morphotype and flowering habit but not to geography. According to AMOVA analysis, 65% of the variation was due to variation within accessions, 25% among accessions, and 10% among groups. A smaller subset of the plant collection, 12 accessions, was also studied with 5727 GBS-SNPs. Diversity indices obtained with GBS-SNPs correlated well with those obtained with Illumina BeadXpress SNPs. The developed SNP markers have already been used and will be used in future plant breeding programs as well as in mapping and diversity studies.