Dataset Information

Integration of metabolome and transcriptome reveals flavonoid accumulation in the intergeneric hybrid between Brassica rapa and Raphanus sativus.

ABSTRACT: Brassica rapa and Raphanus sativus are two important edible vegetables that contain numerous nutritional ingredients. However, the agronomic traits and nutritional components of the intergeneric hybrid of B. rapa and R. sativus remain poorly understood. In this study, we used a stably inherited intergeneric hybrid of B. rapa and R. sativus as a model to study its metabolome and transcriptome profiles. Morphological and cytological analysis showed the intergeneric hybrid had the expected chromosome number and normal meiosis behavior. Moreover, the metabolome analysis showed multiple important secondary metabolites, including flavonoids and glucosinolates, were significantly upregulated in the hybrid. Furthermore, transcriptome data revealed that the expression level of the important genes involved in phenylpropanoid and flavonoid pathways was significantly upregulated in the hybrid. Ultimately, our data indicate the intergeneric hybrid will be a valuable bioengineering resource and promise to become a new-type hybrid vegetable with great medicinal value in future.

SUBMITTER: Zhang L

PROVIDER: S-EPMC6893016 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Integration of metabolome and transcriptome reveals flavonoid accumulation in the intergeneric hybrid between Brassica rapa and Raphanus sativus.

Zhang Libin L Ma Chuang C Chao Hongbo H Long Yan Y Wu Jiangsheng J Li Zaiyun Z Ge Xianhong X Xia Heng H Yin Yongtai Y Batley Jacqueline J Li Maoteng M

Scientific reports 20191204 1

Brassica rapa and Raphanus sativus are two important edible vegetables that contain numerous nutritional ingredients. However, the agronomic traits and nutritional components of the intergeneric hybrid of B. rapa and R. sativus remain poorly understood. In this study, we used a stably inherited intergeneric hybrid of B. rapa and R. sativus as a model to study its metabolome and transcriptome profiles. Morphological and cytological analysis showed the intergeneric hybrid had the expected chromoso ...[more]

PMID: 31797999

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Project description:Hybridization and polyploidization are major driving forces in plant evolution. Allopolyploids can be occasionally formed from a cross between distantly related species but often suffer from chromosome instability and infertility. xBrassicoraphanus is an intergeneric allotetraploid (AARR; 2n = 38) derived from a cross between Brassica rapa (AA; 2n = 20) and Raphanus sativus (RR; 2n = 18). xBrassicoraphanus is fertile and genetically stable, while retaining complete sets of both B. rapa and R. sativus chromosomes. Precise control of meiotic recombination is essential for the production of balanced gametes, and crossovers (COs) must occur exclusively between homologous chromosomes. Many interspecific hybrids have problems with meiotic division at early generations, in which interactions between non-homologous chromosomes often bring about aneuploidy and unbalanced gamete formation. We analyzed meiotic chromosome behaviors in pollen mother cells (PMCs) of allotetraploid and allodiploid F1 individuals of newly synthesized xBrassicoraphanus. Allotetraploid xBrassicoraphanus PMCs showed a normal diploid-like meiotic behavior. By contrast, allodiploid xBrassicoraphanus PMCs displayed abnormal segregation of chromosomes mainly due to the absence of homologous pairs. Notably, during early stages of meiosis I many of allodiploid xBrassicoraphanus chromosomes behave independently with few interactions between B. rapa and R. sativus chromosomes, forming many univalent chromosomes before segregation. Chromosomes were randomly assorted at later stages of meiosis, and tetrads with unequal numbers of chromosomes were formed at completion of meiosis. Immunolocalization of HEI10 protein mediating meiotic recombination revealed that COs were more frequent in synthetic allotetraploid xBrassicoraphanus than in allodiploid, but less than in the stabilized line. These findings suggest that structural dissimilarity between B. rapa and R. sativus chromosomes prevents non-homologous interactions between the parental chromosomes in allotetraploid xBrassicoraphanus, allowing normal diploid-like meiosis when homologous pairing partners are present. This study also suggests that CO suppression between non-homologous chromosomes is required for correct meiotic progression in newly synthesized allopolyploids, which is important for the formation of viable gametes and reproductive success in the hybrid progeny.

Project description:BACKGROUND: Sequence related amplified polymorphism (SRAP) is commonly used to construct high density genetic maps, map genes and QTL of important agronomic traits in crops and perform genetic diversity analysis without knowing sequence information. To combine next generation sequencing technology with SRAP, Illumina's Solexa sequencing was used to sequence tagged SRAP PCR products. RESULTS: Three sets of SRAP primers and three sets of tagging primers were used in 77,568 SRAP PCR reactions and the same number of tagging PCR reactions respectively to produce a pooled sample for Illumina's Solexa sequencing. After sequencing, 1.28 GB of sequence with over 13 million paired-end sequences was obtained and used to match Solexa sequences with their corresponding SRAP markers and to integrate Solexa sequences on an ultradense genetic map. The ultradense genetic bin map with 465 bins was constructed using a recombinant inbred (RI) line mapping population in B. rapa. For this ultradense genetic bin map, 9,177 SRAP markers, 1,737 integrated unique Solexa paired-end sequences and 46 SSR markers representing 10,960 independent genetic loci were assembled and 141 unique Solexa paired-end sequences were matched with their corresponding SRAP markers. The genetic map in B. rapa was aligned with the previous ultradense genetic map in B. napus through common SRAP markers in these two species. Additionally, SSR markers were used to perform alignment of the current genetic map with other five genetic maps in B. rapa and B. napus. CONCLUSION: We used SRAP to construct an ultradense genetic map with 10,960 independent genetic loci in B. rapa that is the most saturated genetic map ever constructed in this species. Using next generation sequencing, we integrated 1,878 Solexa sequences on the genetic map. These integrated sequences will be used to assemble the scaffolds in the B. rapa genome. Additionally, this genetic map may be used for gene cloning and marker development in B. rapa and B. napus.

Dataset Information

Integration of metabolome and transcriptome reveals flavonoid accumulation in the intergeneric hybrid between Brassica rapa and Raphanus sativus.

Publications

Integration of metabolome and transcriptome reveals flavonoid accumulation in the intergeneric hybrid between Brassica rapa and Raphanus sativus.

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