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24 pages, 18506 KiB

Open AccessArticle

Morpho-Physiochemical Indices and Transcriptome Analysis Reveal the Role of Glucosinolate and Erucic Acid in Response to Drought Stress during Seed Germination of Rapeseed

by Xueying Ai, Ali Mahmoud El-Badri, Maria Batool, Hongxiang Lou, Gengdong Gao, Chenyang Bai, Zongkai Wang, Chunji Jiang, Xinhua Zhao, Bo Wang, Jie Kuai, Zhenghua Xu, Jing Wang, Graham John King, Haiqiu Yu, Guangsheng Zhou and Tingdong Fu

Int. J. Mol. Sci. 2024, 25(6), 3308; https://doi.org/10.3390/ijms25063308 - 14 Mar 2024

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Abstract

The global expansion of rapeseed seed quality has been focused on maintaining glucosinolate (GSL) and erucic acid (EA) contents. However, the influence of seed GSL and EA contents on the germination process under drought stress remains poorly understood. Herein, 114 rapeseed accessions were [...] Read more.

The global expansion of rapeseed seed quality has been focused on maintaining glucosinolate (GSL) and erucic acid (EA) contents. However, the influence of seed GSL and EA contents on the germination process under drought stress remains poorly understood. Herein, 114 rapeseed accessions were divided into four groups based on GSL and EA contents to investigate their performance during seed imbibition under drought stress. Our results revealed significant variations in seed germination-related traits, particularly with higher GSL and EA, which exhibited higher germination % (G%) and lower mean germination time (MGT) under drought stress conditions. Moreover, osmoregulation, enzymatic system and hormonal regulation were improved in high GSL and high EA (HGHE) versus low GSL and low EA (LGLE) seeds, indicating the essential protective role of GSL and EA during the germination process in response to drought stress. The transcriptional regulation mechanism for coordinating GSL–EA-related pathways in response to drought stress during seed imbibition was found to involve the differential expression of sugar metabolism-, antioxidant-, and hormone-related genes with higher enrichment in HGHE compared to LGLE seeds. GO enrichment analysis showed higher variations in transcription regulator activity and DNA-binding transcription factors, as well as ATP and microtubule motor activity in GSL–EA-related pathways. Furthermore, KEGG analysis identified cellular processes, environmental information processing, and metabolism categories, with varied gene participation between GSL, EA and GSL–EA-related pathways. For further clarification, QY7 (LGLE) seeds were primed with different concentrations of GSL and EA under drought stress conditions. The results showed that 200 μmol/L of GSL and 400 μmol/L of EA significantly improved G%, MGT, and seedling fresh weight, besides regulating stress and fatty acid responsive genes during the seed germination process under drought stress conditions. Conclusively, exogenous application of GSL and EA is considered a promising method for enhancing the drought tolerance of LGLE seeds. Furthermore, the current investigation could provide a theoretical basis of GSL and EA roles and their underlying mechanisms in stress tolerance during the germination process. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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24 pages, 15683 KiB

Open AccessArticle

Two-Component System Genes in Brassica napus: Identification, Analysis, and Expression Patterns in Response to Abiotic and Biotic Stresses

by Hongfang Liu, Nian Liu, Chen Peng, Jiaquan Huang, Wei Hua, Zhengwei Fu and Jing Liu

Int. J. Mol. Sci. 2023, 24(24), 17308; https://doi.org/10.3390/ijms242417308 - 09 Dec 2023

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Abstract

The two-component system (TCS), consisting of histidine kinases (HKs), histidine phosphotransfer proteins (HPs) and response regulators (RRs) in eukaryotes, plays pivotal roles in regulating plant growth, development, and responses to environment stimuli. However, the TCS genes were poorly characterized in rapeseed, which is [...] Read more.

The two-component system (TCS), consisting of histidine kinases (HKs), histidine phosphotransfer proteins (HPs) and response regulators (RRs) in eukaryotes, plays pivotal roles in regulating plant growth, development, and responses to environment stimuli. However, the TCS genes were poorly characterized in rapeseed, which is an important tetraploid crop in Brassicaceae. In this work, a total of 182 BnaTCS genes were identified, including 43 HKs, 16 HPs, and 123 RRs, which was more than that in other crops due to segmental duplications during the process of polyploidization. It was significantly different in genetic diversity between the three subfamilies, and some members showed substantial genetic differentiation among the three rapeseed ecotypes. Several hormone- and stress-responsive cis-elements were identified in the putative promoter regions of BnaTCS genes. Furthermore, the expression of BnaTCS genes under abiotic stresses, exogenous phytohormone, and biotic stresses was analyzed, and numerous candidate stress-responsive genes were screened out. Meanwhile, using a natural population with 505 B. napus accessions, we explored the genetic effects of BnaTCS genes on salt tolerance by association mapping analysis and detected some significant association SNPs/genes. The result will help to further understand the functions of TCS genes in the developmental and stress tolerance improvement in B. napus. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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17 pages, 3961 KiB

Open AccessArticle

Transcriptome Shock in Developing Embryos of a Brassica napus and Brassica rapa Hybrid

by Weixian Zhou, Libin Zhang, Jianjie He, Wang Chen, Feifan Zhao, Chunhua Fu and Maoteng Li

Int. J. Mol. Sci. 2023, 24(22), 16238; https://doi.org/10.3390/ijms242216238 - 12 Nov 2023

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Abstract

Interspecific crosses that fuse the genomes of two different species may result in overall gene expression changes in the hybrid progeny, called ‘transcriptome shock’. To better understand the expression pattern after genome merging during the early stages of allopolyploid formation, we performed RNA [...] Read more.

Interspecific crosses that fuse the genomes of two different species may result in overall gene expression changes in the hybrid progeny, called ‘transcriptome shock’. To better understand the expression pattern after genome merging during the early stages of allopolyploid formation, we performed RNA sequencing analysis on developing embryos of Brassica rapa, B. napus, and their synthesized allotriploid hybrids. Here, we show that the transcriptome shock occurs in the developing seeds of the hybrids. Of the homoeologous gene pairs, 17.1% exhibit expression bias, with an overall expression bias toward B. rapa. The expression level dominance also biases toward B. rapa, mainly induced by the expression change in homoeologous genes from B. napus. Functional enrichment analysis revealed significant differences in differentially expressed genes (DEGs) related to photosynthesis, hormone synthesis, and other pathways. Further study showed that significant changes in the expression levels of the key transcription factors (TFs) could regulate the overall interaction network in the developing embryo, which might be an essential cause of phenotype change. In conclusion, the present results have revealed the global changes in gene expression patterns in developing seeds of the hybrid between B. rapa and B. napus, and provided novel insights into the occurrence of transcriptome shock for harnessing heterosis. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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11 pages, 1587 KiB

Open AccessArticle

Exploration into Natural Variation Genes Associated with Determinate and Capitulum-like Inflorescence in Brassica napus

by Wei Wan, Haifei Zhao, Kunjiang Yu, Yang Xiang, Wendong Dai, Caifu Du and Entang Tian

Int. J. Mol. Sci. 2023, 24(16), 12902; https://doi.org/10.3390/ijms241612902 - 17 Aug 2023

Cited by 1 | Viewed by 799

Abstract

Brassica napus is a globally important vegetable and oil crop. The research is meaningful for the yield and plant architecture of B. napus. In this study, one natural mutant line with determinate and capitulum-like inflorescence was chosen for further study. Genetic analysis [...] Read more.

Brassica napus is a globally important vegetable and oil crop. The research is meaningful for the yield and plant architecture of B. napus. In this study, one natural mutant line with determinate and capitulum-like inflorescence was chosen for further study. Genetic analysis indicated that the segregation patterns of inflorescences in the F₂ populations supported a digenic inheritance model, which was further approved via the BSA-Seq technique. The BSA-Seq method detected two QTL regions on C02 (14.27–18.41 Mb) and C06 (32.98–33.68 Mb) for the genetic control of determinate inflorescences in MT plants. In addition, the expression profile in MT compared with WT was analyzed, and a total of 133 candidate genes for regulating the flower development (75 genes, 56.4%), shoot meristem development (29 genes, 21.8%), and inflorescence meristem development (13 genes, 9.8%) were identified. Then one joint analysis combing BSA-Seq and RNA-Seq identified two candidate genes of BnaTFL1 and BnaAP1 for regulating the MT phenotype. Furthermore, the potential utilization of the MT plants was also discussed. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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18 pages, 5311 KiB

Open AccessArticle

Transcriptomic Profiling Highlights the ABA Response Role of BnSIP1-1 in Brassica napus

by Chi Zhang, Xiaoqing Yao, Yan Zhang, Shengbo Zhao, Jinghui Liu, Gang Wu, Xiaohong Yan and Junling Luo

Int. J. Mol. Sci. 2023, 24(13), 10641; https://doi.org/10.3390/ijms241310641 - 26 Jun 2023

Cited by 1 | Viewed by 1031

Abstract

BnSIP1-1 is the first identified SIP1 (6b Interacting Protein1) subfamily gene of the trihelix transcription factor family from Brassica napus (B. napus). We previously used a reverse genetic method to reveal its abiotic stress response function in endowing plants resistance to drought and salinity, [...] Read more.

BnSIP1-1 is the first identified SIP1 (6b Interacting Protein1) subfamily gene of the trihelix transcription factor family from Brassica napus (B. napus). We previously used a reverse genetic method to reveal its abiotic stress response function in endowing plants resistance to drought and salinity, as well as ABA (Abscisic acid). However, the molecular mechanisms of BnSIP1-1 are unclear. In this study, the global transcriptome files of BnSIP1-1-overexpressing transgenic and wildtype B. napus seedlings under ABA treatment were constructed using RNA-seq. A total of 1823 and 5512 DEGs (Differentially Expressed Genes) were identified in OE vs. WT and OE_ABA vs. WT_ABA comparison groups, which included 751 and 2567 up-regulated DEGs, and 1072 and 2945 down-regulated DEGs, separately. The impact of overexpressed BnSIP1-1 on plants was amplified by ABA, indicating BnSIP1-1 was an ABA-conditioned responsive gene. More interestingly, we found the reasons for BnSIP1-1 increasing plants’ insensitivity to ABA were not by regulating ABA synthesis and catabolism, but by manipulating ABA transportation, ABA signal perception and transduction, inositol phosphate metabolism, as well as endomembrane trafficking, indirectly suggesting this gene may play roles upstream of the core ABA response pathway. Our results provided new insights into improving the knowledge about the function of BnSIP1-1 and the ABA signaling mechanism in B. napus. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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17 pages, 1868 KiB

Open AccessArticle

Mapping and Identifying Candidate Genes Enabling Cadmium Accumulation in Brassica napus Revealed by Combined BSA-Seq and RNA-Seq Analysis

by Huadong Wang, Jiajia Liu, Juan Huang, Qing Xiao, Alice Hayward, Fuyan Li, Yingying Gong, Qian Liu, Miao Ma, Donghui Fu and Meili Xiao

Int. J. Mol. Sci. 2023, 24(12), 10163; https://doi.org/10.3390/ijms241210163 - 15 Jun 2023

Cited by 1 | Viewed by 1325

Abstract

Rapeseed has the ability to absorb cadmium in the roots and transfer it to aboveground organs, making it a potential species for remediating soil cadmium (Cd) pollution. However, the genetic and molecular mechanisms underlying this phenomenon in rapeseed are still unclear. In this [...] Read more.

Rapeseed has the ability to absorb cadmium in the roots and transfer it to aboveground organs, making it a potential species for remediating soil cadmium (Cd) pollution. However, the genetic and molecular mechanisms underlying this phenomenon in rapeseed are still unclear. In this study, a ‘cadmium-enriched’ parent, ‘P1’, with high cadmium transport and accumulation in the shoot (cadmium root: shoot transfer ratio of 153.75%), and a low-cadmium-accumulation parent, ‘P2’, (with a cadmium transfer ratio of 48.72%) were assessed for Cd concentration using inductively coupled plasma mass spectrometry (ICP-MS). An F₂ genetic population was constructed by crossing ‘P1’ with ‘P2’ to map QTL intervals and underlying genes associated with cadmium enrichment. Fifty extremely cadmium-enriched F₂ individuals and fifty extremely low-accumulation F₂ individuals were selected based on cadmium content and cadmium transfer ratio and used for bulk segregant analysis (BSA) in combination with whole genome resequencing. This generated a total of 3,660,999 SNPs and 787,034 InDels between these two segregated phenotypic groups. Based on the delta SNP index (the difference in SNP frequency between the two bulked pools), nine candidate Quantitative trait loci (QTLs) from five chromosomes were identified, and four intervals were validated. RNA sequencing of ‘P1’ and ‘P2’ in response to cadmium was also performed and identified 3502 differentially expressed genes (DEGs) between ‘P1’ and ‘P2’ under Cd treatment. Finally, 32 candidate DEGs were identified within 9 significant mapping intervals, including genes encoding a glutathione S-transferase (GST), a molecular chaperone (DnaJ), and a phosphoglycerate kinase (PGK), among others. These genes are strong candidates for playing an active role in helping rapeseed cope with cadmium stress. Therefore, this study not only sheds new light on the molecular mechanisms of Cd accumulation in rapeseed but could also be useful for rapeseed breeding programs targeting this trait. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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16 pages, 5798 KiB

Open AccessArticle

Cloning and Functional Characterization of Cold-Inducible MYB-like 17 Transcription Factor in Rapeseed (Brassica napus L.)

by Dan Luo, Ali Raza, Yong Cheng, Xiling Zou and Yan Lv

Int. J. Mol. Sci. 2023, 24(11), 9514; https://doi.org/10.3390/ijms24119514 - 30 May 2023

Cited by 2 | Viewed by 1205

Abstract

Rapeseed (Brassica napus L.) is an important crop for edible oil, vegetables, and biofuel. Rapeseed growth and development require a minimum temperature of ~1–3 °C. Notably, frost damage occurs during overwintering, posing a serious threat to the productivity and yield of rapeseed. [...] Read more.

Rapeseed (Brassica napus L.) is an important crop for edible oil, vegetables, and biofuel. Rapeseed growth and development require a minimum temperature of ~1–3 °C. Notably, frost damage occurs during overwintering, posing a serious threat to the productivity and yield of rapeseed. MYB proteins are important transcription factors (TFs) in plants, and have been proven to be involved in the regulation of stress responses. However, the roles of the MYB TFs in rapeseed under cold stress conditions are yet to be fully elucidated. To better understand the molecular mechanisms of one MYB-like 17 gene, BnaMYBL17, in response to low temperature, the present study found that the transcript level of BnaMYBL17 is induced by cold stress. To characterize the gene’s function, the 591 bp coding sequence (CDS) from rapeseed was isolated and stably transformed into rapeseed. The further functional analysis revealed significant sensitivity in BnaMYBL17 overexpression lines (BnaMYBL17-OE) after freezing stress, suggesting its involvement in freezing response. A total of 14,298 differentially expressed genes relative to freezing response were found based on transcriptomic analysis of BnaMYBL17-OE. Overall, 1321 candidate target genes were identified based on differential expression, including Phospholipases C1 (PLC1), FCS-like zinc finger 8 (FLZ8), and Kinase on the inside (KOIN). The qPCR results confirmed that the expression levels of certain genes showed fold changes ranging from two to six when compared between BnaMYBL17-OE and WT lines after exposure to freezing stress. Furthermore, verification indicated that BnaMYBL17 affects the promoter of BnaPLC1, BnaFLZ8, and BnaKOIN genes. In summary, the results suggest that BnaMYBL17 acts as a transcriptional repressor in regulating certain genes related to growth and development during freezing stress. These findings provide valuable genetic and theoretical targets for molecular breeding to enhance freezing tolerance in rapeseed. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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15 pages, 5051 KiB

Open AccessArticle

QTL Mapping and Transcriptome Analysis Reveal Candidate Genes Regulating Seed Color in Brassica napus

by Fangying Liu, Hao Chen, Liu Yang, Liang You, Jianye Ju, Shujie Yang, Xiaolin Wang and Zhongsong Liu

Int. J. Mol. Sci. 2023, 24(11), 9262; https://doi.org/10.3390/ijms24119262 - 25 May 2023

Cited by 1 | Viewed by 1244

Abstract

Yellow seeds are desirable in rapeseed breeding because of their higher oil content and better nutritional quality than black seeds. However, the underlying genes and formation mechanism of yellow seeds remain unclear. Here, a novel yellow-seeded rapeseed line (Huangaizao, HAZ) was crossed with [...] Read more.

Yellow seeds are desirable in rapeseed breeding because of their higher oil content and better nutritional quality than black seeds. However, the underlying genes and formation mechanism of yellow seeds remain unclear. Here, a novel yellow-seeded rapeseed line (Huangaizao, HAZ) was crossed with a black-seeded rapeseed line (Zhongshuang11, ZS11) to construct a mapping population of 196 F₂ individuals, based on which, a high-density genetic linkage map was constructed. This map, comprising 4174 bin markers, was 1618.33 cM in length and had an average distance of 0.39 cM between its adjacent markers. To assess the seed color of the F₂ population, three methods (imaging, spectrophotometry, and visual scoring) were used and a common major quantitative trait locus (QTL) on chromosome A09, explaining 10.91–21.83% of the phenotypic variance, was detected. Another minor QTL, accounting for 6.19–6.69% of the phenotypic variance, was detected on chromosome C03, only by means of imaging and spectrophotometry. Furthermore, a dynamic analysis of the differential expressions between the parental lines showed that flavonoid biosynthesis-related genes were down-regulated in the yellow seed coats at 25 and 35 days after flowering. A coexpression network between the differentially expressed genes identified 17 candidate genes for the QTL intervals, including a flavonoid structure gene, novel4557 (BnaC03.TT4), and two transcription factor genes, namely, BnaA09G0616800ZS (BnaA09.NFYA8) and BnaC03G0060200ZS (BnaC03.NAC083), that may regulate flavonoid biosynthesis. Our study lays a foundation for further identifying the genes responsible for and understanding the regulatory mechanism of yellow seed formation in Brassica napus. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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15 pages, 4774 KiB

Open AccessArticle

Effects of Exogenous Ergothioneine on Brassica rapa Clubroot Development Revealed by Transcriptomic Analysis

by Yuting Zhang, Guizhu Cao, Xiaonan Li and Zhongyun Piao

Int. J. Mol. Sci. 2023, 24(7), 6380; https://doi.org/10.3390/ijms24076380 - 28 Mar 2023

Cited by 1 | Viewed by 1183

Abstract

Clubroot disease is a soil-borne disease caused by Plasmodiophora brassicae that leads to a serious yield reduction in cruciferous plants. In this study, ergothioneine (EGT) was used to culture P. brassicae resting spores, the germination of which was significantly inhibited. Further exogenous application [...] Read more.

Clubroot disease is a soil-borne disease caused by Plasmodiophora brassicae that leads to a serious yield reduction in cruciferous plants. In this study, ergothioneine (EGT) was used to culture P. brassicae resting spores, the germination of which was significantly inhibited. Further exogenous application of EGT and P. brassicae inoculation in Chinese cabbage showed that EGT promoted root growth and significantly reduced the incidence rate and disease index. To further explore the mechanism by which EGT improves the resistance of Chinese cabbage to clubroot, a Chinese cabbage inbred line BJN3-2 susceptible to clubroot treated with EGT was inoculated, and a transcriptome analysis was conducted. The transcriptome sequencing analysis showed that the differentially expressed genes induced by EGT were significantly enriched in the phenylpropanoid biosynthetic pathway, and the genes encoding related enzymes involved in lignin synthesis were upregulated. qRT-PCR, peroxidase activity, lignin and flavonoid content determination showed that EGT promoted the lignin and flavonoid synthesis of Chinese cabbage and improved its resistance to clubroot. This study provides a new insight for the comprehensive prevention and control of cruciferous clubroot and for further study of the effects of EGT on clubroot disease. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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14 pages, 4614 KiB

Open AccessArticle

BrCWM Mutation Disrupted Leaf Flattening in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

by Yanji Wu, Yue Xin, Jiaqi Zou, Shengnan Huang, Che Wang and Hui Feng

Int. J. Mol. Sci. 2023, 24(6), 5225; https://doi.org/10.3390/ijms24065225 - 09 Mar 2023

Viewed by 1500

Abstract

Leaf flattening plays a vital role in the establishment of plant architecture, which is closely related to plant photosynthesis and, thus, influences the product yield and quality of Chinese cabbage. In this study, we used the doubled haploid line ‘FT’ of Chinese cabbage [...] Read more.

Leaf flattening plays a vital role in the establishment of plant architecture, which is closely related to plant photosynthesis and, thus, influences the product yield and quality of Chinese cabbage. In this study, we used the doubled haploid line ‘FT’ of Chinese cabbage as the wild type for ethyl methanesulfonate (EMS) mutagenesis and obtained a mutant cwm with stably inherited compact and wrinkled leaves. Genetic analysis revealed that the mutated trait was controlled by a single recessive nuclear gene, Brcwm. Brcwm was preliminarily mapped to chromosome A07 based on bulked segregant RNA sequencing (BSR-seq) and fine-mapped to a 205.66 kb region containing 39 genes between Indel12 and Indel21 using SSR and Indel analysis. According to the whole-genome re-sequencing results, we found that there was only one nonsynonymous single nucleotide polymorphism (SNP) (C to T) within the target interval on exon 4 of BraA07g021970.3C, which resulted in a proline to serine amino acid substitution. The mutated trait co-segregated with the SNP. Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) revealed that BraA07g021970.3C expression was dramatically higher in ‘FT’ leaves than that in cwm leaves. BraA07g021970.3C is homologous to AT3G55000 encoding a protein related to cortical microtubule organization. A similar phenotype of dwarfism and wrinkled leaves was observed in the recessive homozygous mutant cwm-f1 of AT3G55000, and its T3 transgenic lines were restored to the Arabidopsis wild-type phenotype through ectopic overexpression of BraA07g021970.3C. These results verified that BraA07g021970.3C was the target gene essential for leaf flattening in Chinese cabbage. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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13 pages, 2419 KiB

Open AccessArticle

Dissecting the Meiotic Recombination Patterns in a Brassica napus Double Haploid Population Using 60K SNP Array

by Shuxiang Yan, Jianjie He, Mi Tang, Bangfa Ming, Huaixin Li, Shipeng Fan, Yiyi Xiong, Hongbo Chao, Libin Zhang, Aihua Wang and Maoteng Li

Int. J. Mol. Sci. 2023, 24(5), 4469; https://doi.org/10.3390/ijms24054469 - 24 Feb 2023

Cited by 1 | Viewed by 1860

Abstract

Meiotic recombination not only maintains the stability of the chromosome structure but also creates genetic variations for adapting to changeable environments. A better understanding of the mechanism of crossover (CO) patterns at the population level is useful for crop improvement. However, there are [...] Read more.

Meiotic recombination not only maintains the stability of the chromosome structure but also creates genetic variations for adapting to changeable environments. A better understanding of the mechanism of crossover (CO) patterns at the population level is useful for crop improvement. However, there are limited cost-effective and universal methods to detect the recombination frequency at the population level in Brassica napus. Here, the Brassica 60K Illumina Infinium SNP array (Brassica 60K array) was used to systematically study the recombination landscape in a double haploid (DH) population of B. napus. It was found that COs were unevenly distributed across the whole genome, and a higher frequency of COs existed at the distal ends of each chromosome. A considerable number of genes (more than 30%) in the CO hot regions were associated with plant defense and regulation. In most tissues, the average gene expression level in the hot regions (CO frequency of greater than 2 cM/Mb) was significantly higher than that in the regions with a CO frequency of less than 1 cM/Mb. In addition, a bin map was constructed with 1995 recombination bins. For seed oil content, Bin 1131 to 1134, Bin 1308 to 1311, Bin 1864 to 1869, and Bin 2184 to 2230 were identified on chromosomes A08, A09, C03, and C06, respectively, which could explain 8.5%, 17.3%, 8.6%, and 3.9% of the phenotypic variation. These results could not only deepen our understanding of meiotic recombination in B. napus at the population level, and provide useful information for rapeseed breeding in the future, but also provided a reference for studying CO frequency in other species. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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14 pages, 3742 KiB

Open AccessArticle

Brassica napus BnaC9.DEWAX1 Negatively Regulates Wax Biosynthesis via Transcriptional Suppression of BnCER1-2

by Saiyu Wang, Chengcheng Bai, Na Luo, Youwei Jiang, Yulu Wang, Yu Liu, Chunjie Chen, Yuxin Wang, Qiaoqiao Gan, Shurong Jin and Yu Ni

Int. J. Mol. Sci. 2023, 24(5), 4287; https://doi.org/10.3390/ijms24054287 - 21 Feb 2023

Cited by 1 | Viewed by 1522

Abstract

Very-long-chain alkane plays an important role as an aliphatic barrier. We previously reported that BnCER1-2 was responsible for alkane biosynthesis in Brassica napus and improved plant tolerance to drought. However, how the expression of BnCER1-2 is regulated is still unknown. Through yeast one-hybrid [...] Read more.

Very-long-chain alkane plays an important role as an aliphatic barrier. We previously reported that BnCER1-2 was responsible for alkane biosynthesis in Brassica napus and improved plant tolerance to drought. However, how the expression of BnCER1-2 is regulated is still unknown. Through yeast one-hybrid screening, we identified a transcriptional regulator of BnCER1-2, BnaC9.DEWAX1, which encodes AP2\ERF transcription factor. BnaC9.DEWAX1 targets the nucleus and displays transcriptional repression activity. Electrophoretic mobility shift and transient transcriptional assays suggested that BnaC9.DEWAX1 repressed the transcription of BnCER1-2 by directly interacting with its promoter. BnaC9.DEWAX1 was expressed predominantly in leaves and siliques, which was similar to the expression pattern of BnCER1-2. Hormone and major abiotic stresses such as drought and high salinity affected the expression of BnaC9.DEWAX1. Ectopic expression of BnaC9.DEWAX1 in Arabidopsis plants down-regulated CER1 transcription levels and resulted in a reduction in alkanes and total wax loads in leaves and stems when compared with the wild type, whereas the wax depositions in the dewax mutant returned to the wild type level after complementation of BnaC9.DEWAX1 in the mutant. Moreover, both altered cuticular wax composition and structure contribute to increased epidermal permeability in BnaC9.DEWAX1 overexpression lines. Collectively, these results support the notion that BnaC9.DEWAX1 negatively regulates wax biosynthesis by binding directly to the BnCER1-2 promoter, which provides insights into the regulatory mechanism of wax biosynthesis in B. napus. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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13 pages, 2845 KiB

Open AccessArticle

Whole-Genome Comparison Reveals Structural Variations behind Heading Leaf Trait in Brassica oleracea

by Gaoxiang Ji, Ying Long, Guangqin Cai, Guixin Yan, Jinfeng Wu, Fugui Zhang, Lixia Li, Hao Li, Qian Huang, Jinxiong Shen and Xiaoming Wu

Int. J. Mol. Sci. 2023, 24(4), 4063; https://doi.org/10.3390/ijms24044063 - 17 Feb 2023

Cited by 3 | Viewed by 1475

Abstract

Brassica oleracea displays remarkable morphological variations. It intrigued researchers to study the underlying cause of the enormous diversification of this organism. However, genomic variations in complex heading traits are less known in B. oleracea. Herein, we performed a comparative population genomics analysis [...] Read more.

Brassica oleracea displays remarkable morphological variations. It intrigued researchers to study the underlying cause of the enormous diversification of this organism. However, genomic variations in complex heading traits are less known in B. oleracea. Herein, we performed a comparative population genomics analysis to explore structural variations (SVs) responsible for heading trait formation in B. oleracea. Synteny analysis showed that chromosomes C1 and C2 of B. oleracea (CC) shared strong collinearity with A01 and A02 of B. rapa (AA), respectively. Two historical events, whole genome triplication (WGT) of Brassica species and differentiation time between AA and CC genomes, were observed clearly by phylogenetic and Ks analysis. By comparing heading and non-heading populations of B. oleracea genomes, we found extensive SVs during the diversification of the B. oleracea genome. We identified 1205 SVs that have an impact on 545 genes and might be associated with the heading trait of cabbage. Overlapping the genes affected by SVs and the differentially expressed genes identified by RNA-seq analysis, we identified six vital candidate genes that may be related to heading trait formation in cabbage. Further, qRT-PCR experiments also verified that six genes were differentially expressed between heading leaves and non-heading leaves, respectively. Collectively, we used available genomes to conduct a comparison population genome analysis and identify candidate genes for the heading trait of cabbage, which provides insight into the underlying reason for heading trait formation in B. oleracea. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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17 pages, 12765 KiB

Open AccessArticle

Investigation of the Key Genes Associated with Anthocyanin Accumulation during Inner Leaf Reddening in Ornamental Kale (Brassica oleracea L. var. acephala)

by Jiaqi Zou, Zhichao Gong, Zhiyong Liu, Jie Ren and Hui Feng

Int. J. Mol. Sci. 2023, 24(3), 2837; https://doi.org/10.3390/ijms24032837 - 02 Feb 2023

Cited by 1 | Viewed by 1618

Abstract

Ornamental kale (Brassica oleracea L. var. acephala) is a popular decorative plant in late autumn and winter. However, only during low-temperature color-changed periods below rough 15 °C can the plant accumulate anthocyanins and exhibit a diverse array of foliar color patterns. [...] Read more.

Ornamental kale (Brassica oleracea L. var. acephala) is a popular decorative plant in late autumn and winter. However, only during low-temperature color-changed periods below rough 15 °C can the plant accumulate anthocyanins and exhibit a diverse array of foliar color patterns. In this study, we probed into the potential mechanism of inner leaf reddening in a red-leaf pure line of ornamental kale by physiological, metabolic, and transcriptomic analyses. Determination of anthocyanin contents in the uncolored new white leaves (S0), the light red leaves (S1) in the reddening period and the red leaves (S2) completing color change, and analysis of anthocyanin metabolites at stage S2, revealed that the coloring of red leaves was mainly attributed to the accumulation of cyanidins. We further used transcriptomic sequencing between the pairwise S0, S1, and S2 stages to identify 21 differentially expressed genes (DEGs) involved in anthocyanin biosynthesis, among which the expression level of 14 DEGs was positively correlated with anthocyanin accumulation, and 6 DEGs were negatively correlated with anthocyanin accumulation. A total of 89 co-expressed genes were screened out, from which three DEGs (BoCHI, Bo4CL3, and BoF3H) were identified as hub genes in co-expression DEGs network. BoDFR and BoCHI were the DEGs with the highest expressions at S2. Moreover, two co-expressed DEGs related to stress response (BoBBX17 and BoCOR47) also exhibited upregulated expressions and positive correlations with anthocyanin accumulation. A deep dive into the underlying regulatory network of anthocyanin accumulation comprising these six upregulated DEGs from S0 to S2 was performed via trend, correlation, and differentially co-expression analysis. This study uncovered the DEGs expression profiles associated with anthocyanin accumulation during ornamental kale inner leaf reddening, which provided a basis for further dissecting the molecular mechanisms of leaf color characteristic change in ornamental kale at low temperatures. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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24 pages, 6321 KiB

Open AccessArticle

Functional Characterization of the Cystine-Rich-Receptor-like Kinases (CRKs) and Their Expression Response to Sclerotinia sclerotiorum and Abiotic Stresses in Brassica napus

by Rehman Sarwar, Lei Li, Jiang Yu, Yijie Zhang, Rui Geng, Qingfeng Meng, Keming Zhu and Xiao-Li Tan

Int. J. Mol. Sci. 2023, 24(1), 511; https://doi.org/10.3390/ijms24010511 - 28 Dec 2022

Cited by 3 | Viewed by 1825

Abstract

Cysteine-rich receptor-like kinases (CRKs) are transmembrane proteins that bind to the calcium ion to regulate stress-signaling and plant development-related pathways, as indicated by several pieces of evidence. However, the CRK gene family hasn’t been inadequately examined in Brassica napus. In [...] Read more.

Cysteine-rich receptor-like kinases (CRKs) are transmembrane proteins that bind to the calcium ion to regulate stress-signaling and plant development-related pathways, as indicated by several pieces of evidence. However, the CRK gene family hasn’t been inadequately examined in Brassica napus. In our study, 27 members of the CRK gene family were identified in Brassica napus, which are categorized into three phylogenetic groups and display synteny relationship to the Arabidopsis thaliana orthologs. All the CRK genes contain highly conserved N-terminal PKINASE domain; however, the distribution of motifs and gene structure were variable conserved. The functional divergence analysis between BnaCRK groups indicates a shift in evolutionary rate after duplication events, demonstrating that BnaCRKs might direct a specific function. RNA-Seq datasets and quantitative real-time PCR (qRT-PCR) exhibit the complex expression profile of the BnaCRKs in plant tissues under multiple stresses. Nevertheless, BnaA06CRK6-1 and BnaA08CRK8 from group B were perceived to play a predominant role in the Brassica napus stress signaling pathway in response to drought, salinity, and Sclerotinia sclerotiorum infection. Insights gained from this study improve our knowledge about the Brassica napus CRK gene family and provide a basis for enhancing the quality of rapeseed. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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19 pages, 3538 KiB

Open AccessArticle

Auxin Biosynthesis Genes in Allotetraploid Oilseed Rape Are Essential for Plant Development and Response to Drought Stress

by Mengyu Hao, Wenxiang Wang, Jia Liu, Hui Wang, Rijin Zhou, Desheng Mei, Li Fu, Qiong Hu and Hongtao Cheng

Int. J. Mol. Sci. 2022, 23(24), 15600; https://doi.org/10.3390/ijms232415600 - 09 Dec 2022

Cited by 4 | Viewed by 1568

Abstract

Crucial studies have verified that IAA is mainly generated via the two-step pathway in Arabidopsis, in which tryptophan aminotransferase (TAA) and YUCCA (YUC) are the two crucial enzymes. However, the role of the TAA (or TAR) and YUC genes in allotetraploid oilseed [...] Read more.

Crucial studies have verified that IAA is mainly generated via the two-step pathway in Arabidopsis, in which tryptophan aminotransferase (TAA) and YUCCA (YUC) are the two crucial enzymes. However, the role of the TAA (or TAR) and YUC genes in allotetraploid oilseed rape underlying auxin biosynthesis and development regulation remains elusive. In the present study, all putative TAR and YUC genes were identified in B. napus genome. Most TAR and YUC genes were tissue that were specifically expressed. Most YUC and TAR proteins contained trans-membrane regions and were confirmed to be endoplasmic reticulum localizations. Enzymatic activity revealed that YUC and TAR protein members were involved in the conversion of IPA to IAA and Trp to IPA, respectively. Transgenic plants overexpressing BnaYUC6a in both Arabidopsis and B. napus displayed high auxin production and reduced plant branch angle, together with increased drought resistance. Moreover, mutation in auxin biosynthesis BnaTARs genes by CRISPR/Cas9 caused development defects. All these results suggest the convergent role of BnaYUC and BnaTAR genes in auxin biosynthesis. Different homoeologs of BnaYUC and BnaTAR may be divergent according to sequence and expression variation. Auxin biosynthesis genes in allotetraploid oilseed rape play a pivotal role in coordinating plant development processes and stress resistance. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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Review

Jump to: Research

14 pages, 1234 KiB

Open AccessReview

Research Progress on the Effect of Nitrogen on Rapeseed between Seed Yield and Oil Content and Its Regulation Mechanism

by Jiarong Zhu, Wenjun Dai, Biyun Chen, Guangqin Cai, Xiaoming Wu and Guixin Yan

Int. J. Mol. Sci. 2023, 24(19), 14504; https://doi.org/10.3390/ijms241914504 - 25 Sep 2023

Cited by 2 | Viewed by 1183

Abstract

Rapeseed (Brassica napus L.) is one of the most important oil crops in China. Improving the oil production of rapeseed is an important way to ensure the safety of edible oil in China. Oil production is an important index that reflects the [...] Read more.

Rapeseed (Brassica napus L.) is one of the most important oil crops in China. Improving the oil production of rapeseed is an important way to ensure the safety of edible oil in China. Oil production is an important index that reflects the quality of rapeseed and is determined by the oil content and yield. Applying nitrogen is an important way to ensure a strong and stable yield. However, the seed oil content has been shown to be reduced in most rapeseed varieties after nitrogen application. Thus, it is critical to screen elite germplasm resources with stable or improved oil content under high levels of nitrogen, and to investigate the molecular mechanisms of the regulation by nitrogen of oil accumulation. However, few studies on these aspects have been published. In this review, we analyze the effect of nitrogen on the growth and development of rapeseed, including photosynthetic assimilation, substance distribution, and the synthesis of lipids and proteins. In this process, the expression levels of genes related to nitrogen absorption, assimilation, and transport changed after nitrogen application, which enhanced the ability of carbon and nitrogen assimilation and increased biomass, thus leading to a higher yield. After a crop enters the reproductive growth phase, photosynthates in the body are transported to the developing seed for protein and lipid synthesis. However, protein synthesis precedes lipid synthesis, and a large number of photosynthates are consumed during protein synthesis, which weakens lipid synthesis. Moreover, we suggest several research directions, especially for exploring genes involved in lipid and protein accumulation under nitrogen regulation. In this study, we summarize the effects of nitrogen at both the physiological and molecular levels, aiming to reveal the mechanisms of nitrogen regulation in oil accumulation and, thereby, provide a theoretical basis for breeding varieties with a high oil content. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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15 pages, 940 KiB

Open AccessReview

Research Progress in High-Efficiency Utilization of Nitrogen in Rapeseed

by Na Zhan, Kun Xu, Gaoxiang Ji, Guixin Yan, Biyun Chen, Xiaoming Wu and Guangqin Cai

Int. J. Mol. Sci. 2023, 24(9), 7752; https://doi.org/10.3390/ijms24097752 - 24 Apr 2023

Cited by 1 | Viewed by 1331

Abstract

Nitrogen (N) is one of the most important mineral elements for plant growth and development and a key factor for improving crop yield. Rapeseed, Brassica napus, is the largest oil crop in China, producing more than 50% of the domestic vegetable oil. [...] Read more.

Nitrogen (N) is one of the most important mineral elements for plant growth and development and a key factor for improving crop yield. Rapeseed, Brassica napus, is the largest oil crop in China, producing more than 50% of the domestic vegetable oil. However, high N fertilizer input with low utilization efficiency not only increases the production cost but also causes serious environmental pollution. Therefore, the breeding of rapeseed with high N efficiency is of great strategic significance to ensure the security of grain and oil and the sustainable development of the rapeseed industry. In order to provide reference for genetic improvement of rapeseed N-efficient utilization, in this article, we mainly reviewed the recent research progress of rapeseed N efficiency, including rapeseed N efficiency evaluation, N-efficient germplasm screening, and N-efficient physiological and molecular genetic mechanisms. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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14 pages, 616 KiB

Open AccessReview

The Flavonoid Biosynthesis and Regulation in Brassica napus: A Review

by Yuan-Yuan Chen, Hai-Qin Lu, Kai-Xuan Jiang, Yi-Ran Wang, You-Ping Wang and Jin-Jin Jiang

Int. J. Mol. Sci. 2023, 24(1), 357; https://doi.org/10.3390/ijms24010357 - 26 Dec 2022

Cited by 10 | Viewed by 2428

Abstract

Brassica napus is an important crop for edible oil, vegetables, biofuel, and animal food. It is also an ornamental crop for its various petal colors. Flavonoids are a group of secondary metabolites with antioxidant activities and medicinal values, and are important to plant [...] Read more.

Brassica napus is an important crop for edible oil, vegetables, biofuel, and animal food. It is also an ornamental crop for its various petal colors. Flavonoids are a group of secondary metabolites with antioxidant activities and medicinal values, and are important to plant pigmentation, disease resistance, and abiotic stress responses. The yellow seed coat, purple leaf and inflorescence, and colorful petals of B. napus have been bred for improved nutritional value, tourism and city ornamentation. The putative loci and genes regulating flavonoid biosynthesis in B. napus have been identified using germplasms with various seed, petal, leaf, and stem colors, or different flavonoid contents under stress conditions. This review introduces the advances of flavonoid profiling, biosynthesis, and regulation during development and stress responses of B. napus, and hopes to help with the breeding of B. napus with better quality, ornamental value, and stress resistances. Full article

(This article belongs to the Special Issue The Gene, Genomics, and Molecular Breeding in Cruciferae Plants)

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