Molecular analysis of anthocyanin biosynthesis-related genes reveal BoTT8 associated with purple hypocotyl of broccoli (Brassica oleracea var. italica L.)

Phyto-nutraceutical promise of Brassica vegetables in post-genomic era: a comprehensive review

MAIN CONCLUSION

Brassica vegetables are one of the possible solutions to tackle the emerging human diseases and malnutrition due to their rich content of phyto-nutraceutaical compounds. The genomics enabled tools have facilitated the elucidation of molecular regulation, mapping of genes/QTLs governing nutraceutical compounds, and development of nutrient-rich Brassica vegetables. The enriched food products or foods as whole termed as functional foods are intended to provide health benefits. The 2500 year old Hippocratic phrase 'let thy food be thy medicine and thy medicine be thy food' remained in anonymity due to lack of sufficient evidence. However, today, we are facing reappraisal of healthy nutritious functional foods in battling diseases. In this context, the Brassica vegetables represent the most extensively investigated class of functional foods. An optimal consumption of Brassica vegetables is associated with lowering the risks of several types of cancer, chronic diseases, cardiovascular disease, and help in autism. In the post-genomic era, the integration of genetic and neoteric omics tools like transcriptomics, metabolomics, and proteomics have illuminated the downstream genetic mechanisms governing functional food value of Brassica vegetables. In this review, we have summarized in brief the phyto-nutraceutical profile and their functionality in Brassica vegetables. This review also highlights the progress made in identification of candidate genes/QTLs for accumulation of bioactive compounds in Brassica vegetables. We summarize the molecular regulation of major phytochemicals and breeding triumphs in delivering multifunctional Brassica vegetables.

Study on the changes of miRNAs and their target genes in regulating anthocyanin synthesis during purple discoloration of cauliflower curd under low temperature stress

Introduction

Cauliflower is widely cultivated all over the world is attributed to its palatable flavor, high levels of anti-cancer compounds, and diverse array of nutrients. Exposure to extremely cold stress during production can result in a more frequent occurrence of purple discoloration in cauliflower curds. In response to cold stress, plants naturally produce anthocyanins to eliminate reactive oxygen species (ROS) generated as a defense mechanism.

Methods

This research involved conducting mRNA sequencing analysis on cauliflower curds both before and after exposure to cold stress treatment.

Results

It was determined that the up-regulation of anthocyanin biosynthesis-related genes CHS, CHI, DFR, ANS, UGFT, PAP1/2, and MYBL2 occurred significantly in response to cold stress, resulting in a significant increase in total anthocyanin content. Subsequently, miRNA sequencing was employed to identify miRNAs in cauliflower curds, followed by differential expression analysis. The results showed that Bna-miR289 and Ath-miR157a may play a key role in regulating the accumulation of anthocyanin in cauliflower curds. Furthermore, we utilized degradome sequencing data to predict the target genes of the identified miRNAs, resulting in the identification of BolK_3g48940.1, BolK_9g11680.1, BolK_7g41780.1, BolK_3g68050.1, and BolK_3g729700.1 as targets. Subsequently, the expression patterns of the miRNAs and their target genes were validated using qRT-PCR, the results showed that Ath-miR157a and its target genes BolK_3g68050.1 and BolK_3g72970.1 may be the key to the purple of cauliflower curds under cold stress.

Discussion

Our preliminary findings identified key miRNAs and their target genes that may be involved in regulating anthocyanin synthesis, thereby enhancing the cold tolerance of cauliflower through mRNA, miRNA, and degradome sequencing. Overall, our study sheds light on the activation of anthocyanin synthesis in flower curds under cold stress conditions as a mechanism to enhance resilience to adverse environmental conditions.

Map-based cloning and CRISPR/Cas9-based editing uncover BoNA1 as the causal gene for the no-anthocyanin-accumulation phenotype in curly kale (Brassica oleracea var. sabellica)

Brassica oleracea comprises several important vegetable and ornamental crops, including curly kale, ornamental kale, cabbage, broccoli, and others. The accumulation of anthocyanins, important secondary metabolites valuable to human health, in these plants varies widely and is responsible for their pink to dark purple colors. Some curly kale varieties lack anthocyanins, making these plants completely green. The genetic basis of this trait is still unknown. We crossed the curly kale inbred line BK2019 (without anthocyanins) with the cabbage inbred line YL1 (with anthocyanins) and the Chinese kale inbred line TO1000 (with anthocyanins) to generate segregating populations. The no-anthocyanin trait was genetically controlled by a recessive gene, bona1. We generated a linkage map and mapped bona1 to a 256-kb interval on C09. We identified one candidate gene, Bo9g058630, in the target genomic region; this gene is homologous to AT5G42800, which encodes a dihydroflavonol-4-reductase-like (DFR-like) protein in Arabidopsis. In BK2019, a 1-bp insertion was observed in the second exon of Bo9g058630 and directly produced a stop codon. To verify the candidate gene function, CRISPR/Cas9 gene editing technology was applied to knock out Bo9g058630. We generated three bona1 mutants, two of which were completely green with no anthocyanins, confirming that Bo9g058630 corresponds to BoNA1. Different insertion/deletion mutations in BoNA1 exons were found in all six of the other no-anthocyanin kale varieties examined, supporting that independent disruption of BoNA1 resulted in no-anthocyanin varieties of B. oleracea. This study improves the understanding of the regulation mechanism of anthocyanin accumulation in B. oleracea subspecies.

Research progress and applications of colorful Brassica crops

MAIN CONCLUSION

We review the application and the molecular regulation of anthocyanins in colorful Brassica crops, the creation of new germplasm resources, and the development and utilization of colorful Brassica crops. Brassica crops are widely cultivated: these include oilseed crops, such as rapeseed, mustards, and root, leaf, and stem vegetable types, such as turnips, cabbages, broccoli, and cauliflowers. Colorful variants exist of these crop species, and asides from increased aesthetic appeal, these may also offer advantages in terms of nutritional content and improved stress resistances. This review provides a comprehensive overview of pigmentation in Brassica as a reference for the selection and breeding of new colorful Brassica varieties for multiple end uses. We summarize the function and molecular regulation of anthocyanins in Brassica crops, the creation of new colorful germplasm resources via different breeding methods, and the development and multifunctional utilization of colorful Brassica crop types.

Genome-wide identification and expression analysis of the bHLH gene family in cauliflower (Brassica oleracea L.)

Basic helix-loop-helix (bHLH) transcription factors (TFs) are one of the largest TF families in plant species, and they play important roles in plant growth, development and stress responses. The present study systematically identified members of the cauliflower (Brassica oleracea L.) bHLH gene family based on genomic data. Analysis of bHLH family gene numbers, evolution, collinearity, gene structures and motifs indicated that cauliflower contained 256 bHLH family genes distributed on 10 chromosomes. Most of these genes have been localized in the nucleus, and they were divided into 18 subgroups which have been relatively conserved during evolution. Promoter analysis showed that most cis-acting elements were related to MeJA and ABA. Expression analysis suggested that 14 bHLH genes may be involved in the transformation of cauliflower curd from white to purple. An expression analysis of these 14 genes in FQ136 material was performed using qRT-PCR, and 9 bHLH genes (BobHLH1, 14, 58, 61, 63, 84, 231, 239 and 243) showed significantly increased or decreased expression in cauliflower from white to purple, which suggests that these 9 genes play important roles in the accumulation of anthocyanins in cauliflower. The coexpression network of these 9 genes and anthocyanin synthesis-related key genes was analyzed using weighted gene coexpression network analysis (WGCNA). In conclusion, our observations suggested that the bHLH gene family plays an important role in the accumulation of anthocyanins in cauliflower and provide an important theoretical basis for further research on the functions of the bHLH gene family and the molecular mechanism of cauliflower coloration.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01238-9.

Development of Novel Markers and Creation of Non-Anthocyanin and Anthocyanin-Rich Broccoli (Brassica oleracea var. italica) Cultivars

In broccoli, anthocyanin pigments can be accumulated in the flower bud epidermis, resulting in a purple-green head. This study aimed to create non-anthocyanin green broccoli varieties and anthocyanin-rich purple broccoli varieties using new F3′H and Pur7.1-K1 molecular markers, respectively. The breeding program started with crosses of the recipient (superior variety and line) LF02 line with the donor line SN60 carrying the recessive allele f3′h and the donor line BT126 carrying the dominant allele Pur7.1. The F1 hybrids were confirmed with molecular markers and backcrossed with the recurrent parent LF02, followed by cycles of foreground and background selection at each stage. A total of 161 green plants with the f3′hf3′h genotype and 152 purple plants with the Pur7.1Pur7.1 genotype were selected from the BC3F2 line. Among these, 34 green plants and 28 purple plants demonstrated >85% background recovery. The identified plants were selfed to obtain 301 green and 416 purple BC3F3 plants for assessment of major agronomic traits. After these investigations, two green broccoli lines without anthocyanin and three anthocyanin-rich purple lines with the best yield/quality characteristics were obtained. The development of these lines might help provide basic materials and the theoretical basis for breeding commercial broccoli varieties.

Advances in Genetics and Molecular Breeding of Broccoli

Broccoli (Brassica oleracea L. var. italica) is one of the most important vegetable crops cultivated worldwide. The market demand for broccoli is still increasing due to its richness in vitamins, anthocyanins, mineral substances, fiber, secondary metabolites and other nutrients. The famous secondary metabolites, glucosinolates, sulforaphane and selenium have protective effects against cancer. Significant progress has been made in fine-mapping and cloning genes that are responsible for important traits; this progress provides a foundation for marker-assisted selection (MAS) in broccoli breeding. Genetic engineering by the well-developed Agrobacterium tumefaciens-mediated transformation in broccoli has contributed to the improvement of quality; postharvest life; glucosinolate and sulforaphane content; and resistance to insects, pathogens and abiotic stresses. Here, we review recent progress in the genetics and molecular breeding of broccoli. Future perspectives for improving broccoli are also briefly discussed.

Intron-retained radish (Raphanus sativus L.) RsMYB1 transcripts found in colored-taproot lines enhance anthocyanin accumulation in transgenic Arabidopsis plants

KEY MESSAGE

Overexpression of the naturally occurring intron-retained (IR) forms of radish RsMYB1 and RsTT8 transcripts in Arabidopsis causes a substantial increase in anthocyanin accumulation. The production of anthocyanins in plants is tightly controlled by the MYB-bHLH-WD40 (MBW) complex. In this study, analysis of four radish (Raphanus sativus L.) inbred lines with different colored taproots revealed that regulatory genes of anthocyanin biosynthesis, RsMYB1 and RsTT8, produce three transcripts, one completely spliced and two intron retention (IR1 and IR2) forms. Transcripts RsMYB1-IR1 and RsMYB1-IR2 retained the 1st (380 nt) and 2nd (149 nt) introns, respectively; RsTT8-IR1 retained the 4th intron (113 nt); RsTT8-IR2 retained both the 3rd (128 nt) and 4th introns. Levels of most IR forms were substantially low in radish samples, but the RsTT8-IR2 level was higher than RsTT8 in red skin/red flesh (RsRf) root. Since all IR forms contained a stop codon within the intron, they were predicted to encode truncated proteins with defective interaction domains, resulting in the inability to form the MBW complex in vivo. However, tobacco leaves transiently co-expressing RsMYB1-IRs and RsTT8-IRs showed substantially higher anthocyanin accumulation than those co-expressing their spliced forms. Consistently, co-expression of constructs encoding truncated proteins with spliced or IR forms of their interaction partner in tobacco leaves did not result in anthocyanin accumulation. Compared with RsMYB1, the overexpression of RsMYB1-IRs in Arabidopsis pap1 mutant increased anthocyanin accumulation by > sevenfold and upregulated the expression of Arabidopsis flavonoid biosynthesis genes including AtTT8. Our results suggest that the stable co-expression of RsMYB1-IRs in fruit trees and vegetable crops could be used to increase their anthocyanin contents.

Alleles disrupting LBD37-like gene by an 136 bp insertion show different distributions between green and purple cabbages (Brassica oleracea var. capitata)

BACKGROUND

In Arabidopsis thaliana (Arabidopsis), clade IIb lateral organ boundary domain (LBD) 37, 38, and 39 proteins negatively regulate anthocyanin biosynthesis and affect nitrogen responses.

OBJECTIVE

To investigate the possible role of LBD genes in anthocyanin accumulations among green and purple cabbages (Brassica oleracea var. capitata), we determined sequence variations and expression levels of cabbage homologs of Arabidopsis LBD37, 38, and 39.

METHODS

DNA and mRNA sequences of BoLBD37, BoLBD37L (BoLBD37-like), BoLBD38, BoLBD38L (BoLBD38-like), and BoLBD39 gene in cabbage were determined. Allelic variations of BoLBD37L alleles in cabbages, resulting from insertions, were validated by genomic DNA PCR. Gene expressions were examined by semi-quantitative reverse transcription (RT-PCR) or quantitative RT-PCR.

RESULTS

Based on the expression analyses, BoLBD37L with two alleles, BoLBD37L-G and BoLBD37L-P, was selected as a candidate gene important for differential anthocyanin accumulation. BoLBD37L-P contains an 136 base pair insertion in the 2nd exon, producing two splicing variants encoding truncated proteins. Most purple cabbage lines were found to have BoLBD37L-P allele as homozygotes or heterozygotes, and only two out of sixty-four purple cabbages were identified as BoLBD37L-G homozygotes. Expression analyses of anthocyanin biosynthesis genes and their upstream regulators, including BoLBD37L, suggest that truncated proteins encoded by splicing variants of BoLBD37L-P may disrupt the BoLBD37L function as repressor.

CONCLUSION

Difference in the C-terminal region of BoLBD37L-G and BolBD37L-P may affect the expression of downstream genes, BoMYB114L and BoTT8, resulting in differential anthocyanin accumulation.

Genome-wide association and transcriptome analysis of root color-related genes in Gossypium arboreum L

The significant number loci and candidate genes of root color in Gossypium arboreum are identified and provide a theoretical basis of root color for cotton. A stimulating phenomenon was observed on the 4th day of sowing in the root color of some G. arboreum accessions that turned red. To disclose the genetic mechanisms of root color formation via genome and transcript levels, we identified the significant number of SNPs and candidate genes that are related to root color through genome-wide association study (GWAS) and RNAseq analysis in G. arboreum. Initially, 215 no. of G. arboreum accessions was collected, and the colors of root on the 4th, 6th and 9th day of germination were recorded. The GWAS demonstrated that 225 significant SNPs and 47 candidate genes have been identified totally. The strongest signal SNP A04_91824 could greatly distinguish the root color with most "C" allele accessions have displayed white and "T" allele accessions displayed red. RNAseq was performed on accessions having the white and red root, and results revealed that 12 and 138 DEGs were detected on 2nd and 4th day, respectively. ACD6, UFGT, and LYM2 were the most related genes of root color, later, verified by qRT-PCR. The mature zone of red and the white roots was observed by the histological section method, and results shown that cells were more closely arranged in the white root, and both average cell length and cell width were longer in the red root. This study will be helpful to cotton breeders for utilization of several elite genes and related SNPs related to root color, in addition to find linkage with economically important traits of interests.

Grown to be Blue-Antioxidant Properties and Health Effects of Colored Vegetables. Part II: Leafy, Fruit, and Other Vegetables

The current trend for substituting synthetic compounds with natural ones in the design and production of functional and healthy foods has increased the research interest about natural colorants. Although coloring agents from plant origin are already used in the food and beverage industry, the market and consumer demands for novel and diverse food products are increasing and new plant sources are explored. Fresh vegetables are considered a good source of such compounds, especially when considering the great color diversity that exists among the various species or even the cultivars within the same species. In the present review we aim to present the most common species of colored vegetables, focusing on leafy and fruit vegetables, as well as on vegetables where other plant parts are commercially used, with special attention to blue color. The compounds that are responsible for the uncommon colors will be also presented and their beneficial health effects and antioxidant properties will be unraveled.

Abscisic acid and ethylene biosynthesis-related genes are associated with anthocyanin accumulation in purple ornamental cabbage (Brassica oleracea var. acephala)

Purple ornamental cabbage (Brassica oleracea var. acephala) is a popular decorative plant, cultivated for its colorful leaf rosettes that persist in cool weather. It is characterized by green outer leaves and purple inner leaves, whose purple pigmentation is due to the accumulation of anthocyanin pigments. Phytohormones play important roles in anthocyanin biosynthesis in other species. Here, we identified 14 and 19 candidate genes putatively involved in abscisic acid (ABA) and ethylene (ET) biosynthesis, respectively, in B. oleracea. We determined the expression patterns of these candidate genes by reverse-transcription quantitative PCR (RT-qPCR). Among candidate ABA biosynthesis-related genes, the expressions of BoNCED2.1, BoNCED2.2, BoNCED6, BoNCED9.1, and BoAAO3.2 were significantly higher in purple compared to green leaves. Likewise, most of the ET biosynthetic genes (BoACS6, BoACS9.1, BoACS11, BoACO1.1, BoACO1.2, BoACO3.1, BoACO4, and BoACO5) had significantly higher expression in purple compared to green leaves. Among these genes, BoNCED2.1, BoNCED2.2, BoACS11, and BoACO4 showed particularly strong associations with total anthocyanin content of the purple inner leaves. Our results suggest that ABA and ET might promote the intense purple pigmentation of the inner leaves of purple ornamental cabbage.