Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L.

Background Seed coat color is an important horticultural trait in Brassica crops, which is divided into two categories: brown/black and yellow. Seeds with yellow seed coat color have higher oil quality, higher protein content and lower fiber content. Yellow seed coat color is therefore considered a desirable trait in hybrid breeding of Brassica rapa, Brassica juncea and Brassica napus. Methods Comprehensive analysis of the abundance transcripts for seed coat color at three development stages by RNA-sequencing (RNA-seq) and corresponding flavonoids compounds by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were carried out in B. rapa. Results We identified 41,286 unigenes with 4,989 differentially expressed genes between brown seeds (B147) and yellow seeds (B80) at the same development stage. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified 19 unigenes associated with the phenylpropanoid, flavonoid, flavone and flavonol biosynthetic pathways as involved in seed coat color formation. Interestingly, expression levels of early biosynthetic genes (BrCHS, BrCHI, BrF3H, BrF3’H and BrFLS) in the flavonoid biosynthetic pathway were down-regulated while late biosynthetic genes (BrDFR, BrLDOX and BrBAN) were hardly or not expressed in seeds of B80. At the same time, BrTT8 and BrMYB5 were down-regulated in B80. Results of LC-MS also showed that epicatechin was not detected in seeds of B80. We validated the accuracy of our RNA-seq data by RT-qPCR of nine critical genes. Epicatechin was not detected in seeds of B80 by LC-MS/MS. Conclusions The expression levels of flavonoid biosynthetic pathway genes and the relative content of flavonoid biosynthetic pathway metabolites clearly explained yellow seed color formation in B. rapa. This study provides a foundation for further research on the molecular mechanism of seed coat color formation.

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Mapping and identification of yellow seed coat color genes in Brassica juncea L.

10.21203/rs.3.rs-25889/v1 ◽

2020 ◽

Author(s):

Zhen Huang ◽

Yang Wang ◽

Hong Lu ◽

Xiang Liu ◽

Lu Liu ◽

...

Keyword(s):

Candidate Gene ◽

Brassica Juncea ◽

Seed Coat ◽

Coat Color ◽

Seed Color ◽

Seed Coat Color ◽

Flavonoid Pathway ◽

Yellow Seed ◽

Color Formation ◽

Yellow Seed Coat

Abstract BackgroundYellow seed breeding is an effective method to improve the oil content in rapeseed. Yellow seed coat color formation is influenced by various factors, and no clear mechanisms are known. In this study, Bulked segregant RNA-Seq (BSR-Seq) of BC9 population of Wuqi mustard (yellow seed) and Wugong mustard (brown seed) was used to identity the candidate genes controlling the yellow seed color in Brassica juncea L.ResultsYellow seed coat color gene was mapped to chromosome A09, and differentially expressed genes (DEGs) between brown and yellow bulks enriched in the flavonoid pathway. A significant correlation between the expression of BjF3H and BjTT5 and the content of the seed coat color related indexes was identified. Two intron polymorphism (IP) markers linked to the target gene were developed around BjF3H. Therefore, BjF3H was considered as the candidate gene. The BjF3H coding sequences (CDS) of Wuqi mustard and Wugong mustard are 1071-1077bp, encoding protein of 356-358 amino acids. One amino acid change (254, F/V) was identified in the conserved domain. This mutation site was detected in four Brassica rapa (B. rapa) and six Brassica juncea (B. juncea) lines, but not in Brassica napus (B. napus).ConclusionsThe results indicated BjF3H is a candidate gene that related to yellow seed coat color formation in Brassica juncea and provided a comprehensive understanding of the yellow seed coat color mechanism.

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Fine-Mapping And Identification of A Candidate Gene Controlling Seed Coat Color In Melon (Cucumis Melo L. Var. Chinensis Pangalo)

10.21203/rs.3.rs-720440/v1 ◽

2021 ◽

Author(s):

Zhicheng Hu ◽

Xueyin Shi ◽

Xuemiao Chen ◽

Jing Zheng ◽

Aiai Zhang ◽

...

Keyword(s):

Candidate Gene ◽

Seed Coat ◽

Coat Color ◽

Bulked Segregant Analysis ◽

Dominant Gene ◽

Seed Coat Color ◽

Gene Encoding ◽

Yellow Seed ◽

Homeobox Protein ◽

Yellow Seed Coat

Abstract Seed coat color is related to flavonoid content which is closely related to seed dormancy. According to the genetic analysis of a six-generation population derived from two parents (IC2508 with a yellow seed coat and IC2518 with a brown seed coat), we discovered that the yellow seed coat trait in melon was controlled by a single dominant gene, named CmBS-1. Bulked segregant analysis sequencing (BSA-Seq) revealed that the gene was located at 11,860,000–15,890,000 bp (4.03 Mb) on Chr 6. The F2 population was genotyped using insertion-deletions (InDels), from which cleaved amplified polymorphic sequence (dCAPS) markers were derived to construct a genetic map. The gene was then fine-mapped to a 233.98 kb region containing 12 genes. Based on gene sequence analysis with two parents, we found that the MELO3C019554 gene encoding a homeobox protein (PHD transcription factor) had a nonsynonymous single nucleotide polymorphism (SNP) mutation in the coding sequence (CDS), and the SNP mutation resulted in the conversion of an amino acid (A→T) at residue 534. In addition, MELO3C019554 exhibited lower relative expression levels in the yellow seed coat than in the brown seed coat. Furthermore, we found that MELO3C019554 was related to 12 flavonoid metabolites. Thus, we predicted that MELO3C019554 is a candidate gene controlling seed coat color in melon. The study lays a foundation for further cloning projects and functional analysis of this gene, as well as marker-assisted selection breeding.

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Identification of SSR markers closely linked to the yellow seed coat color gene in heading Chinese cabbage (Brassica rapaL. ssp.pekinensis)

Biology Open ◽

10.1242/bio.021592 ◽

2017 ◽

Vol 6 (2) ◽

pp. 278-282 ◽

Cited By ~ 3

Author(s):

Yanjing Ren ◽

Junqing Wu ◽

Jing Zhao ◽

Lingyu Hao ◽

Lugang Zhang

Keyword(s):

Ssr Markers ◽

Chinese Cabbage ◽

Seed Coat ◽

Coat Color ◽

Seed Coat Color ◽

Yellow Seed ◽

Heading Chinese Cabbage ◽

Yellow Seed Coat ◽

Coat Color Gene ◽

Color Gene

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Characterization of the BrTT1 gene responsible for seed coat color formation in Dahuang (Brassica rapa L. landrace)

Molecular Breeding ◽

10.1007/s11032-017-0736-3 ◽

2017 ◽

Vol 37 (11) ◽

Cited By ~ 4

Author(s):

Yanhua Wang ◽

Lu Xiao ◽

Xiaoling Dun ◽

Kede Liu ◽

Dezhi Du

Keyword(s):

Brassica Rapa ◽

Seed Coat ◽

Coat Color ◽

Seed Coat Color ◽

Color Formation

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Effect of chilling acclimation on germination and seedlings response to cold in different seed coat colored wheat (Triticum aestivum L.)

BMC Plant Biology ◽

10.1186/s12870-021-03036-z ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Paulina Calderon Flores ◽

Jin Seok Yoon ◽

Dae Yeon Kim ◽

Yong Weon Seo

Keyword(s):

Stress Response ◽

Seed Coat ◽

Biosynthetic Pathway ◽

Coat Color ◽

Chilling Stress ◽

Seed Coat Color ◽

Ros Scavenging ◽

Flavonoid Biosynthetic Pathway ◽

Scavenging Enzymes ◽

Ros Scavenging Enzymes

Abstract Background Flavonoids can protect plants against extreme temperatures and ROS due to their antioxidant activities. We found that deep-purple seed coat color was controlled by two gene interaction (12:3:1) from the cross between yellow and deep-purple seed coat colored inbreds. F2:3 seeds were grouped in 3 by seed coat color and germinated under chilling (4 °C) and non-acclimated conditions (18 °C) for a week, followed by normal conditions (18 °C) for three weeks and a subsequent chilling stress (4 °C) induction. We analyzed mean daily germination in each group. Additionally, to study the acclimation in relationship to the different seed coat colors on the germination ability and seedling performances under the cold temperatures, we measured the chlorophyll content, ROS scavenging activity, and expression levels of genes involved in ROS scavenging, flavonoid biosynthetic pathway, and cold response in seedlings. Results The results of seed color segregation between yellow and deep purple suggested a two-gene model. In the germination study, normal environmental conditions induced the germination of yellow-seed, while under chilling conditions, the germination ratio of deep purple-seed was higher than that of yellow-colored seeds. We also found that the darker seed coat colors were highly responsive to cold acclimation based on the ROS scavenging enzymes activity and gene expression of ROS scavenging enzymes, flavonoid biosynthetic pathway and cold responsive genes. Conclusions We suggest that deep purple colored seed might be in a state of innate pre-acquired stress response state under normal conditions to counteract stresses in a more effective way. Whereas, after the acclimation, another stress should enhance the cold genes expression response, which might result in a more efficient chilling stress response in deep purple seed seedlings. Low temperature has a large impact on the yield of crops. Thus, understanding the benefit of seed coat color response to chilling stress and the identification of limiting factors are useful for developing breeding strategies in order to improve the yield of wheat under chilling stress.

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Genetic Mapping and Identification of the Candidate Gene for White Seed Coat in Cucurbita maxima

International Journal of Molecular Sciences ◽

10.3390/ijms22062972 ◽

2021 ◽

Vol 22 (6) ◽

pp. 2972

Author(s):

Yuzi Shi ◽

Meng Zhang ◽

Qin Shu ◽

Wei Ma ◽

Tingzhen Sun ◽

...

Keyword(s):

Seed Coat ◽

Molecular Breeding ◽

Coat Color ◽

Recessive Gene ◽

Myb Transcription Factor ◽

Cucurbita Maxima ◽

Seed Coat Color ◽

Rna Seq ◽

Edible Seed ◽

Segregating Population

Seed coat color is an important agronomic trait of edible seed pumpkin in Cucurbita maxima. In this study, the development pattern of seed coat was detected in yellow and white seed coat accessions Wuminglv and Agol. Genetic analysis suggested that a single recessive gene white seed coat (wsc) is involved in seed coat color regulation in Cucurbita maxima. An F2 segregating population including 2798 plants was used for fine mapping and a candidate region containing nine genes was identified. Analysis of 54 inbred accessions revealed four main Insertion/Deletion sites in the promoter of CmaCh15G005270 encoding an MYB transcription factor were co-segregated with the phenotype of seed coat color. RNA-seq analysis and qRT-PCR revealed that some genes involved in phenylpropanoid/flavonoid metabolism pathway displayed remarkable distinction in Wuminglv and Agol during the seed coat development. The flanking InDel marker S1548 was developed to predict the seed coat color in the MAS breeding with an accuracy of 100%. The results may provide valuable information for further studies in seed coat color formation and structure development in Cucurbitaceae crops and help the molecular breeding of Cucurbita maxima.

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