scholarly journals Transcriptome and metabolome reveal redirection of flavonoids in a white testa peanut mutant

2019 ◽  
Author(s):  
Liyun Wan ◽  
Yong Lei ◽  
Liying Yan ◽  
Yue Liu ◽  
Manish Kumar Pandey ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Seed Coat ◽  
Coat Color ◽  
Expression Patterns ◽  
Tca Cycle ◽  
Tissue Expression ◽  
Processing Efficiency ◽  
Hormone Synthesis ◽  
Mbw Complex

Abstract Background: Coat color determines both appearance and nutrient quality of peanut. White seed coat in peanut can enhance the processing efficiency and quality of peanut oil.An integrative analysis of transcriptomes, metabolomes and histocytology was performed on wsc mutant and its wild type to investigate the regulatory mechanisms underlying color pigmentation. Result：Metabolomes revealed flavonoids were redirected in wsc, while multi-omics analyses of wsc mutant seeds and testae uncovered WSC influenced the flavonoids biosynthesis in testa as well as suberin formation, glycolysis, the TCA cycle and amino acid metabolism. The mutation also enhanced BR, GA, and JA biosynthesis as well as ABA, AUX, BR and JA signaling. Further, co-expression analysis showed that FLS genes co-expressed with MBW complex member genes. Combining tissue expression patterns, genetic analyses, and the annotation of common DEGs for these three stages revealed that three testa specific expressed candidate genes, Araip.M7RY3, Aradu.R8PMF and Araip.MHR6K were likely responsible for the white testa phenotype. WSC might be regulated expression competition between FLS and DRF by controlling hormone synthesis and signaling as well as the MBW complex. Conclusions: The results of this study therefore provide both candidate genes and novel approaches that can be applied to improve peanut with desirable seed coat color and flavonoid quality.

scholarly journals Transcriptome and metabolome reveal redirection of flavonoids in a white testa peanut mutant

2019 ◽  
Author(s):  
Liyun Wan ◽  
Yong Lei ◽  
Liying Yan ◽  
Yue Liu ◽  
Manish Kumar Pandey ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Seed Coat ◽  
Coat Color ◽  
Expression Patterns ◽  
Tca Cycle ◽  
Tissue Expression ◽  
Processing Efficiency ◽  
Hormone Synthesis ◽  
Mbw Complex

Abstract Background: Coat color determines both appearance and nutrient quality of peanut. White seed coat in peanut can enhance the processing efficiency and quality of peanut oil.An integrative analysis of transcriptomes, metabolomes and histocytology was performed on a white seed coat peanut mutant (wsc) and its wild type to investigate the regulatory mechanisms underlying color pigmentation. Result：Metabolomes revealed flavonoids were redirected in wsc, while multi-omics analyses of wsc mutant seeds and testae uncovered WSC influenced the flavonoids biosynthesis in testa as well as suberin formation, glycolysis, the tricarboxylic acid (TCA) cycle and amino acid metabolism. The mutation also enhanced brassinosteroid (BR), gibberellin (GA), and jasmonic acid (JA) biosynthesis as well as abscisic acid (ABA), auxin (AUX), BR and JA signaling. Further, co-expression analysis showed that flavonol synthase (FLS) genes co-expressed with MYB-bHLH-WD40 (MBW) complex member genes. Combining tissue expression patterns, genetic analyses, and the annotation of common differentially expressed genes (DEGs) for these three stages revealed that three testa specific expressed candidate genes, Araip.M7RY3, Aradu.R8PMF and Araip.MHR6K were likely responsible for the white testa phenotype. WSC might be regulated expression competition between FLS and dihydroflavonol 4-reductase (DRF) by controlling hormone synthesis and signaling as well as the MBW complex. Conclusions: The results of this study therefore provide both candidate genes and novel approaches that can be applied to improve peanut with desirable seed coat color and flavonoid quality.

scholarly journals The Extent and Its Source of Variation for Characteristics Related to Seed Quality of Adzuki Beans. II. Variation of seed coat color among growers lots in Hokkaido area.

1991 ◽  
Vol 60 (2) ◽  
pp. 234-240 ◽  
Author(s):  
Koichi YOSHIDA ◽  
Hisayasu SATO ◽  
Hisashi UESHIMA ◽  
Nobuaki ISHII ◽  
Michinori SATO
Keyword(s):  
Seed Coat ◽  
Seed Quality ◽  
Coat Color ◽  
Seed Coat Color

scholarly journals Integrated Metabolome and Transcriptome Analysis Provide Insights into the Effects of Grafting on Fruit Flavor of Cucumber with Different Rootstocks

2019 ◽  
Vol 20 (14) ◽  
pp. 3592 ◽  
Author(s):  
Li Miao ◽  
Qinghua Di ◽  
Tianshu Sun ◽  
Yansu Li ◽  
Ying Duan ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Expression Patterns ◽  
Sugar Metabolism ◽  
Myb Transcription Factor ◽  
Chemical Production ◽  
Cucumis Sativus L ◽  
Cucumber Fruit ◽  
Valine Biosynthesis ◽  
Fruit Flavor

Rootstocks frequently exert detrimental effects on the fruit quality of grafted cucumber (Cucumis sativus L.) plants. To understand and ultimately correct this deficiency, a transcriptomic and metabolomic comparative analysis was performed among cucumber fruits from non-grafted plants (NG), and fruits from plants grafted onto different rootstocks of No.96 and No.45 (Cucurbita moschata. Duch), known to confer a different aroma and taste. We found remarkable changes in the primary metabolites of sugars, organic acids, amino acids, and alcohols in the fruit of the grafted cucumber plants with different rootstocks, compared to the non-grafted ones, especially No.45. We identified 140, 131, and 244 differentially expressed genes (DEGs) in the comparisons of GNo.96 vs. NG, GNo.45 vs. NG, and GNo.45 vs. GNo.96. The identified DEGs have functions involved in many metabolic processes, such as starch and sucrose metabolism; the biosynthesis of diterpenoid, carotenoid, and zeatin compounds; and plant hormone signal transduction. Members of the HSF, AP2/ERF-ERF, HB-HD-ZIP, and MYB transcription factor families were triggered in the grafted cucumbers, especially in the cucumber grafted on No.96. Based on a correlation analysis of the relationships between the metabolites and genes, we screened 10 candidate genes likely to be involved in sugar metabolism (Fructose-6-phosphate and trehalose), linoleic acid, and amino-acid (isoleucine, proline, and valine) biosynthesis in grafted cucumbers, and then confirmed the gene expression patterns of these genes by qRT-PCR. The levels of TPS15 (Csa3G040850) were remarkably increased in cucumber fruit with No.96 rootstock compared with No.45, suggesting changes in the volatile chemical production. Together, the results of this study improve our understanding of flavor changes in grafted cucumbers, and identify the candidate genes involved in this process.

scholarly journals Transcriptome Dynamics during Black and White Sesame (Sesamum indicum L.) Seed Development and Identification of Candidate Genes Associated with Black Pigmentation

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1399
Author(s):  
Linhai Wang ◽  
Senouwa Segla Koffi Dossou ◽  
Xin Wei ◽  
Yanxin Zhang ◽  
Donghua Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Seed Development ◽  
Seed Coat ◽  
Coat Color ◽  
Sesame Seed ◽  
Sesamum Indicum ◽  
Seed Coat Color ◽  
Black And White ◽  
Pigment Biosynthesis ◽  
Black Pigmentation

Seed coat color is a crucial agronomic trait in sesame (Sesamum indicum L.) since it is strongly linked to seed oil, proteins, and lignans contents, and also influences consumer preferences. In East Asia, black sesame seed is used in the treatment and the prevention of various diseases. However, in sesame, little is known about the establishment of the seed coat color, and only one gene has been reported to control black pigmentation. This study provides an overview of developing seeds transcriptome of two varieties of sesame “Zhongfengzhi No.1” (white seed) and “Zhongzhi No.33” (black seed) and shed light on genes involving in black seed formation. Until eight days post-anthesis (DPA), both the seeds of the two varieties were white. The black sesame seed turned to yellow between 9 and 11 DPA and then black between 12 and 14 DPA. The black and white sesame showed similar trend-expressed genes with the numbers increased at the early stages of seed development. The differentially expressed genes (DEGs) number increased with seed development in the two sesame varieties. We examined the DEGs and uncovered that more were up-regulated at the early stages. The DEGs between the black and white sesame were mainly enriched in 37 metabolic pathways, among which the flavonoid biosynthesis and biosynthesis of secondary metabolites were dominants. Furthermore, we identified 20 candidate genes associated with pigment biosynthesis in black sesame seed, among which 10 were flavonoid biosynthesis and regulatory genes. These genes also include isochorismate and polyphenol oxidase genes. By comparing the phenotypes and genes expressions of the black and white sesame seed at different development stages, this work revealed the important role of 8–14 DPA in black pigment biosynthesis and accumulation. Moreover, it unfolded candidate genes associated with black pigmentation in sesame. These findings provide a vast transcriptome dataset and list of genes that will be targeted for functional studies related to the molecular mechanism involved in biosynthesis and regulation of seed coat color in sesame.

scholarly journals Comparative genomic analysis of the tricarboxylic acid cycle members in four Solanaceae vegetable crops and expression pattern analysis in Solanum tuberosum

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yongming Liu ◽  
Jingtao Qu ◽  
Ziwen Shi ◽  
Peng Zhang ◽  
Maozhi Ren
Keyword(s):  
Solanum Tuberosum ◽  
Tricarboxylic Acid Cycle ◽  
Expression Patterns ◽  
Solanum Melongena ◽  
Genomic Analysis ◽  
Tca Cycle ◽  
Tissue Expression ◽  
Tricarboxylic Acid ◽  
Comparative Genomic ◽  
Vegetable Crops

Abstract Background The tricarboxylic acid (TCA) cycle is crucial for energy supply in animal, plant, and microbial cells. It is not only the main pathway of carbohydrate catabolism but also the final pathway of lipid and protein catabolism. Some TCA genes have been found to play important roles in the growth and development of tomato and potato, but no comprehensive study of TCA cycle genes in Solanaceae crops has been reported. Results In this study, we analyzed TCA cycle genes in four important Solanaceae vegetable crops (potato (Solanum tuberosum), tomato (Solanum lycopersicum), eggplant (Solanum melongena), and pepper (Capsicum annuum)) based on comparative genomics. The four Solanaceae crops had a total of 180 TCA cycle genes: 43 in potato, 44 in tomato, 40 in eggplant, and 53 in pepper. Phylogenetic analysis, collinearity analysis, and tissue expression patterns revealed the conservation of and differences in TCA cycle genes between the four Solanaceae crops and found that there were unique subgroup members in Solanaceae crops that were independent of Arabidopsis genes. The expression analysis of potato TCA cycle genes showed that (1) they were widely expressed in various tissues, and some transcripts like Soltu.DM.01G003320.1(SCoAL) and Soltu.DM.04G021520.1 (SDH) mainly accumulate in vegetative organs, and some transcripts such as Soltu.DM.12G005620.3 (SDH) and Soltu.DM.02G007400.4 (MDH) are preferentially expressed in reproductive organs; (2) several transcripts can be significantly induced by hormones, such as Soltu.DM.08G023870.2 (IDH) and Soltu.DM.06G029290.1 (SDH) under ABA treatment, and Soltu.DM.07G021850.2 (CSY) and Soltu.DM.09G026740.1 (MDH) under BAP treatment, and Soltu.DM.02G000940.1 (IDH) and Soltu.DM.01G031350.4 (MDH) under GA treatment; (3) Soltu.DM.11G024650.1 (SDH) can be upregulated by the three disease resistance inducers including Phytophthora infestans, acibenzolar-S-methyl (BTH), and DL-β-amino-n-butyric acid (BABA); and (4) the levels of Soltu.DM.01G045790.1 (MDH), Soltu.DM.01G028520.3 (CSY), and Soltu.DM.12G028700.1 (CSY) can be activated by both NaCl and mannitol. The subcellular localization results of three potato citrate synthases showed that Soltu.DM.01G028520.3 was localized in mitochondria, while Soltu.DM.12G028700.1 and Soltu.DM.07G021850.1 were localized in the cytoplasm. Conclusions This study provides a scientific foundation for the comprehensive understanding and functional studies of TCA cycle genes in Solanaceae crops and reveals their potential roles in potato growth, development, and stress response.

scholarly journals Identification of candidate genes controlling black seed coat and pod tip color in cowpea (Vigna unguiculata L. Walp)

2018 ◽  
Author(s):  
Ira A Herniter ◽  
María Muñoz-Amatriaín ◽  
Sassoum Lo ◽  
Yi-Ning Guo ◽  
Timothy J Close
Keyword(s):  
Candidate Genes ◽  
Vigna Unguiculata ◽  
Seed Coat ◽  
Coat Color ◽  
Anthocyanin Biosynthesis ◽  
Biosynthesis Pathway ◽  
Seed Coat Color ◽  
Black Seed ◽  
Black Seed Coat ◽  
Myb Domain

ABSTRACTSeed coat color is an important part of consumer preferences for cowpea (Vigna unguiculata L. Walp). Color has been studied in numerous crop species and has often been linked to loci controlling the anthocyanin biosynthesis pathway. This study makes use of available resources, including mapping populations, a reference genome, and a high-density single nucleotide polymorphism genotyping platform, to map the black seed coat and purple pod tip color traits in cowpea. Several gene models encoding MYB domain protein 113 were identified as candidate genes. MYB domain proteins have been shown in other species to control expression of genes encoding enzymes for the final steps in the anthocyanin biosynthesis pathway. PCR analysis indicated that a presence/absence variation of one or more MYB113 genes may control the presence or absence of black pigment. A PCR marker has been developed for black seed coat color in cowpea.

Transcriptome Analysis of Black and White Sesame Seed Reveals Candidate Genes Associated with Black Seed Development in Sesame (Sesamum Indicum)

2020 ◽  
Author(s):  
Senouwa Segla Koffi Dossou ◽  
Linhai Wang ◽  
Xin Wei ◽  
Yanxin Zhang ◽  
Donghua Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Seed Development ◽  
Seed Coat ◽  
Coat Color ◽  
Sesame Seed ◽  
Sesamum Indicum ◽  
Seed Coat Color ◽  
Seed Formation ◽  
Black And White ◽  
Black Seed

Abstract Background: Seed coat color is a key agronomic characteristic in sesame (Sesamum indicum) since it is strongly linked to seed oil, proteins, and lignans content and it influences consumer preferences. Even though some QTL and candidate genes have been detected for sesame seed coat color, the mechanism and regulation of black pigmentation are not entirely understood. This study provides an overview of developing seeds transcriptome of two varieties of sesame “Zhongfengzhi No.1” (white seed) and “Zhongzhi No.33” (black seed) and shed light on genes involving in black seed formation.Results: Both black and white sesame showed similar trend expressed genes with the numbers increased at the early stages of seed development. The differentially expressed genes (DEGs) number increased with seed development in the two sesame varieties. We examined the DEGs and uncovered that the early stage, which is from 8 to 17 days post-anthesis (DPA) plays an important role in black pigment biosynthesis and accumulation. The gene expression patterns were consistent with the seed color change. Besides, we studied the shared DEGs between the black and white sesame. We figured out 17 candidate genes associated with pigments biosynthesis in black sesame seed including 2 chalcone synthase genes SIN_1018961 and SIN_1018959 which may function in the phenylpropanoid pathway. 5 of these candidate genes, SIN_1006242 and SIN_1016759/PPO, SIN_1026689 and SIN_1006025, SIN_1025056 are located on chromosomes 4, 8 and 11 respectively, in conformity with previous QTL mapping. These genes were believed to play a major role in black seed development in sesame. Conclusion: This work illuminated the different expression profiles in black and white sesames and unfolded pivotal stages and a catalog of candidate genes associated with black seed formation in sesame. These findings provide a vast transcriptome dataset and list of genes that will be targeted for functional studies related to the molecular mechanism involved in biosynthesis and regulation of seed coat color in sesame and for molecular breeding of high-quality sesame varieties.

scholarly journals Identification of Candidate Genes Regulating the Seed Coat Color Trait in Sesame (Sesamum indicum L.) Using an Integrated Approach of QTL Mapping and Transcriptome Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Chun Li ◽  
Yinghui Duan ◽  
Hongmei Miao ◽  
Ming Ju ◽  
Libin Wei ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Seed Coat ◽  
Transcriptome Analysis ◽  
Coat Color ◽  
Integrated Approach ◽  
Seed Coat Color ◽  
Seed Formation ◽  
Comparison Results ◽  
Transcriptome Comparison

Seed coat color is an important seed quality trait in sesame. However, the genetic mechanism of seed coat color variation remains elusive in sesame. We conducted a QTL mapping of the seed coat color trait in sesame using an F2 mapping population. With the aid of the newly constructed superdense genetic linkage map comprised of 22,375 bins distributed in 13 linkage groups (LGs), 17 QTLs of the three indices (i.e., L, a, and b values) of seed coat color were detected in seven intervals on four LGs, with a phenotype variance explanation rate of 4.46–41.53%. A new QTL qSCa6.1 on LG 6 and a QTL hotspot containing at least four QTLs on LG 9 were further identified. Variants screening of the target intervals showed that there were 84 genes which possessed the variants that were high-impact and co-segregating with the seed coat color trait. Meanwhile, we performed the transcriptome comparison of the developing seeds of a white- and a black-seeded variety, and found that the differentially expressed genes were significantly enriched in 37 pathways, including three pigment biosynthesis related pathways. Integration of variants screening and transcriptome comparison results suggested that 28 candidate genes probably participated in the regulation of the seed coat color in sesame; of which, 10 genes had been proved or suggested to be involved in pigments biosynthesis or accumulation during seed formation. The findings gave the basis for the mechanism of seed coat color regulation in sesame, and exhibited the effects of the integrated approach of genome resequencing and transcriptome analysis on the genetics analysis of the complex traits.

Sign in / Sign up

Export Citation Format

Share Document