scholarly journals Genetic Analysis and QTL Mapping of Seed Coat Color in Sesame (Sesamum indicum L.)

PLoS ONE ◽  
2013 ◽  
Vol 8 (5) ◽  
pp. e63898 ◽  
Author(s):  
Haiyang Zhang ◽  
Hongmei Miao ◽  
Libin Wei ◽  
Chun Li ◽  
Ruihong Zhao ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Qtl Mapping ◽  
Seed Coat ◽  
Coat Color ◽  
Sesamum Indicum ◽  
Seed Coat Color

scholarly journals A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.)

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Hua Du ◽  
Haiyang Zhang ◽  
Libin Wei ◽  
Chun Li ◽  
Yinghui Duan ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Seed Size ◽  
Genetic Map ◽  
Seed Coat ◽  
Coat Color ◽  
Sesamum Indicum ◽  
High Density ◽  
Oilseed Crop ◽  
Seed Coat Color ◽  
Specific Length

Abstract Background Sesame (Sesamum indicum L., 2n = 2x = 26) is an important oilseed crop with high oil content but small seed size. To reveal the genetic loci of the quantitative seed-related traits, we constructed a high-density single nucleotide polymorphism (SNP) linkage map of an F2 population by using specific length amplified fragment (SLAF) technique and determined the quantitative trait loci (QTLs) of seed-related traits for sesame based on the phenotypes of F3 progeny. Results The genetic map comprised 2159 SNP markers distributed on 13 linkage groups (LGs) and was 2128.51 cM in length, with an average distance of 0.99 cM between adjacent markers. QTL mapping revealed 19 major-effect QTLs with the phenotypic effect (R2) more than 10%, i.e., eight QTLs for seed coat color, nine QTLs for seed size, and two QTLs for 1000-seed weight (TSW), using composite interval mapping method. Particularly, LG04 and LG11 contained collocated QTL regions for the seed coat color and seed size traits, respectively, based on their close or identical locations. In total, 155 candidate genes for seed coat color, 22 for seed size traits, and 54 for TSW were screened and analyzed. Conclusions This report presents the first QTL mapping of seed-related traits in sesame using an F2 population. The results reveal the location of specific markers associated with seed-related traits in sesame and provide the basis for further seed quality traits research.

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.

QTL Mapping of Seed Coat Color for Yellow Seeded Brassica napus

2006 ◽  
Vol 33 (2) ◽  
pp. 181-187 ◽  
Author(s):  
Lie-Zhao LIU ◽  
Jin-Ling MENG ◽  
Na LIN ◽  
Li CHEN ◽  
Zhang-Lin TANG ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Qtl Mapping ◽  
Seed Coat ◽  
Coat Color ◽  
Seed Coat Color

scholarly journals Genetics of seed coat color in sesame (Sesamum indicum L.)

2013 ◽  
Vol 12 (42) ◽  
pp. 6061-6067 ◽  
Author(s):  
K P Sarita ◽  
ey ◽  
Das Arna ◽  
Dasgupta Tapash
Keyword(s):  
Seed Coat ◽  
Coat Color ◽  
Sesamum Indicum ◽  
Seed Coat Color

scholarly journals A genetic analysis of red seed-coat color inPhaseolus vulgaris

Hilgardia ◽  
1939 ◽  
Vol 12 (9) ◽  
pp. 551-621 ◽  
Author(s):  
Francis L. Smith
Keyword(s):  
Genetic Analysis ◽  
Seed Coat ◽  
Coat Color ◽  
Seed Coat Color

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 Genome-wide association study of seed coat color in sesame (Sesamum indicum L.)

2019 ◽  
Author(s):  
Hongxian Mei ◽  
Chengqi Cui ◽  
Yanyang Liu ◽  
Yan Liu ◽  
Xianghua Cui ◽  
...  
Keyword(s):  
Seed Coat ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Coat Color ◽  
Sesame Seed ◽  
Significant Snps ◽  
Sesamum Indicum ◽  
Genome Wide Association ◽  
Seed Coat Color ◽  
Genome Wide

Abstract Background: Sesame (Sesamum indicum L.) is an important and ancient oilseed crop. Sesame seed coat color is an extremely important agronomic trait, and is related to biochemical functions involved in protein and oil metabolism, and antioxidant content. Because of its complication, the genetic basis of sesame seed coat color remains poorly understood.Results: Genome-wide association study (GWAS) using 42,781 SNPs was performed with a diverse association-mapping panel comprising 366 sesame germplasm lines in 12 environments. In total, 224 significant SNPs (P < 2.34×10−7) explaining approximately 13.34% of the phenotypic variation on average were identified, and 35 significant SNPs were detected in more than 6 environments. Out of 224 significant SNPs, 22 were located in the confidence intervals of previous reported quantitative trait loci (QTLs). A total of 92 candidate genes were identified in the vicinity of the 4 SNPs that were most significantly associated with sesame seed coat color. Conclusions: The results in this paper will provide new insights into the genetic basis of sesame seed coat color, and should be useful for molecular breeding in sesame.

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.

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

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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