Verification of Soybean Seed Coat Colour Specific Markers Reveals I Loci Specific Markers Capable for Distinguishing Genotypes Differing in Seed Coated Colour

2020 ◽  
Author(s):  
R. B. Shingare ◽  
V. P. Chimote ◽  
M. P. Deshmukh ◽  
T. J. Bhor ◽  
A. A. Kale
Keyword(s):  
Seed Coat ◽  
Coat Color ◽  
Soybean Seed ◽  
Coat Colour ◽  
Specific Primers ◽  
Seed Coat Colour ◽  
Yellow Seed ◽  
Black Seed ◽  
Soybean Seed Coat ◽  
Yellow Seed Coat

Background: In soybean yellow seed coat is preferred in the market, however, colored ones are currently gaining attention because of their medicinal and nutritive values; besides. Hence it is essential to breed varieties with desired seed coat colour. Methods: Twelve genotypes with six each having yellow and black seed coats were screened with fourteen primers linked to seed coat colour governing loci. Result: Out of them twelve primers showed polymorphism. Monomorphism was observed with both T loci specific and two of the three R loci specific primers. However I locus specific primers i.e. SM303, SM305 and TR showed polymorphism shared by their seed coat color. SM303 amplified a 180 bp sized band in yellow seed coated genotypes and a 130 bp band in black seed coated genotypes. SM305 amplified dual bands with a 200bp band being monomorphic and an additional band (192-216 bp range) present in only yellow seed coated genotypes, of which a 208 bp band was shared by four yellow seed coated genotypes. Cold induced seed coat discoloration specific TR primer generated bands of different size ranges in yellow seed coated (336-344 bp) and black seed coated genotypes (300-320), of which a 340 bp band was shared by four yellow seed coated genotypes.

Biochemical and molecuar marker based screening of seed longevity in soybean [Glycine max ( L.) Merill ]

2018 ◽  
Author(s):  
P. V. Pawar ◽  
R. M. Naik ◽  
M. P. Deshmukh ◽  
R. D. Satbhai ◽  
S. G. Mohite
Keyword(s):  
Lipid Peroxidation ◽  
Seed Coat ◽  
Coat Color ◽  
Soybean Seed ◽  
Coat Colour ◽  
Seed Longevity ◽  
Seed Coat Color ◽  
Seed Coat Colour ◽  
Black Seed ◽  
Black Seed Coat

The soybean seed is highly susceptible to field weathering and mechanical damage which adversely affect its longevity. Mechanical injury can occur at any time during harvesting, drying and storage conditioning of seeds. The seed coat color and leachate conductivity of soybean has been correlated with seed longevity and black seed coat color has been reported to be positively correlated with better seed longevity. In order to understand the physico-chemical attributes related to soybean seed longevity, biochemical and molecular analysis of the parents exhibiting black (Birsasoya-1) and yellow seed coat colour (EC 241780) and the eleven F3 progenies of the cross exhibiting brown, yellow and black seed coat colour was carried out. The results revealed that vita-E, lignin, calcium content and activity of antioxidative enzymes appeared to be positively correlated with soybean seed longevity and levels were higher in black and brown seed coat color progenies. The lipid peroxidation rate was inversely related to membrane injury caused by ROS and comparatively much less lipid peroxidation rate was recorded in black and brown seed coat colour parents and progenies having better seed longevity. The SSR primers Satt162, Satt523 and Satt453 which are either linked with seed coat colour and seed permeability exhibited a specific size allelic fragments in soybean genotypes and crosses with better seed longevity.

Identification of a major gene and RAPD markers for yellow seed coat colour in Brassica napus

Genome ◽  
2001 ◽  
Vol 44 (6) ◽  
pp. 1077-1082 ◽  
Author(s):  
Daryl J. Somers ◽  
Gerhard Rakow ◽  
Vinod K. Prabhu ◽  
Ken R.D. Friesen
Keyword(s):  
Brassica Napus ◽  
Seed Coat ◽  
Rapd Markers ◽  
Major Gene ◽  
Coat Colour ◽  
Seed Coat Colour ◽  
Yellow Seed ◽  
Yellow Seed Coat

Identification of a major gene and RAPD markers for yellow seed coat colour in Brassica napus

Genome ◽  
2001 ◽  
Vol 44 (6) ◽  
pp. 1077-1082 ◽  
Author(s):  
Daryl J Somers ◽  
Gerhard Rakow ◽  
Vinod K Prabhu ◽  
Ken RD Friesen
Keyword(s):  
Brassica Napus ◽  
Seed Coat ◽  
Rapd Markers ◽  
Major Gene ◽  
Coat Colour ◽  
Seed Coat Colour ◽  
Yellow Seed ◽  
Dh Population ◽  
Seed Trait ◽  
Yellow Seed Coat

The development of yellow-seeded Brassica napus for improving the canola-meal quality characteristics of lower fibre content and higher protein content has been restricted because no yellow-seeded forms of B. napus exist, and their conventional development requires interspecific introgression of yellow seed coat colour genes from related species. A doubled-haploid (DH) population derived from the F1 generation of the cross 'Apollo' (black-seeded) × YN90-1016 (yellow-seeded) B. napus was analysed via bulked segregant analysis to identify molecular markers associated with the yellow-seed trait in B. napus for future implementation in marker-assisted breeding. A single major gene (pigment 1) flanked by eight RAPD markers was identified co-segregating with the yellow seed coat colour trait in the population. This gene explained over 72% of the phenotypic variation in seed coat colour. Further analysis of the yellow-seeded portion of this DH population revealed two additional genes favouring 'Apollo' alleles, explaining 11 and 8.5%, respectively, of the yellow seed coat colour variation. The data suggested that there is a dominant, epistatic interaction between the pigment 1 locus and the two additional genes. The potential of the markers to be implemented in plant breeding for the yellow-seed trait in B. napus is discussed.Key words: Brassica napus, yellow seed, RAPD.

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

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.

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

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.

scholarly journals VaSDC1 Is Involved in Modulation of Flavonoid Metabolic Pathways in Black and Red Seed Coats in Adzuki Bean (Vigna angularis L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Liwei Chu ◽  
Pu Zhao ◽  
Kaili Wang ◽  
Bo Zhao ◽  
Yisong Li ◽  
...  
Keyword(s):  
Seed Coat ◽  
Metabolic Pathways ◽  
Nutritional Quality ◽  
Coat Colour ◽  
Myb Transcription Factor ◽  
Adzuki Bean ◽  
Vigna Angularis ◽  
Seed Coat Colour ◽  
Black Seed ◽  
Black Seed Coat

Seed coat colour is an important nutritional quality trait. Variations in anthocyanins and flavonoids induce the diversity of seed coat colour in adzuki bean (Vigna angularis L.). Red seed coat and black seed coat are important adzuki bean cultivars. Insights into the differences of flavonoid metabolic pathways between black and red adzuki bean are significant. In this study, we explored that the difference in seed coat colour between the red (Jingnong6) and the black (AG118) is caused by the accumulation of anthocyanins. The RNA-sequencing (RNA-Seq) and real-time reverse transcription (qRT)-PCR results showed that the Vigna angularis L. seed coat color (VaSDC1) gene, an R2R3-MYB transcription factor, should be the key gene to regulate the black and red seed coat colours. In three different colouring staes of seed development, VaSDC1 was specifically expressed in the black seed coat (AG118) landrace, which activates the structural genes of flavonoid metabolic pathways. As a result, this caused a substantial accumulation of anthocyanins and created a dark blue-black colour. In the red (Jingnong6) seed coat variety, low expression levels of VaSDC1 resulted in a lower accumulation of anthocyanins than in AG118. In addition, VaSDC1 was genetically mapped in the interval between simple-sequence repeat (SSR) markers Sca326-12, Sca326-4, and BAgs007 on chromosome 3 using an F4 segregating population derived from the cross between Jingnong6 and AG118. These results will facilitate the improvement of nutritional quality breeding in adzuki beans.

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

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10770
Author(s):  
Yanjing Ren ◽  
Ning Zhang ◽  
Ru Li ◽  
Xiaomin Ma ◽  
Lugang Zhang
Keyword(s):  
Brassica Rapa ◽  
Seed Coat ◽  
Biosynthetic Pathway ◽  
Coat Color ◽  
Seed Coat Color ◽  
Rna Seq ◽  
Yellow Seed ◽  
Color Formation ◽  
Flavonoid Biosynthetic Pathway ◽  
Yellow Seed Coat

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.

scholarly journals Breeding of Black Soybean with Green Cotyledon and Four Recessive Alleles for Lipoxygenase, Kunitz Trypsin Inhibitor, Lectin, and Stachyose

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 309
Author(s):  
Sang Woo Choi ◽  
Jae Eun Kang ◽  
Seong Kyeong Lee ◽  
Sarath Ly ◽  
Jong Il Chung
Keyword(s):  
Seed Coat ◽  
Coat Color ◽  
Soybean Seed ◽  
Breeding Line ◽  
Seed Coat Color ◽  
Kunitz Trypsin Inhibitor ◽  
Black Soybean ◽  
Black Seed ◽  
Green Cotyledon ◽  
Black Seed Coat

Anthocyanins from the black soybean seed coat are known to have many pharmaceutical effects. However, black soybean seed contains antinutritional factors such as lipoxygenase, Kunitz trypsin inhibitor (KTI), lectin, and stachyose. The genetic removal of these components will improve the nutritional value of black soybean seed. The objective of this research was to breed a soybean strain with the black seed coat color, green cotyledon color, and tetra recessive allele (lox1lox2lox3/lox1lox2lox3-ti/ti-le/le-rs2/rs2) for lipoxygenase, KTI, lectin, and stachyose components. Eight parents were used to breed the tetra null strain. Analysis of lipoxygenase, KTI, lectin, and stachyose components in mature seeds was conducted by SDS-PAGE, Western blot, and HPLC. The soybean line with the black seed coat color, the green cotyledon color, a large seed size, and tetra recessive alleles has purple flowers, a determinate growth habit, and brown pods at maturity. The stem height of the breeding line was 52.3 cm. The 100-seed weight of the breeding line was 35.2 g and the yield (Ton/ha) was 2.50. The stachyose content of the breeding line was 3.30 g/kg. This is the first soybean strain with the black seed coat color, the green cotyledon color, a large seed size, and tetra null alleles (lox1lox2lox3/lox1lox2lox3-ti/ti-le/le-rs2/rs2, low content of stachyose, free of lipoxygenase, KTI, and lectin proteins).

scholarly journals Inheritance of black seed coat colour in lentil

2020 ◽  
Author(s):  
G.N. Suvorova ◽  
Keyword(s):  
Seed Coat ◽  
Coat Colour ◽  
Seed Coat Colour ◽  
Black Seed ◽  
Black Seeds ◽  
Grey Colour ◽  
Black Seed Coat ◽  
Dominant Genes

The purpose of the research was to determine the inheritance of black seed coat colour in lentil variety ‘Beluga’. The seeds collected from F1 plants in cross of ‘Rauza’ (yellow seeds) × ‘Beluga’ (black seeds) were of grey colour with black mottles. F2 ratio of nonblack and black seeds was 62:6, which corresponded to 15:1 dihybrid segregation. It is concluded that the black seed coat colour of ‘Beluga’ is controlled by two dominant genes.

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