scholarly journals A Novel Pinkish-White Flower Color Variant Is Caused by a New Allele of Flower Color Gene W1 in Wild Soybean (Glycine soja)

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1001
Author(s):  
Jagadeesh Sundaramoorthy ◽  
Gyu Tae Park ◽  
Hyun Jo ◽  
Jeong-Dong Lee ◽  
Hak Soo Seo ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Functional Activity ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Flower Color ◽  
Loss Of Function ◽  
Protein Variation ◽  
Color Variant ◽  
Color Gene

The enzyme flavonoid 3′,5′-hydroxylase (F3′5′H) plays an important role in producing anthocyanin pigments in soybean. Loss of function of the W1 locus encoding F3′5′H always produces white flowers. However, few color variations have been reported in wild soybean. In the present study, we isolated a new color variant of wild soybean accession (IT261811) with pinkish-white flowers. We found that the flower’s pinkish-white color is caused by w1-s3, a single recessive allele of W1. The SNP detected in the mutant caused amino acid substitution (A304S) in a highly conserved SRS4 domain of F3′5′H proteins. On the basis of the results of the protein variation effect analyzer (PROVEAN) tool, we suggest that this mutation may lead to hypofunctional F3′5′H activity rather than non-functional activity, which thereby results in its pinkish-white color.

scholarly journals A new allele of flower color gene W1 encoding flavonoid 3'5'-hydroxylase is responsible for light purple flowers in wild soybean Glycine soja

2010 ◽  
Vol 10 (1) ◽  
pp. 155 ◽  
Author(s):  
Ryoji Takahashi ◽  
Joseph G Dubouzet ◽  
Hisakazu Matsumura ◽  
Kentaro Yasuda ◽  
Tsukasa Iwashina
Keyword(s):  
Glycine Soja ◽  
Wild Soybean ◽  
Flower Color ◽  
Color Gene

Evaluation of seed amino acid content and its correlation network analysis in wild soybean (Glycine soja) germplasm in Japan

2021 ◽  
Vol 19 (1) ◽  
pp. 35-43
Author(s):  
Awatsaya Chotekajorn ◽  
Takuyu Hashiguchi ◽  
Masatsugu Hashiguchi ◽  
Hidenori Tanaka ◽  
Ryo Akashi
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Free Amino Acid ◽  
Acid Content ◽  
Free Amino ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Amino Acid Content ◽  
Soybean Seeds ◽  
Free Amino Acid Content

AbstractWild soybean (Glycine soja) is a valuable genetic resource for soybean improvement. Seed composition profiles provide beneficial information for the effective conservation and utilization of wild soybeans. Therefore, this study aimed to assess the variation in free amino acid abundance in the seeds of wild soybean germplasm collected in Japan. The free amino acid content in the seeds from 316 accessions of wild soybean ranged from 0.965 to 5.987 mg/g seed dry weight (DW), representing a 6.2-fold difference. Three amino acids had the highest coefficient of variation (CV): asparagine (1.15), histidine (0.95) and glutamine (0.94). Arginine (0.775 mg/g DW) was the predominant amino acid in wild soybean seeds, whereas the least abundant seed amino acid was glutamine (0.008 mg/g DW). A correlation network revealed significant positive relationships among most amino acids. Wild soybean seeds from different regions of origin had significantly different levels of several amino acids. In addition, a significant correlation between latitude and longitude of the collection sites and the total free amino acid content of seeds was observed. Our study reports diverse phenotypic data on the free amino acid content in seeds of wild soybean resources collected from throughout Japan. This information will be useful in conservation programmes for Japanese wild soybean and for the selection of accessions with favourable characteristics in future legume crop improvement efforts.

scholarly journals Genetic characterization of a novel Tib-derived variant of soybean Kunitz trypsin inhibitor detected in wild soybean (Glycine soja)

Genome ◽  
2004 ◽  
Vol 47 (1) ◽  
pp. 9-14 ◽  
Author(s):  
Ke-Jing Wang ◽  
Tetsuro Yamashita ◽  
Masao Watanabe ◽  
Yoshihito Takahata
Keyword(s):  
Amino Acid ◽  
Trypsin Inhibitor ◽  
Glycine Soja ◽  
Polyacrylamide Gel Electrophoresis ◽  
Wild Soybean ◽  
Amino Acid Sequences ◽  
Kunitz Trypsin Inhibitor ◽  
Variant Type ◽  
New Variant ◽  
Novel Variant

A novel variant of soybean Kunitz trypsin inhibitor (SKTI) was detected in 530 lines of wild soybean (Glycine soja). This variant showed an intermediate electrophoretic mobility between the Tia and Tic types. In isoelectric focusing polyacrylamide gel electrophoresis gels containing urea, this variant had a similar isoelectric point as that of Tia. The genetic analysis of SKTI bands in F2 seeds from crosses of the new variant type with Tia or Tic type showed that this variant type is controlled by a codominant allele at the SKTI locus. We propose the genetic symbol Tif for this novel variant. When the nucleotide sequence of the Tif gene was compared with those of other types of SKTI genes (Tia, Tib, and Tic), the sequence of Tif was identical to that of Tib with the exception of one A[Formula: see text]G transitional mutation occurring at position 676 of Tif. This mutation resulted in an amino acid change from Lys to Glu at the 178 residue. These results suggest that this variant is derived from Tib through a point mutation. In addition, we settled an inconsistency in the number of amino acid differences between Tia and Tib (eight or nine). Analysis of nucleotide and amino acid sequences revealed that Tib was different from Tia by nine amino acids.Key words: soybean Kunitz trypsin inhibitor, polymorphism, gene sequence, soybean, wild soybean.

scholarly journals splitGFP Technology Reveals Dose-Dependent ER-Mitochondria Interface Modulation by α-Synuclein A53T and A30P Mutants

Cells ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 1072 ◽  
Author(s):  
Tito Calì ◽  
Denis Ottolini ◽  
Mattia Vicario ◽  
Cristina Catoni ◽  
Francesca Vallese ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Mitochondrial Function ◽  
Cell Metabolism ◽  
Loss Of Function ◽  
Function Mechanism ◽  
Dose Dependent ◽  
Familial Parkinson’S Disease ◽  
Interface Modulation

Familial Parkinson’s disease (PD) is associated with duplication or mutations of α-synuclein gene, whose product is a presynaptic cytosolic protein also found in mitochondria and in mitochondrial-associated ER membranes. We have originally shown the role of α-syn as a modulator of the ER-mitochondria interface and mitochondrial Ca2+ transients, suggesting that, at mild levels of expression, α-syn sustains cell metabolism. Here, we investigated the possibility that α-syn action on ER-mitochondria tethering could be compromised by the presence of PD-related mutations. The clarification of this aspect could contribute to elucidate key mechanisms underlying PD. The findings reported so far are not consistent, possibly because of the different methods used to evaluate ER-mitochondria connectivity. Here, the effects of the PD-related α-syn mutations A53T and A30P on ER-mitochondria relationship were investigated in respect to Ca2+ handling and mitochondrial function using a newly generated SPLICS sensor and aequorin-based Ca2+measurements. We provided evidence that A53T and A30P amino acid substitution does not affect the ability of α-syn to enhance ER/mitochondria tethering and mitochondrial Ca2+ transients, but that this action was lost as soon as a high amount of TAT-delivered A53T and A30P α-syn mutants caused the redistribution of α-syn from cytoplasm to foci. Our results suggest a loss of function mechanism and highlight a possible connection between α-syn and ER-mitochondria Ca2+ cross-talk impairment to the pathogenesis of PD.

Hubsm: A Novel Amino Acid Substitution Matrix for Comparing Hub Proteins

2017 ◽  
Vol 7 (8) ◽  
pp. 212
Author(s):  
Renganayaki G. ◽  
Achuthsankar S. Nair
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Low Complexity ◽  
Database Search ◽  
Substitution Matrix ◽  
Compositional Bias ◽  
Sequence Alignments ◽  
Amino Acid Substitution Matrix ◽  
Alignment Algorithms ◽  
Hub Proteins

Sequence alignment algorithms and  database search methods use BLOSUM and PAM substitution matrices constructed from general proteins. These de facto matrices are not optimal to align sequences accurately, for the proteins with markedly different compositional bias in the amino acid.   In this work, a new amino acid substitution matrix is calculated for the disorder and low complexity rich region of Hub proteins, based on residue characteristics. Insights into the amino acid background frequencies and the substitution scores obtained from the Hubsm unveils the  residue substitution patterns which differs from commonly used scoring matrices .When comparing the Hub protein sequences for detecting homologs,  the use of this Hubsm matrix yields better results than PAM and BLOSUM matrices. Usage of Hubsm matrix can be optimal in database search and for the construction of more accurate sequence alignments of Hub proteins.

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