scholarly journals Seed Coat Pattern QTL and Development in Cowpea (Vigna unguiculata [L.] Walp.)

2019 ◽  
Author(s):  
Ira A. Herniter ◽  
Ryan Lo ◽  
María Muñoz-Amatriaín ◽  
Sassoum Lo ◽  
Yi-Ning Guo ◽  
...  
Keyword(s):  
Vigna Unguiculata ◽  
Seed Coat ◽  
Consumer Preference ◽  
Single Nucleotide ◽  
Helix Loop Helix ◽  
Genotyping Platform ◽  
Coat Pattern ◽  
Genome Assemblies ◽  
Mapping Populations ◽  
Seed Coat Pattern

AbstractThe appearance of the seed is an important aspect of consumer preference for cowpea (Vigna unguiculata [L.] Walp.). Seed coat pattern in cowpea has been a subject of study for over a century. This study makes use of newly available resources, including mapping populations, a reference genome and additional genome assemblies, and a high-density single nucleotide polymorphism genotyping platform, to map various seed coat pattern traits to three loci, concurrent with the Color Factor (C), Watson (W), and Holstein (H) factors identified previously. Several gene models encoding proteins involved in regulating the later stages of the flavonoid biosynthesis pathway have been identified as candidate genes, including a basic helix-loop-helix gene (Vigun07g110700) for the C locus, a WD-repeat gene (Vigun09g139900) for the W locus and an E3 ubiquitin ligase gene (Vigun10g163900) for the H locus. A model of seed coat development, consisting of six distinct stages, is described to explain some of the observed pattern phenotypes.

scholarly journals Seed Coat Pattern QTL and Development in Cowpea (Vigna unguiculata [L.] Walp.)

2019 ◽  
Vol 10 ◽  
Author(s):  
Ira A. Herniter ◽  
Ryan Lo ◽  
María Muñoz-Amatriaín ◽  
Sassoum Lo ◽  
Yi-Ning Guo ◽  
...  
Keyword(s):  
Vigna Unguiculata ◽  
Seed Coat ◽  
Coat Pattern ◽  
Seed Coat Pattern

scholarly journals Morphological characterization of lentil accessions: Qualitative characters

2013 ◽  
Vol 41 (2) ◽  
pp. 187-190
Author(s):  
S Roy ◽  
MA Islam ◽  
A Sarker ◽  
MR Ismail ◽  
MY Rafii ◽  
...  
Keyword(s):  
Seed Coat ◽  
Flower Colour ◽  
Morphological Characterization ◽  
Normal Green ◽  
Coat Pattern ◽  
Wide Variability ◽  
Qualitative Characters ◽  
Stem Colour ◽  
Seed Coat Pattern

Wide variability was observed for all the characters among 110 lentil accessions. Stem colour varied from normal green (45%) to purple (55%). Prominent and rudimentary tendrils were found in 60% and 40% of the accessions, respectively. Among the characters, flower colour showed the highest variation. White flower colour was observed in 49%, violet in 28%, white with blue veins in 20% accessions and the rest 3% were with blue flowers. Red cotyledon was shown by 90% while with yellow was shown by 10% of the accessions. Green, grey and brown seed coat was observed in 10, 66 and 24% of the accessions, respectively. Seed coat pattern with dots was found in 70% accessions and marbled seed coat pattern was shown by 15.5% while 14.5% did not show any seed coat pattern. DOI: http://dx.doi.org/10.3329/bjb.v41i2.13447 Bangladesh J. Bot. 41(2): 187-190, 2012 (December)

scholarly journals Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 705
Author(s):  
John Carlos I. Ignacio ◽  
Maricris Zaidem ◽  
Carlos Casal ◽  
Shalabh Dixit ◽  
Tobias Kretzschmar ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Rice Varieties ◽  
Single Nucleotide ◽  
Genotyping Platform ◽  
Anaerobic Germination ◽  
Direct Seeded ◽  
Mapping By Sequencing ◽  
Simple Sequence

Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germination (AG). To map the genetic basis of its tolerance, we examined a population of 200 F2:3 families derived from a cross between IR64 and ASD1 using the restriction site-associated DNA sequencing (RAD-seq) technology. This genotyping platform enabled the identification of 1921 single nucleotide polymorphism (SNP) markers to construct a high-resolution genetic linkage map with an average interval of 0.9 cM. Two significant quantitative trait loci (QTLs) were detected on chromosomes 7 and 9, qAG7 and qAG9, with LOD scores of 7.1 and 15.0 and R2 values of 15.1 and 29.4, respectively. Here, we obtained more precise locations of the QTLs than traditional simple sequence repeat and low-density SNP genotyping methods and may help further dissect the genetic factors of these QTLs.

scholarly journals From raw reads to trees: Whole genome SNP phylogenetics across the tree of life

2015 ◽  
Author(s):  
Sanaa Afroz Ahmed ◽  
Chien-Chi Lo ◽  
Po-E Li ◽  
Karen W Davenport ◽  
Patrick S.G. Chain
Keyword(s):  
Ad Hoc ◽  
Phylogenetic Reconstruction ◽  
Clinical Samples ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Complex Samples ◽  
Phylogenetic Characterization ◽  
Genome Wide ◽  
Genome Assemblies

Next-generation sequencing is increasingly being used to examine closely related organisms. However, while genome-wide single nucleotide polymorphisms (SNPs) provide an excellent resource for phylogenetic reconstruction, to date evolutionary analyses have been performed using different ad hoc methods that are not often widely applicable across different projects. To facilitate the construction of robust phylogenies, we have developed a method for genome-wide identification/characterization of SNPs from sequencing reads and genome assemblies. Our phylogenetic and molecular evolutionary (PhaME) analysis software is unique in its ability to take reads and draft/complete genome(s) as input, derive core genome alignments, identify SNPs, construct phylogenies and perform evolutionary analyses. Several examples using genomes and read datasets for bacterial, eukaryotic and viral linages demonstrate the broad and robust functionality of PhaME. Furthermore, the ability to incorporate raw metagenomic reads from clinical samples with suspected infectious agents shows promise for the rapid phylogenetic characterization of pathogens within complex samples.

Genotypic variation for phenolic compounds in developing and whole seeds, and storage conditions influence visual seed quality of yellow dry bean genotypes

2020 ◽  
Vol 100 (3) ◽  
pp. 284-295
Author(s):  
Mei Xiong ◽  
Mengli Zhao ◽  
Zhen-Xiang Lu ◽  
Parthiba Balasubramanian
Keyword(s):  
Antioxidant Activity ◽  
Phenolic Compounds ◽  
Seed Coat ◽  
Storage Temperature ◽  
Condensed Tannin ◽  
Consumer Preference ◽  
Coat Colour ◽  
Seed Coat Colour ◽  
Duration Of Storage

Seed coat colour is an important determinant of the visual quality of dry beans, as seeds are sold as a dry commodity. Phenolic compounds have a major effect on the colour of bean seeds. The objectives of the study were to determine the changes in phenolic compounds during seed development and in whole seeds of yellow bean genotypes with contrasting seed coat colour, and the effects of storage temperature and duration on seed phenolics and colour. Condensed tannin, phenolic acid, flavonoids, and antioxidant activity were observed as early as 10 d after flowering in the developing seeds of Arikara Yellow, which darken at harvest and during postharvest storage. In contrast, for CDC Sol and AAC Y073 seeds which remain yellow, phenolic compounds and antioxidant activity were consistently low. Seed brightness (L*) and yellow colour (b*) were negatively correlated with phenolic compounds and antioxidant activity, and conversely seed redness (a*) was positively correlated with phenolic compounds, confirming a negative influence of phenolic compounds on seed coat colour. Yellow bean genotypes had low anthocyanin but were high in β-carotene. Storage temperature influenced condensed tannin and seed coat colour, whereas the duration of storage influenced phenolic compounds, antioxidant activity, and seed coat colour. Higher temperatures (20 or 30 °C) and longer storage duration (120 or 180 d) generally resulted in darker seeds with increasing redness compared with seeds stored at 6 °C or for 60 d. AAC Y073 and CDC Sol with improved seed coat colour may increase consumer preference, value, and marketability of yellow beans.

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