scholarly journals Tissue Specific Transcriptome Profiling and Genetic Region Marker Discovery of Indian Sesame (Sisemum indicum L.)

2021 ◽  
Author(s):  
Sarika Jaiswal ◽  
Rukam S. Tomar ◽  
Komal Vadukool ◽  
Uma . ◽  
Meenu Chopra ◽  
...  
Keyword(s):  
Crop Improvement ◽  
Transcriptome Profiling ◽  
Flower Bud ◽  
Improvement Program ◽  
Tissue Specific ◽  
Trait Improvement ◽  
Variant Analysis ◽  
Genomic Resource ◽  
Putative Marker ◽  
Marker Discovery

Sesame (Sesamum indicum L.), is rich source of oil, protein and potent antioxidants with wide applications. Molecular approach can be of great use for trait improvement as well more availability for this crop. The present work aims at tissue specific transcriptome profiling along with biochemical pathway analysis and genic region putative marker discovery. We report 14389, 9465 and 5490 DEGs in root, leaf and flower-bud tissues, respectively. 135, 113 and 120 cellular metabolic or signaling pathways having common 118 pathways were found in root-leaf (RL), leaf-flower (LF) and flower-root (FR), respectively. 218, 170 and 180 transcription factors were identified in root, leaf and flower transcriptome, respectively. Among DEGs, microRNA targets predicted were 534, 376 and 173 in root, leaf and flower, respectively. Genic region repeat analysis revealed 379 SSR. Further variant analysis revealed 3371, 5439 and 4975 SNPs and 2257, 2403 and 2411 INDELs in root, leaf and flower, respectively. The present study will aid in understanding the major biochemical pathways operating in different tissues. Genic region putative marker discovery can be a valuable genomic resource for future crop improvement program.

scholarly journals Transcriptomic Analysis of the Anthocyanin Biosynthetic Pathway Reveals the Molecular Mechanism Associated with Purple Color Formation in Dendrobium Nestor

Life ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 113
Author(s):  
Xueqiang Cui ◽  
Jieling Deng ◽  
Changyan Huang ◽  
Xuan Tang ◽  
Xianmin Li ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Developmental Stages ◽  
Anthocyanin Biosynthesis ◽  
Transcriptome Profiling ◽  
Flower Color ◽  
Flower Bud ◽  
Color Formation ◽  
Color Development ◽  
Purple Coloration ◽  
Purple Color

Dendrobium nestor is a famous orchid species in the Orchidaceae family. There is a diversity of flower colorations in the Dendrobium species, but knowledge of the genes involved and molecular mechanism underlying the flower color formation in D. nestor is less studied. Therefore, we performed transcriptome profiling using Illumina sequencing to facilitate thorough studies of the purple color formation in petal samples collected at three developmental stages, namely—flower bud stage (F), half bloom stage (H), and full bloom stage (B) in D. nestor. In addition, we identified key genes and their biosynthetic pathways as well as the transcription factors (TFs) associated with purple flower color formation. We found that the phenylpropanoid–flavonoid–anthocyanin biosynthesis genes such as phenylalanine ammonia lyase, chalcone synthase, anthocyanidin synthase, and UDP-flavonoid glucosyl transferase, were largely up-regulated in the H and B samples as compared to the F samples. This upregulation might partly account for the accumulation of anthocyanins, which confer the purple coloration in these samples. We further identified several differentially expressed genes related to phytohormones such as auxin, ethylene, cytokinins, salicylic acid, brassinosteroid, and abscisic acid, as well as TFs such as MYB and bHLH, which might play important roles in color formation in D. nestor flower. Sturdy upregulation of anthocyanin biosynthetic structural genes might be a potential regulatory mechanism in purple color formation in D. nestor flowers. Several TFs were predicted to regulate the anthocyanin genes through a K-mean clustering analysis. Our study provides valuable resource for future studies to expand our understanding of flower color development mechanisms in D. nestor.

scholarly journals Tissue-Specific Transcriptome Profiling of Plutella Xylostella Third Instar Larval Midgut

2012 ◽  
Vol 8 (8) ◽  
pp. 1142-1155 ◽  
Author(s):  
Wen Xie ◽  
Yanyuan Lei ◽  
Wei Fu ◽  
Zhongxia Yang ◽  
Xun Zhu ◽  
...  
Keyword(s):  
Plutella Xylostella ◽  
Transcriptome Profiling ◽  
Tissue Specific ◽  
Larval Midgut

scholarly journals Economic Benefits of Foreign Sourced Germplasm in Domestic Crop Improvement Program: A Case of an Improved Khumal-4 Rice Variety in Nepal

2016 ◽  
Vol 4 ◽  
pp. 107-120 ◽  
Author(s):  
D Gauchan ◽  
K P Pant ◽  
B K Joshi
Keyword(s):  
Rice Variety ◽  
Crop Improvement ◽  
Market Price ◽  
Economic Benefits ◽  
International Exchange ◽  
Improvement Program ◽  
Economic Surplus ◽  
Rice Area ◽  
Multilateral System ◽  
Yield Gain

This study assesses economic benefits of international exchange and flow of key rice germplasm in Nepal under globally operated multilateral system of facilitated access using a case of an improved rice variety Khumal-4. Khumal-4 rice is popular and widely grown in mid hills region of Nepal which was developed by crossing a high yielding dwarf foreign sourced germplasm IR-28 with a local Nepali variety Pokharilo Masino. Economic benefits of Khumal-4 rice adoption and impact was analysed using economic surplus model, where additional productivity and profitability gained from developing Khumal-4 was estimated in monetary value in comparison with existing farmers’ variety Pokharilo masino. The finding showed that Khumal-4 covered 9% of rice area in the mid-hills and 7% in the mountains during year 2010-12 years covering about 40 thousand hectares of rice area. Data show that there is a clear yield gain of 1.25 mt per hectare with cost in rice yield equivalent when farmers switch from traditional Pokhareli Masino to improved Khumal-4 variety. Estimation of additional revenue per hectare with total adoption area of Khumal-4 in prevailing market price in Nepal was NRs 1.07 billion (US $ 11 million) per annum. This is reasonable economic benefits obtained annually from flow of foreign sourced genes (IR-28) for the development of an improved Khumal-4 rice variety in Nepal. This finding indicates that access to foreign germplasm is important for ensuring national food security and gaining higher economic benefits in the country.Agronomy Journal of Nepal (Agron JN) vol. 4, 2016

scholarly journals Comparative Transcriptome Profiling of High and Low oil yielding Santalum album L.

2021 ◽  
Author(s):  
Tanzeem Fatima ◽  
Rangachari Krishnan ◽  
Ashutosh Srivastava ◽  
Vageeshbabu S. Hanur ◽  
M. Srinivasa Rao
Keyword(s):  
Transcriptome Profiling ◽  
Santalum Album ◽  
Rna Seq ◽  
Improvement Program ◽  
East Indian ◽  
Kegg Pathways ◽  
Oil Biosynthesis ◽  
Genome Wide ◽  
A Genome ◽  
Santalum Album L

East Indian Sandalwood (Santalum album L.) is highly valued for its heartwood and its oil. There have been no efforts to comparative study of high and low oil yielding genetically identical sandalwood trees grown in similar climatic condition. Thus we intend to study a genome wide transcriptome analysis to identify the corresponding genes involved in high oil biosynthesis in S. album. In this study, 15 years old S. album (SaSHc and SaSLc) genotypes were targeted for analysis to understand the contribution of genetic background on high oil biosynthesis in S. album. A total of 28,959187 and 25,598869 raw PE reads were generated by the Illumina sequencing. 2.12 million and 1.811 million coding sequences were obtained in respective accessions. Based on the GO terms, functional classification of the CDS 21262, & 18113 were assigned into 26 functional groups of three GO categories; (4,168; 3,641) for biological process (5,758;4,971) cellular component and (5,108;4,441) for molecular functions. Total 41,900 and 36,571 genes were functionally annotated and KEGG pathways of the DEGs resulted 213 metabolic pathways. In this, 14 pathways were involved in secondary metabolites biosynthesis pathway in S. album. Among 237 cytochrome families, nine groups of cytochromes were participated in high oil biosynthesis. 16,665 differentially expressed genes were commonly detected in both the accessions (SaHc and SaSLc). The results showed that 784 genes were upregulated and 339 genes were downregulated in SaHc whilst 635 upregulated 299 downregulated in SaSLc S. album. RNA-Seq results were further validated by quantitative RT-PCR. Maximum Blast hits were found to be against Vitis vinifera. From this study we have identified additional number of cytochrome family in SaHc. The accessibility of a RNA-Seq for high oil yielding sandalwood accessions will have broader associations for the conservation and selection of superior elite samples/populations for further genetic improvement program.

scholarly journals Population structure and genetic diversity analysis in Sali (Oryza sativa) rice germplasm of Assam using microsatellite markers

2021 ◽  
Vol 58 (2) ◽  
pp. 279-286
Author(s):  
Sandhani Saikia ◽  
Pratap Jyoti Handique ◽  
Mahendra K Modi
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Improvement ◽  
Crop Improvement ◽  
Mean Value ◽  
Diversity Analysis ◽  
Rice Cultivars ◽  
Improvement Program ◽  
Information Index ◽  
Improvement Programs

Genetic diversity is the source of novel allelic combinations that can be efficiently utilized in any crop improvement program. To facilitate future crop improvement programs in rice, a study was designed to identify the underlying genetic variations in the Sali rice germplasms of Assam using SSR markers. The 129 SSR markers that were used in the study amplified a total of 765 fragments with an average of 5.93 alleles per locus. The Shannon's Information Index was found to be in the range from 0.533 to 1.786. The Polymorphism Information Content (PIC) fell into the range from 0.304 to 0.691 with a mean value of 0.55. The overall FST value was found to be 0.519 that indicated the presence of genetic differentiation amongst the genotypes used in the study. The Sali population was divided into two clusters. The information obtained from the present study will facilitate the genetic improvement of Sali rice cultivars.

scholarly journals Mutation Breeding in Tomato: Advances, Applicability and Challenges

Plants ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 128 ◽  
Author(s):  
Juhi Chaudhary ◽  
Alisha Alisha ◽  
Vacha Bhatt ◽  
Sonali Chandanshive ◽  
Nirbhay Kumar ◽  
...  
Keyword(s):  
Genome Editing ◽  
Large Scale ◽  
Insertional Mutagenesis ◽  
Crop Improvement ◽  
Mutation Breeding ◽  
Tomato Crop ◽  
Technological Advances ◽  
Trait Improvement ◽  
Induced Mutagenesis ◽  
Efficient Exploration

Induced mutagenesis is one of the most effective strategies for trait improvement without altering the well-optimized genetic background of the cultivars. In this review, several currently accessible methods such as physical, chemical and insertional mutagenesis have been discussed concerning their efficient exploration for the tomato crop improvement. Similarly, challenges for the adaptation of genome-editing, a newly developed technique providing an opportunity to induce precise mutation, have been addressed. Several efforts of genome-editing have been demonstrated in tomato and other crops, exploring its effectiveness and convenience for crop improvement. Descriptive data compiled here from such efforts will be helpful for the efficient exploration of technological advances. However, uncertainty about the regulation of genome-edited crops is still a significant concern, particularly when timely trait improvement in tomato cultivars is needed. In this regard, random approaches of induced mutagenesis are still promising if efficiently explored in breeding applications. Precise identification of casual mutation is a prerequisite for the molecular understanding of the trait development as well as its utilization for the breeding program. Recent advances in sequencing techniques provide an opportunity for the precise detection of mutagenesis-induced sequence variations at a large scale in the genome. Here, we reviewed several novel next-generation sequencing based mutation mapping approaches including Mutmap, MutChromeSeq, and whole-genome sequencing-based mapping which has enormous potential to accelerate the mutation breeding in tomato. The proper utilization of the existing well-characterized tomato mutant resources combined with novel mapping approaches would inevitably lead to rapid enhancement of tomato quality and yield. This article provides an overview of the principles and applications of mutagenesis approaches in tomato and discusses the current progress and challenges involved in tomato mutagenesis research.

scholarly journals Genetic Diversity of Upland Rice Germplasm in Malaysia Based on Quantitative Traits

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
M. Sohrabi ◽  
M. Y. Rafii ◽  
M. M. Hanafi ◽  
A. Siti Nor Akmar ◽  
M. A. Latif
Keyword(s):  
Genetic Diversity ◽  
Growth Traits ◽  
Upland Rice ◽  
Flag Leaf ◽  
Crop Improvement ◽  
Leaf Length ◽  
Width Ratio ◽  
Improvement Program ◽  
Days To Flowering ◽  
Flag Leaf Length

Genetic diversity is prerequisite for any crop improvement program as it helps in the development of superior recombinants. Fifty Malaysian upland rice accessions were evaluated for 12 growth traits, yield and yield components. All of the traits were significant and highly significant among the accessions. The higher magnitudes of genotypic and phenotypic coefficients of variation were recorded for flag leaf length-to-width ratio, spikelet fertility, and days to flowering. High heritability along with high genetic advance was registered for yield of plant, days to flowering, and flag leaf length-to-width ratio suggesting preponderance of additive gene action in the gene expression of these characters. Plant height showed highly significant positive correlation with most of the traits. According to UPGMA cluster analysis all accessions were clustered into six groups. Twelve morphological traits provided around 77% of total variation among the accessions.

scholarly journals Biodiversity Assessment of Foxtail Millet (Setaria italica L.) Genotypes Based on RAPD Marker

2017 ◽  
Vol 4 (1) ◽  
pp. 21-25 ◽  
Author(s):  
Sintho Wahyuning ARDIE ◽  
Nurul Khumaida ◽  
Nurul Fauziah ◽  
Yudiansyah Yudiansyah
Keyword(s):  
Rapd Markers ◽  
High Salinity ◽  
Rapd Marker ◽  
Crop Improvement ◽  
Foxtail Millet ◽  
Crop Productivity ◽  
Setaria Italica ◽  
Base Pairs ◽  
Improvement Program ◽  
Product Size

Foxtail millet (Setaria italica L.) is an important crop in areas where harsh environmental conditions limit crop productivity, including in high salinity and drought prone areas. In Indonesia millet is cultivated in certain areas; however, superior varieties are less developed in the country. The objective of this study was to analyze the genetic diversity among foxtail genotypes using RAPD markers. Genomic DNA of ten foxtail millet genotypes was amplified using 26 random primers through RAPD analysis. Of these primers, 22 produced reproducible amplicons and were polymorphic among the 10 foxtail millet genotypes. The number of polymorphic markers for each primer varied from 1 (primer E15) to 14 (primer M17). The amplified product size ranged from 120 to 2500 base pairs (bp). A dendrogram constructed based on the UPGMA clustering method put all genotypes in 5 distinct groups at 0.64 coefficient level. Diverse genotypes identified in this study can be used as potential parents in an efficient crop improvement program.

scholarly journals CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259540
Author(s):  
Morad M. Mokhtar ◽  
Alsamman M. Alsamman ◽  
Haytham M. Abd-Elhalim ◽  
Achraf El Allali
Keyword(s):  
Transposable Elements ◽  
Crop Improvement ◽  
Draft Genome ◽  
Structural Variations ◽  
Web Based ◽  
Cicer Echinospermum ◽  
Genome Wide ◽  
Cicer Species ◽  
Trait Improvement ◽  
Made In

Recently, Cicer species have experienced increased research interest due to their economic importance, especially in genetics, genomics, and crop improvement. The Cicer arietinum, Cicer reticulatum, and Cicer echinospermum genomes have been sequenced and provide valuable resources for trait improvement. Since the publication of the chickpea draft genome, progress has been made in genome assembly, functional annotation, and identification of polymorphic markers. However, work is still needed to identify transposable elements (TEs) and make them available for researchers. In this paper, we present CicerSpTEdb, a comprehensive TE database for Cicer species that aims to improve our understanding of the organization and structural variations of the chickpea genome. Using structure and homology-based methods, 3942 C. echinospermum, 3579 C. reticulatum, and 2240 C. arietinum TEs were identified. Comparisons between Cicer species indicate that C. echinospermum has the highest number of LTR-RT and hAT TEs. C. reticulatum has more Mutator, PIF Harbinger, Tc1 Mariner, and CACTA TEs, while C. arietinum has the highest number of Helitron. CicerSpTEdb enables users to search and visualize TEs by location and download their results. The database will provide a powerful resource that can assist in developing TE target markers for molecular breeding and answer related biological questions. Database URL: http://cicersptedb.easyomics.org/index.php

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