Current Trends in Biotechnology: From Genome Sequence to Crop Improvement

2019 ◽  
pp. 91-108
Author(s):  
Swarup Kumar Chakrabarti ◽  
Hemant Kardile ◽  
Jagesh Kumar Tiwari
Keyword(s):  
Genome Sequence ◽  
Crop Improvement ◽  
Current Trends

scholarly journals New hyper-variable SSRs for diversity analysis in mango (Mangifera indica L.)

2021 ◽  
Vol 81 (01) ◽  
pp. 119-126
Author(s):  
Manish Srivastav ◽  
Sanjay K. Singh ◽  
Jai Prakash ◽  
Rakesh Singh ◽  
Neha Sharma ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Polymorphic Information Content ◽  
Mangifera Indica ◽  
Crop Improvement ◽  
Whole Genome Sequence ◽  
Diversity Analysis ◽  
Genome Wide ◽  
Improvement Programme ◽  
The Mean ◽  
Simple Sequence

Whole genome sequence in mango offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, simple sequence repeats (SSRs) were predicted from genome sequence of mango. Based on the SSR length (? 50 bp), highly-variable mango SSRs (MSSRs) were sorted. A sub-set of 129 MSSRs was validated on a set of 24 diverse mango genotypes yielding marker validation and polymorphism of 88.96 and 85.27 per cent, respectively. One hundred and ten polymorphic markers were identified for the present set of mango genotypes. Polymorphic information content (PIC) ranged from 0.10 to 0.78 and the highest value was observed with MSSR133. The mean PIC value was 0.40 but 33 MSSR markers showed PIC values ? 0.5, suggesting that these markers can efficiently measure genetic diversity and serve for mapping of quantitative trait loci (QTLs) in mango. MSSRs data was further used for diversity analysis of mango genotypes belonging to different agro-ecological conditions including chance seedlings, landraces, exotic and indigenous germplasm and hybrids. Cluster analysis using UPGMA of 24 mango genotypes revealed that these MSSRs were informative in diversity analysis and distinguished mango genotypes based on their origin, parentage and embryo types. A novel set of 110 hyper-variable SSR markers have been added to the mango repository depicting usefulness in discriminating closely related mango germplasm and their use in mango improvement programme.

scholarly journals Draft Genome Sequence and intraspecific diversification of the wild crop relative Brassica cretica Lam. using demographic model selection

2019 ◽  
Author(s):  
Antonis Kioukis ◽  
Vassiliki A. Michalopoulou ◽  
Laura Briers ◽  
Stergios Pirintsos ◽  
David J. Studholme ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Sequence Data ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Draft Genome ◽  
Illumina Miseq ◽  
Crop Wild Relatives ◽  
Demographic Model ◽  
Sequencing Data

AbstractCrop wild relatives contain great levels of genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops become more resistant and resilient, and adapt to the new conditions that they will experience due to climate change. An impressive global effort occurs for the conservation of various wild crop relatives and facilitates their use in crop breeding for food security.The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage) is a species native to coastal southern and western Europe that has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves.Brassica cretica Lam. is a wild relative crop in the brassica group and B. cretica subsp. nivea has been suggested as a separate subspecies. The species B. cretica has been proposed as a potential gene donor to a number of crops in the brassica group, including broccoli, Brussels sprout, cabbage, cauliflower, kale, swede, turnip and oilseed rape.Here, we present the draft de novo genome assemblies of four B. cretica individuals, including two B. cretica subsp. nivea and two B. cretica.De novo assembly of Illumina MiSeq genomic shotgun sequencing data yielded 243,461 contigs totalling 412.5 Mb in length, corresponding to 122 % of the estimated genome size of B. cretica (339 Mb). According to synteny mapping and phylogenetic analysis of conserved genes, B. cretica genome based on our sequence data reveals approximately 30.360 proteins.Furthermore, our demographic analysis based on whole genome data, suggests that distinct populations of B. cretica are not isolated. Our findings suggest that the classification of the B. cretica in distinct subspecies is not supported from the genome sequence data we analyzed.

scholarly journals TheSorghum bicolorreference genome: improved assembly and annotations, a transcriptome atlas, and signatures of genome organization

2017 ◽  
Author(s):  
Ryan F. McCormick ◽  
Sandra K. Truong ◽  
Avinash Sreedasyam ◽  
Jerry Jenkins ◽  
Shengqiang Shu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Tandem Repeats ◽  
Reference Genome ◽  
Genetic Model ◽  
Crop Improvement ◽  
Tissue Type ◽  
Genetic Linkage Analysis ◽  
Transcriptome Data ◽  
Reference Genome Sequence ◽  
C4 Grass

2ABSTRACTSorghum bicoloris a drought tolerant C4 grass used for production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (~800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34,211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp. Sub-telomeric repeats with characteristics of Tandem Repeats In Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of the reference genome sequence to 56 resequenced genomes from diverse sorghum genotypes identified ~7.4M SNPs and 1.8M indels. Large scale variant features in euchromatin were identified with periodicities of ~25 kbp. An RNA transcriptome atlas of gene expression was constructed from 47 samples derived from growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement.

scholarly journals The assembled Banana dihaploid mitochondrial genome is compact with a high number of gene copies

2022 ◽  
Author(s):  
Shruthy Priya Prakash ◽  
Vaidheki Chandrasekar ◽  
Selvi Subramanian ◽  
Rahamatthunnisha Ummar
Keyword(s):  
Mitochondrial Genome ◽  
Genome Sequence ◽  
Copy Number ◽  
Ribosomal Proteins ◽  
Tandem Repeats ◽  
Sequence Data ◽  
Crop Improvement ◽  
Whole Genome Sequence ◽  
Trna Genes ◽  
Mt Genome

Banana being a major food crop all around the world, attracts various research interests in crop improvement. In banana, complete genome sequences of Musa accuminata and Musa balbisiana are available. However, the mitochondrial genome is not sequenced or assembled. Mitochondrial (mt) genes play an important role in flower and seed development and in Cytoplasmic Male Sterility. Unraveling banana mt genome architecture will be a foundation for understanding inheritance of traits and their evolution. In this study, the complete banana mt genome is assembled from the whole genome sequence data of the Musa acuminata subsp. malaccensis DH-Pahang. The mt genome sequence acquired by this approach was 409574 bp and it contains, 54 genes coding for 25 respiratory complex proteins 15 ribosomal proteins, 12 tRNA genes and two ribosomal RNA gene. Except atpB, rps11 and rps19 other genes are in multiple copies. The copy number is 12 in tRNA genes. In addition, nearly 25% tandem repeats are also present in it. These mt proteins are identical to the mt proteins present in the other members of AA genome and share 98% sequence similarity with M. balbisiana. The C to U RNA editing is profoundly higher (87 vs 13%) in transcripts of M. balbisiana (BB) compared to M. accuminata (AA). The banana AA mitochondrial genome is tightly packed with 233 genes, with less rearrangements and just 5.3% chloroplast DNA in it. The maintenance of high copy number of functional mt genes suggest that they have a crucial role in the evolution of banana.

scholarly journals Crop improvement in the era of climate change: an integrated, multi-disciplinary approach for common bean (Phaseolus vulgaris)

2011 ◽  
Vol 38 (12) ◽  
pp. 927 ◽  
Author(s):  
Phillip E. McClean ◽  
Jimmy Burridge ◽  
Stephen Beebe ◽  
Idupulapati M. Rao ◽  
Timothy G. Porch
Keyword(s):  
Climate Change ◽  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Association Analysis ◽  
Genome Sequence ◽  
Crop Improvement ◽  
Stress Conditions ◽  
Population Increase ◽  
Improvement Programs ◽  
Global Population

Climate change and global population increase are two converging forces that will jointly challenge researchers to design programs that ensure crop production systems meet the world’s food demand. Climate change will potentially reduce productivity while a global population increase will require more food. If productivity is not improved for future climatic conditions, food insecurity may foster major economic and political uncertainty. Given the importance of grain legumes in general – common bean (Phaseolus vulgaris L.) in particular – a workshop entitled ‘Improving Tolerance of Common Bean to Abiotic Stresses’ was held with the goal of developing an interdisciplinary research agenda designed to take advantage of modern genotyping and breeding approaches that are coupled with large scale phenotyping efforts to improve common bean. Features of the program included a multinational phenotyping effort to evaluate the major common bean core germplasm collections and appropriate genetic populations. The phenotyping effort will emphasise the response of root and shoot traits to individual and combined stress conditions. These populations would also be genotyped using newly emerging high density single nucleotide polymorphism (SNP) marker arrays or next generation sequencing technology. Association analysis of the core collections aims to identify key loci associated with the response to the stress conditions. Companion bi-parental quantitative trait loci (QTL) experiments will act as confirmation experiments for the association analysis. The upcoming release of the genome sequence of common bean will be leveraged by utilising population genomic approaches to discover genomic regions that differentiate stress-responsive and non-responsive genotypes. The genome sequence will also enable global gene expression studies that will highlight specific molecular-based stress responses. This collective knowledge will inform the selection of parental lines to improve the efficiency of common bean improvement programs.

The Rice Genome Sequence as an Indispensable Tool for Crop Improvement

2008 ◽  
pp. 3-12 ◽  
Author(s):  
Takuji Sasaki ◽  
Jianzhong Wu ◽  
Hiroshi Mizuno ◽  
Baltazar A. Antonio ◽  
Takashi Matsumoto
Keyword(s):  
Genome Sequence ◽  
Crop Improvement ◽  
Rice Genome ◽  
Rice Genome Sequence ◽  
Indispensable Tool

Current Trends in the Training and Utilization of Paraprofessionals in Speech and Language Programs

1991 ◽  
Vol 22 (2) ◽  
pp. 51-59 ◽  
Author(s):  
Kathy L. Coufal ◽  
Allen L. Steckelberg ◽  
Stanley F. Vasa
Keyword(s):  
Selection Criteria ◽  
Job Descriptions ◽  
Paraprofessional Training ◽  
Language Programs ◽  
Program Administrators ◽  
Current Trends ◽  
Training And Supervision ◽  
Communicative Disorders ◽  
Supervision Practices ◽  
A Current

Administrators of programs for children with communicative disorders in 11 midwestern states were surveyed to assess trends in the training and utilization of paraprofessionals. Topics included: (a) current trends in employment, (b) paraprofessional training, (c) use of ASHA and state guidelines, and (d) district policies for supervision. Selection criteria, use of job descriptions, training programs, and supervision practices and policies were examined. Results indicate that paraprofessionals are used but that standards for training and supervision are not consistently applied across all programs. Program administrators report minimal training for supervising professionals.

The Graduate Dysphagia Course: Opening the Door to New Frontiers

2016 ◽  
Vol 1 (13) ◽  
pp. 104-112
Author(s):  
Karen A. Ball ◽  
Luis F. Riquelme
Keyword(s):  
Graduate Student ◽  
Paradigm Shifts ◽  
Speech Language Pathology ◽  
Approaches To Teaching ◽  
Graduate Level ◽  
Graduate Curriculum ◽  
Current Trends ◽  
Language Pathology

A graduate-level course in dysphagia is an integral part of the graduate curriculum in speech-language pathology. There are many challenges to meeting the needs of current graduate student clinicians, thus requiring the instructor to explore alternatives. These challenges, suggested paradigm shifts, and potential available solutions are explored. Current trends, lack of evidence for current methods, and the variety of approaches to teaching the dysphagia course are presented.

Molecular Biology and Crop Improvement

1986 ◽  
Author(s):  
R. B. Austin ◽  
R. B. Flavell ◽  
I. E. Henson ◽  
H. J. B. Lowe
Keyword(s):  
Molecular Biology ◽  
Crop Improvement
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