scholarly journals Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy

2016 ◽  
Vol 14 (12) ◽  
pp. 2240-2253 ◽  
Author(s):  
Bradley C. Campbell ◽  
Edward K. Gilding ◽  
Emma S. Mace ◽  
Shuaishuai Tai ◽  
Yongfu Tao ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Starch Biosynthesis ◽  
Biosynthesis Pathway ◽  
Sorghum Genome ◽  
Sequencing Strategy ◽  
Signatures Of Selection ◽  
Storage Starch

Understanding storage starch biosynthesis in plants: a means to quality improvement

2006 ◽  
Vol 84 (8) ◽  
pp. 1167-1185 ◽  
Author(s):  
Ian J. Tetlow
Keyword(s):  
Quality Improvement ◽  
Biosynthetic Pathway ◽  
Current Knowledge ◽  
Industrial Applications ◽  
Starch Biosynthesis ◽  
Starch Structure ◽  
Granule Structure ◽  
The Many ◽  
A Current ◽  
Storage Starch

The many varied uses of starch in food and industrial applications often requires an understanding of its physicochemical properties and the detailed variations in granule structure that underpin these properties. The ability to manipulate storage starch structures depends on understanding the biosynthetic pathway, and in particular, how the many components of the pathway are coordinated and regulated. This article presents a current overview of starch structure and the known enzymes involved in the synthesis of the granule, with an emphasis on how current knowledge on the regulation of the pathway in cereals and other crops may be applied to the production of different functional starches.

scholarly journals Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

2019 ◽  
Author(s):  
Meenu Bhati ◽  
Naveen Kumar Kadri ◽  
Danang Crysnanto ◽  
Hubert Pausch
Keyword(s):  
Whole Genome Sequencing ◽  
Meat Quality ◽  
Genome Sequencing ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Cattle Breeds ◽  
Signatures Of Selection ◽  
Genomic Inbreeding ◽  
Genomic Regions

AbstractBackgroundAutochthonous cattle breeds represent an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution.ResultsWe annotated 15,722,811 million SNPs and 1,580,878 million Indels including 10,738 and 2,763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 × 10-3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding quantified using runs of homozygosity (ROH) was relatively low (FROH=0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in more recent generations of OB cattle (FROH=0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus.ConclusionsWe provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation and adoption of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.

scholarly journals Starch biosynthesis in developing seeds

2010 ◽  
Vol 21 (1) ◽  
pp. 5-32 ◽  
Author(s):  
Ian J. Tetlow
Keyword(s):  
Seedling Establishment ◽  
Biological Function ◽  
Starch Synthesis ◽  
Industrial Applications ◽  
Starch Biosynthesis ◽  
Post Translational Modification ◽  
Developing Seeds ◽  
Starch Structure ◽  
Wide Range ◽  
Storage Starch

AbstractStarch is globally important as a source of food and, in addition, has a wide range of industrial applications. Much of this agriculturally produced starch is synthesized in developing seeds, where its biological function is to provide energy for seedling establishment. Storage starch in developing seeds is synthesized in heterotrophic plastids called amyloplasts and is distinct from the transient synthesis of starch in chloroplasts. This article reviews our current understanding of storage starch biosynthesis occurring in these organelles and discusses recent advances in research in this field. The review discusses starch structure and granule initiation, emerging ideas on the evolution of the pathway, the enzymes of starch synthesis, and the post-translational modification and regulation of key enzymes of amylopectin biosynthesis.

scholarly journals Jekyll or Hyde? The genome (and more) of Nesidiocoris tenuis, a zoophytophagous predatory bug that is both a biological control agent and a pest

2020 ◽  
Author(s):  
K. B. Ferguson ◽  
S. Visser ◽  
M. Dalíková ◽  
I. Provazníková ◽  
A. Urbaneja ◽  
...  
Keyword(s):  
Biological Control ◽  
Genome Sequencing ◽  
Acyrthosiphon Pisum ◽  
Population Genomics ◽  
Biological Control Agent ◽  
Control Agent ◽  
Initial Assessment ◽  
Control Research ◽  
Nesidiocoris Tenuis ◽  
Sequencing Strategy

AbstractNesidiocoris tenuis (Reuter) is an efficient predatory biological control agent used throughout the Mediterranean Basin in tomato crops but regarded as a pest in northern European countries. Belonging to the family Miridae, it is an economically important insect yet very little is known in terms of genetic information – no published genome, population studies, or RNA transcripts. It is a relatively small and long-lived diploid insect, characteristics that complicate genome sequencing. Here, we circumvent these issues by using a linked-read sequencing strategy on a single female N. tenuis. From this, we assembled the 355 Mbp genome and delivered an ab initio, homology-based, and evidence-based annotation. Along the way, the bacterial “contamination” was removed from the assembly, which also revealed potential symbionts. Additionally, bacterial lateral gene transfer (LGT) candidates were detected in the N. tenuis genome. The complete gene set is composed of 24,688 genes; the associated proteins were compared to other hemipterans (Cimex lectularis, Halyomorpha halys, and Acyrthosiphon pisum), resulting in an initial assessment of unique and shared protein clusters. We visualised the genome using various cytogenetic techniques, such as karyotyping, CGH and GISH, indicating a karyotype of 2n=32 with a male-heterogametic XX/XY system. Additional analyses include the localization of 18S rDNA and unique satellite probes via FISH techniques. Finally, population genomics via pooled sequencing further showed the utility of this genome. This is one of the first mirid genomes to be released and the first of a mirid biological control agent, representing a step forward in integrating genome sequencing strategies with biological control research.

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