scholarly journals The genetic basis of cis-regulatory divergence between the subspecies of cultivated rice (Oryza sativa)

2019 ◽  
Author(s):  
Malachy T Campbell ◽  
Qian Du ◽  
Kan Liu ◽  
Sandeep Sharma ◽  
Chi Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phenotypic Variability ◽  
Cultivated Rice ◽  
Regulatory Variation ◽  
Selective Pressures ◽  
Regulatory Variants ◽  
Genome Wide ◽  
Comprehensive Characterization ◽  
Transcriptome Level

AbstractCultivated rice consists of two subspecies, Indica and Japonica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the transcriptome level remains largely unexamined. Here, we provide a comprehensive characterization of transcriptome divergence and cis-regulatory variation within rice using transcriptome data from 91 accessions from a rice diversity panel (RDP1). The transcriptomes of the two subspecies of rice are highly divergent. The expression and genetic diversity was significantly lower within Japonica relative to Indica, which is consistent with the known population bottleneck during Japonica domestication. Moreover, 1,860 and 1,325 genes showed differences in heritability in the broad and narrow sense respectively, between the subspecies, which was driven largely by environmental and genetic effects rather than differences in phenotypic variability. We leveraged high-density genotypic data and transcript levels to identify cis-regulatory variants that may explain the genetic divergence between the subspecies. We identified significantly more eQTL that were specific to the Indica subspecies compared to Japonica, suggesting that the observed differences in expression and genetic variability also extends to cis-regulatory variation. We next explored the potential causes of this cis-regulatory divergence by assessing local genetic diversity for cis-eQTL. Local genetic diversity around subspecies-specific cis-eQTL was significantly lower than genome-wide averages in subspecies lacking the eQTL, suggesting that selective pressures may have shaped regulatory variation in each subspecies. This study provides the first comprehensive characterization of transcriptional and cis-regulatory variation in cultivated rice, and could be an important resource for future studies.

scholarly journals A Comprehensive Characterization of Genome-Wide Copy Number Aberrations in Colorectal Cancer Reveals Novel Oncogenes and Patterns of Alterations

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e42001 ◽  
Author(s):  
Tao Xie ◽  
Giovanni d’ Ario ◽  
John R. Lamb ◽  
Eric Martin ◽  
Kai Wang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Copy Number ◽  
Copy Number Aberrations ◽  
Genome Wide ◽  
Comprehensive Characterization

scholarly journals Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Huayu Zhu ◽  
Pengyao Song ◽  
Dal-Hoe Koo ◽  
Luqin Guo ◽  
Yanman Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeats ◽  
Comparative Mapping ◽  
Diversity Analysis ◽  
Genetic Diversity Analysis ◽  
Genome Wide ◽  
Simple Sequence

scholarly journals Genome-Wide Association Study Reveals Genetic Architecture of Septoria Tritici Blotch Resistance in a Historic Landrace Collection

2021 ◽  
Author(s):  
Anik Dutta ◽  
Daniel Croll ◽  
Bruce A. McDonald ◽  
Simon G. Krattinger
Keyword(s):  
Genetic Diversity ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Phenotypic Variability ◽  
Genome Wide Association ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Genome Wide ◽  
A Genome ◽  
Wheat Landraces

Abstract Septoria tritici blotch (STB), caused by the fungus Zymoseptoria tritici, is a major constraint in global wheat production. The lack of genetic diversity in modern elite wheat cultivars largely hinders the improvement of STB resistance. Wheat landraces are reservoirs of untapped genetic diversity, which can be exploited to find novel STB resistance genes or alleles. Here, we characterized 188 Swiss wheat landraces for resistance to STB using four Swiss Z. tritici isolates. We used a genome-wide association study (GWAS) to identify genetic variants associated with the amount of lesion and pycnidia production by the fungus. The majority of the landraces were highly resistant for both traits to the isolate 1E4, indicating a gene-for-gene relationship, while higher phenotypic variability was observed against other isolates. GWAS detected a significant SNP on chromosome 3A that was associated with both traits in the isolate 1E4. The resistance response against 1E4 was likely controlled by the Stb6 gene. Sanger sequencing revealed that the majority of these ~100-year-old landraces carry the Stb6 resistance allele. This indicates the importance of this gene in Switzerland during the early 1900s for disease control in the field. Our study demonstrates the importance of characterizing historic landrace collections for STB resistance to provide valuable information on resistance variability and contributing alleles. This will help breeders in the future to make decisions on integrating such germplasms in STB resistance breeding.

Molecular characterization of China aster (Callistephus chinensis (L.) Nees) genotypes using SSR markers

2021 ◽  
pp. 1-10
Author(s):  
Veluru Bhargav ◽  
Rajiv Kumar ◽  
Anuradha Sane ◽  
T. Manjunatha Rao ◽  
T. Usha Bharathi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Mapping ◽  
Ssr Markers ◽  
Crop Improvement ◽  
Flower Color ◽  
Target Populations ◽  
Genome Wide ◽  
China Aster ◽  
Simple Sequence

Abstract Understanding genetic diversity in target populations is of great importance in breeding and a prerequisite for association mapping of traits. In this study, 57 cross species simple sequence repeat (SSR) markers were screened for amplification in China aster. Twenty six polymorphic markers were used to estimate the genetic diversity in forty two China aster genotypes. The observed and expected heterozygosities within the genotypes were ranged from 0.00 to 0.80 and 0.17 to 0.50, respectively. Weighted Neighbor Joining method, grouped China aster genotypes into five major clusters which coincided for morphological traits mostly flower color and form, but not correlated for their geographical locations. The results suggested that, population may be useful for the genome-wide marker–trait association mapping. These set of cross species transferable SSR markers would enable the application of the SSR technique in China aster crop improvement.

scholarly journals Phenotypic variability in chorea-acanthocytosis associated with novel VPS13A mutations

2020 ◽  
Vol 6 (3) ◽  
pp. e426
Author(s):  
Valter Niemelä ◽  
Ammar Salih ◽  
Daniela Solea ◽  
Björn Lindvall ◽  
Jan Weinberg ◽  
...  
Keyword(s):  
Fdg Pet ◽  
Potential Role ◽  
Phenotypic Variability ◽  
Resonance Spectroscopy ◽  
Novel Mutations ◽  
Genetic Studies ◽  
Clinical Assessments ◽  
Comprehensive Characterization ◽  
Deep Brain

ObjectiveTo perform a comprehensive characterization of a cohort of patients with chorea-acanthocytosis (ChAc) in Sweden.MethodsClinical assessments, targeted genetic studies, neuroimaging with MRI, [18F]-fluorodeoxyglucose (FDG) PET, and dopamine transporter with 123I FP-CIT (DaTscan) SPECT. One patient underwent magnetic resonance spectroscopy (MRS).ResultsFour patients living in Sweden but with different ethnical backgrounds were included. Their clinical features were variable. Biallelic VPS13A mutations were confirmed in all patients, including 3 novel mutations. All tested patients had either low or absent chorein levels. One patient had progressive caudate atrophy. Investigation using FDG-PET revealed severe bilateral striatal hypometabolism, and DaTscan SPECT displayed presynaptic dopaminergic deficiency in 3 patients. MRS demonstrated reduced N-acetylaspartate/creatine (Cr) ratio and mild elevation of both choline/Cr and combined glutamate and glutamine/Cr in the striatum in 1 case. One patient died during sleep, and another was treated with deep brain stimulation, which transiently attenuated feeding dystonia but not his gait disorder or chorea.ConclusionsLarger longitudinal neuroimaging studies with different modalities, particularly MRS, are needed to determine their potential role as biomarkers for ChAc.

scholarly journals Testing the ‘caves as islands’ model in two cave-obligate invertebrates with a genomic approach

2020 ◽  
Author(s):  
Andras Balogh ◽  
Lam Ngo ◽  
Kirk S. Zigler ◽  
Groves Dixon
Keyword(s):  
Genetic Diversity ◽  
Genetic Divergence ◽  
Nucleotide Diversity ◽  
Dense Region ◽  
Cumberland Plateau ◽  
Small Areas ◽  
Selective Pressures ◽  
Genome Wide ◽  
Genomic Approach ◽  
Good Sample

AbstractCaves offer selective pressures that are distinct from the surface. Organisms that have evolved to exist under these pressures typically exhibit a suite of convergent characteristics, including a loss or reduction of eyes and pigmentation. As a result, cave-obligate taxa, termed troglobionts, are no longer viable on the surface. This circumstance has led to a “caves as islands” model of troglobiont evolution that predicts extreme genetic divergence between cave populations even across relatively small areas. An effective test of this model would involve (1) common troglobionts from (2) nearby caves in a cave-dense region, (3) good sample sizes per cave, (4) multiple taxa, and (5) genome-wide characterization. With these criteria in mind, we used RAD-seq to genotype an average of ten individuals of the troglobiotic spider Nesticus barri and the troglobiotic beetle Ptomaphagus hatchi, each from four closely located caves (ranging from 3-13 km apart) in the cave-rich southern Cumberland Plateau of Tennessee, USA. Consistent with the caves as islands model, we find that populations from separate caves are indeed highly genetically isolated. In addition, nucleotide diversity was correlated to cave length, suggesting that cave size is a dominant force shaping troglobiont population size and genetic diversity. Our results support the idea of caves as natural laboratories for the study of parallel evolutionary processes.

scholarly journals High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq.

2016 ◽  
Author(s):  
Rafal Gumienny ◽  
Dominik Jedlinski ◽  
Georges Martin ◽  
Arnau Vina-Villaseca ◽  
Mihaela Zavolan
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Expression Patterns ◽  
Ribonucleoprotein Complexes ◽  
Short Rnas ◽  
Genome Wide ◽  
The Many ◽  
Nucleolar Rnas ◽  
Comprehensive Characterization

Identification of long and short RNAs, their processing and expression patterns have been greatly facilitated by high-throughput sequencing. Frequently, these RNAs act as guides for ribonucleoprotein complexes that regulate the expression or processing of target RNAs. However, to determine the targets of the many newly discovered regulatory RNAs in high-throughput remains a challenge. To globally assign guide small nucleolar RNAs to site of 2'-O-ribose methylation in human cells, we here developed novel computational methods for the analysis of data that was generated with protocols designed to capture direct small RNA-target interactions and to identify the sites of 2'-O-ribose methylation genome-wide. We thereby determined that many "orphan" snoRNAs appear to guide 2'-O-ribose methylation at sites that are targeted by other snoRNAs and that snoRNAs can be reliably captured in interaction with many mRNAs, in which a subsequent 2'-O-methylation cannot be detected. Our study provides a reliable approach to the comprehensive characterization of snoRNA-target interactions in species beyond those in which these interactions have been traditionally studied and contribute to the rapidly developing field of "epitranscriptomics".

scholarly journals Genome-wide characterization of simple sequence repeats in Pyrus bretschneideri and their application in an analysis of genetic diversity in pear

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Huabai Xue ◽  
Pujuan Zhang ◽  
Ting Shi ◽  
Jian Yang ◽  
Long Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeats ◽  
Genome Wide ◽  
Simple Sequence

scholarly journals Exploring functional variation affecting ceRNA regulation in humans

2015 ◽  
Author(s):  
Mulin Jun Li ◽  
Jiexing Wu ◽  
Peng Jiang ◽  
Wei Li ◽  
Yun Zhu ◽  
...  
Keyword(s):  
Genetic Effect ◽  
Systematic Investigation ◽  
Human Populations ◽  
Functional Variation ◽  
Regulatory Variants ◽  
Genome Wide ◽  
Competing Endogenous Rnas ◽  
Mirna Sponges ◽  
Cis And Trans

MicroRNA (miRNA) sponges have been shown to function as competing endogenous RNAs (ceRNAs) to regulate the expression of other miRNA targets in the network by sequestering available miRNAs. As the first systematic investigation of the genome-wide genetic effect on ceRNA regulation, we applied multivariate response regression and identified widespread genetic variations that are associated with ceRNA competition using 462 Geuvadis RNA-seq data in multiple human populations. We showed that SNPs in gene 3’UTRs at the miRNA seed binding regions can simultaneously regulate gene expression changes in both cis and trans by the ceRNA mechanism. We termed these loci as endogenous miRNA sponge expression quantitative trait loci or “emsQTLs”, and found that a large number of them were unexplored in conventional eQTL mapping. We identified many emsQTLs are undergoing recent positive selection in different human populations. Using GWAS results, we found that emsQTLs are significantly enriched in traits/diseases associated loci. Functional prediction and prioritization extend our understanding on causality of emsQTL allele in disease pathways. We illustrated that emsQTL can synchronously regulate the expression of tumor suppressor and oncogene through ceRNA competition in angiogenesis. Together these results provide a distinct catalog and characterization of functional noncoding regulatory variants that control ceRNA crosstalk.

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