scholarly journals MSH1-Induced Non-Genetic Variation Provides a Source of Phenotypic Diversity in Sorghum bicolor

PLoS ONE ◽  
2014 ◽  
Vol 9 (10) ◽  
pp. e108407 ◽  
Author(s):  
Roberto de la Rosa Santamaria ◽  
Mon-Ray Shao ◽  
Guomei Wang ◽  
David O. Nino-Liu ◽  
Hardik Kundariya ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Sorghum Bicolor ◽  
Phenotypic Diversity

scholarly journals A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing

2021 ◽  
Author(s):  
Chao Yuan ◽  
Zengkui Lu ◽  
Tingting Guo ◽  
Yaojing Yue ◽  
Xijun Wang ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Complex Traits ◽  
Phenotypic Diversity ◽  
Average Length ◽  
Global Analysis ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Nutrient Metabolism ◽  
Relaxin Family

Abstract Background Copy number variation (CNV) is an important source of genetic variation that has a significant influence on phenotypic diversity, economically important traits and the evolution of livestock species. In this study, the genome-wide CNV distribution characteristics of 32 fine-wool sheep from three breeds were analyzed using resequencing.Results A total of 1,747,604 CNVs were detected in this study, and 7,228 CNV regions (CNVR) were obtained after merging overlapping CNVs; these regions accounted for 2.17% of the sheep reference genome. The average length of the CNVRs was 4,307.17 bp. “Deletion” events took place more frequently than “duplication” or “both” events. The CNVRs obtained overlapped with previously reported sheep CNVRs to variable extents (4.39%–55.46%). Functional enrichment analysis showed that the CNVR-harboring genes were mainly involved in sensory perception systems, nutrient metabolism processes, and growth and development processes. Furthermore, 1,855 of the CNVRs were associated with 166 quantitative trait loci (QTL), including milk QTLs, carcass QTLs, and health-related QTLs, among others. In addition, the 32 fine-wool sheep were divided into horned and polled groups to analyze for the selective sweep of CNVRs, and it was found that the relaxin family peptide receptor 2 (RXFP2) gene was strongly influenced by selection.Conclusions In summary, we constructed a genomic CNV map for Chinese indigenous fine-wool sheep using resequencing, thereby providing a valuable genetic variation resource for sheep genome research, which will contribute to the study of complex traits in sheep.

scholarly journals Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)

2011 ◽  
Vol 12 (11) ◽  
pp. R114 ◽  
Author(s):  
Lei-Ying Zheng ◽  
Xiao-Sen Guo ◽  
Bing He ◽  
Lian-Jun Sun ◽  
Yao Peng ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Sorghum Bicolor ◽  
Grain Sorghum ◽  
Genome Wide

Rapd variation of late-maturing sorghum [ Sorghum bicolor (L.) Moench] landraces from Ethiopia

2007 ◽  
Vol 55 (3) ◽  
pp. 375-382 ◽  
Author(s):  
S. Mamo ◽  
A. Ayana ◽  
T. Tesso
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Sorghum Bicolor ◽  
Rapd Markers ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
The Mean ◽  
Polymorphic Bands ◽  
High Degree ◽  
Sorghum Bicolor L

A study on the extent and pattern of genetic variability in late-maturing sorghum [ Sorghum bicolor (L.) Moench] landraces collected from the Wello and Hararge areas of Ethiopia was conducted using random amplified polymorphic DNA (RAPD) markers for 70 individuals representing 14 populations. Four oligonucleotide primers generated a total of 55 polymorphic bands with 13–19 bands per primer and a mean of 16 bands across the 70 individuals. The value of the Shannon diversity index among the populations (0.26) and between the two regions (0.24) was low to moderate, despite the high degree of polymorphic bands per primer. The mean genetic distance (0.25) between the populations was found to be low. The low genetic variation may be due to the reduced population size of late-maturing sorghum landraces in the two regions of Ethiopia because of farmers’ decisions in the process of planting, managing, harvesting and processing their crops. Partitioning of the genetic variation into variation between and within the population revealed that 92.9% and 7.10% of the variation was found to be between and within the populations, respectively. Cluster analysis of genetic distance estimates further confirmed a low level of differentiation in late-maturing sorghum populations both between and within the regions. The implications of the results for genetic conservation purposes are discussed.

scholarly journals Genetic and Phenotypic Diversity in Downy-mildew-resistant Sorghum (Sorghum bicolor (L.) Moench) Germplasm

2006 ◽  
Vol 53 (6) ◽  
pp. 1243-1253 ◽  
Author(s):  
V. Kamala ◽  
P. J. Bramel ◽  
S. Sivaramakrishnan ◽  
S. Chandra ◽  
Seetha Kannan ◽  
...  
Keyword(s):  
Sorghum Bicolor ◽  
Downy Mildew ◽  
Phenotypic Diversity ◽  
Sorghum Bicolor L

Host genetic variation contributes to phenotypic diversity in myeloproliferative disorders

Blood ◽  
2008 ◽  
Vol 111 (5) ◽  
pp. 2785-2789 ◽  
Author(s):  
Animesh Pardanani ◽  
Brooke L. Fridley ◽  
Terra L. Lasho ◽  
D. Gary Gilliland ◽  
Ayalew Tefferi
Keyword(s):  
Genetic Variation ◽  
Odds Ratio ◽  
Phenotypic Diversity ◽  
Primary Myelofibrosis ◽  
Myeloproliferative Disorders ◽  
Single Nucleotide ◽  
Disease Allele ◽  
Phenotype Analysis ◽  
Host Genetic ◽  
Stimulating Factor

JAK2V617F is an acquired mutation associated with polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). We tested the hypothesis that the paradox of a single disease allele associated with 3 distinctive clinical phenotypes could be explained in part by host-modifying influences. We screened for genetic variation within 4 candidate genes involved in JAK-STAT signaling, including receptors for erythropoietin (EPOR), thrombopoietin (MPL), and granulocyte colony-stimulating factor (GCSFR), and JAK2. We genotyped 32 linkage disequilibrium tag single nucleotide polymorphism (SNP) loci in 179 white patients: 84 had PV, 58 had PMF, and 37 had ET. Genotype-phenotype analysis showed 3 JAK2 SNPs (rs7046736, rs10815148, and rs12342421) to be significantly but reciprocally associated with PV (P < .001 for all; odds ratio = 0.16, 2.72, and 2.46, respectively) and ET (P < .001 for all; odds ratio = 3.05, 0.29, and 0.30, respectively) but not with PMF. Three additional JAK2 SNPs (rs10758669, rs3808850, and rs10974947) and a single EPOR SNP (rs318699) were also significantly associated with PV but not with ET or PMF. Finally, intragene haplotypes in JAK2 were significantly associated with PV only. Thus, host genetic variation may contribute to phenotypic diversity among myeloproliferative disorders, including in the presence of a shared disease allele.

scholarly journals Analysis of genetic variation in sorghum (Sorghum bicolor (L.) Moench) genotypes with various agronomical traits using SPAR methods

Gene ◽  
2016 ◽  
Vol 576 (1) ◽  
pp. 581-585 ◽  
Author(s):  
Lakkakula Satish ◽  
Jayabalan Shilpha ◽  
Subramani Pandian ◽  
Arockiam Sagina Rency ◽  
Periyasamy Rathinapriya ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Sorghum Bicolor ◽  
Agronomical Traits ◽  
Sorghum Bicolor L

scholarly journals Human genetic variation within neural crest enhancers: molecular and phenotypic implications

2013 ◽  
Vol 368 (1620) ◽  
pp. 20120360 ◽  
Author(s):  
Alvaro Rada-Iglesias ◽  
Sara L. Prescott ◽  
Joanna Wysocka
Keyword(s):  
Genetic Variation ◽  
Neural Crest ◽  
Phenotypic Diversity ◽  
Regulatory Elements ◽  
Embryonic Cell ◽  
Human Genetic Variation ◽  
Nucleotide Polymorphisms ◽  
Cooperative Relationships ◽  
Developmental Gene Expression ◽  
Genome Wide

Developmental gene expression programmes are coordinated by the specialized distal cis -regulatory elements called enhancers, which integrate lineage- and signalling-dependent inputs to guide morphogenesis. In previous work, we characterized the genome-wide repertoire of active enhancers in human neural crest cells (hNCC), an embryonic cell population with critical roles in craniofacial development. We showed that in hNCC, co-occupancy of a master regulator TFAP2A with nuclear receptors NR2F1 and NR2F2 correlates with the presence of permissive enhancer chromatin states. Here, we take advantage of pre-existing human genetic variation to further explore potential cooperation between TFAP2A and NR2F1/F2. We demonstrate that isolated single nucleotide polymorphisms affecting NR2F1/F2-binding sites within hNCC enhancers can alter TFAP2A occupancy and overall chromatin features at the same enhancer allele. We propose that a similar strategy can be used to elucidate other cooperative relationships between transcription factors involved in developmental transitions. Using the neural crest and its major contribution to human craniofacial phenotypes as a paradigm, we discuss how genetic variation might modulate the molecular properties and activity of enhancers, and ultimately impact human phenotypic diversity.

Genetic diversity in Puccinia striiformis Westend. f.sp. tritici revealed by pathogen genome-specific repetitive sequence

1998 ◽  
Vol 76 (4) ◽  
pp. 587-595 ◽  
Author(s):  
Wei-xing Shan ◽  
Shou-yi Chen ◽  
Zhen-sheng Kang ◽  
Li-ren Wu ◽  
Zhen-qi Li
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Dna Fingerprinting ◽  
Puccinia Striiformis ◽  
Phenotypic Diversity ◽  
Molecular Evidence ◽  
Polymorphism Analysis ◽  
Dna Fingerprints ◽  
High Level ◽  
Virulence Variation

DNA fingerprinting was used to examine genetic variation in populations of Puccinia striiformis Westend. f.sp. tritici, an obligate fungus that causes wheat stripe rust, using as a probe a moderately repetitive DNA sequence PSR331 that shows species specificity in the genome of this pathogen. One hundred and sixty isolates sampled from six provinces throughout China were examined for genetic variation over 26 putative genetic loci defined by PSR331 and the restriction enzyme BglII. Because of the dikaryotic nature of this fungus, DNA fingerprints can not differentiate heterozygotes from homozygotes. We refer to the PSR DNA fingerprints as phenotypes rather than genotypes. Phenotypic diversity analysis revealed a high level of genetic variation. A total of 97 phenotypes was detected among 160 isolates. Phenotypic diversity varied among regions, ranging from 0.3742 in Shaanxi to 0.9380 in Gansu, as calculated with the normalized Shannon's index. Genetic subdivision analysis revealed a low level of genetic differentiation (GST = 0.0084) among regions (Gansu, Henan, Shaanxi, Sichuan, and Yunnan provinces) as well as within regions (Gansu and Sichuan provinces). This, together with the detection of the same phenotypes among regions, provided the molecular evidence for gene flow in P. striiformis f.sp. tritici. The results support conclusions from virulence surveys that Tianshui of southern Gansu is probably the most important "hotspot" area with respect to the potential to generate and maintain virulence variation. DNA polymorphism analysis also detected potential hotspot areas in addition to southern Gansu. This may result in more difficulties in management of genetic variation and thus the potential virulence variation in P. striiformis f.sp. tritici as well as providing opportunities for searching disease resistance factors.Key words: genetic diversity, Puccinia striiformis, DNA fingerprinting, virulence variation.

scholarly journals Slc1a3-2A-CreERT2 mice reveal unique features of Bergmann glia and augment a growing collection of Cre drivers and effectors in the 129S4 genetic background

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lech Kaczmarczyk ◽  
Nicole Reichenbach ◽  
Nelli Blank ◽  
Maria Jonson ◽  
Lars Dittrich ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Phenotypic Diversity ◽  
Expression Patterns ◽  
Cell Types ◽  
Inbred Strains ◽  
Brain Regions ◽  
Genetically Engineered ◽  
Disease Models ◽  
Calcium Indicator ◽  
High Consistency

AbstractGenetic variation is a primary determinant of phenotypic diversity. In laboratory mice, genetic variation can be a serious experimental confounder, and thus minimized through inbreeding. However, generalizations of results obtained with inbred strains must be made with caution, especially when working with complex phenotypes and disease models. Here we compared behavioral characteristics of C57Bl/6—the strain most widely used in biomedical research—with those of 129S4. In contrast to 129S4, C57Bl/6 demonstrated high within-strain and intra-litter behavioral hyperactivity. Although high consistency would be advantageous, the majority of disease models and transgenic tools are in C57Bl/6. We recently established six Cre driver lines and two Cre effector lines in 129S4. To augment this collection, we genetically engineered a Cre line to study astrocytes in 129S4. It was validated with two Cre effector lines: calcium indicator gCaMP5g-tdTomato and RiboTag—a tool widely used to study cell type-specific translatomes. These reporters are in different genomic loci, and in both the Cre was functional and astrocyte-specific. We found that calcium signals lasted longer and had a higher amplitude in cortical compared to hippocampal astrocytes, genes linked to a single neurodegenerative disease have highly divergent expression patterns, and that ribosome proteins are non-uniformly expressed across brain regions and cell types.

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