scholarly journals A Genome Scan for Genes Underlying Adult Body Size Differences between Central African Pygmies and their Non-Pygmy Neighbors

2017 ◽  
Author(s):  
Trevor J. Pemberton ◽  
Paul Verdu ◽  
Noémie S. Becker ◽  
Cristen J. Willer ◽  
Barry S. Hewlett ◽  
...  
Keyword(s):  
Body Size ◽  
Genomic Region ◽  
Growth Patterns ◽  
Genetic Admixture ◽  
Leg Length ◽  
Standing Height ◽  
Reduced Body ◽  
Sitting Height ◽  
A Genome ◽  
African Pygmies

AbstractBackgroundCentral African hunter-gatherer Pygmy populations have reduced body size compared with their often much larger agricultural non-Pygmy neighbors, potentially reflecting adaptation to the anatomical and physiological constraints of their lifestyle in tropical rainforests. Earlier studies investigating the genetics of the pygmy phenotype have focused on standing height, one aspect of this complex phenotype that is itself a composite of skeletal components with different growth patterns. Here, we extend the investigations of standing height to the variability and genetic architecture of sitting height and subischial leg length as well as body mass index (BMI) in a sample of 406 unrelated West Central African Pygmies and non-Pygmies.ResultsIn addition to their significantly reduced standing height compared with non-Pygmies, we find Pygmies to have significantly shorter sitting heights and subischial leg lengths as well as higher sitting/standing height ratios than non-Pygmies. However, while male Pygmies had significantly lower BMI compared with male non-Pygmies, the BMI of females were instead similar. Consistent with prior observations with standing height, sitting height and subischial leg length were strongly correlated with inferred levels of non-Pygmy genetic admixture while BMI was instead weakly correlated, likely reflecting the greater contribution of non-genetic factors to the determination of body weight compared with height. Using 196,725 SNPs on the Illumina Cardio-MetaboChip with genotypes on 358 Pygmy and 169 non-Pygmy individuals together with single-and multi-marker association approaches, we identified a single genomic region and seven genes associated with Pygmy/non-Pygmy categorization as well as 9, 10, 9, and 10 genes associated with standing and sitting height, sitting/standing height ratio, and subischial leg length, respectively. Many of the genes identified have putative functions consistent with a role in determining their associated trait as well as the complex Central African pygmy phenotype.ConclusionsThese findings highlight the potential of modestly sized datasets of Pygmies and non-Pygmies to detect biologically meaningful associations with traits contributing to the Central African pygmy phenotype. Moreover, they provide new insights into the phenotypic and genetic bases of the complex pygmy phenotype and offer new opportunities to facilitate our understanding of its complex evolutionary origins.

scholarly journals Growth impairment in children with atopic eczema

1987 ◽  
Vol 80 (1) ◽  
pp. 9-12 ◽  
Author(s):  
F Kristmundsdottir ◽  
T J David
Keyword(s):  
Topical Corticosteroid ◽  
Atopic Eczema ◽  
Linear Growth ◽  
Skeletal Maturity ◽  
National Formulary ◽  
Leg Length ◽  
Standing Height ◽  
Growth Impairment ◽  
Topical Corticosteroids ◽  
Sitting Height

Growth was studied in 89 children with atopic eczema aged 1–16 years. Nine (10%) had a standing height below the 3rd centile. Both boys and girls had significantly reduced sitting height but normal subischial leg length, and both sexes had significantly delayed skeletal maturity scores. Impaired growth was particularly associated with widespread eczema, but also with the presence of asthma and the potency of topical corticosteroid. Six of the 15 patients with a corrected height centile below the 10th centile had been receiving potent (British National Formulary category I or II) topical corticosteroids. This study suggests that impaired linear growth is a feature of atopic eczema. While the causes of the growth impairment are unclear, there is a need for caution in the use of potent topical corticosteroids in children.

scholarly journals Genome-Wide Association Study (GWAS) for Examining the Genomics Controlling Prickle Production in Red Raspberry (Rubus idaeus L.)

Agronomy ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 27
Author(s):  
Archana Khadgi ◽  
Courtney A. Weber
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genomic Region ◽  
Rubus Idaeus ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Red Raspberry ◽  
Genome Wide ◽  
A Genome ◽  
Genotype By Sequencing

Red raspberry (Rubus idaeus L.) is an expanding high-value berry crop worldwide. The presence of prickles, outgrowths of epidermal tissues lacking vasculature, on the canes, petioles, and undersides of leaves complicates both field management and harvest. The utilization of cultivars with fewer prickles or prickle-free canes simplifies production. A previously generated population segregating for prickles utilizing the s locus between the prickle-free cultivar Joan J (ss) and the prickled cultivar Caroline (Ss) was analyzed to identify the genomic region associated with prickle development in red raspberry. Genotype by sequencing (GBS) was combined with a genome-wide association study (GWAS) using fixed and random model circulating probability unification (FarmCPU) to analyze 8474 single nucleotide polymorphisms (SNPs) and identify significant markers associated with the prickle-free trait. A total of four SNPs were identified on chromosome 4 that were associated with the phenotype and were located near or in annotated genes. This study demonstrates how association genetics can be used to decipher the genetic control of important horticultural traits in Rubus, and provides valuable information about the genomic region and potential genes underlying the prickle-free trait.

scholarly journals An FGA Frameshift Variant Associated with Afibrinogenemia in Dachshunds

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1065
Author(s):  
Reinhard Mischke ◽  
Julia Metzger ◽  
Ottmar Distl
Keyword(s):  
Protein Sequence ◽  
Sanger Sequencing ◽  
Selective Breeding ◽  
Genome Wide Association Study ◽  
Frameshift Mutation ◽  
Homozygosity Mapping ◽  
Genomic Region ◽  
Severe Bleeding ◽  
Genome Wide ◽  
A Genome

Congenital fibrinogen disorders are very rare in dogs. Cases of afibrinogenemia have been reported in Bernese Mountain, Bichon Frise, Cocker Spaniel, Collie, Lhasa Apso, Viszla, and St. Bernard dogs. In the present study, we examined four miniature wire-haired Dachshunds with afibrinogenemia and ascertained their pedigree. Homozygosity mapping and a genome-wide association study identified a candidate genomic region at 50,188,932–64,187,680 bp on CFA15 harboring FGB (fibrinogen beta chain), FGA (fibrinogen alpha chain), and FGG (fibrinogen gamma-B chain). Sanger sequencing of all three fibrinogen genes in two cases and validation of the FGA-associated mutation (FGA:g.6296delT, NC_006597.3:g.52240694delA, rs1152388481) in pedigree members showed a perfect co-segregation with afibrinogenemia-affected phenotypes, obligate carriers, and healthy animals. In addition, the rs1152388481 variant was validated in 393 Dachshunds and samples from 33 other dog breeds. The rs1152388481 variant is predicted to modify the protein sequence of both FGA transcripts (FGA201:p.Ile486Met and FGA-202:p.Ile555Met) leading to proteins truncated by 306 amino acids. The present data provide evidence for a novel FGA truncating frameshift mutation that is very likely to explain the cases of severe bleeding due to afibrinogenemia in a Dachshund family. This mutation has already been spread in Dachshunds through carriers before cases were ascertained. Genetic testing allows selective breeding to prevent afibrinogenemia-affected puppies in the future.

Relationship between circadian period and body size in the tau-mutant golden hamster

2014 ◽  
Vol 92 (1) ◽  
pp. 27-33
Author(s):  
Roberto Refinetti
Keyword(s):  
Body Size ◽  
Single Gene ◽  
Pleiotropic Effect ◽  
Circadian Period ◽  
Golden Syrian Hamster ◽  
Casein Kinase 1 ◽  
Reduced Body ◽  
Short Period ◽  
Casein Kinase 1 Epsilon ◽  
Tau Mutation

The tau mutation in the golden (Syrian) hamster is a single gene mutation that drastically affects the speed of the circadian clock, in such a way that homozygous mutants have an endogenous circadian period of 20 h (compared with 24 h for wild-type hamsters). While studying the circadian system of tau-mutant hamsters during the past 25 years, several authors have noted an apparent relationship between circadian period and body size in these animals. This study, based on 181 hamsters from 24 litters, confirmed previous observations that a shorter circadian period is associated with smaller body size, documented a sex difference in this association, and evaluated several mechanisms that might explain the phenomenon (such as different organ sizes, body composition, and metabolic rate). The obtained evidence suggests that the reduced body size of short-period hamsters is likely a pleiotropic effect of the tau allele (an allele of the casein kinase 1 epsilon gene) rather than a consequence of the shortened circadian period.

Ituglanis compactus, a new species of catfish (Siluriformes: Trichomycteridae) from the rio Jari drainage, lower Amazon, Brazil 

Zootaxa ◽  
2017 ◽  
Vol 4244 (2) ◽  
pp. 207 ◽  
Author(s):  
ÍTHALO DA SILVA CASTRO ◽  
WOLMAR BENJAMIN WOSIACKI
Keyword(s):  
New Species ◽  
Body Size ◽  
Head Length ◽  
New Taxon ◽  
Pectoral Fin ◽  
Reduced Body ◽  
Weberian Apparatus ◽  
Fin Rays ◽  
A New Species ◽  
Pectoral Fin Rays

A new species of Ituglanis is described from rio Iratapuru, near the rio Jari, Amapá, Brazil. The new species is distinguished from all congeners by the reduced number of post-Weberian apparatus vertebrae (36 or 37); the low number of paired ribs (2); the low number of interopercular odontodes (12–15); the number of branchiostegal rays (7 or 8); the presence of elongated fontanel in parieto-supraoccipital; the pectoral-fin rays (i,5); head length (18.9–25.0); and the presence of pores supraorbital s1, infraorbitals i1 and i3 of the laterosensory system. The new taxon has a reduced body size and fully ossified skeleton, but does not display a large number of paedomorphic traits compared to congeners. Comments about taxonomy and intrageneric comparisons are made, and paedomorphic in Ituglanis is discussed. Thoughts about conservation of the new species are presented. 

Genome-Wide Prediction of Coaxial Helical Stacking Using Random Forests and Covariance Models

2014 ◽  
Vol 23 (03) ◽  
pp. 1460008
Author(s):  
Kevin Byron ◽  
Jason T. L. Wang ◽  
Dongrong Wen
Keyword(s):  
Random Forests ◽  
Life Science ◽  
Science Research ◽  
Genomic Region ◽  
Computational Approach ◽  
Search Method ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search ◽  
Covariance Models

Developing effective artificial intelligence tools to find motifs in DNA, RNA and proteins poses a challenging yet important problem in life science research. In this paper, we present a computational approach for finding RNA tertiary motifs in genomic sequences. Specifically, we predict genomic coordinate locations for coaxial helical stackings in 3-way RNA junctions. These predictions are provided by our tertiary motif search package, named CSminer, which utilizes two versatile methodologies: random forests and covariance models. A coaxial helical stacking tertiary motif occurs in a 3-way RNA junction where two separate helical elements form a pseudocontiguous helix and provide thermodynamic stability to the RNA molecule as a whole. Our CSminer tool first uses a genome-wide search method based on covariance models to find a genomic region that may potentially contain a coaxial helical stacking tertiary motif. CSminer then uses a random forests classifier to predict whether the genomic region indeed contains the tertiary motif. Experimental results demonstrate the effectiveness of our approach.

scholarly journals Changing the relative size of the body parts of Drosophila by selection

1962 ◽  
Vol 3 (2) ◽  
pp. 169-180 ◽  
Author(s):  
Forbes W. Robertson
Keyword(s):  
Body Size ◽  
Relative Size ◽  
Cell Number ◽  
High Ratio ◽  
Growth Patterns ◽  
The Body ◽  
Mass Selection ◽  
Body Parts ◽  
Wing Size ◽  
Thorax Length

1. Mass selection for both high- and low-ratio of wing to thorax length has been carried out on a population of Drosophila melanogaster. The response to selection was immediate and sustained. When the experiment was stopped after ten generations, the wing area in the two selected lines differed by about 30%. The heritability estimate worked out at 0·56 ± 0·08.2. Thorax length remained comparatively unchanged during selection nor was there any change in wing shape. There was some evidence of assymetry of response since there was a relatively greater change in favour of smaller rather than larger size.3. The tibia length of all pairs of legs showed correlated changes so that the lines with larger or smaller wing sizes had also larger and smaller legs.4. The normal allometric relation between wing and thorax length, associated with variation in body-size, apparently also changed, so that for a given change in thorax length there was a greater or smaller proportional change in wing size in the high- or low-ratio lines.5. The changes in relative wing size are due to changes in cell number.6. It is suggested that the genetic changes due to selection act in the early pupal period when the imaginal discs are undergoing differentiation and proliferation to form imaginal hypoderm and appendages.7. Tests of genetic behaviour failed to show any departure from additivity in crosses which involved the unselected population and the high-ratio line. But highly significant departures existed in the cross to the low-ratio line. Relatively smaller wing size behaves as largely recessive. Stability of the normal wing/thorax ratio involves dominance and probably also epistasis. The genetic properties of the relative size of the appendage are apparently similar to those which characterize body-size as a whole.8. It is suggested that selection provides a valuable tool for studying the constancy or lability of the growth patterns which determine morphology.

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