scholarly journals Comparative Transcriptome Analysis Identifies Candidate Genes Related to Skin Color Differentiation in Red Tilapia

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Wenbin Zhu ◽  
Lanmei Wang ◽  
Zaijie Dong ◽  
Xingting Chen ◽  
Feibiao Song ◽  
...  
Keyword(s):  
Skin Color ◽  
Molecular Mechanisms ◽  
Skin Pigmentation ◽  
Color Variation ◽  
Pigment Synthesis ◽  
Red Tilapia ◽  
Specific Strain ◽  
Molecular Selection ◽  
Aquaculture Production ◽  
Selection Of

Abstract Red tilapia is becoming more popular for aquaculture production in China in recent years. However, the pigmentation differentiation in genetic breeding is the main problem limiting its development of commercial red tilapia culture and the genetic basis of skin color variation is still unknown. In this study, we conducted Illumina sequencing of transcriptome on three color variety red tilapia. A total of 224,895,758 reads were generated, resulting in 160,762 assembled contigs that were used as reference contigs. The contigs of red tilapia transcriptome had hits in the range of 53.4% to 86.7% of the unique proteins of zebrafish, fugu, medaka, three-spined stickleback and tilapia. And 44,723 contigs containing 77,423 simple sequence repeats (SSRs) were identified, with 16,646 contigs containing more than one SSR. Three skin transcriptomes were compared pairwise and the results revealed that there were 148 common significantly differentially expressed unigenes and several key genes related to pigment synthesis, i.e. tyr, tyrp1, silv, sox10, slc24a5, cbs and slc7a11, were included. The results will facilitate understanding the molecular mechanisms of skin pigmentation differentiation in red tilapia and accelerate the molecular selection of the specific strain with consistent skin colors.

scholarly journals Transcriptome Analysis of Skin Color Variation During and after Overwintering of Malaysian Red Tilapia

2021 ◽  
Author(s):  
bingjie Jiang ◽  
lanmei Wang ◽  
mingkun Luo ◽  
jianjun Fu ◽  
wenbin Zhu ◽  
...  
Keyword(s):  
Skin Color ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Color Variation ◽  
Future Research ◽  
Red Tilapia ◽  
Pink Color ◽  
Pathway Analyses ◽  
Specificity Measure ◽  
Black Color

Abstract The commercial value of red tilapia is hampered by variations in skin color during overwintering. In this study, three types skin of red tilapia, including the skin remained pink color during and after overwintering (WP), the skin changed from pink color to black color during overwintering and remained black color after overwintering (PB), and the skin changed from pink color to black color during overwintering but recovered to pink color when the temperature rose after overwintering (BP), were used to analyze their molecular mechanisms of color variation. The transcriptome results revealed that the PB, WP, and BP libraries had 42, 43, and 43 million clean reads, respectively. The top 10 abundance mRNAs and specific mRNAs (specificity measure SPM > 0.9) were screened. After comparing intergroup gene expression levels, there were 2528, 1924 and 1939 differentially expressed genes (DEGs) between BP and PB, BP and WP, and PB and WP, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of color-related mRNAs showed that a number of DEGs, including tyrp1, tyr, pmel, mitf, mc1r, asip, tat, hpdb and foxd3, might play a potential role in pigmentation. Additionally, the co-expression patterns of genes were detected within the pigment-related pathways by PPI network from PB_WP group. Furthermore, DEGs from the apoptosis and autophagy pathways, such as baxα, beclin1, and atg7, might be involved in the fading of red tilapia melanocytes. The findings will aid in understanding the molecular mechanism underlying skin color variation in red tilapia during and after overwintering, as well as lay a foundation for future research aimed at improving red tilapia skin color characteristics.

scholarly journals Characterization of Chicken Skin Yellowness and Exploration of Genes Involved in Skin Yellowness Deposition in Chicken

2021 ◽  
Vol 12 ◽  
Author(s):  
Jingwen Wu ◽  
Zetong Lin ◽  
Genghua Chen ◽  
Qingbin Luo ◽  
Qinghua Nie ◽  
...  
Keyword(s):  
Skin Color ◽  
Skin Pigmentation ◽  
Differentially Expressed ◽  
Economic Trait ◽  
Chicken Skin ◽  
Before And After ◽  
Skin Coloration ◽  
Insight Into ◽  
Selection Of

Skin color is an important economic trait in meat-type chickens. A uniform bright skin color can increase the sales value of chicken. Chickens with bright yellow skin are more popular in China, especially in the broiler market of South China. However, the skin color of chickens can vary because of differences in breeds, diet, health, and individual genetics. To obtain greater insight into the genetic factors associated with the process of skin pigmentation in chickens, we used a colorimeter and high-resolution skin photographs to measure and analyze the skin color of chickens. By analyzing 534 chickens of the same breed, age, and feed condition, we found that the yellowness values of the chickens varied within this population. A significant positive correlation was found between the cloacal skin yellowness values before and after slaughter, and the cloacal skin yellowness value of live chickens was positively correlated with the overall body skin yellowness value. Additionally, chicken skin yellowness exhibited low heritability, ranging from 0.07 to 0.27. Through RNA sequencing, 882 genes were found to be differentially expressed between the skin with the highest and lowest yellowness values. Some of these differentially expressed genes may play an important role in yellow pigment deposition in chicken skin, which included TLR2B, IYD, SMOC1, ALDH1A3, CYP11A1, FHL2, TECRL, ACACB, TYR, PMEL, and GPR143. In addition, we found that the expression and variations of the BCO2 gene, which is referred to as the yellow skin gene, cannot be used to estimate the skin yellowness value of chickens in this population. These data will help to further our understanding of chicken skin yellowness and might contribute to the selection of specific chicken strains with consistent skin coloration.

scholarly journals Skin color variation: A study on Eastern and North East India

2019 ◽  
Vol 10 (3) ◽  
pp. 13-16
Author(s):  
Sumit Maitra ◽  
Diptendu Chatterjee ◽  
Arup Ratan Bandyopadhyay
Keyword(s):  
Ethnic Groups ◽  
Skin Color ◽  
Skin Pigmentation ◽  
Color Space ◽  
Color Variation ◽  
Phenotypic Traits ◽  
North East India ◽  
North East ◽  
Wide Range ◽  
Significant Difference

Background: Skin pigmentation is one of the most variable phenotypic traits and most noticeable of human polymorphisms. Skin pigmentation in humans is largely determined by the quantity and distribution of the pigment melanin. The literature review on skin color variation revealed a few works on skin pigmentation variation has been conducted in India from Southern, Western and Northern part. Aims and Objectives: To best of the knowledge, the present discourse is the first attempt to understand skin color variation from Eastern and North Eastern part of India among three populations. Materials and Methods: The present study consisted of 312 participants from Chakma and Tripuri groups of Tripura, North East India, and participants from Bengalee Hindu caste population from West Bengal. Skin color was measured by Konica Minolta CR-10 spectrophotometer which measures and quantifies the colors with a 3D color space (CIELAB) color space created by 3 axes. All the skin color measurements from each participant were taken from unexposed (underarm) left and right to get a mean and exposed (forehead) to sunlight. Results: The distribution of skin color variation among the three populations demonstrated significant (p<0.05) difference in lightness for unexposed and exposed indicating lightness in unexposed area. Furthermore, the present study revealed significant difference (p<0.05) in skin color among the ethnic groups across the body location and all three attributes (lightness, redness and yellowness). Conclusion: Generally, skin color variation may be elucidated by two main factors: individual differences in lightness and yellowness and by and large due to ethnicity, where diversity in redness is due to primarily due to different body locations. Variation in lightness have more characteristic probability. The present study first time reports the wide range of quantitative skin color variation among the three ethnic groups from Eastern and North East India and highest yellowness (b*) among the population from North East India.

Skin Color Correction for Tissue Spectroscopy: Demonstration of a Novel Approach with Tissue-Mimicking Phantoms

2005 ◽  
Vol 59 (2) ◽  
pp. 237-244 ◽  
Author(s):  
Olusola O. Soyemi ◽  
Michelle R. Landry ◽  
Ye Yang ◽  
Patrick O. Idwasi ◽  
Babs R. Soller
Keyword(s):  
Skin Color ◽  
Near Infrared ◽  
Skin Pigmentation ◽  
Nir Spectroscopy ◽  
Bottom Layer ◽  
Correction Method ◽  
Color Variation ◽  
Absorption Properties ◽  
Novel Approach ◽  
Components Analysis

The application of partial least squares (PLS) regression to visible–near-infrared (VIS-NIR) spectroscopy for modeling important blood and tissue parameters is generally complicated by the variation in skin pigmentation (melanin) across the human population. An orthogonal correction method for removing the influence of skin pigmentation has been demonstrated in diffuse reflectance spectra from two-layer tissue-mimicking phantoms. The absorption properties of the phantoms were defined by lyophilized human hemoglobin (bottom layer) and synthetic melanin (top layer). Tissue-like scattering was simulated in both layers with intralipid™. The approach uses principal components analysis (PCA) loading vectors from a separate set of phantom spectra that encode the unwanted melanin variation to remove the effect of melanin from the test phantoms. The preprocessing of phantom spectra using this orthogonal correction method resulted in PLS models with reduced complexity and enhanced prediction performance. Preliminary results from a separate study that evaluates the feasibility of defining skin color variation in an experiment with a single human subject are also presented.

scholarly journals Analysis of Skin Pigmentation and Genetic Ancestry in Three Subpopulations from Pakistan: Punjabi, Pashtun, and Baloch

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 733
Author(s):  
Muhammad Adnan Shan ◽  
Olivia Strunge Meyer ◽  
Mie Refn ◽  
Niels Morling ◽  
Jeppe Dyrberg Andersen ◽  
...  
Keyword(s):  
Skin Color ◽  
Multiple Testing ◽  
African Ancestry ◽  
Skin Pigmentation ◽  
Genetic Distances ◽  
Color Variation ◽  
European Ancestry ◽  
Upper Arm ◽  
South Central ◽  
Sub Saharan

Skin pigmentation is one of the most prominent and variable phenotypes in humans. We compared the alleles of 163 SNPs and indels from the Human Pigmentation (HuPi) AmpliSeq™ Custom panel, and biogeographic ancestry with the quantitative skin pigmentation levels on the upper arm, lower arm, and forehead of 299 Pakistani individuals from three subpopulations: Baloch, Pashtun, and Punjabi. The biogeographic ancestry of each individual was estimated using the Precision ID Ancestry Panel. All individuals were mainly of mixed South-Central Asian and European ancestry. However, the Baloch individuals also had an average proportion of Sub-Saharan African ancestry of approximately 10%, whereas it was <1% in the Punjabi and Pashtun individuals. The pairwise genetic distances between the Pashtun, Punjabi, and Baloch subpopulations based on the ancestry markers were statistically significantly different. Individuals from the Pashtun subpopulation had statistically significantly lower skin pigmentation than individuals from the Punjabi and Baloch subpopulations (p < 0.05). The proportions of European and Sub-Saharan African ancestry and five SNPs (rs1042602, rs10831496, rs1426654, rs16891982, and rs12913832) were statistically significantly associated with skin pigmentation at either the upper arm, lower arm or forehead in the Pakistani population after correction for multiple testing (p < 10−3). A model based on four of these SNPs (rs1426654, rs1042602, rs16891982, and rs12913832) explained 33% of the upper arm skin pigmentation. The four SNPs and the proportions of European and Sub-Saharan African ancestry explained 37% of the upper arm skin pigmentation. Our results indicate that the four likely causative SNPs, rs1426654, rs1042602, rs16891982, and rs12913832 located in SLC24A5, TYR, SLC45A2, and HERC2, respectively, are essential for skin color variation in the admixed Pakistani subpopulations.

scholarly journals Comparative Transcriptome Analysis Identifies Candidate Genes Related to Black-Spotted Pattern Formation in Spotted Scat (Scatophagus argus)

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 765
Author(s):  
Xiaozhan Lin ◽  
Changxu Tian ◽  
Yang Huang ◽  
Hongjuan Shi ◽  
Guangli Li
Keyword(s):  
Signaling Pathway ◽  
Fish Species ◽  
Molecular Mechanisms ◽  
Skin Pigmentation ◽  
Wnt Signaling Pathway ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Marine Aquaculture ◽  
Pigment Synthesis ◽  
Scatophagus Argus

Spotted scat (Scatophagus argus) is an economically important marine aquaculture and ornamental fish species in Asia, especially in southeast China. In this study, skin transcriptomes of S. argus were obtained for three types of skin, including black-spotted skin (A), non-spotted skin (B) and caudal fin (C). A total of nine complementary DNA (cDNA) libraries were obtained by Illumina sequencing. Bioinformatics analysis revealed that 1358, 2086 and 487 genes were differentially expressed between A and B, A and C, and B and C, respectively. The results revealed that there were 134 common significantly differentially expressed genes (DEGs) and several key genes related to pigment synthesis and pigmentation, including tyrp1, mitf, pmel, slc7a2, tjp1, hsp70 and mart-1. Of these, some DEGs were associated with pigmentation-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, such as tyrosine metabolism, melanogenesis, the Wnt signaling pathway and the mitogen-activated protein kinase (MAPK) signaling pathway. The results will facilitate understanding the molecular mechanisms of skin pigmentation differentiation in S. argus and provide valuable information for skin coloration, especially the formation of spotted patterns on other marine fish species.

scholarly journals Combining QTL Mapping and Gene Expression Analysis to Elucidate the Genetic Control of ‘Crumbly’ Fruit in Red Raspberry (Rubus idaeus L.)

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 794
Author(s):  
Luca M. Scolari ◽  
Robert D. Hancock ◽  
Pete E. Hedley ◽  
Jenny Morris ◽  
Kay Smith ◽  
...  
Keyword(s):  
Genetic Control ◽  
Developmental Disorder ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Microarray Experiment ◽  
Rubus Idaeus ◽  
Red Raspberry ◽  
Genotype By Sequencing ◽  
First Time ◽  
Selection Of

‘Crumbly’ fruit is a developmental disorder in raspberry that results in malformed and unsaleable fruits. For the first time, we define two distinct crumbly phenotypes as part of this work. A consistent crumbly fruit phenotype affecting the majority of fruits every season, which we refer to as crumbly fruit disorder (CFD) and a second phenotype where symptoms vary across seasons as malformed fruit disorder (MFD). Here, segregation of crumbly fruit of the MFD phenotype was examined in a full-sib family and three QTL (Quantitative Trait Loci) were identified on a high density GbS (Genotype by Sequencing) linkage map. This included a new QTL and more accurate location of two previously identified QTLs. A microarray experiment using normal and crumbly fruit at three different developmental stages identified several genes that were differentially expressed between the crumbly and non-crumbly phenotypes within the three QTL. Analysis of gene function highlighted the importance of processes that compromise ovule fertilization as triggers of crumbly fruit. These candidate genes provided insights regarding the molecular mechanisms involved in the genetic control of crumbly fruit in red raspberry. This study will contribute to new breeding strategies and diagnostics through the selection of molecular markers associated with the crumbly trait.

“Because I’m Light Skin . . . They Think I’m Italian”

2016 ◽  
Vol 52 (4) ◽  
pp. 460-490 ◽  
Author(s):  
Edward Fergus
Keyword(s):  
Skin Color ◽  
Color Variation ◽  
Ethnic Identification ◽  
Opportunity Structure ◽  
Mexican Students ◽  
Light Skin ◽  
Racial Ethnic

Discussions on Latino/a students’ interpretation of the opportunity structure and schooling treat racial/ethnic identification among Latino/as as static, despite skin color variation. This article provides findings from interviews with six Mexican students who discussed teachers identifying them as “White-looking” or “Hispanic/Mexican-looking.” Both groups shared belief in the achievement ideology and understood the opportunity structure as fraught with barriers. However, the “White-looking” students perceived themselves as being able to permeate such barriers meanwhile the “Hispanic/Mexican-looking” students believed such barriers affect their ability to “make it” regardless of their aspirations. This study raises questions regarding theories on academic variability of Latino/a students.

First person – Fanny Jaudon and Martina Albini

2021 ◽  
Vol 134 (16) ◽  
Keyword(s):  
Neurotrophic Factor ◽  
Neurological Disorders ◽  
Molecular Mechanisms ◽  
Neurological Diseases ◽  
Early Career ◽  
First Person ◽  
Early Career Researchers ◽  
And Function ◽  
The University ◽  
Selection Of

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. Fanny Jaudon and Martina Albini are co-first authors on ‘ A developmental stage- and Kidins220-dependent switch in astrocyte responsiveness to brain-derived neurotrophic factor’, published in JCS. Fanny is a postdoc at the University of Trieste in the lab of Lorenzo A. Cingolani at Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy, investigating the molecular mechanisms controlling development and function of neuronal circuits and implementing genome-editing approaches for the treatment of neurological disorders. Martina is a PhD student at the Istituto Italiano di Tecnologia in the lab of Fabio Benfenati and Fabrizia Cesca investigating neurotrophin biology and its involvement in neurological diseases.

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