Further insight into the global variability of the OCA2-HERC2 locus for human pigmentation from multiallelic markers

AbstractThe OCA2-HERC2 locus is responsible for the greatest proportion of eye color variation in humans. Numerous studies extensively described both functional SNPs and associated patterns of variation over this region. The goal of our study is to examine how these haplotype structures and allelic associations vary when highly variable markers such as microsatellites are used. Eleven microsatellites spanning 357 Kb of OCA2-HERC2 genes are analyzed in 3029 individuals from worldwide populations. We found that several markers display large differences in allele frequency (10% to 35% difference) among Europeans, East Asians and Africans. In Europe, the alleles showing increased frequency can also discriminate individuals with (IrisPlex) predicted blue and brown eyes. Distinct haplotypes are identified around the variants C and T of the functional SNP rs12913832 (associated to blue eyes), with linkage disequilibrium r2 values significant up to 237 Kb. The haplotype carrying the allele rs12913832 C has high frequency (76%) in blue eye predicted individuals (30% in brown eye predicted individuals), while the haplotype associated to the allele rs12913832 T is restricted to brown eye predicted individuals. Finally, homozygosity values reach levels of 91% near rs12913832. Odds ratios show values of 4.2, 7.4 and 10.4 for four markers around rs12913832 and 7.1 for their core haplotype. Hence, this study provides an example on the informativeness of multiallelic markers that, despite their current limited potential contribution to forensic eye color prediction, supports the use of microsatellites for identifying causing variants showing similar genetic features and history.

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Transcriptomic and chemical analyses to identify candidate genes involved in color variation of sainfoin flowers

BMC Plant Biology ◽

10.1186/s12870-021-02827-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yu Qiao ◽

Qiming Cheng ◽

Yutong Zhang ◽

Wei Yan ◽

Fengyan Yi ◽

...

Keyword(s):

Regulatory Networks ◽

Flower Color ◽

Color Variation ◽

Anthocyanin Synthesis ◽

Flower Formation ◽

Factors Affecting ◽

Phenylpropanoid Biosynthesis ◽

Molecular Information ◽

Illumina Hiseq4000 ◽

Insight Into

Abstract Background Sainfoin (Onobrychis viciifolia Scop) is not only a high-quality legume forage, but also a nectar-producing plant. Therefore, the flower color of sainfoin is an important agronomic trait, but the factors affecting its flower phenotype are still unclear. To gain insights into the regulatory networks associated with metabolic pathways of coloration compounds (flavonoids or anthocyanins) and identify the key genes, we conducted a comprehensive analysis of the phenotype, metabolome and transcriptome of WF and AF of sainfoin. Results Delphinidin, petunidin and malvidin derivatives were the main anthocyanin compounds in the AF of sainfoin. These substances were not detected in the WF of sainfoin. The transcriptomes of WF and AF in sainfoin at the S1 and S3 stages were obtained using the Illumina HiSeq4000 platform. Overall, 10,166 (4273 upregulated and 5893 downregulated) and 15,334 (8174 upregulated and 7160 downregulated) DEGs were identified in flowers at S1 and S3 stages, respectively (WF-VS-AF). KEGG pathway annotations showed that 6396 unigenes were annotated to 120 pathways and contained 866 DEGs at S1 stages, and 6396 unigenes were annotated to 131 pathways and included 1546 DEGs at the S3 stage. Nine DEGs belonging to the “flavonoid biosynthesis”and “phenylpropanoid biosynthesis” pathways involved in flower color formation were identified and verified by RT-qPCR analyses. Among these DEGs, 4CL3, FLS, ANS, CHS, DFR and CHI2 exhibited downregulated expression, and F3H exhibited upregulated expression in the WF compared to the AF, resulting in a decrease in anthocyanin synthesis and the formation of WF in sainfoin. Conclusions This study is the first to use transcriptome technology to study the mechanism of white flower formation in sainfoin. Our transcriptome data will be a great enrichment of the genetic information for sainfoin. In addition, the data presented herein will provide valuable molecular information for genetic breeding and provide insight into the future study of flower color polymorphisms in sainfoin.

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Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color

Science Advances ◽

10.1126/sciadv.abd1239 ◽

2021 ◽

Vol 7 (11) ◽

pp. eabd1239

Author(s):

Mark Simcoe ◽

Ana Valdes ◽

Fan Liu ◽

Nicholas A. Furlotte ◽

David M. Evans ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Color Variation ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Melanin Pigmentation ◽

Eye Color ◽

Human Eye ◽

Genome Wide ◽

Genomic Regions

Human eye color is highly heritable, but its genetic architecture is not yet fully understood. We report the results of the largest genome-wide association study for eye color to date, involving up to 192,986 European participants from 10 populations. We identify 124 independent associations arising from 61 discrete genomic regions, including 50 previously unidentified. We find evidence for genes involved in melanin pigmentation, but we also find associations with genes involved in iris morphology and structure. Further analyses in 1636 Asian participants from two populations suggest that iris pigmentation variation in Asians is genetically similar to Europeans, albeit with smaller effect sizes. Our findings collectively explain 53.2% (95% confidence interval, 45.4 to 61.0%) of eye color variation using common single-nucleotide polymorphisms. Overall, our study outcomes demonstrate that the genetic complexity of human eye color considerably exceeds previous knowledge and expectations, highlighting eye color as a genetically highly complex human trait.

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Insight into Inflammatory Bowel Disease Pathogenesis: Is the Answer Blowing in the Wind?

Inflammatory Bowel Diseases ◽

10.1093/ibd/izab183 ◽

2021 ◽

Author(s):

Sari M Herman ◽

Karver Zaborniak ◽

Charles N Bernstein

Keyword(s):

Ulcerative Colitis ◽

Atopic Disease ◽

Immune Dysregulation ◽

Potential Contribution ◽

Food Allergens ◽

Disease Pathogenesis ◽

Bowel Diseases ◽

Inflammatory Bowel ◽

Immunomodulatory Therapies ◽

Insight Into

Abstract Inflammatory bowel diseases (IBD) including Crohn’s disease and ulcerative colitis are conditions characterized by immune dysregulation to a trigger in those with a genetic predisposition. Environmental factors are thought to contribute to IBD, but no definite trigger has been identified. Aeroallergens have not been thoroughly investigated in their potential contribution to the pathogenesis to IBD. The geographic distribution of aeroallergens and IBD, the association of atopic disease with IBD, seasonality and IBD, and cross-reactive food allergens require further study with implications for targeted dietary and immunomodulatory therapies.

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Application of six IrisPlex SNPs and comparison of two eye color prediction systems in diverse Eurasia populations

International Journal of Legal Medicine ◽

10.1007/s00414-013-0953-1 ◽

2014 ◽

Vol 128 (3) ◽

pp. 447-453 ◽

Cited By ~ 18

Author(s):

Libing Yun ◽

Yan Gu ◽

Haseena Rajeevan ◽

Kenneth K. Kidd

Keyword(s):

Eye Color ◽

Prediction Systems ◽

Color Prediction

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Eye color prediction using single nucleotide polymorphisms in Saudi population

Saudi Journal of Biological Sciences ◽

10.1016/j.sjbs.2018.09.011 ◽

2019 ◽

Vol 26 (7) ◽

pp. 1607-1612

Author(s):

Jahad Alghamdi ◽

Manal Amoudi ◽

Ahmad Ch. Kassab ◽

Mansour Al Mufarrej ◽

Saleh Al Ghamdi

Keyword(s):

Single Nucleotide Polymorphisms ◽

Saudi Population ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Eye Color ◽

Color Prediction

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Comparative Transcriptomics Provides Insight into Floral Color Polymorphism in a Pleione limprichtii Orchid Population

International Journal of Molecular Sciences ◽

10.3390/ijms21010247 ◽

2019 ◽

Vol 21 (1) ◽

pp. 247 ◽

Cited By ~ 2

Author(s):

Yiyi Zhang ◽

Tinghong Zhou ◽

Zhongwu Dai ◽

Xiaoyu Dai ◽

Wei Li ◽

...

Keyword(s):

Distribution Pattern ◽

Expression Patterns ◽

Color Polymorphism ◽

Color Variation ◽

Similar Species ◽

Color Formation ◽

Floral Color ◽

Species Evolution ◽

Different Color ◽

Insight Into

Floral color polymorphism can provide great insight into species evolution from a genetic and ecological standpoint. Color variations between species are often mediated by pollinators and are fixed characteristics, indicating their relevance to adaptive evolution, especially between plants within a single population or between similar species. The orchid genus Pleione has a wide variety of flower colors, from violet, rose-purple, pink, to white, but their color formation and its evolutionary mechanism are unclear. Here, we selected the P. limprichtii population in Huanglong, Sichuan Province, China, which displayed three color variations: Rose-purple, pink, and white, providing ideal material for exploring color variations with regard to species evolution. We investigated the distribution pattern of the different color morphs. The ratio of rose-purple:pink:white-flowered individuals was close to 6:3:1. We inferred that the distribution pattern may serve as a reproductive strategy to maintain the population size. Metabolome analysis was used to reveal that cyanindin derivatives and delphidin are the main color pigments involved. RNA sequencing was used to characterize anthocyanin biosynthetic pathway-related genes and reveal different color formation pathways and transcription factors in order to identify differentially-expressed genes and explore their relationship with color formation. In addition, qRT-PCR was used to validate the expression patterns of some of the genes. The results show that PlFLS serves as a crucial gene that contributes to white color formation and that PlANS and PlUFGT are related to the accumulation of anthocyanin which is responsible for color intensity, especially in pigmented flowers. Phylogenetic and co-expression analyses also identified a R2R3-MYB gene PlMYB10, which is predicted to combine with PlbHLH20 or PlbHLH26 along with PlWD40-1 to form an MBW protein complex (MYB, bHLH, and WDR) that regulates PlFLS expression and may serve as a repressor of anthocyanin accumulation-controlled color variations. Our results not only explain the molecular mechanism of color variation in P. limprichtii, but also contribute to the exploration of a flower color evolutionary model in Pleione, as well as other flowering plants.

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On High Frequency Polar Motion and Length of Day Variations

International Astronomical Union Colloquium ◽

10.1017/s0252921100061716 ◽

2000 ◽

Vol 178 ◽

pp. 545-554

Author(s):

K. Arfa-Kaboodvand ◽

E. Groten

Keyword(s):

Frequency Spectrum ◽

Earth Rotation ◽

High Frequency ◽

Polar Motion ◽

Length Of Day ◽

Physical Processes ◽

Earth Orientation ◽

Tidal Forces ◽

Diurnal Range ◽

Insight Into

AbstractThe 0.042-day Earth rotation data (diurnal and semidiurnal) computed by the International GPS Service were used to analyze the daily/sub-daily variations of polar motion (PM) and length of day (LOD). Systematic and advanced spectral analytical investigations of the degree of periodic variability have been carried out. They show that the prominent periodical components can be found at the tidal frequencies of zonal, tesseral and sectorial waves. These investigations should give better insight into the physical processes, which influence Earth orientation (i.e. due to the atmospheric and oceanic motions, tidal forces etc.). It should be the basis for the detailed modeling of excitation functions in the sub-diurnal range of the high-frequency spectrum.

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