Color Genes Research Articles

Differential level of oxidative stress markers in skin tissue of zebu and crossbreed cattle during thermal stress

Abstract The study aimed to evaluate oxidative stress markers (ROS, GPx, GRx) in skin tissue of cattle with different coat colors during different seasons. Ten each of Tharparkar (zebu) and Karan Fries (crossbred) heifers were selected from NDRI herd, Karnal. Animals were maintained under standard managemental practices followed at the farm. Skin biopsies were aseptically collected from each animal during winter, spring and summer. ROS, GPx, GRx were determined by ELISA. Real time PCR was performed to examine the expression of skin color genes (MC1R and PMEL) in skin tissue. In both the breeds, significantly higher (P

A functional single nucleotide polymorphism in the tyrosinase gene promoter affects skin color and transcription activity in the black-boned chicken

The tyrosinase (TYR) gene is the major melanogenesis-related gene for skin (fur) or plumage color in mammals and birds. Genetic variation in the promoter region of a gene may affect gene expression and phenotypes. This study compared the TYR promoter region between pooled DNA (n = 8) of chickens (Gallus gallus) with black and white skin using direct sequencing. The single nucleotide polymorphism (SNP) c.-2228A>T was found to have the opposite allele distribution in the two groups. The results of genotyping in a larger population (n = 188) revealed that SNP c.-2228A>T was associated with the skin color of the black-boned chicken. Individuals with genotypes AA and AT had greater TYR expression than those with genotype TT. A luciferase assay of the promoter activity revealed that genotype AA had greater activity than genotype TT. Transcription factor binding site analyses showed that the c.-2228A allele has a putative binding site for transcription factor AT-rich interaction domain 3a (Arid3a), while the c.-2228T allele has sites for GS homeobox 2 (GSX2), homeobox D9 (Hoxd9), and mix paired-like homeobox (MIXL1). We concluded that the TYR promoter polymorphism affects skin color. SNP c.-2228A>T could be used as a genetic marker for marker-assisted selection of skin color in the black-boned chicken.

Mosaic genome evolution in a recent and rapid avian radiation.

Recent genomic analyses of evolutionary radiations suggest that ancestral or standing genetic variation may facilitate rapid diversification, particularly in cases involving convergence in ecological traits. Likewise, lateral transfer of alleles via hybridization may also facilitate adaptive convergence, but little is known about the role of ancestral variation in examples of explosive diversification that primarily involve the evolution of species recognition traits. Here, we show that genomic regions distinguishing sympatric species in an extraordinary radiation of small finches called munias (genus Lonchura) have phylogenetic histories that are discordant with each other, with the overall pattern of autosomal differentiation among species, and with sex-linked and mitochondrial components of the genome. Genome-wide data for 11 species sampled in Australia and Papua New Guinea indicate substantial autosomal introgression between sympatric species, but also identify a limited number of divergent autosomal regions, several of which overlap known colour genes (ASIP,EDN3, IGSF11,KITLG, MC1R andSOX10). Phylogenetic analysis of these outlier regions shows that different munia species have acquired unique combinations of alleles across a relatively small set of phenotypically relevant genes. Our results demonstrate that the recombination of ancestral genetic variation across multiple loci may be an important mechanism for generating phenotypic novelty and diversity.

Regulatory pathway analysis of coat color genes in Mongolian horses

BackgroundStudies on the molecular genetics of horse skin pigmentation have typically focused on very few genes and proteins. In this study, we used Illumina sequencing to determine the global gene expression profiles in horses with white-colored coats and those with black-colored coats, with the goal of identifying novel genes that could regulate horse coat color.ResultsGenes encoding ribosomal-associated proteins were highly expressed in horse skin. We found a total of 231 unigenes that were differentially expressed between horses with white coats and horses with black coats; 119 were down-regulated, and 112 were up-regulated. Many of the up-regulated genes in black horses, such as genes related to tyrosine metabolism, may directly regulate dark coat color. Keratin genes, MIA family genes, fatty acid-related genes, and melanoma-associated genes were also differentially regulated, which suggests that they may play important roles in coat color formation.ConclusionsThese findings show that the transcription profiles from white and black horse skin provide useful information to understand the genetics underlying the control of skin melanin synthesis in horses, which may enhance our knowledge of human skin diseases, such as melanoma and albinism.

Characterization of a composite population of beef cattle in subtropical south Texas and the effect of genes for coat type and color on preweaning growth and influence of summer breeding on sex ratio

ABSTRACT In the wake of global climate change, it is paramount that breeders use breed types with optimal performance ability. This investigation describes a unique 3-breed composite population of cattle in south Texas composed of Red Angus and tropically adapted Senepol and Tuli breeds. Under a low-input production system, trend analyses revealed that between 2005 and 2015 total direct costs per cow decreased by $180 due largely to reduction of feed costs (−9.40 ± 4.3 $/yr; P 0.05). However, where either or both the calf and dam were red colored, a larger combined mean difference of 14.3 ± 5.2 kg (P

Beyond mean allelic effects: A locus at the major color gene MC1R associates also with differing levels of phenotypic and genetic (co)variance for coloration in barn owls.

The mean phenotypic effects of a discovered variant help to predict major aspects of the evolution and inheritance of a phenotype. However, differences in the phenotypic variance associated to distinct genotypes are often overlooked despite being suggestive of processes that largely influence phenotypic evolution, such as interactions between the genotypes with the environment or the genetic background. We present empirical evidence for a mutation at the melanocortin-1-receptor gene, a major vertebrate coloration gene, affecting phenotypic variance in the barn owl, Tyto alba. The white MC1R allele, which associates with whiter plumage coloration, also associates with a pronounced phenotypic and additive genetic variance for distinct color traits. Contrarily, the rufous allele, associated with a rufous coloration, relates to a lower phenotypic and additive genetic variance, suggesting that this allele may be epistatic over other color loci. Variance differences between genotypes entailed differences in the strength of phenotypic and genetic associations between color traits, suggesting that differences in variance also alter the level of integration between traits. This study highlights that addressing variance differences of genotypes in wild populations provides interesting new insights into the evolutionary mechanisms and the genetic architecture underlying the phenotype.

The Identification of SNPs in BCDO2 Gene for Skin Color in Chinese Indigenous Chicken

A complete linkage disequilibrium between the SNP (SNP B) in BCDO2 gene and the yellow skin phenotype in European domestic chicken has been reported. Here, we genotyped the reported SNPs (SNP A, SNP B, and SNP C) of the BCDO2 gene in 183 Chinese Indigenous chickens from 11 breeds/populations, including 57 yellow, 17 white, and 109 black skin chickens. The frequency of all three SNPs were significantly different between yellow and white skin chickens (p<0.01). In black skin chickens, a high frequency of the heterozygous genotype (AG) in SNP A (0.51) and SNP B (0.48) was observed. A total of three haplotypes (AAA, AGA, and GAA) from these three SNPs were obtained. Frequencies of the proposed yellow skin-associated haplotype AGA in yellow skin, white skin, and black skin chickens were 0.81, 0.35, and 0.56, respectively. The results showed that the yellow skin phenotype of the evaluated birds has not been under selection, and that the BCDO2 gene in black skin chickens, evolutionally may undergo a transition phase from yellow to white skin chicken. We concluded that, the SNPs of BCDO2 gene not only can be used to determine whether the chicken was subjected to selection, but may also be used as a marker when selecting for the preferred skin color in chicken breeding programs.

Standardization of Methodology for Polymorphism Detection in ASIP, MC1R and MATP Genes in Relation to Colour in Horses

The basic colour in horses, such as black, brown and chestnut is affected by only two genes MC1R and ASIP. Other colours in horses are affected by modifying genes, such as dilution gene MATP. In this paper genotypes of 133 horses were determined using PCR‑RFLP for MATP (membrane‑associated transporter protein) gene and duplex PCR‑RFLP for MC1R (melanocortin 1 receptor) and ASIP (agouti signaling protein) genes. The allele and genotype frequencies were detected in a group of horses of 6 different breeds. In animals, which was not influenced by modification allele of another colour gene, we found the concordance between detected genotypes and phenotypes observed in summer and in winter. But in some animals, it was difficult to derive genotypes from their colour and therefore DNA analysis could be necessary.

The white gene controls copulation success in Drosophila melanogaster

Characteristics of male courtship behavior in Drosophila melanogaster have been well-described, but the genetic basis of male-female copulation is largely unknown. Here we show that the white (w) gene, a classical gene for eye color, is associated with copulation success. 82.5% of wild-type Canton-S flies copulated within 60 minutes in circular arenas, whereas few white-eyed mutants mated successfully. The w+ allele exchanged to the X chromosome or duplicated to the Y chromosome in the white-eyed genetic background rescued the defect of copulation success. The w+-associated copulation success was independent of eye color phenotype. Addition of the mini-white (mw+) gene to the white-eyed mutant rescued the defect of copulation success in a manner that was mw+ copy number-dependent. Lastly, male-female sexual experience mimicked the effects of w+/mw+ in improving successful copulation. These data suggest that the w+ gene controls copulation success in Drosophila melanogaster.

English

Data from the snail farm of the University of Calabar, Nigeria were collected and utilized to investigate the distribution and gene frequencies of egg shell colour of two ectotypes of Giant African Land Snails (Archachatina marginata var. saturalis), black skinned (BS) × black skinned mating group, and white skinned (WS) × white skinned mating group. The eggs collected were scored for the presence of yellow (Yp), light yellow (Lp) and milky white (Mp) egg shell colour. The egg shell colour distributions between the two ectotypes (BS × BS and WS × WS) were 46.50 vs. 3.77%, 42.68 vs. 48.11% and 10.83 vs. 48.11% for yellow, light yellow and milky white, respectively. In both ectotypes, the dominant gene for yellow, light yellow and milky white egg shell colour segregated at low frequencies (0.26 vs. 0.02, 0.24 vs. 0.31 and 0.06 vs. 0.31). The lowest value being yellow shell of the white skinned × white skinned mating group with frequency of 0.02, followed by milky white shell of the black skinned × black skinned mating group with frequency of 0.06. These values were much lower than the Mendelian value of 0.75. This is an indication that snails have not been purified through artificial breeding. Estimate of genetic distance between the two ectotypes were 0.060, 0.005 and 0.063 at yellow, light yellow and milky white loci, respectively. This shows that the ectotypes are closely related at the egg shell colour loci. Key words: Genotype, phenotype, snail egg, shell colour, variations.

Genetic characterization of coat color genes in Brazilian Crioula sheep from a conservation nucleus

Abstract: The objective of this work was to identify single nucleotide polymorphisms (SNPs) in resequencing data from MC1R, ASIP, and TYRP1 genes derived from Crioula sheep (Ovis aris) with different coat colors. Polymorphisms in the ASIP (agouti-signaling protein), MC1R (melanocortin 1 receptor), and TRYP1 (tyrosinase-related protein 1) genes were analyzed in 115 sheep from Embrapa’s conservation nucleus of crioula sheep, in Brazil. A total of 7,914 bp were sequenced per animal, and 14 SNPs were identified. Two additional assays were performed to detect duplications and deletions in the ASIP gene. Ninety-five percent of the coat color variation was explained by epistatic interactions observed between specific alleles in the MC1R and ASIP genes. Evidence suggests an important role of TYRP1 variants for wool color, despite their low frequencies. The marker panel was efficient enough in predicting coat color in the studied animals and, therefore, can be used to implement a marker-assisted selection program in the conservation nucleus of sheep of the crioula breed.

Whole-genome re-sequencing and fine mapping of an orange petal color gene (Bnpc1) in spring Brassica napus L. to a 151-kb region

The petal color of B. napus is usually yellow, but white, cream, golden yellow, orange, and other colors have also been reported. The pigmentation mechanisms and evolutionary processes of petal color in B. napus remain elusive. An analysis of the inheritance of the orange petal color (OPC) trait indicated that this trait was controlled by two recessive genes, termed Bnpc1 and Bnpc2. For fine mapping of the Bnpc1 gene, two backcrossing populations, BC4 and BC5, were developed from the cross between an OPC parent, X118, and a yellow petal color parent, R258. Whole-genome re-sequencing with bulked segregation analysis using BC4 individuals was conducted, and as a result, two major candidate intervals of Bnpc1 were identified on chromosome C09 of B. napus (C09: 1.000–5.464 and 6.491–7.777 Mb). Subsequently, the genetic and physical linkage maps were constructed for the BC5 population using 10 simple sequence repeat, two sequence-characterized amplified region and 12 insertion-deletion (InDel) markers. The Bnpc1 gene was located in scaffold_38 on C09 of B. napus and flanked by Indel-31 and Indel-5, with genetic distances of 0.083 and 0.042 cM, respectively. The interval distance between the two markers was 151 kb (4.624–4.775 Mb) and was included in the first re-sequenced candidate region (C09: 1.000–5.464 Mb). The present study may facilitate cloning of the Bnpc1 gene as well as marker-assisted selection for developing OPC B. napus varieties and revealing the mechanism of petal color formation in B. napus.

Identification and genetic mapping of a novel incompletely dominant yellow leaf color gene, Y1718, on chromosome 2BS in wheat

The yellow-green leaf color mutant (Ygm) is a spontaneous mutant derived from the common wheat (Triticum aestivum L.) cultivar Xinong1718. Genetic analysis has shown that a novel single incompletely dominant gene (Y1718) is responsible for the yellow leaf color phenotype. The progeny of Ygm exhibit three distinct leaf color phenotypes, i.e., yellow (Y), yellow-green (Yg), and normal green (G). Y plants have yellow-green leaves in the seedling stage, which become yellow or a strong gold-yellow in the booting stage, with dwarfism and thin tillers until the flowering stage, and underdeveloped thylakoid membranes without well-structured grana in the chloroplasts. Yg plants always have a yellow-green phenotype with a number of well-structured grana that are loosely connected with stroma lamellae in the chloroplasts, where their main agronomic traits are the same as Xinong1718 and G plants, but the seed yield is low. Compared with Xinong1718 and G plants, Y and Yg plants had much lower chlorophyll (Chl) a, Chl b, and carotenoid contents in the booting stage. Molecular analysis using an F2 population and F2:3 lines derived from a cross of Yg and Shannong1 indicated that the Y1718 gene is located on chromosome 2BS, where it is flanked by the simple sequence repeat marker Xwmc25 and expressed sequence tag-sequence tagged sites marker BE498358 at genetic distances of 1.7 and 4.0 cM, respectively. Our results facilitate the fine mapping and gene cloning of Y1718 to explore chlorophyll synthesis, metabolism, and development in wheat.

Profiling of anthocyanins in transgenic purple-fleshed sweet potatoes by HPLC-MS/MS.

Anthocyanins in purple-fleshed sweet potato (PSP) are beneficial to human health. The leaf color (Lc) gene is a transcription factor involved in regulating anthocyanin biosynthesis. The anthocyanin profiles of wild-type PSP of Ayamurasaki and its three Lc-transgenic lines were investigated by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). In vitro antioxidant activities of wild-type and Lc-transgenic lines, including reducing power activity, DPPH radical scavenging activity, hydroxyl radical scavenging activity, linoleic acid autoxidation inhibition activity, ABTS free radical scavenging activity and oxygen radical absorbance capacity activity, were measured. The results showed that the total anthocyanin contents increased 1.5-1.9 times in three transgenic lines compared with that in wild-type PSP. Seventeen anthocyanins were found in wild-type PSP, while 19 in Lc-transgenic lines including cyanidin-based, peonidin-based and pelargonidin-based anthocyanins. Three pelargonidin-based anthocyanins were detected in three Lc-transgenic lines. Among them, the relative contents of cyanidin-based and pelargonidin-based anthocyanins increased 1.9-2.0 and 3.4-4.5 times respectively, while peonidin-based anthocyanins decreased 1.8-1.9 times in Lc-transgenic lines, compared with wild-type PSP. PSP from wild-type Ayamurasaki and three Lc-transgenic lines exhibited potent antioxidant activities, whereas there was no distinct difference among them. The transgene Lc significantly increased the content of total anthocyanins and remarkably changed the anthocyanin profiles in Ayamurasaki. Such novel and high content of anthocyanins obtained in the Lc-transgenic lines with potent antioxidant activities may provide unique functional products with potential helpful for human health. © 2017 Society of Chemical Industry.

Morphological and molecular evolution and their consequences for conservation and taxonomy in the Le Conte's thrasher Toxostoma lecontei

We evaluated geographic variation and subspecific taxonomy in the Le Conte's thrasher Toxostoma lecontei by analyzing DNA sequences from 16 nuclear loci, one mitochondrial DNA locus, and four study skin characters, and compared these data sets with previously published data on plumage coloration and different mtDNA genes. Morphological support for the southernmost taxon, T. l. arenicola, is relatively weak: multivariate analyses of morphometrics or back coloration do not provide diagnostic support, although one color character differs statistically. However, combined DNA analyses indicate that T. l. arenicola is diagnosable and reciprocally monophyletic, diverging from T. l. lecontei at least 140 000 yr ago. Little to no past introgression across a very short geographic distance despite the long period of isolation is strong evidence of independently evolving taxa. We suggest that the lack of morphological divergence in traits related to niche use has prevented the two taxa from invading each other's range. Despite relatively weak morphological differences we suggest that these two deeply divergent lineages merit species status, and we suggest Vizcaíno thrasher for the common name corresponding to T. l. arenicola. The population size of T. l. arenicola is small and the taxon is in need of preservation attention.

Profiling the Phenolic Compounds of the Four Major Seed Coat Types and Their Relation to Color Genes in Lentil.

Phenolic compounds can provide antioxidant health benefits for humans, and foods such as lentils can be valuable dietary sources of different subclasses of these secondary metabolites. This study used LC-MS analyses to compare the phenolic profiles of lentil genotypes with four seed coat background colors (green, gray, tan, and brown) and two cotyledon colors (red and yellow) grown at two locations. The mean area ratio per mg sample (MARS) values of various phenolic compounds in lentil seeds varied with the different seed coat colors conferred by specific genotypes. Seed coats of lentil genotypes with the homozygous recessive tgc allele (green and gray seed coats) had higher MARS values of flavan-3-ols, proanthocyanidins, and some flavonols. This suggests lentils featuring green and gray seed coats might be more promising as health-promoting foods.

Novel Alleles for Black and Gray Seed Color Genes in Common Bean

Seed coat color is one of the most important characteristics of common bean (Phaseolus vulgaris L.). To understand the genetic basis of this trait a cross was made of two small seeded Mesoamerican bean plants from China, the varieties Longyundou 4 (Long 4) with black seed and Longyundou 5 (Long 5) with white seed. Using phenotypic classification, the genetic analysis showed that the inheritance of black, gray, and white seed color could be explained primarily by two independent genes in an additive‐dominant, two gene epistasis model with a significant (χ2 = 1.65, p = 0.44) fit to the 12:3:1 segregation ratio. We also analyzed seed color as a quantitative trait to see whether significant loci aligned with any known seed color genes. To that end we developed 2357 new physically confirmed simple sequence repeat (SSR) markers (BMp series) based on the whole‐genome sequences of common bean and genetically mapped 105 into the F2 bean map. Combining the results of the phenotypic analysis and the new genetic map, two major additive quantitative trait loci (QTL) were found on chromosome Pv07; near the markers BMg87, BMp7s201, and BMp7s206 that explained more than 38% of the phenotypic variation. This region may contain the Asp gene but was distal to the P gene. Several other epistatic QTL for seed color were detected on chromosome Pv08 possibly related to the V locus and on chromosome Pv11. The new linked markers would accelerate the cloning of seed coat color genes of common bean and their selection.

Fine mapping the BjPl1 gene for purple leaf color in B2 of Brassica juncea L. through comparative mapping and whole-genome re-sequencing

Purple plants with higher anthocyanin content have attracted increasing attention in recent years due to their advantageous biological functions and nutritional value. A spontaneous mutant with purple leaves, designated 1280-1, was discovered in Brassica juncea line 1280. A previous genetic analysis indicated that the purple leaf trait in 1280-1 was controlled by a dominant gene (BjPl1). In the present study, an analysis of total anthocyanin content further indicated that the purple leaf trait was controlled by a complete dominance gene. According to a survey of 426 primers available from public resources, BjPl1 was assigned to linkage group B2 of B. juncea. In the early stage of this research, based on comparative mapping in Brassica, two simple sequence repeat (SSR) markers developed from A2 of B. rapa delimited the BjPl1 gene to a 0.7-cM genetic interval in the corresponding linkage map. According to information on the B. juncea genome released recently, the location of BjPl1 was further narrowed to a 225-kb interval (17.74–17.97 Mb). Within the target region, whole-genome re-sequencing identified two candidate regions (17.74–17.78 Mb and 17.93–17.96 Mb). Through Blast analysis of the two candidate intervals, four homologous anthocyanin biosynthetic genes were identified and localized to a 17.93–17.96 Mb interval of B2 (approximately 27 kb), which might include BjPl1. This work lays the foundation for the isolation of BjPl1 and will further improve our understanding of the molecular mechanisms of the anthocyanin metabolic pathway in Brassica.

A single gene controls leaf background color in caladium (Araceae) and is tightly linked to genes for leaf main vein color, spotting and rugosity

Modern cultivated caladiums (Caladium×hortulanum) are grown for their long-lasting and colorful leaves. Understanding the mode of inheritance for caladium leaf characteristics is critical for plant breeders to select appropriate parents, predict progeny performance, estimate breeding population sizes needed, and increase breeding efficiencies. This study was conducted to determine the mode of inheritance of two leaf background colors (lemon and green) in caladium and to understand their relationships with four other important leaf characteristics including leaf shape, main vein color, spotting, and rugosity. Seven caladium cultivars and three breeding lines were used as parents in 19 crosses, and their progeny were phenotyped for segregation of leaf traits. Results showed that the two leaf background colors are controlled by a single nuclear locus, with two alleles, LEM and lem, which control the dominant lemon and the recessive green leaf background color, respectively. The lemon-colored cultivar ‘Miss Muffet’ and breeding lines UF-52 and UF-53 have a heterozygous genotype LEMlem. Chi-square tests showed that the leaf background color locus LEM is independent from the leaf shape locus F, but is tightly linked to three loci (S, V and RLF) controlling leaf spotting, main vein color, and rugosity in caladium. A linkage map that consists of four loci controlling major caladium leaf characteristics and extends ~15 cM was developed based on the observed recombination frequencies. This is the first report on the mode of inheritance of leaf background colors in caladium and in the Araceae family. The information gained in this study will be very useful for caladium breeding and study of the inheritance of leaf colors in other ornamental aroids, an important group of ornamental plants in the world.

Genetics of Flower Color in Periwinkle &amp;lt;i&amp;gt;Catharanthus roseus&amp;lt;/i&amp;gt; (L) G. Don

Genetics of flower Color in winka Catharanthus roseus (L) G.Don were investigate by inheritance two types (strains) of plants with different flowers color were used in this study, violet (V) and White (W) color as parents, to determine the number of genes involved. This study was conducted at the Department of Chemistry & Biology at the Faculty of Education, University of Kassala, kassala State, Sudan, during: the autumn, seasons for two years 2010- 2012. First the two parents were covered to ensure self pollination. Reciprocal cross has been carried out between the two inbred parents. The study showed that a single pair of genes is probably involved in flower colour and that gene for violet color is incompletely dominant over that for white color. The reciprocal crosses gave the same results indicating no role of cytoplasmic genes in the inheritance of these colors.