Project description:Regenerating feathers of the Gouldian finches were collected from heads of moulting individuals from an Australian captive population. Affymetrix microarrays were used to examine gene expression differences between black and red morphs.
Project description:The domesticated rock pigeon (Columba livia) has been bred for hundreds of years to display an immense variety of ornamental attributes such as feather color and color patterns. Color is influenced by multiple loci that impact the type and amount of melanin deposited on the feathers. Pigeons homozygous for the “recessive red” mutation, which causes downregulation of Sox10, display brilliant red feathers instead of blue/black feathers. Sox10 encodes a transcription factor important for melanocyte differentiation and function, but the genes that mediate its promotion of black vs. red pigment are unknown. Here, we present a transcriptomic comparison of regenerating feathers from wild-type and recessive red pigeons to identify candidate SOX10 targets. Our results identify both known and novel targets, including many genes not previously implicated in pigmentation. These data highlight the value of using novel, emerging model organisms to gain insight into the genetic basis of pigment variation.
Project description:Comparative transcriptome profile of genes differentially expressed in longissimus dorsi muscles between Japanese black (Wagyu) and Chinese Red Steppes cattle by RNA-seq
Project description:We analyzed expression change of the genes which involved in anthocyanin and pro-anthocyanin biosynthesis to search an origin of black rice. The submitted samples were transcriptome data in black and red rice pericarps. Rice pericarps were harvested in 7 and 14 days after heading, respectively.
Project description:Rice is a major component of the human diet and feeds more than 50 million people across the globe. Therefore, efforts are being made to improve the nutritional quality of rice seeds in order to make a super-rice cultivar rich in antioxidants and vitamins. We previously developed two rice cultivars, Super-hongmi (red seeds) and Super-jami (black seeds), that were highly rich in antioxidants and exhibited high levels of radical scavenging activities. However, the molecular mechanism underlying the color development and accumulation of different antioxidants in these rice cultivars remains largely elusive. Here, we report the proteome profiles of mature Super-hongmi, and Super-jami seeds and compared with the Hopum (white seeds) using a label-free quantitative proteomics approach. This approach led to the identification of 5127 rice seed proteins of which 1628 showed significant changes (ANOVA, Benjamini-Hochberg FDR ≤ 0.01, fold change ≥ 1.5). Functional annotation of the differentially modulated proteins led to the identification of a phytoene desaturase (PDS3) that was highly enriched in the red seeds and was decreased in the black seeds as compared to the control white seeds. PDS3 is involved in the conversion of phytoene to ζ-carotene which may be responsible for the accumulation of red color in red seeds. Moreover, black seeds seem to accumulate higher levels of anthocyanins because of the higher abundance of dihydroflavonol 4-reductase. In addition, proteins associated with lignin and tocopherol biosynthesis were found to be highly increased in both red and black cultivars. Taken together, these data report the seed proteome of three different colored rice seeds and identify novel components associated with pigment accumulation.
Project description:We performed a comparative genome-wide methylation analysis of longissimus dorsi muscles between the Japanese Black (Wagyu) and Chinese Red Steppes cattle, which exhibit significant differences in meat quality traits. This will allow us to better understand the correlation between DNA methylation variants and meat quality traits.
Project description:The aim of the experiment is to identify genes that are contributing too variation in the intensity of reddish/brown colouration seen in feathers from a wild x domestic advanced intercross line of chickens. RNA was isolated from growing feathers with varying levels of reddish/brown colouration (eg. dark red, red, orange, yellow). The intensity of the colour was measured relative to a true red colour chart and expressed as percentage of the reference colour. A lower colour score indicates a darker red colour(~0,30) and a pure white gives a score of ~0,95. QTL regions for the peak and average colour score measured across the wing were obtained from a mapping population. An eQTL analysis was performed by using the gene expression levels from all genes located within the previously identified QTL confidence intervals. The gene expression values for the genes located within the confidence intervals are available in the data file.
Project description:Purpose: Identify differentially expressed genes between 5 pea aphid morphs Methods: Collected whole bodies of 30 adult aphids of each of the five pea morphs and three clones (total of 15 samples)
Project description:Purpose: Identify differentially expressed genes between 5 pea aphid morphs Methods: Collected whole bodies of 30 adult aphids of each of the five pea morphs and three clones (total of 15 samples) 5 pea aphid morphs * 3 genotypes = 15 samples