Transcriptome Sequencing Analysis of Differentially Expressed Genes Associated with Differential Color Feather Bulbs in Ducks (Anas platyrhynchos)
JIANG Bing-Bing1, 2, HUANG Man-Man1, 2, BAI Tian2, ZENG Tao2, CHEN Li2, SHEN Jun-Da2, TAO Zheng-Rong2, ZHOU Wei3, LIU Guo-Fa3, LU Li-Zhi2, *, LI Hai-Ying1, *
1 College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; 2 Institude of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; 3 Jiangsu Guiliu Animal Husbandry Group Co., Ltd., Xuzhou 221600, China
Abstract：As an important economic trait and breed characteristic of duck (Anas platyrhynchos), plumage color has important research significance, but its genetic mechanism is still unclear. In order to study the differences in the transcriptome of white and black feather bulbs and offer new information related to gene expression profiles in black and white feather bulbs in ducks, 4 F1 white-black plumage crossbred ducks of 'Liancheng white duck' and 'Cherry Valley duck' were selected to analyze the transcriptome characteristics of white and black feather bulbs in the same individual in this study. 457 208 376 raw cleans were obtained in 8 samples. After removing sequencing adaptors and the low-quality reads, 449 067 116 clean reads were obtained, accounting for 98.23% of the raw reads. The total base number of which was 67.36 Gb, and each sample obtained bases above 7.4 Gb, with the average GC content of 8 samples being 52%, the Q20 base percentage at 96.73% and above, and average 73.94% being successfully mapped to the duck genome. 70.85% of the mapped reads were uniquely aligned to the duck genome. The expression genes were screened using FPKM (expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced)≧1 as the threshold. It was found that 14 296 genes were expressed in one sample at least. 231 significantly differentially expressed genes were identified (P≦0.05, |log2Fold Change|≧1) between white and black feather bulbs, including 56 down-regulated and 175 up-regulated in black feather bulbs when compared with the white feather bulbs. Several genes related to melanogenesis were found in these differentially expressed genes, such as tyrosinase-related protein1 (TYRP1), tyrosinase (TYR), stem cell factor receptor (KIT), melanophilin (MLPH), dopachrome tautomerase (DCT/TYRP2), melan-A (MLANA), transient receptor potential cation channel subfamily M member 1 (TRPM1), oculocutaneous albinism typeⅡ(OCA2), SOX gene family member 10 (SOX10) and so on, and the expression of these genes in black feather bulbs was significantly higher than that in white feather bulbs. With Gene Ontology (GO) annotation, 19 differentially expressed genes were significantly enriched in 8 GO terms, including G-protein coupled receptor signaling pathway, transmembrane receptor activity, molecular transducer activity, and so on. Analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway showed that 3 pathways were enriched significantly, including neuroactive ligand-receptor interaction signaling pathway, tyrosine metabolism signaling pathway and melanogenesis signaling pathway. The melanogenesis and tyrosine metabolism signaling pathway played an important role in the formation of duck plumage color, and 5 differentially expressed genes including TYRP1, TYR, KIT, DCT etc. were involved in melanogenesis signaling pathway; TYRP1, TYR, DCT were involved in tyrosine metabolism signaling pathway. qRT-PCR was performed to verify the accuracy of results from RNA-seq and carried out for 6 randomly selected genes, including TYR, TYRP1, MLANA, synaptoporin (SYNPR), OCA2 and solute carrier family 38 member 11 (SLC38A11). Results of qRT-PCR were consistent with the data of RNA-seq. The results showed that down-regulation of TYRP1, TYR, KIT, DCT, SLC45A2, TRPM1, OCA2, SOX10, MLANA, MLPH and other genes in feather bulbs might be one of the causes of white plumage in the duck, revealed that tyrosine metabolism and melanogenesis signaling pathway played an important role in the formation of duck plumage color phenotype. This study would offer new information related to gene expression profiles in black and white feather bulbs in the duck, and provide basic materials for exploring the genetic mechanism and molecular marker breeding of duck feather color traits.
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