Identification of genes related to white and black plumage formation by RNA-Seq from white and black feather bulbs in ducks

To elucidate the genes involved in the formation of white and black plumage in ducks, RNA from white and black feather bulbs of an F(2) population were analyzed using RNA-Seq. A total of 2,642 expressed sequence tags showed significant differential expression between white and black feather bulbs. Among these tags, 186 matched 133 annotated genes that grouped into 94 pathways. A number of genes controlling melanogenesis showed differential expression between the two types of feather bulbs. This differential expression was confirmed by qPCR analysis and demonstrated that Tyr (Tyrosinase) and Tyrp1 (Tyrosinase-related protein-1) were expressed not in W-W (white feather bulb from white dorsal plumage) and W-WB (white feather bulb from white-black dorsal plumage) but in B-B (black feather bulb from black dorsal plumage) and B-WB (black feather bulb from white-black dorsal plumage) feather bulbs. Tyrp2 (Tyrosinase-related protein-2) gene did not show expression in the four types of feather bulbs but expressed in retina. C-kit (The tyrosine kinase receptor) expressed in all of the samples but the relative mRNA expression in B-B or B-WB was approximately 10 fold higher than that in W-W or W-WB. Additionally, only one of the two Mitf isoforms was associated with plumage color determination. Downregulation of c-Kit and Mitf in feather bulbs may be the cause of white plumage in the duck.     

Grey plumage colouration in the duck is genetically determined by the alleles on two different, interacting loci

Based on the observation of a grey phenotype in the F₁ generation from a cross between two white plumage duck varieties, the white Kaiya and the white Liancheng , we hypothesized a possible interaction between two autosomal loci that determine grey plumage. Using the parental and F₁ individuals, seven testing combinations including five different F₁ intercrosses (F₂) and two different backcrosses (BC₁ and BC₂) were designed to test our hypothesis. It was demonstrated by chi-squared analysis that six test matings produced offspring in the expected ratios between the grey and white, with P- values ranging from 0.50 to 0.99. Another mating, where all white offspring were expected, produced 33 white individuals. These results verified that the interaction between two loci produced the grey phenotype. The C locus, which carries the recessive allele ( c ), was previously thought to be the only gene responsible for white plumage in the duck. This is the first report that an allele ( t ), carried by the white Liancheng at a different autosomal locus, also determines white plumage in ducks. Furthermore, the dominant alleles at both loci can interact with each other to produce the grey phenotype, and a new dark phenotype, observed in some F₂ individuals, can be attributed to the dosage effect of the T allele.     

Non‐synonymous SNPs in MC1R gene are associated with the extended black variant in domestic ducks (Anas platyrhynchos)

In this study, we performed a sequence characterization of the duck melanocortin 1 receptor (alpha‐melanocyte stimulating hormone receptor) (MC1R) gene to analyze the relationship between MC1R polymorphism and the extended black variant in domestic ducks based on the extended black (E) and non‐extended black (e⁺) allele hypothesis of the duck MC1R gene. Both c.52G>A and c.376G>A substitutions are highly associated with the duck extended black variant (P < 0.01), but the novel c.52G>A substitution is more of a fit for the allele hypothesis of the duck MC1R gene.     

Melanocortin 1-receptor (MC1R) mutations are associated with plumage colour in chicken

The co-segregation of plumage colour and sequence polymorphism in the melanocortin 1-receptor gene (MC1R) was investigated using an intercross between the red junglefowl and White Leghorn chickens. The results provided compelling evidence that the Extended black (E) locus controlling plumage colour is equivalent to MC1R. E/MC1R was assigned to chromosome 11 with overwhelming statistical support. Sequence analysis indicated that the E92K substitution, causing a constitutively active receptor in the sombre mouse, is the most likely causative mutation for the Extended black allele carried by the White Leghorn founders in this intercross. The MC1R sequence associated with the recessive buttercup (ebc) allele indicated that this allele evolved from a dominant Extended black allele as it shared the E92K and M71T substitutions with some E alleles. It also carried a third missense mutation H215P which thus may interfere with the constitutive activation of the receptor caused by E92K (and possibly M71T).     

兰州熊蜂蜂王头部产卵相关microRNA生物信息学分析

【目的】头部是熊蜂感觉和取食中心,也是生理行为的指挥中心。microRNA（miRNA）参与重要生理行为的调控。本研究初步探索了产卵和未产卵兰州熊蜂Bombus lantschouensis蜂王头部差异表达miRNA及其靶基因,以期探明蜂王头部miRNA在产卵过程中作用。【方法】以本土优良蜂种兰州熊蜂 B. lantschouensis 为材料,利用Solexa高通量测序技术对产卵和未产卵蜂王头部miRNA进行测序,运用生物信息学软件对miRNA及其靶基因进行预测;并应用qPCR技术验证极显著差异表达的miRNA。【结果】共获得兰州熊蜂产卵和未产卵蜂王头部miRNA的clean data数,分别为14 228 864和21 431 031 条reads;长度分析表明,在19~24 nt序列中22 nt序列数量最多,分别占产卵和未产卵蜂王序列的45.8%和45.1%。miRNA预测结果显示,共获得297个miRNA,其中270个为已知miRNA,有92个存在于蜜蜂中,其余178个分别存在于蜜蜂以外的其他物种中;另外27个为新的miRNA。在蜜蜂92个已知的miRNA中,在产卵蜂王头部中表达的共有91个,特异表达的有2个;在未产卵蜂王头部中表达的共有90个,特异表达的有1个。27个新的miRNA中,在产卵蜂王头部中表达的共有22个,特异表达的有2个;未产卵蜂王头部中表达的共有25个,特异表达的有5个。miRNA差异表达分析表明,在产卵与未产卵蜂王头部,共有8个已知miRNA表达量达到差异极显著水平（P<0.01）。qPCR结果表明,这8个表达差异极显著的miRNA均存在于熊蜂体内。在8个差异极显著的miRNA中,3个miRNA进行靶基因预测,发现它们共同调控9个靶基因,这些基因主要参与GTP结合和转录调控。【结论】本研究首次利用高通量测序技术鉴定了熊蜂头部组织的miRNA,并发现蜂王产卵与否受到miRNA差异表达的调控。结果为今后深入开展熊蜂miRNA功能验证及产卵调控机制研究奠定了基础。     

Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer

MicroRNAs (miRNAs) are small regulatory RNAs that are essential in all studied metazoans. Research has focused on the prediction and identification of novel miRNAs, while little has been done to validate, annotate, and characterize identified miRNAs. Using Illumina sequencing, ～20 million small RNA sequences were obtained from Caenorhabditis elegans. Of the 175 miRNAs listed on the miRBase database, 106 were validated as deriving from a stem-loop precursor with hallmark characteristics of miRNAs. This result suggests that not all sequences identified as miRNAs belong in this category of small RNAs. Our large data set of validated miRNAs facilitated the determination of general sequence and structural characteristics of miRNAs and miRNA precursors. In contrast to previous observations, we did not observe a preference for the 5' nucleotide of the miRNA to be unpaired compared to the 5' nucleotide of the miRNA*, nor a preference for the miRNA to be on either the 5' or 3' arm of the miRNA precursor stem-loop. We observed that steady-state pools of miRNAs have fairly homogeneous termini, especially at their 5' end. Nearly all mature miRNA-miRNA* duplexes had two nucleotide 3' overhangs, and there was a preference for a uracil in the first and ninth position of the mature miRNA. Finally, we observed that specific nucleotides and structural distortions were overrepresented at certain positions adjacent to Drosha and Dicer cleavage sites. Our study offers a comprehensive data set of C. elegans miRNAs and their precursors that significantly decreases the uncertainty associated with the identity of these molecules in existing databases.     

Identification and profiling of novel microRNAs in the Brassica rapagenome based on small RNA deep sequencing

Background

Cowpea is a highly inbred crop. It is part of a crop-weed complex, whose origin and dynamics is unknown, which is distributed across the African continent. This study examined outcrossing rates and genetic structures in 35 wild cowpea (Vigna unguiculata ssp. unguiculata var. spontanea) populations from West Africa, using 21 isozyme loci, 9 of them showing polymorphism.

Results

Outcrossing rates ranged from 1% to 9.5% (mean 3.4%), which classifies the wild cowpea breeding system as primarily selfing, though rare outcrossing events were detected in each population studied. Furthermore, the analyses of both the genetic structure of populations and the relationships between the wild and domesticated groups suggest possibilities of gene flow that are corroborated by field observations.

Conclusions

As expected in a predominantly inbred breeding system, wild cowpea shows high levels of genetic differentiation and low levels of genetic diversity within populations. Gene flow from domesticated to wild cowpea does occur, although the lack of strong genetic swamping and modified seed morphology in the wild populations suggest that these introgressions should be rare.     

基于小RNA测序的风轮菜microRNA及其靶基因分析

本研究以风轮菜(Clinopodium chinense (Benth.) O. Kuntze)为材料,采用BGISEQ-500测序平台对风轮菜根、茎和叶的小RNA进行转录组测序,并对其黄酮类物质合成途径中参与调控的microRNA(miRNA)及其靶基因进行了分析。结果显示,鉴定出的保守miRNA有86个,属于26个家族,新发现miRNA 8个,筛选出风轮菜黄酮类物质合成途径中调控3个关键酶的候选miRNA(novel＿mir3、miR167d-5p、miR396h)。通过对靶基因编码的关键酶4-香豆酸辅酶A连接酶进行序列分析和同源建模,发现其具有高度保守的底物结合区域、催化结构域及两个保守的肽基序。     

Telomere length is reflected by plumage coloration and predicts seasonal reproductive success in the barn swallow

Individuals differ in realized fitness but the genetic/phenotypic traits that underpin such variation are often unknown. Telomere dynamics may be a major source of variation in fitness traits because physiological telomere shortening depends on environmental and genetic factors and may impair individual performance. Here, we showed that, in a population of a socially monogamous, biparental passerine bird, the barn swallow (Hirundo rustica), breeding in northern Italy, telomere length (TL) of both adult males and females positively correlated with seasonal reproductive and fledging success, as expected because long telomeres are supposed to boost performance. Telomere length was correlated with sexually dimorphic coloration in both sexes, showing for the first time in any species that coloration reliably reflects TL and may mediate mutual mate choice, leading to the observed positive assortative mating for TL in the barn swallow. Thus, TL appears to be associated with variation in a major fitness trait and may be an ultimate target of mate choice, as individuals of both sexes can use coloration to adaptively choose high‐quality mates that possess long telomeres.     

Frequency of mallard-black duck hybrids along the atlantic coast determined by electrophoresis and plumage analysis

The frequency of mallard and black duck hybrids along the Atlantic flyway was estimated based on serum protein and serum esterase electrophoresis and plumage analysis. Hybrid frequencies for black ducks were low (below 10%) in Nova Scotia - Maine, Ontario and New Jersey and high (above 10%) in Maryland and Massachusetts. Plumage estimates tended to be higher for black ducks in Massachusetts and Maryland than estimates based on the electrophoretic work.