PubMed | Biomarker Technologies Co., Macquarie University and Jiangxi Agricultural University
Type: | Journal: Scientific reports | Year: 2016
Cooperative brood care is diagnostic of animal societies. This is particularly true for the advanced social insects, and the honey bee is the best understood of the insect societies. A brood pheromone signaling the presence of larvae in a bee colony has been characterised and well studied, but here we explored whether honey bee larvae actively signal their food needs pheromonally to workers. We show that starving honey bee larvae signal to workers via increased production of the volatile pheromone E--ocimene. Analysis of volatile pheromones produced by food-deprived and fed larvae with gas chromatography-mass spectrometry showed that starving larvae produced more E--ocimene. Behavioural analyses showed that adding E--ocimene to empty cells increased the number of worker visits to those cells, and similarly adding E--ocimene to larvae increased worker visitation rate to the larvae. RNA-seq and qRT-PCR analysis identified 3 genes in the E--ocimene biosynthetic pathway that were upregulated in larvae following 30minutes of starvation, and these genes also upregulated in 2-day old larvae compared to 4-day old larvae (2-day old larvae produce the most E--ocimene). This identifies a pheromonal mechanism by which brood can beg for food from workers to influence the allocation of resources within the colony.
Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum)
PubMed | Biomarker Technologies Corporation, Chinese Academy of Agricultural Sciences and Anyang Institute of Technology
Type: | Journal: BMC plant biology | Year: 2016
Upland Cotton (Gossypium hirsutum) is one of the most important worldwide crops it provides natural high-quality fiber for the industrial production and everyday use. Next-generation sequencing is a powerful method to identify single nucleotide polymorphism markers on a large scale for the construction of a high-density genetic map for quantitative trait loci mapping.In this research, a recombinant inbred lines population developed from two upland cotton cultivars 0-153 and sGK9708 was used to construct a high-density genetic map through the specific locus amplified fragment sequencing method. The high-density genetic map harbored 5521 single nucleotide polymorphism markers which covered a total distance of 3259.37cM with an average marker interval of 0.78cM without gaps larger than 10cM. In total 18 quantitative trait loci of boll weight were identified as stable quantitative trait loci and were detected in at least three out of 11 environments and explained 4.15-16.70% of the observed phenotypic variation. In total, 344 candidate genes were identified within the confidence intervals of these stable quantitative trait loci based on the cotton genome sequence. These genes were categorized based on their function through gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and eukaryotic orthologous groups analysis.This research reported the first high-density genetic map for Upland Cotton (Gossypium hirsutum) with a recombinant inbred line population using single nucleotide polymorphism markers developed by specific locus amplified fragment sequencing. We also identified quantitative trait loci of boll weight across 11 environments and identified candidate genes within the quantitative trait loci confidence intervals. The results of this research would provide useful information for the next-step work including fine mapping, gene functional analysis, pyramiding breeding of functional genes as well as marker-assisted selection.
PubMed | Hebei Academy of Agricultural & Forestry science Hebei Branch of China National Sorghum Improvement Center, Biomarker Technologies Corporation and Hebei Academy of Agricultural & Forestry science
Type: Journal Article | Journal: BMC genomics | Year: 2017
Sorghum is mainly used as a human food and beverage source, playing an important role in the production of ethanol and other bio-industrial products. Thus it is regarded as a model crop for energy plants. Genetic map construction is the foundation for marker-assisted selection and gene cloning. So far several sorghum linkage maps have been reported using different kinds of molecular markers. However marker numbers and chromosome coverage are limited. As a result, it is difficult to get consistent results and the maps are hard to unify. In the present study, the genomes of 130 individuals consisting an FA high-throughput sequencing method was adopted to screen SLAF markers with 130FA high density sorghum genetic map was constructed in this study. The total length was 2158.1cM covering all 10 chromosomes with a total number of 2246 SLAF markers. The construction of this map can provide detailed information for accurate gene localization and cloning and application of marker-assisted breeding.
PubMed | Stanford University, Hainan Normal University, Biomarker Technologies Corporation and Northeast Normal University
Type: | Journal: Scientific reports | Year: 2016
Owls (Strigiformes) represent a fascinating group of birds that are the ecological night-time counterparts to diurnal raptors (Accipitriformes). The nocturnality of owls, unusual within birds, has favored an exceptional visual system that is highly tuned for hunting at night, yet the molecular basis for this adaptation is lacking. Here, using a comparative evolutionary analysis of 120 vision genes obtained by retinal transcriptome sequencing, we found strong positive selection for low-light vision genes in owls, which contributes to their remarkable nocturnal vision. Not surprisingly, we detected gene loss of the violet/ultraviolet-sensitive opsin (SWS1) in all owls we studied, but two other color vision genes, the red-sensitive LWS and the blue-sensitive SWS2, were found to be under strong positive selection, which may be linked to the spectral tunings of these genes toward maximizing photon absorption in crepuscular conditions. We also detected the only other positively selected genes associated with motion detection in falcons and positively selected genes associated with bright-light vision and eye protection in other diurnal raptors (Accipitriformes). Our results suggest the adaptive evolution of vision genes reflect differentiated activity time and distinct hunting behaviors.
PubMed | Biomarker Technologies Corporation, Shanghai Ocean University, Shanghai Mudbeach Institute of Biological Resource Exploitation and Shanghai Fisheries Research Institute
Type: | Journal: Scientific reports | Year: 2017
The Chinese mitten crab Eriocheir sinensis is the most economically important cultivated crab species in China, and its genome has a high number of chromosomes (2n=146). To obtain sufficient markers for construction of a dense genetic map for this species, we employed the recently developed specific-locus amplified fragment sequencing (SLAF-seq) method for large-scale SNPs screening and genotyping in a F1 full-sib family of 149 individuals. SLAF-seq generated 127,677 polymorphic SNP markers, of which 20,803 valid markers were assigned into five segregation types and were used together with previous SSR markers for linkage map construction. The final integrated genetic map included 17,680 SNP and 629 SSR markers on the 73 linkage groups (LG), and spanned 14,894.9cM with an average marker interval of 0.81cM. QTL mapping localized three significant growth-related QTL to a 1.2cM region in LG53 as well as 146 sex-linked markers in LG48. Genome-wide QTL-association analysis further identified four growth-related QTL genes named LNX2, PAK2, FMRFamide and octopamine receptors. These genes are involved in a variety of different signaling pathways including cell proliferation and growth. The map and SNP markers described here will be a valuable resource for the E. sinensis genome project and selective breeding programs.
PubMed | Biomarker Technologies Corporation, University of Western Australia and Zhejiang University
Type: Journal Article | Journal: Plant biology (Stuttgart, Germany) | Year: 2016
The genus Brassica has many species that are important for oil, vegetable and other food products. Three mitochondrial genome types (mitotype) originated from its common ancestor. In this paper, a B.nigra mitochondrial main circle genome with 232,407bp was generated through de novo assembly. Synteny analysis showed that the mitochondrial genomes of B.rapa and B.oleracea had a better syntenic relationship than B.nigra. Principal components analysis and development of a phylogenetic tree indicated maternal ancestors of three allotetraploid species in Us triangle of Brassica. Diversified mitotypes were found in allotetraploid B.napus, in which napus-type B.napus was derived from B.oleracea, while polima-type B.napus was inherited from B.rapa. In addition, the mitochondrial genome of napus-type B.napus was closer to botrytis-type than capitata-type B.oleracea. The sub-stoichiometric shifting of several mitochondrial genes suggested that mitochondrial genome rearrangement underwent evolutionary selection during domestication and/or plant breeding. Our findings clarify the role of diploid species in the maternal origin of allotetraploid species in Brassica and suggest the possibility of breeding selection of the mitochondrial genome.
Zhang Y.,Chinese Academy of Agricultural Sciences |
Wang L.,Chinese Academy of Agricultural Sciences |
Xin H.,Biomarker Technologies Corporation |
Li D.,Chinese Academy of Agricultural Sciences |
And 4 more authors.
BMC Plant Biology | Year: 2013
Background: The genetics and molecular biology of sesame has only recently begun to be studied even though sesame is an important oil seed crop. A high-density genetic map for sesame has not been published yet due to a lack of sufficient molecular markers. Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for large-scale de novo SNP discovery and genotyping. SLAF-seq was employed in this study to obtain sufficient markers to construct a high-density genetic map for sesame.Results: In total, 28.21 Gb of data containing 201,488,285 pair-end reads was obtained after sequencing. The average coverage for each SLAF marker was 23.48-fold in the male parent, 23.38-fold in the female parent, and 14.46-fold average in each F2 individual. In total, 71,793 high-quality SLAFs were detected of which 3,673 SLAFs were polymorphic and 1,272 of the polymorphic markers met the requirements for use in the construction of a genetic map. The final map included 1,233 markers on the 15 linkage groups (LGs) and was 1,474.87 cM in length with an average distance of 1.20 cM between adjacent markers. To our knowledge, this map is the densest genetic linkage map to date for sesame. 'SNP_only' markers accounted for 87.51% of the markers on the map. A total of 205 markers on the map showed significant (P < 0.05) segregation distortion.Conclusions: We report here the first high-density genetic map for sesame. The map was constructed using an F2 population and the SLAF-seq approach, which allowed the efficient development of a large number of polymorphic markers in a short time. Results of this study will not only provide a platform for gene/QTL fine mapping, map-based gene isolation, and molecular breeding for sesame, but will also serve as a reference for positioning sequence scaffolds on a physical map, to assist in the process of assembling the sesame genome sequence. © 2013 Zhang et al.; licensee BioMed Central Ltd.
Construction of a high-density genetic map based on large-scale markers developed by specific length amplified fragment sequencing (SLAF-seq) and its application to QTL analysis for isoflavone content in Glycine max
Li B.,Chinese Academy of Agricultural Sciences |
Tian L.,Chinese Academy of Agricultural Sciences |
Zhang J.,Chinese Academy of Agricultural Sciences |
Huang L.,Biomarker Technologies Corporation |
And 5 more authors.
BMC Genomics | Year: 2014
Background: Quantitative trait locus (QTL) mapping is an efficient approach to discover the genetic architecture underlying complex quantitative traits. However, the low density of molecular markers in genetic maps has limited the efficiency and accuracy of QTL mapping. In this study, specific length amplified fragment sequencing (SLAF-seq), a new high-throughput strategy for large-scale SNP discovery and genotyping based on next generation sequencing (NGS), was employed to construct a high-density soybean genetic map using recombinant inbred lines (RILs, Luheidou2 × Nanhuizao, F5:8). With this map, the consistent QTLs for isoflavone content across various environments were identified. Results: In total, 23 Gb of data containing 87,604,858 pair-end reads were obtained. The average coverage for each SLAF marker was 11.20-fold for the female parent, 12.51-fold for the male parent, and an average of 3.98-fold for individual RILs. Among the 116,216 high-quality SLAFs obtained, 9,948 were polymorphic. The final map consisted of 5,785 SLAFs on 20 linkage groups (LGs) and spanned 2,255.18 cM in genome size with an average distance of 0.43 cM between adjacent markers. Comparative genomic analysis revealed a relatively high collinearity of 20 LGs with the soybean reference genome. Based on this map, 41 QTLs were identified that contributed to the isoflavone content. The high efficiency and accuracy of this map were evidenced by the discovery of genes encoding isoflavone biosynthetic enzymes within these loci. Moreover, 11 of these 41 QTLs (including six novel loci) were associated with isoflavone content across multiple environments. One of them, qIF20-2, contributed to a majority of isoflavone components across various environments and explained a high amount of phenotypic variance (8.7% - 35.3%). This represents a novel major QTL underlying isoflavone content across various environments in soybean. Conclusions: Herein, we reported a high-density genetic map for soybean. This map exhibited high resolution and accuracy. It will facilitate the identification of genes and QTLs underlying essential agronomic traits in soybean. The novel major QTL for isoflavone content is useful not only for further study on the genetic basis of isoflavone accumulation, but also for marker-assisted selection (MAS) in soybean breeding in the future. © 2014 Li et al.
PubMed | Northwest Agriculture and Forestry University, Biomarker Technologies Corporation and Institute of Cotton Research of CAAS
Type: | Journal: Scientific reports | Year: 2016
Fiber quality is one of the most important agronomic traits of cotton, and understanding the genetic basis of its target traits will accelerate improvements to cotton fiber quality. In this study, a panel comprising 355 upland cotton accessions was used to perform genome-wide association studies (GWASs) of five fiber quality traits in four environments. A total of 16, 10 and 7 SNPs were associated with fiber length (FL), fiber strength (FS) and fiber uniformity (FU), respectively, based on the mixed linear model (MLM). Most importantly, two major genomic regions (MGR1 and MGR2) on chromosome D