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王博  孙广宇 《菌物学报》2016,(12):1434-1440
群体基因组学能够从全基因组水平揭示种群结构与进化、物种形成、适应性机制等。随着高通量技术的不断发展,基因组测序成本不断降低,大规模测序已成为可能。近几年被全基因组测序的真菌数量迅速增加,极大地促进了真菌群体基因组学的发展,加深了人们对植物病原真菌起源、遗传多样性、选择作用、致病性、毒力因子、杀菌剂抗药性、寄主专化型等生物学特性的认识。本文简要介绍了植物病原真菌的全基因测序以及比较基因组学的研究进展,重点综述了基于高通量测序的病原真菌群体基因组学的最新研究动态。群体基因组学将成为植物病原真菌一个新的研究方向。  相似文献   
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Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 F7 recombinant in-bred lines (RILs) from a cross of japonica rice line ‘SNUSG1’ and indica rice line ‘Milyang23’. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.  相似文献   
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Identifying the factors that cause reproductive isolation and their relative importance in species divergence is crucial to our understanding of speciation processes. In most species, natural selection is commonly considered to play a large role in driving speciation. Based on whole genome re-sequencing data from 27 Populus alba and 28 Populus adenopoda individuals, we explored the factors related to reproductive isolation of these two closely related species. The results showed that the two species diverged ~5–10 million years ago (Ma), when the Qinghai–Tibet Plateau reached a certain height and the inland climate of the Asian continent became arid. In highly differentiated genomic regions, the relative divergence (FST) and absolute divergence (dxy) were significantly higher than the genomic background, θπ and shared polymorphisms decreased whereas fixed differences increased, which indicated that natural selection played a key role in the reproductive isolation of the two species. In addition, we found several genes that were related to reproduction that may be involved in explaining the reproductive isolation. Using phylogenetic trees resolved from haplotype data of Populus tomentosa and P. adenopoda, the maternal origin of P. tomentosa from P. adenopoda was likely to be located in Hubei and Chongqing Provinces.  相似文献   
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Having a deep genetic structure evolved during its domestication and adaptation, the Asian cultivated rice (Oryza sativa) displays considerable physiological and morphological variations. Here, we describe deep whole-genome sequencing of the aus rice cultivar Kasalath by using the advanced next-generation sequencing (NGS) technologies to gain a better understanding of the sequence and structural changes among highly differentiated cultivars. The de novo assembled Kasalath sequences represented 91.1% (330.55 Mb) of the genome and contained 35 139 expressed loci annotated by RNA-Seq analysis. We detected 2 787 250 single-nucleotide polymorphisms (SNPs) and 7393 large insertion/deletion (indel) sites (>100 bp) between Kasalath and Nipponbare, and 2 216 251 SNPs and 3780 large indels between Kasalath and 93-11. Extensive comparison of the gene contents among these cultivars revealed similar rates of gene gain and loss. We detected at least 7.39 Mb of inserted sequences and 40.75 Mb of unmapped sequences in the Kasalath genome in comparison with the Nipponbare reference genome. Mapping of the publicly available NGS short reads from 50 rice accessions proved the necessity and the value of using the Kasalath whole-genome sequence as an additional reference to capture the sequence polymorphisms that cannot be discovered by using the Nipponbare sequence alone.  相似文献   
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Next-generation sequencing (NGS) technologies al ow the cost-effective sequencing of whole genomes and have expanded the scope of genomics to novel applications, such as the genome-wide characterizatio...  相似文献   
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Peanut (Arachis hypogaea L.) is an oil and economic crop of vital importance, and peanut pod is the key organ influencing the yield and processing quality. Hence, the Pod-related traits (PRTs) are considered as important agronomic traits in peanut breeding. To broaden the variability of PRTs in current peanut germplasms, three elite peanut cultivars were used to construct Ethyl methane sulfonate (EMS)-induced mutant libraries in this study. The optimal EMS treatment conditions for the three peanut varieties were determined. It was found that the median lethal dose (LD50) of EMS treatment varied greatly among different genotypes. Finally, the EMS-induced peanut mutant libraries were constructed and a total of 124 mutant lines for PRTs were identified and evaluated. Furthermore, “M-8070”, one of the mutant lines for pod constriction, was re-sequenced via high-throughput sequencing technology. The genome-wide variations between “M-8070” and its wild parent “Fuhua 8” (FH 8) were detected. 2994 EMS-induced single nucleotide polymorphisms (SNPs) and 1188 insertion-deletions (InDels) between “M-8070” and its wild parent were identified. The predominant SNP mutation type was C/G to T/A transitions, while the predominant InDel mutation type was “1-bp”. We analyzed the distribution of identified mutations and annotated their functions. Most of the mutations (91.68% of the SNPs and 77.69% of the InDels) were located in the intergenic region. 72 SNPs were identified in the exonic region, leading to 27 synonymous, 43 non-synonymous and 2 stop-gain variation for gene structure. 13 Indels were identified in the exonic region, leading to 4 frame-shift, 8 non-frame-shift and 1 stop-gain variations of genes. These mutations may lead to the phenotypic variation of “M-8070”. Our study provided valuable resources for peanut improvement and functional genomic research.  相似文献   
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DOGSET is an online resource that provides access to primer sequences that have been computationally mined from the reference genome using heuristic algorithms. The electronic repository includes PCR primers corresponding to 32 135 markers for genetic mapping and 334 657 sequence-tagged gene elements for targeted re-sequencing and mutation discovery. A customized report that tailors primer design to wet bench protocols can be exported for a region of interest by specifying genome coordinates in a graphical user interface.  相似文献   
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With the aim of understanding relationship between genetic and phenotypic variations in cultivated tomato, single nucleotide polymorphism (SNP) markers covering the whole genome of cultivated tomato were developed and genome-wide association studies (GWAS) were performed. The whole genomes of six tomato lines were sequenced with the ABI-5500xl SOLiD sequencer. Sequence reads covering ∼13.7× of the genome for each line were obtained, and mapped onto tomato reference genomes (SL2.40) to detect ∼1.5 million SNP candidates. Of the identified SNPs, 1.5% were considered to confer gene functions. In the subsequent Illumina GoldenGate assay for 1536 SNPs, 1293 SNPs were successfully genotyped, and 1248 showed polymorphisms among 663 tomato accessions. The whole-genome linkage disequilibrium (LD) analysis detected highly biased LD decays between euchromatic (58 kb) and heterochromatic regions (13.8 Mb). Subsequent GWAS identified SNPs that were significantly associated with agronomical traits, with SNP loci located near genes that were previously reported as candidates for these traits. This study demonstrates that attractive loci can be identified by performing GWAS with a large number of SNPs obtained from re-sequencing analysis.  相似文献   
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