SNP挖掘与过滤 通过与粳稻Nipponbare(NipRef)和籼稻9311参考基因组的比对,从3KRGP(3024份水稻材料)的NGS测序数据中挖掘了>18.9 M个高质量的SNP(比对质量>20,深度>2,MAF>0.001)和InDel位点。从中过滤出约2.5 M个多态性SNP位点用于基因芯片设计。 SNP挑选和验证 为了确保开发的芯片能够满足水稻基因分型的多种应用需...
The map-based genome sequence of the japonica rice cultivar Nipponbare remains to date as the only monocot genome that has been sequenced to a high-quality level. It has become the reference sequence for understanding the diversity among thousands of rice cultivars and its wild relatives as well...
Nipponbare IRGSP 1.0 reference genome19 to identify polymorphisms. When compared with 100-fold sequencing data, 35-fold sequencing data could capture 96.70% of high-quality single-nucleotide polymorphisms (SNPs), with accuracy estimated at 95.21% and 94.72% for all and heterozygous loci (Supplementary...
For GW5, the functional polymorphism is a 1,212 bp deletion in the reference genome (cv. Nipponbare) that removes the only exon of the gene, resulting in a short, wide, heavy grain38,40. For GS5, polymorphisms in the promoter region leading to differential gene expression were associated...
(2016) The Nipponbare genome and the next generation of rice genOmics research in Japan. Rice 9: 33.Matsumoto, T., J. Wu, T. Itoh, H. Numa, B. Antonio and T. Sasaki (2016) The Nipponbare genome and the next-generation of rice genomics research in Japan. Rice (N Y)...
The WRC accessions were sequenced as described previously (Tanaka et al.2020). The paired-end reads were mapped against Os-Nipponbare-Reference-IRGSP-1.0 (Kawahara et al.2013) pseudomolecules using the bwa mem (Li and Durbin2009), and the duplicates were removed using Picard MarkDuplicates (http...
将其与两个现有组装Nipponbare和R498进行对比,我们发现了水稻基因组变异和驯化的隐藏遗产。我们充分利用我们的泛基因组规模的资源建立了一个基于图的基因组,并且推断出了整个Oryza sativa种质的SV派生状态。我们也分析了SV的分布,并评估了SV形成的机理和SV的在基因表达上的影响。我们提供了SV和gCNV在如何直接塑造环境...
1e–h). Similarly, drought decreased total root length, root surface area and root volume of Nipponbare more than those of Luodao 998. Effects of Drought and Genotype on Rhizosphere Bacterial Communities The alpha diversity of the rhizosphere bacterial communities was not regulated by drought (...
Interestingly, the segregation ratios of the two genotype classes in most loci fitted the expected Mendelian ratio of 3 (Nipponbare): 1 (Kasalath). (The percentage of Nipponbare genome in each line had varied from 49.3% to 91.3% average: 74.2%.) They identified five putative QTLs affecting ...
(three samples per lane). Reads were mapped to the Nipponbare IRGSP v. 1 reference genome with BWA software [46], sorted and indexed with SAMtools [47]. To improve the raw alignment binary forms of SAM (BAMs) for variant calling, we realigned indels and recalibrated base quality scores ...