scholarly journals Rapid identification of lettuce seed germination mutants by bulked segregant analysis and whole genome sequencing

2016 ◽  
Vol 88 (3) ◽  
pp. 345-360 ◽  
Author(s):  
Heqiang Huo ◽  
Isabelle M. Henry ◽  
Eric R. Coppoolse ◽  
Miriam Verhoef-Post ◽  
Johan W. Schut ◽  
...  
Keyword(s):  
Seed Germination ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bulked Segregant Analysis ◽  
Rapid Identification ◽  
Whole Genome ◽  
Lettuce Seed ◽  
Lettuce Seed Germination

scholarly journals Bulked Segregant Analysis Coupled with Whole-Genome Sequencing (BSA-Seq) Mapping Identifies a Novel pi21 Haplotype Conferring Basal Resistance to Rice Blast Disease

2020 ◽  
Vol 21 (6) ◽  
pp. 2162 ◽  
Author(s):  
Tingmin Liang ◽  
Wenchao Chi ◽  
Likun Huang ◽  
Mengyu Qu ◽  
Shubiao Zhang ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rice Blast ◽  
Molecular Mechanisms ◽  
Bulked Segregant Analysis ◽  
Durable Resistance ◽  
Blast Disease ◽  
Whole Genome ◽  
Rice Varieties ◽  
Basal Resistance

Basal or partial resistance has been considered race-non-specific and broad-spectrum. Therefore, the identification of genes or quantitative trait loci (QTLs) conferring basal resistance and germplasm containing them is of significance in breeding crops with durable resistance. In this study, we performed a bulked segregant analysis coupled with whole-genome sequencing (BSA-seq) to identify QTLs controlling basal resistance to blast disease in an F2 population derived from two rice varieties, 02428 and LiXinGeng (LXG), which differ significantly in basal resistance to rice blast. Four candidate QTLs, qBBR-4, qBBR-7, qBBR-8, and qBBR-11, were mapped on chromosomes 4, 7, 8, and 11, respectively. Allelic and genotypic association analyses identified a novel haplotype of the durable blast resistance gene pi21 carrying double deletions of 30 bp and 33 bp in 02428 (pi21-2428) as a candidate gene of qBBR-4. We further assessed haplotypes of Pi21 in 325 rice accessions, and identified 11 haplotypes among the accessions, of which eight were novel types. While the resistant pi21 gene was found only in japonica before, three Chinese indica varieties, ShuHui881, Yong4, and ZhengDa4Hao, were detected carrying the resistant pi21-2428 allele. The pi21-2428 allele and pi21-2428-containing rice germplasm, thus, provide valuable resources for breeding rice varieties, especially indica rice varieties, with durable resistance to blast disease. Our results also lay the foundation for further identification and functional characterization of the other three QTLs to better understand the molecular mechanisms underlying rice basal resistance to blast disease.

scholarly journals Rapid identification, capsular typing and molecular characterization of Streptococcus pneumoniae by using whole genome nanopore sequencing

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
S. Garcia-Garcia ◽  
A. Perez-Arguello ◽  
D. Henares ◽  
N. Timoneda ◽  
C. Muñoz-Almagro
Keyword(s):  
Streptococcus Pneumoniae ◽  
Whole Genome Sequencing ◽  
Real Time ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Rapid Identification ◽  
Whole Genome ◽  
Genomic Epidemiology ◽  
Capsular Typing

Abstract Background Whole genome sequencing has emerged as a useful tool for identification and molecular characterization of pathogens. MinION (Oxford Nanopore) is a real-time third generation sequencer whose portability, affordability and speed in data production make of it an attractive device for whole genome sequencing. The objective of this study is to evaluate MinION sequencer for pathogen identification and molecular characterization of Streptococcus pneumoniae isolated at a children’s Hospital. Whole genome sequencing of 32 Streptococcus pneumoniae invasive isolates, previously characterized by standard methods (Quellung reaction, Multiplex PCR and Sanger-MLST), were performed. DNA was extracted using ZymoBIOMICS DNA Microprep kit. Quantification and purity of DNA was assessed by Qubit and Nanodrop, respectively. Library preparation was performed using the Rapid Barcoding Kit. Real-time workflow EPI2ME platform “What’s it in my pot” was used for species identification. Fast5 sequences were converted into FASTQ by Albacore software. Reads were assembled using CANU software. PathogenWatch, genomic epidemiology and pubmlst online tools were used for capsular typing and/or whole genome-MLST profile. Results Rapid identification of Streptococcus pneumoniae was achieved by “What’s in my pot”. Capsular typing was correctly assigned with PathogenWatch in all 32 isolates at serogroup level and 24 at serotype level. Whole genome-MLST results obtained by genomic epidemiology and pubmlst were consistent with double locus variant clonal complex obtained by Sanger-MLST in 31 isolates. Conclusion MinION sequencer provides a rapid, cost-effective and promising pathway for performing WGS by a pocked-sized device for epidemiological purposes but improving its sequencing accuracy will make it more appealing to be used in clinical microbiology laboratories.

scholarly journals Bulked-Segregant Analysis Coupled to Whole Genome Sequencing (BSA-Seq) for Rapid Gene Cloning in Maize

2018 ◽  
Author(s):  
Harry Klein ◽  
Yuguo Xiao ◽  
Phillip A Conklin ◽  
Rajanikanth Govindarajulu ◽  
Jacob A Kelly ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Gene Cloning ◽  
Genome Sequencing ◽  
Gene Networks ◽  
Bulked Segregant Analysis ◽  
Forward Genetics ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Simple Strategy ◽  
Mutant Genes

Forward genetics remains a powerful method for revealing the genes underpinning organismal form and function, and for revealing how these genes are tied together in gene networks. In maize, forward genetics has been tremendously successful, but the size and complexity of the maize genome made identifying mutant genes an often arduous process with traditional methods. The next generation sequencing revolution has allowed for the gene cloning process to be significantly accelerated in many organisms, even when genomes are large and complex. Here, we describe a bulked-segregant analysis sequencing (BSA-Seq) protocol for cloning mutant genes in maize. Our simple strategy can be used to quickly identify a mapping interval and candidate single nucleotide polymorphisms (SNPs) from whole genome sequencing of pooled F2 individuals. We employed this strategy to identify narrow odd dwarf as an enhancer of teosinte branched1 , and to identify a new allele of defective kernel1 . Our method provides a quick, simple way to clone genes in maize.

scholarly journals Bulked-Segregant Analysis Coupled to Whole Genome Sequencing (BSA-Seq) for Rapid Gene Cloning in Maize

2018 ◽  
Vol 8 (11) ◽  
pp. 3583-3592 ◽  
Author(s):  
Harry Klein ◽  
Yuguo Xiao ◽  
Phillip A. Conklin ◽  
Rajanikanth Govindarajulu ◽  
Jacob A. Kelly ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Gene Cloning ◽  
Genome Sequencing ◽  
Bulked Segregant Analysis ◽  
Whole Genome
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