Identification of a locus for seed shattering in rice (Oryza sativa L.) by combining bulked segregant analysis with whole-genome sequencing

2019 ◽  
Vol 39 (3) ◽  
Author(s):  
Feng Li ◽  
Hisataka Numa ◽  
Naho Hara ◽  
Naoki Sentoku ◽  
Takurou Ishii ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Oryza Sativa L ◽  
Bulked Segregant Analysis ◽  
Whole Genome ◽  
Seed Shattering

scholarly journals Whole genome sequencing data of Oryza sativa L. cv. Takanari

Data in Brief ◽  
2019 ◽  
Vol 27 ◽  
pp. 104546
Author(s):  
Hiromi Kajiya-Kanegae ◽  
Shiori Yabe ◽  
Hiroe Yoshida ◽  
Kaworu Ebana ◽  
Masanori Yamasaki ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Oryza Sativa L ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data

scholarly journals Whole genome sequencing of Oryza sativa L. cv. Seeragasamba identifies a new fragrance allele in rice

PLoS ONE ◽  
2017 ◽  
Vol 12 (11) ◽  
pp. e0188920 ◽  
Author(s):  
Ganigara Bindusree ◽  
Purushothaman Natarajan ◽  
Sukesh Kalva ◽  
Parani Madasamy
Keyword(s):  
Oryza Sativa ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Oryza Sativa L ◽  
Whole Genome

Identification and Characterization of γ-Ray-Induced Mutations in Rice Cytoplasmic Genomes by Whole-Genome Sequencing

2020 ◽  
Vol 160 (2) ◽  
pp. 100-109 ◽  
Author(s):  
Yunchao Zheng ◽  
Shan Li ◽  
Jianzhong Huang ◽  
Longjiang Fan ◽  
Qingyao Shu
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Oryza Sativa L ◽  
Whole Genome Sequencing Data ◽  
Mutation Induction ◽  
Whole Genome ◽  
Induced Mutations ◽  
Genomic Level ◽  
Γ Rays ◽  
Γ Ray

Chloroplasts and mitochondria are semi-autonomous organelles and have their own genomes (cytoplasmic genomes). Physical radiations (e.g., γ-rays) have been widely used in artificial mutation induction for plant germplasm enhancement and for breeding new cultivars. However, little is known at the genomic level about which kind of cytoplasmic mutations and/or characteristics could be induced in plants. The present study aimed to investigate the type, number, and distribution of inheritable cytoplasmic mutations induced by γ-rays in rice (Oryza sativa L.). Six plants were selected from the 2nd generation (M2) populations after γ-ray (137Cs) irradiation of the rice cultivar Nipponbare, 2 each for the 3 irradiation doses (150, 250, and 350 Gy), and their genomes were sequenced on an Illumina platform. Together with the whole-genome sequencing data of 3 external Nipponbare control plants, single-base substitutions (SBSs) and insertions/deletions (InDels) in chloroplast (cp) and mitochondrial (mt) genomes were identified and analyzed in-depth using bioinformatic tools. The majority of SBSs and InDels identified were background mutations in the 6 M2 plants, and the number of induced mutations varied greatly among the plants. Most induced mutations were present in a heterogeneous state, reflecting the fact that multiple cp and mt copies existed in the progenitor cells. The induced mutations were distributed in different genomic regions in the 6 M2 plants, including exonic regions, but none of them was predicted to cause nonsynonymous mutations or frameshifts. Our study thus revealed, at the genomic level, characteristics of cytoplasmic mutations induced by γ-rays in rice.

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 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 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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