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A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize
To better understand maize endosperm filling and maturation, we used γ-irradiation of the B73 maize reference line to generate mutants with opaque endosperm and reduced kernel fill phenotypes, and created a population of 1788 lines including 39 Mo17 × F2s showing stable, segregating, and viable kern...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Genetics Society of America
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978893/ https://www.ncbi.nlm.nih.gov/pubmed/27261000 http://dx.doi.org/10.1534/g3.116.030528 |
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author | Jia, Shangang Li, Aixia Morton, Kyla Avoles-Kianian, Penny Kianian, Shahryar F. Zhang, Chi Holding, David |
author_facet | Jia, Shangang Li, Aixia Morton, Kyla Avoles-Kianian, Penny Kianian, Shahryar F. Zhang, Chi Holding, David |
author_sort | Jia, Shangang |
collection | PubMed |
description | To better understand maize endosperm filling and maturation, we used γ-irradiation of the B73 maize reference line to generate mutants with opaque endosperm and reduced kernel fill phenotypes, and created a population of 1788 lines including 39 Mo17 × F2s showing stable, segregating, and viable kernel phenotypes. For molecular characterization of the mutants, we developed a novel functional genomics platform that combined bulked segregant RNA and exome sequencing (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. To exemplify the utility of the mutants and provide proof-of-concept for the bioinformatics platform, we present detailed characterization of line 937, an opaque mutant harboring a 6203 bp in-frame deletion covering six exons within the Opaque-1 gene. In addition, we describe mutant line 146 which contains a 4.8 kb intragene deletion within the Sugary-1 gene and line 916 in which an 8.6 kb deletion knocks out a Cyclin A2 gene. The publically available algorithm developed in this work improves the identification of causative deletions and its corresponding gaps within mapping peaks. This study demonstrates the utility of γ-irradiation for forward genetics in large nondense genomes such as maize since deletions often affect single genes. Furthermore, we show how this classical mutagenesis method becomes applicable for functional genomics when combined with state-of-the-art genomics tools. |
format | Online Article Text |
id | pubmed-4978893 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
spelling | pubmed-49788932016-08-18 A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize Jia, Shangang Li, Aixia Morton, Kyla Avoles-Kianian, Penny Kianian, Shahryar F. Zhang, Chi Holding, David G3 (Bethesda) Investigations To better understand maize endosperm filling and maturation, we used γ-irradiation of the B73 maize reference line to generate mutants with opaque endosperm and reduced kernel fill phenotypes, and created a population of 1788 lines including 39 Mo17 × F2s showing stable, segregating, and viable kernel phenotypes. For molecular characterization of the mutants, we developed a novel functional genomics platform that combined bulked segregant RNA and exome sequencing (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. To exemplify the utility of the mutants and provide proof-of-concept for the bioinformatics platform, we present detailed characterization of line 937, an opaque mutant harboring a 6203 bp in-frame deletion covering six exons within the Opaque-1 gene. In addition, we describe mutant line 146 which contains a 4.8 kb intragene deletion within the Sugary-1 gene and line 916 in which an 8.6 kb deletion knocks out a Cyclin A2 gene. The publically available algorithm developed in this work improves the identification of causative deletions and its corresponding gaps within mapping peaks. This study demonstrates the utility of γ-irradiation for forward genetics in large nondense genomes such as maize since deletions often affect single genes. Furthermore, we show how this classical mutagenesis method becomes applicable for functional genomics when combined with state-of-the-art genomics tools. Genetics Society of America 2016-06-01 /pmc/articles/PMC4978893/ /pubmed/27261000 http://dx.doi.org/10.1534/g3.116.030528 Text en Copyright © 2016 Jia et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Investigations Jia, Shangang Li, Aixia Morton, Kyla Avoles-Kianian, Penny Kianian, Shahryar F. Zhang, Chi Holding, David A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize |
title | A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize |
title_full | A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize |
title_fullStr | A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize |
title_full_unstemmed | A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize |
title_short | A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize |
title_sort | population of deletion mutants and an integrated mapping and exome-seq pipeline for gene discovery in maize |
topic | Investigations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978893/ https://www.ncbi.nlm.nih.gov/pubmed/27261000 http://dx.doi.org/10.1534/g3.116.030528 |
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