Genome Sequencing-based Coverage Analyses Facilitate High-resolution Detection of Causal Deletions in Gamma-Irradiated Wheat Mutants Article Swipe
S Komura
,
Hironobu Jinno
,
Tatsuya Sonoda
,
Yoko Oono
,
Hirokazu Handa
,
Shigeo Takumi
,
Kentaro Yoshida
,
Fuminori Kobayashi
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-551628/v1
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-551628/v1
Background Gamma-irradiated mutants of hexaploid wheat, Triticum aestivum L., have been providing novel and agriculturally important traits and are used for breeding materials. However, identification of causative genomic regions of mutant phenotypes was challenging due to the large and complicated genome of hexaploid wheat. Recently, the combined use of high-quality reference genome sequences of common wheat and cost-effective resequencing technologies has made it possible to evaluate genome-wide polymorphisms even in hexaploid wheat. Results To investigate whether genome sequencing approach can effectively detect structural variations such as deletions that are frequently caused by gamma irradiation, we selected a grain-hardness mutant from gamma-irradiated population of Japanese elite wheat cultivar “Kitahonami”. It is known that a Hardness ( Ha ) locus including puroindoline protein-encoding genes Pina-D1 and Pinb-D1 on the short arm of chromosome 5D mainly regulates the grain hardness variation in common wheat. We performed short-read genome sequencings of the wild-type and the grain-hardness mutant, and then aligned their short reads to the reference genome of wheat cultivar “Chinese Spring.” The genome-wide comparisons of depth-of-coverage between wild-type and the mutant detected a ~130 Mbp deletion on the short arm of chromosome 5D in the mutant genome. Molecular markers for this deletion were applied to the progeny populations generated by a crosse between wild-type and the mutant. The large deletion in the region including the Ha locus was exactly associated with the mutant phenotype, indicating that genome sequencing approach is powerful and efficient to detect a causal deletion of a gamma-irradiated mutant. We also investigated a pre-harvest sprouting tolerance mutant and identified a 67.8 Mbp deletion on chromosome 3B where Viviparous-B1 and GRAS family transcription factor are located. Co-dominant markers designed to detect the deletion-polymorphism clearly confirmed an association with the low germination rate led to pre-harvest sprouting tolerance. Conclusions Short-read-based genome sequencings of gamma-irradiated mutants facilitate the identification of large deletions responsible for mutant phenotypes when combined with segregation analyses in progeny populations. The method we adopted in this study allows the effective application of mutants with agriculturally important traits to breeding with marker-assisted selection.
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- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.21203/rs.3.rs-551628/v1
- https://www.researchsquare.com/article/rs-551628/latest.pdf
- OA Status
- green
- References
- 43
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3171543059
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Raw OpenAlex JSON
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https://openalex.org/W3171543059Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.21203/rs.3.rs-551628/v1Digital Object Identifier
- Title
-
Genome Sequencing-based Coverage Analyses Facilitate High-resolution Detection of Causal Deletions in Gamma-Irradiated Wheat MutantsWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
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2021Year of publication
- Publication date
-
2021-06-01Full publication date if available
- Authors
-
S Komura, Hironobu Jinno, Tatsuya Sonoda, Yoko Oono, Hirokazu Handa, Shigeo Takumi, Kentaro Yoshida, Fuminori KobayashiList of authors in order
- Landing page
-
https://doi.org/10.21203/rs.3.rs-551628/v1Publisher landing page
- PDF URL
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https://www.researchsquare.com/article/rs-551628/latest.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.researchsquare.com/article/rs-551628/latest.pdfDirect OA link when available
- Concepts
-
Genome, Biology, Genetics, Mutant, Locus (genetics), Gene, Common wheat, Reference genome, ChromosomeTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
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43Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.including | 119, 221 |
| abstract_inverted_index.performed | 143 |
| abstract_inverted_index.providing | 12 |
| abstract_inverted_index.reference | 51, 162 |
| abstract_inverted_index.regulates | 134 |
| abstract_inverted_index.sequences | 53 |
| abstract_inverted_index.sprouting | 255, 295 |
| abstract_inverted_index.tolerance | 256 |
| abstract_inverted_index.variation | 138 |
| abstract_inverted_index.wild-type | 149, 175, 211 |
| abstract_inverted_index.Background | 1 |
| abstract_inverted_index.Spring.” | 168 |
| abstract_inverted_index.associated | 227 |
| abstract_inverted_index.chromosome | 131, 189, 265 |
| abstract_inverted_index.facilitate | 304 |
| abstract_inverted_index.frequently | 90 |
| abstract_inverted_index.identified | 259 |
| abstract_inverted_index.indicating | 232 |
| abstract_inverted_index.materials. | 23 |
| abstract_inverted_index.phenotype, | 231 |
| abstract_inverted_index.phenotypes | 32, 313 |
| abstract_inverted_index.population | 102 |
| abstract_inverted_index.selection. | 343 |
| abstract_inverted_index.sequencing | 78, 235 |
| abstract_inverted_index.short-read | 144 |
| abstract_inverted_index.structural | 83 |
| abstract_inverted_index.tolerance. | 296 |
| abstract_inverted_index.variations | 84 |
| abstract_inverted_index.“Chinese | 167 |
| abstract_inverted_index.Co-dominant | 276 |
| abstract_inverted_index.Conclusions | 297 |
| abstract_inverted_index.application | 332 |
| abstract_inverted_index.association | 286 |
| abstract_inverted_index.challenging | 34 |
| abstract_inverted_index.comparisons | 171 |
| abstract_inverted_index.complicated | 40 |
| abstract_inverted_index.effectively | 81 |
| abstract_inverted_index.genome-wide | 67, 170 |
| abstract_inverted_index.germination | 290 |
| abstract_inverted_index.investigate | 75 |
| abstract_inverted_index.populations | 205 |
| abstract_inverted_index.pre-harvest | 254, 294 |
| abstract_inverted_index.responsible | 310 |
| abstract_inverted_index.segregation | 317 |
| abstract_inverted_index.sequencings | 146, 300 |
| abstract_inverted_index.high-quality | 50 |
| abstract_inverted_index.investigated | 252 |
| abstract_inverted_index.irradiation, | 94 |
| abstract_inverted_index.populations. | 321 |
| abstract_inverted_index.puroindoline | 120 |
| abstract_inverted_index.resequencing | 59 |
| abstract_inverted_index.technologies | 60 |
| abstract_inverted_index.Viviparous-B1 | 268 |
| abstract_inverted_index.polymorphisms | 68 |
| abstract_inverted_index.transcription | 272 |
| abstract_inverted_index.agriculturally | 15, 336 |
| abstract_inverted_index.cost-effective | 58 |
| abstract_inverted_index.grain-hardness | 98, 152 |
| abstract_inverted_index.identification | 25, 306 |
| abstract_inverted_index.marker-assisted | 342 |
| abstract_inverted_index.Gamma-irradiated | 2 |
| abstract_inverted_index.Short-read-based | 298 |
| abstract_inverted_index.gamma-irradiated | 101, 248, 302 |
| abstract_inverted_index.protein-encoding | 121 |
| abstract_inverted_index.depth-of-coverage | 173 |
| abstract_inverted_index.“Kitahonami”. | 108 |
| abstract_inverted_index.deletion-polymorphism | 282 |
| cited_by_percentile_year | |
| corresponding_author_ids | https://openalex.org/A5057560499 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 8 |
| corresponding_institution_ids | https://openalex.org/I1323638106, https://openalex.org/I4210119666, https://openalex.org/I4210156466, https://openalex.org/I65837984 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/2 |
| sustainable_development_goals[0].score | 0.550000011920929 |
| sustainable_development_goals[0].display_name | Zero hunger |
| citation_normalized_percentile.value | 0.04197219 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |