A sorghum mutant resource as an efficient platform for gene discovery in grasses

Yinping Jiao; John Burke; Ratan Chopra; Gloria Burow; Junping Chen; Bo Wang; Chad Hayes; Yves Emendack; Doreen Ware; Zhanguo Xin

doi:10.1105/tpc.16.00373

A sorghum mutant resource as an efficient platform for gene discovery in grasses

Yinping Jiao, John Burke, Ratan Chopra, Gloria Burow, Junping Chen, Bo Wang, Chad Hayes, Yves Emendack, Doreen Ware, Zhanguo Xin

Research output: Contribution to journal › Article › peer-review

78 Scopus citations

Abstract

Sorghum (Sorghum bicolor) is a versatile C4 crop and a model for research in family Poaceae. High-quality genome sequence is available for the elite inbred line BTx623, but functional validation of genes remains challenging due to the limited genomic and germplasm resources available for comprehensive analysis of induced mutations. In this study, we generated 6400 pedigreed M4 mutant pools from EMS-mutagenized BTx623 seeds through single-seed descent. Whole-genome sequencing of 256 phenotyped mutant lines revealed >1.8 million canonical EMS-induced mutations, affecting >95% of genes in the sorghum genome. The vast majority (97.5%) of the induced mutations were distinct from natural variations. To demonstrate the utility of the sequenced sorghum mutant resource, we performed reverse genetics to identify eight genes potentially affecting drought tolerance, three of which had allelic mutations and two of which exhibited exact cosegregation with the phenotype of interest. Our results establish that a large-scale resource of sequenced pedigreed mutants provides an efficient platform for functional validation of genes in sorghum, thereby accelerating sorghum breeding. Moreover, findings made in sorghum could be readily translated to other members of the Poaceae via integrated genomics approaches.

Original language	English (US)
Pages (from-to)	1551-1562
Number of pages	12
Journal	Plant Cell
Volume	28
Issue number	7
DOIs	https://doi.org/10.1105/tpc.16.00373
State	Published - Jul 2016
Externally published	Yes

Bibliographical note

Funding Information:
We thank Lan Liu-Gitz and Halee Hughes (USDA-ARS) for technical support and Veronica Acosta-Martinez (USDA-ARS) for technical assistance with GC analysis of waxes. The project was funded by ARS in-house project 6208-21000-020-00D and the United Sorghum Checkoff Program. We also acknowledge the funding from National Science Foundation IOS1127112 (Y.J. and B.W.) and USDA-ARS1907-21000-030-00D (D.W.) for data analysis. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA.

Publisher Copyright:
© 2016 American Society of Plant Biologists. All rights reserved.

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title = "A sorghum mutant resource as an efficient platform for gene discovery in grasses",

abstract = "Sorghum (Sorghum bicolor) is a versatile C4 crop and a model for research in family Poaceae. High-quality genome sequence is available for the elite inbred line BTx623, but functional validation of genes remains challenging due to the limited genomic and germplasm resources available for comprehensive analysis of induced mutations. In this study, we generated 6400 pedigreed M4 mutant pools from EMS-mutagenized BTx623 seeds through single-seed descent. Whole-genome sequencing of 256 phenotyped mutant lines revealed >1.8 million canonical EMS-induced mutations, affecting >95% of genes in the sorghum genome. The vast majority (97.5%) of the induced mutations were distinct from natural variations. To demonstrate the utility of the sequenced sorghum mutant resource, we performed reverse genetics to identify eight genes potentially affecting drought tolerance, three of which had allelic mutations and two of which exhibited exact cosegregation with the phenotype of interest. Our results establish that a large-scale resource of sequenced pedigreed mutants provides an efficient platform for functional validation of genes in sorghum, thereby accelerating sorghum breeding. Moreover, findings made in sorghum could be readily translated to other members of the Poaceae via integrated genomics approaches.",

author = "Yinping Jiao and John Burke and Ratan Chopra and Gloria Burow and Junping Chen and Bo Wang and Chad Hayes and Yves Emendack and Doreen Ware and Zhanguo Xin",

note = "Funding Information: We thank Lan Liu-Gitz and Halee Hughes (USDA-ARS) for technical support and Veronica Acosta-Martinez (USDA-ARS) for technical assistance with GC analysis of waxes. The project was funded by ARS in-house project 6208-21000-020-00D and the United Sorghum Checkoff Program. We also acknowledge the funding from National Science Foundation IOS1127112 (Y.J. and B.W.) and USDA-ARS1907-21000-030-00D (D.W.) for data analysis. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. Publisher Copyright: {\textcopyright} 2016 American Society of Plant Biologists. All rights reserved.",

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AU - Jiao, Yinping

AU - Burke, John

AU - Chopra, Ratan

AU - Burow, Gloria

AU - Chen, Junping

AU - Wang, Bo

AU - Hayes, Chad

AU - Emendack, Yves

AU - Ware, Doreen

AU - Xin, Zhanguo

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A sorghum mutant resource as an efficient platform for gene discovery in grasses

Abstract

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