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The Sorghum QTL Atlas: a powerful tool for trait dissection, comparative genomics and crop improvement

  • Emma Mace
  • David Innes
  • Colleen Hunt
  • Xuemin Wang
  • Yongfu Tao
  • Jared Baxter
  • Michael Hassall
  • Adrian Hathorn
  • David Jordan
Research Article
Part of the following topical collections:
  1. New technologies for plant breeding

Key message

We describe the development and application of the Sorghum QTL Atlas, a high-resolution, open-access research platform to facilitate candidate gene identification across three cereal species, sorghum, maize and rice.

Abstract

The mechanisms governing the genetic control of many quantitative traits are only poorly understood and have yet to be fully exploited. Over the last two decades, over a thousand QTL and GWAS studies have been published in the major cereal crops including sorghum, maize and rice. A large body of information has been generated on the genetic basis of quantitative traits, their genomic location, allelic effects and epistatic interactions. However, such QTL information has not been widely applied by cereal improvement programs and genetic researchers worldwide. In part this is due to the heterogeneous nature of QTL studies which leads QTL reliability variation from study to study. Using approaches to adjust the QTL confidence interval, this platform provides access to the most updated sorghum QTL information than any database available, spanning 23 years of research since 1995. The QTL database provides information on the predicted gene models underlying the QTL CI, across all sorghum genome assembly gene sets and maize and rice genome assemblies and also provides information on the diversity of the underlying genes and information on signatures of selection in sorghum. The resulting high-resolution, open-access research platform facilitates candidate gene identification across 3 cereal species, sorghum, maize and rice. Using a number of trait examples, we demonstrate the power and resolution of the resource to facilitate comparative genomics approaches to provide a bridge between genomics and applied breeding.

Notes

Author Contribution statement

EM collated the QTL and GWAS data and wrote the manuscript, XW and YT projected QTL locations and co-wrote the manuscript, CH and AH undertook statistical analysis of the data, DI, JB and MH developed the web application and DJ provided the original concept and co-wrote the manuscript.

Acknowledgements

We would like to acknowledge funding support for this activity from the University of Queensland and the Department of Agriculture and Fisheries.

Compliance with ethical standards

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Supplementary material

122_2018_3212_MOESM1_ESM.docx (100 kb)
Fig. S1 QTL density plots along the maize genome. A. On the genetic linkage scale (number of QTL/0.5 cM). B. On the physical scale (number of QTL/0.5Mbp) (DOCX 100 kb)
122_2018_3212_MOESM2_ESM.docx (105 kb)
Fig. S2 QTL density plots (number of QTL/0.5 cM) along the rice genome. A. On the genetic linkage scale (number of QTL/0.5 cM). B. On the physical scale (number of QTL/0.1Mbp) (DOCX 104 kb)
122_2018_3212_MOESM3_ESM.docx (36 kb)
Fig. S3 Visual site map of AusSORGM QTL Atlas (DOCX 35 kb)
122_2018_3212_MOESM4_ESM.docx (1.5 mb)
Fig. S4 A histogram plot of the distance of 70 height QTL on SBI-07 from dw3 (DOCX 1553 kb)
122_2018_3212_MOESM5_ESM.xlsx (1.4 mb)
Table S1 Details of all of the traits within each trait category (XLSX 1465 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandWarwickAustralia
  2. 2.Department of Agriculture and FisheriesHermitage Research FacilityWarwickAustralia
  3. 3.Department of Agriculture and FisheriesEcosciences PrecinctBrisbaneAustralia
  4. 4.Department of Agriculture and FisheriesLeslie Research FacilityToowoombaAustralia
  5. 5.Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandSt Lucia, BrisbaneAustralia

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