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Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement

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Abstract

A comprehensive analysis was conducted using 48 sorghum QTL studies published from 1995 to 2010 to make information from historical sorghum QTL experiments available in a form that could be more readily used by sorghum researchers and plant breeders. In total, 771 QTL relating to 161 unique traits from 44 studies were projected onto a sorghum consensus map. Confidence intervals (CI) of QTL were estimated so that valid comparisons could be made between studies. The method accounted for the number of lines used and the phenotypic variation explained by individual QTL from each study. In addition, estimated centimorgan (cM) locations were calculated for the predicted sorghum gene models identified in Phytozome (JGI GeneModels SBI v1.4) and compared with QTL distribution genome-wide, both on genetic linkage (cM) and physical (base-pair/bp) map scales. QTL and genes were distributed unevenly across the genome. Heterochromatic enrichment for QTL was observed, with approximately 22% of QTL either entirely or partially located in the heterochromatic regions. Heterochromatic gene enrichment was also observed based on their predicted cM locations on the sorghum consensus map, due to suppressed recombination in heterochromatic regions, in contrast to the euchromatic gene enrichment observed on the physical, sequence-based map. The finding of high gene density in recombination-poor regions, coupled with the association with increased QTL density, has implications for the development of more efficient breeding systems in sorghum to better exploit heterosis. The projected QTL information described, combined with the physical locations of sorghum sequence-based markers and predicted gene models, provides sorghum researchers with a useful resource for more detailed analysis of traits and development of efficient marker-assisted breeding strategies.

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Acknowledgments

The authors would like to acknowledge Colleen Hunt for her assistance in generating the heat maps, and Jerry Franckowiak, Mandy Christopher, Tracey Shatte, Ian Godwin and Peter Prentis for their critical review of the manuscript. We would also like to thank the anonymous reviewers for their comments and suggestions. We also acknowledge the Australian Grains Research and Development Cooperation (GRDC; http://www.grdc.com.au) for contributing a part of the funding for this research.

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  1. Department of Employment, Economic Development and Innovation, Hermitage Research Station, 604 Yangan Road, Warwick, QLD, 4370, Australia

    E. S. Mace

  2. Queensland Alliance for Agriculture and Food Innovation, Hermitage Research Station, 604 Yangan Road, Warwick, QLD, 4370, Australia

    D. R. Jordan

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  1. E. S. Mace
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Correspondence to E. S. Mace.

Additional information

Communicated by E. Guiderdoni.

Electronic supplementary material

Below is the link to the electronic supplementary material.

122_2011_1575_MOESM1_ESM.xlsx

Table S1. Description of 771 QTL identified. File format: XLS. Description: Excel spreadsheet containing a list of all 771 QTL identified across 44 studies, and their features including whether there are unique or part of an mQTL, their location, LOD, R 2, publication, source, additive effect, flanking markers in original publication, published symbol and Gramene accession ID. (XLSX 134 kb)

122_2011_1575_MOESM2_ESM.xlsx

Table S2. Locus positions in the expanded consensus map. File format: XLS. Description: Excel spreadsheet containing a list of all consensus map loci and their features; data include the chromosome and position of each locus, details of whether the marker was a bridge marker in the original consensus map (Mace et al. 2009), marker type and multicopy marker details. (XLSX 160 kb)

122_2011_1575_MOESM3_ESM.xlsx

Table S3. 8504 Integrated sequence-mapped markers. File format: XLS. Description: Excel spreadsheet containing a list of all publicly available sequence-mapped SSR markers, together with CISP and selected gene markers, collated by Ramu et al. (2010), integrated with the 2335 sequenced markers placed on the consensus map, and their features; data include the start location of the marker in bp, the chromosome, the location on the consensus map, multicopy marker details and details of overlapping SSRs and duplicates as detailed in Ramu et al. (2010). (XLSX 398 kb)

122_2011_1575_MOESM4_ESM.xlsx

Table S4. The number of QTL per publication and per trait category. File format: XLS. Description: Excel spreadsheet containing a list of QTL for 194 traits, categorised into eight broad categories, identified in 44 publications. (XLSX 83 kb)

122_2011_1575_MOESM5_ESM.xlsx

Table S5. Chi-square statistics for QTL distribution genome-wide. File format: XLS. Description: This file contains two spreadsheets. The first spreadsheet (“All 771 QTL”) is based on the distribution of all 771 QTL and details chi-square statistics and probability values for QTL distribution genome-wide, for each chromosome, heterochromatic and euchromatic regions on each chromosome and heterochromatic and euchromatic regions overall. The second spreadsheet (“mQTL and unique”) is based on the distribution of 125mQTL and 371 unique QTL and details chi-square statistics and probability values for QTL distribution for each chromosome. (XLSX 32 kb)

122_2011_1575_MOESM6_ESM.xlsx

Table S6. Details of the mQTL identified. File format: XLS. Description: Excel spreadsheet containing a list of 125 mQTL and their features, including location and trait category. (XLSX 19 kb)

122_2011_1575_MOESM7_ESM.ppt

Figure S1. Plots of estimated CIs of 771 QTL and 125 mQTL, projected onto the sorghum consensus map. File format: PPT. Description: Plot of 771 QTL and 125 mQTL against the expanded sorghum consensus map. The QTL are colour coded by trait category as follows: grain, red; leaf, dark blue; maturity, yellow; panicle, pink; abiotic stress resistance, bright green; biotic stress resistance, brown; stem composition, bright blue; stem morphology, dark green. The 35 major effect genes identified in Mace and Jordan (2010) are also highlighted in red. (PPT 616 kb)

122_2011_1575_MOESM8_ESM.ppt

Figure S2. QTL and gene density comparisons per chromosome. File format: PPT. Description: Figure S2A. Mean QTL and gene density plots in the heterochromatin and euchromatin per 0.5 cM per chromosome. The total number of QTL with their peak CI position in the heterochromatin is also indicated. Figure S2B. Mean QTL and gene density plots in the heterochromatin and euchromatin per 0.5Mbp per chromosome. The total number of QTL with their peak CI position in the heterochromatin is also indicated. (PPT 165 kb)

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Mace, E.S., Jordan, D.R. Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement. Theor Appl Genet 123, 169–191 (2011). https://doi.org/10.1007/s00122-011-1575-y

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  • DOI: https://doi.org/10.1007/s00122-011-1575-y

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