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Comparative genetic analysis of a wheat seed dormancy QTL with rice and Brachypodium identifies candidate genes for ABA perception and calcium signaling

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Abstract

Wheat preharvest sprouting (PHS) occurs when seed germinates on the plant before harvest resulting in reduced grain quality. In wheat, PHS susceptibility is correlated with low levels of seed dormancy. A previous mapping of quantitative trait loci (QTL) revealed a major PHS/seed dormancy QTL, QPhs.cnl-2B.1, located on wheat chromosome 2B. A comparative genetic study with the related grass species rice (Oryza sativa L.) and Brachypodium distachyon at the homologous region to the QPhs.cnl-2B.1 interval was used to identify the candidate genes for marker development and subsequent fine mapping. Expressed sequence tags and a comparative mapping were used to design 278 primer pairs, of which 22 produced polymorphic amplicons that mapped to the group 2 chromosomes. Fourteen mapped to chromosome 2B, and ten were located in the QTL interval. A comparative analysis revealed good macrocollinearity between the PHS interval and 3 million base pair (mb) region on rice chromosomes 7 and 3, and a 2.7-mb region on Brachypodium Bd1. The comparative intervals in rice were found to contain three previously identified rice seed dormancy QTL. Further analyses of the interval in rice identified genes that are known to play a role in seed dormancy, including a homologue for the putative Arabidopsis ABA receptor ABAR/GUN5. Additional candidate genes involved in calcium signaling were identified and were placed in a functional protein association network that includes additional proteins critical for ABA signaling and germination. This study provides promising candidate genes for seed dormancy in both wheat and rice as well as excellent molecular markers for further comparative and fine mapping.

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Acknowledgments

This research was partially supported by Hatch project149402 and a USDA National Research Initiative Competitive grant from the USDA Cooperative State Research, Education, and Extension Service Coordinated Agriculture Project grants 2005-05130 and 2006-55606-16629.

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Authors and Affiliations

  1. National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand

    Suthasinee Somyong

  2. Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY, 14853, USA

    Jesse D. Munkvold

  3. Department of Plant Breeding and Genetics, Cornell University, 240 Emerson Hall, Ithaca, NY, 14853, USA

    James Tanaka, David Benscher & Mark E. Sorrells

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  1. Suthasinee Somyong
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  2. Jesse D. Munkvold
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  4. David Benscher
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  5. Mark E. Sorrells
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Corresponding author

Correspondence to Mark E. Sorrells.

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Supplementary Table 1

New markers designed from wheat ESTs, their contigs, and wheat transcripts. The PCR annealing temperatures were 56°C except where indicated otherwise. The estimated DNA fragment size is based on a 4% PAGE gel. F, forward primer; R, reverse primer, and chr, chromosome (DOC 75 kb)

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Somyong, S., Munkvold, J.D., Tanaka, J. et al. Comparative genetic analysis of a wheat seed dormancy QTL with rice and Brachypodium identifies candidate genes for ABA perception and calcium signaling. Funct Integr Genomics 11, 479–490 (2011). https://doi.org/10.1007/s10142-011-0219-2

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  • DOI: https://doi.org/10.1007/s10142-011-0219-2

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