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Accelerated rates of protein evolution in barley grain and pistil biased genes might be legacy of domestication

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Abstract

Traits related to grain and reproductive organs in grass crops have been under continuous directional selection during domestication. Barley is one of the oldest domesticated crops in human history. Thus genes associated with the grain and reproductive organs in barley may show evidence of dramatic evolutionary change. To understand how artificial selection contributes to protein evolution of biased genes in different barley organs, we used Digital Gene Expression analysis of six barley organs (grain, pistil, anther, leaf, stem and root) to identify genes with biased expression in specific organs. Pairwise comparisons of orthologs between barley and Brachypodium distachyon, as well as between highland and lowland barley cultivars mutually indicated that grain and pistil biased genes show relatively higher protein evolutionary rates compared with the median of all orthologs and other organ biased genes. Lineage-specific protein evolutionary rates estimation showed similar patterns with elevated protein evolution in barley grain and pistil biased genes, yet protein sequences generally evolve much faster in the lowland barley cultivar. Further functional annotations revealed that some of these grain and pistil biased genes with rapid protein evolution are related to nutrient biosynthesis and cell cycle/division. Our analyses provide insights into how domestication differentially shaped the evolution of genes specific to different organs of a crop species, and implications for future functional studies of domestication genes.

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Acknowledgments

We thank Dr. Jianquan Liu (Lanzhou University) for providing server on computational analyses and Kun Wang (Lanzhou University) for managing technical issues related to computational analyses on the server. We thank Wendy Chen (Lanzhou University) for reading and giving comments on the paper. This work was supported by the National Basic Research Program of China [Grant 2011CB915401 to Jia Li], the National Natural Science Foundation of China [Grant 91317311 to Jia Li], and China Postdoctoral Science Foundation [Grant 132867 to Tao Shi].

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Authors and Affiliations

  1. Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China

    Tao Shi, Yinling Zhang, Jing Yi, Xiaoping Gou & Jia Li

  2. Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA

    Ivan Dimitrov & Frans E. Tax

  3. School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA

    Frans E. Tax

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  1. Tao Shi
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  2. Ivan Dimitrov
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  6. Xiaoping Gou
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  7. Jia Li
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Correspondence to Jia Li.

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Shi, T., Dimitrov, I., Zhang, Y. et al. Accelerated rates of protein evolution in barley grain and pistil biased genes might be legacy of domestication. Plant Mol Biol 89, 253–261 (2015). https://doi.org/10.1007/s11103-015-0366-2

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  • DOI: https://doi.org/10.1007/s11103-015-0366-2

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