title: Accelerated rates of protein evolution in barley grain and pistil biased genes might be legacy of domestication.
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.
authors.affiliation: Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Shi
authors.affiliation: Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA.
authors.forename: Ivan
authors.initials: I
authors.lastname: Dimitrov
authors.affiliation: Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
authors.forename: Yinling
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA.|School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
authors.forename: Frans E
authors.initials: FE
authors.lastname: Tax
authors.affiliation: Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Yi
authors.affiliation: Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Gou
authors.affiliation: Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China. lijia@lzu.edu.cn.
authors.forename: Jia
authors.initials: J
authors.lastname: Li
mesh_terms: D005075:Biological Evolution; D035264:Flowers / Q000378:metabolism; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D001467:Hordeum / Q000378:metabolism*; D018515:Plant Leaves / Q000378:metabolism; D018547:Plant Stems / Q000378:metabolism; D012313:RNA / Q000235:genetics / Q000378:metabolism; D012639:Seeds / Q000502:physiology*; D012641:Selection, Genetic; D059467:Transcriptome
chemical_list: D012313:RNA
keywords: Barley; Domestication; Organ biased genes; Protein evolutionary rates