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

Tao Shi, Ivan Dimitrov, Yinling Zhang, Frans Tax, Jing Yi, Xiaoping Gou, Jia Li

Research output: Contribution to journalArticle

4 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)253-261
Number of pages9
JournalPlant Molecular Biology
Volume89
Issue number3
DOIs
StatePublished - Oct 29 2015

Fingerprint

pistil
Hordeum
domestication
barley
Genes
Proteins
genes
proteins
Brachypodium
gonads
lowlands
crops
Brachypodium distachyon
Domestication
artificial selection
Poaceae
cultivars
anthers
Cell Cycle
History

Keywords

  • Barley
  • Domestication
  • Organ biased genes
  • Protein evolutionary rates

ASJC Scopus subject areas

  • Plant Science
  • Agronomy and Crop Science
  • Genetics

Cite this

Accelerated rates of protein evolution in barley grain and pistil biased genes might be legacy of domestication. / Shi, Tao; Dimitrov, Ivan; Zhang, Yinling; Tax, Frans; Yi, Jing; Gou, Xiaoping; Li, Jia.

In: Plant Molecular Biology, Vol. 89, No. 3, 29.10.2015, p. 253-261.

Research output: Contribution to journalArticle

Shi, Tao ; Dimitrov, Ivan ; Zhang, Yinling ; Tax, Frans ; Yi, Jing ; Gou, Xiaoping ; Li, Jia. / Accelerated rates of protein evolution in barley grain and pistil biased genes might be legacy of domestication. In: Plant Molecular Biology. 2015 ; Vol. 89, No. 3. pp. 253-261.
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