title: Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy.
abstract: Next-generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either 'Landraces' or 'Wild and Weedy' genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP-glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well-characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.
authors.affiliation: School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Qld, Australia.
authors.forename: Bradley C
authors.initials: BC
authors.lastname: Campbell
authors.affiliation: School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Qld, Australia.
authors.forename: Edward K
authors.initials: EK
authors.lastname: Gilding
authors.affiliation: Department of Agriculture and Fisheries (DAF), Warwick, Qld, Australia.
authors.forename: Emma S
authors.initials: ES
authors.lastname: Mace
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Shuaishuai
authors.initials: S
authors.lastname: Tai
authors.affiliation: Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, Qld, Australia.
authors.forename: Yongfu
authors.initials: Y
authors.lastname: Tao
authors.affiliation: Science and Engineering Faculty, Queensland University of Technology (QUT), Brisbane, Qld, Australia.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Prentis
authors.affiliation: Australian Centre for Plant Functional Genomics, Glen Osmond, SA, Australia.
authors.forename: Pauline
authors.initials: P
authors.lastname: Thomelin
authors.affiliation: Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, Qld, Australia.
authors.forename: David R
authors.initials: DR
authors.lastname: Jordan
authors.affiliation: School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Qld, Australia.
authors.forename: Ian D
authors.initials: ID
authors.lastname: Godwin
mesh_terms: D018745:Genome, Plant / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism*; D045868:Sorghum / Q000235:genetics* / Q000378:metabolism*; D013213:Starch / Q000378:metabolism*
chemical_list: D010940:Plant Proteins; D013213:Starch
keywords: Sorghum (Sorghum bicolor); domestication; metabolic pathway; selection; starch synthesis; whole-genome sequencing