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Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy

Campbell, Bradley C. and Gilding, Edward K. and Mace, Emma S. and Tai, Shuaishuai and Tao, Yongfu and Prentis, Peter J. and Thomelin, Pauline and Jordan, David R. and Godwin, Ian D. (2016) Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy. Plant Biotechnology Journal . n/a-n/a. ISSN 1467-7652

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Article Link(s): http://dx.doi.org/10.1111/pbi.12578

Publisher URL: http://dx.doi.org/10.1111/pbi.12578

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.

Item Type:Article
Business groups:Crop and Food Science
Keywords:Sorghum (Sorghum bicolor) domestication starch synthesis whole-genome sequencing selection metabolic pathway
Subjects:Science > Botany > Genetics
Plant culture > Field crops > Grain. Cereals
Deposited On:22 Jul 2016 04:01
Last Modified:22 Jul 2016 04:01

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