Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum

Abstract

The domestication of diverse grain crops from wild grasses was a result of artificial selection for a suite of overlapping traits producing changes referred to in aggregate as 'domestication syndrome'. Parallel phenotypic change can be accomplished by either selection on orthologous genes or selection on non-orthologous genes with parallel phenotypic effects. To determine how often artificial selection for domestication traits in the grasses targeted orthologous genes, we employed resequencing data from wild and domesticated accessions of Zea (maize) and Sorghum (sorghum). Many 'classic' domestication genes identified through quantitative trait locus mapping in populations resulting from wild/domesticated crosses indeed show signatures of parallel selection in both maize and sorghum. However, the overall number of genes showing signatures of parallel selection in both species is not significantly different from that expected by chance. This suggests that while a small number of genes will extremely large phenotypic effects have been targeted repeatedly by artificial selection during domestication, the optimization part of domestication targeted small and largely non-overlapping subsets of all possible genes which could produce equivalent phenotypic alterations.

Maize Biochemical Defences against a Rootworm Were Mediated by Domestication, Spread, and Breeding

“…In contrast, constitutive (and total induced) levels of 9-oxylipins (except AZA), but not 13oxylipins, were consistently higher in MXLR compared to BTEO (see Figure 3), which suggests that the 9-LOX pathway was under positive selection during domestication. This observation is in line with recent evidence showing the 9-LOXs ZmLOX3 and its orthologue to be under parallel selection in both maize and sorghum during their domestication [67]. In addition to their roles as signals, 10-OPEA and derivatives also possess strong insecticidal activity [22], and although the net induced levels of these 9oxylipins were consistently near nil in the maizes, the corresponding induced levels of 10-OPDA and 10-OPEA were significantly higher in BTEO compared to MXLR (see Figure 3).…”

“…total induced levels were lower than constitutive levels), which raises the possibility that COU is used as substrate for non-salicylate phenylpropanoid [69], especially given that SA levels are not dramatically changed in maize roots following WCR feeding (see Figure 3K, 4; [33]). Similar to LOX3, the phenylpropanoid biosynthetic enzymes, PAL4 and PAL6, also appear to be under selection pressure during the domestication of maize [67].…”

Identifying loci with breeding potential across temperate and tropical adaptation via EigenGWAS and EnvGWAS

“…Previous reports employed only a limited number of maize accessions to identify potential adaptation and domestication signals. For example, 56 maize accessions including 30 improved lines, 19 landraces and seven wild relatives were used to investigate how often domestication traits were artificially selected (Lai, Yan, Lu, & Schnable, 2018); 62…”

“…Although many selection signatures had been detected before, it remains difficult to fully explain the maize selection and adaptation process and its molecular mechanism. Thus, it is necessary and important to uncover the architecture of selection signatures to understand maize breeding and adaptation (Gage et al, 2018;Hufford et al, 2012;Lai et al, 2018).…”

Reconstructing the transcriptional ontogeny of maize and sorghum supports an inverse hourglass model of inflorescence development

“…In systems where morphologically unique taxa are interfertile, for example, wild 53 relatives of agricultural domesticates or allopatric species distributions, researchers have used 54 quantitative genetics to identify mutations and even possible mechanisms underlying mutation 55 rates that underlie morphological diversification (Hubbard et Andropogoneae, sorghum and maize shared a common ancestor 12-16 million years ago, 68 reflected in their extensive genomic synteny, with more than 11,000 identified maize-sorghum 69 syntenic orthologs (Zhang et al, 2017). Despite this genomic similarity, maize and sorghum 70 have distinct terminal inflorescence architectures, leading to differences in their agricultural use 71 and possibly reflecting differences in their speciation/domestication histories (Lai et al, 2017;72 Lin et al, 2012). While much is known about the genetic underpinning of tassel morphogenesis 73 in maize, little of that information has been applied to understanding the sorghum panicle, 74 perhaps due to its morphological complexity .…”