Convergent loss of anthocyanin pigments is controlled by the same MYB gene in cereals

Abstract

Loss of anthocyanin pigments is a common transition during cereal domestication, diversification, and improvement. However, the genetic basis for this convergent transition in cereal remains largely unknown. Here, we identified a chromosomal syntenic block across different species that contained R2R3-MYB genes (c1/pl1) responsible for the convergent decoloring of anthocyanins in cereals. Quantitative trait locus (QTL) mapping identified a major QTL for aerial root color corresponding to pl1 and a major QTL for spikelet color corresponding to c1 on maize chromosomes 6 and 9, respectively. One insertion in the regulatory region that led to transcriptional down-regulation was present in maize pl1, and several insertions in the coding region resulting in loss of function occurred in maize c1. A transposable element insertion in the third exon of c1, leading to three new non-functional transcripts, was responsible for decoloring in foxtail millet. The c1/pl1 genes enhanced the transcription of the core enzyme-encoding genes, including pr1, fht1, a1, a2, bz1, and aat1 in the anthocyanin pathway, while they repressed the expression of fnsii1 in flavones, sm2 in maysin, and bx3, bx4, bx5, and bx10 in DIMBOA. Our results indicated that the convergent decoloring of these plants shared the same genetic basis across different cereal species.

Keywords: Cereals; comparative genomics; convergent loss of anthocyanin pigments; domestication syndrome; gene regulatory network; natural functional variant.