Abstract
Sweet maize and popcorn retain tillering growth habit during maize diversification. However, the underlying molecular genetic mechanism remains unknown. Here, we show that the retention of maize tillering is controlled by a major quantitative trait locus (QTL), tin1, which encodes a C2H2-zinc-finger transcription factor that acts independently of tb1. In sweet maize, a splice-site variant from G/GT to C/GT leads to intron retention, which enhances tin1 transcript levels and consequently increases tiller number. Comparative genomics analysis and DNA diversity analysis reveal that tin1 is under parallel selection across different cereal species. tin1 is involved in multiple pathways, directly represses two tiller-related genes, gt1 and Laba1/An-2, and interacts with three TOPLESS proteins to regulate the outgrowth of tiller buds. Our results support that maize tin1, derived from a standing variation in wild progenitor teosinte population, determines tillering retention during maize diversification.
Highlights
Sweet maize and popcorn retain tillering growth habit during maize diversification
Our results suggest that maize tin[1], derived from a standing variation in wild progenitor teosinte population, retains tillering after the fixation of the key gene tb[1] during maize diversification
All the above results suggested that the intron retention originated from the splice-site variant of C/GT greatly enhanced the mRNA stability of tin[1], might elevate the transcript levels of tin[1], to increase tiller number in maize
Summary
All the above results suggested that the intron retention originated from the splice-site variant of C/GT greatly enhanced the mRNA stability of tin[1], might elevate the transcript levels of tin[1], to increase tiller number in maize. Phylogenetic analysis revealed a high level of similarity among maize, rice, foxtail millet, and sorghum TIN1 proteins Most of these proteins contained two highly conserved zinc-finger and EAR-like domains (Fig. 6b and Supplementary Fig. 14), signifying that the tin[1] genes might have a conserved function in the regulation of tiller development. QTL mapping identified a major QTL for tiller number in this tin[1] syntenic block between wild and domesticated sorghums, which accounted for 6.5% of the total phenotypic variation (Supplementary Fig. 16) These results suggested that the function of tin[1] remains conserved among these cereals. This result signified that the splice-site variant C/ GT in maize tin[1] was derived from a standing variation in the wild progenitor, teosinte
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