Abstract
Cold stress is a major factor limiting production and geographic distribution of rice (Oryza sativa). Although the growth range of japonica subspecies has expanded northward compared to modern wild rice (O. rufipogon), the molecular basis of the adaptation remains unclear. Here we report bZIP73, a bZIP transcription factor-coding gene with only one functional polymorphism (+511 G>A) between the two subspecies japonica and indica, may have facilitated japonica adaptation to cold climates. We show the japonica version of bZIP73 (bZIP73Jap) interacts with bZIP71 and modulates ABA levels and ROS homeostasis. Evolutionary and population genetic analyses suggest bZIP73 has undergone balancing selection; the bZIP73Jap allele has firstly selected from standing variations in wild rice and likely facilitated cold climate adaptation during initial japonica domestication, while the indica allele bZIP73Ind was subsequently selected for reasons that remain unclear. Our findings reveal early selection of bZIP73Jap may have facilitated climate adaptation of primitive rice germplasms.
Highlights
Cold stress is a major factor limiting production and geographic distribution of rice (Oryza sativa)
Evolutionary and population genetic analyses suggest that the two alleles of bZIP73 have undergone several rounds of artificial selection in both common wild rice and cultivated rice, indicating that balancing selection may have occurred on this gene
From the high-density single-nucleotide polymorphism (SNP) set (2.3 M) we previously generated for the combined population[34], a total of 27,008 SNPs including 1010 non-synonymous substitutions were identified in the coding region of 91 basic leucine zipper (bZIP) genes
Summary
Cold stress is a major factor limiting production and geographic distribution of rice (Oryza sativa). Evolutionary and population genetic analyses suggest bZIP73 has undergone balancing selection; the bZIP73Jap allele has firstly selected from standing variations in wild rice and likely facilitated cold climate adaptation during initial japonica domestication, while the indica allele bZIP73Ind was subsequently selected for reasons that remain unclear. A potential contribution of bZIP TFs to the northward expansion of japonica has not yet been investigated To fill this gap, we combined association studies, population genetics, and stress-response profiling for the identification of candidate bZIP genes. Molecular and transgenic studies revealed that the japonica version of bZIP73 (bZIP73Jap) interacts with bZIP71 and functions by modulating abscisic acid (ABA) level and reactive oxygen species (ROS) homeostasis, which could significantly enhance rice tolerance to cold. Selection of bZIP73Jap in the direct ancestor of japonica suggests that the gene may have contributed to cold climate adaptation during the early stages of japonica domestication
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