Evolution of Plant Architecture in Oryza Driven by the PROG1 Locus

Abstract

The genetic control of plant architecture in crops is critical for agriculture and understanding morphological evolution. This study showed that an open reading frame (ORF) of the rice domestication gene PROG1 appeared 3.4-3.9 million years ago (Mya). Subsequently, it acquired a novel protein-coding gene function in the genome of O. rufipogon (˜0.3-0.4 Mya). This extremely young gene and its paralogous C2H2 genes located nearby define the prostrate architecture of O. rufipogon and, thus, are of adaptive significance for wild rice in swamp and water areas. However, selection for dense planting and high yield during rice domestication silenced the PROG1 gene and caused the loss of the RPAD locus containing functional C2H2 paralogs; hence, domesticated lines exhibit an erect plant architecture. Analysis of the stepwise origination process of PROG1 and its evolutionary genetics revealed that this zincfinger coding gene may have rapidly evolved under positive selection and promoted the transition from non-or semi-prostrate growth to prostrate growth. A transgenic assay showed that PROG1 from O. rufipogon exerts a stronger function compared with PROG1 sequences from other Oryza species. However, the analysis of the expression levels of PROG1 in different Oryza species suggests that the transcriptional regulation of PROG1 has played an important role in its evolution. This study provides the first strong case showing how a fundamental morphological trait evolved in Oryza species driven by a gene locus.

A High-Quality Haplotype-Resolved Genome of Common Bermudagrass (Cynodon dactylon L.) Provides Insights Into Polyploid Genome Stability and Prostrate Growth

“…Blast searches indicated that key tiller-angle-regulating genes reported in rice and other plants, including PROG1 , LA1 , and TAC1 , were highly conserved in C. dactylon ( Figure 5B ). Similar to prostrate growing wild rice species, clustering of PROG1 -like C 2 H 2 transcription factor genes in adjacent positions of chromosomes were observed in C. dactylon ( Wu et al, 2018 ; Huang et al, 2020 ; Figure 5C and Supplementary Figure S15 ). By contrast, LA1 -like genes that promote erect growth not only experienced gene copy lost due to large chromosomal fragment deletions but also mutated to form truncated proteins ( Figure 5D and Supplementary Figure S16 ).…”

Height to first pod: A review of genetic and breeding approaches to improve combine harvesting in legume crops

“…However, the majority of legumes have a semi-prostrate habit, where both HFP and trigonometric prediction of stem position with pods at harvest have to be taken into consideration (Ramteke et al, 2012). It is important to note that the erect-prostrate type of stem growth has independent genetic mechanisms (Upadhyaya et al, 2017;Zhang B. et al, 2017;Huang et al, 2020). However, recent results revealed that two auxin-related genes (transporter and transport inhibitor) were more active in plants with a prostrate habit than those with erect stems in plants of the perennial legume Astragalus adsurgens Pall., a Chinese native forage crop (Ma et al, 2020).…”

Genetic and molecular factors in determining grain number per panicle of rice

“…Interestingly, many GN-associated genes were involved in the regulation of other domestication related traits. PROG1 ( PROSTRATE GROWTH 1 ) is a key gene in the process of rice domestication, which controls the critical transition from prostrate to erect growth, and changes the plant architecture ( Tan et al, 2008 ; Huang et al, 2020 ). PROG1 is predominantly expressed in the axillary meristems, and promotes GN through increasing the number of primary and secondary branches ( Jin et al, 2008 ).…”