Tetraploid rice re-sequencing and transcriptome

Whole genome duplication (WGD) overcomes hybrid sterility and facilitates reproductive isolation during allopolyploidization. Homoeologous as well as homologous meiotic pairing occurs in many allopolyploids, facilitating homoeologous exchanges (HE) that can generate phenotypically variable progeny, hence potentially increasing evolvability. We analyzed the genome composition and phenotypes of 202 euploid segmental allopolyploid individuals from the 4th selfed generation following genome doubling of reciprocal F1 hybrids of crosses between rice subspecies. We describe the rampant occurrence of HEs that generate extensive and individualized genomic mosaicism across the analyzed tetraploids. We show that the resulting homoeolog copy number alteration affects phenotypically relevant genes and their interactions, in the process creating extraordinary phenotypic diversity at the allopolyploid level following a single initial hybridization. Our results underscore HE as an important mechanism that may fuel rapid phenotypic diversification accompanying the early stages of allopolyploid evolution.