Phenotypic Diversity And Genomic Variation In Progenies Of Japoniaca-indica Synthetic Tetraploids In Rice

Hybridization and polyploidization are widely spread phenomena in nature.It’s believed they are driving forces to speciation and evolution of angiosperm.Rapid genetic and epigenetic changes along with altered gene expression pattern can be triggered by the two processes which may further consequently cause phenotypic novelty in hybrids or polyploids.Compare with diploid parents,some polyploid species exhibit an obvious phenotypic diversity at population level,the reason behind it still remains unclear.Rice as one of the important crops feeds over half of the world’s population.Understanding the genetic basis of agronomic traits is important to both rice breeding and world food security.Here we used a novel inter-subspecies tetraploid rice population which derived from Oryza sativa ssp.japonica and Oryza sativa ssp.indica subspecies.In measured 21 agronomic traits the tetraploid population showed a clearly aggrandized phenotypic diversity relative to the population of F1 hybrids and parents.To explore the reason for the phenotypic diversity of newly synthetic tetraploids,we performed DNA-resequencing on 314 tetraploid individuals,results showed 126 plants of them were aneuploids accounting for 40.13%,the rest 186 plants were euploids.Next we took homeologous ratios between two parental homeologs in the tetraploids as markers based on each 5kb size window to perform genome-wide association studies(GWAS)trying to:1)explore loci that significantly associate with phenotypic trait;2)explain the phenotypic diversity in newly synthetic tetraploids.In this study,by analyzing the types out of the 128 aneuploidy,56 aneuploidy types were found,the most common type was one chromosome minus or plus,namely trisomy or pentasomy in this case.Meanwhile the most complicated cases were aneuploidization happened on the whole three chromosomes or four partial chromosomes(long arm and short arm of a chromosome).In the background of tetraploidy,if only considering the cases of trisomy and pentasomy,there was no significant difference between the probability of chromosome addition or lack;if take all cases into consideration,the probability of chromosome addition is significantly higher than chromosome lack.This result implies the additional or lack one chromosome doesn’t affect plant growth significantly in the background of tetraploidy,but for the extreme cases,the lack of chromosome is possibly fatal to plant,or the additional chromosome cases always happen with other aneuploidization changes.Moreover,rare aneuploidization happened on chromosome 1 and 3,on the contrary,chromosome 4,9 and 11 incline to happen aneuploidization.This result implies the chromosome length,the number of genes and the interaction/compensation between chromosomes are highly attribute to aneuploidization.In this study by using statistical analysis,we found aneuploidization indeed affect the plant phenotypes.We found the loci that are significantly associated with 12 out of 21 agronomic traits through the GWAS analysis on 186 plants of tetraploid population which are exclusively composed of euploids.Some of the loci are known/cloned genes,some of them are newly found loci.The GWAS results are solid to prove that most of the phenotype control genes are sensitive to allelic/homeologous copy number,together with the extensive recombination between Nipponbare and 93-11 chromosome fragments is the main reason for phenotypic diversity within tetraploid rice population.To sum up,the aneuploidization is an inevitable intermediate phase during reproduction process of new polyploid.By passing the impact to progenitors,aneuploidization will prompt population diversity and adaptation to new environment.Moreover,genes that are sensitive to relative homeologous copy number also play important role in better fitness,evolution and even speciation.