| Autotetraploid rice is one new germplasm by diploid rice chromosome doubling.Compared with diploid rice,autotetraploid rice has stronger growth potential,larger leaf area,thicker leaves and stems,which has potential to increase production.But it is hard to be applied for its low seed setting rate.There has been a lo t of research on the reproductive property of autotetraploid rice.But it has not been reported whether genome mutation affects its reproduction and leads to low fertility.For the purpose,this study utilized diploid rice E252 and autotetraploid rice T452,which has been doubled and self-crossed more than 10 generations by our laboratory.The diploid rice E252,and corresponding autotetraploid rice T452,were used to explore agronomic traits and pollen fertility,pollen mother cell meiosis,whole genome sequencing variation.The main results are as follows:(1)Agronomic traits and pollen fertility of T452.Comprared with E252,some agronomic traits of T452 increased significantly,including grain length,grain width,grain aspect ratio,main spike length,the average values were 9.70 mm,3.04 mm,3.20,22.85 cm respectively.While seed setting,plant height,effective number of panicles per plant and 1000-grain weight,significantly reduced,the average values were 23.34%,78.30 cm,2.90,17.71 g.Correlation analysis showed that those exist significant linear positive correlation between seed setting of T452 and effective number of panicles per plant,filled grains per panicle,1000-grain weight and plant height.Coefficient variation of seed setting in T452,which was 41.77%,while it was 7.12% in E252.Different individuals in T452 have significant difference.It has the potential for genetic improvement.The pollen fertility of T452 was 69.22%,while it was 95.24% in E252,Pollen fertility of T452 reduced significantly after doubling.(2)The PMC meiosis observation of T452.Meiotic process of T452 is the same as dioploid E252,the process is as follows: prophaseⅠ,metaphaseⅠ,anaphase Ⅰ,telophaseⅠ,prophaseⅡ,metaphaseⅡ,anaphaseⅡ,telophaseⅡ.During meiosis,the chromosome of PMCs in T452 exist various abnormal behaviors,including chromosome dragging,chromosome lagging,abnormal spindle,out of step and asymmetric cell division.Abnormal rate of chromosome behavior increased during metaphaseⅠ,anaphase Ⅰ,metaphaseⅡ and anaphaseⅡ.Abnormal rates were as follows: 27.72%,38.04%,56.06%,69.23%.The PMCs chromosome synapsis during meiosis of T452 exists various types.Most pairs become tetravalent and bivalent,part of univalent and trivalent.Most synapsis form of E252 is bivalent,little univalent,which was separated from bivalent.These univale nt had a close distance or distributed randomly.The mean meiotic configurations of T452 and E252 at diakinesis was(0.89±1.31)Ⅰ+(8.60±4.44)Ⅱ+(0.25±0.60)Ⅲ﹢(7.24±2.25)Ⅳ;(0.18±0.74)Ⅰ+(11.88±0.49)Ⅱ;The mean meiotic configurations of T452 and E252 at metaphaseⅠwas(1.23±1.46)Ⅰ+(12.67±4.50)Ⅱ﹢(0.50±0.87)Ⅲ﹢(4.99±0.50)Ⅳ;(0.41±0.94)Ⅰ+(11.83±0.62)Ⅱ.(3)The whole genome variation analysis of T452.Compared with E252,hundreds of millions of variations were obtained in T452.A total of 233226778 raw reads were abtaind by whole-genome re-sequencing.Besides 232340464 clean reads were detected,meanwhile Q30 came to 84.53%,nearly 96.27% of the bases properly mapped to the IRGSP genome.The average cover depth was 39 X.Whole genome polymorphism and genetic differences in T452 were significantly higher than E252.A total of 62675 SNPs and 18197 Indels were detected,compared to E252.Heterozygous mutation accounted for 99.54% and 92.06% of total mutation of SNPs and Indels respectively.During the whole genome,there were 10979 mutation genes,which existed SNP or Indel variation.There existed 32 mutant genes,which regulate meiosis chromosome behavior.Meanwhile RAD17,MEL1 and RAD51A1 had high effect mutation.Protein interaction analysis revealed a total of 105 mutation genes had strong direct interaction relations with meiotic genes.K EGG enrichment analysis showed 105 mutation genes refered to DN A replication,Mismatch repair,Homologous recombination,Homologous recombination,Non-homologous end-joining,Base excision repair.Among mutation genes with more than 20 relevancy,a total of 4 genes were associated with DNA repair proteins Rad51.CNV variation in T452 was slightly lower t han E252 during whole genome.CNV variation areas involved 369 genes,mainly enriched to eight related to photosynthesis pathways,which may result in higher photosynthetic rate in autotetraploid rice.Compare to E252,there existed 13888 SV in T452,of which 10232 SV were detected in intergenic,accounted for 73.68% of the whole genome structure variation,involved 57 genes refered to methylation.In words,Autotetraploid rice posess low seed setting,low pollen fetility,high abnormal rate of meiotic chro mosome behavior.But higher genome polymorphism,higher genetic differences and higher photosynthetic rate,which make autotetraploid rice have a broad prospect of genetic improvement.The relationship between genome variation and agronomic traits alter,which need to be further studied. |
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