QTL Mapping For Hypoxic Germination And Submergence Tolerance Using Chromosome Segment Substitution Lines In Rice

Rice is one of the main food crops in the world.China is the largest producer and consumer of rice.With the advance of industrialization,direct-seeding technology is more and more praised for its simplicity,water saving and labor saving.However,when applying direct-seeding,rice seeds often suffer from hypoxic stress that may cause low seedling emergence rate and reduced yield.In order to solve this problem,a set of 153 chromosome segment substitution lines（CSSLs）,which was derived from the cross between indica rice variety ZS97 and Malaysian common wild rice （IRGC105491,ACC10）,was used to analyze quantitative trait loci（QTL）of rice submergence tolerance related traits.The genome coverage of chromosome segment were also improved by developing additional CSSLs.The main results are as follows:（1）Large variation and transgressive segregation in submergence tolerance related traits,such as dry weight,seedling rate,fresh weight,average dry weight,average fresh weight,coleoptile length,seedling length and root length,are observed in the CSSL population,indicating that this population is feasible to map QTL for submergence tolerance traits.（2）Correlation analysis of phenotypic data was performed using cor function in R.The seedling traits of rice seeds under submergence stress were significantly correlated.The anaerobic germination trait,coleoptile length,and seedling traits of rice under the submergence stress,such as seedling rate,root length and seedling length were significantly correlated.（3）A new method was established to evaluate germination ability of rice under hypoxic stress generated by sodium sulfite（Na₂SO₃）treatment.（4）QTL analysis using a ridge regression method detected a total of 21 QTLs for seedling submergence tolerance traits,including four QTLs controlling seedling rate,eight QTLs for root length,two QTLs for average dry seedling weight and seven QTLs for seedling height,each of which explained a range of 1.62%and 8.05%;Five QTLs were detected for anaerobic germination traits,explained a range of 1.76%and 5.5%.Ten alleles derived from ACC10 had positive effects;16 ACC10 alleles had negative effects on seedling traits of interest.（5）The effects of 4 loci were verified.Expression analysis of two selected NILs carrying only one segment contianing a target locus were conducted to screen candidate genes.Three genes（Os PIP2;4、Os Clp C2 and Os12g0189300）were predicted as candidates to be submergence response genes.（6）Backcrossing introgression lines consisting of 40 lines were also developed from the cross of ACC10/ZS97 or ZS97/NIP with a molecular marker-assisted selection strategy.The results of submergence tolerance loci identified lay a theoretical and practical foundation for developing rice varieties by genomic breeding adapted to direct seeding requirement.