Mining Of Submergence-tolerant Resource And Association Analysis At Seed Germination Stage In India Rice

Rice(Oryza sativa L.)is one of the most important economic crops in the word,and it is also a semiaquatic species.Flooding is one of the most common stresses in the rice production,especially in direct seeding methods.Breeding rice varieties with high submergence tolerance can improve the seedling establishment and seedling vigor under submergence stress,which has a decisive role on the final crop yield.India rice is mainly distributed in the south China areas,where constantly happening waterlogging.Therefore,the mining of submergence-tolerant resource and association analysis were conducted at seed germination stage using 113 indica rice accessions.The main results were as follows:The relative seedling percentage(rSP),relative seedling height(rSH)and relative root length(rRL)were used to evaluate the submergence tolerance of indica rice submerged 5 cm and 10 cm at seed germination stage.The results showed that there were significant variations of submergence tolerance among the 113 indica rice accessions at seed germination stage.By comparison,the submergence tolerance is decreased gradually with the increase of water depth.Based on the standars of rSP>0.95,rSH>0.60 and rRL>0.30 for submergence tolerance while the standars of rSP<0.30,rSH<0.30 and rRL<0.30 for submergence sensitive,a total of 7 submergence-tolerant and 17 submergence-sensitive accessiones were identified.Of them,Daihao 90 and Cungu had good submergence tolerances under both submergence treatments simultaneously.Further correlation analysis indicated that the rSP was significantly and positively correlated with seedling height under 5 cm submergence conditions,as well as the rSP and rSH was significantly and positively correlated with grain weight.Meanwhile,the rSP was significantly and negatively correlated with seedling height under 10 cm submergence conditions,while the rSP,rSH and rRL are significantly correlated with grain weight.There is no significant correlation between submergence tolerance and plant height at the mature stage.Two submergence-tolerant(Cungu and Luoka76)and two submergence-sensitive accessions(Lvzhenzhanl,Chenghui 448)were used to analyze the changes of ROS in seeds at seed germination stage under submergence conditions.The results showed that the relative contents of malondialdehyde(MDA),relative hydrogen peroxide(H2O2)and superoxide dismutase(SOD)activity were not significant changing during seed germination process(24h-72h)under submergence condition.In contrast,the relative MDA content in submergence-sensitive rice seed was higher than that of submergence-tolerant rice,but without significant level changes.There were no regularly differences of the relative H2O2 content between submergence-tolerant and submergence-sensitive accessions,but the most sensitive accession Chenghui448 had the significant lower relative H2O2 content compared to other three accessions.However,the relative SOD activity is significantly lower in submergence-sensitive accessions than that of submergence-tolerant accessions under both submergence conditions.With the SSR genotypes and the phenotypes among the 113 indica accessions,the association mapping was conducted to detect the QTLs for submergence tolerance at seed germination stage in rice.The results showed that the 113 indica accessions were divided into 2 subgroups,and two subgroups existed linkage disequilibrium.A total of 14 SSR markers closely linked with the rSP,rSH and rRL were identified under 5cm and 10cm submergence conditions.Of them,6,5 and 2 SSR markers wer closely linked with the rSP,rSH and rRL,respectively,and the markers RM15280 and RM17803 were simultaneously associated with rSP and rSH.In contrast,9 loci were detected under 5cm submergence condition:RM10208,RM14461,RM17803,RM22839,RM25545,RM10021,RM15280,RM17803 and RM15894;while 5 loci were detected under 10cm submergence condition:RM15280,RM22839,RM21249 and RM209 and RM14230.Among them,3 loci were simultaneously detected under two conditions:RM17803,RM22839 and RM15280.Compared with the previous reports,the here 11 loci were co-located with the previous reported submergence-tolerant QTLs or genes.However,the RM10208 on chromosome 1 had no reported QTLs or genes,suggesting it might be a novle gene.Further analysis indicated that the 7 submergence-tolerant accessions(Daihao90,Cungu,Tesanai2,Rizyoto,Guangyeqing,Shengtai 1 and Luoka 76)had 4 to 11 elite alleles.Furthermore,the elite agronomic traits were observed in Cungu,Tesanai2,Guangyeqing and Shengtail,which suggested that these accessions are the excellent resources for the mprovement of rice submergence tolerance at seed germination stage in the future.