| Rice(Oryza sativa L.)is one of the most important crops in the world and the staple of over half of the global population.The production of rice expends a great amount of manpower and resources.Wet-direct seeding is an environment-friendly and integrated technology that significantly reduces labor costs and greatly improves the production efficiency.In the case of wet-direct seeding,rodents and birds are prevented from eating rice seeds.In addition,due to the oxygen deficit in the submergent condition,it can inhibit the growth of weeds in the field for a period of time after sowing,thus greatly reducing the use of herbicide.Furthermore,using the rice germplasm with excellent submergence-resistance can greatly save labor and avoid mechanical damage caused by transplanting.Seed germination under water layer and soil layer will be subject to anoxic stress,resulting in low seedling emergence rate and poor seedling uniformity of direct seeding.This is an important factor that restrict the spread of this technology.Some progress has been made in the research on the flood resistance of rice at the bud stage,and some genes have been found.However,the submergence resistance of rice is a complex quantitative trait,and there are still many problems to be solved.Therefore,it is of great significance to study the submergence-tolerant germination characteristics and genetic mechanism of rice to provide support for the selection and breeding of new rice varieties adapted to the system of wet-direct seeding cultivation technology.In this study,a natural population containing 250 rice varietiesmarked with high-densitymolecular markers was used to conduct a genome-wide association analysis(GWAS)to investigate into the genetic mechanisms related characteristics.Transcriptome analysis was also used to provide further support to the prediction of candidate genes flanking to signicantly associated SNP markers.The main results are:(1)Using a convenient method for germplasm screening,characteristics related to germination under submergence were evaluated in the natural population containing 250 varieties.There were rich phenotypic variations among varieties within xian or geng subspecies.The coleoptile elongation of geng varieties was generally higher than that of xian varieties.(2)Four varieties with tolerance to germination under submergence were screened out from the population based on an experiment under the condition simulating the anaerobic environment in paddy field.i.e.‘Longhuamaohu',‘Lijiangxintuanheigu',‘Gaoyangdiandao' and ‘Huangpinuo',listed in descendant order of coleoptile elongation of seedlings germinated under submergence.(3)A natural population containing 250 rice varieties was used to measure the difference in the length of the coleoptile between the submergence conditions and the aerobic control conditions,and accurately measured respectively in three biological replicates.High-density genotype data consisting of 1019883 SNP loci was calculated by genome-wide association analysis using GAPIT package in R software and high-efficiency mixed linear model.A total of 12 independent genetic loci were detected,respectively located at 1?2?3?5?6?7?9 and 11 chromosome,to be possibly related to the genetic regulation during submergence germination.(4)According to the length of coleoptiles during submergence germination,the following extreme examples were selected: long coleoptile variety 'Longhuamaohu' and short coleoptile variety 'JUMAL1'.The transcriptome analysis was performed respectively on each example for submergence treatment and aerobic control.Refering to the expression data of the transcriptome,candidate genes' selection was performed based on the GWAS significant SNP flanking interval.A total of 22 significant genes were found,in addition,Os07g0440100 and Os07g0439100 may be the key genes in response to submergence. |
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