Mining Of Elite Alleles For Mesocotyl Elongation Length And Shoot Length In Rice(Oryza Sativa L.)Cultivars Through Association Analysis

Rice(Oryza sativa L.)feeds more than half the world's population,and accounts for 20%of the world's total calorie intake.To meet the global rice demand,it is estimated that about 114 million tons of additional milled rice need to be produced by 2035,which is equivalent to an overall increase of 26%in the next 17years.The possibility of expanding the area under rice in the near future is limited.Therefore,this extra rice production needed has to come from a productivity gain.The major challenge is to achieve this gain with less water,labor,and chemicals,thereby ensuring long-term sustainability.Direct seeding of rice(DSR)has become more and more popular among rice farmers in Asian countries although it is widely practiced in the United States and South America.However,poor emergence and inadequate seedling establishment can lead to yield loss in direct-seeding cultivation by dry drill-sowing,and no varietal selection and breeding efforts have been made for developing rice cultivars suitable for DSR in Asia.Germination and seedling development start when seed dormancy has been broken and the seed absorbs adequate water and is exposed to a temperature ranging from 10 to 40?.The mesocotyl is the embryonic tissue located between the coleoptilar node and the basal part of the seedling,and it can directly push the shoot tip above the soil surface during germination.Mesocotyl elongation has great significance in rice direct-seeding production.Under field conditions,elongation of the mesocotyl elevates the coleoptile to a point within a few millimeters of the soil surface.The coleoptile then extends outwards,making contact with the atmosphere and allows the primary leaves to emerge.In this study,262 pairs of simple sequence repeat(S SR)markers and 543 rice accession from different ecological regions were assessed on genetic diversity,population structure and linkage disequilibrium.543 rice varieties were harvested from Jiangpu Experimental Farm,Nanjing Agricultural University.We investigated phenotypic variation of mesocotyl elongation length(MEL)and shoot length(SL)among 543 rice accessions under growth chamber condition(GCC),and the relationship of MEL obtained from GCC with that obtained from soil condition.Genome-wide association mapping for MEL and SL with SSR markers was performed to identify elite alleles for the two traits.The main results are summarized as follows:1.Abundant phenotypic and genetic variations were found in the studied population for the two traits.The mean of MEL over the 543 accessions was 0.11 cm,with range from 0.0 to 1.8cm.2.Among the 543 accessions,130(23.9%)showed mesocotyl elongation under GCC.The result obtained in GCC could basically represent the results obtained under soil condition(rGCC-SC=0.485**).3.Mesocotyl lengths for the two groups were different with respect to the sowing depth.The long mesocotyl group had a higher emergence rate than that of the short mesocotyl group observed.The longer the MEL the higher the speed of emergence(SOE).4.A total of 2649 alleles were detected by 262 pairs of SSR markers in the population studied.These alleles ranged from 2 among the 543 varieties to 25 alleles with an average of 10.1 per marker locus.The average gene diversity of population was 0.734 ranging from 0.0802 to 0.9429,An average of PIC was 0.706 which range from 0.0770 to 0.940.5.Five subpopulations were detected in the entire population constituted of 543 rice varieties by using two methods,i.e.,STRUCTURE 2.3 analysis method(based on Bayersian model)and the Neighbor-Joining cluster method(based on genetic distance).Linkage disequilibrium at certain extent was found between SSR marker loci either intra-chromosome or inter-chromosome within each subpopulations.The average D' values,i.e.,the standard disequilibrium coefficients from subpopulation 1 to subpopulation 5 were 0.625,0.633,0.660,0.718,and 0.628 respectively.The minimum distance(D'<0.5)of decay from subpopulation 1 to subpopulation 5 were 17.5 cM,33.2 cM,29.4 cM,16.5 cM,and 20.1 cM,respectively.6.Genome-wide association mapping detected 11 marker-trait association(MTAs)loci for MEL.A total of 30 elite alleles were discovered for MEL.Elite allele RM265-140 showed the highest phenotypic effect of 1.89 cm with Yuedao 46 as the carrier accession.We found seven out of eleven SSR markers detected for MEL were novel and the rest were located near chromosome segments harboring QTLs for MEL.These elite alleles could be used to improve direct seeding traits by stacking or substituting methods(independent of possible epistatic effects).7.For SL,three MTAs and 12 elite alleles were detected.One SSR marker for SL was novel and the other two were located near the chromosome regions harboring QTLs for SL.Elite allele RM3331-145 showed the highest phenotypic effect(4.2cm)for SL and Yuedao 60 was the carrier variety.