Mining Genes For Elongation Lengths Of Mesocotyl And Coleoptile And Their Sensitivities To Exogenous GA₃ In Rice

Rice is one of the most important food crops in the world.For thousands of years,rice cultivation has been based on transplanting seedlings.With the development of social economy and the shortage of labor force,the demand for direct seedling is getting stronger and stronger.Modern varieties formed under the selection pressure of long-term transplanting tend to be insufficient topsoil capacity and low seedling rate for direct cultivation,which affects the establishment of the desired population.The elongation ability of mesocotyl is closely related to the ability of topsoil and seedling rate.In this study,fresh rice seeds were obtained from a natural population composed of 173 domestic and foreign rice varieties in two environments（Nanjing and Hefei）.The seeds were soaked in water and 1.5μM GA₃solution respectively for 24 hours,and then buried under 5cm soil for 7days-germination.Then elongation lengths of the mesocotyl and coleoptile were investigated.Combined with the molecular data of 173 varieties,r MVP and GHap were used for genome-wide association analysis,respectively,to detect the SNP markers and haplotype markers determined by the degree of linkage disequilibrium（r²）between SNP markers,which were significantly associated with target traits.For a single SNP marker,the gene in which the SNP was located or the closest genes on both sides of the SNP was considered as a preliminary candidate gene.For haplotype marker,all genes within the marker region were considered as preliminary candidate genes.These preliminary candidate genes were further identified by the significance test of phenotypic value difference,that is,taking genes as a unit,haplotypes were performed according to the non-synonymous mutations in the coding region,and the phenotypic values of 173 varieties in natural population were grouped by gene haplotypes by t-test.The candidate genes were screened out according to the results.The main results are as follows:1.After H₂O treatment,nine SNP markers and eight haplotype markers were significantly associated with variation of H₂O-treated mesocotyl（HM）under 5 cm sowing-depth in total.Two candidate genes,LOC＿OS02G47850 and LOC＿OS07G37580,their favorable haplotypes,LOC＿OS02G47850^Hap2 and LOC＿OS07G37580^Hap2 were detected.2.After GA₃ treatment,Seven SNP markers and two haplotype markers were significantly associated with the variation of GA-treated mesocotyl（GM）under 5 cm sowing-depth in total.Two candidate genes,LOC＿OS03G49126 and LOC＿OS12G30130,and their favorable haplotypes,LOC＿OS03G49126^Hap4 and LOC＿OS12G30130 ^Hap2 were detected.3.Twelve SNP markers were significantly associated with GA sensitivity index of mesocotyl（GSIM）variation at 5 cm sowing-depth in total.One candidate gene LOC＿OS11G08250 and its favorable haplotype LOC＿OS11G08250^Hap2 were detected.4.Six SNP markers were significantly associated with the Difference of mesocotyl（DM）variation under 5 cm sowing-depth,and 1 candidate gene LOC＿OS01G09860 and its favorable haplotype LOC＿OS01G09860 ^Hap3 were detected for SNP markers.5.After H₂O treatment,three SNP markers and five haplotype markers were significantly associated with variation in H₂O-treated coleoptile（HC）under 5 cm sowing-depth in total.One candidate gene LOC＿OS04G35160 and its favorable haplotype LOC＿OS04G35160^Hap2were detected.6.After GA₃ treatment,twelve SNP markers and five haplotype markers were significantly associated with variation of GA-treated coleoptile（GC）under 5 cm sowing-depth,and four candidate genes,LOC＿OS04G35160、LOC＿OS04G35190、LOC＿OS04G35210、LOC＿OS04G36640,and their favorable haplotypes,LOC＿OS04G35160^Hap2、LOC＿OS04G35190^Hap2,LOC＿OS04G35210^Hap2,LOC＿OS04G36640^Hap2 were detected in total.LOC＿OS04G35160 is also a candidate gene for HC,which is a one-cause polypotency gene.7.Nine SNP markers were significantly associated with GA sensitivity index of coleoptile（GSIC）variation,and a total of three candidate genes,LOC＿OS05G33460、LOC＿OS03G29570、LOC＿OS07G33450,and their favorable haplotypes,LOC＿OS05G33460^Hap2、LOC＿OS03G29570^Hap2、LOC＿OS07G33450^Hap2,were detected under 5cm sowing-depth.8.Eight SNP markers were significantly associated with the Difference of coleoptile length（DC）variation,and 3 candidate genes,LOC＿OS11G41330、LOC＿OS02G38940 and LOC＿OS03G62314,and their favorable haplotypes,LOC＿OS11G41330^Hap1、LOC＿OS02G38940^Hap3、LOC＿OS03G62314^Hap3 and LOC＿OS03G62314^Hap4were detected at the sowing depth of 5 cm.In conclusion,6 genes controlling mesocotyl elongation or its sensitivity to GA and 10genes controlling coleoptile elongation or its sensitivity to GA were detected,one of which was one factor polypotency.This research laid a foundation for further research on the genes controlling the elongation of rice mesocotyl and coleoptile and their GA sensitivity for molecular breeding to improve the target traits.