Quantitative Trait Loci Analysis For Cooking,eating And Nutritional Quality Traits In Rice (Oryza Sativa L.)

Rice(Oryza sativa L.)leading food crops of the world as more than half of the world’s population relies on rice as the major daily source of calories and protein.The cooking and eating quality of rice has attracted more attention recently.In a comprehensive effort to unravel its genetic basis,a population of recombinant inbred lines(RILs)derived from the cross between Japonica rice Nipponbare(NIP)and Indica rice Zhongjiazao17(YK 17)was used to analyze the genomic regions for amylose content(AC),gel consistency(GC),gelatinization temperature(GT),and protein content(PC)under three environment.Besides,crude protein and fractions of proteins are integral components to determine the nutritional quality aspects.However,the synergetic relationship of PC with AC affects the taste of cooked rice and therefore,important to be studied with phenotype and genetic basis of cooking and eating quality(ECQs)properties.The main results obtained from the present studies are listed below:1.A sum of 33 main effect quantitative trait loci(M-QTLs)were detected for AC,GC,GT and PC on all chromosomes except chromosome 8,10 and 12,respectively with single QTL explaining 1.56-89.51 % of the phenotypic variation,respectively.2.From total,15 of them were identified in all three environmental conditions.The marker interval RM7158-RM3414 harbors most of the detected QTLs and it may host the Waxy(Wx)gene along with Alk are the major determinant for ECQs.3.Four QTLs(qAC6,qGT6.2,qPC6 and qPC7)showed highly significant additive × environment interaction providing evidence of environment effect.Moreover,7 epistatic QTL pairs including 3 for AC,3 for GT and 1 for PC were also detected.4.The Wx gene sequencing results showed that the promoter region of Wx gene in YK17 contains three Indels along with two SNPs on Exon 9 and Exon 10 in comparison to NIP,which lead to the significant difference on ECQs of the two parents of RIL.5.The fraction of protein exhibited highly positive significant correlation with each other indicating that these traits are related to each other.6.A total of 44 QTLs with relation to PC,GLU,GLO,ALB and PRO were detected on all 12 chromosomes,with single QTL explaining 3.70-12.47 % of phenotypic variation.Most of the detected QTLs located in the region of RM7158-RM3414 which includes Wx gene along with qPC1,the major QTLs affecting contents of protein and different protein fractions.7.Three QTLs(qPC6,qPC7 and qGLU6)showed highly significant additive × environment interaction providing evidence of environment effect,which suggesting that the QTLs expression of PC and GLU were influenced by the environmental conditions.Two epistatic QTL pairs,1 for GLO and 1 for PRO were also detected.8.Above all,the present study results confirmed that QTLs located on chromosome 6 which might be linked with the Wx gene are the major determinant for ECQs,protein and its fractions.