Analysis Of Additive Effect And Epistatic QTL For Oil And Protein Contents Using Two Associated RIL Populations Of Soybean

Seed protein and oil contents are the two important quantitative traits determining the quality and value of soybean,which controlled by polygenes and environment,it is great significance to study its genetic basis for soybean molecular design and breeding.Therefore,in this study,using soybean-associated recombinant inbred lines RIL3613 and RIL6013 which were constructed by Dongnong L13,Heihe 36 and Henong 60 RIL?Recombinant inbred lines?as experimental materials,and genetic linkage map constructed by SSR and Soy Bead660 K Bead Chip SNP markers,respectively.Oil content and protein content phenotypes were obtained from planting in 8 environments for multi-environment joint analysis to identify additive and epistatic-effect?additive×additive?quantitative trait loci?QTLs?as well as their interaction with environments.Within the physical intervals of QTL markers in the genome,identified potential candidate genes in seed protein and oil by analyzing the expression levels in soybean seeds.The results are as follows:SSR?Simple Sequence Repeats?genetic maps?RIL3613,134 lines,150 markers,2849.54 c M total marker length,RIL6013,156 lines,137 markers,and 1886.80 c M total map length?were used to perform additive and epistatic effect QTLs as well as their interaction with environments mapping of protein and oil contents using the Inclusive composite interval mapping and Mixed model composite interval mapping analysis method simultaneously.50 protein and 23 oil content additive effect QTLs located on 18 of the 20 soybean chromosomes?except K and N?explained 2.54%-13.88% and 2.99%-38.44% of phenotypic variance,respectively,in RIL3613 and RIL6013.These included 32 common QTLs with overlapping regions in both RIL populations;the remaining 41 QTLs were located only in one population.A total of 56 QTLs were consistent with results from previous studies,among which 12 were hotspot regions.Additionally,13 significantly epistatic QTL pairs related to protein and 5 for oil were identified,including 2 pairs composed of two significantly additive QTLs,6 composed of the significantly additive QTL and one non-significantly-additive QTL,and 5 composed of two non-significantly-additive QTLs.An high-density genetic map of soybean with 2212 markers distributed on 20 linkage groups and spanned 5718.01 c M with an average distance of 2.61 c M between markers using two associated RIL populations?120 lines of RIL3613 and 139 lines of RIL6013?:A total of 64 additive QTLs for oil content and 43 additive QTLs for protein content as well as their interaction with environments were common detected by the ICIM and IM methods.38 and 27 additive effect QTLs for oil content were found to be distributed on 19 and 12 chromosomes in RIL3613 and RIL6013 populations,respectively,explaining the phenotypic variation of 1.29%-10.75%,and the q Oil-5-1?maker interval Gm05₄062384-Gm05₅158657?was detected simultaneously in two genetic backgrounds and methods.Additionally,19 common additive effect QTLs?including q Oil-5-1?of overlapping marker regions were detected in two populations.29 and 14 additive effect QTLs for protein content were found to be distributed on 15 and 12 chromosomes in RIL3613 and RIL6013 populations,respectively,explaining the phenotypic variation of 0.51%-10.07%.Additionally,4 common additive effect QTLs?including q Oil-5-1?of overlapping marker regions were detected in two populations.Comparison with the previous additive QTL based on SSR mapping,it was found that 8 oil content and 8 protein contents QTLs shortened the localization interval and improved the detection efficiency.A total of 23 pairs oil and 329 pairs protein contents epistatic?additive × additive?QTLs as well as their interaction with environments were found by ICIM in two related recombinant inbred line populations.Among them,7 pairs oil content epistasis effect and their interaction with the environments QTLs distributed on the same chromosome,while the other 16 pairs QTLs distributed between the different chromosomes,and the 7 epistasis QTLs had the phenomenon of "1 to many"?1 QTL had epistasis interaction with multiple QTLs?,additionally,two significantly additive QTLs?q Oil-9-2 and q Oil-15-1?were detected to participate in epistatic interaction.30 pairs protein content epistasis effect and their interaction with the environments QTLs distributed on the same chromosome,while the other QTLs distributed between the different chromosomes,and the 165 epistasis QTLs had the phenomenon of "1 to many".Additionally,1 significantly additive QTL?q Pro-12-3?was detected to participate in epistatic interaction.The common QTLs were involved in epistatic interaction in the two RIL populations,which were distributed on chromosomes 3,4,7,8,9,11,12,16,17,18 and 20.There were 23 pairs of co-located epistatic QTLs controlling the protein and oil contents simultaneously of soybean,including 2 pairs of them shared the same QTL mapping regions,and the other 21 pairs of them shared one same marker,indicating that epistatic QTLs were also involved in the negative relationships between seed protein and oil contents in soybean.24 common additive effect QTLs?including involved in significant additive epistatic interactions QTL,q Pro-12-3?of overlapping marker regions or with the same chain marker were detected in two populations comparing with results of Soy Base database,found that 16 oil content and 4 protein content QTLs was reported by previous researches,4 QTL was the new found.16 oil content and 2 protein content additive QTLs were used for the prediction of candidate genes,and we found 1008 and 44 genes with medium and high expression in seeds,respectively.Based on the pathway analysis of the KEGG website?www.kegg.jp?,a total of 14 potential candidate genes related to seed oil and 1 potential candidate gene related to seed protein were identified.The above research results,combined with the high-density genetic map,could better understand the genetic architecture of soybean seed oil and protein,could be the primary target for further fine mapping,candidate gene information and molecular mechanism,which is helpful to improve the quality of soybean.