Unconditional And Conditional Mapping QTL Underlying Protein And Oil Content And Candidate Gene Prediction In Soybean

Soybean,as an important source of protein and oil for humans in everyday life,creates high economic value.In the wake of growing population and increased living standards,the demand for protein and oil is also on the rise.Therefore,it is a critical goal for breeders to improve the content of protein and oil in soybean.However,the protein content of soybean presents a significant negative correlation with its oil content.In this context,the effects of correlated traits on target traits were eliminated by means of conditional variables.A four-way recombinant inbred line(FW-RIL)population with 144 families and a population containing 455 soybean germplasm collections were created by using(Kenfeng 14×Kenfeng 15)×(Heinong 48× Kenfeng 19).The QTL that affect the protein and oil contents of soybean were identified by linkage analysis and genome-wide association study(GWAS).The results are as follows:(1)By analyzing the phenotypic data of protein and oil contents of FW-RIL population in 14 environments and germplasm collections in 2 environments,it was found that the phenotypic data varied greatly in different populations and environments.A correlation analysis confirmed a significant negative correlation between protein and oil contents,suggesting that the protein and oil contents interact with each other.Analysis of variance(ANOVA)was performed to investigate the phenotypic data treated with conditional variables and the original phenotypic data.The results showed that both the genotype variance of two traits and the interaction variance of genotype and environment presented a significant difference,suggesting that the data is suitable for QTL/QTN localization.(2)A genetic map containing 20 chromosomes of soybean was created by using the FW-RIL with 2,332 markers.The map had a total length of 3539.66 cM and contained 2,332 markers.Each linkage group had 20-316 SNP markers and the average length of interval ranged 1.92-10.93 cM.(3)The map above was used to perform linkage analysis on the phenotypic data of protein and oil contents of FW-RIL population.The results showed that a total of 103 QTL related to soybean protein synthesis were located to 20 chromosomes in 14 environments.They included 27 unconditional QTL,15 conditional QTL and 61 QTL detected simultaneously by conditional and unconditional variables;The results showed that a total of 157 QTL related to soybean oil synthesis were located to 20 chromosomes in 14 environments.They included 72 unconditional QTL,67 conditional QTL and 18 QTL detected simultaneously by conditional and unconditional variables.(4)The phenotypic data of protein and oil contents of FW-RIL population in 14 environments were analyzed by using 5 multiple-locus GWAS methods.The results showed that a total of 77 QTN related to protein synthesis were distributed on 19 chromosomes.They included 13 QTN detected by conditional variables,27 unconditional QTN,and 38 QTN detected simultaneously by conditional and unconditional variables;The results showed that a total of 115 QTN related to oil synthesis were distributed on 20 chromosomes.They included 55 QTN detected by conditional variables,59 unconditional QTN,and 1QTN detected simultaneously by conditional and unconditional variables.(5)The phenotypic data of protein and oil contents of germplasm population in 2 environments were analyzed by using 5 multiple-locus GWAS methods.The results showed that a total of 123 QTN related to protein synthesis were distributed on 19 chromosomes.They included 50 QTN detected by conditional variables,69 unconditional QTN,and 4 QTN detected simultaneously by conditional and unconditional variables;The results showed that a total of 124 QTN related to oil synthesis were distributed on 20 chromosomes.They included 59 QTN detected by conditional variables,67 unconditional QTN,and 10 QTN detected simultaneously by conditional and unconditional variables.(6 The analysis on structure of germplasm collections(Q)showed that the collections were divided into two subgroups.The linkage disequilibrium(LD)analysis indicated that if the physical distance corresponding to half of the maximum LD coefficient(r~2)was used as the standard,the LD attenuation distance at the genome-wide level was about 86 Kb.(7)The QTL/QTN located in the four-way population and the QTN located in the germplasm collections were compared within the attenuation range.The results showed that: a total of 6 QTN related to protein synthesis were repeatedly located in the two populations.Based on the 6 QTN,4 candidate genes(Glyma.05G236000.1,Glyma.05G222400.1,Glyma.06G183900.1 and Glyma.05G235400.1)related to protein synthesis were found;a total of 5 QTN related to oil synthesis were repeatedly located in the two populations.Based on the 5 QTN,4 candidate genes(Glyma.08G044100.1,Glyma.11G103500.1,Glyma.11G104800.1 and Glyma.10G159900.1)related to oil synthesis were found.In this study,a total of 8 candidate genes related to protein and oil synthesis were found.These findings are helpful for soybean analysis and breeding.