Genetic Analysis of Genotype-Specific Parameters in the DSSTA-CROPGRO-soybean Phenology Simulation Model Via a Multi-Gwas Method

Context: Genotype-specific parameters (GSP) are the fundamental elements for phenotypic prediction in the DSSAT-CROPGRO soybean phenology simulation model (DCS-PSM). Yet, it is unclear about the quantitative relationship between GSP and genomics, which limits the crop models used for breeding research.Objective: Exploring the genetic composition of GSP related to four soybean phenological traits in DCS-PSM for providing a basis for whether GSP are genetic coefficient. Highlighting the breeding value of DCS-PSM from a genetic perspective and strengthening its genetic understanding, which could support a further crop model assisted molecular breeding.Methods: We conducted a multi-genome-wide association study (GWAS) method by intrgrating the single-locus with multi-locus GWAS models for GSP associated quantitative trait nucleotides (QTN) detection. And the heritability, functional annotation of QTN and genotype-environment interaction (GEI) effect were further analyzed. Results: (i). All GSP had high broad-sense heritability, ranging form 88.20-98.80%. (ii). Multi-locus GWAS significantly increased the QTN detection efficiency, the GSP associated QTN detected by multi-GWAS method contributed 22.11-50.25% phenotypic variation explained (PVE) of GSP. Besides, the GSP associated QTN accounted for a high PVE of four phenological traits, ranging from 54.25% to 74.75%. (iii). Most QTN overlapped with the function-known genes which regulate soybean phenology through photoperiod-temperature pathways. (iv). GSP associated QTN could reveal the GEI effect and contributed 1.45-6.27% PVE of soybean phenology. Conclusions: This study indicated that the genetic factor was the primary source of GSP's variation, and the multiGWAS method could be an alternative way for the genetic analysis of GSP. Phenology-related GSP had genetic potential and could be regarded as genetic coefficients and breeding targets.