Integrated eQTL mapping approach reveals genomic regions regulating candidate genes of the locus in soybean.

Deciphering the gene regulatory networks of critical quantitative trait loci associated with early maturity provides information for breeders to unlock soybean's ( (L.) Merr.) northern potential and expand its cultivation range. The locus is a genomic region regulating the number of days to maturity under constant short-day photoperiodic conditions in two early-maturing soybean populations (QS15524 and QS15544) belonging to maturity groups MG00 and MG000. In this study, we developed a combinatorial expression quantitative trait loci mapping approach using three algorithms (ICIM, IM, and GCIM) to identify the regions that regulate three candidate genes of the locus (/, /, and /). Using this approach, a total of 2,218 (2,061 genes)/7 (7 genes) and 4,073 (2,842 genes)/3,083 (2,418 genes) interactions were mapped in the QS15524 and QS15544 populations, respectively. From these interactions, we successfully identified two hotspots (F2_GM15:49,385,092-49,442,237 and F2_GM18:1,434,182-1,935,386) and three minor regions (RIL_GM04:17,227,512-20,251,662, RIL_GM04:31,408,946-31,525,671 and RIL_GM13:37,289,785-38,620,690) regulating the candidate genes of and several of their homologs. Based on co-expression network and single nucleotide variant analyses, we identified () and () as the best candidates for the F2_GM15:49,385,092-49,442,237 and F2_GM18:1,434,182-1,935,386 hotspots. These findings demonstrate that a few key regions are involved in the regulation of the E8-r3 candidates , , and .