Marker-Assisted Selection of Soybean E-Locus Alleles Using Functional and Linked Markers: Phenotypic Validation Under High-Latitude Conditions

Abstract

Photoperiod sensitivity is one of the main factors limiting soybean adaptation to high-latitude conditions. The aim of this study was to perform marker-assisted selection (MAS) at the E1, E3, E4, and E7 loci in three soybean F2 populations (F10, F13, and U4), followed by field evaluation of their F3 progenies in Northern Kazakhstan. Individual plants were genotyped with functional PCR-based markers for E1, E3, and E4, and with linked SSR markers for E7. This allowed us to select plants carrying target alleles and marker profiles. In total, 110 F3 progenies were tested in the Kostanay Region, and 80 of them (72.7%) reached full maturity. The phenotypic associations of the E loci and differed among genetic backgrounds. In F10, e3-fs was strongly associated with earlier flowering and completion of maturation. In F13, e4-SORE-I was associated with earlier flowering, a higher frequency of completed maturation, and earlier maturity. Also in F13, SSR marker classes associated with E7 were significantly related to maturity status and days to maturity. Among the multilocus classes in F13, the target combination e3-fs/e3-fs e4-SORE-I/e4-SORE-I together with the SSR marker profile associated with e7/e7, showed the earliest mean flowering and maturation times. Based on the field results, 14 F3 progenies were selected for further breeding work. These progenies completed maturation within 90–110 days and met additional agronomic selection criteria. Hybridization combined with MAS enabled targeted selection of breeding material carrying the valuable alleles e1-nl, e3-fs, and e4-SORE-I, as well as favorable multilocus profiles. The results highlight the value of combining multilocus MAS with field evaluation in the target environment for developing early-maturing, photoperiod-adapted soybean breeding material for Northern Kazakhstan.