Strategic Marker-Assisted Selection for Elite Soybean Development: I. Parental Polymorphism Survey Using Core SSR Markers for Null KTI and LOX2 Alleles

Abstract

This study aimed to develop soybean lines deficient in both KTI and lipoxygenase-2 (Lox2) using marker-assisted selection (MAS) with trait-specific simple sequence repeat (SSR) markers. The research was conducted at the Biotechnology Centre and RRC Amravati, Dr. PDKV, Akola, using three genotypes: AMS-100-39 (recipient; high-protein, charcoal rot resistant), NRC-127 (KTI-null donor), and NRC-109 (Lox2-null donor). Controlled hybridizations were carried out during Kharif 2023, and F₁ plants were grown in the Rabi season. A total of 318 SSR markers spanning 20 linkage groups were screened in a parental polymorphism survey (PPS). Genomic DNA was extracted using the CTAB method, and marker analysis revealed 113 polymorphic SSR loci, with polymorphism rates ranging from 29.55% (AMS-100-39 × NRC-127) to 31.76% (AMS-100-39 × NRC-109). Linkage groups D1b and D2 exhibited the highest polymorphism. Molecular validation confirmed hybridity in 17 F₁ plants from AMS-100-39 × NRC-127 and 7 from AMS-100-39 × NRC-109. The results underscore the limited genetic diversity within Indian soybean germplasm and highlight the utility of SSR markers for accurate hybrid identification and background selection. This work paves the way for developing KTI- and Lox2-deficient soybean genotypes with improved nutritional quality, enhanced palatability, and greater suitability for sustainable food and feed applications.