Identification and Confirmation of Quantitative Trait Loci for Seed Protein and Oil Content of Soybean

Protein and oil are the major chemical constituents of soybean seed that affect the quality of soyfood, feed, and oil products. Therefore, soybean cultivars with high protein and/or high oil are desirable for the soyfood and feed markets. Use of molecular-marker-assisted selection will facilitate the breeding process of such cultivar development. The objectives of this research were to identify new quantitative trait loci (QTL) and confirm previously reported QTL associated with seed protein and oil content by using simple sequence repeat (SSR) markers and single nucleotide polymorphism (SNP) markers. Two recombinant inbred line (RIL) populations consisting of 242 individuals from R05-1415 (high protein/low oil) x R05-638 (low protein/high oil) (population 1) and 214 individuals from R05-4256 (high oil/low protein) x V97-1346 (low oil/high protein) (population 2) were used in QTL mapping. F2 plants from the mapping populations were used for SSR/SNP genotyping. In the marker screening, 120 out of 626 SSR and 1652 out of 5361 SNP markers were polymorphic. The RILs from both populations were grown in a randomized complete block design in Argentina in 2010, Stuttgart and Keiser, AR in 2011 and 2012. Seed from F2:3, F2:4 and F2:5 lines were tested for protein and oil content by using near infrared transmittance technique based on 13% moisture. Protein and oil content in both RIL populations exhibited a typical normal distribution. Single marker analysis (SMA) and composite interval mapping (CIM) revealed two novel oil QTL on chromosomes 14 and 6 in population 2 which account for 17% and 13% of the oil content variation, respectively. A minor protein QTL was confirmed on chromosome 14. One major QTL with large effect was confirmed on chromosome 20 across genetic populations, locations, and years; this QTL has opposite effects on seed protein and oil content. Eight new SNP markers flanking this QTL region on chromosome 20 were identified in population 2. These new and confirmed QTL along with linked molecular markers for seed protein and oil content can be used for marker-assisted selection for seed composition improvement in soybean breeding programs.