QTL and heritability analysis of Essex x Williams F₂ and F₄:₆ soybean progenies

The use of molecular markers in plant breeding for indirect selection of agronomically important traits could have a large impact on the efficiency of plant breeding systems. Most agronomically important traits are polygenic (quantitative) traits and the improvement of these traits through marker assisted breeding would have the greatest impact because traditional plant breeding for quantitative traits is usually slow and difficult.

The purpose of this research is to 1) identify quantitative trait loci (QTL)for the quantitative traits yield, plant height, seed protein concentration, seed oil concentration, seed size, and maturity, in an F₂ population from a cross between the soybean cultivars 'Essex’ and 'Williams’ 2) conduct a field test on F_4:6 pure lines to assess heritability and genetic variance for each quantitative trait, and 3) compare simple sequence repeat (SSR) markers which were found to be significant QTL's in the F₂ population will also be analyzed with field data from F_4:6 lines to identify whether early generation (F₂) molecular marker selection is effective and consistent with measured traits from more inbred (F_4:6) lines.

DNA was extracted from young F₂ generation soybean leaves and amplified via polymerase chain reaction (PCR) using SSR markers. The amplified products were then run on polyacrylamide gels and silver stained to visualize bands. The F_2:3 seeds were sent to Costa Rica for three generations of advancement during the winter of 1998-1999. The F_4:6 seeds were grown in Knoxville and Springfield, TN in summer of 1999. Markers that were polymorphic between the parents were then analyzed against the F₂ and F_4:6 generation trait data using the general linear model procedure of SAS. Additive and dominant effects were partitioned by utilizing a general QTL model and a maturity covariate model to detect QTL's. The genetic variance and heritability were calculated for each trait in the F_4:6 generation, over two environments, using the mixed model procedure of SAS.

For the F₂ population, significant additive QTL's were Satt540 (maturity), Satt52 (height), Satt239 (yield; seed size), Satt373 (oil; seed size; height), and significant dominant QTL's were Satt540 (maturity; yield; seed size), Satt52 (maturity; protein; oil), Satt373 (height), Sctt9 (height). However, soybean is cultivated as a pure-line crop. Hence, additive QTL's in later generations, and which are significant over environments, may provide the greatest utility to breeders. In the F_4:6 generation, averaged over both environments, the following significant additive QTL's were identified: SattSO (yield, r² = 1.8%), Satt251 (protein, r² = 2.6%), Satt353 (seed size, r² = 2.5%), Sattl4 (seed size, r² = 11.3%), and Satt239 (height, r² = 2.6%).

Molecular breeding is becoming more practical as better technology emerges. Great progress has been made in the construction of genetic maps in many plant species, including all major crops. Most of these maps are constructed with RFLP markers, however many new maps are being constructed with both RADP and microsatellite markers. Continued molecular genetics and genomics research with our Essex x Williams population may further help to develop applied, molecular marker-assisted approaches for the benefit of soybean breeders.