Genetics of soybean agronomic traits: I. Comparison of three related recombinant inbred populations

Molecular markers provide a rapid approach to breeding for desired agronomi c traits. To use them, it is necessary to determine the linkage between qua ntitative trait loci (QTLs) and such markers. The objective of this researc h was to determine such linkage in recombinant inbred (RI) soybean [Glycine max (L,) Merrill] populations. To do this, RI soybean segregants were char acterized for molecular genetic markers and traits measured in several diff erent environments. QTLs then were identified by interval mapping. Agronomi c traits were measured and compared in large (about 230 segregants) RI popu lations derived from crosses between the cultivars Minsoy and Noir 1 (MN po pulation), Minsoy and Archer (MA population), and Noir 1 and Archer (NA pop ulation). The MA and NA populations were grown together as two replications in each of four environments, Measurements from the MN population mere rep orted previously and were taken from three replications grown in four envir onments, Traits measured were plant height, lodging, date of flowering, rep roductive period, maturity, yield, seed weight, seed oil, seed protein, lea f length, and leaf width, Additional traits were derived from these primary measurements. Each of the three RI populations was also characterized by a large (>400) number of molecular genetic markers including RFLP (restricti on fragment length polymorphism) and SSR (simple sequence repeat polymorphi sms). QTLs were identified for all of the primary and derived traits at a s ignificance level greater than or equal to LOD 3 on 17 of the 20 linkage gr oups and tended to be clustered on three. QTLs with major effects (R-2 > 10 %) were identified for all traits, and for many, these explained more than half of the heritable variation. Comparison of QTLs between the three RI po pulations established that for the majority of the traits, only two alleles could be identified. In only a fen instances could a third allele be detec ted. Many of the significant QTLs identified in one population were confirm ed in another. However, an almost equal number were found in only one popul ation, suggesting that a dependence on the genetic background for expressio n (epistasis) was common.