An additive-dominance model to determine chromosomal effects in chromosome substitution lines and other gemplasms

When using chromosome substitution (CS) lines in a crop breeding improvement program, one needs to separate the effects of the substituted chromosome from the remaining chromosomes. This cannot be done with the traditional additive-dominance (AD) model where CS lines, recurrent parent, and their hybrids are used. In this study, we develop a new genetic model and software, called a modified AD model with genotype x environment interactions, which can predict additive and dominance genetic effects attributed to a substituted alien chromosome in a CS line as well as the overall genetic effects of the non-substituted chromosomes. In addition, this model will predict the additive and dominance effects of the same chromosome of interest (i.e. chromosome 25 of cotton in this study) in an inbred line, as well as the effects of the remaining chromosomes in the inbred line. The model requires a CS line, its recurrent parent and their F-1 and/or F-2 hybrids between the substitution lines and several inbred lines. Monte Carlo simulation results showed that genetic variance components were estimated with no or slight bias when we considered this modified AD model as random. The correlation coefficient between predicted effects and true effects due to the chromosomes of interest varied from zero to greater than 0.90 and it was positively relative to the difference between the CS line and the recurrent line. To illustrate the use of this new genetic model, an upland cotton, Gossypium hirsusum L, CS line (CS-B25), TM-1 (the recurrent parent), five elite cultivars, and the F-2 hybrids from test-crossing these two lines with the five elite cultivars were grown in two environments in Mississippi. Agronomic and fiber data were collected and analyzed. The results showed that the CS line, CS-B25, which has chromosome 25 from line 3 to 79, Gossypium barbadense substituted into TM-1, had positive genetic associations with several fiber traits. We also determined that Chromosome 25 from FiberMax 966 had significantly positive associations with fiber length and strength; whereas, chromosome 25 from TM-1 and SureGrow 747 had detectable negative genetic effects on fiber strength. The new model will be useful to determine effects of the chromosomes of interest in various inbred lines in any diploid or amphidiploid crop for which CS lines are available.