From means to QTL: the Illinois long-term selection experiment as a case study in quantitative genetics

Divergent selection for oil and protein concentration in the corn (Zea mays L.) kernel was initiated at the University of Illinois in 1896 by C.G. Hopkins. In 2005, 106 generations of selection had been completed for high oil and 105 for high protein Limits to selection for low oil and low protein were reached but not for high oil or high protein. Over the more than 100 yr of the existence of the program a number of attempts have been made to analyze the experiment using quantitative genetic tools. The purpose of this paper is to trace the use of Quantitative genetic techniques to analyze the results of divergent long-term selection for oil and protein, to relate results to the question of the need for divergent parents for quantitative trait locus (QTL) analysis, and to provide a new look at the reasons for long-continued progress from selection. Key findings include (i) progress from selection was much greater than could nave been predicted; (ii) based on both classical quantitative genetic analysis and QTL studies, a large number of QTL are involved in control of the three traits; (iii) the number of QTL identified in a given study cannot be predicted by the magnitude of genetic variance or the divergence of the parents but is a function of the number of markers used and the number of lines evaluated; and (iv) epistasis may be an important factor in explaining long-term response to selection.