NCSU HS 541 - Case Study in Quantitative Genetics

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From Means to QTL: The Illinois Long-Term Selection Experiment as a Case Study in Quantitative GeneticsJ.W. DUDLEY*Dep. of Crop Sciences, Univ. of Illinois, Urbana, IL 61801. This research was supported by the Illinois Agric. Exp. Stn. and a grant from Renessen, LLC. Received 9 July 2007. *Corresponding author ([email protected]).Published in Crop Sci. 47(S3) S20–S31 (2007).doi: 10.2135/cropsci2007.04.0003IPBS© Crop Science Society of America677 S. Segoe Rd., Madison, WI 53711 USAINTERNATIONAL PLANT BREEDING SYMPOSIUM • DECEMBER 2007 S-21ivergent 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 fi nd-ings include (i) progress from selection was much greater than could have 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 identifi ed in a given study cannot be predicted by the magnitude of genetic variance or the diver-gence 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.DS-22 INTERNATIONAL PLANT BREEDING SYMPOSIUM • DECEMBER 2007Divergent long-term selection is a tool for understanding genetic control of a trait and for concentrating alleles for contrasting versions of the trait. Th e Illinois long-term selec-tion experiment for kernel oil and protein concentration is a classic example of use of divergent selection to understand genetic control of traits. Th e history of this experiment was reviewed extensively in the proceedings of a symposium on long-term selection (Dudley and Lambert, 2004). Details of selection intensity, breeding procedure, and methods of chemical analysis are found in those proceedings. Briefl y, the experiment was started by C.G. Hopkins in 1896 (Hop-kins, 1899). Th e open-pollinated corn cultivar Burr’s White was the founder population. Four selected strains were estab-lished: Illinois High Oil (IHO), Illinois Low Oil (ILO), Illinois High Protein (IHP), and Illinois Low Protein (ILP). Selection in each strain was in the direction indicated by the name of the strain (e.g., IHO was selected for high oil concentration in the kernel). Mass selection, based on analysis of individual ears, was used with a selection intensity of approximately one ear out of fi ve (12 ears out of 60 most recently) for most of the experiment (Dudley and Lambert, 2004). Aft er 48 genera-tions, reverse selection was started in each strain to establish the Reverse High Oil (RHO), Reverse Low Oil (RLO), Reverse High Protein (RHP), and Reverse Low Protein (RLP) strains (Woodworth et al., 1952). Aft er seven generations of selection in RHO, selection was again reversed to create the Switchback High Oil strain (SHO). Th e objective of the reverse selection strains was to determine whether genetic variability had been exhausted in the selected strains.Th e tools of quantitative genetics include means, regression analysis, variance estimation (particularly genetic variances), genetic correlations, mating designs, random mating, and more recently QTL analysis. Th e pur-pose 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 concentration in the corn (Zea mays L.) kernel at the University of Illinois, to relate results to the question of the need to use divergent parents for QTL analysis, and to provide a new look at the reasons for long-continued progress from selection.ResultsTh e results are discussed under the major headings of Classical Quantitative Genetics, QTL Studies, Explana-tions of Long-Term Response, and Conclusions. Th e mate-rials and methods used in the studies discussed are in the original papers.Classical Quantitative GeneticsMeansFor the duration of the experiment, means of ears sampled each cycle are plotted against generations in Fig. 1 and 2 for the oil and protein strains, respectively. Th e earliest report of results from this experiment (Hopkins, 1899) compared means of IHO cycle 2 with ILO cycle 2 for oil and IHP cycle 2 with ILP cycle 2 for protein. For the IHO-ILO com-parison, a diff erence of 11.5 g kg–1 oil was found while for the IHP-ILP comparison, the diff erence in protein was 5.0 g kg–1. From these results Hopkins concluded that selec-tion for oil and protein was eff ective even though there was no test of signifi cance of the observed diff erences. Aft er 10 generations of selection Smith (1908) found a diff erence of 56.2 g kg–1 protein between IHP and ILP and a diff erence of 47.1 g kg–1 oil between IHO and ILO. Th ese results were based on means of the ears grown in 1906 in each strain and again there was no statistical test of the signifi cance of diff erences between means. Aft er 28 generations of selec-tion the diff erence in means between IHO and ILO was 83.5 g kg–1 oil and the diff erence between IHP and ILP was 82.2 g kg–1 protein (Winter, 1929). Aft er 50 generations of selection the diff erence between IHO and ILO was 143.5 g kg–1 oil and the diff erence between IHP and ILP was 145.4 g kg–1 protein (Woodworth et al., 1952). Results of two cycles of reverse selection (selection within a strain in the opposite direction, e.g., selection for low protein in IHP) showed apparent progress in RHO, RHP, and RLP but little progress in RLO.Leng (1962) attempted to apply the results of 61 gen-erations of selection to breeding theory. At 61


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NCSU HS 541 - Case Study in Quantitative Genetics

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