Correcting for Classification Errors when Estimating the Number of Genes Using Recombinant Inbred Chromosome Lines

controlling economically important quantitative traits (Law, 1966). Recombinant inbred chromosome lines are Techniques based on intercultivar chromosome substitution lines partial substitution lines that carry one or a few chromoin wheat (Triticum aestivum L.) have been used to identify and locate the genes controlling quantitative traits on a specific chromosome. For somal segments instead of the whole substitution chroa particular trait, the number of segregating loci affecting differences mosome in an otherwise common genetic background. between two parental lines are generally determined by the frequency Generally, two strategies have been adopted to deterdistribution of recombinant inbred chromosome lines (RICLs). Remine the number and location of genes on a chromocombinant inbred chromosome lines are the inbred progeny of crosses some using RICL populations, namely, (i) interpreting between a chromosome substitution line and its parent cultivar. The the phenotypic distribution of the trait and (ii) following determination of the presence and the number of segregating loci the mongenic inheritance of marker genes (e.g., disease becomes difficult (i) when the distribution exhibits no clear discrete resistance genes) linked to the quantitative trait of interclasses, (ii) when there is a considerable chance of misclassifying lines est (Law, 1966, 1967; Law et al., 1976; Snape et al., into parental and recombinant types, and (iii) when loci are linked. 1985). However, these approaches are restrictive for the We describe an approach to estimate the number of segregating loci responsible for the difference between a chromosome substitution determination of gene number and the nature of gene line and parental cultivar using the derived RICLs when classification action. Since the first approach depends entirely on the errors are likely. We also discuss the effects of linked loci on the recognition of discrete classes, where such discontinuestimates. The method was used to estimate the number of genes on ities are often not found it is difficult to estimate the chromosome 3A controlling grain yield, kernels spike21, kernel number of genes controlling a quantitative trait. In the weight, spikes m22, grain volume weight, plant height and anthesis second case, for a single chromosome, there often are date in wheat. not enough gene markers available in wheat. The need to overcome this difficulty is important and it would be useful for plant breeders, using RICLs, to know the F a better understanding of the genetics of connumber of loci (k) that differ between the chromosome tinuous variation, it is important that the genes consubstitution line and the parent cultivar that control a trolling quantitative characters be identified so that their desired quantitative trait. individual properties may be investigated. Techniques The method of Wehrhahn and Allard (1965) may be based on the use of intercultivar chromosome substituused to estimate the number of segregating loci respontion lines have been used to locate genes controlling sible for differences between a chromosome substitution important agronomic traits in wheat (Law, 1966; Zemeline and a parent cultivar and to test hypotheses. The tra et al., 1986; Berke et al., 1992; Muira and Worland, Wehrhahn and Allard method has several advantages 1994). This technique exploited an intercultivar chromoover other biometrical approaches, such as the Castlesome substitution line in which a single homologous Wright model, since the method can circumvent probpair of chromosomes in one cultivar has been replaced lems due to transgressive segregation and variation by its homologues from a second cultivar (Sears, 1953). among loci for allelic effects (Lynch and Walsh, 1998). However, this technique provides information only conHowever, the Wehrhahn and Allard method has several cerning the chromosomal location of genes, rather than limitations when using RICLs. With field data, there is their number and linkage relationship on the chromooften a considerable chance of incorrectly classifying some. Identifying the number and location of genes RICLs as either parental or nonparental types. Wehrfor agronomic traits on a chromosome is important for hahn and Allard’s method does not account for these breeding strategies. Recombinant inbred chromosome errors, and the estimate of k can be seriously biased lines developed between a chromosome substitution when the probability of misclassification is large. In adline (containing the chromosome of interest) and the dition, Wehrhahn and Allard’s method is based on the parental cultivar (containing the homologue for the assumption of unlinked loci. However, RICLs differ chromosome of interest) provide a useful tool to deterby only one chromosome, or a part of a chromosome, mine the number of genes and nature of gene action, resulting in a good chance of tightly linked loci, which may seriously bias Wehrhahn and Allard’s estimate. K.M. Eskridge and D.A Travnicek, Dep. of Biometry, University of The objective of this study was to describe an apNebraska, Lincoln, NE 68583; M.M. Shah and P.S. Baenziger, Dep. of proach to estimate and test hypotheses about the numAgronomy, University of Nebraska, Lincoln, NE 68583. Contributions ber of loci with genes that differ between a parent cultifrom NE, Agriculture Research Division, Journal Series no. 12525. Received 23 Apr. 1999. *Corresponding author (keskridge1@unl. Abbreviations: ANOVA, analysis of variance; CNN, ‘Cheyenne’; G 3 edu). E, genotype 3 environment interaction; RICLs, recombinant inbred chromosome lines; WI, ‘Wichita’. Published in Crop Sci. 40:398–403 (2000).