Abstract
In a line or a hybrid breeding program superior lines are selected from a breeding pool as parental lines for the next breeding cycle. From a cross of two parental lines, new lines are derived by single-seed descent (SSD) or doubled haploid (DH) technology. However, not all possible crosses between the parental lines can be carried out due to limited resources. Our objectives were to present formulas to characterize a cross by the mean and variance of the genotypic values of the lines derived from the cross, and to apply the formulas to predict means and variances of flowering time traits in recombinant inbred line families of a publicly available data set in maize. We derived formulas which are based on the expected linkage disequilibrium (LD) between two loci and which can be used for arbitrary mating systems. Results were worked out for SSD and DH lines derived from a cross after an arbitrary number of intermating generations. The means and variances were highly correlated with results obtained by the simulation software PopVar. Compared with these simulations, computation time for our closed formulas was about ten times faster. The means and variances for flowering time traits observed in the recombinant inbred line families of the investigated data set showed correlations of around 0.9 for the means and of 0.46 and 0.65 for the standard deviations with the estimated values. We conclude that our results provide a framework that can be exploited to increase the efficiency of hybrid and line breeding programs by extending genomic selection approaches to the selection of crossing partners.
Highlights
In each cycle of a line or a hybrid breeding program, lines are selected which serve as the parents of the crosses from which the base population of the breeding cycle is derived
Our objectives were to (1) present an analytical derivation of s2g that is based on the expected linkage disequilibrium (LD) between two loci, and that can be used for arbitrary mating systems, (2) provide formulas for the genetic variance s2g in populations of doubled haploid (DH) and single-seed descent (SSD) lines derived from a cross after t generations of intermating, and (3) illustrate the use of the formulas with published data of the nested association mapping (NAM) population in maize [9]
The means and variances estimated with Eqs 1 and 2 showed correlations between 0.98 and 1 with the average of the 25 simulated estimates obtained from PopVar (Fig 1)
Summary
In each cycle of a line or a hybrid breeding program, lines are selected which serve as the parents of the crosses from which the base population of the breeding cycle is derived. The decision which parental lines to cross is an essential factor that determines the selection gain in a breeding program. The usefulness of a cross [1] is defined as U = μ + iσgh, where μ is the expectation and σg the standard deviation of the genetic values of the lines derived from the cross, i is the selection. Buckler_etal_2009_Science_flowering_time_data090807.zip The direct URL for downloading the marker genotypes of the 282 lines of the association panel is http://cbsusrv04.tc.cornell.edu/ users/panzea/download.aspx?filegroupid=7 The data used in our manuscript is contained in the file SNP55K_maize282_AGP3_20190904.hmp.txt.gz Buckler_etal_2009_Science_flowering_time_data090807.zip The direct URL for downloading the marker genotypes of the 282 lines of the association panel is http://cbsusrv04.tc.cornell.edu/ users/panzea/download.aspx?filegroupid=7 The data used in our manuscript is contained in the file SNP55K_maize282_AGP3_20190904.hmp.txt.gz
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