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Strain engineering for industrial production requires a targeted improvement of multiple complex traits, which range from pathway flux to tolerance to mixed sugar utilization.
Quantitative genetic methods enable more effective selection on single or multiple complex traits than selection on phenotypes because of the estimation of additive genetic variance in the population (the chief cause of resemblance of relatives and the only genetic component that can be estimated from observations on the population) and estimated breeding values of individuals.
Thus, females may base their choice on multiple complex traits, but few studies have shown if this preference leads to an increase in reproductive success and/or offspring fitness [8].
Monozygotic twin mice (genetically identical mice that are generated from a single zygote by dividing the blastocyst at the 8-cell stage to produce 2 viable embryos) are significantly more alike for multiple complex traits than are dizygotic twin mice (genetically identical mice obtained from different zygotes) [5].
The parental lines of popular varieties and selected genetic mapping populations were also included; 400 of which were parental lines for genome-wide introgression lines for multiple complex traits developed using novel molecular breeding strategies [ 7].
The distance between recombination events decreases with each generation of breeding, such that HS mice and rats have been used to map multiple complex traits to generally <5 Mb (Talbot et al. 1999, 2003; Demarest et al. 2001; Valdar et al. 2006; Solberg Woods et al. 2010, 2012; Johnsen et al. 2011; Baud et al. 2013).
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Additionally, gene mapping information could increase the relative weight of specific gene-rich regions in predictive Genomic Selection models to assist forest tree breeding programs for multiple complex quantitative traits [ 51].
Since then, epigenetic alterations have been reported in many other types of cancer [ 15], autoimmune diseases [ 16], diabetes [ 17], Alzheimer's disease [ 18], Parkinson's disease [ 19], asthma [ 20], and multiple other human complex traits [ 21- 23].
This approach demonstrated the power of X-QTL mapping to dissect multiple loci contributing to complex traits.
MR also has relatively low statistical power and may be affected by weak instrument bias as only the small percentage of phenotypic variance is explained by single (or often multiple) genotypes for most complex traits.
The recent identification of multiple epistatic QTL controlling complex traits in mice [ 1- 4], chickens [ 5, 6], and in model organisms such as yeast [ 7] and Drosophila melanogaster [ 8, 9] has been a major achievement in the understanding of the genetic nature of complex traits.
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