Abstract
Deleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring of a cross between two inbred parents. We test these ideas using evolutionary measures of sequence conservation to ask whether incorporating information about putatively deleterious alleles can inform genomic selection (GS) models and improve phenotypic prediction. We measured a number of agronomic traits in both the inbred parents and hybrids of an elite maize partial diallel population and re-sequenced the parents of the population. Inbred elite maize lines vary for more than 350,000 putatively deleterious sites, but show a lower burden of such sites than a comparable set of traditional landraces. Our modeling reveals widespread evidence for incomplete dominance at these loci, and supports theoretical models that more damaging variants are usually more recessive. We identify haplotype blocks using an identity-by-decent (IBD) analysis and perform genomic prediction analyses in which we weigh blocks on the basis of complementation for segregating putatively deleterious variants. Cross-validation results show that incorporating sequence conservation in genomic selection improves prediction accuracy for grain yield and other fitness-related traits as well as heterosis for those traits. Our results provide empirical support for an important role for incomplete dominance of deleterious alleles in explaining heterosis and demonstrate the utility of incorporating functional annotation in phenotypic prediction and plant breeding.
Highlights
Understanding the genetic basis of phenotypic variation is critical to many biological endeavors from human health to conservation and agriculture
We measured plant height (PHT, in cm), height of primary ear (EHT, in cm), days to 50% pollen shed (DTP), days to 50% silking (DTS), anthesis-silking interval (ASI, in days), grain yield adjusted to 15.5% moisture (GY, in bu/A), and test weight (TW, weight of 1 bushel of grain in pounds)
We measured a number of agronomically relevant phenotypes in both parents and hybrids, including flowering time, plant size, test weight (TW; a measure of quality based on grain density), and grain yield (GY)
Summary
Understanding the genetic basis of phenotypic variation is critical to many biological endeavors from human health to conservation and agriculture. The long-term burden of deleterious variants is relatively insensitive to demography [3], population bottlenecks and expansion may lead to an increased abundance of deleterious alleles over shorter time scales such as those associated with domestication [4], postglacial colonization [5] or recent human migration [6]. Even when the impacts on total load are minimal, demographic change may have important consequences for the contribution of deleterious variants to phenotypic variation [3, 7,8,9]. Together, these considerations point to a potentially important role for deleterious variants in determining patterns of phenotypic variation, especially for traits closely related to fitness. Substantial evidence suggests an abundance of deleterious alleles present in modern germplasm, from the observed maintenance of heterozygosity during the processes of inbreeding [16, 17] and selection [18] to genome-wide association results that reveal an excess of associations with genes segregating for damaging protein-coding variants [19]
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