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Incomplete Dominance of Deleterious Alleles Contributes Substantially to Trait Variation and Heterosis in Maize

View ORCID ProfileJinliang Yang, Sofiane Mezmouk, Andy Baumgarten, Edward S. Buckler, Katherine E. Guill, Michael D. McMullen, Rita H. Mumm, Jeffrey Ross-Ibarra
doi: https://doi.org/10.1101/086132
Jinliang Yang
1Department of Plant Sciences, University of California, Davis, CA 95616, USA,
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  • For correspondence: jolyang@ucdavis.edu rossibarra@ucdavis.edu
Sofiane Mezmouk
1Department of Plant Sciences, University of California, Davis, CA 95616, USA,
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Andy Baumgarten
2DuPont Pioneer, Johnston, IA 50131, USA,
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Edward S. Buckler
3US Department of Agriculture, Agricultural Research Service, Ithaca, NY 14853, USA,
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Katherine E. Guill
4US Department of Agriculture, Agricultural Research Service, Columbia, MO 65211, USA,
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Michael D. McMullen
4US Department of Agriculture, Agricultural Research Service, Columbia, MO 65211, USA,
5Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA,
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Rita H. Mumm
6Department of Crop Sciences and the Illinois Plant Breeding Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,
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Jeffrey Ross-Ibarra
1Department of Plant Sciences, University of California, Davis, CA 95616, USA,
7Center for Population Biology and Genome Center, University of California, Davis, CA 95616, USA.
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  • For correspondence: jolyang@ucdavis.edu rossibarra@ucdavis.edu
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Abstract

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 by crossing 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 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.

Author Summary A key long-term goal of biology is understanding the genetic basis of phenotypic variation. Although most new mutations are likely disadvantageous, their prevalence and importance in explaining patterns of phenotypic variation is controversial and not well understood. In this study we combine whole genome-sequencing and field evaluation of a maize mapping population to investigate the contribution of deleterious mutations to phenotype. We show that a priori prediction of deleterious alleles correlates well with effect sizes for grain yield and that variants predicted to be more damaging are on average more recessive. We develop a simple model allowing for variation in the heterozygous effects of deleterious mutations and demonstrate its improved ability to predict both phenotypes and hybrid vigor. Our results help reconcile alternative explanations for hybrid vigor and highlight the use of leveraging evolutionary history to facilitate breeding for crop improvement.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted June 09, 2017.
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Incomplete Dominance of Deleterious Alleles Contributes Substantially to Trait Variation and Heterosis in Maize
Jinliang Yang, Sofiane Mezmouk, Andy Baumgarten, Edward S. Buckler, Katherine E. Guill, Michael D. McMullen, Rita H. Mumm, Jeffrey Ross-Ibarra
bioRxiv 086132; doi: https://doi.org/10.1101/086132
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Incomplete Dominance of Deleterious Alleles Contributes Substantially to Trait Variation and Heterosis in Maize
Jinliang Yang, Sofiane Mezmouk, Andy Baumgarten, Edward S. Buckler, Katherine E. Guill, Michael D. McMullen, Rita H. Mumm, Jeffrey Ross-Ibarra
bioRxiv 086132; doi: https://doi.org/10.1101/086132

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