Deleterious Mutation Burden and Its Association with Complex Traits in Sorghum (Sorghum bicolor)

Valluru, Ravi; Gazave, Elodie E.; Fernandes, Samuel B.; Ferguson, John N.; Lozano, Roberto; Hirannaiah, Pradeep; Zuo, Tao; Brown, Patrick J.; Leakey, Andrew D.  B.; Gore, Michael A.; Buckler, Edward S.; Bandillo, Nonoy

doi:10.1534/genetics.118.301742

Title: Deleterious Mutation Burden and Its Association with Complex Traits in Sorghum (Sorghum bicolor)

Journal Article · 28 February 2019 · Genetics

DOI: https://doi.org/10.1534/genetics.118.301742 · OSTI ID:1510283

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Cornell Univ., Ithaca, NY (United States). Inst. for Genomic Diversity; University of Illinois at Urbana-Champaign
Cornell Univ., Ithaca, NY (United States). Plant Breeding and Genetics Section. School of Integrative Plant Science
Univ. of Illinois, Urbana, IL (United States). Dept. of Plant Biology
Univ. of Illinois, Urbana, IL (United States). Dept. of Plant Biology. Dept. of Crop Sciences. Inst. for Genomic Biology
Cornell Univ., Ithaca, NY (United States). Inst. for Genomic Diversity
Univ. of California, Davis, CA (United States). Section of Agricultural Plant Biology. Dept. of Plant Sciences
Cornell Univ., Ithaca, NY (United States). Inst. for Genomic Diversity. Plant Breeding and Genetics Section. School of Integrative Plant Science; USDA Agricultural Research Service, Ithaca, NY (United States)

Sorghum (Sorghum bicolor L.) is a major food cereal for millions of people worldwide. The sorghum genome, like other species, accumulates deleterious mutations, likely impacting its fitness. The lack of recombination, drift, and the coupling with favorable loci impede the removal of deleterious mutations from the genome by selection. To study how deleterious variants impact phenotypes, we identified putative deleterious mutations among ~5.5 M segregating variants of 229 diverse biomass sorghum lines. We provide the whole-genome estimate of the deleterious burden in sorghum, showing that ~33% of nonsynonymous substitutions are putatively deleterious. The pattern of mutation burden varies appreciably among racial groups. Across racial groups, the mutation burden correlated negatively with biomass, plant height, specific leaf area (SLA), and tissue starch content (TSC), suggesting that deleterious burden decreases trait fitness. Putatively deleterious variants explain roughly one-half of the genetic variance. However, there is only moderate improvement in total heritable variance explained for biomass (7.6%) and plant height (average of 3.1% across all stages). There is no advantage in total heritable variance for SLA and TSC. The contribution of putatively deleterious variants to phenotypic diversity therefore appears to be dependent on the genetic architecture of traits. Overall, these results suggest that incorporating putatively deleterious variants into genomic models slightly improves prediction accuracy because of extensive linkage. Knowledge of deleterious variants could be leveraged for sorghum breeding through either genome editing and/or conventional breeding that focuses on the selection of progeny with fewer deleterious alleles.

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Research Organization:: Univ. of Illinois, Urbana, IL (United States)

Sponsoring Organization:: USDOE Advanced Research Projects Agency - Energy (ARPA-E)

Grant/Contract Number:: AR0000598; AR0000661

OSTI ID:: 1510283

Journal Information:: Genetics, Journal Name: Genetics Journal Issue: 3 Vol. 211; ISSN 0016-6731

Publisher:: Genetics Society of AmericaCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
deleterious mutations
genetic load
genome-wide predictions
mutation burden
sorghum

Supplemental Material for Valluru et al., 2019 Valluru, Ravi; Gazave, Elodie; Fernandes, Samuel B. https://doi.org/10.25386/genetics.7638122 The current record is supplemented by this collection	collection	January 2019
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Title: Deleterious Mutation Burden and Its Association with Complex Traits in Sorghum (Sorghum bicolor)

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