Deleterious mutation burden and its association with complex traits in sorghum (Sorghum bicolor)

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

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1075-1087
Number of pages13
JournalGenetics
Volume211
Issue number3
DOIs
StatePublished - Mar 2019

Fingerprint

Sorghum
Mutation
Biomass
Genome
Starch
Breeding
Genetic Recombination
Alleles
Phenotype
Food

Keywords

  • Deleterious mutations
  • Genetic load
  • Genome-wide predictions
  • Mutation burden
  • Sorghum

ASJC Scopus subject areas

  • Genetics

Cite this

Valluru, R., Gazave, E. E., Fernandes, S. B., Ferguson, J. N., Lozano, R., Hirannaiah, P., ... Bandillo, N. (2019). Deleterious mutation burden and its association with complex traits in sorghum (Sorghum bicolor). Genetics, 211(3), 1075-1087. https://doi.org/10.1534/genetics.118.301742

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; Gore, Michael A.; Buckler, Edward S.; Bandillo, Nonoy.

In: Genetics, Vol. 211, No. 3, 03.2019, p. 1075-1087.

Research output: Contribution to journalArticle

Valluru, R, Gazave, EE, Fernandes, SB, Ferguson, JN, Lozano, R, Hirannaiah, P, Zuo, T, Brown, PJ, Leakey, A, Gore, MA, Buckler, ES & Bandillo, N 2019, 'Deleterious mutation burden and its association with complex traits in sorghum (Sorghum bicolor)', Genetics, vol. 211, no. 3, pp. 1075-1087. https://doi.org/10.1534/genetics.118.301742
Valluru R, Gazave EE, Fernandes SB, Ferguson JN, Lozano R, Hirannaiah P et al. Deleterious mutation burden and its association with complex traits in sorghum (Sorghum bicolor). Genetics. 2019 Mar;211(3):1075-1087. https://doi.org/10.1534/genetics.118.301742
Valluru, Ravi ; Gazave, Elodie E. ; Fernandes, Samuel B. ; Ferguson, John N. ; Lozano, Roberto ; Hirannaiah, Pradeep ; Zuo, Tao ; Brown, Patrick J. ; Leakey, Andrew ; Gore, Michael A. ; Buckler, Edward S. ; Bandillo, Nonoy. / Deleterious mutation burden and its association with complex traits in sorghum (Sorghum bicolor). In: Genetics. 2019 ; Vol. 211, No. 3. pp. 1075-1087.
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