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

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 thatmore » 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.« less

Authors:
ORCiD logo [1];  [2]; ORCiD logo [3]; ORCiD logo [4]; ORCiD logo [2]; ORCiD logo [4]; ORCiD logo [1]; ORCiD logo [5]; ORCiD logo [4]; ORCiD logo [2]; ORCiD logo [6]; ORCiD logo [1]
  1. Cornell Univ., Ithaca, NY (United States). Inst. for Genomic Diversity
  2. Cornell Univ., Ithaca, NY (United States). Plant Breeding and Genetics Section. School of Integrative Plant Science
  3. Univ. of Illinois, Urbana, IL (United States). Dept. of Plant Biology
  4. Univ. of Illinois, Urbana, IL (United States). Dept. of Plant Biology. Dept. of Crop Sciences. Inst. for Genomic Biology
  5. Univ. of California, Davis, CA (United States). Section of Agricultural Plant Biology. Dept. of Plant Sciences
  6. 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)
Publication Date:
Research Org.:
Univ. of Illinois at Urbana-Champaign, IL (United States)
Sponsoring Org.:
USDOE Advanced Research Projects Agency - Energy (ARPA-E)
OSTI Identifier:
1510283
Grant/Contract Number:  
AR0000598; AR0000661
Resource Type:
Accepted Manuscript
Journal Name:
Genetics
Additional Journal Information:
Journal Volume: 211; Journal Issue: 3; Journal ID: ISSN 0016-6731
Publisher:
Genetics Society of America
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; deleterious mutations; genetic load; genome-wide predictions; mutation burden; sorghum

Citation Formats

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., and Bandillo, Nonoy. Deleterious Mutation Burden and Its Association with Complex Traits in Sorghum (Sorghum bicolor). United States: N. p., 2019. Web. doi: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 D. B., Gore, Michael A., Buckler, Edward S., & Bandillo, Nonoy. Deleterious Mutation Burden and Its Association with Complex Traits in Sorghum (Sorghum bicolor). United States. doi: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 D. B., Gore, Michael A., Buckler, Edward S., and Bandillo, Nonoy. Fri . "Deleterious Mutation Burden and Its Association with Complex Traits in Sorghum (Sorghum bicolor)". United States. doi:10.1534/genetics.118.301742. https://www.osti.gov/servlets/purl/1510283.
@article{osti_1510283,
title = {Deleterious Mutation Burden and Its Association with Complex Traits in Sorghum (Sorghum bicolor)},
author = {Valluru, Ravi and Gazave, Elodie E. and Fernandes, Samuel B. and Ferguson, John N. and Lozano, Roberto and Hirannaiah, Pradeep and Zuo, Tao and Brown, Patrick J. and Leakey, Andrew D. B. and Gore, Michael A. and Buckler, Edward S. and Bandillo, Nonoy},
abstractNote = {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.},
doi = {10.1534/genetics.118.301742},
journal = {Genetics},
number = 3,
volume = 211,
place = {United States},
year = {2019},
month = {3}
}

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    Works referencing / citing this record:

    Plant regeneration from sorghum anther cultures and field evaluation of progeny
    journal, February 1994

    • Kumaravadivel, N.; Sree Rangasamy, S. R.
    • Plant Cell Reports, Vol. 13, Issue 5
    • DOI: 10.1007/bf00233321

    Genetic structure among sorghum landraces as revealed by morphological variation and microsatellite markers in three agroclimatic regions of Burkina Faso
    journal, February 2010

    • Barro-Kondombo, Clarisse; Sagnard, Fabrice; Chantereau, Jacques
    • Theoretical and Applied Genetics, Vol. 120, Issue 8
    • DOI: 10.1007/s00122-010-1272-2

    Deleterious amino acid polymorphisms in Arabidopsis thaliana and rice
    journal, March 2010


    Efficiency of multi-trait, indirect, and trait-assisted genomic selection for improvement of biomass sorghum
    journal, December 2017

    • Fernandes, Samuel B.; Dias, Kaio O. G.; Ferreira, Daniel F.
    • Theoretical and Applied Genetics, Vol. 131, Issue 3
    • DOI: 10.1007/s00122-017-3033-y

    GCTA: A Tool for Genome-wide Complex Trait Analysis
    journal, January 2011

    • Yang, Jian; Lee, S. Hong; Goddard, Michael E.
    • The American Journal of Human Genetics, Vol. 88, Issue 1
    • DOI: 10.1016/j.ajhg.2010.11.011

    Characteristics of Neutral and Deleterious Protein-Coding Variation among Individuals and Populations
    journal, October 2014

    • Fu, Wenqing; Gittelman, Rachel M.; Bamshad, Michael J.
    • The American Journal of Human Genetics, Vol. 95, Issue 4
    • DOI: 10.1016/j.ajhg.2014.09.006

    The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication
    journal, March 2006


    Genomics and the Contrasting Dynamics of Annual and Perennial Domestication
    journal, December 2015

    • Gaut, Brandon S.; Díez, Concepción M.; Morrell, Peter L.
    • Trends in Genetics, Vol. 31, Issue 12
    • DOI: 10.1016/j.tig.2015.10.002

    Plant height and evolutionary games
    journal, July 2003


    Breeding systems and genome evolution
    journal, December 2001


    Accumulation of mutations in sexual and asexual populations
    journal, April 1987


    The genetic basis of inbreeding depression
    journal, December 1999


    Saharan exploitation of plants 8,000 years BP
    journal, October 1992

    • Wendorf, Fred; Close, Angela E.; Schild, Romuald
    • Nature, Vol. 359, Issue 6397
    • DOI: 10.1038/359721a0

    The cost of inbreeding in Arabidopsis
    journal, April 2002

    • Bustamante, Carlos D.; Nielsen, Rasmus; Sawyer, Stanley A.
    • Nature, Vol. 416, Issue 6880
    • DOI: 10.1038/416531a

    Proportionally more deleterious genetic variation in European than in African populations
    journal, February 2008

    • Lohmueller, Kirk E.; Indap, Amit R.; Schmidt, Steffen
    • Nature, Vol. 451, Issue 7181
    • DOI: 10.1038/nature06611

    The Sorghum bicolor genome and the diversification of grasses
    journal, January 2009

    • Paterson, Andrew H.; Bowers, John E.; Bruggmann, Rémy
    • Nature, Vol. 457, Issue 7229
    • DOI: 10.1038/nature07723

    A polygenic burden of rare disruptive mutations in schizophrenia
    journal, January 2014

    • Purcell, Shaun M.; Moran, Jennifer L.; Fromer, Menachem
    • Nature, Vol. 506, Issue 7487
    • DOI: 10.1038/nature12975

    Rare and low-frequency coding variants alter human adult height
    journal, February 2017

    • Marouli, Eirini; Graff, Mariaelisa; Medina-Gomez, Carolina
    • Nature, Vol. 542, Issue 7640
    • DOI: 10.1038/nature21039

    Dysregulation of expression correlates with rare-allele burden and fitness loss in maize
    journal, March 2018

    • Kremling, Karl A. G.; Chen, Shu-Yun; Su, Mei-Hsiu
    • Nature, Vol. 555, Issue 7697
    • DOI: 10.1038/nature25966

    Maize HapMap2 identifies extant variation from a genome in flux
    journal, June 2012

    • Chia, Jer-Ming; Song, Chi; Bradbury, Peter J.
    • Nature Genetics, Vol. 44, Issue 7
    • DOI: 10.1038/ng.2313

    The Capsella rubella genome and the genomic consequences of rapid mating system evolution
    journal, June 2013

    • Slotte, Tanja; Hazzouri, Khaled M.; Ågren, J. Arvid
    • Nature Genetics, Vol. 45, Issue 7
    • DOI: 10.1038/ng.2669

    The deleterious mutation load is insensitive to recent population history
    journal, February 2014

    • Simons, Yuval B.; Turchin, Michael C.; Pritchard, Jonathan K.
    • Nature Genetics, Vol. 46, Issue 3
    • DOI: 10.1038/ng.2896

    LD Score regression distinguishes confounding from polygenicity in genome-wide association studies
    journal, February 2015

    • Bulik-Sullivan, Brendan K.; Loh, Po-Ru; Finucane, Hilary K.
    • Nature Genetics, Vol. 47, Issue 3
    • DOI: 10.1038/ng.3211

    Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data
    journal, March 2017

    • Huang, Yi-Fei; Gulko, Brad; Siepel, Adam
    • Nature Genetics, Vol. 49, Issue 4
    • DOI: 10.1038/ng.3810

    Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation
    journal, April 2017

    • Ramu, Punna; Esuma, Williams; Kawuki, Robert
    • Nature Genetics, Vol. 49, Issue 6
    • DOI: 10.1038/ng.3845

    Genomic prediction contributing to a promising global strategy to turbocharge gene banks
    journal, October 2016


    SIFT missense predictions for genomes
    journal, December 2015

    • Vaser, Robert; Adusumalli, Swarnaseetha; Leng, Sim Ngak
    • Nature Protocols, Vol. 11, Issue 1
    • DOI: 10.1038/nprot.2015.123

    Crop genomics: advances and applications
    journal, December 2011

    • Morrell, Peter L.; Buckler, Edward S.; Ross-Ibarra, Jeffrey
    • Nature Reviews Genetics, Vol. 13, Issue 2
    • DOI: 10.1038/nrg3097

    Drought susceptibility of modern rice varieties: an effect of linkage of drought tolerance with undesirable traits
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    Experiments on the role of deleterious mutations as stepping stones in adaptive evolution
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    Distance from sub-Saharan Africa predicts mutational load in diverse human genomes
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    Evaluating the contribution of rare variants to type 2 diabetes and related traits using pedigrees
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    Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize
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    Extensive Variation in the Density and Distribution of DNA Polymorphism in Sorghum Genomes
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    Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP
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