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Title: Genome-Wide Association Mapping of Anthracnose (Colletotrichum sublineolum) Resistance in NPGS Ethiopian Sorghum Germplasm

Abstract

The National Plant Germplasm System (NPGS) Ethiopian sorghum [Sorghum bicolor (L.) Moench] collection of the United States is an important genetic resource for sorghum improvement. Anthracnose (Colletotrichum sublineolum) is one of the most harmful fungal diseases in humid sorghum production regions. Although multiple resistance sources have been identified in temperate-adapted germplasm in the Sorghum Association Panel (SAP), these resistance loci explain a limited portion of the total variation, and sources of resistance from tropical germplasm are not available for breeding programs at temperate regions. Using a core set of 335 previously genotyped NPGS Ethiopian accessions, we identified 169 accessions resistant to anthracnose. To identify resistance loci, we merged the genotypic and anthracnose response data for both NPGS Ethiopian germplasm and the SAP and performed genome-wide association scans using 219,037 single nucleotide polymorphisms and 617 accessions. The integrated data set enabled the detection of a locus on chromosome 9 present in the SAP at a low frequency. The locus explains a limited portion of the observed phenotypic variation ($r^2$ = 0.31), suggesting the presence of other resistance loci. The locus in chromosome 9 was constituted by three R genes clustered within a 47-kb region. The presence of multiple sources of resistancemore » in NPGS Ethiopian germplasm and SAP requires the inclusion of other resistance response evaluation that could revealed others low frequency resistance alleles in the panel.« less

Authors:
ORCiD logo [1];  [1];  [1]
  1. USDA-ARS, College Station, TX (United States). Southern Plains Agricultural Research Center
Publication Date:
Research Org.:
USDA-ARS, Mayaguez (Puerto Rico); USDA-ARS, College Station, TX (United States). Southern Plains Agricultural Research Center
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1593833
Report Number(s):
USDA-ARS-CRIS-6090-21000-053-00-D
Journal ID: ISSN 2160-1836
Grant/Contract Number:  
SC0014171
Resource Type:
Accepted Manuscript
Journal Name:
G3
Additional Journal Information:
Journal Volume: 9; Journal Issue: 9; Journal ID: ISSN 2160-1836
Publisher:
Genetics Society of America
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Sorghum; GWAS; Anthracnose; NPGS; Ethiopia

Citation Formats

Cuevas, Hugo E., Prom, Louis K., and Cruet-Burgos, Clara M. Genome-Wide Association Mapping of Anthracnose (Colletotrichum sublineolum) Resistance in NPGS Ethiopian Sorghum Germplasm. United States: N. p., 2019. Web. https://doi.org/10.1534/g3.119.400350.
Cuevas, Hugo E., Prom, Louis K., & Cruet-Burgos, Clara M. Genome-Wide Association Mapping of Anthracnose (Colletotrichum sublineolum) Resistance in NPGS Ethiopian Sorghum Germplasm. United States. https://doi.org/10.1534/g3.119.400350
Cuevas, Hugo E., Prom, Louis K., and Cruet-Burgos, Clara M. Wed . "Genome-Wide Association Mapping of Anthracnose (Colletotrichum sublineolum) Resistance in NPGS Ethiopian Sorghum Germplasm". United States. https://doi.org/10.1534/g3.119.400350. https://www.osti.gov/servlets/purl/1593833.
@article{osti_1593833,
title = {Genome-Wide Association Mapping of Anthracnose (Colletotrichum sublineolum) Resistance in NPGS Ethiopian Sorghum Germplasm},
author = {Cuevas, Hugo E. and Prom, Louis K. and Cruet-Burgos, Clara M.},
abstractNote = {The National Plant Germplasm System (NPGS) Ethiopian sorghum [Sorghum bicolor (L.) Moench] collection of the United States is an important genetic resource for sorghum improvement. Anthracnose (Colletotrichum sublineolum) is one of the most harmful fungal diseases in humid sorghum production regions. Although multiple resistance sources have been identified in temperate-adapted germplasm in the Sorghum Association Panel (SAP), these resistance loci explain a limited portion of the total variation, and sources of resistance from tropical germplasm are not available for breeding programs at temperate regions. Using a core set of 335 previously genotyped NPGS Ethiopian accessions, we identified 169 accessions resistant to anthracnose. To identify resistance loci, we merged the genotypic and anthracnose response data for both NPGS Ethiopian germplasm and the SAP and performed genome-wide association scans using 219,037 single nucleotide polymorphisms and 617 accessions. The integrated data set enabled the detection of a locus on chromosome 9 present in the SAP at a low frequency. The locus explains a limited portion of the observed phenotypic variation ($r^2$ = 0.31), suggesting the presence of other resistance loci. The locus in chromosome 9 was constituted by three R genes clustered within a 47-kb region. The presence of multiple sources of resistance in NPGS Ethiopian germplasm and SAP requires the inclusion of other resistance response evaluation that could revealed others low frequency resistance alleles in the panel.},
doi = {10.1534/g3.119.400350},
journal = {G3},
number = 9,
volume = 9,
place = {United States},
year = {2019},
month = {9}
}

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Works referenced in this record:

The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes
journal, September 2014


Enrichment of statistical power for genome-wide association studies
journal, October 2014


Inheritance and molecular mapping of anthracnose resistance genes present in sorghum line SC112-14
journal, July 2014


Linking the emergence of fungal plant diseases with ecological speciation
journal, July 2010

  • Giraud, Tatiana; Gladieux, Pierre; Gavrilets, Sergey
  • Trends in Ecology & Evolution, Vol. 25, Issue 7
  • DOI: 10.1016/j.tree.2010.03.006

Evaluation of Malian Sorghum Germplasm for Resistance Against Anthracnose
journal, February 2004


Anthracnose Resistance in Sorghum Germplasm from the Segou Region of Mali
journal, May 2012


TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline
journal, February 2014


Population genomic and genome-wide association studies of agroclimatic traits in sorghum
journal, December 2012

  • Morris, G. P.; Ramu, P.; Deshpande, S. P.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 2
  • DOI: 10.1073/pnas.1215985110

Molecular mapping of Cg1, a gene for resistance to anthracnose (Colletotrichum sublineolum) in sorghum
journal, August 2008


Dissecting Genome-Wide Association Signals for Loss-of-Function Phenotypes in Sorghum Flavonoid Pigmentation Traits
journal, September 2013

  • Morris, Geoffrey P.; Rhodes, Davina H.; Brenton, Zachary
  • G3: Genes|Genomes|Genetics, Vol. 3, Issue 11
  • DOI: 10.1534/g3.113.008417

Genetic diversity and pathotype determination of Colletotrichum sublineolum isolates causing anthracnose in sorghum
journal, January 2012

  • Prom, L. K.; Perumal, R.; Erattaimuthu, S. R.
  • European Journal of Plant Pathology, Vol. 133, Issue 3
  • DOI: 10.1007/s10658-012-9946-z

Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production
journal, June 2013


Elicitors, Effectors, and R Genes: The New Paradigm and a Lifetime Supply of Questions
journal, September 2007


PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
journal, September 2007

  • Purcell, Shaun; Neale, Benjamin; Todd-Brown, Kathe
  • The American Journal of Human Genetics, Vol. 81, Issue 3
  • DOI: 10.1086/519795

Enhancements and modifications of primer design program Primer3
journal, March 2007


Plant disease resistance genes: Current status and future directions
journal, April 2012

  • Gururani, Mayank Anand; Venkatesh, Jelli; Upadhyaya, Chandrama Prakash
  • Physiological and Molecular Plant Pathology, Vol. 78
  • DOI: 10.1016/j.pmpp.2012.01.002

Quantitative Trait Loci Associated with Anthracnose Resistance in Sorghum
journal, February 2017


GAPIT: genome association and prediction integrated tool
journal, July 2012


Using Genotyping by Sequencing to Map Two Novel Anthracnose Resistance Loci in Sorghum bicolor
journal, May 2016

  • J. Felderhoff, Terry; M. McIntyre, Lauren; Saballos, Ana
  • G3: Genes|Genomes|Genetics, Vol. 6, Issue 7
  • DOI: 10.1534/g3.116.030510

Sequencing of an Anthracnose-Resistant Sorghum Genotype and Mapping of a Major QTL Reveal Strong Candidate Genes for Anthracnose Resistance
journal, March 2015


Genome-Wide Association Mapping of Anthracnose ( Colletotrichum sublineolum ) Resistance in the U.S. Sorghum Association Panel
journal, July 2018


Assessments of genetic diversity and anthracnose disease response among Zimbabwe sorghum germplasm
journal, January 2014

  • Cuevas, Hugo E.; Prom, Louis K.; Erpelding, John E.
  • Plant Breeding, Vol. 133, Issue 2
  • DOI: 10.1111/pbr.12133

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
journal, April 2011

  • Letunic, I.; Bork, P.
  • Nucleic Acids Research, Vol. 39, Issue suppl
  • DOI: 10.1093/nar/gkr201

A Pictorial Technique for Mass Screening of Sorghum Germplasm for Anthracnose (Colletotrichum sublineolum) Resistance
journal, April 2009


Population structure of the NPGS Senegalese sorghum collection and its evaluation to identify new disease resistant genes
journal, February 2018


p Athogen p Opulation g Enetics , e Volutionary p Otential, and d Urable r Esistance
journal, September 2002


Community Resources and Strategies for Association Mapping in Sorghum
journal, January 2008