Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection
Abstract
The United States Department of Agriculture (USDA) National Plant Germplasm System (NPGS) sorghum core collection contains 3011 accessions randomly selected from 77 countries. Genomic and phenotypic characterization of this core collection is necessary to encourage and facilitate its utilization in breeding programs and to improve conservation efforts. In this study, we examined the genome sequences of 318 accessions belonging to the NPGS Sudan sorghum core set, and characterized their agronomic traits and anthracnose resistance response. We identified 183,144 single nucleotide polymorphisms (SNPs) located within or in proximity of 25,124 annotated genes using the genotyping-by-sequencing (GBS) approach. The core collection was genetically highly diverse, with an average pairwise genetic distance of 0.76 among accessions. Population structure and cluster analysis revealed five ancestral populations within the Sudan core set, with moderate to high level of genetic differentiation. In total, 171 accessions (54%) were assigned to one of these populations, which covered 96% of the total genomic variation. Genome scan based on Tajima’s D values revealed two populations under balancing selection. Phenotypic analysis showed differences in agronomic traits among the populations, suggesting that these populations belong to different ecogeographical regions. A total of 55 accessions were resistant to anthracnose; these accessions could representmore »
- Authors:
-
[1];
- USDA-ARS, Tropical Agriculture Research Station, Mayaguez, PR (United States)
- USDA-ARS, Southern Plains Agriculture Research Center, College Station, TX (United States)
- Publication Date:
- Research Org.:
- US Dept. of Agriculture (USDA), Washington, DC (United States). Agricultural Research Service (ARS)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1802575
- Grant/Contract Number:
- SC0014171
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Genomics
- Additional Journal Information:
- Journal Volume: 21; Journal Issue: 1; Journal ID: ISSN 1471-2164
- Publisher:
- Springer
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; anthracnose; population structure; genome-wide association analysis; NPGS sorghum germplasm; genotyping-by-sequencing
Citation Formats
Cuevas, Hugo E., and Prom, Louis K. Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection. United States: N. p., 2020.
Web. doi:10.1186/s12864-020-6489-0.
Cuevas, Hugo E., & Prom, Louis K. Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection. United States. https://doi.org/10.1186/s12864-020-6489-0
Cuevas, Hugo E., and Prom, Louis K. Tue .
"Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection". United States. https://doi.org/10.1186/s12864-020-6489-0. https://www.osti.gov/servlets/purl/1802575.
@article{osti_1802575,
title = {Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection},
author = {Cuevas, Hugo E. and Prom, Louis K.},
abstractNote = {The United States Department of Agriculture (USDA) National Plant Germplasm System (NPGS) sorghum core collection contains 3011 accessions randomly selected from 77 countries. Genomic and phenotypic characterization of this core collection is necessary to encourage and facilitate its utilization in breeding programs and to improve conservation efforts. In this study, we examined the genome sequences of 318 accessions belonging to the NPGS Sudan sorghum core set, and characterized their agronomic traits and anthracnose resistance response. We identified 183,144 single nucleotide polymorphisms (SNPs) located within or in proximity of 25,124 annotated genes using the genotyping-by-sequencing (GBS) approach. The core collection was genetically highly diverse, with an average pairwise genetic distance of 0.76 among accessions. Population structure and cluster analysis revealed five ancestral populations within the Sudan core set, with moderate to high level of genetic differentiation. In total, 171 accessions (54%) were assigned to one of these populations, which covered 96% of the total genomic variation. Genome scan based on Tajima’s D values revealed two populations under balancing selection. Phenotypic analysis showed differences in agronomic traits among the populations, suggesting that these populations belong to different ecogeographical regions. A total of 55 accessions were resistant to anthracnose; these accessions could represent multiple resistance sources. Genome-wide association study based on fixed and random model Circulating Probability (farmCPU) identified genomic regions associated with plant height, flowering time, panicle length and diameter, and anthracnose resistance response. Integrated analysis of the Sudan core set and sorghum association panel indicated that a large portion of the genetic variation in the Sudan core set might be present in breeding programs but remains unexploited within some clusters of accessions. The NPGS Sudan core collection comprises genetically and phenotypically diverse germplasm with multiple anthracnose resistance sources. Population genomic analysis could be used to improve screening efforts and identify the most valuable germplasm for breeding programs. The new GBS data set generated in this study represents a novel genomic resource for plant breeders interested in mining the genetic diversity of the NPGS sorghum collection.},
doi = {10.1186/s12864-020-6489-0},
journal = {BMC Genomics},
number = 1,
volume = 21,
place = {United States},
year = {Tue Jan 28 00:00:00 EST 2020},
month = {Tue Jan 28 00:00:00 EST 2020}
}
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Works referenced in this record:
Presence of tannins in sorghum grains is conditioned by different natural alleles of Tannin1
journal, June 2012
- Wu, Y.; Li, X.; Xiang, W.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 26
TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline
journal, February 2014
- Glaubitz, Jeffrey C.; Casstevens, Terry M.; Lu, Fei
- PLoS ONE, Vol. 9, Issue 2
Inheritance and molecular mapping of anthracnose resistance genes present in sorghum line SC112-14
journal, July 2014
- Cuevas, Hugo E.; Prom, Louis K.; Erpelding, John E.
- Molecular Breeding, Vol. 34, Issue 4
Genome-Wide Association Study on Resistance to Stalk Rot Diseases in Grain Sorghum
journal, April 2015
- Adeyanju, A.; Little, C.; Yu, J.
- G3: Genes|Genomes|Genetics, Vol. 5, Issue 6
Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection: implications for germplasm conservation, evaluation, and utilization in crop improvement
journal, January 2017
- Cuevas, Hugo E.; Rosa-Valentin, Giseiry; Hayes, Chad M.
- BMC Genomics, Vol. 18, Issue 1
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
journal, May 2011
- Elshire, Robert J.; Glaubitz, Jeffrey C.; Sun, Qi
- PLoS ONE, Vol. 6, Issue 5, Article No. e19379
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
hierfstat, a package for r to compute and test hierarchical F-statistics
journal, March 2005
- Goudet, Jerome
- Molecular Ecology Notes, Vol. 5, Issue 1
Core Collection of Sorghum: I. Stratification Based on Eco‐Geographical Data
journal, January 2001
- Grenier, C.; Bramel‐Cox, P. J.; Hamon, P.
- Crop Science, Vol. 41, Issue 1
Inference of Population Structure Using Multilocus Genotype Data
journal, June 2000
- Pritchard, Jonathan K.; Stephens, Matthew; Donnelly, Peter
- Genetics, Vol. 155, Issue 2
Detecting the number of clusters of individuals using the software structure: a simulation study
journal, July 2005
- Evanno, G.; Regnaut, S.; Goudet, J.
- Molecular Ecology, Vol. 14, Issue 8
Additional file 2: Table S1 of Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection: implications for germplasm conservation, evaluation, and utilization in crop improvement
dataset, January 2017
- Cuevas, Hugo; Rosa-Valentin, Giseiry; Hayes, Chad
- Figshare
Strigolactone promotes cytokinin degradation through transcriptional activation of CYTOKININ OXIDASE/DEHYDROGENASE 9 in rice
journal, June 2019
- Duan, Jingbo; Yu, Hong; Yuan, Kun
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 28
Registration of Partially Converted Germplasm from 44 Accessions of the USDA‐ARS Ethiopian and Sudanese Sorghum Collections
journal, July 2013
- Klein, R. R.; Miller, F. R.; Klein, P. E.
- Journal of Plant Registrations, Vol. 7, Issue 3
GAPIT: genome association and prediction integrated tool
journal, July 2012
- Lipka, Alexander E.; Tian, Feng; Wang, Qishan
- Bioinformatics, Vol. 28, Issue 18
Genome-Wide Association Mapping of Anthracnose ( Colletotrichum sublineolum ) Resistance in the U.S. Sorghum Association Panel
journal, July 2018
- Cuevas, Hugo E.; Prom, Louis K.; Cooper, Elizabeth A.
- The Plant Genome, Vol. 11, Issue 2
Inheritance of Anthracnose Resistance for the Sorghum Cultivar Redlan
journal, March 2007
- Erpelding, John E.
- Plant Pathology Journal, Vol. 6, Issue 2
Estimation of fixation indices and gene diversities
journal, July 1983
- Nei, M.; Chesser, R. K.
- Annals of Human Genetics, Vol. 47, Issue 3
Genome-Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm
journal, July 2016
- Boyles, Richard E.; Cooper, Elizabeth A.; Myers, Matthew T.
- The Plant Genome, Vol. 9, Issue 2
ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE
journal, November 1984
- Weir, B. S.; Cockerham, C. Clark
- Evolution, Vol. 38, Issue 6
A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement
journal, June 2001
- Upadhyaya, H. D.; Ortiz, R.
- Theoretical and Applied Genetics, Vol. 102, Issue 8
A web-based survey on various symptoms of computer vision syndrome and the genetic understanding based on a multi-trait genome-wide association study
journal, May 2021
- Yoshimura, Keito; Morita, Yuji; Konomi, Kenji
- Scientific Reports, Vol. 11, Issue 1
Variation in inflorescence architecture associated with yield components in a sorghum germplasm
journal, June 2013
- Witt Hmon, Khaing Pann; Shehzad, Tariq; Okuno, Kazutoshi
- Plant Genetic Resources, Vol. 11, Issue 3
Genome-Wide Association Study of Grain Polyphenol Concentrations in Global Sorghum [ Sorghum bicolor (L.) Moench] Germplasm
journal, October 2014
- Rhodes, Davina H.; Hoffmann, Leo; Rooney, William L.
- Journal of Agricultural and Food Chemistry, Vol. 62, Issue 45
TASSEL: software for association mapping of complex traits in diverse samples
journal, June 2007
- Bradbury, P. J.; Zhang, Z.; Kroon, D. E.
- Bioinformatics, Vol. 23, Issue 19
The USDA Barley Core Collection: Genetic Diversity, Population Structure, and Potential for Genome-Wide Association Studies
journal, April 2014
- Muñoz-Amatriaín, María; Cuesta-Marcos, Alfonso; Endelman, Jeffrey B.
- PLoS ONE, Vol. 9, Issue 4
Genome-Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm
journal, July 2016
- Boyles, Richard E.; Cooper, Elizabeth A.; Myers, Matthew T.
- The Plant Genome, Vol. 9, Issue 2
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
Comparison of Representative and Custom Methods of Generating Core Subsets of a Carrot Germplasm Collection
journal, May 2019
- Corak, K. E.; Ellison, S. L.; Simon, P. W.
- Crop Science, Vol. 59, Issue 3
Population structure and strong divergent selection shape phenotypic diversification in maize landraces
journal, December 2003
- Pressoir, G.; Berthaud, J.
- Heredity, Vol. 92, Issue 2
Core Collection of Sorghum: II. Comparison of Three Random Sampling Strategies
journal, January 2001
- Grenier, C.; Hamon, P.; Bramel‐Cox, P. J.
- Crop Science, Vol. 41, Issue 1
Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants
journal, May 2016
- Uricchio, Lawrence H.; Zaitlen, Noah A.; Ye, Chun Jimmie
- Genome Research, Vol. 26, Issue 7
Genome-environment associations in sorghum landraces predict adaptive traits
text, January 2015
- Lasky, Jesse R.; Upadhyaya, Hari D.; Ramu, Punna
- Columbia University
Identification of diverse germplasm lines for agronomic traits in a chickpea (Cicer arietinum L.) core collection for use in crop improvement
journal, February 2007
- Upadhyaya, H. D.; Dwivedi, S. L.; Gowda, C. L. L.
- Field Crops Research, Vol. 100, Issue 2-3
Transcriptomic and genome-wide association study reveal long noncoding RNAs responding to nitrogen deficiency in maize
journal, February 2021
- Ma, Peng; Zhang, Xiao; Luo, Bowen
- BMC Plant Biology, Vol. 21, Issue 1
Genome-Wide Association Mapping of Anthracnose ( Colletotrichum sublineolum ) Resistance in the U.S. Sorghum Association Panel
journal, July 2018
- Cuevas, Hugo E.; Prom, Louis K.; Cooper, Elizabeth A.
- The Plant Genome, Vol. 11, Issue 2
GWAS analysis of sorghum association panel lines identifies SNPs associated with disease response to Texas isolates of Colletotrichum sublineola
journal, January 2019
- Prom, Louis K.; Ahn, Ezekiel; Isakeit, Thomas
- Theoretical and Applied Genetics, Vol. 132, Issue 5
Status and Prospects of Association Mapping in Plants
journal, January 2008
- Zhu, Chengsong; Gore, Michael; Buckler, Edward S.
- The Plant Genome Journal, Vol. 1, Issue 1
Classification and inheritance of genetic resistance to anthracnose in sorghum
journal, July 2005
- Mehta, Pushpak J.; Wiltse, Curtis C.; Rooney, William L.
- Field Crops Research, Vol. 93, Issue 1
Population genomics of sorghum ( Sorghum bicolor ) across diverse agroclimatic zones of Niger
journal, April 2018
- Maina, Fanna; Bouchet, Sophie; Marla, Sandeep R.
- Genome, Vol. 61, Issue 4
Core collections: a practical approach to genetic resources management
journal, January 1989
- Brown, A. H. D.
- Genome, Vol. 31, Issue 2
A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy
journal, June 2016
- Brenton, Zachary W.; Cooper, Elizabeth A.; Myers, Mathew T.
- Genetics, Vol. 204, Issue 1
Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies
journal, February 2016
- Liu, Xiaolei; Huang, Meng; Fan, Bin
- PLOS Genetics, Vol. 12, Issue 2
Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures
journal, September 2015
- Zhu, Bo; Zhang, Wenli; Zhang, Tao
- The Plant Cell, Vol. 27, Issue 9
Sequencing of an Anthracnose-Resistant Sorghum Genotype and Mapping of a Major QTL Reveal Strong Candidate Genes for Anthracnose Resistance
journal, March 2015
- Burrell, A. Millie; Sharma, Arun; Patil, Nikhil Y.
- Crop Science, Vol. 55, Issue 2
Registration of Partially Converted Germplasm from 44 Accessions of the USDA‐ARS Ethiopian and Sudanese Sorghum Collections
journal, July 2013
- Klein, R. R.; Miller, F. R.; Klein, P. E.
- Journal of Plant Registrations, Vol. 7, Issue 3
SSR individual identification system construction and population genetics analysis for Chamaecyparis formosensis
journal, March 2022
- Huang, Chiun-Jr; Chu, Fang-Hua; Huang, Yi-Shiang
- Scientific Reports, Vol. 12, Issue 1
Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection: implications for germplasm conservation, evaluation, and utilization in crop improvement
journal, January 2017
- Cuevas, Hugo E.; Rosa-Valentin, Giseiry; Hayes, Chad M.
- BMC Genomics, Vol. 18, Issue 1
The Ensembl Variant Effect Predictor
journal, June 2016
- McLaren, William; Gil, Laurent; Hunt, Sarah E.
- Genome Biology, Vol. 17, Issue 1
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
Detecting the Genetic Signature of Natural Selection in Human Populations: Models, Methods, and Data
journal, October 2008
- Hancock, Angela M.; Di Rienzo, Anna
- Annual Review of Anthropology, Vol. 37, Issue 1
Registration of 40 Converted Germplasm Sources from the Reinstated Sorghum Conversion Program
journal, December 2015
- Klein, R. R.; Miller, F. R.; Bean, S.
- Journal of Plant Registrations, Vol. 10, Issue 1
Conserved Noncoding Sequences among Cultivated Cereal Genomes Identify Candidate Regulatory Sequence Elements and Patterns of Promoter Evolution
journal, April 2003
- Guo, Hena; Moose, Stephen P.
- The Plant Cell, Vol. 15, Issue 5
Inheritance of Resistance of Three Sorghum Lines to Pathotypes of Colletotrichum sublineola, Causal Agent of Anthracnose
journal, April 2018
- K. Prom, Louis; Cuevas, Hugo; Perumal, Ramasamy
- Plant Pathology Journal, Vol. 17, Issue 2
Population structure of the NPGS Senegalese sorghum collection and its evaluation to identify new disease resistant genes
journal, February 2018
- Cuevas, Hugo E.; Prom, Louis K.; Rosa-Valentin, Giseiry
- PLOS ONE, Vol. 13, Issue 2
Community Resources and Strategies for Association Mapping in Sorghum
journal, January 2008
- Casa, Alexandra M.; Pressoir, Gael; Brown, Patrick J.
- Crop Science, Vol. 48, Issue 1
hierfstat, a package for r to compute and test hierarchical F-statistics
journal, March 2005
- Goudet, Jerome
- Molecular Ecology Notes, Vol. 5, Issue 1
qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots
journal, May 2018
- D. Turner, Stephen
- Journal of Open Source Software, Vol. 3, Issue 25
Analysis of cardiac magnetic resonance imaging in 36,000 individuals yields genetic insights into dilated cardiomyopathy
journal, May 2020
- Pirruccello, James P.; Bick, Alexander; Wang, Minxian
- Nature Communications, Vol. 11, Issue 1
A sorghum NAC gene is associated with variation in biomass properties and yield potential
journal, July 2018
- Xia, Jingnu; Zhao, Yunjun; Burks, Payne
- Plant Direct, Vol. 2, Issue 7
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
TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline
journal, February 2014
- Glaubitz, Jeffrey C.; Casstevens, Terry M.; Lu, Fei
- PLoS ONE, Vol. 9, Issue 2
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
Detecting the Genetic Signature of Natural Selection in Human Populations: Models, Methods, and Data
journal, October 2008
- Hancock, Angela M.; Di Rienzo, Anna
- Annual Review of Anthropology, Vol. 37, Issue 1
Registration of 40 Converted Germplasm Sources from the Reinstated Sorghum Conversion Program
journal, December 2015
- Klein, R. R.; Miller, F. R.; Bean, S.
- Journal of Plant Registrations, Vol. 10, Issue 1
A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement
journal, June 2001
- Upadhyaya, H. D.; Ortiz, R.
- Theoretical and Applied Genetics, Vol. 102, Issue 8
In situ estimation of outcrossing rate in sorghum landraces using microsatellite markers
journal, August 2004
- Djè, Yao; Heuertz, Myriam; Ater, Mohamed
- Euphytica, Vol. 138, Issue 3
Presence of tannins in sorghum grains is conditioned by different natural alleles of Tannin1
journal, June 2012
- Wu, Y.; Li, X.; Xiang, W.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 26
A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy
journal, June 2016
- Brenton, Zachary W.; Cooper, Elizabeth A.; Myers, Mathew T.
- Genetics, Vol. 204, Issue 1
Quantitative Trait Loci Associated with Anthracnose Resistance in Sorghum
journal, February 2017
- Patil, Nikhil Y.; Klein, Robert R.; Williams, Crescenda L.
- Crop Science, Vol. 57, Issue 2
Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal
journal, April 2019
- Faye, Jacques M.; Maina, Fanna; Hu, Zhenbin
- Ecology and Evolution, Vol. 9, Issue 10
Population structure of the NPGS Senegalese sorghum collection and its evaluation to identify new disease resistant genes
journal, February 2018
- Cuevas, Hugo E.; Prom, Louis K.; Rosa-Valentin, Giseiry
- PLOS ONE, Vol. 13, Issue 2
Sequencing of an Anthracnose-Resistant Sorghum Genotype and Mapping of a Major QTL Reveal Strong Candidate Genes for Anthracnose Resistance
journal, March 2015
- Burrell, A. Millie; Sharma, Arun; Patil, Nikhil Y.
- Crop Science, Vol. 55, Issue 2
Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies
journal, February 2016
- Liu, Xiaolei; Huang, Meng; Fan, Bin
- PLOS Genetics, Vol. 12, Issue 2
Sorghum Dw2 Encodes a Protein Kinase Regulator of Stem Internode Length
journal, July 2017
- Hilley, Josie L.; Weers, Brock D.; Truong, Sandra K.
- Scientific Reports, Vol. 7, Issue 1
Conserved Noncoding Sequences among Cultivated Cereal Genomes Identify Candidate Regulatory Sequence Elements and Patterns of Promoter Evolution
journal, April 2003
- Guo, Hena; Moose, Stephen P.
- The Plant Cell, Vol. 15, Issue 5
Genome-Wide Association Mapping of Anthracnose ( Colletotrichum sublineolum ) Resistance in NPGS Ethiopian Sorghum Germplasm
journal, September 2019
- Cuevas, Hugo E.; Prom, Louis K.; Cruet-Burgos, Clara M.
- G3 Genes|Genomes|Genetics, Vol. 9, Issue 9
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
ADZE: a rarefaction approach for counting alleles private to combinations of populations
journal, September 2008
- Szpiech, Z. A.; Jakobsson, M.; Rosenberg, N. A.
- Bioinformatics, Vol. 24, Issue 21
STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method
journal, October 2011
- Earl, Dent A.; vonHoldt, Bridgett M.
- Conservation Genetics Resources, Vol. 4, Issue 2
Core Collection of Sorghum: I. Stratification Based on Eco‐Geographical Data
journal, January 2001
- Grenier, C.; Bramel‐Cox, P. J.; Hamon, P.
- Crop Science, Vol. 41, Issue 1
Genome-environment associations in sorghum landraces predict adaptive traits
journal, July 2015
- Lasky, Jesse R.; Upadhyaya, Hari D.; Ramu, Punna
- Science Advances, Vol. 1, Issue 6
Status and Prospects of Association Mapping in Plants
journal, January 2008
- Zhu, Chengsong; Gore, Michael; Buckler, Edward S.
- The Plant Genome Journal, Vol. 1, Issue 1
Genome-Wide Association Study of Grain Polyphenol Concentrations in Global Sorghum [ Sorghum bicolor (L.) Moench] Germplasm
journal, October 2014
- Rhodes, Davina H.; Hoffmann, Leo; Rooney, William L.
- Journal of Agricultural and Food Chemistry, Vol. 62, Issue 45
Genome‐Wide Association Mapping of Grain Mold Resistance in the US Sorghum Association Panel
journal, June 2019
- Cuevas, Hugo E.; Fermin‐Pérez, Ramon A.; Prom, Louis K.
- The Plant Genome, Vol. 12, Issue 2
Classification and inheritance of genetic resistance to anthracnose in sorghum
journal, July 2005
- Mehta, Pushpak J.; Wiltse, Curtis C.; Rooney, William L.
- Field Crops Research, Vol. 93, Issue 1
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
Comparison of Representative and Custom Methods of Generating Core Subsets of a Carrot Germplasm Collection
journal, May 2019
- Corak, K. E.; Ellison, S. L.; Simon, P. W.
- Crop Science, Vol. 59, Issue 3
Development of a Sorghum Core Collection: Refinement and Evaluation of a Subset from Sudan
journal, December 2004
- Dahlberg, J. A.; Burke, J. J.; Rosenow, D. T.
- Economic Botany, Vol. 58, Issue 4
The USDA Barley Core Collection: Genetic Diversity, Population Structure, and Potential for Genome-Wide Association Studies
journal, April 2014
- Muñoz-Amatriaín, María; Cuesta-Marcos, Alfonso; Endelman, Jeffrey B.
- PLoS ONE, Vol. 9, Issue 4
Genome‐Wide Association Mapping of Grain Mold Resistance in the US Sorghum Association Panel
journal, June 2019
- Cuevas, Hugo E.; Fermin‐Pérez, Ramon A.; Prom, Louis K.
- The Plant Genome, Vol. 12, Issue 2
CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure
journal, May 2007
- Jakobsson, M.; Rosenberg, N. A.
- Bioinformatics, Vol. 23, Issue 14
Conversion of Alien Sorghums to Early Combine Genotypes1
journal, January 1967
- Stephens, J. C.; Miller, F. R.; Rosenow, D. T.
- Crop Science, Vol. 7, Issue 4
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
Genome-environment associations in sorghum landraces predict adaptive traits
journal, July 2015
- Lasky, Jesse R.; Upadhyaya, Hari D.; Ramu, Punna
- Science Advances, Vol. 1, Issue 6
Estimation of fixation indices and gene diversities
journal, July 1983
- Nei, M.; Chesser, R. K.
- Annals of Human Genetics, Vol. 47, Issue 3
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens
journal, March 2021
- Papalexi, Efthymia; Mimitou, Eleni P.; Butler, Andrew W.
- Nature Genetics, Vol. 53, Issue 3
A Simplified Classification of Cultivated Sorghum1
journal, January 1972
- Harlan, J. R.; de Wet, J. M. J.
- Crop Science, Vol. 12, Issue 2
Core collections: a practical approach to genetic resources management
journal, January 1989
- Brown, A. H. D.
- Genome, Vol. 31, Issue 2
Inheritance of Anthracnose Resistance for the Sorghum Cultivar Redlan
journal, March 2007
- Erpelding, John E.
- Plant Pathology Journal, Vol. 6, Issue 2
Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought
journal, September 2018
- Spindel, Jennifer E.; Dahlberg, Jeffery; Colgan, Matthew
- BMC Genomics, Vol. 19, Issue 1
GWAS analysis of sorghum association panel lines identifies SNPs associated with disease response to Texas isolates of Colletotrichum sublineola
journal, January 2019
- Prom, Louis K.; Ahn, Ezekiel; Isakeit, Thomas
- Theoretical and Applied Genetics, Vol. 132, Issue 5
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
Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures
journal, September 2015
- Zhu, Bo; Zhang, Wenli; Zhang, Tao
- The Plant Cell, Vol. 27, Issue 9
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
journal, May 2011
- Elshire, Robert J.; Glaubitz, Jeffrey C.; Sun, Qi
- PLoS ONE, Vol. 6, Issue 5, Article No. e19379
Comprehensive genotyping of the USA national maize inbred seed bank
journal, June 2013
- Romay, Maria C.; Millard, Mark J.; Glaubitz, Jeffrey C.
- Genome Biology, Vol. 14, Issue 6
Core Collection of Sorghum: II. Comparison of Three Random Sampling Strategies
journal, January 2001
- Grenier, C.; Hamon, P.; Bramel‐Cox, P. J.
- Crop Science, Vol. 41, Issue 1
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
Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants
journal, May 2016
- Uricchio, Lawrence H.; Zaitlen, Noah A.; Ye, Chun Jimmie
- Genome Research, Vol. 26, Issue 7
TASSEL: software for association mapping of complex traits in diverse samples
journal, June 2007
- Bradbury, P. J.; Zhang, Z.; Kroon, D. E.
- Bioinformatics, Vol. 23, Issue 19
Inheritance and molecular mapping of anthracnose resistance genes present in sorghum line SC112-14
journal, July 2014
- Cuevas, Hugo E.; Prom, Louis K.; Erpelding, John E.
- Molecular Breeding, Vol. 34, Issue 4
Inference of Population Structure Using Multilocus Genotype Data
journal, June 2000
- Pritchard, Jonathan K.; Stephens, Matthew; Donnelly, Peter
- Genetics, Vol. 155, Issue 2