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Ruperao P, Gandham P, Odeny DA, Mayes S, Selvanayagam S, Thirunavukkarasu N, Das RR, Srikanda M, Gandhi H, Habyarimana E, Manyasa E, Nebie B, Deshpande SP, Rathore A. Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources. FRONTIERS IN PLANT SCIENCE 2023; 14:1143512. [PMID: 37008459 PMCID: PMC10063887 DOI: 10.3389/fpls.2023.1143512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/22/2023] [Indexed: 06/19/2023]
Abstract
Due to evolutionary divergence, sorghum race populations exhibit significant genetic and morphological variation. A k-mer-based sorghum race sequence comparison identified the conserved k-mers of all 272 accessions from sorghum and the race-specific genetic signatures identified the gene variability in 10,321 genes (PAVs). To understand sorghum race structure, diversity and domestication, a deep learning-based variant calling approach was employed in a set of genotypic data derived from a diverse panel of 272 sorghum accessions. The data resulted in 1.7 million high-quality genome-wide SNPs and identified selective signature (both positive and negative) regions through a genome-wide scan with different (iHS and XP-EHH) statistical methods. We discovered 2,370 genes associated with selection signatures including 179 selective sweep regions distributed over 10 chromosomes. Co-localization of these regions undergoing selective pressure with previously reported QTLs and genes revealed that the signatures of selection could be related to the domestication of important agronomic traits such as biomass and plant height. The developed k-mer signatures will be useful in the future to identify the sorghum race and for trait and SNP markers for assisting in plant breeding programs.
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Affiliation(s)
- Pradeep Ruperao
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prasad Gandham
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, LA, United States
| | - Damaris A. Odeny
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sean Mayes
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Nepolean Thirunavukkarasu
- Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research (ICAR) - Indian Institute of Millets Research, Hyderabad, India
| | - Roma R. Das
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Manasa Srikanda
- Department of Statistics, Osmania University, Hyderabad, India
| | - Harish Gandhi
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Eric Manyasa
- Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Baloua Nebie
- International Maize and Wheat Improvement Center (CIMMYT), Dakar, Senegal
| | | | - Abhishek Rathore
- Excellence in Breeding, International Maize and Wheat Improvement Center (CIMMYT), Hyderabad, India
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Zhang Z, Pope M, Shakoor N, Pless R, Mockler TC, Stylianou A. Comparing Deep Learning Approaches for Understanding Genotype × Phenotype Interactions in Biomass Sorghum. Front Artif Intell 2022; 5:872858. [PMID: 35860344 PMCID: PMC9289439 DOI: 10.3389/frai.2022.872858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
We explore the use of deep convolutional neural networks (CNNs) trained on overhead imagery of biomass sorghum to ascertain the relationship between single nucleotide polymorphisms (SNPs), or groups of related SNPs, and the phenotypes they control. We consider both CNNs trained explicitly on the classification task of predicting whether an image shows a plant with a reference or alternate version of various SNPs as well as CNNs trained to create data-driven features based on learning features so that images from the same plot are more similar than images from different plots, and then using the features this network learns for genetic marker classification. We characterize how efficient both approaches are at predicting the presence or absence of a genetic markers, and visualize what parts of the images are most important for those predictions. We find that the data-driven approaches give somewhat higher prediction performance, but have visualizations that are harder to interpret; and we give suggestions of potential future machine learning research and discuss the possibilities of using this approach to uncover unknown genotype × phenotype relationships.
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Affiliation(s)
- Zeyu Zhang
- Department of Computer Science, George Washington University, Washington, DC, United States
| | - Madison Pope
- Department of Computer Science, Saint Louis University, Saint Louis, MO, United States
| | - Nadia Shakoor
- Donald Danforth Plant Science Center, Mockler Lab, Saint Louis, MO, United States
| | - Robert Pless
- Department of Computer Science, George Washington University, Washington, DC, United States
| | - Todd C. Mockler
- Donald Danforth Plant Science Center, Mockler Lab, Saint Louis, MO, United States
| | - Abby Stylianou
- Department of Computer Science, Saint Louis University, Saint Louis, MO, United States
- *Correspondence: Abby Stylianou
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Torkamaneh D, Laroche J, Valliyodan B, O'Donoughue L, Cober E, Rajcan I, Vilela Abdelnoor R, Sreedasyam A, Schmutz J, Nguyen HT, Belzile F. Soybean (Glycine max) Haplotype Map (GmHapMap): a universal resource for soybean translational and functional genomics. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:324-334. [PMID: 32794321 DOI: 10.1101/534578] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 07/24/2020] [Accepted: 08/07/2020] [Indexed: 05/27/2023]
Abstract
Here, we describe a worldwide haplotype map for soybean (GmHapMap) constructed using whole-genome sequence data for 1007 Glycine max accessions and yielding 14.9 million variants as well as 4.3 M tag single-nucleotide polymorphisms (SNPs). When sampling random subsets of these accessions, the number of variants and tag SNPs plateaued beyond approximately 800 and 600 accessions, respectively. This suggests extensive coverage of diversity within the cultivated soybean. GmHapMap variants were imputed onto 21 618 previously genotyped accessions with up to 96% success for common alleles. A local association analysis was performed with the imputed data using markers located in a 1-Mb region known to contribute to seed oil content and enabled us to identify a candidate causal SNP residing in the NPC1 gene. We determined gene-centric haplotypes (407 867 GCHs) for the 55 589 genes and showed that such haplotypes can help to identify alleles that differ in the resulting phenotype. Finally, we predicted 18 031 putative loss-of-function (LOF) mutations in 10 662 genes and illustrated how such a resource can be used to explore gene function. The GmHapMap provides a unique worldwide resource for applied soybean genomics and breeding.
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Affiliation(s)
- Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Jérôme Laroche
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
| | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Louise O'Donoughue
- CÉROM, Centre de recherche Sur Les Grains Inc., Saint-Mathieu de Beloeil, QC, Canada
| | - Elroy Cober
- Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Ricardo Vilela Abdelnoor
- Brazilian Corporation of Agricultural Research (Embrapa Soja), Warta County, PR, Brazil
- Londrina State University (UEL), Londrina, PR, Brazil
| | | | - Jeremy Schmutz
- Institute for Biotechnology, HudsonAlpha, Huntsville, AL, USA
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Henry T Nguyen
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - François Belzile
- Département de Phytologie, Université Laval, Québec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
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Faye JM, Maina F, Hu Z, Fonceka D, Cisse N, Morris GP. Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal. Ecol Evol 2019; 9:6038-6051. [PMID: 31161017 PMCID: PMC6540697 DOI: 10.1002/ece3.5187] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/22/2019] [Accepted: 03/29/2019] [Indexed: 02/01/2023] Open
Abstract
Uncovering the genomic basis of climate adaptation in traditional crop varieties can provide insight into plant evolution and facilitate breeding for climate resilience. In the African cereal sorghum (Sorghum bicolor L. [Moench]), the genomic basis of adaptation to the semiarid Sahelian zone versus the subhumid Soudanian zone is largely unknown. To address this issue, we characterized a large panel of 421 georeferenced sorghum landrace accessions from Senegal and adjacent locations at 213,916 single-nucleotide polymorphisms (SNPs) using genotyping-by-sequencing. Seven subpopulations distributed along the north-south precipitation gradient were identified. Redundancy analysis found that climate variables explained up to 8% of SNP variation, with climate collinear with space explaining most of this variation (6%). Genome scans of nucleotide diversity suggest positive selection on chromosome 2, 4, 5, 7, and 10 in durra sorghums, with successive adaptation during diffusion along the Sahel. Putative selective sweeps were identified, several of which colocalize with stay-green drought tolerance (Stg) loci, and a priori candidate genes for photoperiodic flowering and inflorescence morphology. Genome-wide association studies of photoperiod sensitivity and panicle compactness identified 35 and 13 associations that colocalize with a priori candidate genes, respectively. Climate-associated SNPs colocalize with Stg3a, Stg1, Stg2, and Ma6 and have allelic distribution consistent with adaptation across Sahelian and Soudanian zones. Taken together, the findings suggest an oligogenic basis of adaptation to Sahelian versus Soudanian climates, underpinned by variation in conserved floral regulatory pathways and other systems that are less understood in cereals.
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Affiliation(s)
- Jacques M. Faye
- Department of AgronomyKansas State UniversityManhattanKansas
| | - Fanna Maina
- Department of AgronomyKansas State UniversityManhattanKansas
- Institut National de la Recherche Agronomique du NigerNiameyNiger
| | - Zhenbin Hu
- Department of AgronomyKansas State UniversityManhattanKansas
| | - Daniel Fonceka
- Centre d'Étude Régional pour l'Amélioration de l'Adaptation à la SécheresseThièsSénégal
- CIRADUMR AGAPMontpellierFrance
| | - Ndiaga Cisse
- Centre d'Étude Régional pour l'Amélioration de l'Adaptation à la SécheresseThièsSénégal
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Dwivedi SL, Scheben A, Edwards D, Spillane C, Ortiz R. Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes. FRONTIERS IN PLANT SCIENCE 2017; 8:1461. [PMID: 28900432 PMCID: PMC5581882 DOI: 10.3389/fpls.2017.01461] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/07/2017] [Indexed: 05/03/2023]
Abstract
There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses.
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Affiliation(s)
| | - Armin Scheben
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, PerthWA, Australia
| | - David Edwards
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, PerthWA, Australia
| | - Charles Spillane
- Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland GalwayGalway, Ireland
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural SciencesAlnarp, Sweden
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