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Pugh NA, Young A, Ojha M, Emendack Y, Sanchez J, Xin Z, Puppala N. Yield prediction in a peanut breeding program using remote sensing data and machine learning algorithms. Front Plant Sci 2024; 15:1339864. [PMID: 38444530 PMCID: PMC10912196 DOI: 10.3389/fpls.2024.1339864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/02/2024] [Indexed: 03/07/2024]
Abstract
Peanut is a critical food crop worldwide, and the development of high-throughput phenotyping techniques is essential for enhancing the crop's genetic gain rate. Given the obvious challenges of directly estimating peanut yields through remote sensing, an approach that utilizes above-ground phenotypes to estimate underground yield is necessary. To that end, this study leveraged unmanned aerial vehicles (UAVs) for high-throughput phenotyping of surface traits in peanut. Using a diverse set of peanut germplasm planted in 2021 and 2022, UAV flight missions were repeatedly conducted to capture image data that were used to construct high-resolution multitemporal sigmoidal growth curves based on apparent characteristics, such as canopy cover and canopy height. Latent phenotypes extracted from these growth curves and their first derivatives informed the development of advanced machine learning models, specifically random forest and eXtreme Gradient Boosting (XGBoost), to estimate yield in the peanut plots. The random forest model exhibited exceptional predictive accuracy (R2 = 0.93), while XGBoost was also reasonably effective (R2 = 0.88). When using confusion matrices to evaluate the classification abilities of each model, the two models proved valuable in a breeding pipeline, particularly for filtering out underperforming genotypes. In addition, the random forest model excelled in identifying top-performing material while minimizing Type I and Type II errors. Overall, these findings underscore the potential of machine learning models, especially random forests and XGBoost, in predicting peanut yield and improving the efficiency of peanut breeding programs.
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Affiliation(s)
- N. Ace Pugh
- United States Department of Agriculture, Crop Stress Research Laboratory, Lubbock, TX, United States
| | - Andrew Young
- United States Department of Agriculture, Crop Stress Research Laboratory, Lubbock, TX, United States
| | - Manisha Ojha
- Agricultural Science Center at Clovis, New Mexico State University, Clovis, NM, United States
| | - Yves Emendack
- United States Department of Agriculture, Crop Stress Research Laboratory, Lubbock, TX, United States
| | - Jacobo Sanchez
- United States Department of Agriculture, Crop Stress Research Laboratory, Lubbock, TX, United States
| | - Zhanguo Xin
- United States Department of Agriculture, Crop Stress Research Laboratory, Lubbock, TX, United States
| | - Naveen Puppala
- Agricultural Science Center at Clovis, New Mexico State University, Clovis, NM, United States
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2
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Triplett E, Hayes C, Emendack Y, Longing S, Monclova C, Simpson C, Laza HE. Leaf structural traits mediating pre-existing physical innate resistance to sorghum aphid in sorghum under uninfested conditions. Planta 2023; 258:46. [PMID: 37468707 DOI: 10.1007/s00425-023-04194-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/23/2023] [Indexed: 07/21/2023]
Abstract
KEY MESSAGE We found four indicative traits of innate immunity. Sorghum-resistant varieties had a greater trichome, stomatal and chloroplast density, and smaller mesophyll intercellular width than susceptible varieties. The sorghum aphid (SA), Melanaphis sorghi (Theobald), can severely reduce sorghum yield. The contribution of structural traits to SA resistance has not been extensively studied. Moreover, the current screening method for resistance is inherently subjective for resistance and requires infestation in plants. Quantifying the microanatomical basis of innate SA resistance is crucial for developing reliable screening tools requiring no infestation. The goal of this study was to identify structural traits linked to physical innate SA resistance in sorghum. We conducted controlled environment and field experiments under no SA infestation conditions, with two resistant (R. LBK1 and R. Tx2783) and two susceptible (R. Tx7000 and R. Tx430) varieties. Leaf tissues collected at the fifth leaf stage in the controlled environment experiment were analyzed for the epidermal and mesophyll traits using light and transmission electron microscopy. Leaf tissues collected at physiological maturity in the field experiment were analyzed for surface traits using scanning electron microscopy. Our results showed that stomatal density, trichome density, trichome length, and chloroplast density are key leaf structural traits indicative of physical innate SA resistance. We found that resistant varieties had a greater density of trichomes (39%), stomata (31%), and chloroplast (42%), and smaller mesophyll intercellular width (- 52%) than susceptible varieties. However, the chloroplast, mitochondria, and epidermal cell ultrastructural traits were ineffective indicators of SA resistance. Our findings provide the foundation for developing an objective high-throughput method for SA resistance screening. We suggest a follow-up validation experiment to confirm our outcomes under SA infestation conditions.
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Affiliation(s)
- Ethan Triplett
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Chad Hayes
- Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA
| | - Yves Emendack
- Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA
| | - Scott Longing
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | | | - Catherine Simpson
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Haydee E Laza
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
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Sm I, Bean S, loerger B, Hayes C, Emendack Y, Svk J. Comparative assessment of grain quality in tannin versus non‐tannin sorghums in the sorghum association panel. Cereal Chem 2023. [DOI: 10.1002/cche.10643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Impa Sm
- Department of Plant and Soil ScienceTexas Tech UniversityLubbockTX79410USA
| | - S.R. Bean
- Center for Grain and Animal Health Research, USDA‐ARSManhattanKS66502
| | - B.P. loerger
- Center for Grain and Animal Health Research, USDA‐ARSManhattanKS66502
| | - C Hayes
- USDA‐ARS, Cropping Systems Research LabLubbockTX79415USA
| | - Y Emendack
- USDA‐ARS, Cropping Systems Research LabLubbockTX79415USA
| | - Jagadish Svk
- Department of Plant and Soil ScienceTexas Tech UniversityLubbockTX79410USA
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Gladman N, Olson A, Wei S, Chougule K, Lu Z, Tello-Ruiz M, Meijs I, Van Buren P, Jiao Y, Wang B, Kumar V, Kumari S, Zhang L, Burke J, Chen J, Burow G, Hayes C, Emendack Y, Xin Z, Ware D. SorghumBase: a web-based portal for sorghum genetic information and community advancement. Planta 2022; 255:35. [PMID: 35015132 PMCID: PMC8752523 DOI: 10.1007/s00425-022-03821-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/27/2021] [Indexed: 05/05/2023]
Abstract
SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Public research and development in agriculture rely on proper data and resource sharing within stakeholder communities. For plant breeders, agronomists, molecular biologists, geneticists, and bioinformaticians, centralizing desirable data into a user-friendly hub for crop systems is essential for successful collaborations and breakthroughs in germplasm development. Here, we present the SorghumBase web portal ( https://www.sorghumbase.org ), a resource for the sorghum research community. SorghumBase hosts a wide range of sorghum genomic information in a modular framework, built with open-source software, to provide a sustainable platform. This initial release of SorghumBase includes: (1) five sorghum reference genome assemblies in a pan-genome browser; (2) genetic variant information for natural diversity panels and ethyl methanesulfonate (EMS)-induced mutant populations; (3) search interface and integrated views of various data types; (4) links supporting interconnectivity with other repositories including genebank, QTL, and gene expression databases; and (5) a content management system to support access to community news and training materials. SorghumBase offers sorghum investigators improved data collation and access that will facilitate the growth of a robust research community to support genomics-assisted breeding.
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Affiliation(s)
- Nicholas Gladman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Zhenyuan Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | | | - Ivar Meijs
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Peter Van Buren
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Yinping Jiao
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, 79409, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Vivek Kumar
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - John Burke
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX, 79415, USA
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX, 79415, USA
| | - Gloria Burow
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX, 79415, USA
| | - Chad Hayes
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX, 79415, USA
| | - Yves Emendack
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX, 79415, USA
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX, 79415, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
- U.S. Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, 14853, USA.
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Chaudhuri S, Roy M, McDonald LM, Emendack Y. Coping Behaviours and the concept of Time Poverty: a review of perceived social and health outcomes of food insecurity on women and children. Food Secur 2021. [DOI: 10.1007/s12571-021-01171-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Emendack Y, Sanchez J, Hayes C, Nesbitt M, Laza H, Burke J. Seed-to-seed early-season cold resiliency in sorghum. Sci Rep 2021; 11:7801. [PMID: 33833364 PMCID: PMC8032771 DOI: 10.1038/s41598-021-87450-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 11/14/2022] Open
Abstract
Early planted sorghum usually experiences cooler day/night temperatures, which may result in delayed growth, floral initiation, and infertile pollen, limiting productivity in high altitudes and temperate regions. Genetic variability for cold tolerance in sorghum has been evaluated by characterizing germination, emergence, vigor, and seedling growth under sub-optimal temperatures. However, the compounded effect of early season cold on plant growth and development and subsequent variability in potential grain yield losses has not been evaluated. Agro-morphological and physiological responses of sorghum grown under early-, mid-, and standard planting dates in West Texas were characterized from seed-to-seed. A set of diverse lines and hybrids with two major sources of tolerance, and previously selected for seedling cold tolerance were used. These were evaluated with a standard commercial hybrid known for its seedling cold tolerance and some cold susceptible breeding lines as checks. Variabilities in assessed parameters at seedling, early vegetative, and maturity stages were observed across planting dates for genotypes and sources of cold tolerance. Panicle initiation was delayed, and panicle size reduced, resulting in decreased grain yields under early and mid-planting dates. Coupled with final germination percent, panicle width and area were significant unique predictors of yield under early and mid-planting dates. Significant variability in performance was observed not only between cold tolerant and susceptible checks, but noticeably between sources of cold tolerance, with the Ethiopian highland sources having lesser yield penalties than their Chinese counterparts. Thus, screening for cold tolerance should not be limited to early seedling characterization but should also consider agronomic traits that may affect yield penalties depending on the sources of tolerance.
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Affiliation(s)
- Yves Emendack
- Cropping Systems Research Laboratory, USDA-ARS, 3810 4th Street, Lubbock, TX, USA.
| | - Jacobo Sanchez
- Cropping Systems Research Laboratory, USDA-ARS, 3810 4th Street, Lubbock, TX, USA
| | - Chad Hayes
- Cropping Systems Research Laboratory, USDA-ARS, 3810 4th Street, Lubbock, TX, USA
| | - Matthew Nesbitt
- Cropping Systems Research Laboratory, USDA-ARS, 3810 4th Street, Lubbock, TX, USA
| | - Haydee Laza
- Department of Plant and Soil Sciences, Texas Tech University, Lubbock, TX, USA
| | - John Burke
- Cropping Systems Research Laboratory, USDA-ARS, 3810 4th Street, Lubbock, TX, USA
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Naoura G, Emendack Y, Baloua N, Vom Brocke K, Hassan MA, Sawadogo N, Doyam Nodjasse A, Djinodji R, Trouche G, Echevarria Laza H. Characterization of semi-arid Chadian sweet sorghum accessions as potential sources for sugar and ethanol production. Sci Rep 2020; 10:14947. [PMID: 32917934 PMCID: PMC7486407 DOI: 10.1038/s41598-020-71506-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 07/08/2020] [Indexed: 11/24/2022] Open
Abstract
Sweet sorghum (Sorghum bicolor (L.) Moench) is an important crop in Chad that plays an economic role in the countryside were stalks are produced mainly for human consumption without any processing. Unfortunately, very little information exists on its genetic diversity and brix content. Studies performed in 2014 and 2015 showed that there were significant variations (p < 0.001) for all assessed quantitative traits. Potential grain yield (0.12–1.67 t ha−1), days to 50% flowering (68.3–126.3 days), and plant height (128.9–298.3 cm) were among traits that exhibited broader variability. Brix content range from 5.5 to 16.7% across accessions, was positively correlated to stalk diameter and plant height, but negatively correlated to moisture content in fresh stalk and potential grain yield. Fresh stalk yield range from 16.8 to 115.7 Mg ha−1, with a mean value of 58.3 Mg ha−1 across accession. Moisture content in fresh stalk range from 33.7 to 74.4% but was negatively correlated to fresh stalk yield. Potential sugar yield range from 0.5 to 5.3 Mg ha−1 across accession with an average of 2.2 Mg ha−1. Theoretical ethanol yield range from 279.5 to 3,101.2 L ha−1 across accession with an average of 1,266.3 L ha−1 which is significantly higher than values reported under similar semiarid conditions. Overall, grain yields were comparatively low. However, two accessions had grain yield of more than 1.5 t ha−1; which is greater than the average 1.0 t ha−1 for local grain sorghum varieties in Chad. These could have multi-purpose uses; grains, sugar and bioenergy production.
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Affiliation(s)
- Gapili Naoura
- Institut Tchadien de Recherche Agronomique Pour le Développement (ITRAD), B.P. 5400, N'Djaména, Chad
| | - Yves Emendack
- Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA.
| | - Nébié Baloua
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Bamako, Mali
| | - Kirsten Vom Brocke
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, 34090, Montpellier, France.,CIRAD, UMR AGAP, 34398, Montpellier, France
| | - Mahamat Alhabib Hassan
- Institut Tchadien de Recherche Agronomique Pour le Développement (ITRAD), B.P. 5400, N'Djaména, Chad
| | - Nerbewende Sawadogo
- Laboratoire Biosciences, Équipe Génétique et Amélioration des Plantes, Université Joseph KI-ZERBO, 03 BP 7021, Ouagadougou 03, Burkina Faso
| | - Amos Doyam Nodjasse
- Institut Tchadien de Recherche Agronomique Pour le Développement (ITRAD), B.P. 5400, N'Djaména, Chad
| | - Reoungal Djinodji
- Institut Tchadien de Recherche Agronomique Pour le Développement (ITRAD), B.P. 5400, N'Djaména, Chad
| | - Gilles Trouche
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, 34090, Montpellier, France.,CIRAD, UMR AGAP, 34398, Montpellier, France
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Mauget S, Kothari K, Leiker G, Emendack Y, Xin Z, Hayes C, Ale S, Louis Baumhardt R. Optimizing Dryland Crop Management to Regional Climate. Part II: U.S. Southern High Plains Grain Sorghum Production. Front Sustain Food Syst 2020. [DOI: 10.3389/fsufs.2019.00119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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9
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Naoura G, Sawadogo N, Atchozou EA, Emendack Y, Hassan MA, Reoungal D, Amos DN, Djirabaye N, Tabo R, Laza H. Assessment of agro-morphological variability of dry-season sorghum cultivars in Chad as novel sources of drought tolerance. Sci Rep 2019; 9:19581. [PMID: 31863053 PMCID: PMC6925278 DOI: 10.1038/s41598-019-56192-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/08/2019] [Indexed: 11/17/2022] Open
Abstract
Dry-season sorghum is a type of sorghum whose establishment ends at the end of the rainy season and its development takes place during the dry and cold harmattan period. Its root system is particularly well developed with deep penetration for water withdrawal. This study was conducted to assess the level of genetic diversity present among dry-season sorghum in Chad’s Sudanese zone using phenotypic traits, and to identify new sources of drought tolerance that could be used in sorghum breeding programs. A high variability in qualitative traits was observed except for the botanical race which showed that all cultivars were of durra race. It was also observed that most cultivars had compact panicles (66.67%), mostly black glumes (66.67%), glume hairiness (58.33%) and did not have aristation (91.67%). Most qualitative traits showed a coefficient of variation of less than 30%, and the analysis of the variance showed that at 0.1% probability, there were significant differences between cultivars for all traits except botanical race. It was observed that the potential productivity of dry-season sorghum of this collection was strongly related to their staygreen characteristic; a trait of enormous importance in breeding for postflowering drought tolerance in sorghum. Plant height was highly heritable (91.9%), followed by the peduncle length (90.2%), panicle length (87.5%) and the internodes number (86.5%). Structuring of diversity separated the cultivars into four statistically distinct groups; with group 2 clustering cultivars with panicle productivity, early maturity and high staygreen, and other traits that contribute to the performance of cultivars. The findings will help to enhance the selection and production of dry-season sorghum in Chad and also provide alternative sources for staygreen introgression into the larger sorghum breeding community.
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Affiliation(s)
- Gapili Naoura
- Institut Tchadien de Recherche Agronomique pour le Développement (ITRAD), B.P. 5400, N'Djaména, Tchad
| | - Nerbewende Sawadogo
- Equipe Génétique et Amélioration des plantes, Laboratoire Biosciences, Université Ouaga I Pr Joseph KI-ZERBO 03 BP 7021, Ouagadougou, 03, Burkina Faso
| | | | - Yves Emendack
- USDA-ARS, Cropping Systems Research Laboratory, Lubbock, TX, USA.
| | - Mahamat A Hassan
- Institut Tchadien de Recherche Agronomique pour le Développement (ITRAD), B.P. 5400, N'Djaména, Tchad
| | - Djinodji Reoungal
- Institut Tchadien de Recherche Agronomique pour le Développement (ITRAD), B.P. 5400, N'Djaména, Tchad
| | - Doyam N Amos
- Institut Tchadien de Recherche Agronomique pour le Développement (ITRAD), B.P. 5400, N'Djaména, Tchad
| | - Nadjiam Djirabaye
- Institut Tchadien de Recherche Agronomique pour le Développement (ITRAD), B.P. 5400, N'Djaména, Tchad
| | - Ramadjita Tabo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Bamako, BP 320, Bamako, Mali
| | - Haydee Laza
- USDA-ARS, Cropping Systems Research Laboratory, Lubbock, TX, USA
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Emendack Y, Burke J, Bean S, Wilson J, Hayes C, Laza H. Composition, functional components, and physical characteristics of grain from staygreen and senescent sorghum lines grown under variable water availability. Cereal Chem 2018. [DOI: 10.1002/cche.10077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yves Emendack
- Plant Stress and Germplasm Development Research; USDA-ARS; Lubbock Texas
| | - John Burke
- Plant Stress and Germplasm Development Research; USDA-ARS; Lubbock Texas
| | - Scott Bean
- Grain Quality and Structure Research; USDA-ARS; Manhattan Kansas
| | - Jeff Wilson
- Grain Quality and Structure Research; USDA-ARS; Manhattan Kansas
| | - Chad Hayes
- Plant Stress and Germplasm Development Research; USDA-ARS; Lubbock Texas
| | - Haydee Laza
- Plant and Soil Science Department; Texas Tech University; Lubbock Texas
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Jiao Y, Burke J, Chopra R, Burow G, Chen J, Wang B, Hayes C, Emendack Y, Ware D, Xin Z. A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses. Plant Cell 2016; 28:1551-62. [PMID: 27354556 PMCID: PMC4981137 DOI: 10.1105/tpc.16.00373] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/23/2016] [Accepted: 06/23/2016] [Indexed: 05/20/2023]
Abstract
Sorghum (Sorghum bicolor) is a versatile C4 crop and a model for research in family Poaceae. High-quality genome sequence is available for the elite inbred line BTx623, but functional validation of genes remains challenging due to the limited genomic and germplasm resources available for comprehensive analysis of induced mutations. In this study, we generated 6400 pedigreed M4 mutant pools from EMS-mutagenized BTx623 seeds through single-seed descent. Whole-genome sequencing of 256 phenotyped mutant lines revealed >1.8 million canonical EMS-induced mutations, affecting >95% of genes in the sorghum genome. The vast majority (97.5%) of the induced mutations were distinct from natural variations. To demonstrate the utility of the sequenced sorghum mutant resource, we performed reverse genetics to identify eight genes potentially affecting drought tolerance, three of which had allelic mutations and two of which exhibited exact cosegregation with the phenotype of interest. Our results establish that a large-scale resource of sequenced pedigreed mutants provides an efficient platform for functional validation of genes in sorghum, thereby accelerating sorghum breeding. Moreover, findings made in sorghum could be readily translated to other members of the Poaceae via integrated genomics approaches.
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Affiliation(s)
- Yinping Jiao
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - John Burke
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415
| | - Ratan Chopra
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415
| | - Gloria Burow
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Chad Hayes
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415
| | - Yves Emendack
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 U.S. Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York 14853
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415
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Chopra R, Burow G, Hayes C, Emendack Y, Xin Z, Burke J. Transcriptome profiling and validation of gene based single nucleotide polymorphisms (SNPs) in sorghum genotypes with contrasting responses to cold stress. BMC Genomics 2015; 16:1040. [PMID: 26645959 PMCID: PMC4673766 DOI: 10.1186/s12864-015-2268-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 12/01/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Sorghum is a versatile cereal crop, with excellent heat and drought tolerance. However, it is susceptible to early-season cold stress (12-15 °C) which limits stand-establishment and seedling growth. To gain further insights on the molecular mechanism of cold tolerance in sorghum we performed transcriptome profiling between known cold sensitive and tolerant sorghum lines using RNA sequencing technology under control and cold stress treatments. RESULTS Here we report on the identification of differentially expressed genes (DEGs) between contrasting sorghum genotypes, HongkeZi (cold tolerant) and BTx623 (cold sensitive) under cool and control temperatures using RNAseq approach to elucidate the molecular basis of sorghum response to cold stress. Furthermore, we validated bi-allelic variants in the form of single nucleotide polymorphism (SNPs) between the cold susceptible and tolerant lines of sorghum. An analysis of transcriptome profile showed that in response to cold, a total of 1910 DEGs were detected under cold and control temperatures in both genotypes. We identified a subset of genes under cold stress for downstream analysis, including transcription factors that exhibit differential abundance between the sensitive and tolerant genotypes. We identified transcription factors including Dehydration-responsive element-binding factors, C-repeat binding factors, and Ethylene responsive transcription factors as significantly upregulated during cold stress in cold tolerant HKZ. Additionally, specific genes such as plant cytochromes, glutathione s-transferases, and heat shock proteins were found differentially regulated under cold stress between cold tolerant and susceptible genotype of sorghum. A total of 41,603 SNP were identified between the cold sensitive and tolerant genotypes with minimum read of four. Approximately 89 % of the 114 SNP sites selected for evaluation were validated using endpoint genotyping technology. CONCLUSION A new strategy which involved an integrated analysis of differential gene expression and identification of bi-allelic single nucleotide polymorphism (SNP) was conducted to determine and analyze differentially expressed genes and variation involved in cold stress response of sorghum. The results gathered provide an insight into the complex mechanisms associated with cold response in sorghum, which involve an array of transcription factors and genes which were previously related to abiotic stress response. This study also offers resource for gene based SNP that can be applied towards targeted genomic studies of cold tolerance in sorghum and other cereal crops.
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Affiliation(s)
- Ratan Chopra
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA
| | - Gloria Burow
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA.
| | - Chad Hayes
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA
| | - Yves Emendack
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA
| | - Zhanguo Xin
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA
| | - John Burke
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA
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Mirik M, Emendack Y, Attia A, Chaudhuri S, Roy M, Backoulou GF, Cui S. Detecting Musk Thistle (Carduus nutans) Infestation Using a Target Recognition Algorithm. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ars.2014.33008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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