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Lee D, Lara L, Moseley D, Vuong TD, Shannon G, Xu D, Nguyen HT. Novel genetic resources associated with sucrose and stachyose content through genome-wide association study in soybean ( Glycine max (L.) Merr.). FRONTIERS IN PLANT SCIENCE 2023; 14:1294659. [PMID: 38023839 PMCID: PMC10646508 DOI: 10.3389/fpls.2023.1294659] [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: 09/15/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023]
Abstract
The nutritional value of soybean [Glycine max (L.) Merr.] for animals is influenced by soluble carbohydrates, such as sucrose and stachyose. Although sucrose is nutritionally desirable, stachyose is an antinutrient causing diarrhea and flatulence in non-ruminant animals. We conducted a genome-wide association study of 220 soybean accessions using 21,317 single nucleotide polymorphisms (SNPs) from the SoySNP50K iSelect Beadchip data to identify significant SNPs associated with sucrose and stachyose content. Seven significant SNPs were identified for sucrose content across chromosomes (Chrs.) 2, 8, 12, 17, and 20, while thirteen significant SNPs were identified for stachyose content across Chrs. 2, 5, 8, 9, 10, 13, 14, and 15. Among those significant SNPs, three sucrose-related SNPs on Chrs. 8 and 17 were novel, while twelve stachyose-related SNPs on Chrs. 2, 5, 8, 9, 10, 13, 14, and 15 were novel. Based on Phytozome, STRING, and GO annotation, 17 and 24 candidate genes for sucrose and stachyose content, respectively, were highly associated with the carbohydrate metabolic pathway. Among these, the publicly available RNA-seq Atlas database highlighted four candidate genes associated with sucrose (Glyma.08g361200 and Glyma.17g258100) and stachyose (Glyma.05g025300 and Glyma.13g077900) content, which had higher gene expression levels in developing seed and multiple parts of the soybean plant. The results of this study will extend knowledge of the molecular mechanism and genetic basis underlying sucrose and stachyose content in soybean seed. Furthermore, the novel candidate genes and SNPs can be valuable genetic resources that soybean breeders may utilize to modify carbohydrate profiles for animal and human usage.
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Affiliation(s)
- Dongho Lee
- Fisher Delta Research, Extension, and Education Center, Division of Plant Science and Technology, University of Missouri, Portageville, MO, United States
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Laura Lara
- Agrícola Los Alpes, Chimaltenango, Guatemala
| | - David Moseley
- Dean Lee Research and Extension Center, LSU AgCenter, Alexandria, LA, United States
| | - Tri D. Vuong
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Grover Shannon
- Fisher Delta Research, Extension, and Education Center, Division of Plant Science and Technology, University of Missouri, Portageville, MO, United States
| | - Dong Xu
- Department of Electrical Engineering and Computer Sciences, Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO, United States
| | - Henry T. Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
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2
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Patel S, Patel J, Bowen K, Koebernick J. Deciphering the genetic architecture of resistance to Corynespora cassiicola in soybean ( Glycine max L.) by integrating genome-wide association mapping and RNA-Seq analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1255763. [PMID: 37828935 PMCID: PMC10565807 DOI: 10.3389/fpls.2023.1255763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/04/2023] [Indexed: 10/14/2023]
Abstract
Target spot caused by Corynespora cassiicola is a problematic disease in tropical and subtropical soybean (Glycine max) growing regions. Although resistant soybean genotypes have been identified, the genetic mechanisms underlying target spot resistance has not yet been studied. To address this knowledge gap, this is the first genome-wide association study (GWAS) conducted using the SoySNP50K array on a panel of 246 soybean accessions, aiming to unravel the genetic architecture of resistance. The results revealed significant associations of 14 and 33 loci with resistance to LIM01 and SSTA C. cassiicola isolates, respectively, with six loci demonstrating consistent associations across both isolates. To identify potential candidate genes within GWAS-identified loci, dynamic transcriptome profiling was conducted through RNA-Seq analysis. The analysis involved comparing gene expression patterns between resistant and susceptible genotypes, utilizing leaf tissue collected at different time points after inoculation. Integrating results of GWAS and RNA-Seq analyses identified 238 differentially expressed genes within a 200 kb region encompassing significant quantitative trait loci (QTLs) for disease severity ratings. These genes were involved in defense response to pathogen, innate immune response, chitinase activity, histone H3-K9 methylation, salicylic acid mediated signaling pathway, kinase activity, and biosynthesis of flavonoid, jasmonic acid, phenylpropanoid, and wax. In addition, when combining results from this study with previous GWAS research, 11 colocalized regions associated with disease resistance were identified for biotic and abiotic stress. This finding provides valuable insight into the genetic resources that can be harnessed for future breeding programs aiming to enhance soybean resistance against target spot and other diseases simultaneously.
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Affiliation(s)
- Sejal Patel
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Jinesh Patel
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Kira Bowen
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
| | - Jenny Koebernick
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
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3
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Wu T, Lu S, Cai Y, Xu X, Zhang L, Chen F, Jiang B, Zhang H, Sun S, Zhai H, Zhao L, Xia Z, Hou W, Kong F, Han T. Molecular breeding for improvement of photothermal adaptability in soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:60. [PMID: 37496825 PMCID: PMC10366068 DOI: 10.1007/s11032-023-01406-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023]
Abstract
Soybean (Glycine max (L.) Merr.) is a typical short-day and temperate crop that is sensitive to photoperiod and temperature. Responses of soybean to photothermal conditions determine plant growth and development, which affect its architecture, yield formation, and capacity for geographic adaptation. Flowering time, maturity, and other traits associated with photothermal adaptability are controlled by multiple major-effect and minor-effect genes and genotype-by-environment interactions. Genetic studies have identified at least 11 loci (E1-E4, E6-E11, and J) that participate in photoperiodic regulation of flowering time and maturity in soybean. Molecular cloning and characterization of major-effect flowering genes have clarified the photoperiod-dependent flowering pathway, in which the photoreceptor gene phytochrome A, circadian evening complex (EC) components, central flowering repressor E1, and FLOWERING LOCUS T family genes play key roles in regulation of flowering time, maturity, and adaptability to photothermal conditions. Here, we provide an overview of recent progress in genetic and molecular analysis of traits associated with photothermal adaptability, summarizing advances in molecular breeding practices and tools for improving these traits. Furthermore, we discuss methods for breeding soybean varieties with better adaptability to specific ecological regions, with emphasis on a novel strategy, the Potalaization model, which allows breeding of widely adapted soybean varieties through the use of multiple molecular tools in existing elite widely adapted varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01406-z.
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Affiliation(s)
- Tingting Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Sijia Lu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Yupeng Cai
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xin Xu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lixin Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Fulu Chen
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Bingjun Jiang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Honglei Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shi Sun
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
| | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education of China, Northeast Agricultural University, Harbin, 150030 China
| | - Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
| | - Wensheng Hou
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Tianfu Han
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Bhat JA, Feng X, Mir ZA, Raina A, Siddique KHM. Recent advances in artificial intelligence, mechanistic models, and speed breeding offer exciting opportunities for precise and accelerated genomics-assisted breeding. PHYSIOLOGIA PLANTARUM 2023; 175:e13969. [PMID: 37401892 DOI: 10.1111/ppl.13969] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/11/2023] [Accepted: 06/27/2023] [Indexed: 07/05/2023]
Abstract
Given the challenges of population growth and climate change, there is an urgent need to expedite the development of high-yielding stress-tolerant crop cultivars. While traditional breeding methods have been instrumental in ensuring global food security, their efficiency, precision, and labour intensiveness have become increasingly inadequate to address present and future challenges. Fortunately, recent advances in high-throughput phenomics and genomics-assisted breeding (GAB) provide a promising platform for enhancing crop cultivars with greater efficiency. However, several obstacles must be overcome to optimize the use of these techniques in crop improvement, such as the complexity of phenotypic analysis of big image data. In addition, the prevalent use of linear models in genome-wide association studies (GWAS) and genomic selection (GS) fails to capture the nonlinear interactions of complex traits, limiting their applicability for GAB and impeding crop improvement. Recent advances in artificial intelligence (AI) techniques have opened doors to nonlinear modelling approaches in crop breeding, enabling the capture of nonlinear and epistatic interactions in GWAS and GS and thus making this variation available for GAB. While statistical and software challenges persist in AI-based models, they are expected to be resolved soon. Furthermore, recent advances in speed breeding have significantly reduced the time (3-5-fold) required for conventional breeding. Thus, integrating speed breeding with AI and GAB could improve crop cultivar development within a considerably shorter timeframe while ensuring greater accuracy and efficiency. In conclusion, this integrated approach could revolutionize crop breeding paradigms and safeguard food production in the face of population growth and climate change.
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Affiliation(s)
| | - Xianzhong Feng
- Zhejiang Lab, Hangzhou, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Zahoor A Mir
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Aamir Raina
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, Perth, Western Australia, Australia
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5
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Wang X, Zhou S, Wang J, Lin W, Yao X, Su J, Li H, Fang C, Kong F, Guan Y. Genome-wide association study for biomass accumulation traits in soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:33. [PMID: 37312748 PMCID: PMC10248709 DOI: 10.1007/s11032-023-01380-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/04/2023] [Indexed: 06/15/2023]
Abstract
Soybean is one of the most versatile crops for oil production, human diets, and feedstocks. The vegetative biomass of soybean is an important determinant of seed yield and is crucial for the forage usages. However, the genetic control of soybean biomass is not well explained. In this work, we used a soybean germplasm population, including 231 improved cultivars, 207 landraces, and 121 wild soybeans, to investigate the genetic basis of biomass accumulation of soybean plants at the V6 stage. We found that biomass-related traits, including NDW (nodule dry weight), RDW (root dry weight), SDW (shoot dry weight), and TDW (total dry weight), were domesticated during soybean evolution. In total, 10 loci, encompassing 47 putative candidate genes, were detected for all biomass-related traits by a genome-wide association study. Among these loci, seven domestication sweeps and six improvement sweeps were identified. Glyma.05G047900, a purple acid phosphatase, was a strong candidate gene to improve biomass for future soybean breeding. This study provided new insights into the genetic basis of biomass accumulation during soybean evolution. Supplementary information The online version contains supplementary material available at 10.1007/s11032-023-01380-6.
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Affiliation(s)
- Xin Wang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Shaodong Zhou
- College of Resources and Environment, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Jie Wang
- College of Resources and Environment, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- FAFU-UCR Joint Center for Horticultural Plant Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Wenxin Lin
- College of Resources and Environment, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xiaolei Yao
- College of Resources and Environment, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Jiaqing Su
- College of Resources and Environment, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Haiyang Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Chao Fang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Yuefeng Guan
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- FAFU-UCR Joint Center for Horticultural Plant Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
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6
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Abstract
Resistance to the soybean cyst nematode (SCN) is a topic incorporating multiple mechanisms and multiple types of science. It is also a topic of substantial agricultural importance, as SCN is estimated to cause more yield damage than any other pathogen of soybean, one of the world's main food crops. Both soybean and SCN have experienced jumps in experimental tractability in the past decade, and significant advances have been made. The rhg1-b locus, deployed on millions of farm acres, has been durable and will remain important, but local SCN populations are gradually evolving to overcome rhg1-b. Multiple other SCN resistance quantitative trait loci (QTL) of proven value are now in play with soybean breeders. QTL causal gene discovery and mechanistic insights into SCN resistance are contributing to both basic and applied disciplines. Additional understanding of SCN and other cyst nematodes will also grow in importance and lead to novel disease control strategies.
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Affiliation(s)
- Andrew F Bent
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA;
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Bhat JA, Adeboye KA, Ganie SA, Barmukh R, Hu D, Varshney RK, Yu D. Genome-wide association study, haplotype analysis, and genomic prediction reveal the genetic basis of yield-related traits in soybean (Glycine max L.). Front Genet 2022; 13:953833. [PMID: 36419833 PMCID: PMC9677453 DOI: 10.3389/fgene.2022.953833] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/22/2022] [Indexed: 11/09/2022] Open
Abstract
Identifying the genetic components underlying yield-related traits in soybean is crucial for improving its production and productivity. Here, 211 soybean genotypes were evaluated across six environments for four yield-related traits, including seed yield per plant (SYP), number of pods per plant number of seeds per plant and 100-seed weight (HSW). Genome-wide association study (GWAS) and genomic prediction (GP) analyses were performed using 12,617 single nucleotide polymorphism markers from NJAU 355K SoySNP Array. A total of 57 SNPs were significantly associated with four traits across six environments and a combined environment using five Genome-wide association study models. Out of these, six significant SNPs were consistently identified in more than three environments using multiple GWAS models. The genomic regions (±670 kb) flanking these six consistent SNPs were considered stable QTL regions. Gene annotation and in silico expression analysis revealed 15 putative genes underlying the stable QTLs that might regulate soybean yield. Haplotype analysis using six significant SNPs revealed various allelic combinations regulating diverse phenotypes for the studied traits. Furthermore, the GP analysis revealed that accurate breeding values for the studied soybean traits is attainable at an earlier generation. Our study paved the way for increasing soybean yield performance within a short breeding cycle.
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Affiliation(s)
- Javaid Akhter Bhat
- Soybean Research Institution, National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- International Genome Center, Jiangsu University, Zhenjiang, China
- *Correspondence: Javaid Akhter Bhat, ; Rajeev K. Varshney, ; Deyue Yu,
| | | | - Showkat Ahmad Ganie
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Surrey, United Kingdom
| | - Rutwik Barmukh
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Dezhou Hu
- Soybean Research Institution, National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Murdoch’s Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Perth, WA, Australia
- *Correspondence: Javaid Akhter Bhat, ; Rajeev K. Varshney, ; Deyue Yu,
| | - Deyue Yu
- Soybean Research Institution, National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Javaid Akhter Bhat, ; Rajeev K. Varshney, ; Deyue Yu,
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Sandhu KS, Shiv A, Kaur G, Meena MR, Raja AK, Vengavasi K, Mall AK, Kumar S, Singh PK, Singh J, Hemaprabha G, Pathak AD, Krishnappa G, Kumar S. Integrated Approach in Genomic Selection to Accelerate Genetic Gain in Sugarcane. PLANTS 2022; 11:plants11162139. [PMID: 36015442 PMCID: PMC9412483 DOI: 10.3390/plants11162139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/08/2022] [Accepted: 08/08/2022] [Indexed: 11/30/2022]
Abstract
Marker-assisted selection (MAS) has been widely used in the last few decades in plant breeding programs for the mapping and introgression of genes for economically important traits, which has enabled the development of a number of superior cultivars in different crops. In sugarcane, which is the most important source for sugar and bioethanol, marker development work was initiated long ago; however, marker-assisted breeding in sugarcane has been lagging, mainly due to its large complex genome, high levels of polyploidy and heterozygosity, varied number of chromosomes, and use of low/medium-density markers. Genomic selection (GS) is a proven technology in animal breeding and has recently been incorporated in plant breeding programs. GS is a potential tool for the rapid selection of superior genotypes and accelerating breeding cycle. However, its full potential could be realized by an integrated approach combining high-throughput phenotyping, genotyping, machine learning, and speed breeding with genomic selection. For better understanding of GS integration, we comprehensively discuss the concept of genetic gain through the breeder’s equation, GS methodology, prediction models, current status of GS in sugarcane, challenges of prediction accuracy, challenges of GS in sugarcane, integrated GS, high-throughput phenotyping (HTP), high-throughput genotyping (HTG), machine learning, and speed breeding followed by its prospective applications in sugarcane improvement.
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Affiliation(s)
- Karansher Singh Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA
| | - Aalok Shiv
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Mintu Ram Meena
- Regional Center, ICAR-Sugarcane Breeding Institute, Karnal 132001, India
| | - Arun Kumar Raja
- Division of Crop Production, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Krishnapriya Vengavasi
- Division of Crop Production, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Ashutosh Kumar Mall
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Sanjeev Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Praveen Kumar Singh
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Jyotsnendra Singh
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Govind Hemaprabha
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Ashwini Dutt Pathak
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Gopalareddy Krishnappa
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
- Correspondence: (G.K.); (S.K.)
| | - Sanjeev Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
- Correspondence: (G.K.); (S.K.)
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9
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Singer WM, Shea Z, Yu D, Huang H, Mian MAR, Shang C, Rosso ML, Song QJ, Zhang B. Genome-Wide Association Study and Genomic Selection for Proteinogenic Methionine in Soybean Seeds. FRONTIERS IN PLANT SCIENCE 2022; 13:859109. [PMID: 35557723 PMCID: PMC9088226 DOI: 10.3389/fpls.2022.859109] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
Soybean [Glycine max (L.) Merr.] seeds have an amino acid profile that provides excellent viability as a food and feed protein source. However, low concentrations of an essential amino acid, methionine, limit the nutritional utility of soybean protein. The objectives of this study were to identify genomic associations and evaluate the potential for genomic selection (GS) for methionine content in soybean seeds. We performed a genome-wide association study (GWAS) that utilized 311 soybean accessions from maturity groups IV and V grown in three locations in 2018 and 2019. A total of 35,570 single nucleotide polymorphisms (SNPs) were used to identify genomic associations with proteinogenic methionine content that was quantified by high-performance liquid chromatography (HPLC). Across four environments, 23 novel SNPs were identified as being associated with methionine content. The strongest associations were found on chromosomes 3 (ss715586112, ss715586120, ss715586126, ss715586203, and ss715586204), 8 (ss715599541 and ss715599547) and 16 (ss715625009). Several gene models were recognized within proximity to these SNPs, such as a leucine-rich repeat protein kinase and a serine/threonine protein kinase. Identification of these linked SNPs should help soybean breeders to improve protein quality in soybean seeds. GS was evaluated using k-fold cross validation within each environment with two SNP sets, the complete 35,570 set and a subset of 248 SNPs determined to be associated with methionine through GWAS. Average prediction accuracy (r 2) was highest using the SNP subset ranging from 0.45 to 0.62, which was a significant improvement from the complete set accuracy that ranged from 0.03 to 0.27. This indicated that GS utilizing a significant subset of SNPs may be a viable tool for soybean breeders seeking to improve methionine content.
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Affiliation(s)
- William M. Singer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Zachary Shea
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Dajun Yu
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, United States
| | - Haibo Huang
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, United States
| | - M. A. Rouf Mian
- Soybean and Nitrogen Fixation Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Raleigh, NC, United States
| | - Chao Shang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Maria L. Rosso
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Qijan J. Song
- Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD, United States
| | - Bo Zhang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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10
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Škrabišová M, Dietz N, Zeng S, Chan YO, Wang J, Liu Y, Biová J, Joshi T, Bilyeu KD. A novel Synthetic phenotype association study approach reveals the landscape of association for genomic variants and phenotypes. J Adv Res 2022; 42:117-133. [PMID: 36513408 PMCID: PMC9788956 DOI: 10.1016/j.jare.2022.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/14/2022] [Accepted: 04/08/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Genome-Wide Association Studies (GWAS) identify tagging variants in the genome that are statistically associated with the phenotype because of their linkage disequilibrium (LD) relationship with the causative mutation (CM). When both low-density genotyped accession panels with phenotypes and resequenced data accession panels are available, tagging variants can assist with post-GWAS challenges in CM discovery. OBJECTIVES Our objective was to identify additional GWAS evaluation criteria to assess correspondence between genomic variants and phenotypes, as well as enable deeper analysis of the localized landscape of association. METHODS We used genomic variant positions as Synthetic phenotypes in GWAS that we named "Synthetic phenotype association study" (SPAS). The extreme case of SPAS is what we call an "Inverse GWAS" where we used CM positions of cloned soybean genes. We developed and validated the Accuracy concept as a measure of the correspondence between variant positions and phenotypes. RESULTS The SPAS approach demonstrated that the genotype status of an associated variant used as a Synthetic phenotype enabled us to explore the relationships between tagging variants and CMs, and further, that utilizing CMs as Synthetic phenotypes in Inverse GWAS illuminated the landscape of association. We implemented the Accuracy calculation for a curated accession panel to an online Accuracy calculation tool (AccuTool) as a resource for gene identification in soybean. We demonstrated our concepts on three examples of soybean cloned genes. As a result of our findings, we devised an enhanced "GWAS to Genes" analysis (Synthetic phenotype to CM strategy, SP2CM). Using SP2CM, we identified a CM for a novel gene. CONCLUSION The SP2CM strategy utilizing Synthetic phenotypes and the Accuracy calculation of correspondence provides crucial information to assist researchers in CM discovery. The impact of this work is a more effective evaluation of landscapes of GWAS associations.
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Affiliation(s)
- Mária Škrabišová
- Department of Biochemistry, Faculty of Science, Palacky University Olomouc, Olomouc 78371, Czech Republic
| | - Nicholas Dietz
- Division of Plant Sciences, University of Missouri, Columbia, MO 65201, USA
| | - Shuai Zeng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65212, USA,Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA
| | - Yen On Chan
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA,MU Data Science and Informatics Institute, University of Missouri, Columbia, MO 65212, USA
| | - Juexin Wang
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65212, USA,Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA
| | - Yang Liu
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA,MU Data Science and Informatics Institute, University of Missouri, Columbia, MO 65212, USA
| | - Jana Biová
- Department of Biochemistry, Faculty of Science, Palacky University Olomouc, Olomouc 78371, Czech Republic
| | - Trupti Joshi
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65212, USA,Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA,MU Data Science and Informatics Institute, University of Missouri, Columbia, MO 65212, USA,Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO 65212, USA,Corresponding authors at: Department of Health Management and Informatics, School of Medicine, 1201 E Rollins St, 271B Life Science Center, Columbia, MO 65201, USA (T. Joshi). Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, 110 Waters Hall, University of Missouri, Columbia, MO 65211, USA (K.D. Bilyeu).
| | - Kristin D. Bilyeu
- Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, MO 65211, USA,Corresponding authors at: Department of Health Management and Informatics, School of Medicine, 1201 E Rollins St, 271B Life Science Center, Columbia, MO 65201, USA (T. Joshi). Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, 110 Waters Hall, University of Missouri, Columbia, MO 65211, USA (K.D. Bilyeu).
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11
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Shi A, Bhattarai G, Xiong H, Avila CA, Feng C, Liu B, Joshi V, Stein L, Mou B, du Toit LJ, Correll JC. Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN spinach germplasm. HORTICULTURE RESEARCH 2022; 9:uhac069. [PMID: 35669703 PMCID: PMC9157682 DOI: 10.1093/hr/uhac069] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/09/2022] [Indexed: 06/15/2023]
Abstract
White rust, caused by Albugo occidentalis, is one of the major yield-limiting diseases of spinach (Spinacia oleracea) in some major commercial production areas, particularly in southern Texas in the United States. The use of host resistance is the most economical and environment-friendly approach to managing white rust in spinach production. The objectives of this study were to conduct a genome-wide associating study (GWAS), to identify single nucleotide polymorphism (SNP) markers associated with white rust resistance in spinach, and to perform genomic prediction (GP) to estimate the prediction accuracy (PA). A GWAS panel of 346 USDA (US Dept. of Agriculture) germplasm accessions was phenotyped for white rust resistance under field conditions and GWAS was performed using 13 235 whole-genome resequencing (WGR) generated SNPs. Nine SNPs, chr2_53 049 132, chr3_58 479 501, chr3_95 114 909, chr4_9 176 069, chr4_17 807 168, chr4_83 938 338, chr4_87 601 768, chr6_1 877 096, and chr6_31 287 118, located on chromosomes 2, 3, 4, and 6 were associated with white rust resistance in this GWAS panel. Four scenarios were tested for PA using Pearson's correlation coefficient (r) between the genomic estimation breeding value (GEBV) and the observed values: (1) different ratios between the training set and testing set (fold), (2) different GP models, (3) different SNP numbers in three different SNP sets, and (4) the use of GWAS-derived significant SNP markers. The results indicated that a 2- to 10-fold difference in the various GP models had similar, although not identical, averaged r values in each SNP set; using GWAS-derived significant SNP markers would increase PA with a high r-value up to 0.84. The SNP markers and the high PA can provide valuable information for breeders to improve spinach by marker-assisted selection (MAS) and genomic selection (GS).
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Affiliation(s)
- Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Gehendra Bhattarai
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Haizheng Xiong
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Carlos A Avila
- Department of Horticultural Sciences, Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596, USA
| | - Chunda Feng
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, USA
| | - Bo Liu
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, USA
| | - Vijay Joshi
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 77801, USA
| | - Larry Stein
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 77801, USA
| | - Beiquan Mou
- Crop Improvement and Protection Research Unit, USDA-ARS, Salinas, CA 93905, USA
| | | | - James C Correll
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, USA
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12
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Sandhu KS, Merrick LF, Sankaran S, Zhang Z, Carter AH. Prospectus of Genomic Selection and Phenomics in Cereal, Legume and Oilseed Breeding Programs. Front Genet 2022. [PMCID: PMC8814369 DOI: 10.3389/fgene.2021.829131] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The last decade witnessed an unprecedented increase in the adoption of genomic selection (GS) and phenomics tools in plant breeding programs, especially in major cereal crops. GS has demonstrated the potential for selecting superior genotypes with high precision and accelerating the breeding cycle. Phenomics is a rapidly advancing domain to alleviate phenotyping bottlenecks and explores new large-scale phenotyping and data acquisition methods. In this review, we discuss the lesson learned from GS and phenomics in six self-pollinated crops, primarily focusing on rice, wheat, soybean, common bean, chickpea, and groundnut, and their implementation schemes are discussed after assessing their impact in the breeding programs. Here, the status of the adoption of genomics and phenomics is provided for those crops, with a complete GS overview. GS’s progress until 2020 is discussed in detail, and relevant information and links to the source codes are provided for implementing this technology into plant breeding programs, with most of the examples from wheat breeding programs. Detailed information about various phenotyping tools is provided to strengthen the field of phenomics for a plant breeder in the coming years. Finally, we highlight the benefits of merging genomic selection, phenomics, and machine and deep learning that have resulted in extraordinary results during recent years in wheat, rice, and soybean. Hence, there is a potential for adopting these technologies into crops like the common bean, chickpea, and groundnut. The adoption of phenomics and GS into different breeding programs will accelerate genetic gain that would create an impact on food security, realizing the need to feed an ever-growing population.
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Affiliation(s)
- Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
- *Correspondence: Karansher S. Sandhu,
| | - Lance F. Merrick
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Sindhuja Sankaran
- Department of Biological System Engineering, Washington State University, Pullman, WA, United States
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Arron H. Carter
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
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Payne WZ, Dou T, Cason JM, Simpson CE, McCutchen B, Burow MD, Kurouski D. A Proof-of-Principle Study of Non-invasive Identification of Peanut Genotypes and Nematode Resistance Using Raman Spectroscopy. FRONTIERS IN PLANT SCIENCE 2022; 12:664243. [PMID: 35058940 PMCID: PMC8765701 DOI: 10.3389/fpls.2021.664243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 11/24/2021] [Indexed: 05/11/2023]
Abstract
Identification of peanut cultivars for distinct phenotypic or genotypic traits whether using visual characterization or laboratory analysis requires substantial expertise, time, and resources. A less subjective and more precise method is needed for identification of peanut germplasm throughout the value chain. In this proof-of-principle study, the accuracy of Raman spectroscopy (RS), a non-invasive, non-destructive technique, in peanut phenotyping and identification is explored. We show that RS can be used for highly accurate peanut phenotyping via surface scans of peanut leaves and the resulting chemometric analysis: On average 94% accuracy in identification of peanut cultivars and breeding lines was achieved. Our results also suggest that RS can be used for highly accurate determination of nematode resistance and susceptibility of those breeding lines and cultivars. Specifically, nematode-resistant peanut cultivars can be identified with 92% accuracy, whereas susceptible breeding lines were identified with 81% accuracy. Finally, RS revealed substantial differences in biochemical composition between resistant and susceptible peanut cultivars. We found that resistant cultivars exhibit substantially higher carotenoid content compared to the susceptible breeding lines. The results of this study show that RS can be used for quick, accurate, and non-invasive identification of genotype, nematode resistance, and nutrient content. Armed with this knowledge, the peanut industry can utilize Raman spectroscopy for expedited breeding to increase yields, nutrition, and maintaining purity levels of cultivars following release.
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Affiliation(s)
- William Z. Payne
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Tianyi Dou
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - John M. Cason
- Texas A&M AgriLife Research, Stephenville, TX, United States
| | | | - Bill McCutchen
- Texas A&M AgriLife Research, Stephenville, TX, United States
| | - Mark D. Burow
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
- Texas A&M AgriLife Research, Lubbock, TX, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
- The Institute for Quantum Science and Engineering, Texas A&M University, College Station, TX, United States
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14
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Ferreira EGC, Marcelino-Guimarães FC. Mapping Major Disease Resistance Genes in Soybean by Genome-Wide Association Studies. Methods Mol Biol 2022; 2481:313-340. [PMID: 35641772 DOI: 10.1007/978-1-0716-2237-7_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Soybean is one of the most valuable agricultural crops in the world. Besides, this legume is constantly attacked by a wide range of pathogens (fungi, bacteria, viruses, and nematodes) compromising yield and increasing production costs. One of the major disease management strategies is the genetic resistance provided by single genes and quantitative trait loci (QTL). Identifying the genomic regions underlying the resistance against these pathogens on soybean is one of the first steps performed by molecular breeders. In the past, genetic mapping studies have been widely used to discover these genomic regions. However, over the last decade, advances in next-generation sequencing technologies and their subsequent cost decreasing led to the development of cost-effective approaches to high-throughput genotyping. Thus, genome-wide association studies applying thousands of SNPs in large sets composed of diverse soybean accessions have been successfully done. In this chapter, a comprehensive review of the majority of GWAS for soybean diseases published since this approach was developed is provided. Important diseases caused by Heterodera glycines, Phytophthora sojae, and Sclerotinia sclerotiorum have been the focus of the several GWAS. However, other bacterial and fungi diseases also have been targets of GWAS. As such, this GWAS summary can serve as a guide for future studies of these diseases. The protocol begins by describing several considerations about the pathogens and bringing different procedures of molecular characterization of them. Advice to choose the best isolate/race to maximize the discovery of multiple R genes or to directly map an effective R gene is provided. A summary of protocols, methods, and tools to phenotyping the soybean panel is given to several diseases. We also give details of options of DNA extraction protocols and genotyping methods, and we describe parameters of SNP quality to soybean data. Websites and their online tools to obtain genotypic and phenotypic data for thousands of soybean accessions are highlighted. Finally, we report several tricks and tips in Subheading 4, especially related to composing the soybean panel as well as generating and analyzing the phenotype data. We hope this protocol will be helpful to achieve GWAS success in identifying resistance genes on soybean.
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15
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Qin J, Wang F, Zhao Q, Shi A, Zhao T, Song Q, Ravelombola W, An H, Yan L, Yang C, Zhang M. Identification of Candidate Genes and Genomic Selection for Seed Protein in Soybean Breeding Pipeline. FRONTIERS IN PLANT SCIENCE 2022; 13:882732. [PMID: 35783963 PMCID: PMC9244705 DOI: 10.3389/fpls.2022.882732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/16/2022] [Indexed: 05/13/2023]
Abstract
Soybean is a primary meal protein for human consumption, poultry, and livestock feed. In this study, quantitative trait locus (QTL) controlling protein content was explored via genome-wide association studies (GWAS) and linkage mapping approaches based on 284 soybean accessions and 180 recombinant inbred lines (RILs), respectively, which were evaluated for protein content for 4 years. A total of 22 single nucleotide polymorphisms (SNPs) associated with protein content were detected using mixed linear model (MLM) and general linear model (GLM) methods in Tassel and 5 QTLs using Bayesian interval mapping (IM), single-trait multiple interval mapping (SMIM), single-trait composite interval mapping maximum likelihood estimation (SMLE), and single marker regression (SMR) models in Q-Gene and IciMapping. Major QTLs were detected on chromosomes 6 and 20 in both populations. The new QTL genomic region on chromosome 6 (Chr6_18844283-19315351) included 7 candidate genes and the Hap.X AA at the Chr6_19172961 position was associated with high protein content. Genomic selection (GS) of protein content was performed using Bayesian Lasso (BL) and ridge regression best linear unbiased prediction (rrBULP) based on all the SNPs and the SNPs significantly associated with protein content resulted from GWAS. The results showed that BL and rrBLUP performed similarly; GS accuracy was dependent on the SNP set and training population size. GS efficiency was higher for the SNPs derived from GWAS than random SNPs and reached a plateau when the number of markers was >2,000. The SNP markers identified in this study and other information were essential in establishing an efficient marker-assisted selection (MAS) and GS pipelines for improving soybean protein content.
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Affiliation(s)
- Jun Qin
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Hebei Laboratory of Crop Genetics and Breeding, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Fengmin Wang
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Hebei Laboratory of Crop Genetics and Breeding, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Qingsong Zhao
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Hebei Laboratory of Crop Genetics and Breeding, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
- *Correspondence: Ainong Shi,
| | - Tiantian Zhao
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Hebei Laboratory of Crop Genetics and Breeding, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Qijian Song
- Soybean Genomics and Improvement Lab, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Beltsville, MD, United States
| | - Waltram Ravelombola
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Hongzhou An
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Hebei Laboratory of Crop Genetics and Breeding, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Long Yan
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Hebei Laboratory of Crop Genetics and Breeding, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Chunyan Yang
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Hebei Laboratory of Crop Genetics and Breeding, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Chunyan Yang,
| | - Mengchen Zhang
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Hebei Laboratory of Crop Genetics and Breeding, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Mengchen Zhang,
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Shi A, Gepts P, Song Q, Xiong H, Michaels TE, Chen S. Genome-Wide Association Study and Genomic Prediction for Soybean Cyst Nematode Resistance in USDA Common Bean ( Phaseolus vulgaris) Core Collection. FRONTIERS IN PLANT SCIENCE 2021; 12:624156. [PMID: 34163495 PMCID: PMC8215670 DOI: 10.3389/fpls.2021.624156] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 05/14/2021] [Indexed: 05/16/2023]
Abstract
Soybean cyst nematode (SCN, Heterodera glycines) has become the major yield-limiting biological factor in soybean production. Common bean is also a good host of SCN, and its production is challenged by this emerging pest in many regions such as the upper Midwest USA. The use of host genetic resistance has been the most effective and environmentally friendly method to manage SCN. The objectives of this study were to evaluate the SCN resistance in the USDA common bean core collection and conduct a genome-wide association study (GWAS) of single nucleotide polymorphism (SNP) markers with SCN resistance. A total of 315 accessions of the USDA common bean core collection were evaluated for resistance to SCN HG Type 0 (race 6). The common bean core set was genotyped with the BARCBean6K_3 Infinium BeadChips, consisting of 4,654 SNPs. Results showed that 15 accessions were resistant to SCN with a Female Index (FI) at 4.8 to 9.4, and 62 accessions were moderately resistant (10 < FI < 30) to HG Type 0. The association study showed that 11 SNP markers, located on chromosomes Pv04, 07, 09, and 11, were strongly associated with resistance to HG Type 0. GWAS was also conducted for resistance to HG Type 2.5.7 and HG Type 1.2.3.5.6.7 based on the public dataset (N = 276), consisting of a diverse set of common bean accessions genotyped with the BARCBean6K_3 chip. Six SNPs associated with HG Type 2.5.7 resistance on Pv 01, 02, 03, and 07, and 12 SNPs with HG Type 1.2.3.5.6.7 resistance on Pv 01, 03, 06, 07, 09, 10, and 11 were detected. The accuracy of genomic prediction (GP) was 0.36 to 0.49 for resistance to the three SCN HG types, indicating that genomic selection (GS) of SCN resistance is feasible. This study provides basic information for developing SCN-resistant common bean cultivars, using the USDA core germ plasm accessions. The SNP markers can be used in molecular breeding in common beans through marker-assisted selection (MAS) and GS.
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Affiliation(s)
- Ainong Shi
- Department of Horticulture, PTSC316, University of Arkansas, Fayetteville, AR, United States
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Qijian Song
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Haizheng Xiong
- Department of Horticulture, PTSC316, University of Arkansas, Fayetteville, AR, United States
| | - Thomas E. Michaels
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States
| | - Senyu Chen
- Southern Research and Outreach Center, University of Minnesota, Waseca, MN, United States
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Gartner U, Hein I, Brown LH, Chen X, Mantelin S, Sharma SK, Dandurand LM, Kuhl JC, Jones JT, Bryan GJ, Blok VC. Resisting Potato Cyst Nematodes With Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:661194. [PMID: 33841485 PMCID: PMC8027921 DOI: 10.3389/fpls.2021.661194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/03/2021] [Indexed: 05/17/2023]
Abstract
Potato cyst nematodes (PCN) are economically important pests with a worldwide distribution in all temperate regions where potatoes are grown. Because above ground symptoms are non-specific, and detection of cysts in the soil is determined by the intensity of sampling, infestations are frequently spread before they are recognised. PCN cysts are resilient and persistent; their cargo of eggs can remain viable for over two decades, and thus once introduced PCN are very difficult to eradicate. Various control methods have been proposed, with resistant varieties being a key environmentally friendly and effective component of an integrated management programme. Wild and landrace relatives of cultivated potato have provided a source of PCN resistance genes that have been used in breeding programmes with varying levels of success. Producing a PCN resistant variety requires concerted effort over many years before it reaches what can be the biggest hurdle-commercial acceptance. Recent advances in potato genomics have provided tools to rapidly map resistance genes and to develop molecular markers to aid selection during breeding. This review will focus on the translation of these opportunities into durably PCN resistant varieties.
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Affiliation(s)
- Ulrike Gartner
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Ingo Hein
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Lynn H. Brown
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Xinwei Chen
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Sophie Mantelin
- INRAE UMR Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - Sanjeev K. Sharma
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Louise-Marie Dandurand
- Entomology, Plant Pathology and Nematology Department, University of Idaho, Moscow, ID, United States
| | - Joseph C. Kuhl
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States
| | - John T. Jones
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Glenn J. Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Vivian C. Blok
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Vivian C. Blok,
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