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Wang L, Tu W, Jin P, Liu Y, Du J, Zheng J, Wang YH, Li J. Genome-wide association study of plant color in Sorghum bicolor. FRONTIERS IN PLANT SCIENCE 2024; 15:1320844. [PMID: 38660439 PMCID: PMC11039782 DOI: 10.3389/fpls.2024.1320844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024]
Abstract
Introduction Sorghum plant color is the leaf sheath/leaf color and is associated with seed color, tannin and phenol content, head blight disease incidence, and phytoalexin production. Results In this study, we evaluated plant color of the sorghum mini core collection by scoring leaf sheath/leaf color at maturity as tan, red, or purple across three testing environments and performed genome-wide association mapping (GWAS) with 6,094,317 SNPs markers. Results and Discussion Eight loci, one each on chromosomes 1, 2, 4, and 6 and two on chromosomes 5 and 9, were mapped. All loci contained one to three candidate genes. In qPC5-1, Sobic.005G165632 and Sobic.005G165700 were located in the same linkage disequilibrium (LD) block. In qPC6, Sobic.006G149650 and Sobic.006G149700 were located in the different LD block. The single peak in qPC6 covered one gene, Sobic.006G149700, which was a senescence regulator. We found a loose correlation between the degree of linkage and tissue/organ expression of the underlying genes possibly related to the plant color phenotype. Allele analysis indicated that none of the linked SNPs can differentiate between red and purple accessions whereas all linked SNPs can differentiate tan from red/purple accessions. The candidate genes and SNP markers may facilitate the elucidation of plant color development as well as molecular plant breeding.
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Affiliation(s)
- Lihua Wang
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
- Anhui Province International Joint Research Center of Forage Bio-breeding, Chuzhou, China
| | - Wenmiao Tu
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
- Anhui Province International Joint Research Center of Forage Bio-breeding, Chuzhou, China
| | - Peng Jin
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
- Anhui Province International Joint Research Center of Forage Bio-breeding, Chuzhou, China
| | - Yanlong Liu
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
- Anhui Province International Joint Research Center of Forage Bio-breeding, Chuzhou, China
| | - Junli Du
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
- Anhui Province International Joint Research Center of Forage Bio-breeding, Chuzhou, China
| | - Jiacheng Zheng
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
- Anhui Province International Joint Research Center of Forage Bio-breeding, Chuzhou, China
| | - Yi-Hong Wang
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, United States
| | - Jieqin Li
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
- Anhui Province International Joint Research Center of Forage Bio-breeding, Chuzhou, China
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Ahn E, Prom LK, Park S, Hu Z, Magill CW. Genome-Wide Association Analysis Uncovers Genes Associated with Resistance to Head Smut Pathotype 5 in Senegalese Sorghum Accessions. PLANTS (BASEL, SWITZERLAND) 2024; 13:977. [PMID: 38611506 PMCID: PMC11013943 DOI: 10.3390/plants13070977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/18/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
A newly documented pathotype 5 of the soil-borne fungus Sporisorium reilianum, causing head smut in sorghum, was tested against 153 unexplored Senegalese sorghum accessions. Among the 153 sorghum accessions tested, 63 (41%) exhibited complete resistance, showing no signs of infection by the fungus. The remaining 90 accessions (59%) displayed varying degrees of susceptibility. Sorghum responses against S. reilianum were explored to analyze the potential link with previously known seed morphology-related traits and new phenotype data from 59 lines for seed weight. A genome-wide association study (GWAS) screened 297,876 SNPs and identified highly significant associations (p < 1 × 10-5) with head smut resistance in sorghum. By mapping these significant SNPs to the reference genome, this study revealed 35 novel candidate defense genes potentially involved in disease resistance.
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Affiliation(s)
- Ezekiel Ahn
- USDA-ARS Sustainable Perennial Crops Laboratory, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
| | - Louis K. Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX 77845, USA;
| | - Sunchung Park
- USDA-ARS Sustainable Perennial Crops Laboratory, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
| | - Zhenbin Hu
- USDA-ARS Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
| | - Clint W. Magill
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77843, USA
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Madhusudhana R, Padmaja PG. Multi-trait stability index for the identification of shoot fly (Atherigona soccata) resistant sorghum lines from a mini core collection. PEST MANAGEMENT SCIENCE 2023; 79:4319-4327. [PMID: 37368500 DOI: 10.1002/ps.7629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/14/2023] [Accepted: 06/27/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND On sorghum, shoot fly (Atherigona soccata Rondani) is the most destructive insect pest causing enormous economic losses. Breeding for host plant resistance is the best and economically viable strategy to control shoot fly damage. For improving resistance, there is a need to identify better donors with resistance, stability and adaptability. Sorghum mini core set representing global genetic diversity offers opportunity to understand genetic diversity of resistance component traits, their genotype × year (G × Y), and to identify better donors based on mean performance of multiple shoot fly resistance traits coupled with stability. RESULTS Significant genetic variability and G × Y interaction was detected for all traits in the mini core set. Broad sense heritability and accuracy of selection for traits was high. Genetic correlation between deadhearts and leaf surface glossiness and with seedling height were negative while genetic correlation of deadhearts with oviposition was positive. The sorghum races did not establish any inherent relation with shoot fly resistance. Based on multiple trait stability index (MTSI), the study identified 12 stable resistant accessions. Selection differential and selection gains in the selected genotypes were positive for both glossiness and seedling height and were negative for deadhearts and Eggs. CONCLUSION The MTSI selected new sources of resistance may constitute a breeding population for providing a dynamic gene pool of different resistance mechanisms for improving shoot fly resistance in sorghum. © 2023 Society of Chemical Industry.
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Ahn E, Botkin J, Ellur V, Lee Y, Poudel K, Prom LK, Magill C. Genome-Wide Association Study of Seed Morphology Traits in Senegalese Sorghum Cultivars. PLANTS (BASEL, SWITZERLAND) 2023; 12:2344. [PMID: 37375969 DOI: 10.3390/plants12122344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Sorghum is considered the fifth most important crop in the world. Despite the potential value of Senegalese germplasm for various traits, such as resistance to fungal diseases, there is limited information on the study of sorghum seed morphology. In this study, 162 Senegalese germplasms were evaluated for seed area size, length, width, length-to-width ratio, perimeter, circularity, the distance between the intersection of length & width (IS) and center of gravity (CG), and seed darkness and brightness by scanning and analyzing morphology-related traits with SmartGrain software at the USDA-ARS Plant Science Research Unit. Correlations between seed morphology-related traits and traits associated with anthracnose and head smut resistance were analyzed. Lastly, genome-wide association studies were performed on phenotypic data collected from over 16,000 seeds and 193,727 publicly available single nucleotide polymorphisms (SNPs). Several significant SNPs were found and mapped to the reference sorghum genome to uncover multiple candidate genes potentially associated with seed morphology. The results indicate clear correlations among seed morphology-related traits and potential associations between seed morphology and the defense response of sorghum. GWAS analysis listed candidate genes associated with seed morphologies that can be used for sorghum breeding in the future.
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Affiliation(s)
- Ezekiel Ahn
- USDA-ARS Plant Science Research Unit, St. Paul, MN 55108, USA
| | - Jacob Botkin
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Vishnutej Ellur
- Molecular Plant Sciences, Washington State University, Pullman, WA 99164, USA
| | - Yoonjung Lee
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Kabita Poudel
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Louis K Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX 77845, USA
| | - Clint Magill
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
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Guden B, Yol E, Erdurmus C, Lucas SJ, Uzun B. Construction of a high-density genetic linkage map and QTL mapping for bioenergy-related traits in sweet sorghum [ Sorghum bicolor (L.) Moench]. FRONTIERS IN PLANT SCIENCE 2023; 14:1081931. [PMID: 37342135 PMCID: PMC10278949 DOI: 10.3389/fpls.2023.1081931] [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: 10/27/2022] [Accepted: 05/15/2023] [Indexed: 06/22/2023]
Abstract
Sorghum is an important but arguably undervalued cereal crop, grown in large areas in Asia and Africa due to its natural resilience to drought and heat. There is growing demand for sweet sorghum as a source of bioethanol as well as food and feed. The improvement of bioenergy-related traits directly affects bioethanol production from sweet sorghum; therefore, understanding the genetic basis of these traits would enable new cultivars to be developed for bioenergy production. In order to reveal the genetic architecture behind bioenergy-related traits, we generated an F2 population from a cross between sweet sorghum cv. 'Erdurmus' and grain sorghum cv. 'Ogretmenoglu'. This was used to construct a genetic map from SNPs discovered by double-digest restriction-site associated DNA sequencing (ddRAD-seq). F3 lines derived from each F2 individual were phenotyped for bioenergy-related traits in two different locations and their genotypes were analyzed with the SNPs to identify QTL regions. On chromosomes 1, 7, and 9, three major plant height (PH) QTLs (qPH1.1, qPH7.1, and qPH9.1) were identified, with phenotypic variation explained (PVE) ranging from 10.8 to 34.8%. One major QTL (qPJ6.1) on chromosome 6 was associated with the plant juice trait (PJ) and explained 35.2% of its phenotypic variation. For fresh biomass weight (FBW), four major QTLs (qFBW1.1, qFBW6.1, qFBW7.1, and qFBW9.1) were determined on chromosomes 1, 6, 7, and 9, which explained 12.3, 14.5, 10.6, and 11.9% of the phenotypic variation, respectively. Moreover, two minor QTLs (qBX3.1 and qBX7.1) of Brix (BX) were mapped on chromosomes 3 and 7, explaining 8.6 and 9.7% of the phenotypic variation, respectively. The QTLs in two clusters (qPH7.1/qBX7.1 and qPH7.1/qFBW7.1) overlapped for PH, FBW and BX. The QTL, qFBW6.1, has not been previously reported. In addition, eight SNPs were converted into cleaved amplified polymorphic sequences (CAPS) markers, which can be easily detected by agarose gel electrophoresis. These QTLs and molecular markers can be used for pyramiding and marker-assisted selection studies in sorghum, to develop advanced lines that include desirable bioenergy-related traits.
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Affiliation(s)
- Birgul Guden
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Engin Yol
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Cengiz Erdurmus
- Department of Field Crops, West Mediterranean Agricultural Research Institute, Antalya, Türkiye
| | - Stuart James Lucas
- Sabanci University Nanotechnology Research and Application Centre, Sabanci University, Istanbul, Türkiye
| | - Bulent Uzun
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
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Ahn E, Prom LK, Magill C. Multi-Trait Genome-Wide Association Studies of Sorghum bicolor Regarding Resistance to Anthracnose, Downy Mildew, Grain Mold and Head Smut. Pathogens 2023; 12:779. [PMID: 37375469 DOI: 10.3390/pathogens12060779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/18/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Multivariate linear mixed models (mvLMMs) are widely applied for genome-wide association studies (GWAS) to detect genetic variants affecting multiple traits with correlations and/or different plant growth stages. Subsets of multiple sorghum populations, including the Sorghum Association Panel (SAP), the Sorghum Mini Core Collection and the Senegalese sorghum population, have been screened against various sorghum diseases such as anthracnose, downy mildew, grain mold and head smut. Still, these studies were generally performed in a univariate framework. In this study, we performed GWAS based on the principal components of defense-related multi-traits against the fungal diseases, identifying new potential SNPs (S04_51771351, S02_66200847, S09_47938177, S08_7370058, S03_72625166, S07_17951013, S04_66666642 and S08_51886715) associated with sorghum's defense against these diseases.
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Affiliation(s)
- Ezekiel Ahn
- USDA-ARS Plant Science Research Unit, St. Paul, MN 55108, USA
| | - Louis K Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX 77845, USA
| | - Clint Magill
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
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Baloch FS, Altaf MT, Liaqat W, Bedir M, Nadeem MA, Cömertpay G, Çoban N, Habyarimana E, Barutçular C, Cerit I, Ludidi N, Karaköy T, Aasim M, Chung YS, Nawaz MA, Hatipoğlu R, Kökten K, Sun HJ. Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding. Front Genet 2023; 14:1150616. [PMID: 37252661 PMCID: PMC10213934 DOI: 10.3389/fgene.2023.1150616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world.
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Affiliation(s)
- Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Waqas Liaqat
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Mehmet Bedir
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Gönül Cömertpay
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Nergiz Çoban
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Celaleddin Barutçular
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Ibrahim Cerit
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ndomelele Ludidi
- Plant Stress Tolerance Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
- DSI-NRF Centre of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
| | | | - Rüştü Hatipoğlu
- Kırşehir Ahi Evran Universitesi Ziraat Fakultesi Tarla Bitkileri Bolumu, Kırşehir, Türkiye
| | - Kağan Kökten
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Hyeon-Jin Sun
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
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Ge F, Xie P, Wu Y, Xie Q. Genetic architecture and molecular regulation of sorghum domestication. ABIOTECH 2023; 4:57-71. [PMID: 37220542 PMCID: PMC10199992 DOI: 10.1007/s42994-022-00089-y] [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: 09/28/2022] [Accepted: 11/28/2022] [Indexed: 05/25/2023]
Abstract
Over time, wild crops have been domesticated by humans, and the knowledge gained from parallel selection and convergent domestication-related studies in cereals has contributed to current techniques used in molecular plant breeding. Sorghum (Sorghum bicolor (L.) Moench) is the world's fifth-most popular cereal crop and was one of the first crops cultivated by ancient farmers. In recent years, genetic and genomic studies have provided a better understanding of sorghum domestication and improvements. Here, we discuss the origin, diversification, and domestication processes of sorghum based on archeological discoveries and genomic analyses. This review also comprehensively summarized the genetic basis of key genes related to sorghum domestication and outlined their molecular mechanisms. It highlights that the absence of a domestication bottleneck in sorghum is the result of both evolution and human selection. Additionally, understanding beneficial alleles and their molecular interactions will allow us to quickly design new varieties by further de novo domestication.
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Affiliation(s)
- Fengyong Ge
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Peng Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yaorong Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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Odesola KA, Olawuyi OJ, Paliwal R, Oyatomi OA, Abberton MT. Genome-Wide association analysis of phenotypic traits in Bambara groundnut under drought-stressed and non-stressed conditions based on DArTseq SNP. FRONTIERS IN PLANT SCIENCE 2023; 14:1104417. [PMID: 36866383 PMCID: PMC9972976 DOI: 10.3389/fpls.2023.1104417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/05/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Bambara groundnut (BG) (Vigna subterranea [L.] Verdc) is an indigenous, resilient, but underutilized leguminous crop that occurs mostly as genetically heterogeneous landraces with limited information on the drought tolerant attributes. This study elucidates the associations between sequencing-based diversity array technology (DArTseq) and phenotypic character as well as differing indices related to drought tolerance in one hundred accessions of Bambara groundnut. METHODS The field experiments were conducted at IITA research stations in Kano and Ibadan between 2016 and 2018 planting seasons. The experiments were arranged in randomised complete block design with three replications, under the different water regimes. The phenotypic traits evaluated was further to construct the dendrogram. Genome-wide association mapping was conducted based on 5927 DArTs loci with < 20% missing data. RESULTS AND DISCUSSIONS The genome wide association study predicted drought tolerance in Bambara accessions for geometric mean productivity (GMP) and stress tolerance index (STI). TVSu-423 had the highest GMP and STI values (28.50, 2.40), while TVSu-2017 had the lowest at GMP (1.74) and STI (0.01) respectively. The relative water content (%) was significantly higher for accessions; TVSu-266 (60.35, 61.49), TVSu-2 (58.29, 53.94), and TVSu-411 (55.17, 58.92) in 2016/2017 and 2017/2018, respectively. The phenotypic characters studied delineated the accessions into two major clusters and five distinct sub-clusters, indicating variations across all the geographical locations. The 5,927 DArTseq genomic markers in association with STI further grouped the 100 accessions into two main clusters. TVSu-1897 from Botswana (Southern Africa) was in the first cluster, while the remaining 99 accessions from Western, Central, and Eastern Africa made up the second cluster. The eight significant Quantitative Trait Loci (QTLs) (24346377|F|0-22:A>G-22:A>G, 24384105|F|0-56:A>G33 :A> G, 24385643|F|0-53:G>C-53:G>C, 24385696|F|0-43:A>G-43:A>G, 4177257|F|0-44:A>T-44:A>T, 4182070|F|0-66:G>A-66:G>A, 4183483|F|0-24:G>A-24:G>A, 4183904|F|0-11:C>T-11:C>T) identified with Bonferroni threshold was in association with STI, indicative of variations under the drought-stressed condition. The observation of consistent SNPs in the 2016 and 2017 planting seasons, as well as in combination with the 2016 and 2017 planting seasons, led to the designation of these QTLs as significant. The drought selected accessions could form basis for hybridization breeding. The identified quantitative trait loci could be useful in marker-assisted selection in drought molecular breeding programs.
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Affiliation(s)
- Kafilat Abiodun Odesola
- Department of Biological Sciences, Bells University of Technology, Sango Otta, Ogun State, Nigeria
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Oyo State, Nigeria
- Department of Botany, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | - Rajneesh Paliwal
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Oyo State, Nigeria
| | - Olaniyi Ajewole Oyatomi
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Oyo State, Nigeria
| | - Michael T. Abberton
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Oyo State, Nigeria
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Ahn E, Fall C, Prom LK, Magill C. A Genome-Wide Association Study of Senegalese Sorghum Seedlings Responding to Pathotype 5 of Sporisorium reilianum. PLANTS (BASEL, SWITZERLAND) 2022; 11:2999. [PMID: 36365456 PMCID: PMC9654544 DOI: 10.3390/plants11212999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Sporisorium reilianum is a fungal pathogen that causes head smut in sorghum. In addition to pathotypes (P) 1-4, P5 and P6 were identified recently. In this study, seedlings of Senegalese sorghum, comprising 163 accessions, were evaluated for response to Sporisorium reilianum. Teliospores of pathotype P5 of the pathogen in dilute agar were pipetted onto seedling shoots while still in soil, and inoculated seedlings were submerged under water at 4 days post-inoculation. Signs of infection (noticeable spots) on the first leaf were checked daily up to 6 days post submergence. A genome-wide association study (GWAS) was conducted using 193,727 single-nucleotide polymorphisms (SNPs) throughout the genome based on two types of phenotypic data: whether noticeable spots were shown or not and the average time for an observation of the spots across 163 accessions. When mapped back to the reference sorghum genome, most of the top candidate SNP loci were associated with plant defense or plant stress response-related genes. The identified SNP loci were associated with spot appearance in sorghum seedlings under flooding following inoculation with P5 of Sporisorium reilianum.
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Affiliation(s)
- Ezekiel Ahn
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Coumba Fall
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Louis K. Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX 77845, USA
| | - Clint Magill
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77843, USA
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Ali A, Altaf MT, Nadeem MA, Karaköy T, Shah AN, Azeem H, Baloch FS, Baran N, Hussain T, Duangpan S, Aasim M, Boo KH, Abdelsalam NR, Hasan ME, Chung YS. Recent advancement in OMICS approaches to enhance abiotic stress tolerance in legumes. FRONTIERS IN PLANT SCIENCE 2022; 13:952759. [PMID: 36247536 PMCID: PMC9554552 DOI: 10.3389/fpls.2022.952759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023]
Abstract
The world is facing rapid climate change and a fast-growing global population. It is believed that the world population will be 9.7 billion in 2050. However, recent agriculture production is not enough to feed the current population of 7.9 billion people, which is causing a huge hunger problem. Therefore, feeding the 9.7 billion population in 2050 will be a huge target. Climate change is becoming a huge threat to global agricultural production, and it is expected to become the worst threat to it in the upcoming years. Keeping this in view, it is very important to breed climate-resilient plants. Legumes are considered an important pillar of the agriculture production system and a great source of high-quality protein, minerals, and vitamins. During the last two decades, advancements in OMICs technology revolutionized plant breeding and emerged as a crop-saving tool in wake of the climate change. Various OMICs approaches like Next-Generation sequencing (NGS), Transcriptomics, Proteomics, and Metabolomics have been used in legumes under abiotic stresses. The scientific community successfully utilized these platforms and investigated the Quantitative Trait Loci (QTL), linked markers through genome-wide association studies, and developed KASP markers that can be helpful for the marker-assisted breeding of legumes. Gene-editing techniques have been successfully proven for soybean, cowpea, chickpea, and model legumes such as Medicago truncatula and Lotus japonicus. A number of efforts have been made to perform gene editing in legumes. Moreover, the scientific community did a great job of identifying various genes involved in the metabolic pathways and utilizing the resulted information in the development of climate-resilient legume cultivars at a rapid pace. Keeping in view, this review highlights the contribution of OMICs approaches to abiotic stresses in legumes. We envisage that the presented information will be helpful for the scientific community to develop climate-resilient legume cultivars.
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Affiliation(s)
- Amjad Ali
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Hajra Azeem
- Department of Plant Pathology, Faculty of Agricultural Sciences & Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Nurettin Baran
- Bitkisel Uretim ve Teknolojileri Bolumu, Uygulamali Bilimler Faku Itesi, Mus Alparslan Universitesi, Mus, Turkey
| | - Tajamul Hussain
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Thailand
| | - Saowapa Duangpan
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Thailand
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Kyung-Hwan Boo
- Subtropical/Tropical Organism Gene Bank, Department of Biotechnology, College of Applied Life Science, Jeju National University, Jeju, South Korea
| | - Nader R. Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Mohamed E. Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, South Korea
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12
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Amombo E, Ashilenje D, Hirich A, Kouisni L, Oukarroum A, Ghoulam C, El Gharous M, Nilahyane A. Exploring the correlation between salt tolerance and yield: research advances and perspectives for salt-tolerant forage sorghum selection and genetic improvement. PLANTA 2022; 255:71. [PMID: 35190912 PMCID: PMC8860782 DOI: 10.1007/s00425-022-03847-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/25/2022] [Indexed: 05/18/2023]
Abstract
Some salt stress response mechanisms can translate into sorghum forage yield and thus act as targets for genetic improvement. Sorghum is a drought-tolerant cereal that is widely grown in the vast Africa's arid and semi-arid areas. Apart from drought, salinity is a major abiotic factor that, in addition to natural causes, has been exacerbated by increased poor anthropological activities. The importance of sorghum as a forage crop in saline areas has yet to be fully realized. Despite intraspecific variation in salt tolerance, sorghum is generally moderately salt-tolerant, and its productivity in saline soils can be remarkably limited. This is due to the difficulty of replicating optimal field saline conditions due to the great heterogeneity of salt distribution in the soil. As a promising fodder crop for saline areas, classic phenotype-based selection methods can be integrated with modern -omics in breeding programs to simultaneously address salt tolerance and production. To enable future manipulation, selection, and genetic improvement of sorghum with high yield and salt tolerance, here, we explore the potential positive correlations between the reliable indices of sorghum performance under salt stress at the phenotypic and genotypic level. We then explore the potential role of modern selection and genetic improvement programs in incorporating these linked salt tolerance and yield traits and propose a mechanism for future studies.
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Affiliation(s)
- Erick Amombo
- African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco
| | - Dennis Ashilenje
- African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco
| | - Abdelaziz Hirich
- African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco
| | - Lamfeddal Kouisni
- African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco
| | - Abdallah Oukarroum
- AgroBioSciences Department (AgBS), Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Cherki Ghoulam
- AgroBioSciences Department (AgBS), Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
- Center of Agrobiotechnology and Bioengineering, Labelled Research Unit CNRST, Cadi Ayyad University (UCA), Marrakech, Morocco
| | - Mohamed El Gharous
- Agricultural Innovation and Technology Transfer Center (AITTC), Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Abdelaziz Nilahyane
- African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco.
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13
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Ahn E, Prom LK, Hu Z, Odvody G, Magill C. Genome-wide association analysis for response of Senegalese sorghum accessions to Texas isolates of anthracnose. THE PLANT GENOME 2021; 14:e20097. [PMID: 33900689 DOI: 10.1002/tpg2.20097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Anthracnose disease of sorghum is caused by Colletotrichum sublineola, a filamentous fungus. The genetic basis of resistance to anthracnose in sorghum is largely unclear, especially in Senegalese sorghum germplasm. In this study, 163 Senegalese sorghum accessions were evaluated for response to C. sublineola, and a genome-wide association study (GWAS) was performed to identify genetic variation associated with response to C. sublineola using 193,727 single nucleotide polymorphisms (SNPs) throughout the genome. Germplasm diversity analysis showed low genetic diversity and slow linkage disequilibrium (LD) decay among the Senegalese accessions. Phenotypic analysis resulted in relatively low differences to C. sublineola among the tested population. Genome-wide association study did not identify any significant association based on a strict threshold for the number of SNPs available. However, individual analysis of the top eight SNPs associated with relative susceptibility and resistance identified candidate genes that have been shown to play important roles in plant stress tolerance in previous studies. This study identifies sorghum genes whose annotated properties have known roles in host defense and thus identify them as candidates for use in breeding for resistance to anthracnose.
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Affiliation(s)
- Ezekiel Ahn
- Dep. of Plant Pathology & Microbiology, Texas A&M Univ., College Station, TX, 77843, USA
| | - Louis K Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX, 77845, USA
| | - Zhenbin Hu
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
| | - Gary Odvody
- Texas A&M AgriLife Research, Corpus Christi, TX, 78406, USA
| | - Clint Magill
- Dep. of Plant Pathology & Microbiology, Texas A&M Univ., College Station, TX, 77843, USA
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14
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Hao H, Li Z, Leng C, Lu C, Luo H, Liu Y, Wu X, Liu Z, Shang L, Jing HC. Sorghum breeding in the genomic era: opportunities and challenges. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1899-1924. [PMID: 33655424 PMCID: PMC7924314 DOI: 10.1007/s00122-021-03789-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/05/2021] [Indexed: 05/04/2023]
Abstract
The importance and potential of the multi-purpose crop sorghum in global food security have not yet been fully exploited, and the integration of the state-of-art genomics and high-throughput technologies into breeding practice is required. Sorghum, a historically vital staple food source and currently the fifth most important major cereal, is emerging as a crop with diverse end-uses as food, feed, fuel and forage and a model for functional genetics and genomics of tropical grasses. Rapid development in high-throughput experimental and data processing technologies has significantly speeded up sorghum genomic researches in the past few years. The genomes of three sorghum lines are available, thousands of genetic stocks accessible and various genetic populations, including NAM, MAGIC, and mutagenised populations released. Functional and comparative genomics have elucidated key genetic loci and genes controlling agronomical and adaptive traits. However, the knowledge gained has far away from being translated into real breeding practices. We argue that the way forward is to take a genome-based approach for tailored designing of sorghum as a multi-functional crop combining excellent agricultural traits for various end uses. In this review, we update the new concepts and innovation systems in crop breeding and summarise recent advances in sorghum genomic researches, especially the genome-wide dissection of variations in genes and alleles for agronomically important traits. Future directions and opportunities for sorghum breeding are highlighted to stimulate discussion amongst sorghum academic and industrial communities.
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Affiliation(s)
- Huaiqing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zhigang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chuanyuan Leng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Cheng Lu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Luo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanming Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhiquan Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Li Shang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- Engineering Laboratory for Grass-based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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15
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Olatoye MO, Hu Z, Morris GP. Genome-wide mapping and prediction of plant architecture in a sorghum nested association mapping population. THE PLANT GENOME 2020; 13:e20038. [PMID: 33217207 DOI: 10.1002/tpg2.20038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 06/11/2023]
Abstract
Modifying plant architecture is often necessary for yield improvement and climate adaptation, but we lack understanding of the genotype-phenotype map for plant morphology in sorghum. Here, we use a nested association mapping (NAM) population that captures global allelic diversity of sorghum to characterize the genetics of leaf erectness, leaf width (at two stages), and stem diameter. Recombinant inbred lines (n = 2200) were phenotyped in multiple environments (35,200 observations) and joint linkage mapping was performed with ∼93,000 markers. Fifty-four QTL of small to large effect were identified for trait BLUPs (9-16 per trait) each explaining 0.4-4% of variation across the NAM population. While some of these QTL colocalize with sorghum homologs of grass genes (e.g., those involved in transcriptional regulation of hormone synthesis [rice SPINDLY] and transcriptional regulation of development [rice Ideal plant architecture1]), most QTL did not colocalize with an a priori candidate gene (92%). Genomic prediction accuracy was generally high in five-fold cross-validation (0.65-0.83), and varied from low to high in leave-one-family-out cross-validation (0.04-0.61). The findings provide a foundation to identify the molecular basis of architecture variation in sorghum and establish genomic-enabled breeding for improved plant architecture.
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Affiliation(s)
- Marcus O Olatoye
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
- Current address: Department of Crop Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Geoffrey P Morris
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
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Habyarimana E, De Franceschi P, Ercisli S, Baloch FS, Dall’Agata M. Genome-Wide Association Study for Biomass Related Traits in a Panel of Sorghum bicolor and S. bicolor × S. halepense Populations. FRONTIERS IN PLANT SCIENCE 2020; 11:551305. [PMID: 33281836 PMCID: PMC7688983 DOI: 10.3389/fpls.2020.551305] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 10/26/2020] [Indexed: 05/08/2023]
Abstract
The efficient use of sorghum as a renewable energy source requires high biomass yields and reduced agricultural inputs. Hybridization of Sorghum bicolor with wild Sorghum halepense can help meet both requirements, generating high-yielding and environment friendly perennial sorghum cultivars. Selection efficiency, however, needs to be improved to exploit the genetic potential of the derived recombinant lines and remove weedy and other wild traits. In this work, we present the results from a Genome-Wide Association Study conducted on a diversity panel made up of S. bicolor and an advanced population derived from S. bicolor × S. halepense multi-parent crosses. The objective was to identify genetic loci controlling biomass yield and biomass-relevant traits for breeding purposes. Plants were phenotyped during four consecutive years for dry biomass yield, dry mass fraction of fresh material, plant height and plant maturity. A genotyping-by-sequencing approach was implemented to obtain 92,383 high quality SNP markers used in this work. Significant marker-trait associations were uncovered across eight of the ten sorghum chromosomes, with two main hotspots near the end of chromosomes 7 and 9, in proximity of dwarfing genes Dw1 and Dw3. No significant marker was found on chromosomes 2 and 4. A large number of significant marker loci associated with biomass yield and biomass-relevant traits showed minor effects on respective plant characteristics, with the exception of seven loci on chromosomes 3, 8, and 9 that explained 5.2-7.8% of phenotypic variability in dry mass yield, dry mass fraction of fresh material, and maturity, and a major effect (R 2 = 16.2%) locus on chromosome 1 for dry mass fraction of fresh material which co-localized with a zinc-finger homeodomain protein possibly involved in the expression of the D (Dry stalk) locus. These markers and marker haplotypes identified in this work are expected to boost marker-assisted selection in sorghum breeding.
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Affiliation(s)
- Ephrem Habyarimana
- CREA Research Center for Cereal and Industrial Crops, Bologna, Italy
- *Correspondence: Ephrem Habyarimana,
| | | | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
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17
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Wang RJ, Gao XF, Yang J, Kong XR. Genome-Wide Association Study to Identify Favorable SNP Allelic Variations and Candidate Genes That Control the Timing of Spring Bud Flush of Tea ( Camellia sinensis) Using SLAF-seq. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10380-10391. [PMID: 31464444 DOI: 10.1021/acs.jafc.9b03330] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The timing of spring bud flush (TBF) is of economic importance for tea plant (Camellia sinensis) breeding. We employed a genome-wide association study (GWAS) to identify favorable single nucleotide polymorphism (SNP) allelic variations as well as candidate genes that control TBF of C. sinensis using specific-locus-amplified fragment sequencing (SLAF-seq) in a diversity panel comprising 151 tea plant germplasm resources. GWAS analysis revealed 26 SNPs associated with TBF in three years, and we eventually identified a final significant SNP for TBF. To identify candidate genes possibly related to TBF, we screened seven candidate genes within 100 kb regions surrounding the trait-related SNP loci. Furthermore, the favorable allelic variation, the "TT" genotype in the SNP loci, was discovered, and a derived cleaved amplified polymorphism (dCAPS) marker was designed that cosegregated with TBF, which could be used for marker-assisted selection (MAS) breeding in C. sinensis. The results obtained from this study can provide a theoretical and applied basis for the MAS of early breeding in tea plants in the future.
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Affiliation(s)
- Rang Jian Wang
- Institute of Tea , Fujian Academy of Agricultural Sciences , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
- Fujian Branch , National Center for Tea Improvement , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
| | - Xiang Feng Gao
- Institute of Tea , Fujian Academy of Agricultural Sciences , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
- Fujian Branch , National Center for Tea Improvement , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
| | - Jun Yang
- Institute of Tea , Fujian Academy of Agricultural Sciences , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
- Fujian Branch , National Center for Tea Improvement , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
| | - Xiang Rui Kong
- Institute of Tea , Fujian Academy of Agricultural Sciences , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
- Fujian Branch , National Center for Tea Improvement , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
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18
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Ahn E, Hu Z, Perumal R, Prom LK, Odvody G, Upadhyaya HD, Magill C. Genome wide association analysis of sorghum mini core lines regarding anthracnose, downy mildew, and head smut. PLoS One 2019; 14:e0216671. [PMID: 31086384 PMCID: PMC6516728 DOI: 10.1371/journal.pone.0216671] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/26/2019] [Indexed: 02/04/2023] Open
Abstract
In previous studies, a sorghum mini core collection was scored over several years for response to Colletotrichum sublineola, Peronosclerospora sorghi, and Sporisorium reilianum, the causal agents of the disease anthracnose, downy mildew, and head smut, respectively. The screening results were combined with over 290,000 Single nucleotide polymorphic (SNP) loci from an updated version of a publicly available genotype by sequencing (GBS) dataset available for the mini core collection. GAPIT (Genome Association and Prediction Integrated Tool) R package was used to identify chromosomal locations that differ in disease response. When the top scoring SNPs were mapped to the most recent version of the published sorghum genome, in each case, a nearby and most often the closest annotated gene has precedence for a role in host defense.
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Affiliation(s)
- Ezekiel Ahn
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
| | - Ramasamy Perumal
- Kansas State University, Agricultural Research Center, Hays, Kansas, United States of America
| | - Louis K. Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, Texas, United States of America
| | - Gary Odvody
- Texas A&M AgriLife Research, Corpus Christi, Texas, United States of America
| | - Hari D. Upadhyaya
- ICRISAT, Patancheru, Telangana, India
- King Abdulaziz University, Jeddah, Saudi Arabia
| | - Clint Magill
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, Texas, United States of America
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19
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Chong X, Su J, Wang F, Wang H, Song A, Guan Z, Fang W, Jiang J, Chen S, Chen F, Zhang F. Identification of favorable SNP alleles and candidate genes responsible for inflorescence-related traits via GWAS in chrysanthemum. PLANT MOLECULAR BIOLOGY 2019; 99:407-420. [PMID: 30701353 DOI: 10.1007/s11103-019-00826-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 01/19/2019] [Indexed: 05/21/2023]
Abstract
81 SNPs were identified for three inflorescence-related traits, in which 15 were highly favorable. Two dCAPS markers were developed for future MAS breeding, and six candidate genes were predicted. Chrysanthemum is a leading ornamental species worldwide and demonstrates a wealth of morphological variation. Knowledge about the genetic basis of its phenotypic variation for key horticultural traits can contribute to its effective management and genetic improvement. In this study, we conducted a genome-wide association study (GWAS) based on two years of phenotype data and a set of 92,617 single nucleotide polymorphisms (SNPs) using a panel of 107 diverse cut chrysanthemums to dissect the genetic control of three inflorescence-related traits. A total of 81 SNPs were significantly associated with the three inflorescence-related traits (capitulum diameter, number of ray florets and flowering time) in at least one environment, with an individual allele explaining 22.72-38.67% of the phenotypic variation. Fifteen highly favorable alleles were identified for the three target traits by computing the phenotypic effect values for the stable associations detected in 2 year-long trials at each locus. Dosage pyramiding effects of the highly favorable SNP alleles and significant linear correlations between highly favorable allele numbers and corresponding phenotypic performance were observed. Two highly favorable SNP alleles correlating to flowering time and capitulum diameter were converted to derived cleaved amplified polymorphic sequence (dCAPS) markers to facilitate future breeding. Finally, six putative candidate genes were identified that contribute to flowering time and capitulum diameter. These results serve as a foundation for analyzing the genetic mechanisms underlying important horticultural traits and provide valuable insights into molecular marker-assisted selection (MAS) in chrysanthemum breeding programs.
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Affiliation(s)
- Xinran Chong
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Jiangshuo Su
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Fan Wang
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Fei Zhang
- College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China.
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Su J, Zhang F, Chong X, Song A, Guan Z, Fang W, Chen F. Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums. HORTICULTURE RESEARCH 2019; 6:21. [PMID: 30729011 PMCID: PMC6355785 DOI: 10.1038/s41438-018-0101-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 08/06/2018] [Accepted: 10/09/2018] [Indexed: 05/05/2023]
Abstract
Chrysanthemums are sensitive to waterlogging stress, and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breeding. To understand the genetic basis of waterlogging tolerance (WT) in chrysanthemums, we performed a genome-wide association study (GWAS) using 92,811 single nucleotide polymorphisms (SNPs) in a panel of 88 chrysanthemum accessions, including 64 spray cut and 24 disbud chrysanthemums. The results showed that the average MFVW (membership function value of waterlogging) of the disbud type (0.65) was significantly higher than that of the spray type (0.55) at P < 0.05, and the MFVW of the Asian accessions (0.65) was significantly higher than that of the European accessions (0.48) at P < 0.01. The GWAS performed using the general linear model (GLM) and mixed linear model (MLM) identified 137 and 14 SNP loci related to WT, respectively, and 11 associations were commonly predicted. By calculating the phenotypic effect values for 11 common SNP loci, six highly favorable SNP alleles that explained 12.85-21.85% of the phenotypic variations were identified. Furthermore, the dosage-pyramiding effects of the favorable alleles and the significant linear correlations between the numbers of highly favorable alleles and phenotypic values were identified (r 2 = 0.45; P < 0.01). A major SNP locus (Marker6619-75) was converted into a derived cleaved amplified polymorphic sequence (dCAPS) marker that cosegregated with WT with an average efficiency of 78.9%. Finally, four putative candidate genes in the WT were identified via quantitative real-time PCR (qRT-PCR). The results presented in this study provide insights for further research on WT mechanisms and the application of molecular marker-assisted selection (MAS) in chrysanthemum WT breeding programs.
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Affiliation(s)
- Jiangshuo Su
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Fei Zhang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Xinran Chong
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
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Su J, Zhang F, Chong X, Song A, Guan Z, Fang W, Chen F. Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums. HORTICULTURE RESEARCH 2019. [PMID: 30729011 DOI: 10.1038/s41438-018-0101-107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Chrysanthemums are sensitive to waterlogging stress, and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breeding. To understand the genetic basis of waterlogging tolerance (WT) in chrysanthemums, we performed a genome-wide association study (GWAS) using 92,811 single nucleotide polymorphisms (SNPs) in a panel of 88 chrysanthemum accessions, including 64 spray cut and 24 disbud chrysanthemums. The results showed that the average MFVW (membership function value of waterlogging) of the disbud type (0.65) was significantly higher than that of the spray type (0.55) at P < 0.05, and the MFVW of the Asian accessions (0.65) was significantly higher than that of the European accessions (0.48) at P < 0.01. The GWAS performed using the general linear model (GLM) and mixed linear model (MLM) identified 137 and 14 SNP loci related to WT, respectively, and 11 associations were commonly predicted. By calculating the phenotypic effect values for 11 common SNP loci, six highly favorable SNP alleles that explained 12.85-21.85% of the phenotypic variations were identified. Furthermore, the dosage-pyramiding effects of the favorable alleles and the significant linear correlations between the numbers of highly favorable alleles and phenotypic values were identified (r 2 = 0.45; P < 0.01). A major SNP locus (Marker6619-75) was converted into a derived cleaved amplified polymorphic sequence (dCAPS) marker that cosegregated with WT with an average efficiency of 78.9%. Finally, four putative candidate genes in the WT were identified via quantitative real-time PCR (qRT-PCR). The results presented in this study provide insights for further research on WT mechanisms and the application of molecular marker-assisted selection (MAS) in chrysanthemum WT breeding programs.
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Affiliation(s)
- Jiangshuo Su
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Fei Zhang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Xinran Chong
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
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22
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Spindel JE, Dahlberg J, Colgan M, Hollingsworth J, Sievert J, Staggenborg SH, Hutmacher R, Jansson C, Vogel JP. Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought. BMC Genomics 2018; 19:679. [PMID: 30223789 PMCID: PMC6142696 DOI: 10.1186/s12864-018-5055-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/04/2018] [Indexed: 11/10/2022] Open
Abstract
Background Sorghum bicolor is the fifth most commonly grown cereal worldwide and is remarkable for its drought and abiotic stress tolerance. For these reasons and the large size of biomass varieties, it has been proposed as a bioenergy crop. However, little is known about the genes underlying sorghum’s abiotic stress tolerance and biomass yield. Results To uncover the genetic basis of drought tolerance in sorghum at a genome-wide level, we undertook a high-density phenomics genome wide association study (GWAS) in which 648 diverse sorghum lines were phenotyped at two locations in California once per week by drone over the course of a growing season. Biomass, height, and leaf area were measured by drone for individual field plots, subjected to two drought treatments and a well-watered control. The resulting dataset of ~ 171,000 phenotypic data-points was analyzed along with 183,989 genotype by sequence markers to reveal 213 high-quality, replicated, and conserved GWAS associations. Conclusions The genomic intervals defined by the associations include many strong candidate genes, including those encoding heat shock proteins, antifreeze proteins, and other domains recognized as important to plant stress responses. The markers identified by our study can be used for marker assisted selection for drought tolerance and biomass. In addition, our results are a significant step toward identifying specific sorghum genes controlling drought tolerance and biomass yield. Electronic supplementary material The online version of this article (10.1186/s12864-018-5055-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jennifer E Spindel
- DOE Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA, 94598, USA.,Present Address: Monsanto, St. Louis, MO, USA
| | - Jeffery Dahlberg
- UC-ANR Kearney Agricultural Research and Extension Center, 9240 S Riverbend Ave, Parlier, CA, 93648, USA
| | - Matthew Colgan
- Blue River Technology, 575 N Pastoria Ave, Sunnyvale, CA, 94085, USA
| | - Joy Hollingsworth
- UC-ANR Kearney Agricultural Research and Extension Center, 9240 S Riverbend Ave, Parlier, CA, 93648, USA
| | - Julie Sievert
- UC-ANR Kearney Agricultural Research and Extension Center, 9240 S Riverbend Ave, Parlier, CA, 93648, USA
| | | | - Robert Hutmacher
- UC-ANR West Side Research & Extension Center, 17353 W Oakland Ave, Five Points, CA, 93624, USA
| | - Christer Jansson
- Pacific Northwest National Laboratory: Environmental Molecular Sciences Laboratory, 902 Battelle Blvd, Richland, WA, 99354, USA
| | - John P Vogel
- DOE Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA, 94598, USA.
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Ambreen H, Kumar S, Kumar A, Agarwal M, Jagannath A, Goel S. Association Mapping for Important Agronomic Traits in Safflower ( Carthamus tinctorius L.) Core Collection Using Microsatellite Markers. FRONTIERS IN PLANT SCIENCE 2018; 9:402. [PMID: 29651296 PMCID: PMC5885069 DOI: 10.3389/fpls.2018.00402] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 03/13/2018] [Indexed: 05/27/2023]
Abstract
Carthamus tinctorius L. (safflower) is an important oilseed crop producing seed oil rich in unsaturated fatty acids. Scarcity of identified marker-trait associations is a major limitation toward development of successful marker-assisted breeding programs in safflower. In the present study, a safflower panel (CartAP) comprising 124 accessions derived from two core collections was assayed for its suitability for association mapping. Genotyping of CartAP using microsatellite markers revealed significant genetic diversity indicated by Shannon information index (H = 0.7537) and Nei's expected heterozygosity (I = 0.4432). In Principal Coordinate Analysis, the CartAP accessions were distributed homogeneously in all quadrants indicating their diverse nature. Distance-based Neighbor Joining analysis did not delineate the CartAP accessions in consonance with their geographical origin. Bayesian analysis of population structure of CartAP demonstrated the unstructured nature of the association panel. Kinship analysis at population (Gij ) and individual level (Fij ) revealed absence of or weak relatedness between the CartAP accessions. The above parameters established the suitability of CartAP for association mapping. We performed association mapping using phenotypic data for eight traits of agronomic value (viz., seed oil content, oleic acid, linoleic acid, plant height, number of primary branches, number of capitula per plant, 100-seed weight and days to 50% flowering) available for two growing seasons (2011-2012 and 2012-2013) through General Linear Model and Mixed Linear Model. Our study identified ninety-six significant marker-trait associations (MTAs; P < 0.05) of which, several MTAs with correlation coefficient (R2) > 10% were consistently represented in both models and in both seasons for traits viz., oil content, oleic acid content, linoleic acid content and number of primary branches. Several MTAs with high R2-values were detected either in a majority or in some environments (models and/or seasons). Many MTAs were also common between traits (viz., oleic/linoleic acid content; plant height/days to 50% flowering; number of primary branches/number of capitula per plant) that showed positive or negative correlation in their phenotypic values. The marker-trait associations identified in this study will facilitate marker-assisted breeding and identification of genetic determinants of trait variability.
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Chopra R, Burow G, Burke JJ, Gladman N, Xin Z. Genome-wide association analysis of seedling traits in diverse Sorghum germplasm under thermal stress. BMC PLANT BIOLOGY 2017; 17:12. [PMID: 28086798 PMCID: PMC5237230 DOI: 10.1186/s12870-016-0966-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 12/23/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Climate variability due to fluctuation in temperature is a worldwide concern that imperils crop production. The need to understand how the germplasm variation in major crops can be utilized to aid in discovering and developing breeding lines that can withstand and adapt to temperature fluctuations is more necessary than ever. Here, we analyzed the genetic variation associated with responses to thermal stresses in a sorghum association panel (SAP) representing major races and working groups to identify single nucleotide polymorphisms (SNPs) that are associated with resilience to temperature stress in a major cereal crop. RESULTS The SAP exhibited extensive variation for seedling traits under cold and heat stress. Genome-wide analyses identified 30 SNPs that were strongly associated with traits measured at seedling stage under cold stress and tagged genes that act as regulators of anthocyanin expression and soluble carbohydrate metabolism. Meanwhile, 12 SNPs were significantly associated with seedling traits under heat stress and these SNPs tagged genes that function in sugar metabolism, and ion transport pathways. Evaluation of co-expression networks for genes near the significantly associated SNPs indicated complex gene interactions for cold and heat stresses in sorghum. We focused and validated the expression of four genes in the network of Sb06g025040, a basic-helix-loop-helix (bHLH) transcription factor that was proposed to be involved in purple color pigmentation of leaf, and observed that genes in this network were upregulated during cold stress in a moderately tolerant line as compared to the more sensitive line. CONCLUSION This study facilitated the tagging of genome regions associated with variation in seedling traits of sorghum under cold and heat stress. These findings show the potential of genotype information for development of temperature resilient sorghum cultivars and further characterization of genes and their networks responsible for adaptation to thermal stresses. Knowledge on the gene networks from this research can be extended to the other cereal crops to better understand the genetic basis of resilience to temperature fluctuations during plant developmental stages.
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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.
| | - John J Burke
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA
| | - Nicholas Gladman
- 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
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Tracing QTLs for Leaf Blast Resistance and Agronomic Performance of Finger Millet (Eleusine coracana (L.) Gaertn.) Genotypes through Association Mapping and in silico Comparative Genomics Analyses. PLoS One 2016; 11:e0159264. [PMID: 27415007 PMCID: PMC4944987 DOI: 10.1371/journal.pone.0159264] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 06/29/2016] [Indexed: 02/04/2023] Open
Abstract
Finger millet is one of the small millets with high nutritive value. This crop is vulnerable to blast disease caused by Pyricularia grisea, which occurs annually during rainy and winter seasons. Leaf blast occurs at early crop stage and is highly damaging. Mapping of resistance genes and other quantitative trait loci (QTLs) for agronomic performance can be of great use for improving finger millet genotypes. Evaluation of one hundred and twenty-eight finger millet genotypes in natural field conditions revealed that leaf blast caused severe setback on agronomic performance for susceptible genotypes, most significant traits being plant height and root length. Plant height was reduced under disease severity while root length was increased. Among the genotypes, IE4795 showed superior response in terms of both disease resistance and better agronomic performance. A total of seven unambiguous QTLs were found to be associated with various agronomic traits including leaf blast resistance by association mapping analysis. The markers, UGEP101 and UGEP95, were strongly associated with blast resistance. UGEP98 was associated with tiller number and UGEP9 was associated with root length and seed yield. Cross species validation of markers revealed that 12 candidate genes were associated with 8 QTLs in the genomes of grass species such as rice, foxtail millet, maize, Brachypodium stacei, B. distachyon, Panicum hallii and switchgrass. Several candidate genes were found proximal to orthologous sequences of the identified QTLs such as 1,4-β-glucanase for leaf blast resistance, cytokinin dehydrogenase (CKX) for tiller production, calmodulin (CaM) binding protein for seed yield and pectin methylesterase inhibitor (PMEI) for root growth and development. Most of these QTLs and their putatively associated candidate genes are reported for first time in finger millet. On validation, these novel QTLs may be utilized in future for marker assisted breeding for the development of fungal resistant and high yielding varieties of finger millet.
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Using Genotyping by Sequencing to Map Two Novel Anthracnose Resistance Loci in Sorghum bicolor. G3-GENES GENOMES GENETICS 2016; 6:1935-46. [PMID: 27194807 PMCID: PMC4938647 DOI: 10.1534/g3.116.030510] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Colletotrichum sublineola is an aggressive fungal pathogen that causes anthracnose in sorghum [Sorghum bicolor (L.) Moench]. The obvious symptoms of anthracnose are leaf blight and stem rot. Sorghum, the fifth most widely grown cereal crop in the world, can be highly susceptible to the disease, most notably in hot and humid environments. In the southeastern United States the acreage of sorghum has been increasing steadily in recent years, spurred by growing interest in producing biofuels, bio-based products, and animal feed. Resistance to anthracnose is, therefore, of paramount importance for successful sorghum production in this region. To identify anthracnose resistance loci present in the highly resistant cultivar ‘Bk7’, a biparental mapping population of F3:4 and F4:5 sorghum lines was generated by crossing ‘Bk7’ with the susceptible inbred ‘Early Hegari-Sart’. Lines were phenotyped in three environments and in two different years following natural infection. The population was genotyped by sequencing. Following a stringent custom filtering protocol, totals of 5186 and 2759 informative SNP markers were identified in the two populations. Segregation data and association analysis identified resistance loci on chromosomes 7 and 9, with the resistance alleles derived from ‘Bk7’. Both loci contain multiple classes of defense-related genes based on sequence similarity and gene ontologies. Genetic analysis following an independent selection experiment of lines derived from a cross between ‘Bk7’ and sweet sorghum ‘Mer81-4’ narrowed the resistance locus on chromosome 9 substantially, validating this QTL. As observed in other species, sorghum appears to have regions of clustered resistance genes. Further characterization of these regions will facilitate the development of novel germplasm with resistance to anthracnose and other diseases.
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27
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Kulwal PL. Association Mapping and Genomic Selection—Where Does Sorghum Stand? COMPENDIUM OF PLANT GENOMES 2016. [DOI: 10.1007/978-3-319-47789-3_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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28
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Upadhyaya HD, Wang YH, Sastry DVSSR, Dwivedi SL, Prasad PVV, Burrell AM, Klein RR, Morris GP, Klein PE. Association mapping of germinability and seedling vigor in sorghum under controlled low-temperature conditions. Genome 2015; 59:137-45. [PMID: 26758024 DOI: 10.1139/gen-2015-0122] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sorghum is one of the world's most important food, feed, and fiber crops as well as a potential feedstock for lignocellulosic bioenergy. Early-season planting extends sorghum's growing season and increases yield in temperate regions. However, sorghum's sensitivity to low soil temperatures adversely impacts seed germination. In this study, we evaluated the 242 accessions of the ICRISAT sorghum mini core collection for seed germination and seedling vigor at 12 °C as a measure of cold tolerance. Genome-wide association analysis was performed with approximately 162,177 single nucleotide polymorphism markers. Only one marker locus (Locus 7-2) was significantly associated with low-temperature germination and none with vigor. The linkage of Locus 7-2 to low-temperature germination was supported by four lines of evidence: strong association in three independent experiments, co-localization with previously mapped cold tolerance quantitative trait loci (QTL) in sorghum, a candidate gene that increases cold tolerance and germination rate when its wheat homolog is overexpressed in tobacco, and its syntenic region in rice co-localized with two cold tolerance QTL in rice. This locus may be useful in developing tools for molecular breeding of sorghums with improved low-temperature germinability.
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Affiliation(s)
- Hari D Upadhyaya
- a International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Andhra Pradesh, India.,b Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA.,c UWA Institute of Agriculture, the University of Western Australia, Crawley WA 6009, Australia
| | - Yi-Hong Wang
- d Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Dintyala V S S R Sastry
- a International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Andhra Pradesh, India
| | - Sangam L Dwivedi
- a International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Andhra Pradesh, India
| | - P V Vara Prasad
- b Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - A Millie Burrell
- e Department of Horticulture and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Robert R Klein
- f USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX 77845, USA
| | - Geoffrey P Morris
- b Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Patricia E Klein
- e Department of Horticulture and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
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Li X, Li X, Fridman E, Tesso TT, Yu J. Dissecting repulsion linkage in the dwarfing gene Dw3 region for sorghum plant height provides insights into heterosis. Proc Natl Acad Sci U S A 2015; 112:11823-8. [PMID: 26351684 PMCID: PMC4586871 DOI: 10.1073/pnas.1509229112] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterosis is a main contributor to yield increase in many crop species. Different mechanisms have been proposed for heterosis: dominance, overdominance, epistasis, epigenetics, and protein metabolite changes. However, only limited examples of molecular dissection and validation of these mechanisms are available. Here, we present an example of discovery and validation of heterosis generated by a combination of repulsion linkage and dominance. Using a recombinant inbred line population, a separate quantitative trait locus (QTL) for plant height (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 gene. With two loci having repulsion linkage between two inbreds, heterosis in the hybrid can appear as a single locus with an overdominance mode of inheritance (i.e., pseudo-overdominance). Individually, alleles conferring taller plant height exhibited complete dominance over alleles conferring shorter height. Detailed analyses of different height components demonstrated that qHT7.1 affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. Computer simulations show that repulsion linkage could influence QTL detection and estimation of effect in segregating populations. Guided by findings in linkage mapping, a genome-wide association study of plant height with a sorghum diversity panel pinpointed genomic regions underlying the trait variation, including Dw1, Dw2, Dw3, Dw4, and qHT7.1. Multilocus mixed model analysis confirmed the advantage of complex trait dissection using an integrated approach. Besides identifying a specific genetic example of heterosis, our research indicated that integrated molecular dissection of complex traits in different population types can enable plant breeders to fine tune the breeding process for crop production.
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Affiliation(s)
- Xin Li
- Department of Agronomy, Iowa State University, Ames, IA 50011
| | - Xianran Li
- Department of Agronomy, Iowa State University, Ames, IA 50011
| | - Eyal Fridman
- Institute of Plant Science, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel
| | - Tesfaye T Tesso
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA 50011;
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Anami SE, Zhang L, Xia Y, Zhang Y, Liu Z, Jing H. Sweet sorghum ideotypes: genetic improvement of the biofuel syndrome. Food Energy Secur 2015. [DOI: 10.1002/fes3.63] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Sylvester Elikana Anami
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
- Institute of Biotechnology Research Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya
| | - Li‐Min Zhang
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Yan Xia
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Yu‐Miao Zhang
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Zhi‐Quan Liu
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Hai‐Chun Jing
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
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Wang X, Mace E, Hunt C, Cruickshank A, Henzell R, Parkes H, Jordan D. Two distinct classes of QTL determine rust resistance in sorghum. BMC PLANT BIOLOGY 2014; 14:366. [PMID: 25551674 PMCID: PMC4335369 DOI: 10.1186/s12870-014-0366-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 12/05/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND Agriculture is facing enormous challenges to feed a growing population in the face of rapidly evolving pests and pathogens. The rusts, in particular, are a major pathogen of cereal crops with the potential to cause large reductions in yield. Improving stable disease resistance is an on-going major and challenging focus for many plant breeding programs, due to the rapidly evolving nature of the pathogen. Sorghum is a major summer cereal crop that is also a host for a rust pathogen Puccinia purpurea, which occurs in almost all sorghum growing areas of the world, causing direct and indirect yield losses in sorghum worldwide, however knowledge about its genetic control is still limited. In order to further investigate this issue, QTL and association mapping methods were implemented to study rust resistance in three bi-parental populations and an association mapping set of elite breeding lines in different environments. RESULTS In total, 64 significant or highly significant QTL and 21 suggestive rust resistance QTL were identified representing 55 unique genomic regions. Comparisons across populations within the current study and with rust QTL identified previously in both sorghum and maize revealed a high degree of correspondence in QTL location. Negative phenotypic correlations were observed between rust, maturity and height, indicating a trend for both early maturing and shorter genotypes to be more susceptible to rust. CONCLUSIONS The significant amount of QTL co-location across traits, in addition to the consistency in the direction of QTL allele effects, has provided evidence to support pleiotropic QTL action across rust, height, maturity and stay-green, supporting the role of carbon stress in susceptibility to rust. Classical rust resistance QTL regions that did not co-locate with height, maturity or stay-green QTL were found to be significantly enriched for the defence-related NBS-encoding gene family, in contrast to the lack of defence-related gene enrichment in multi-trait effect rust resistance QTL. The distinction of disease resistance QTL hot-spots, enriched with defence-related gene families from QTL which impact on development and partitioning, provides plant breeders with knowledge which will allow for fast-tracking varieties with both durable pathogen resistance and appropriate adaptive traits.
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Affiliation(s)
- Xuemin Wang
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, Australia.
| | - Emma Mace
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | - Colleen Hunt
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, Australia.
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | - Alan Cruickshank
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | - Robert Henzell
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | - Heidi Parkes
- Department of Agriculture, Fisheries & Forestry (DAFF), Stanthorpe, QLD, Australia.
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, Australia.
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Sbei H, Sato K, Shehzad T, Harrabi M, Okuno K. Detection of QTLs for salt tolerance in Asian barley (Hordeum vulgare L.) by association analysis with SNP markers. BREEDING SCIENCE 2014; 64:378-88. [PMID: 25914593 PMCID: PMC4267313 DOI: 10.1270/jsbbs.64.378] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/08/2014] [Indexed: 05/30/2023]
Abstract
Two hundred ninety-six Asian barley (Hordeum vulgare L.) accessions were assessed to detect QTLs underlying salt tolerance by association analysis using a 384 single nucleotide polymorphism (SNP) marker system. The experiment was laid out at the seedling stage in a hydroponic solution under control and 250 mM NaCl solution with three replications of four plants each. Salt tolerance was assessed by leaf injury score (LIS) and salt tolerance indices (STIs) of the number of leaves (NL), shoot length (SL), root length (RL), shoot dry weight (SDW) and root dry weight (RDW). LIS was scored from 1 to 5 according to the severity of necrosis and chlorosis observed on leaves. There was a wide variation in salt tolerance among Asian barley accessions. LIS and STI (SDW) were the most suitable traits for screening salt tolerance. Association was estimated between markers and traits to detect QTLs for LIS and STI (SDW). Seven significant QTLs were located on chromosomes 1H (2 QTLs), 2H (2 QTLs), 3H (1 QTL), 4H (1 QTL) and 5H (1 QTL). Five QTLs were associated with LIS and 2 QTLs with STI (SDW). Two QTLs associated with LIS were newly identified on chromosomes 3H and 4H.
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Affiliation(s)
- Hanen Sbei
- Graduate School of Life and Environmental Sciences, University of Tsukuba,
Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572,
Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University,
Chuo 2-20-1, Kurashiki, Okayama 710-0046,
Japan
| | - Tariq Shehzad
- Graduate School of Life and Environmental Sciences, University of Tsukuba,
Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572,
Japan
- The Alliance for Research on North Africa, University of Tsukuba,
Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572,
Japan
| | - Moncef Harrabi
- National Institute of Agriculture at Tunis,
43 Avenue Charles Nicolle, Mahrajene City, 1082Tunisia
| | - Kazutoshi Okuno
- The Alliance for Research on North Africa, University of Tsukuba,
Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572,
Japan
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33
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Nayak SN, Song J, Villa A, Pathak B, Ayala-Silva T, Yang X, Todd J, Glynn NC, Kuhn DN, Glaz B, Gilbert RA, Comstock JC, Wang J. Promoting utilization of Saccharum spp. genetic resources through genetic diversity analysis and core collection construction. PLoS One 2014; 9:e110856. [PMID: 25333358 PMCID: PMC4205016 DOI: 10.1371/journal.pone.0110856] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/25/2014] [Indexed: 12/22/2022] Open
Abstract
Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance.
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Affiliation(s)
- Spurthi N. Nayak
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - Jian Song
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
- College of Life Sciences, Dezhou University, Dezhou, Shandong, China
| | - Andrea Villa
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - Bhuvan Pathak
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - Tomas Ayala-Silva
- Subtropical Horticulture Research Station, USDA-ARS, Miami, Florida, United States of America
| | - Xiping Yang
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - James Todd
- Everglades Research and Education Center, University of Florida, Belle Glade, Florida, United States of America
| | - Neil C. Glynn
- Sugarcane Field Station, USDA-ARS, Canal Point, Florida, United States of America
| | - David N. Kuhn
- Subtropical Horticulture Research Station, USDA-ARS, Miami, Florida, United States of America
| | - Barry Glaz
- Sugarcane Field Station, USDA-ARS, Canal Point, Florida, United States of America
| | - Robert A. Gilbert
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - Jack C. Comstock
- Sugarcane Field Station, USDA-ARS, Canal Point, Florida, United States of America
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
- Genetics Institute, Plant Molecular and Biology Program, University of Florida, Gainesville, Florida, United States of America
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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34
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Li F, Chen B, Xu K, Wu J, Song W, Bancroft I, Harper AL, Trick M, Liu S, Gao G, Wang N, Yan G, Qiao J, Li J, Li H, Xiao X, Zhang T, Wu X. Genome-wide association study dissects the genetic architecture of seed weight and seed quality in rapeseed (Brassica napus L.). DNA Res 2014; 21:355-67. [PMID: 24510440 PMCID: PMC4131830 DOI: 10.1093/dnares/dsu002] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/08/2014] [Indexed: 11/12/2022] Open
Abstract
Association mapping can quickly and efficiently dissect complex agronomic traits. Rapeseed is one of the most economically important polyploid oil crops, although its genome sequence is not yet published. In this study, a recently developed 60K Brassica Infinium(®) SNP array was used to analyse an association panel with 472 accessions. The single-nucleotide polymorphisms (SNPs) of the array were in silico mapped using 'pseudomolecules' representative of the genome of rapeseed to establish their hypothetical order and to perform association mapping of seed weight and seed quality. As a result, two significant associations on A8 and C3 of Brassica napus were detected for erucic acid content, and the peak SNPs were found to be only 233 and 128 kb away from the key genes BnaA.FAE1 and BnaC.FAE1. BnaA.FAE1 was also identified to be significantly associated with the oil content. Orthologues of Arabidopsis thaliana HAG1 were identified close to four clusters of SNPs associated with glucosinolate content on A9, C2, C7 and C9. For seed weight, we detected two association signals on A7 and A9, which were consistent with previous studies of quantitative trait loci mapping. The results indicate that our association mapping approach is suitable for fine mapping of the complex traits in rapeseed.
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Affiliation(s)
- Feng Li
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Biyun Chen
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Kun Xu
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Jinfeng Wu
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Weilin Song
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Ian Bancroft
- Department of Biology, University of York, York, UK
| | | | - Martin Trick
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Shengyi Liu
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Guizhen Gao
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Nian Wang
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Guixin Yan
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Jiangwei Qiao
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Jun Li
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Hao Li
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Xin Xiao
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Tianyao Zhang
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
| | - Xiaoming Wu
- Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No. 2 Xudong Second Road, Hubei Province, Wuhan 430062, China
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35
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Wang YH, Acharya A, Burrell AM, Klein RR, Klein PE, Hasenstein KH. Mapping and candidate genes associated with saccharification yield in sorghum. Genome 2013; 56:659-65. [PMID: 24299105 DOI: 10.1139/gen-2013-0134] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is a high-yielding, stress tolerant energy crop for lignocellulosic-based biofuel production. Saccharification is a process by which hydrolytic enzymes break down lignocellulosic materials to fermentable sugars for biofuel production, and mapping and identifying genes underlying saccharification yield is an important first step to genetically improve the plant for higher biofuel productivity. In this study, we used the ICRISAT sorghum mini core germplasm collection and 14 739 single nucleotide polymorphism markers to map saccharification yield. Seven marker loci were associated with saccharification yield and five of these loci were syntenic with regions in the maize genome that contain quantitative trait loci underlying saccharification yield and cell wall component traits. Candidate genes from the seven loci were identified but must be validated, with the most promising candidates being β-tubulin, which determines the orientation of cellulose microfibrils in plant secondary cell walls, and NST1, a master transcription factor controlling secondary cell wall biosynthesis in fibers. Other candidate genes underlying the different saccharification loci included genes that play a role in vascular development and suberin deposition in plants. The identified loci and candidate genes provide information into the factors controlling saccharification yield and may facilitate increasing biofuel production in sorghum.
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Affiliation(s)
- Yi-Hong Wang
- a Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
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