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Kumar N, Boatwright JL, Sapkota S, Brenton ZW, Ballén-Taborda C, Myers MT, Cox WA, Jordan KE, Kresovich S, Boyles RE. Discovering useful genetic variation in the seed parent gene pool for sorghum improvement. Front Genet 2023; 14:1221148. [PMID: 37790706 PMCID: PMC10544336 DOI: 10.3389/fgene.2023.1221148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/04/2023] [Indexed: 10/05/2023] Open
Abstract
Multi-parent populations contain valuable genetic material for dissecting complex, quantitative traits and provide a unique opportunity to capture multi-allelic variation compared to the biparental populations. A multi-parent advanced generation inter-cross (MAGIC) B-line (MBL) population composed of 708 F6 recombinant inbred lines (RILs), was recently developed from four diverse founders. These selected founders strategically represented the four most prevalent botanical races (kafir, guinea, durra, and caudatum) to capture a significant source of genetic variation to study the quantitative traits in grain sorghum [Sorghum bicolor (L.) Moench]. MBL was phenotyped at two field locations for seven yield-influencing traits: panicle type (PT), days to anthesis (DTA), plant height (PH), grain yield (GY), 1000-grain weight (TGW), tiller number per meter (TN) and yield per panicle (YPP). High phenotypic variation was observed for all the quantitative traits, with broad-sense heritabilities ranging from 0.34 (TN) to 0.84 (PH). The entire population was genotyped using Diversity Arrays Technology (DArTseq), and 8,800 single nucleotide polymorphisms (SNPs) were generated. A set of polymorphic, quality-filtered markers (3,751 SNPs) and phenotypic data were used for genome-wide association studies (GWAS). We identified 52 marker-trait associations (MTAs) for the seven traits using BLUPs generated from replicated plots in two locations. We also identified desirable allelic combinations based on the plant height loci (Dw1, Dw2, and Dw3), which influences yield related traits. Additionally, two novel MTAs were identified each on Chr1 and Chr7 for yield traits independent of dwarfing genes. We further performed a multi-variate adaptive shrinkage analysis and 15 MTAs with pleiotropic effect were identified. The five best performing MBL progenies were selected carrying desirable allelic combinations. Since the MBL population was designed to capture significant diversity for maintainer line (B-line) accessions, these progenies can serve as valuable resources to develop superior sorghum hybrids after validation of their general combining abilities via crossing with elite pollinators. Further, newly identified desirable allelic combinations can be used to enrich the maintainer germplasm lines through marker-assisted backcross breeding.
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Affiliation(s)
- Neeraj Kumar
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - J. Lucas Boatwright
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Sirjan Sapkota
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
| | - Zachary W. Brenton
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Carolina Seed Systems, Darlington, SC, United States
| | - Carolina Ballén-Taborda
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
- Pee Dee Research and Education Center, Clemson University, Florence, SC, United States
| | - Matthew T. Myers
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - William A. Cox
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Kathleen E. Jordan
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Stephen Kresovich
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
- Feed the Future Innovation Lab for Crop Improvement, Cornell University, Ithaca, NY, United States
| | - Richard E. Boyles
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
- Pee Dee Research and Education Center, Clemson University, Florence, SC, United States
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Krishna TPA, Veeramuthu D, Maharajan T, Soosaimanickam M. The Era of Plant Breeding: Conventional Breeding to Genomics-assisted Breeding for Crop Improvement. Curr Genomics 2023; 24:24-35. [PMID: 37920729 PMCID: PMC10334699 DOI: 10.2174/1389202924666230517115912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/31/2023] [Accepted: 04/14/2023] [Indexed: 11/04/2023] Open
Abstract
Plant breeding has made a significant contribution to increasing agricultural production. Conventional breeding based on phenotypic selection is not effective for crop improvement. Because phenotype is considerably influenced by environmental factors, which will affect the selection of breeding materials for crop improvement. The past two decades have seen tremendous progress in plant breeding research. Especially the availability of high-throughput molecular markers followed by genomic-assisted approaches significantly contributed to advancing plant breeding. Integration of speed breeding with genomic and phenomic facilities allowed rapid quantitative trait loci (QTL)/gene identifications and ultimately accelerated crop improvement programs. The advances in sequencing technology helps to understand the genome organization of many crops and helped with genomic selection in crop breeding. Plant breeding has gradually changed from phenotype-to-genotype-based to genotype-to-phenotype-based selection. High-throughput phenomic platforms have played a significant role in the modern breeding program and are considered an essential part of precision breeding. In this review, we discuss the rapid advance in plant breeding technology for efficient crop improvements and provide details on various approaches/platforms that are helpful for crop improvement. This review will help researchers understand the recent developments in crop breeding and improvements.
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Affiliation(s)
| | - Duraipandiyan Veeramuthu
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, Tamil Nadu, India
| | - Theivanayagam Maharajan
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, Tamil Nadu, India
| | - Mariapackiam Soosaimanickam
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, Tamil Nadu, India
- Department of Advanced Zoology & Biotechnology, Loyola College, Nungambakkam, Chennai, 600034, India
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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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Zhang Y, Fan X, Liang D, Guo Q, Zhang X, Nie M, Li C, Meng S, Zhang X, Xu P, Guo W, Wang H, Liu Q, Wu Y. The Identification of a Yield-Related Gene Controlling Multiple Traits Using GWAS in Sorghum ( Sorghum bicolor L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1557. [PMID: 37050183 PMCID: PMC10097259 DOI: 10.3390/plants12071557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Sorghum bicolor (L.) is one of the oldest crops cultivated by human beings which has been used in food and wine making. To understand the genetic diversity of sorghum breeding resources and further guide molecular-marker-assisted breeding, six yield-related traits were analyzed for 214 sorghum germplasm from all over the world, and 2,811,016 single-nucleotide polymorphisms (SNPs) markers were produced by resequencing these germplasms. After controlling Q and K, QTLs were found to be related to the traits using three algorisms. Interestingly, an important QTL was found which may affect multiple traits in this study. It was the most likely candidate gene for the gene SORBI_3008G116500, which was a homolog of Arabidopsis thaliana gene-VIP5 found by analyzing the annotation of the gene in the LD block. The haplotype analysis showed that the SORBI_3008G116500hap3 was the elite haplotype, and it only existed in Chinese germplasms. The traits were proven to be more associated with the SNPs of the SORBI_3008G116500 promoter through gene association studies. Overall, the QTLs and the genes identified in this study would benefit molecular-assisted yield breeding in sorghum.
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Affiliation(s)
- Yizhong Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Xinqi Fan
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Du Liang
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Qi Guo
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Xiaojuan Zhang
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Mengen Nie
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Chunhong Li
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Shan Meng
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xianggui Zhang
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Peng Xu
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Wenqi Guo
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Huiyan Wang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Qingshan Liu
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Yuxiang Wu
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
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5
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Genetic Architecture of Grain Yield-Related Traits in Sorghum and Maize. Int J Mol Sci 2022; 23:ijms23052405. [PMID: 35269548 PMCID: PMC8909957 DOI: 10.3390/ijms23052405] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/06/2022] [Accepted: 02/18/2022] [Indexed: 02/08/2023] Open
Abstract
Grain size, grain number per panicle, and grain weight are crucial determinants of yield-related traits in cereals. Understanding the genetic basis of grain yield-related traits has been the main research object and nodal in crop science. Sorghum and maize, as very close C4 crops with high photosynthetic rates, stress tolerance and large biomass characteristics, are extensively used to produce food, feed, and biofuels worldwide. In this review, we comprehensively summarize a large number of quantitative trait loci (QTLs) associated with grain yield in sorghum and maize. We placed great emphasis on discussing 22 fine-mapped QTLs and 30 functionally characterized genes, which greatly hinders our deep understanding at the molecular mechanism level. This review provides a general overview of the comprehensive findings on grain yield QTLs and discusses the emerging trend in molecular marker-assisted breeding with these QTLs.
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Somegowda VK, Prasad KVSV, Naravula J, Vemula A, Selvanayagam S, Rathore A, Jones CS, Gupta R, Deshpande SP. Genetic Dissection and Quantitative Trait Loci Mapping of Agronomic and Fodder Quality Traits in Sorghum Under Different Water Regimes. FRONTIERS IN PLANT SCIENCE 2022; 13:810632. [PMID: 35251083 PMCID: PMC8892184 DOI: 10.3389/fpls.2022.810632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 01/03/2022] [Indexed: 06/01/2023]
Abstract
Livestock provides an additional source of income for marginal cropping farmers, but crop residues that are used as a main source of animal feed are characteristically low in digestibility and protein content. This reduces the potential livestock product yield and quality. The key trait, which influences the quality and the cost of animal feed, is digestibility. In this study, we demonstrate that sorghum breeding can be directed to achieve genetic gains for both fodder biomass and digestibility without any trade-offs. The genotypic variance has shown significant differences for biomass across years (13,035 in 2016 and 3,395 in 2017) while in vitro organic matter digestibility (IVOMD) showed significant genotypic variation in 2016 (0.253) under drought. A range of agronomic and fodder quality traits was found to vary significantly in the population within both the control and drought conditions and across both years of the study. There was significant genotypic variance (σg2) and genotypic × treatment variance (σgxt2) in dry matter production in a recombinant inbred line (RIL) population in both study years, while there was only significant σg2 and σgxt2 in IVOMD under the control conditions. There was no significant correlation identified between biomass and digestibility traits under the control conditions, but there was a positive correlation under drought. However, a negative relation was observed between digestibility and grain yield under the control conditions, while there was no significant correlation under drought population, which was genotyped using the genotyping-by-sequencing (GBS) technique, and 1,141 informative single nucleotide polymorphism (SNP) markers were identified. A linkage map was constructed, and a total of 294 quantitative trait loci (QTLs) were detected, with 534 epistatic interactions, across all of the traits under study. QTL for the agronomic traits fresh and dry weight, together with plant height, mapped on to the linkage group (LG) 7, while QTL for IVOMD mapped on to LG1, 2, and 8. A number of genes previously reported to play a role in nitrogen metabolism and cell wall-related functions were found to be associated with these QTL.
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Affiliation(s)
- Vinutha K. Somegowda
- International Crops Research Institute for the Semi-arid Tropics-HQ, Patancheru, India
- Department of Biotechnology, Vignan University, Vadlamudi, India
| | - Kodukula V. S. V. Prasad
- International Livestock Research Institute (ILRI), International Crops Research Institute for the Semi-arid Tropics Campus, Patancheru, India
| | - Jalaja Naravula
- Department of Biotechnology, Vignan University, Vadlamudi, India
| | - Anilkumar Vemula
- International Crops Research Institute for the Semi-arid Tropics-HQ, Patancheru, India
| | | | - Abhishek Rathore
- International Crops Research Institute for the Semi-arid Tropics-HQ, Patancheru, India
| | - Chris S. Jones
- International Livestock Research Institute (ILRI), International Crops Research Institute for the Semi-arid Tropics Campus, Patancheru, India
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-arid Tropics-HQ, Patancheru, India
| | - Santosh P. Deshpande
- International Crops Research Institute for the Semi-arid Tropics-HQ, Patancheru, India
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Chiluwal A, Perumal R, Poudel HP, Muleta K, Ostmeyer T, Fedenia L, Pokharel M, Bean SR, Sebela D, Bheemanahalli R, Oumarou H, Klein P, Rooney WL, Jagadish SVK. Genetic control of source-sink relationships in grain sorghum. PLANTA 2022; 255:40. [PMID: 35038036 DOI: 10.1007/s00425-022-03822-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
QTL hotspots identified for selected source-sink-related traits provide the opportunity for pyramiding favorable alleles for improving sorghum productivity under diverse environments. A sorghum bi-parental mapping population was evaluated under six different environments at Hays and Manhattan, Kansas, USA, in 2016 and 2017, to identify genomic regions controlling source-sink relationships. The population consisted of 210 recombinant inbred lines developed from US elite post-flowering drought susceptible (RTx430) and a known post-flowering drought tolerant cultivar (SC35). Selected physiological traits related to source (effective quantum yield of photosystem II and chlorophyll index), sink (grain yield per panicle) and panicle neck diameter were recorded during grain filling. The results showed strong phenotypic and genotypic association between panicle neck diameter and grain yield per panicle during mid-grain filling and at maturity. Multiple QTL model revealed 5-12 including 2-5 major QTL for each trait. Among them 3, 7 and 8 QTL for quantum yield, panicle neck diameter and chlorophyll index, respectively, have not been identified previously in sorghum. Phenotypic variation explained by QTL identified across target traits ranged between 5.5 and 25.4%. Panicle neck diameter and grain yield per panicle were positively associated, indicating the possibility of targeting common co-localized QTL to improve both traits simultaneously through marker-assisted selection. Three major QTL hotspots, controlling multiple traits were identified on chromosome 1 (52.23-61.18 Mb), 2 (2.52-11.43 Mb) and 3 (1.32-3.95 Mb). The identified genomic regions and underlying candidate genes can be utilized in pyramiding favorable alleles for improving source-sink relationships in sorghum under diverse environments.
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Affiliation(s)
- Anuj Chiluwal
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Ramasamy Perumal
- Agricultural Research Center, Kansas State University, Hays, KS, 67601, USA
| | - Hari P Poudel
- Agriculture and Agri-Food Canada, 5403 First Ave. South, Lethbridge, AB, T1J 4B1, Canada
| | - Kebede Muleta
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Troy Ostmeyer
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Lauren Fedenia
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Meghnath Pokharel
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Scott R Bean
- Grain Quality and Structure Research Unit, CGAHR, USDA-ARS, 1515 College Avenue, Manhattan, KS, 66502, USA
| | - David Sebela
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Raju Bheemanahalli
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Halilou Oumarou
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Patricia Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - William L Rooney
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - S V Krishna Jagadish
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA.
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8
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Drought Tolerance and Application of Marker-Assisted Selection in Sorghum. BIOLOGY 2021; 10:biology10121249. [PMID: 34943164 PMCID: PMC8699005 DOI: 10.3390/biology10121249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/07/2021] [Accepted: 10/07/2021] [Indexed: 12/30/2022]
Abstract
Simple Summary Sorghum is a climate-resilient crop grown in limited rainfall areas globally. However, climate change has increased temperature and shortened rainfall durations, which has constrained crop yield. We reviewed mechanisms of drought tolerance and application of marker-assisted selection in sorghum. Marker-assisted selection uses DNA molecular markers to map quantitative trait loci (QTL) associated with stay-green. Stg1, Stg2, Stg3, Stg4, Stg3A, and Stg3B QTLs associated with stay-green and high yield, have been mapped in sorghum. These QTLs are used for introgression into the senescent sorghum varieties through marker-assisted backcrossing. Abstract Sorghum is an important staple food crop in drought prone areas of Sub-Saharan Africa, which is characterized by erratic rainfall with poor distribution. Sorghum is a drought-tolerant crop by nature with reasonable yield compared to other cereal crops, but such abiotic stress adversely affects the productivity. Some sorghum varieties maintain green functional leaves under post-anthesis drought stress referred to as stay-green, which makes it an important crop for food and nutritional security. Notwithstanding, it is difficult to maintain consistency of tolerance over time due to climate change, which is caused by human activities. Drought in sorghum is addressed by several approaches, for instance, breeding drought-tolerant sorghum using conventional and molecular technologies. The challenge with conventional methods is that they depend on phenotyping stay-green, which is complex in sorghum, as it is constituted by multiple genes and environmental effects. Marker assisted selection, which involves the use of DNA molecular markers to map QTL associated with stay-green, has been useful to supplement stay-green improvement in sorghum. It involves QTL mapping associated with the stay-green trait for introgression into the senescent sorghum varieties through marker-assisted backcrossing by comparing with phenotypic field data. Therefore, this review discusses mechanisms of drought tolerance in sorghum focusing on physiological, morphological, and biochemical traits. In addition, the review discusses the application of marker-assisted selection techniques, including marker-assisted backcrossing, QTL mapping, and QTL pyramiding for addressing post-flowering drought in sorghum.
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Wang L, Upadhyaya HD, Zheng J, Liu Y, Singh SK, Gowda CLL, Kumar R, Zhu Y, Wang YH, Li J. Genome-Wide Association Mapping Identifies Novel Panicle Morphology Loci and Candidate Genes in Sorghum. FRONTIERS IN PLANT SCIENCE 2021; 12:743838. [PMID: 34675951 PMCID: PMC8525895 DOI: 10.3389/fpls.2021.743838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Panicle morphology is an important trait in racial classification and can determine grain yield and other agronomic traits in sorghum. In this study, we performed association mapping of panicle length, panicle width, panicle compactness, and peduncle recurving in the sorghum mini core panel measured in multiple environments with 6,094,317 single nucleotide polymorphism (SNP) markers. We mapped one locus each on chromosomes 7 and 9 to recurving peduncles and eight loci for panicle length, panicle width, and panicle compactness. Because panicle length was positively correlated with panicle width, all loci for panicle length and width were colocalized. Among the eight loci, two each were on chromosomes 1, 2, and 6, and one each on chromosomes 8 and 10. The two loci on chromosome 2, i.e., Pm 2-1 and Pm 2-2, were detected in 7 and 5 out of 11 testing environments, respectively. Pm 2-2 colocalized with panicle compactness. Candidate genes were identified from both loci. The rice Erect Panicle2 (EP2) ortholog was among the candidate genes in Pm 2-2. EP2 regulates panicle erectness and panicle length in rice and encodes a novel plant-specific protein with unknown functions. The results of this study may facilitate the molecular identification of panicle morphology-related genes and the enhancement of yield and adaptation in sorghum.
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Affiliation(s)
- Lihua Wang
- College of Agriculture, Anhui Science and Technology University, Chuzhou, China
| | - Hari D. Upadhyaya
- Gene Bank, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheruvu, India
| | - Jian Zheng
- College of Agriculture, Anhui Science and Technology University, Chuzhou, China
| | - Yanlong Liu
- College of Agriculture, Anhui Science and Technology University, Chuzhou, China
| | - Shailesh Kumar Singh
- Gene Bank, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheruvu, India
| | - C. L. L. Gowda
- Gene Bank, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheruvu, India
| | - Rajendra Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Yongqun Zhu
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences (SAAS), Chengdu, 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, Chuzhou, China
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10
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Genetic dissection of QTLs associated with spikelet-related traits and grain size in sorghum. Sci Rep 2021; 11:9398. [PMID: 33931706 PMCID: PMC8087780 DOI: 10.1038/s41598-021-88917-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
Although spikelet-related traits such as size of anther, spikelet, style, and stigma are associated with sexual reproduction in grasses, no QTLs have been reported in sorghum. Additionally, there are only a few reports on sorghum QTLs related to grain size, such as grain length, width, and thickness. In this study, we performed QTL analyses of nine spikelet-related traits (length of sessile spikelet, pedicellate spikelet, pedicel, anther, style, and stigma; width of sessile spikelet and stigma; and stigma pigmentation) and six grain-related traits (length, width, thickness, length/width ratio, length/thickness ratio, and width/thickness ratio) using sorghum recombinant inbred lines. We identified 36 and 7 QTLs for spikelet-related traits and grain-related traits, respectively, and found that most sorghum spikelet organ length- and width-related traits were partially controlled by the dwarf genes Dw1 and Dw3. Conversely, we found that these Dw genes were not strongly involved in the regulation of grain size. The QTLs identified in this study aid in understanding the genetic basis of spikelet- and grain-related traits in sorghum.
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11
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Pandian BA, Varanasi A, Vennapusa AR, Sathishraj R, Lin G, Zhao M, Tunnell M, Tesso T, Liu S, Prasad PVV, Jugulam M. Characterization, Genetic Analyses, and Identification of QTLs Conferring Metabolic Resistance to a 4-Hydroxyphenylpyruvate Dioxygenase Inhibitor in Sorghum ( Sorghum bicolor). FRONTIERS IN PLANT SCIENCE 2020; 11:596581. [PMID: 33362828 PMCID: PMC7756693 DOI: 10.3389/fpls.2020.596581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/09/2020] [Indexed: 05/24/2023]
Abstract
Postemergence grass weed control continues to be a major challenge in grain sorghum [Sorghum bicolor (L.) Moench], primarily due to lack of herbicide options registered for use in this crop. The development of herbicide-resistant sorghum technology to facilitate broad-spectrum postemergence weed control can be an economical and viable solution. The 4-hydroxyphenylpyruvate dioxygenase-inhibitor herbicides (e.g., mesotrione or tembotrione) can control a broad spectrum of weeds including grasses, which, however, are not registered for postemergence application in sorghum due to crop injury. In this study, we identified two tembotrione-resistant sorghum genotypes (G-200, G-350) and one susceptible genotype (S-1) by screening 317 sorghum lines from a sorghum association panel (SAP). These tembotrione-resistant and tembotrione-susceptible genotypes were evaluated in a tembotrione dose-response [0, 5.75, 11.5, 23, 46, 92 (label recommended dose), 184, 368, and 736 g ai ha-1] assay. Compared with S-1, the genotypes G-200 and G-350 exhibited 10- and seven fold more resistance to tembotrione, respectively. To understand the inheritance of tembotrione-resistant trait, crosses were performed using S-1 and G-200 or G-350 to generate F1 and F2 progeny. The F1 and F2 progeny were assessed for their response to tembotrione treatment. Genetic analyses of the F1 and F2 progeny demonstrated that the tembotrione resistance in G-200 and G-350 is a partially dominant polygenic trait. Furthermore, cytochrome P450 (CYP)-inhibitor assay using malathion and piperonyl butoxide suggested possible CYP-mediated metabolism of tembotrione in G-200 and G-350. Genotype-by-sequencing based quantitative trait loci (QTL) mapping revealed QTLs associated with tembotrione resistance in G-200 and G-350 genotypes. Overall, the genotypes G-200 and G-350 confer a high level of metabolic resistance to tembotrione and controlled by a polygenic trait. There is an enormous potential to introgress the tembotrione resistance into breeding lines to develop agronomically desirable sorghum hybrids.
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Affiliation(s)
| | | | | | | | - Guifang Lin
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Mingxia Zhao
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Madison Tunnell
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Tesfaye Tesso
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - P. V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
- Sustainable Intensification Innovation Lab, Kansas State University, Manhattan, KS, United States
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
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12
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Venkata BP, Polzin R, Wilkes R, Fearn A, Blumenthal D, Rohrbough S, Taylor NJ. Heterologous Overexpression of Arabidopsis cel1 Enhances Grain Yield, Biomass and Early Maturity in Setaria viridis. FRONTIERS IN PLANT SCIENCE 2020; 11:515078. [PMID: 33240288 PMCID: PMC7683425 DOI: 10.3389/fpls.2020.515078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Heterologous overexpression of Arabidopsis cellulase 1 (Atcel1) results in enhanced yield, early maturity, and increased biomass in dicotyledonous species like poplar and eucalyptus but has not been demonstrated in monocots. We produced transgenic Setaria viridis accession A10.1 plants overexpressing a monocotyledonous codon optimized (MCO) Atcel1. Agronomic characterization of the transgenic events showed that heterologous overexpression of MCOAtcel1 caused enhanced grain yield, shoot biomass, and accelerated maturation rate in the model grass species S. viridis under growth chamber conditions. The agronomic trait differences observed were consistent with previous reports in dicots but are here described in a monocot species and associated with increased seed yield. Overexpression of Atcel1 in S. viridis was shown to increase the number of panicles and seeds by 24-30%, enhance overall grain yield by up to 26%, and lead to a shoot dry biomass increase of 16-19%. Overexpression also reduced time to plant maturation and senescence by 12.5%. Our findings in S. viridis suggest that manipulation of Atcel1 has potential for developing early-maturing and higher-yielding monocotyledonous biomass crops suitable for climate-smart agriculture.
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Affiliation(s)
- Bala P. Venkata
- Donald Danforth Plant Science Center, St. Louis, MO, United States
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13
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Zou G, Zhai G, Yan S, Li S, Zhou L, Ding Y, Liu H, Zhang Z, Zou J, Zhang L, Chen J, Xin Z, Tao Y. Sorghum qTGW1a encodes a G-protein subunit and acts as a negative regulator of grain size. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5389-5401. [PMID: 32497208 DOI: 10.1093/jxb/eraa277] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Grain size is a major determinant of grain yield in sorghum and other cereals. Over 100 quantitative trait loci (QTLs) of grain size have been identified in sorghum. However, no gene underlying any grain size QTL has been cloned. Here, we describe the fine mapping and cloning of one grain size QTL. From an F8 recombinant inbred line population derived from a cross between inbred lines 654 and LTR108, we identified 44 grain size QTLs. One QTL, qTGW1a, was detected consistently on the long arm of chromosome 1 in the span of 4 years. Using the extreme recombinants from an F2:3 fine-mapping population, qTGW1a was delimited within a ~33 kb region containing three predicted genes. One of them, SORBI_3001G341700, predicted to encode a G-protein γ subunit and homologous to GS3 in rice, is likely to be the causative gene for qTGW1a. qTGW1a appears to act as a negative regulator of grain size in sorghum. The functional allele of the putatively causative gene of qTGW1a from inbred line 654 decreased grain size, plant height, and grain yield in transgenic rice. Identification of the gene underlying qTGW1a advances our understanding of the regulatory mechanisms of grain size in sorghum and provides a target to manipulate grain size through genome editing.
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Affiliation(s)
- Guihua Zou
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guowei Zhai
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Song Yan
- Rice National Engineering Laboratory, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Sujuan Li
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lengbo Zhou
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yanqing Ding
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Heqin Liu
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhipeng Zhang
- Chinese National Sorghum Improvement Center, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Jianqiu Zou
- Chinese National Sorghum Improvement Center, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Liyi Zhang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Junping Chen
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, USA
| | - Zhanguo Xin
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, USA
| | - Yuezhi Tao
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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14
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Kajiya-Kanegae H, Takanashi H, Fujimoto M, Ishimori M, Ohnishi N, Wacera W F, Omollo EA, Kobayashi M, Yano K, Nakano M, Kozuka T, Kusaba M, Iwata H, Tsutsumi N, Sakamoto W. RAD-seq-Based High-Density Linkage Map Construction and QTL Mapping of Biomass-Related Traits in Sorghum using the Japanese Landrace Takakibi NOG. PLANT & CELL PHYSIOLOGY 2020; 61:1262-1272. [PMID: 32353144 DOI: 10.1093/pcp/pcaa056] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
Sorghum [Sorghum bicolor (L.) Moench] grown locally by Japanese farmers is generically termed Takakibi, although its genetic diversity compared with geographically distant varieties or even within Takakibi lines remains unclear. To explore the genomic diversity and genetic traits controlling biomass and other physiological traits in Takakibi, we focused on a landrace, NOG, in this study. Admixture analysis of 460 sorghum accessions revealed that NOG belonged to the subgroup that represented Asian sorghums, and it was only distantly related to American/African accessions including BTx623. In an attempt to dissect major traits related to biomass, we generated a recombinant inbred line (RIL) from a cross between BTx623 and NOG, and we constructed a high-density linkage map based on 3,710 single-nucleotide polymorphisms obtained by restriction-site-associated DNA sequencing of 213 RIL individuals. Consequently, 13 fine quantitative trait loci (QTLs) were detected on chromosomes 2, 3, 6, 7, 8 and 9, which included five QTLs for days to heading, three for plant height (PH) and total shoot fresh weight and two for Brix. Furthermore, we identified two dominant loci for PH as being identical to the previously reported dw1 and dw3. Together, these results corroborate the diversified genome of Japanese Takakibi, while the RIL population and high-density linkage map generated in this study will be useful for dissecting other important traits in sorghum.
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Affiliation(s)
- Hiromi Kajiya-Kanegae
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8517, Japan
| | - Hideki Takanashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Masaru Fujimoto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Motoyuki Ishimori
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Norikazu Ohnishi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046 Japan
| | - Fiona Wacera W
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046 Japan
| | - Everlyne A Omollo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046 Japan
| | - Masaaki Kobayashi
- Department of Life Sciences Faculty of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571 Japan
| | - Kentaro Yano
- Department of Life Sciences Faculty of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571 Japan
| | - Michiharu Nakano
- Graduate School of Integral Science for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526 Japan
| | - Toshiaki Kozuka
- Graduate School of Integral Science for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526 Japan
| | - Makoto Kusaba
- Graduate School of Integral Science for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526 Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Nobuhiro Tsutsumi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046 Japan
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15
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Zhou L, Wang C, Gao X, Ding Y, Cheng B, Zhang G, Cao N, Xu Y, Shao M, Zhang L. Genome-wide variations analysis of sorghum cultivar Hongyingzi for brewing Moutai liquor. Hereditas 2020; 157:19. [PMID: 32410666 PMCID: PMC7227080 DOI: 10.1186/s41065-020-00130-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/14/2020] [Indexed: 11/28/2022] Open
Abstract
Background Hongyingzi is a sorghum (Sorghum bicolor L. Moench) cultivar for brewing Moutai liquor. For an overall understanding of the whole genome of Hongyingzi, we performed whole-genome resequencing technology to reveal its comprehensive variations. Results Compared with the BTx623 reference genome, we uncovered 1,885,774 single nucleotide polymorphisms (SNPs), 309,381 small fragments insertions and deletions (Indels), 31,966 structural variations (SVs), and 217,273 copy number variations (CNVs). These alterations conferred 29,614 gene variations. It was also predicted that 35 gene variations were related to the multidrug and toxic efflux (MATE) transporter, chalcone synthase (CHS), ATPase isoform 10 (AHA10) transporter, dihydroflavonol-4-reductase (DFR), the laccase 15 (LAC15), flavonol 3′-hydroxylase (F3′H), flavanone 3-hydroxylase (F3H), O-methyltransferase (OMT), flavonoid 3′5′ hydroxylase (F3′5′H), UDP-glucose:sterol-glucosyltransferase (SGT), flavonol synthase (FLS), and chalcone isomerase (CHI) involved in the tannin synthesis. Conclusions These results would provide theoretical supports for the molecular markers developments and gene function studies related to the tannin synthesis, and the genetic improvement of liquor-making sorghum based on the genome editing technology.
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Affiliation(s)
- Lingbo Zhou
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Can Wang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Xu Gao
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Yanqing Ding
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Bin Cheng
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Guobing Zhang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Ning Cao
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Yan Xu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Mingbo Shao
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China
| | - Liyi Zhang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China.
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16
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Tao Y, Zhao X, Wang X, Hathorn A, Hunt C, Cruickshank AW, van Oosterom EJ, Godwin ID, Mace ES, Jordan DR. Large-scale GWAS in sorghum reveals common genetic control of grain size among cereals. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1093-1105. [PMID: 31659829 PMCID: PMC7061873 DOI: 10.1111/pbi.13284] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/30/2019] [Accepted: 10/24/2019] [Indexed: 05/20/2023]
Abstract
Grain size is a key yield component of cereal crops and a major quality attribute. It is determined by a genotype's genetic potential and its capacity to fill the grains. This study aims to dissect the genetic architecture of grain size in sorghum. An integrated genome-wide association study (GWAS) was conducted using a diversity panel (n = 837) and a BC-NAM population (n = 1421). To isolate genetic effects associated with genetic potential of grain size, rather than the genotype's capacity to fill the grains, a treatment of removing half of the panicle was imposed during flowering. Extensive and highly heritable variation in grain size was observed in both populations in 5 field trials, and 81 grain size QTL were identified in subsequent GWAS. These QTL were enriched for orthologues of known grain size genes in rice and maize, and had significant overlap with SNPs associated with grain size in rice and maize, supporting common genetic control of this trait among cereals. Grain size genes with opposite effect on grain number were less likely to overlap with the grain size QTL from this study, indicating the treatment facilitated identification of genetic regions related to the genetic potential of grain size. These results enhance understanding of the genetic architecture of grain size in cereal, and pave the way for exploration of underlying molecular mechanisms and manipulation of this trait in breeding practices.
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Affiliation(s)
- Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
| | - Xianrong Zhao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
| | - Xuemin Wang
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
| | - Adrian Hathorn
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
| | - Colleen Hunt
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
- Agri‐Science QueenslandDepartment of Agriculture and Fisheries (DAF)Hermitage Research FacilityWarwickQldAustralia
| | - Alan W. Cruickshank
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
- Agri‐Science QueenslandDepartment of Agriculture and Fisheries (DAF)Hermitage Research FacilityWarwickQldAustralia
| | - Erik J. van Oosterom
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandBrisbaneQldAustralia
| | - Ian D. Godwin
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandBrisbaneQldAustralia
| | - Emma S. Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
- Agri‐Science QueenslandDepartment of Agriculture and Fisheries (DAF)Hermitage Research FacilityWarwickQldAustralia
| | - David R. Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
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17
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Zhang Z, Li J, Jamshed M, Shi Y, Liu A, Gong J, Wang S, Zhang J, Sun F, Jia F, Ge Q, Fan L, Zhang Z, Pan J, Fan S, Wang Y, Lu Q, Liu R, Deng X, Zou X, Jiang X, Liu P, Li P, Iqbal MS, Zhang C, Zou J, Chen H, Tian Q, Jia X, Wang B, Ai N, Feng G, Wang Y, Hong M, Li S, Lian W, Wu B, Hua J, Zhang C, Huang J, Xu A, Shang H, Gong W, Yuan Y. Genome-wide quantitative trait loci reveal the genetic basis of cotton fibre quality and yield-related traits in a Gossypium hirsutum recombinant inbred line population. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:239-253. [PMID: 31199554 PMCID: PMC6920336 DOI: 10.1111/pbi.13191] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 05/30/2019] [Accepted: 06/11/2019] [Indexed: 05/02/2023]
Abstract
Cotton is widely cultivated globally because it provides natural fibre for the textile industry and human use. To identify quantitative trait loci (QTLs)/genes associated with fibre quality and yield, a recombinant inbred line (RIL) population was developed in upland cotton. A consensus map covering the whole genome was constructed with three types of markers (8295 markers, 5197.17 centimorgans (cM)). Six fibre yield and quality traits were evaluated in 17 environments, and 983 QTLs were identified, 198 of which were stable and mainly distributed on chromosomes 4, 6, 7, 13, 21 and 25. Thirty-seven QTL clusters were identified, in which 92.8% of paired traits with significant medium or high positive correlations had the same QTL additive effect directions, and all of the paired traits with significant medium or high negative correlations had opposite additive effect directions. In total, 1297 genes were discovered in the QTL clusters, 414 of which were expressed in two RNA-Seq data sets. Many genes were discovered, 23 of which were promising candidates. Six important QTL clusters that included both fibre quality and yield traits were identified with opposite additive effect directions, and those on chromosome 13 (qClu-chr13-2) could increase fibre quality but reduce yield; this result was validated in a natural population using three markers. These data could provide information about the genetic basis of cotton fibre quality and yield and help cotton breeders to improve fibre quality and yield simultaneously.
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19
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Mohammed R, Are AK, Bhavanasi R, Munghate RS, Kavi Kishor PB, Sharma HC. Quantitative genetic analysis of agronomic and morphological traits in sorghum, Sorghum bicolor. FRONTIERS IN PLANT SCIENCE 2015; 6:945. [PMID: 26579183 PMCID: PMC4630571 DOI: 10.3389/fpls.2015.00945] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/17/2015] [Indexed: 05/26/2023]
Abstract
The productivity in sorghum is low, owing to various biotic and abiotic constraints. Combining insect resistance with desirable agronomic and morphological traits is important to increase sorghum productivity. Therefore, it is important to understand the variability for various agronomic traits, their heritabilities and nature of gene action to develop appropriate strategies for crop improvement. Therefore, a full diallel set of 10 parents and their 90 crosses including reciprocals were evaluated in replicated trials during the 2013-14 rainy and postrainy seasons. The crosses between the parents with early- and late-flowering flowered early, indicating dominance of earliness for anthesis in the test material used. Association between the shoot fly resistance, morphological, and agronomic traits suggested complex interactions between shoot fly resistance and morphological traits. Significance of the mean sum of squares for GCA (general combining ability) and SCA (specific combining ability) of all the studied traits suggested the importance of both additive and non-additive components in inheritance of these traits. The GCA/SCA, and the predictability ratios indicated predominance of additive gene effects for majority of the traits studied. High broad-sense and narrow-sense heritability estimates were observed for most of the morphological and agronomic traits. The significance of reciprocal combining ability effects for days to 50% flowering, plant height and 100 seed weight, suggested maternal effects for inheritance of these traits. Plant height and grain yield across seasons, days to 50% flowering, inflorescence exsertion, and panicle shape in the postrainy season showed greater specific combining ability variance, indicating the predominance of non-additive type of gene action/epistatic interactions in controlling the expression of these traits. Additive gene action in the rainy season, and dominance in the postrainy season for days to 50% flowering and plant height suggested G X E interactions for these traits.
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Affiliation(s)
- Riyazaddin Mohammed
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
- Department of Genetics, Osmania UniversityHyderabad, India
| | - Ashok K. Are
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Ramaiah Bhavanasi
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Rajendra S. Munghate
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | | | - Hari C. Sharma
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
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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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Rama Reddy NR, Ragimasalawada M, Sabbavarapu MM, Nadoor S, Patil JV. Detection and validation of stay-green QTL in post-rainy sorghum involving widely adapted cultivar, M35-1 and a popular stay-green genotype B35. BMC Genomics 2014; 15:909. [PMID: 25326366 PMCID: PMC4219115 DOI: 10.1186/1471-2164-15-909] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 09/24/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Sorghum [Sorghum bicolor (L.) Moench] is an important dry-land cereal of the world providing food, fodder, feed and fuel. Stay-green (delayed-leaf senescence) is a key attribute in sorghum determining its adaptation to terminal drought stress. The objective of this study was to validate sorghum stay-green quantitative trait loci (QTL) identified in the past, and to identify new QTL in the genetic background of a post-rainy adapted genotype M35-1. RESULTS A genetic linkage map based on 245 F9 Recombinant Inbred Lines (RILs) derived from a cross between M35-1 (more senescent) and B35 (less senescent) with 237 markers consisting of 174 genomic, 60 genic and 3 morphological markers was used. The phenotypic data collected for three consecutive post-rainy crop seasons on the RIL population (M35-1 × B35) was used for QTL analysis. Sixty-one QTL were identified for various measures of stay-green trait and each trait was controlled by one to ten QTL. The phenotypic variation explained by each QTL ranged from 3.8 to 18.7%. Co-localization of QTL for more than five traits was observed on two linkage groups i.e. on SBI-09-3 flanked by S18 and Xgap206 markers and, on SBI-03 flanked by XnhsbSFCILP67 and Xtxp31. QTL identified in this study were stable across environments and corresponded to sorghum stay-green and grain yield QTL reported previously. Of the 60 genic SSRs mapped, 14 were closely linked with QTL for ten traits. A genic marker, XnhsbSFCILP67 (Sb03g028240) encoding Indole-3-acetic acid-amido synthetase GH3.5, was co-located with QTL for GLB, GLM, PGLM and GLAM on SBI-03. Genes underlying key enzymes of chlorophyll metabolism were also found in the stay-green QTL regions. CONCLUSIONS We validated important stay-green QTL reported in the past in sorghum and detected new QTL influencing the stay-green related traits consistently. Stg2, Stg3 and StgB were prominent in their expression. Collectively, the QTL/markers identified are likely candidates for subsequent verification for their involvement in stay-green phenotype using NILs and to develop drought tolerant sorghum varieties through marker-assisted breeding for terminal drought tolerance in sorghum.
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Affiliation(s)
- Nagaraja Reddy Rama Reddy
- />Marker-assisted selection Lab, ICAR-Directorate of Sorghum Research (DSR), Rajendranagar, Hyderabad, 500 030 India
- />ICAR-Directorate of Medicinal and Aromatic Plants Research (DMAPR), Anand, Gujarat 387 310 India
| | - Madhusudhana Ragimasalawada
- />Marker-assisted selection Lab, ICAR-Directorate of Sorghum Research (DSR), Rajendranagar, Hyderabad, 500 030 India
| | - Murali Mohan Sabbavarapu
- />Marker-assisted selection Lab, ICAR-Directorate of Sorghum Research (DSR), Rajendranagar, Hyderabad, 500 030 India
| | - Seetharama Nadoor
- />Marker-assisted selection Lab, ICAR-Directorate of Sorghum Research (DSR), Rajendranagar, Hyderabad, 500 030 India
| | - Jagannatha Vishnu Patil
- />Marker-assisted selection Lab, ICAR-Directorate of Sorghum Research (DSR), Rajendranagar, Hyderabad, 500 030 India
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