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Li R, Wang Y, Li D, Guo Y, Zhou Z, Zhang M, Zhang Y, Würschum T, Liu W. Meta-Quantitative Trait Loci Analysis and Candidate Gene Mining for Drought Tolerance-Associated Traits in Maize ( Zea mays L.). Int J Mol Sci 2024; 25:4295. [PMID: 38673880 PMCID: PMC11049847 DOI: 10.3390/ijms25084295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Drought is one of the major abiotic stresses with a severe negative impact on maize production globally. Understanding the genetic architecture of drought tolerance in maize is a crucial step towards the breeding of drought-tolerant varieties and a targeted exploitation of genetic resources. In this study, 511 quantitative trait loci (QTL) related to grain yield components, flowering time, and plant morphology under drought conditions, as well as drought tolerance index were collected from 27 published studies and then projected on the IBM2 2008 Neighbors reference map for meta-analysis. In total, 83 meta-QTL (MQTL) associated with drought tolerance in maize were identified, of which 20 were determined as core MQTL. The average confidence interval of MQTL was strongly reduced compared to that of the previously published QTL. Nearly half of the MQTL were confirmed by co-localized marker-trait associations from genome-wide association studies. Based on the alignment of rice proteins related to drought tolerance, 63 orthologous genes were identified near the maize MQTL. Furthermore, 583 candidate genes were identified within the 20 core MQTL regions and maize-rice homologous genes. Based on KEGG analysis of candidate genes, plant hormone signaling pathways were found to be significantly enriched. The signaling pathways can have direct or indirect effects on drought tolerance and also interact with other pathways. In conclusion, this study provides novel insights into the genetic and molecular mechanisms of drought tolerance in maize towards a more targeted improvement of this important trait in breeding.
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Affiliation(s)
- Ronglan Li
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Yueli Wang
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Dongdong Li
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yuhang Guo
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhipeng Zhou
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Mi Zhang
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Yufeng Zhang
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Tobias Würschum
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599 Stuttgart, Germany
| | - Wenxin Liu
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Sanya 572025, China
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Karnatam KS, Mythri B, Un Nisa W, Sharma H, Meena TK, Rana P, Vikal Y, Gowda M, Dhillon BS, Sandhu S. Silage maize as a potent candidate for sustainable animal husbandry development-perspectives and strategies for genetic enhancement. Front Genet 2023; 14:1150132. [PMID: 37303948 PMCID: PMC10250641 DOI: 10.3389/fgene.2023.1150132] [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: 01/23/2023] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Maize is recognized as the queen of cereals, with an ability to adapt to diverse agroecologies (from 58oN to 55oS latitude) and the highest genetic yield potential among cereals. Under contemporary conditions of global climate change, C4 maize crops offer resilience and sustainability to ensure food, nutritional security, and farmer livelihood. In the northwestern plains of India, maize is an important alternative to paddy for crop diversification in the wake of depleting water resources, reduced farm diversity, nutrient mining, and environmental pollution due to paddy straw burning. Owing to its quick growth, high biomass, good palatability, and absence of anti-nutritional components, maize is also one of the most nutritious non-legume green fodders. It is a high-energy, low-protein forage commonly used for dairy animals like cows and buffalos, often in combination with a complementary high-protein forage such as alfalfa. Maize is also preferred for silage over other fodders due to its softness, high starch content, and sufficient soluble sugars required for proper ensiling. With a rapid population increase in developing countries like China and India, there is an upsurge in meat consumption and, hence, the requirement for animal feed, which entails high usage of maize. The global maize silage market is projected to grow at a compound annual growth rate of 7.84% from 2021 to 2030. Factors such as increasing demand for sustainable and environment-friendly food sources coupled with rising health awareness are fueling this growth. With the dairy sector growing at about 4%-5% and the increasing shortage faced for fodder, demand for silage maize is expected to increase worldwide. The progress in improved mechanization for the provision of silage maize, reduced labor demand, lack of moisture-related marketing issues as associated with grain maize, early vacancy of farms for next crops, and easy and economical form of feed to sustain household dairy sector make maize silage a profitable venture. However, sustaining the profitability of this enterprise requires the development of hybrids specific for silage production. Little attention has yet been paid to breeding for a plant ideotype for silage with specific consideration of traits such as dry matter yield, nutrient yield, energy in organic matter, genetic architecture of cell wall components determining their digestibility, stalk standability, maturity span, and losses during ensiling. This review explores the available information on the underlying genetic mechanisms and gene/gene families impacting silage yield and quality. The trade-offs between yield and nutritive value in relation to crop duration are also discussed. Based on available genetic information on inheritance and molecular aspects, breeding strategies are proposed to develop maize ideotypes for silage for the development of sustainable animal husbandry.
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Affiliation(s)
- Krishna Sai Karnatam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Bikkasani Mythri
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Wajhat Un Nisa
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Heena Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Tarun Kumar Meena
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Prabhat Rana
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - M. Gowda
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Baldev Singh Dhillon
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Surinder Sandhu
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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Sarkar B, Varalaxmi Y, Vanaja M, RaviKumar N, Prabhakar M, Yadav SK, Maheswari M, Singh VK. Mapping of QTLs for morphophysiological and yield traits under water-deficit stress and well-watered conditions in maize. FRONTIERS IN PLANT SCIENCE 2023; 14:1124619. [PMID: 37223807 PMCID: PMC10200936 DOI: 10.3389/fpls.2023.1124619] [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: 12/15/2022] [Accepted: 03/27/2023] [Indexed: 05/25/2023]
Abstract
Maize productivity is significantly impacted by drought; therefore, improvement of drought tolerance is a critical goal in maize breeding. To achieve this, a better understanding of the genetic basis of drought tolerance is necessary. Our study aimed to identify genomic regions associated with drought tolerance-related traits by phenotyping a mapping population of recombinant inbred lines (RILs) for two seasons under well-watered (WW) and water-deficit (WD) conditions. We also used single nucleotide polymorphism (SNP) genotyping through genotyping-by-sequencing to map these regions and attempted to identify candidate genes responsible for the observed phenotypic variation. Phenotyping of the RILs population revealed significant variability in most of the traits, with normal frequency distributions, indicating their polygenic nature. We generated a linkage map using 1,241 polymorphic SNPs distributed over 10 chromosomes (chrs), covering a total genetic distance of 5,471.55 cM. We identified 27 quantitative trait loci (QTLs) associated with various morphophysiological and yield-related traits, with 13 QTLs identified under WW conditions and 12 under WD conditions. We found one common major QTL (qCW2-1) for cob weight and a minor QTL (qCH1-1) for cob height that were consistently identified under both water regimes. We also detected one major and one minor QTL for the Normalized Difference Vegetation Index (NDVI) trait under WD conditions on chr 2, bin 2.10. Furthermore, we identified one major QTL (qCH1-2) and one minor QTL (qCH1-1) on chr 1 that were located at different genomic positions to those identified in earlier studies. We found co-localized QTLs for stomatal conductance and grain yield on chr 6 (qgs6-2 and qGY6-1), while co-localized QTLs for stomatal conductance and transpiration rate were identified on chr 7 (qgs7-1 and qTR7-1). We also attempted to identify the candidate genes responsible for the observed phenotypic variation; our analysis revealed that the major candidate genes associated with QTLs detected under water deficit conditions were related to growth and development, senescence, abscisic acid (ABA) signaling, signal transduction, and transporter activity in stress tolerance. The QTL regions identified in this study may be useful in designing markers that can be utilized in marker-assisted selection breeding. In addition, the putative candidate genes can be isolated and functionally characterized so that their role in imparting drought tolerance can be more fully understood.
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Sheoran S, Gupta M, Kumari S, Kumar S, Rakshit S. Meta-QTL analysis and candidate genes identification for various abiotic stresses in maize ( Zea mays L.) and their implications in breeding programs. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:26. [PMID: 37309532 PMCID: PMC10248626 DOI: 10.1007/s11032-022-01294-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/26/2022] [Indexed: 06/14/2023]
Abstract
Global climate change leads to the concurrence of a number of abiotic stresses including moisture stress (drought, waterlogging), temperature stress (heat, cold), and salinity stress, which are the major factors affecting maize production. To develop abiotic stress tolerance in maize, many quantitative trait loci (QTL) have been identified, but very few of them have been utilized successfully in breeding programs. In this context, the meta-QTL analysis of the reported QTL will enable the identification of stable/real QTL which will pave a reliable way to introgress these QTL into elite cultivars through marker-assisted selection. In this study, a total of 542 QTL were summarized from 33 published studies for tolerance to different abiotic stresses in maize to conduct meta-QTL analysis using BiomercatorV4.2.3. Among those, only 244 major QTL with more than 10% phenotypic variance were preferably utilised to carry out meta-QTL analysis. In total, 32 meta-QTL possessing 1907 candidate genes were detected for different abiotic stresses over diverse genetic and environmental backgrounds. The MQTL2.1, 5.1, 5.2, 5.6, 7.1, 9.1, and 9.2 control different stress-related traits for combined abiotic stress tolerance. The candidate genes for important transcription factor families such as ERF, MYB, bZIP, bHLH, NAC, LRR, ZF, MAPK, HSP, peroxidase, and WRKY have been detected for different stress tolerances. The identified meta-QTL are valuable for future climate-resilient maize breeding programs and functional validation of candidate genes studies, which will help to deepen our understanding of the complexity of these abiotic stresses. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01294-9.
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Affiliation(s)
- Seema Sheoran
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 141004 India
- Present Address: ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, 132001 India
| | - Mamta Gupta
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 141004 India
| | - Shweta Kumari
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Sandeep Kumar
- Present Address: ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, 132001 India
- ICAR-Indian Institute of Pulses Research, Regional Station, Phanda, Bhopal, 462030 India
| | - Sujay Rakshit
- ICAR-Indian Institute of Maize Research, PAU Campus, Ludhiana, 141004 India
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Sheoran S, Kaur Y, Kumar S, Shukla S, Rakshit S, Kumar R. Recent Advances for Drought Stress Tolerance in Maize ( Zea mays L.): Present Status and Future Prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:872566. [PMID: 35707615 PMCID: PMC9189405 DOI: 10.3389/fpls.2022.872566] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/26/2022] [Indexed: 05/04/2023]
Abstract
Drought stress has severely hampered maize production, affecting the livelihood and economics of millions of people worldwide. In the future, as a result of climate change, unpredictable weather events will become more frequent hence the implementation of adaptive strategies will be inevitable. Through utilizing different genetic and breeding approaches, efforts are in progress to develop the drought tolerance in maize. The recent approaches of genomics-assisted breeding, transcriptomics, proteomics, transgenics, and genome editing have fast-tracked enhancement for drought stress tolerance under laboratory and field conditions. Drought stress tolerance in maize could be considerably improved by combining omics technologies with novel breeding methods and high-throughput phenotyping (HTP). This review focuses on maize responses against drought, as well as novel breeding and system biology approaches applied to better understand drought tolerance mechanisms and the development of drought-tolerant maize cultivars. Researchers must disentangle the molecular and physiological bases of drought tolerance features in order to increase maize yield. Therefore, the integrated investments in field-based HTP, system biology, and sophisticated breeding methodologies are expected to help increase and stabilize maize production in the face of climate change.
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Kamphorst SH, do Amaral Junior AT, de Lima VJ, Carena MJ, Azeredo VC, Mafra GS, Santos PHAD, Leite JT, Schmitt KFM, dos Santos Junior DR, Bispo RB, Santos TDO, de Oliveira UA, Pereira JL, Lamêgo DL, Carvalho CM, Gomes LP, Silva JGDS, Campostrini E. Driving Sustainable Popcorn Breeding for Drought Tolerance in Brazil. FRONTIERS IN PLANT SCIENCE 2021; 12:732285. [PMID: 34621285 PMCID: PMC8491626 DOI: 10.3389/fpls.2021.732285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Drought currently affects several regions worldwide and tends to be more frequent due to climate change. It might compromise food security and the economic structure related to agribusiness. Popcorn has a crucial role in the Brazilian economy, but the cultivars that adapt to water stress, the most prejudicial abiotic stress for crop productivity, are unknown to date. This deficit of popcorn varieties adapted to heat and drought stresses will become more limiting with climate change. Given this scenario, knowing the genetic basis of agronomic traits under stress conditions is essential in promoting crop productivity and plant adaptation to abiotic stresses. Under two contrasting water conditions (WC) and different crop seasons (CS), we aimed to generate information about the combining ability of 10 popcorn progenitors and 15 hybrids through a partial diallel-mating design. The water stress was initiated at the male pre-anthesis stage. Significant genotype*crop seasons (G*CS), genotype*water condition (G*WC), and genotype*crop seasons*water condition (G*CS*WC) interactions were present. Regardless of CS and WC, non-additive effects controlled grain yield (GY), grain number per row (GN), ear length and diameter (ED), and 100-grain weight, while additive effects were present for popping expansion (PE). For each CS, regardless of WC, the cause-effect of GN (2018) and ED (2020) on GY seems to be an opportunity for indirect selection. Utilizing genetically broad-based hybrids is also a good opportunity for obtaining superior genotypes for GY and PE as it is possible to select inbred lines for both of these traits. We recommend the L76 × L61 hybrid for the Brazilian agribusiness context due to its greater productivity and dominance deviations.
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Affiliation(s)
- Samuel Henrique Kamphorst
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | - Antônio Teixeira do Amaral Junior
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | - Valter Jário de Lima
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | | | - Valdinei Cruz Azeredo
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | - Gabrielle Sousa Mafra
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | - Pedro Henrique Araújo Diniz Santos
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | - Jhean Torres Leite
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | - Kátia Fabiane Medeiros Schmitt
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | - Divino Rosa dos Santos Junior
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | - Rosimeire Barboza Bispo
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | - Talles de Oliveira Santos
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | - Uéliton Alves de Oliveira
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | - Jacymara Lopes Pereira
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | - Danielle Leal Lamêgo
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | - Carolina Macedo Carvalho
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | - Letícia Peixoto Gomes
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | - José Gabriel de Souza Silva
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
| | - Eliemar Campostrini
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF, Campos dos Goytacazes, Brazil
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Siddiqui MN, Léon J, Naz AA, Ballvora A. Genetics and genomics of root system variation in adaptation to drought stress in cereal crops. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1007-1019. [PMID: 33096558 PMCID: PMC7904151 DOI: 10.1093/jxb/eraa487] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 10/19/2020] [Indexed: 05/03/2023]
Abstract
Cereals are important crops worldwide that help meet food demands and nutritional needs. In recent years, cereal production has been challenged globally by frequent droughts and hot spells. A plant's root is the most relevant organ for the plant adaptation to stress conditions, playing pivotal roles in anchorage and the acquisition of soil-based resources. Thus, dissecting root system variations and trait selection for enhancing yield and sustainability under drought stress conditions should aid in future global food security. This review highlights the variations in root system attributes and their interplay with shoot architecture features to face water scarcity and maintain thus yield of major cereal crops. Further, we compile the root-related drought responsive quantitative trait loci/genes in cereal crops including their interspecies relationships using microsynteny to facilitate comparative genomic analyses. We then discuss the potential of an integrated strategy combining genomics and phenomics at genetic and epigenetic levels to explore natural genetic diversity as a basis for knowledge-based genome editing. Finally, we present an outline to establish innovative breeding leads for the rapid and optimized selection of root traits necessary to develop resilient crop varieties.
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Affiliation(s)
- Md Nurealam Siddiqui
- Institute of Crop Science and Resource Conservation (INRES) – Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Jens Léon
- Institute of Crop Science and Resource Conservation (INRES) – Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Ali A Naz
- Institute of Crop Science and Resource Conservation (INRES) – Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation (INRES) – Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
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Su J, Yang X, Zhang F, Wu S, Xiong S, Shi L, Guan Z, Fang W, Chen F. Dynamic and epistatic QTL mapping reveals the complex genetic architecture of waterlogging tolerance in chrysanthemum. PLANTA 2018; 247:899-924. [PMID: 29273861 DOI: 10.1007/s00425-017-2833-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/14/2017] [Indexed: 05/21/2023]
Abstract
37 unconditional QTLs, 51 conditional QTLs and considerable epistatic QTLs were detected for waterlogging tolerance, and six favourable combinations were selected accelerating the possible application of MAS in chrysanthemum breeding. Chrysanthemum is seriously impacted by soil waterlogging. To determine the genetic characteristics of waterlogging tolerance (WAT) in chrysanthemum, a population of 162 F1 lines was used to construct a genetic map to identify the dynamic and epistatic quantitative trait loci (QTLs) for four WAT traits: wilting index (WI), dead leaf ratio (DLR), chlorosis score (Score) and membership function value of waterlogging (MFVW). The h B2 for the WAT traits ranged from 0.49 to 0.64, and transgressive segregation was observed in both directions. A total of 37 unconditional consensus QTLs with 5.81-18.21% phenotypic variation explanation (PVE) and 51 conditional consensus QTLs with 5.90-24.56% PVE were detected. Interestingly, three unconditional consensus QTLs were consistently identified across different stages, whereas no conditional consensus QTLs were consistently expressed. In addition, considerable epistatic QTLs, all with PVE values ranging from 0.01 to 8.87%, were detected by a joint analysis of WAT phenotypes. These results illustrated that the QTLs (genes) controlling WAT were environmentally dependent and selectively expressed at different times and indicated that both additive and epistatic effects underlie the inheritance of WAT in chrysanthemum. The findings of the current study provide insights into the complex genetic architecture of WAT, and the identification of favourable alleles represents an important step towards the application of molecular marker-assisted selection (MAS) and QTL pyramiding in chrysanthemum WAT breeding programmes.
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Affiliation(s)
- Jiangshuo Su
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xincheng Yang
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Fei Zhang
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Shaofang Wu
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Siyi Xiong
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Liming Shi
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Zhiyong Guan
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Weimin Fang
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Fadi Chen
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People's Republic of China.
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Wang H, Qin F. Genome-Wide Association Study Reveals Natural Variations Contributing to Drought Resistance in Crops. FRONTIERS IN PLANT SCIENCE 2017; 8:1110. [PMID: 28713401 PMCID: PMC5491614 DOI: 10.3389/fpls.2017.01110] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/08/2017] [Indexed: 05/18/2023]
Abstract
Crops are often cultivated in regions where they will face environmental adversities; resulting in substantial yield loss which can ultimately lead to food and societal problems. Thus, significant efforts have been made to breed stress tolerant cultivars in an attempt to minimize these problems and to produce more stability with respect to crop yields across broad geographies. Since stress tolerance is a complex and multi-genic trait, advancements with classical breeding approaches have been challenging. On the other hand, molecular breeding, which is based on transgenics, marker-assisted selection and genome editing technologies; holds great promise to enable farmers to better cope with these challenges. However, identification of the key genetic components underlying the trait is critical and will serve as the foundation for future crop genetic improvement. Recently, genome-wide association studies have made significant contributions to facilitate the discovery of natural variation contributing to stress tolerance in crops. From these studies, the identified loci can serve as targets for genomic selection or editing to enable the molecular design of new cultivars. Here, we summarize research progress on this issue and focus on the genetic basis of drought tolerance as revealed by genome-wide association studies and quantitative trait loci mapping. Although many favorable loci have been identified, elucidation of their molecular mechanisms contributing to increased stress tolerance still remains a challenge. Thus, continuous efforts are still required to functionally dissect this complex trait through comprehensive approaches, such as system biological studies. It is expected that proper application of the acquired knowledge will enable the development of stress tolerant cultivars; allowing agricultural production to become more sustainable under dynamic environmental conditions.
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Affiliation(s)
- Hongwei Wang
- Agricultural College, Yangtze UniversityJingzhou, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze UniversityJingzhou, China
| | - Feng Qin
- College of Biological Sciences, China Agricultural UniversityBeijing, China
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Babasaheb Aglawe S, Bangale U, Sagili Jayasree Satya RD, Balija V, Vijay Pal B, Susheel Kumar S, Pawan Kumar S, Sudhir Kumar, Maddamshetty S, Maganti SM. Identification of novel QTLs conferring field resistance for rice leaf and neck blast from an unique landrace of India. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Tsai KJ, Lu MYJ, Yang KJ, Li M, Teng Y, Chen S, Ku MSB, Li WH. Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance. Sci Rep 2016; 6:35076. [PMID: 27734962 PMCID: PMC5062080 DOI: 10.1038/srep35076] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/23/2016] [Indexed: 12/23/2022] Open
Abstract
The diploid C4 plant foxtail millet (Setaria italica L. Beauv.) is an important crop in many parts of Africa and Asia for the vast consumption of its grain and ability to grow in harsh environments, but remains understudied in terms of complete genomic architecture. To date, there have been only two genome assembly and annotation efforts with neither assembly reaching over 86% of the estimated genome size. We have combined de novo assembly with custom reference-guided improvements on a popular cultivar of foxtail millet and have achieved a genome assembly of 477 Mbp in length, which represents over 97% of the estimated 490 Mbp. The assembly anchors over 98% of the predicted genes to the nine assembled nuclear chromosomes and contains more functional annotation gene models than previous assemblies. Our annotation has identified a large number of unique gene ontology terms related to metabolic activities, a region of chromosome 9 with several growth factor proteins, and regions syntenic with pearl millet or maize genomic regions that have been previously shown to affect growth. The new assembly and annotation for this important species can be used for detailed investigation and future innovations in growth for millet and other grains.
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Affiliation(s)
- Kevin J. Tsai
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 11574 Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, 11221 Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Kai-Jung Yang
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Mengyun Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Yuchuan Teng
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Shihmay Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Maurice S. B. Ku
- Department of Bioagricultural Science, National Chiayi University, Chiayi, 60004 Taiwan
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
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Vaughan MM, Christensen S, Schmelz EA, Huffaker A, McAuslane HJ, Alborn HT, Romero M, Allen LH, Teal PEA. Accumulation of terpenoid phytoalexins in maize roots is associated with drought tolerance. PLANT, CELL & ENVIRONMENT 2015; 38:2195-207. [PMID: 25392907 DOI: 10.1111/pce.12482] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 11/04/2014] [Accepted: 11/05/2014] [Indexed: 05/25/2023]
Abstract
Maize (Zea mays) production, which is of global agro-economic importance, is largely limited by herbivore pests, pathogens and environmental conditions, such as drought. Zealexins and kauralexins belong to two recently identified families of acidic terpenoid phytoalexins in maize that mediate defence against both pathogen and insect attacks in aboveground tissues. However, little is known about their function in belowground organs and their potential to counter abiotic stress. In this study, we show that zealexins and kauralexins accumulate in roots in response to both biotic and abiotic stress including, Diabrotica balteata herbivory, Fusarium verticillioides infection, drought and high salinity. We find that the quantity of drought-induced phytoalexins is positively correlated with the root-to-shoot ratio of different maize varieties, and further demonstrate that mutant an2 plants deficient in kauralexin production are more sensitive to drought. The induction of phytoalexins in response to drought is root specific and does not influence phytoalexin levels aboveground; however, the accumulation of phytoalexins in one tissue may influence the induction capacity of other tissues.
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Affiliation(s)
- Martha M Vaughan
- Bacterial Foodborne Pathogens and Mycology, Agricultural Research Service, United States Department of Agriculture, Peoria, IL, 61604, USA
| | - Shawn Christensen
- Chemistry Research Unit, Center of Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, Gainesville, FL, 32608, USA
| | - Eric A Schmelz
- Chemistry Research Unit, Center of Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, Gainesville, FL, 32608, USA
| | - Alisa Huffaker
- Chemistry Research Unit, Center of Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, Gainesville, FL, 32608, USA
| | - Heather J McAuslane
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, 32611, USA
| | - Hans T Alborn
- Chemistry Research Unit, Center of Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, Gainesville, FL, 32608, USA
| | - Maritza Romero
- Chemistry Research Unit, Center of Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, Gainesville, FL, 32608, USA
| | - Leon Hartwell Allen
- Chemistry Research Unit, Center of Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, Gainesville, FL, 32608, USA
| | - Peter E A Teal
- Chemistry Research Unit, Center of Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, Gainesville, FL, 32608, USA
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13
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Sun X, Du Z, Ren J, Amombo E, Hu T, Fu J. Association of SSR markers with functional traits from heat stress in diverse tall fescue accessions. BMC PLANT BIOLOGY 2015; 15:116. [PMID: 25957573 PMCID: PMC4425909 DOI: 10.1186/s12870-015-0494-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 04/17/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Heat stress is a critical threat to tall fescue in transitional and warm climate zones. Identification of association between molecular markers and heat tolerance-related functional traits would promote the efficient selection of heat tolerant tall fescue cultivars. Association analysis of heat tolerance-related traits was conducted in 100 diverse tall fescue accessions consisting of 93 natural genotypes originating from 33 countries and 7 turf-type commercial cultivars. RESULTS The panel displayed significant genetic variations in growth rate (GR), turfgrass quality (TQ), survival rate (SR), chlorophyll content (CHL) and evapotranspiration rate (ET) in greenhouse and growth chamber trials. Two subpopulations were detected in the panel of accessions by 1010 SSR alleles with 90 SSR markers, but no obvious relative kinship was observed. 97 and 67 marker alleles associated with heat tolerance-related traits were identified in greenhouse trial and growth chamber trial (P < 0.01) using mix linear model, respectively. Due to different experimental conditions of the two trials, 2 SSR marker alleles associated with GR and ET were simultaneously identified at P < 0.01 level in two trials in response to heat stress. CONCLUSION High-temperature induced great variations of functional traits in tall fescue accessions. And the identified marker alleles associated with functional traits could provide important information about heat tolerance genetic pathways, and be used for molecular assisted breeding to enhance tall fescue performance under heat stress.
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Affiliation(s)
- Xiaoyan Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, Hubei, P.R. China.
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, China.
| | - Zhimin Du
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, Hubei, P.R. China.
| | - Jin Ren
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, Hubei, P.R. China.
| | - Erick Amombo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, Hubei, P.R. China.
| | - Tao Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, Hubei, P.R. China.
| | - Jinmin Fu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, 430074, Hubei, P.R. China.
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Petrarulo M, Marone D, Ferragonio P, Cattivelli L, Rubiales D, De Vita P, Mastrangelo AM. Genetic analysis of root morphological traits in wheat. Mol Genet Genomics 2014; 290:785-806. [PMID: 25416422 DOI: 10.1007/s00438-014-0957-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 11/11/2014] [Indexed: 02/05/2023]
Abstract
Traits related to root architecture are of great importance for yield performance of crop species, although they remain poorly understood. The present study is aimed at identifying the genomic regions involved in the control of root morphological traits in durum wheat (Triticum durum Desf.). A set of 123 recombinant inbred lines derived from the durum wheat cross of cvs. 'Creso' × 'Pedroso' were grown hydroponically to two growth stages, and were phenotypically evaluated for a number of root traits. In addition, meta-(M)QTL analysis was performed that considered the results of other root traits studies in wheat, to compare with the 'Creso' × 'Pedroso' cross and to increase the QTL detection power. Eight quantitative trait loci (QTL) for traits related to root morphology were identified on chromosomes 1A, 1B, 2A, 3A, 6A and 6B in the 'Creso' × 'Pedroso' segregating population. Twenty-two MQTL that comprised from two to six individual QTL that had widely varying confidence intervals were found on 14 chromosomes. The data from the present study provide a detailed analysis of the genetic basis of morphological root traits in wheat. This study of the 'Creso' × 'Pedroso' durum-wheat population has revealed some QTL that had not been previously identified.
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Affiliation(s)
- Maria Petrarulo
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura-Cereal Research Centre, SS 673 km 25.200, 71122, Foggia, Italy
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15
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Osman KA, Tang B, Wang Y, Chen J, Yu F, Li L, Han X, Zhang Z, Yan J, Zheng Y, Yue B, Qiu F. Dynamic QTL analysis and candidate gene mapping for waterlogging tolerance at maize seedling stage. PLoS One 2013; 8:e79305. [PMID: 24244474 PMCID: PMC3828346 DOI: 10.1371/journal.pone.0079305] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 09/22/2013] [Indexed: 11/19/2022] Open
Abstract
Soil waterlogging is one of the major abiotic stresses adversely affecting maize growth and yield. To identify dynamic expression of genes or quantitative trait loci (QTL), QTL associated with plant height, root length, root dry weight, shoot dry weight and total dry weight were identified via conditional analysis in a mixed linear model and inclusive composite interval mapping method at three respective periods under waterlogging and control conditions. A total of 13, 19 and 23 QTL were detected at stages 3D|0D (the period during 0-3 d of waterlogging), 6D|3D and 9D|6D, respectively. The effects of each QTL were moderate and distributed over nine chromosomes, singly explaining 4.14-18.88% of the phenotypic variation. Six QTL (ph6-1, rl1-2, sdw4-1, sdw7-1, tdw4-1 and tdw7-1) were identified at two consistent stages of seedling development, which could reflect a continuous expression of genes; the remaining QTL were detected at only one stage. Thus, expression of most QTL was influenced by the developmental status. In order to provide additional evidence regarding the role of corresponding genes in waterlogging tolerance, mapping of Expressed Sequence Tags markers and microRNAs were conducted. Seven candidate genes were observed to co-localize with the identified QTL on chromosomes 1, 4, 6, 7 and 9, and may be important candidate genes for waterlogging tolerance. These results are a good starting point for understanding the genetic basis for selectively expressing of QTL in different stress periods and the common genetic control mechanism of the co-localized traits.
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Affiliation(s)
- Khalid A. Osman
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Bin Tang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yaping Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Juanhua Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Feng Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Liu Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xuesong Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jianbin Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yonglian Zheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Bing Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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16
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Xue Y, Warburton ML, Sawkins M, Zhang X, Setter T, Xu Y, Grudloyma P, Gethi J, Ribaut JM, Li W, Zhang X, Zheng Y, Yan J. Genome-wide association analysis for nine agronomic traits in maize under well-watered and water-stressed conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2587-96. [PMID: 23884600 DOI: 10.1007/s00122-013-2158-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 07/12/2013] [Indexed: 05/03/2023]
Abstract
Drought can cause severe reduction in maize production, and strongly threatens crop yields. To dissect this complex trait and identify superior alleles, 350 tropical and subtropical maize inbred lines were genotyped using a 1536-SNP array developed from drought-related genes and an array of 56,110 random SNPs. The inbred lines were crossed with a common tester, CML312, and the testcrosses were phenotyped for nine traits under well-watered and water-stressed conditions in seven environments. Using genome-wide association mapping with correction for population structure, 42 associated SNPs (P ≤ 2.25 × 10(-6) 0.1/N) were identified, located in 33 genes for 126 trait × environment × treatment combinations. Of these genes, three were co-localized to drought-related QTL regions. Gene GRMZM2G125777 was strongly associated with ear relative position, hundred kernel weight and timing of male and female flowering, and encodes NAC domain-containing protein 2, a transcription factor expressed in different tissues. These results provide some good information for understanding the genetic basis for drought tolerance and further studies on identified candidate genes should illuminate mechanisms of drought tolerance and provide tools for designing drought-tolerant maize cultivars tailored to different environmental scenarios.
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Affiliation(s)
- Yadong Xue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Fakrudin B, Kavil SP, Girma Y, Arun SS, Dadakhalandar D, Gurusiddesh BH, Patil AM, Thudi M, Bhairappanavar SB, Narayana YD, Krishnaraj PU, Khadi BM, Kamatar MY. Molecular mapping of genomic regions harbouring QTLs for root and yield traits in sorghum (Sorghum bicolor L. Moench). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2013; 19:409-19. [PMID: 24431509 PMCID: PMC3715642 DOI: 10.1007/s12298-013-0188-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Root system is a vital part of plants for absorbing soil moisture and nutrients and it influences the drought tolerance. Identification of the genomic regions harbouring quantitative trait loci (QTLs) for root and yield traits, and the linked markers can facilitate sorghum improvement through marker-assisted selection (MAS) besides the deeper understanding of the plant response to drought stress. A population of 184 recombinant inbred lines (RILs), derived from E36-1 × SPV570, along with parents were phenotyped for component traits of yield in field and root traits in an above ground rhizotron. High estimates of heritability and genetic advance for all the root traits and for most of the yield traits, presents high scope for improvement of these traits by simple selection. A linkage map constructed with 104 marker loci comprising 50 EST-SSRs, 34 non-genic nuclear SSRs and 20 SNPs, and QTL analysis was performed using composite interval mapping (CIM) approach. A total of eight and 20 QTLs were mapped for root and yield related traits respectively. The QTLs for root volume, root fresh weight and root dry weight were found co-localized on SBI-04, supported by a positive correlation among these traits. Hence, these traits can be improved using the same linked markers. The lack of overlap between the QTLs of component traits of root and yield suggested that these two sets of parameters are independent in their influence and the possibility of combining these two traits might enhance productivity of sorghum under receding moisture condition.
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Affiliation(s)
- B. Fakrudin
- />Institute of Agri-Biotechnology, University of Agricultural Sciences, Dharwad, Dharwad, 580 005 Karnataka India
| | - S. P. Kavil
- />Institute of Agri-Biotechnology, University of Agricultural Sciences, Dharwad, Dharwad, 580 005 Karnataka India
| | - Y. Girma
- />School of Plant Sciences and NRMES, Haramaya University, Alemaya City, Ethiopia
| | - S. S. Arun
- />Bioinformatics Core, Purdue University, West Lafayette, IN 47907 USA
| | - D. Dadakhalandar
- />Institute of Agri-Biotechnology, University of Agricultural Sciences, Dharwad, Dharwad, 580 005 Karnataka India
| | - B. H. Gurusiddesh
- />Institute of Agri-Biotechnology, University of Agricultural Sciences, Dharwad, Dharwad, 580 005 Karnataka India
| | - A. M. Patil
- />Institute of Agri-Biotechnology, University of Agricultural Sciences, Dharwad, Dharwad, 580 005 Karnataka India
| | - M. Thudi
- />International Crop Research Institute for Semi-Arid Tropics, Patancheru, Hyderabad, India
| | - S. B. Bhairappanavar
- />Institute of Agri-Biotechnology, University of Agricultural Sciences, Dharwad, Dharwad, 580 005 Karnataka India
| | - Y. D. Narayana
- />All India Coordinated Sorghum Improvement Programme, Main Agricultural Research Station, Dharwad, India
| | - P. U. Krishnaraj
- />Institute of Agri-Biotechnology, University of Agricultural Sciences, Dharwad, Dharwad, 580 005 Karnataka India
| | - B. M. Khadi
- />University of Agricultural Sciences, Dharwad, Dharwad, India
| | - M. Y. Kamatar
- />All India Coordinated Sorghum Improvement Programme, Main Agricultural Research Station, Dharwad, India
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Deschamps S, Llaca V, May GD. Genotyping-by-Sequencing in Plants. BIOLOGY 2012; 1:460-83. [PMID: 24832503 PMCID: PMC4009820 DOI: 10.3390/biology1030460] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 08/07/2012] [Accepted: 09/13/2012] [Indexed: 12/12/2022]
Abstract
The advent of next-generation DNA sequencing (NGS) technologies has led to the development of rapid genome-wide Single Nucleotide Polymorphism (SNP) detection applications in various plant species. Recent improvements in sequencing throughput combined with an overall decrease in costs per gigabase of sequence is allowing NGS to be applied to not only the evaluation of small subsets of parental inbred lines, but also the mapping and characterization of traits of interest in much larger populations. Such an approach, where sequences are used simultaneously to detect and score SNPs, therefore bypassing the entire marker assay development stage, is known as genotyping-by-sequencing (GBS). This review will summarize the current state of GBS in plants and the promises it holds as a genome-wide genotyping application.
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Affiliation(s)
- Stéphane Deschamps
- DuPont Agricultural Biotechnology, Experimental Station, PO Box 80353, 200 Powder Mill Road, Wilmington, DE 19880-0353, USA.
| | - Victor Llaca
- DuPont Agricultural Biotechnology, Experimental Station, PO Box 80353, 200 Powder Mill Road, Wilmington, DE 19880-0353, USA.
| | - Gregory D May
- DuPont Pioneer, 7300 NW 62nd Ave., P.O. Box 1004, Johnston, IA 50131-1004, USA.
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Tuberosa R. Phenotyping for drought tolerance of crops in the genomics era. Front Physiol 2012; 3:347. [PMID: 23049510 PMCID: PMC3446691 DOI: 10.3389/fphys.2012.00347] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 08/09/2012] [Indexed: 12/11/2022] Open
Abstract
Improving crops yield under water-limited conditions is the most daunting challenge faced by breeders. To this end, accurate, relevant phenotyping plays an increasingly pivotal role for the selection of drought-resilient genotypes and, more in general, for a meaningful dissection of the quantitative genetic landscape that underscores the adaptive response of crops to drought. A major and universally recognized obstacle to a more effective translation of the results produced by drought-related studies into improved cultivars is the difficulty in properly phenotyping in a high-throughput fashion in order to identify the quantitative trait loci that govern yield and related traits across different water regimes. This review provides basic principles and a broad set of references useful for the management of phenotyping practices for the study and genetic dissection of drought tolerance and, ultimately, for the release of drought-tolerant cultivars.
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Affiliation(s)
- Roberto Tuberosa
- Department of Agroenvironmental Science and Technology, University of BolognaBologna, Italy
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