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Khan A, Ahmad M, Shani MY, Khan MKR, Rahimi M, Tan DKY. Identifying the physiological traits associated with DNA marker using genome wide association in wheat under heat stress. Sci Rep 2024; 14:20134. [PMID: 39209932 PMCID: PMC11362520 DOI: 10.1038/s41598-024-70630-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Heat stress poses a significant environmental challenge that profoundly impacts wheat productivity. It disrupts vital physiological processes such as photosynthesis, by impeding the functionality of the photosynthetic apparatus and compromising plasma membrane stability, thereby detrimentally affecting grain development in wheat. The scarcity of identified marker trait associations pertinent to thermotolerance presents a formidable obstacle in the development of marker-assisted selection strategies against heat stress. To address this, wheat accessions were systematically exposed to both normal and heat stress conditions and phenotypic data were collected on physiological traits including proline content, canopy temperature depression, cell membrane injury, photosynthetic rate, transpiration rate (at vegetative and reproductive stage and 'stay-green'. Principal component analysis elucidated the most significant contributors being proline content, transpiration rate, and canopy temperature depression, which exhibited a synergistic relationship with grain yield. Remarkably, cluster analysis delineated the wheat accessions into four discrete groups based on physiological attributes. Moreover, to explore the relationship between physiological traits and DNA markers, 158 wheat accessions were genotyped with 186 SSRs. Allelic frequency and polymorphic information content value were found to be highest on genome A (4.94 and 0.688), chromosome 1A (5.00 and 0.712), and marker Xgwm44 (13.0 and 0.916). Population structure, principal coordinate analysis and cluster analysis also partitioned the wheat accessions into four subpopulations based on genotypic data, highlighting their genetic homogeneity. Population diversity and presence of linkage disequilibrium established the suitability of population for association mapping. Additionally, linkage disequilibrium decay was most pronounced within a 15-20 cM region on chromosome 1A. Association mapping revealed highly significant marker trait associations at Bonferroni correction P < 0.00027. Markers Xwmc418 (located on chromosome 3D) and Xgwm233 (chromosome 7A) demonstrated associations with transpiration rate, while marker Xgwm494 (chromosome 3A) exhibited an association with photosynthetic rates at both vegetative and reproductive stages under heat stress conditions. Additionally, markers Xwmc201 (chromosome 6A) and Xcfa2129 (chromosome 1A) displayed robust associations with canopy temperature depression, while markers Xbarc163 (chromosome 4B) and Xbarc49 (chromosome 5A) were strongly associated with cell membrane injury at both stages. Notably, marker Xbarc49 (chromosome 5A) exhibited a significant association with the 'stay-green' trait under heat stress conditions. These results offers the potential utility in marker-assisted selection, gene pyramiding and genomic selection models to predict performance of wheat accession under heat stress conditions.
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Affiliation(s)
- Adeel Khan
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, 38950, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan.
- Department of Plant Breeding and Genetics, PMAS-Arid Agriculture University, Rawalpindi, 46300, Pakistan.
| | - Munir Ahmad
- Department of Plant Breeding and Genetics, PMAS-Arid Agriculture University, Rawalpindi, 46300, Pakistan
| | - Muhammad Yousaf Shani
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, 38950, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Muhammad Kashif Riaz Khan
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, 38950, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Mehdi Rahimi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
| | - Daniel K Y Tan
- Plant Breeding Institute, Sydney Institute of Agriculture, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
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Atsbeha G, Mekonnen T, Kebede M, Haileselassie T, Goodwin SB, Tesfaye K. Genetic architecture of adult-plant resistance to stripe rust in bread wheat ( Triticum aestivum L.) association panel. FRONTIERS IN PLANT SCIENCE 2023; 14:1256770. [PMID: 38130484 PMCID: PMC10733515 DOI: 10.3389/fpls.2023.1256770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a severe disease in wheat worldwide, including Ethiopia, causing up to 100% wheat yield loss in the worst season. The use of resistant cultivars is considered to be the most effective and durable management technique for controlling the disease. Therefore, the present study targeted the genetic architecture of adult plant resistance to yellow rust in 178 wheat association panels. The panel was phenotyped for yellow rust adult-plant resistance at three locations. Phonological, yield, yield-related, and agro-morphological traits were recorded. The association panel was fingerprinted using the genotyping-by-sequencing (GBS) platform, and a total of 6,788 polymorphic single nucleotide polymorphisms (SNPs) were used for genome-wide association analysis to identify effective yellow rust resistance genes. The marker-trait association analysis was conducted using the Genome Association and Prediction Integrated Tool (GAPIT). The broad-sense heritability for the considered traits ranged from 74.52% to 88.64%, implying the presence of promising yellow rust resistance alleles in the association panel that could be deployed to improve wheat resistance to the disease. The overall linkage disequilibrium (LD) declined within an average physical distance of 31.44 Mbp at r2 = 0.2. Marker-trait association (MTA) analysis identified 148 loci significantly (p = 0.001) associated with yellow rust adult-plant resistance. Most of the detected resistance quantitative trait loci (QTLs) were located on the same chromosomes as previously reported QTLs for yellow rust resistance and mapped on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6A, 6B, 7A, and 7D. However, 12 of the discovered MTAs were not previously documented in the wheat literature, suggesting that they could represent novel loci for stripe rust resistance. Zooming into the QTL regions in IWGSC RefSeq Annotation v1 identified crucial disease resistance-associated genes that are key in plants' defense mechanisms against pathogen infections. The detected QTLs will be helpful for marker-assisted breeding of wheat to increase resistance to stripe rust. Generally, the present study identified putative QTLs for field resistance to yellow rust and some important agronomic traits. Most of the discovered QTLs have been reported previously, indicating the potential to improve wheat resistance to yellow rust by deploying the QTLs discovered by marker-assisted selection.
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Affiliation(s)
- Genet Atsbeha
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Tilahun Mekonnen
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mulugeta Kebede
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Stephen B. Goodwin
- USDA-Agricultural Research Service, Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Bio and Emerging Technology Institute. Affiliated with the Institute of Biotechnology, Addis Ababa, University, Addis Ababa, Ethiopia
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Gangurde SS, Xavier A, Naik YD, Jha UC, Rangari SK, Kumar R, Reddy MSS, Channale S, Elango D, Mir RR, Zwart R, Laxuman C, Sudini HK, Pandey MK, Punnuri S, Mendu V, Reddy UK, Guo B, Gangarao NVPR, Sharma VK, Wang X, Zhao C, Thudi M. Two decades of association mapping: Insights on disease resistance in major crops. FRONTIERS IN PLANT SCIENCE 2022; 13:1064059. [PMID: 37082513 PMCID: PMC10112529 DOI: 10.3389/fpls.2022.1064059] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/10/2022] [Indexed: 05/03/2023]
Abstract
Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties.
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Affiliation(s)
- Sunil S. Gangurde
- Crop Genetics and Breeding Research, United States Department of Agriculture (USDA) - Agriculture Research Service (ARS), Tifton, GA, United States
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Alencar Xavier
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | | | - Uday Chand Jha
- Indian Council of Agricultural Research (ICAR), Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | | | - Raj Kumar
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - M. S. Sai Reddy
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - Sonal Channale
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
| | - Dinakaran Elango
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Reyazul Rouf Mir
- Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST), Sopore, India
| | - Rebecca Zwart
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
| | - C. Laxuman
- Zonal Agricultural Research Station (ZARS), Kalaburagi, University of Agricultural Sciences, Raichur, Karnataka, India
| | - Hari Kishan Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Manish K. Pandey
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Somashekhar Punnuri
- College of Agriculture, Family Sciences and Technology, Dr. Fort Valley State University, Fort Valley, GA, United States
| | - Venugopal Mendu
- Department of Plant Science and Plant Pathology, Montana State University, Bozeman, MT, United States
| | - Umesh K. Reddy
- Department of Biology, West Virginia State University, West Virginia, WV, United States
| | - Baozhu Guo
- Crop Genetics and Breeding Research, United States Department of Agriculture (USDA) - Agriculture Research Service (ARS), Tifton, GA, United States
| | | | - Vinay K. Sharma
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - Xingjun Wang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
| | - Mahendar Thudi
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
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Rashid Z, Babu V, Sharma SS, Singh PK, Nair SK. Identification and validation of a key genomic region on chromosome 6 for resistance to Fusarium stalk rot in tropical maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4549-4563. [PMID: 36271945 PMCID: PMC9734215 DOI: 10.1007/s00122-022-04239-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/15/2022] [Indexed: 06/16/2023]
Abstract
A key genomic region was identified for resistance to FSR at 168 Mb on chromosome 6 in GWAS and haplotype regression analysis, which was validated by QTL mapping in two populations. Fusarium stalk rot (FSR) of maize is an economically important post-flowering stalk rot (PFSR) disease caused by Fusarium verticillioides. The pathogen invades the plant individually, or in combination with other stalk rot pathogens or secondary colonizers, thereby making it difficult to make accurate selection for resistance. For identification and validation of genomic regions associated with FSR resistance, a genome-wide association study (GWAS) was conducted with 342 maize lines. The panel was screened for FSR in three environments using standard artificial inoculation methodology. GWAS using the mixed linear model corrected for population structure and kinship was done, in which 290,626 SNPs from genotyping-by-sequencing were used. A total of 7 SNPs, five on chromosome 6 showing strong LD at 168 Mb, were identified to be associated with FSR. Haplotype regression analysis identified 32 haplotypes with a significant effect on the trait. In a QTL mapping experiment in two populations for validating the identified variants, QTLs were identified with confidence intervals having overlapped physical coordinates in both the populations on chromosome 6, which was closely located to the GWAS-identified variants on chromosome 6. It makes this genomic region a crucial one to further investigate the possibility of developing trait markers for deployment in breeding pipelines. It was noted that previously reported QTLs for other stalk rots in maize mapped within the same physical intervals of several haplotypes identified for FSR resistance in this study. The possibility of QTLs controlling broad-spectrum resistance for PFSR in general requires further investigation.
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Affiliation(s)
- Zerka Rashid
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater, Hyderabad, 502324, Telangana, India
| | - Veerendra Babu
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater, Hyderabad, 502324, Telangana, India
| | - Shyam Sundar Sharma
- Maharana Pratap University of Agriculture and Technology (MPUAT), Udaipur, 313001, Rajasthan, India
| | - Pradeep Kumar Singh
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater, Hyderabad, 502324, Telangana, India
- Corteva Agriscience Seeds India Pvt Ltd., Madhapur, Hyderabad, 500081, Telangana, India
| | - Sudha Krishnan Nair
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater, Hyderabad, 502324, Telangana, India.
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Jadhav KP, Saykhedkar GR, Tamilarasi PM, Devasree S, Ranjani RV, Sarankumar C, Bharathi P, Karthikeyan A, Arulselvi S, Vijayagowri E, Ganesan KN, Paranidharan V, Nair SK, Babu R, Ramalingam J, Raveendran M, Senthil N. GBS-Based SNP Map Pinpoints the QTL Associated With Sorghum Downy Mildew Resistance in Maize (Zea mays L.). Front Genet 2022; 13:890133. [PMID: 35937985 PMCID: PMC9348272 DOI: 10.3389/fgene.2022.890133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 06/13/2022] [Indexed: 12/04/2022] Open
Abstract
Sorghum downy mildew (SDM), caused by the biotrophic fungi Peronosclerospora sorghi, threatens maize production worldwide, including India. To identify quantitative trait loci (QTL) associated with resistance to SDM, we used a recombinant inbred line (RIL) population derived from a cross between resistant inbred line UMI936 (w) and susceptible inbred line UMI79. The RIL population was phenotyped for SDM resistance in three environments [E1-field (Coimbatore), E2-greenhouse (Coimbatore), and E3-field (Mandya)] and also utilized to construct the genetic linkage map by genotyping by sequencing (GBS) approach. The map comprises 1516 SNP markers in 10 linkage groups (LGs) with a total length of 6924.7 cM and an average marker distance of 4.57 cM. The QTL analysis with the phenotype and marker data detected nine QTL on chromosome 1, 2, 3, 5, 6, and 7 across three environments. Of these, QTL namely qDMR1.2, qDMR3.1, qDMR5.1, and qDMR6.1 were notable due to their high phenotypic variance. qDMR3.1 from chromosome 3 was detected in more than one environment (E1 and E2), explaining the 10.3% and 13.1% phenotypic variance. Three QTL, qDMR1.2, qDMR5.1, and qDMR6.1 from chromosomes 1, 5, and 6 were identified in either E1 or E3, explaining 15.2%–18% phenotypic variance. Moreover, genome mining on three QTL (qDMR3.1, qDMR5.1, and qDMR6.1) reveals the putative candidate genes related to SDM resistance. The information generated in this study will be helpful for map-based cloning and marker-assisted selection in maize breeding programs.
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Affiliation(s)
- Kashmiri Prakash Jadhav
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Gajanan R. Saykhedkar
- Asian Regional Maize Program, International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, India
| | | | - Subramani Devasree
- Department of Millets, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | - Rajagopalan Veera Ranjani
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Chandran Sarankumar
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Pukalenthy Bharathi
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Adhimoolam Karthikeyan
- Department of Biotechnology, Centre of Innovation, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Soosai Arulselvi
- Agricultural College and Research Institute, Thanjavur, Tamil Nadu Agricultural University, Thanjavur, India
| | - Esvaran Vijayagowri
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Kalipatty Nalliappan Ganesan
- Department of Forage Crops, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | - Vaikuntavasan Paranidharan
- Department of Plant Pathology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, India
| | - Sudha K. Nair
- Asian Regional Maize Program, International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, India
| | - Raman Babu
- Corteva Agrisciences, Multi Crop Research Centre, Hyderabad, India
| | - Jegadeesan Ramalingam
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Muthurajan Raveendran
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Natesan Senthil
- Department of Biotechnology, Centre of Innovation, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
- *Correspondence: Natesan Senthil,
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Zaidi PH, Shahid M, Seetharam K, Vinayan MT. Genomic Regions Associated With Salinity Stress Tolerance in Tropical Maize ( Zea Mays L.). FRONTIERS IN PLANT SCIENCE 2022; 13:869270. [PMID: 35712555 PMCID: PMC9194767 DOI: 10.3389/fpls.2022.869270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Being a widely cultivated crop globally under diverse climatic conditions and soil types, maize is often exposed to an array of biotic and abiotic stresses. Soil salinity is one of the challenges for maize cultivation in many parts of lowland tropics that significantly affects crop growth and reduces economic yields. Breeding strategies integrated with molecular approach might accelerate the process of identifying and developing salinity-tolerant maize cultivars. In this study, an association mapping panel consisting of 305 diverse maize inbred lines was phenotyped in a managed salinity stress phenotyping facility at International Center for Biosaline Agriculture (ICBA), Dubai, United Arab Emirates (UAE). Wide genotypic variability was observed in the panel under salinity stress for key phenotypic traits viz., grain yield, days to anthesis, anthesis-silking interval, plant height, cob length, cob girth, and kernel number. The panel was genotyped following the genome-based sequencing approach to generate 955,690 SNPs. Total SNPs were filtered to 213,043 at a call rate of 0.85 and minor allele frequency of 0.05 for association analysis. A total of 259 highly significant (P ≤ 1 × 10-5) marker-trait associations (MTAs) were identified for seven phenotypic traits. The phenotypic variance for MTAs ranged between 5.2 and 9%. A total of 64 associations were found in 19 unique putative gene expression regions. Among them, 12 associations were found in gene models with stress-related biological functions.
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Affiliation(s)
- Pervez H. Zaidi
- Asia Regional Maize Program, International Maize & Wheat Improvement Center (CIMMYT), Hyderabad, India
| | - Mohammed Shahid
- International Centre for Biosaline Agriculture (ICBA), Dubai, United Arab Emirates
| | - Kaliyamoorthy Seetharam
- Asia Regional Maize Program, International Maize & Wheat Improvement Center (CIMMYT), Hyderabad, India
| | - Madhumal Thayil Vinayan
- Asia Regional Maize Program, International Maize & Wheat Improvement Center (CIMMYT), Hyderabad, India
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Sadessa K, Beyene Y, Ifie BE, Suresh LM, Olsen MS, Ogugo V, Wegary D, Tongoona P, Danquah E, Offei SK, Prasanna BM, Gowda M. Identification of Genomic Regions Associated with Agronomic and Disease Resistance Traits in a Large Set of Multiple DH Populations. Genes (Basel) 2022; 13:genes13020351. [PMID: 35205395 PMCID: PMC8872035 DOI: 10.3390/genes13020351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Breeding maize lines with the improved level of desired agronomic traits under optimum and drought conditions as well as increased levels of resistance to several diseases such as maize lethal necrosis (MLN) is one of the most sustainable approaches for the sub-Saharan African region. In this study, 879 doubled haploid (DH) lines derived from 26 biparental populations were evaluated under artificial inoculation of MLN, as well as under well-watered (WW) and water-stressed (WS) conditions for grain yield and other agronomic traits. All DH lines were used for analyses of genotypic variability, association studies, and genomic predictions for the grain yield and other yield-related traits. Genome-wide association study (GWAS) using a mixed linear FarmCPU model identified SNPs associated with the studied traits i.e., about seven and eight SNPs for the grain yield; 16 and 12 for anthesis date; seven and eight for anthesis silking interval; 14 and 5 for both ear and plant height; and 15 and 5 for moisture under both WW and WS environments, respectively. Similarly, about 13 and 11 SNPs associated with gray leaf spot and turcicum leaf blight were identified. Eleven SNPs associated with senescence under WS management that had depicted drought-stress-tolerant QTLs were identified. Under MLN artificial inoculation, a total of 12 and 10 SNPs associated with MLN disease severity and AUDPC traits, respectively, were identified. Genomic prediction under WW, WS, and MLN disease artificial inoculation revealed moderate-to-high prediction accuracy. The findings of this study provide useful information on understanding the genetic basis for the MLN resistance, grain yield, and other agronomic traits under MLN artificial inoculation, WW, and WS conditions. Therefore, the obtained information can be used for further validation and developing functional molecular markers for marker-assisted selection and for implementing genomic prediction to develop superior elite lines.
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Affiliation(s)
- Kassahun Sadessa
- Ethiopian Institute of Agricultural Research (EIAR), Ambo Agricultural Research Center, Ambo P.O. Box 37, West Shoa, Ethiopia;
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, P.O. Box 1041-00621, Nairobi 00100, Kenya; (Y.B.); (L.M.S.); (M.S.O.); (V.O.); (B.M.P.)
- International Maize and Wheat Improvement Center (CIMMYT), 12.5 KM Peg, Harare P.O. Box MP163, Zimbabwe;
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, P.O. Box LG23, Accra 00233, Ghana; (B.E.I.); (P.T.); (E.D.); (S.K.O.)
| | - Yoseph Beyene
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, P.O. Box 1041-00621, Nairobi 00100, Kenya; (Y.B.); (L.M.S.); (M.S.O.); (V.O.); (B.M.P.)
| | - Beatrice E. Ifie
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, P.O. Box LG23, Accra 00233, Ghana; (B.E.I.); (P.T.); (E.D.); (S.K.O.)
| | - L. M. Suresh
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, P.O. Box 1041-00621, Nairobi 00100, Kenya; (Y.B.); (L.M.S.); (M.S.O.); (V.O.); (B.M.P.)
| | - Michael S. Olsen
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, P.O. Box 1041-00621, Nairobi 00100, Kenya; (Y.B.); (L.M.S.); (M.S.O.); (V.O.); (B.M.P.)
| | - Veronica Ogugo
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, P.O. Box 1041-00621, Nairobi 00100, Kenya; (Y.B.); (L.M.S.); (M.S.O.); (V.O.); (B.M.P.)
| | - Dagne Wegary
- International Maize and Wheat Improvement Center (CIMMYT), 12.5 KM Peg, Harare P.O. Box MP163, Zimbabwe;
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, P.O. Box LG23, Accra 00233, Ghana; (B.E.I.); (P.T.); (E.D.); (S.K.O.)
| | - Eric Danquah
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, P.O. Box LG23, Accra 00233, Ghana; (B.E.I.); (P.T.); (E.D.); (S.K.O.)
| | - Samuel Kwame Offei
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, P.O. Box LG23, Accra 00233, Ghana; (B.E.I.); (P.T.); (E.D.); (S.K.O.)
| | - Boddupalli M. Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, P.O. Box 1041-00621, Nairobi 00100, Kenya; (Y.B.); (L.M.S.); (M.S.O.); (V.O.); (B.M.P.)
| | - Manje Gowda
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, P.O. Box 1041-00621, Nairobi 00100, Kenya; (Y.B.); (L.M.S.); (M.S.O.); (V.O.); (B.M.P.)
- Correspondence: ; Tel.: +254-727019454
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Rashid Z, Kaur H, Babu V, Singh PK, Harlapur SI, Nair SK. Identification and Validation of Genomic Regions Associated With Charcoal Rot Resistance in Tropical Maize by Genome-Wide Association and Linkage Mapping. FRONTIERS IN PLANT SCIENCE 2021; 12:726767. [PMID: 34691105 PMCID: PMC8531636 DOI: 10.3389/fpls.2021.726767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/30/2021] [Indexed: 06/01/2023]
Abstract
Charcoal rot is a post-flowering stalk rot (PFSR) disease of maize caused by the fungal pathogen, Macrophomina phaseolina. It is a serious concern for smallholder maize cultivation, due to significant yield loss and plant lodging at harvest, and this disease is expected to surge with climate change effects like drought and high soil temperature. For identification and validation of genomic variants associated with charcoal rot resistance, a genome-wide association study (GWAS) was conducted on CIMMYT Asia association mapping panel comprising 396 tropical-adapted lines, especially to Asian environments. The panel was phenotyped for disease severity across two locations with high disease prevalence in India. A subset of 296,497 high-quality SNPs filtered from genotyping by sequencing was correcting for population structure and kinship matrices for single locus mixed linear model (MLM) of GWAS analysis. A total of 19 SNPs were identified to be associated with charcoal rot resistance with P-value ranging from 5.88 × 10-06 to 4.80 × 10-05. Haplotype regression analysis identified 21 significant haplotypes for the trait with Bonferroni corrected P ≤ 0.05. For validating the associated variants and identifying novel QTLs, QTL mapping was conducted using two F2:3 populations. Two QTLs with overlapping physical intervals, qMSR6 and qFMSR6 on chromosome 6, identified from two different mapping populations and contributed by two different resistant parents, were co-located with the SNPs and haplotypes identified at 103.51 Mb on chromosome 6. Similarly, several SNPs/haplotypes identified on chromosomes 3, 6 and 8 were also found to be physically co-located within QTL intervals detected in one of the two mapping populations. The study also noted that several SNPs/haplotypes for resistance to charcoal rot were located within physical intervals of previously reported QTLs for Gibberella stalk rot resistance, which opens up a new possibility for common disease resistance mechanisms for multiple stalk rots.
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Affiliation(s)
- Zerka Rashid
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Hyderabad, India
| | - Harleen Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Veerendra Babu
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Hyderabad, India
| | - Pradeep Kumar Singh
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Hyderabad, India
| | | | - Sudha K. Nair
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Hyderabad, India
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Mekonnen T, Sneller CH, Haileselassie T, Ziyomo C, Abeyo BG, Goodwin SB, Lule D, Tesfaye K. Genome-Wide Association Study Reveals Novel Genetic Loci for Quantitative Resistance to Septoria Tritici Blotch in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:671323. [PMID: 34630445 PMCID: PMC8500178 DOI: 10.3389/fpls.2021.671323] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Septoria tritici blotch, caused by the fungus Zymoseptoria titici, poses serious and persistent challenges to wheat cultivation in Ethiopia and worldwide. Deploying resistant cultivars is a major component of controlling septoria tritici blotch (STB). Thus, the objective of this study was to elucidate the genomic architecture of STB resistance in an association panel of 178 bread wheat genotypes. The association panel was phenotyped for STB resistance, phenology, yield, and yield-related traits in three locations for 2 years. The panel was also genotyped for single nucleotide polymorphism (SNP) markers using the genotyping-by-sequencing (GBS) method, and a total of 7,776 polymorphic SNPs were used in the subsequent analyses. Marker-trait associations were also computed using a genome association and prediction integrated tool (GAPIT). The study then found that the broad-sense heritability for STB resistance ranged from 0.58 to 0.97 and 0.72 to 0.81 at the individual and across-environment levels, respectively, indicating the presence of STB resistance alleles in the association panel. Population structure and principal component analyses detected two sub-groups with greater degrees of admixture. A linkage disequilibrium (LD) analysis in 338,125 marker pairs also detected the existence of significant (p ≤ 0.01) linkage in 27.6% of the marker pairs. Specifically, in all chromosomes, the LD between SNPs declined within 2.26-105.62 Mbp, with an overall mean of 31.44 Mbp. Furthermore, the association analysis identified 53 loci that were significantly (false discovery rate, FDR, <0.05) associated with STB resistance, further pointing to 33 putative quantitative trait loci (QTLs). Most of these shared similar chromosomes with already published Septoria resistance genes, which were distributed across chromosomes 1B, 1D, 2A, 2B, 2D, 3A,3 B, 3D, 4A, 5A, 5B, 6A, 7A, 7B, and 7D. However, five of the putative QTLs identified on chromosomes 1A, 5D, and 6B appeared to be novel. Dissecting the detected loci on IWGSC RefSeq Annotation v2.1 revealed the existence of disease resistance-associated genes in the identified QTL regions that are involved in plant defense responses. These putative QTLs explained 2.7-13.2% of the total phenotypic variation. Seven of the QTLs (R 2 = 2.7-10.8%) for STB resistance also co-localized with marker-trait associations (MTAs) for agronomic traits. Overall, this analysis reported on putative QTLs for adult plant resistance to STB and some important agronomic traits. The reported and novel QTLs have been identified previously, indicating the potential to improve STB resistance by pyramiding QTLs by marker-assisted selection.
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Affiliation(s)
- Tilahun Mekonnen
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Clay H. Sneller
- Biosciences Eastern and Central Africa (BecA), Nairobi, Kenya
| | | | - Cathrine Ziyomo
- Biosciences Eastern and Central Africa (BecA), Nairobi, Kenya
| | - Bekele G. Abeyo
- International Maize and Wheat Improvement Center- CIMMYT (Ethiopia), Addis Ababa, Ethiopia
| | - Stephen B. Goodwin
- United States Department of Agriculture (USDA)-Agricultural Research Service, West Lafayette, IN, United States
| | - Dagnachew Lule
- Oromia Agricultural Research Institute (OARI), Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute (EBTi), Addis Ababa, Ethiopia
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10
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Genomic regions associated with heat stress tolerance in tropical maize (Zea mays L.). Sci Rep 2021; 11:13730. [PMID: 34215789 PMCID: PMC8253795 DOI: 10.1038/s41598-021-93061-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/21/2021] [Indexed: 11/20/2022] Open
Abstract
With progressive climate change and the associated increase in mean temperature, heat stress tolerance has emerged as one of the key traits in the product profile of the maize breeding pipeline for lowland tropics. The present study aims to identify the genomic regions associated with heat stress tolerance in tropical maize. An association mapping panel, called the heat tolerant association mapping (HTAM) panel, was constituted by involving a total of 543 tropical maize inbred lines from diverse genetic backgrounds, test-crossed and phenotyped across nine locations in South Asia under natural heat stress. The panel was genotyped using a genotyping-by-sequencing (GBS) platform. Considering the large variations in vapor pressure deficit (VPD) at high temperature (Tmax) across different phenotyping locations, genome-wide association study (GWAS) was conducted separately for each location. The individual location GWAS identified a total of 269 novel significant single nucleotide polymorphisms (SNPs) for grain yield under heat stress at a p value of < 10–5. A total of 175 SNPs were found in 140 unique gene models implicated in various biological pathway responses to different abiotic stresses. Haplotype trend regression (HTR) analysis of the significant SNPs identified 26 haplotype blocks and 96 single SNP variants significant across one to five locations. The genomic regions identified based on GWAS and HTR analysis considering genomic region x environment interactions are useful for breeding efforts aimed at developing heat stress resilient maize cultivars for current and future climatic conditions through marker-assisted introgression into elite genetic backgrounds and/or genome-wide selection.
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11
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Berhe M, Dossa K, You J, Mboup PA, Diallo IN, Diouf D, Zhang X, Wang L. Genome-wide association study and its applications in the non-model crop Sesamum indicum. BMC PLANT BIOLOGY 2021; 21:283. [PMID: 34157965 PMCID: PMC8218510 DOI: 10.1186/s12870-021-03046-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/17/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Sesame is a rare example of non-model and minor crop for which numerous genetic loci and candidate genes underlying features of interest have been disclosed at relatively high resolution. These progresses have been achieved thanks to the applications of the genome-wide association study (GWAS) approach. GWAS has benefited from the availability of high-quality genomes, re-sequencing data from thousands of genotypes, extensive transcriptome sequencing, development of haplotype map and web-based functional databases in sesame. RESULTS In this paper, we reviewed the GWAS methods, the underlying statistical models and the applications for genetic discovery of important traits in sesame. A novel online database SiGeDiD ( http://sigedid.ucad.sn/ ) has been developed to provide access to all genetic and genomic discoveries through GWAS in sesame. We also tested for the first time, applications of various new GWAS multi-locus models in sesame. CONCLUSIONS Collectively, this work portrays steps and provides guidelines for efficient GWAS implementation in sesame, a non-model crop.
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Affiliation(s)
- Muez Berhe
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China
- Humera Agricultural Research Center of Tigray Agricultural Research Institute, Humera, Tigray, Ethiopia
| | - Komivi Dossa
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China.
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal.
- Laboratory of Genetics, Horticulture and Seed Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526, Cotonou, Republic of Benin.
| | - Jun You
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Pape Adama Mboup
- Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal
| | - Idrissa Navel Diallo
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal
- Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China.
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Longmei N, Gill GK, Zaidi PH, Kumar R, Nair SK, Hindu V, Vinayan MT, Vikal Y. Genome wide association mapping for heat tolerance in sub-tropical maize. BMC Genomics 2021; 22:154. [PMID: 33663389 PMCID: PMC7934507 DOI: 10.1186/s12864-021-07463-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 02/22/2021] [Indexed: 01/06/2023] Open
Abstract
Background Heat tolerance is becoming increasingly important where maize is grown under spring season in India which coincide with grain filling stage of crop resulting in tassel blast, reduced pollen viability, pollination failure and barren ears that causes devastating yield losses. So, there is need to identify the genomic regions associated with heat tolerance component traits which could be further employed in maize breeding program. Results An association mapping panel, consisting of 662 doubled haploid (DH) lines, was evaluated for yield contributing traits under normal and natural heat stress conditions. Genome wide association studies (GWAS) carried out using 187,000 SNPs and 130 SNPs significantly associated for grain yield (GY), days to 50% anthesis (AD), days to 50% silking (SD), anthesis-silking interval (ASI), plant height (PH), ear height (EH) and ear position (EPO) were identified under normal conditions. A total of 46 SNPs strongly associated with GY, ASI, EH and EPO were detected under heat stress conditions. Fifteen of the SNPs was found to have common association with more than one trait such as two SNPs viz. S10_1,905,273 and S10_1,905,274 showed colocalization with GY, PH and EH whereas S10_7,132,845 SNP associated with GY, AD and SD under normal conditions. No such colocalization of SNP markers with multiple traits was observed under heat stress conditions. Haplotypes trend regression analysis revealed 122 and 85 haplotype blocks, out of which, 20 and 6 haplotype blocks were associated with more than one trait under normal and heat stress conditions, respectively. Based on SNP association and haplotype mapping, nine and seven candidate genes were identified respectively, which belongs to different gene models having different biological functions in stress biology. Conclusions The present study identified significant SNPs and haplotype blocks associated with yield contributing traits that help in selection of donor lines with favorable alleles for multiple traits. These results provided insights of genetics of heat stress tolerance. The genomic regions detected in the present study need further validation before being applied in the breeding pipelines. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07463-y.
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Affiliation(s)
- Ningthaipuilu Longmei
- Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Gurjit Kaur Gill
- Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pervez Haider Zaidi
- International Maize and Wheat Improvement Centre (CIMMYT), Asia Regional Office, Hyderabad, India
| | - Ramesh Kumar
- Indian Institutes of Maize, Ludhiana, Punjab, India
| | - Sudha Krishnan Nair
- International Maize and Wheat Improvement Centre (CIMMYT), Asia Regional Office, Hyderabad, India
| | - Vermuri Hindu
- International Maize and Wheat Improvement Centre (CIMMYT), Asia Regional Office, Hyderabad, India
| | - Madhumal Thayil Vinayan
- International Maize and Wheat Improvement Centre (CIMMYT), Asia Regional Office, Hyderabad, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India.
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Genome wide association study and genomic prediction for stover quality traits in tropical maize (Zea mays L.). Sci Rep 2021; 11:686. [PMID: 33436870 PMCID: PMC7804097 DOI: 10.1038/s41598-020-80118-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 12/15/2020] [Indexed: 11/09/2022] Open
Abstract
Maize is rapidly replacing traditionally cultivated dual purpose crops of South Asia, primarily due to the better economic remuneration. This has created an impetus for improving maize for both grain productivity and stover traits. Molecular techniques can largely assist breeders in determining approaches for effectively integrating stover trait improvement in their existing breeding pipeline. In the current study we identified a suite of potential genomic regions associated to the two major stover quality traits-in-vitro organic matter digestibility (IVOMD) and metabolizable energy (ME) through genome wide association study. However, considering the fact that the loci identified for these complex traits all had smaller effects and accounted only a small portion of phenotypic variation, the effectiveness of following a genomic selection approach for these traits was evaluated. The testing set consists of breeding lines recently developed within the program and the training set consists of a panel of lines from the working germplasm comprising the founder lines of the newly developed breeding lines and also an unrelated diversity set. The prediction accuracy as determined by the Pearson's correlation coefficient between observed and predicted values of these breeding lines were high even at lower marker density (200 random SNPs), when the training and testing set were related. However, the accuracies were dismal, when there was no relationship between the training and the testing set.
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14
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Rashid Z, Sofi M, Harlapur SI, Kachapur RM, Dar ZA, Singh PK, Zaidi PH, Vivek BS, Nair SK. Genome-wide association studies in tropical maize germplasm reveal novel and known genomic regions for resistance to Northern corn leaf blight. Sci Rep 2020; 10:21949. [PMID: 33319847 PMCID: PMC7738672 DOI: 10.1038/s41598-020-78928-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/26/2020] [Indexed: 02/08/2023] Open
Abstract
Northern Corn Leaf Blight (NCLB) caused by Setosphaeria turcica, is one of the most important diseases of maize world-wide, and one of the major reasons behind yield losses in maize crop in Asia. In the present investigation, a high-resolution genome wide association study (GWAS) was conducted for NCLB resistance in three association mapping panels, predominantly consisting of tropical lines adapted to different agro-ecologies. These panels were phenotyped for disease severity across three locations with high disease prevalence in India. High density SNPs from Genotyping-by-sequencing were used in GWAS, after controlling for population structure and kinship matrices, based on single locus mixed linear model (MLM). Twenty-two SNPs were identified, that revealed a significant association with NCLB in the three mapping panels. Haplotype regression analysis revealed association of 17 significant haplotypes at FDR ≤ 0.05, with two common haplotypes across three maize panels. Several of the significantly associated SNPs/haplotypes were found to be co-located in chromosomal bins previously reported for major genes like Ht2, Ht3 and Htn1 and QTL for NCLB resistance and multiple foliar disease resistance. Phenotypic variance explained by these significant SNPs/haplotypes ranged from low to moderate, suggesting a breeding strategy of combining multiple resistance alleles towards resistance for NCLB.
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Affiliation(s)
- Zerka Rashid
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad Telangana, 502324, India
| | - Mehrajuddin Sofi
- High Mountain Arid Agricultural Research Institute (HMAARI) Stakna, SKUAST-Kashmir, Leh, 194101, India
| | - Sharanappa I Harlapur
- University of Agricultural Sciences, Krishi Nagar, Dharwad, Karnataka, 580005, India
| | | | - Zahoor Ahmed Dar
- Sher-E-Kashmir University of Agriculture Sciences and Technology (SKUAST), Srinagar, Jammu and Kashmir, 190001, India
| | - Pradeep Kumar Singh
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad Telangana, 502324, India
| | - Pervez Haider Zaidi
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad Telangana, 502324, India
| | - Bindiganavile Sampath Vivek
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad Telangana, 502324, India
| | - Sudha Krishnan Nair
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad Telangana, 502324, India.
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15
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Kibe M, Nair SK, Das B, Bright JM, Makumbi D, Kinyua J, Suresh LM, Beyene Y, Olsen MS, Prasanna BM, Gowda M. Genetic Dissection of Resistance to Gray Leaf Spot by Combining Genome-Wide Association, Linkage Mapping, and Genomic Prediction in Tropical Maize Germplasm. FRONTIERS IN PLANT SCIENCE 2020; 11:572027. [PMID: 33224163 PMCID: PMC7667048 DOI: 10.3389/fpls.2020.572027] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/29/2020] [Indexed: 05/05/2023]
Abstract
Gray leaf spot (GLS) is one of the major maize foliar diseases in sub-Saharan Africa. Resistance to GLS is controlled by multiple genes with additive effect and is influenced by both genotype and environment. The objectives of the study were to dissect the genetic architecture of GLS resistance through linkage mapping and genome-wide association study (GWAS) and assessing the potential of genomic prediction (GP). We used both biparental populations and an association mapping panel of 410 diverse tropical/subtropical inbred lines that were genotyped using genotype by sequencing. Phenotypic evaluation in two to four environments revealed significant genotypic variation and moderate to high heritability estimates ranging from 0.43 to 0.69. GLS was negatively and significantly correlated with grain yield, anthesis date, and plant height. Linkage mapping in five populations revealed 22 quantitative trait loci (QTLs) for GLS resistance. A QTL on chromosome 7 (qGLS7-105) is a major-effect QTL that explained 28.2% of phenotypic variance. Together, all the detected QTLs explained 10.50, 49.70, 23.67, 18.05, and 28.71% of phenotypic variance in doubled haploid (DH) populations 1, 2, 3, and F3 populations 4 and 5, respectively. Joint linkage association mapping across three DH populations detected 14 QTLs that individually explained 0.10-15.7% of phenotypic variance. GWAS revealed 10 significantly (p < 9.5 × 10-6) associated SNPs distributed on chromosomes 1, 2, 6, 7, and 8, which individually explained 6-8% of phenotypic variance. A set of nine candidate genes co-located or in physical proximity to the significant SNPs with roles in plant defense against pathogens were identified. GP revealed low to moderate prediction correlations of 0.39, 0.37, 0.56, 0.30, 0.29, and 0.38 for within IMAS association panel, DH pop1, DH pop2, DH pop3, F3 pop4, and F3 po5, respectively, and accuracy was increased substantially to 0.84 for prediction across three DH populations. When the diversity panel was used as training set to predict the accuracy of GLS resistance in biparental population, there was 20-50% reduction compared to prediction within populations. Overall, the study revealed that resistance to GLS is quantitative in nature and is controlled by many loci with a few major and many minor effects. The SNPs/QTLs identified by GWAS and linkage mapping can be potential targets in improving GLS resistance in breeding programs, while GP further consolidates the development of high GLS-resistant lines by incorporating most of the major- and minor-effect genes.
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Affiliation(s)
- Maguta Kibe
- International Maize and Wheat Improvement Center, Nairobi, Kenya
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Sudha K. Nair
- International Maize and Wheat Improvement Center, Hyderabad, India
| | - Biswanath Das
- International Maize and Wheat Improvement Center, Nairobi, Kenya
| | - Jumbo M. Bright
- International Maize and Wheat Improvement Center, Nairobi, Kenya
| | - Dan Makumbi
- International Maize and Wheat Improvement Center, Nairobi, Kenya
| | - Johnson Kinyua
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - L. M. Suresh
- International Maize and Wheat Improvement Center, Nairobi, Kenya
| | - Yoseph Beyene
- International Maize and Wheat Improvement Center, Nairobi, Kenya
| | - Michael S. Olsen
- International Maize and Wheat Improvement Center, Nairobi, Kenya
| | | | - Manje Gowda
- International Maize and Wheat Improvement Center, Nairobi, Kenya
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Kim HC, Kim KH, Song K, Kim JY, Lee BM. Identification and Validation of Candidate Genes Conferring Resistance to Downy Mildew in Maize ( Zea mays L.). Genes (Basel) 2020; 11:E191. [PMID: 32053973 PMCID: PMC7074223 DOI: 10.3390/genes11020191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/05/2020] [Accepted: 02/05/2020] [Indexed: 11/16/2022] Open
Abstract
Downy mildew (DM) is a major disease of maize that causes significant yield loss in subtropical and tropical regions around the world. A variety of DM strains have been reported, and the resistance to them is polygenically controlled. In this study, we analyzed the quantitative trait loci (QTLs) involved in resistance to Peronosclerospora sorghi (sorghum DM), P. maydis (Java DM), and Sclerophthora macrospora (crazy top DM) using a recombinant inbred line (RIL) from a cross between B73 (susceptible) and Ki11 (resistant), and the candidate genes for P. sorghi, P. maydis, and S. macrospora resistance were discovered. The linkage map was constructed with 234 simple sequence repeat (SSR) and restriction fragment length polymorphism (RFLP) markers, which was identified seven QTLs (chromosomes 2, 3, 6, and 9) for three DM strains. The major QTL, located on chromosome 2, consists of 12.95% of phenotypic variation explained (PVE) and a logarithm of odds (LOD) score of 14.12. Sixty-two candidate genes for P. sorghi, P. maydis, and S. macrospora resistance were obtained between the flanked markers in the QTL regions. The relative expression level of candidate genes was evaluated by quantitative real-time polymerase chain reaction (qRT-PCR) using resistant (CML228, Ki3, and Ki11) and susceptible (B73 and CML270) genotypes. For the 62 candidate genes, 15 genes were upregulated in resistant genotypes. Among these, three (GRMZM2G028643, GRMZM2G128315, and GRMZM2G330907) and AC210003.2_FG004 were annotated as leucine-rich repeat (LRR) and peroxidase (POX) genes, respectively. These candidate genes in the QTL regions provide valuable information for further studies related to P. sorghi, P. maydis, and S. macrospora resistance.
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Affiliation(s)
- Hyo Chul Kim
- Department of Life Science, Dongguk University-Seoul, Seoul 04620, Korea; (H.C.K.); (K.-H.K.); (K.S.)
| | - Kyung-Hee Kim
- Department of Life Science, Dongguk University-Seoul, Seoul 04620, Korea; (H.C.K.); (K.-H.K.); (K.S.)
| | - Kitae Song
- Department of Life Science, Dongguk University-Seoul, Seoul 04620, Korea; (H.C.K.); (K.-H.K.); (K.S.)
| | - Jae Yoon Kim
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea;
| | - Byung-Moo Lee
- Department of Life Science, Dongguk University-Seoul, Seoul 04620, Korea; (H.C.K.); (K.-H.K.); (K.S.)
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Ye X, Li J, Cheng Y, Yao F, Long L, Wang Y, Wu Y, Li J, Wang J, Jiang Q, Kang H, Li W, Qi P, Lan X, Ma J, Liu Y, Jiang Y, Wei Y, Chen X, Liu C, Zheng Y, Chen G. Genome-wide association study reveals new loci for yield-related traits in Sichuan wheat germplasm under stripe rust stress. BMC Genomics 2019; 20:640. [PMID: 31395029 PMCID: PMC6688255 DOI: 10.1186/s12864-019-6005-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 07/29/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As one of the most important food crops in the world, increasing wheat (Triticum aestivum L.) yield is an urgent task for global food security under the continuous threat of stripe rust (caused by Puccinia striiformis f. sp. tritici) in many regions of the world. Molecular marker-assisted breeding is one of the most efficient ways to increase yield. Here, we identified loci associated to multi-environmental yield-related traits under stripe rust stress in 244 wheat accessions from Sichuan Province through genome-wide association study (GWAS) using 44,059 polymorphic markers from the 55 K single nucleotide polymorphism (SNP) chip. RESULTS A total of 13 stable quantitative trait loci (QTLs) were found to be highly associating to yield-related traits, including 6 for spike length (SL), 3 for thousand-kernel weight (TKW), 2 for kernel weight per spike (KWPS), and 2 for both TKW and KWPS, in at least two test environments under stripe rust stress conditions. Of them, ten QTLs were overlapped or very close to the reported QTLs, three QTLs, QSL.sicau-1AL, QTKW.sicau-4AL, and QKWPS.sicau-4AL.1, were potentially novel through the physical location comparison with previous QTLs. Further, 21 candidate genes within three potentially novel QTLs were identified, they were mainly involved in the regulation of phytohormone, cell division and proliferation, meristem development, plant or organ development, and carbohydrate transport. CONCLUSIONS QTLs and candidate genes detected in our study for yield-related traits under stripe rust stress will facilitate elucidating genetic basis of yield-related trait and could be used in marker-assisted selection in wheat yield breeding.
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Affiliation(s)
- Xueling Ye
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jian Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yukun Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Fangjie Yao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Li Long
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yuqi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yu Wu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jing Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Houyang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Pengfei Qi
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Xiujin Lan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yunfeng Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Xianming Chen
- US Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit; and Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Chunji Liu
- CSIRO Agriculture and Food, St Lucia, Queensland, 4067, Australia
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China.
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China.
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SNP-based mixed model association of growth- and yield-related traits in popcorn. PLoS One 2019; 14:e0218552. [PMID: 31237892 PMCID: PMC6592533 DOI: 10.1371/journal.pone.0218552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/04/2019] [Indexed: 12/26/2022] Open
Abstract
The identification of the genes responsible for complex traits is highly promising to accelerate crop breeding, but such information is still limited for popcorn. Thus, in the present study, a mixed linear model-based association analysis (MLMA) was applied for six important popcorn traits: plant and ear height, 100-grain weight, popping expansion, grain yield and expanded popcorn volume per hectare. To this end, 196 plants of the open-pollinated popcorn population UENF-14 were sampled, selfed (S1), and then genotyped with a panel of 10,507 single nucleotide polymorphisms (SNPs) markers distributed throughout the genome. The six traits were studied under two environments [Campos dos Goytacazes-RJ (ENV1) and Itaocara-RJ (ENV2)] in an incomplete block design. Based on the phenotypic data of the S1 progenies and on the genetic characteristics of the parents, the MLMA was performed. Thereafter, genes annotated in the MaizeGDB platform were screened for potential linkage disequilibrium with the SNPs associated to the six evaluated traits. Overall, seven and eight genes were identified as associated with the traits in ENV1 and ENV2, respectively, and proteins encoded by these genes were evaluated for their function. The results obtained here contribute to increase knowledge on the genetic architecture of the six evaluated traits and might be used for marker-assisted selection in breeding programs.
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19
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Long L, Yao F, Yu C, Ye X, Cheng Y, Wang Y, Wu Y, Li J, Wang J, Jiang Q, Li W, Ma J, Liu Y, Deng M, Wei Y, Zheng Y, Chen G. Genome-Wide Association Study for Adult-Plant Resistance to Stripe Rust in Chinese Wheat Landraces ( Triticum aestivum L.) From the Yellow and Huai River Valleys. FRONTIERS IN PLANT SCIENCE 2019; 10:596. [PMID: 31156668 PMCID: PMC6532019 DOI: 10.3389/fpls.2019.00596] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/24/2019] [Indexed: 05/21/2023]
Abstract
Stripe rust (also known as yellow rust), caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), is a common and serious fungal disease of wheat (Triticum aestivum L.) worldwide. To identify effective stripe rust resistance loci, a genome-wide association study was performed using 152 wheat landraces from the Yellow and Huai River Valleys in China based on Diversity Arrays Technology and simple sequence repeat markers. Phenotypic evaluation of the degree of resistance to stripe rust at the adult-plant stage under field conditions was carried out in five environments. In total, 19 accessions displayed stable, high degrees of resistance to stripe rust development when exposed to mixed races of Pst at the adult-plant stage in multi-environment field assessments. A marker-trait association analysis indicated that 51 loci were significantly associated with adult-plant resistance to stripe rust. These loci included 40 quantitative trait loci (QTL) regions for adult-plant resistance. Twenty identified resistance QTL were linked closely to previously reported yellow rust resistance genes or QTL regions, which were distributed across chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4A, 4B, 5B, 6B, 7A, 7B, and 7D. Six multi-trait QTL were detected on chromosomes 1B, 1D, 2B, 3A, 3B, and 7D. Twenty QTL were mapped to chromosomes 1D, 2A, 2D, 4B, 5B, 6A, 6B, 6D, 7A, 7B, and 7D, distant from previously identified yellow rust resistance genes. Consequently, these QTL are potentially novel loci for stripe rust resistance. Among the 20 potentially novel QTL, five (QDS.sicau-2A, QIT.sicau-4B, QDS.sicau-4B.2, QDS.sicau-6A.3, and QYr.sicau-7D) were associated with field responses at the adult-plant stage in at least two environments, and may have large effects on stripe rust resistance. The novel effective QTL for adult-plant resistance to stripe rust will improve understanding of the genetic mechanisms that control the spread of stripe rust, and will aid in the molecular marker-assisted selection-based breeding of wheat for stripe rust resistance.
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Affiliation(s)
- Li Long
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Fangjie Yao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Can Yu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Xueling Ye
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Yukun Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Yuqi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Yu Wu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Jing Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - YaXi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Guoyue Chen,
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Hindu V, Palacios-Rojas N, Babu R, Suwarno WB, Rashid Z, Usha R, Saykhedkar GR, Nair SK. Identification and validation of genomic regions influencing kernel zinc and iron in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1443-1457. [PMID: 29574570 PMCID: PMC6004279 DOI: 10.1007/s00122-018-3089-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 03/16/2018] [Indexed: 05/19/2023]
Abstract
KEY MESSAGE Genome-wide association study (GWAS) on 923 maize lines and validation in bi-parental populations identified significant genomic regions for kernel-Zinc and-Iron in maize. Bio-fortification of maize with elevated Zinc (Zn) and Iron (Fe) holds considerable promise for alleviating under-nutrition among the world's poor. Bio-fortification through molecular breeding could be an economical strategy for developing nutritious maize, and hence in this study, we adopted GWAS to identify markers associated with high kernel-Zn and Fe in maize and subsequently validated marker-trait associations in independent bi-parental populations. For GWAS, we evaluated a diverse maize association mapping panel of 923 inbred lines across three environments and detected trait associations using high-density Single nucleotide polymorphism (SNPs) obtained through genotyping-by-sequencing. Phenotyping trials of the GWAS panel showed high heritability and moderate correlation between kernel-Zn and Fe concentrations. GWAS revealed a total of 46 SNPs (Zn-20 and Fe-26) significantly associated (P ≤ 5.03 × 10-05) with kernel-Zn and Fe concentrations with some of these associated SNPs located within previously reported QTL intervals for these traits. Three double-haploid (DH) populations were developed using lines identified from the panel that were contrasting for these micronutrients. The DH populations were phenotyped at two environments and were used for validating significant SNPs (P ≤ 1 × 10-03) based on single marker QTL analysis. Based on this analysis, 11 (Zn) and 11 (Fe) SNPs were found to have significant effect on the trait variance (P ≤ 0.01, R2 ≥ 0.05) in at least one bi-parental population. These findings are being pursued in the kernel-Zn and Fe breeding program, and could hold great value in functional analysis and possible cloning of high-value genes for these traits in maize.
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Affiliation(s)
- Vemuri Hindu
- Asia Regional Maize Program, International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Hyderabad, Telangana 502324 India
- Sri Padmavati Mahila Visvavidyalayam (Women’s University), Tirupati, Andhra Pradesh 517502 India
| | - Natalia Palacios-Rojas
- International Maize and Wheat Improvement Center (CIMMYT), Km 45 Carretera Mexico-Veracruz, 56130 Texcoco, Mexico
| | - Raman Babu
- Asia Regional Maize Program, International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Hyderabad, Telangana 502324 India
- Present Address: Multi-Crop Research Center (MCRC), DuPont Pioneer, Hyderabad, Telangana 500078 India
| | - Willy B. Suwarno
- International Maize and Wheat Improvement Center (CIMMYT), Km 45 Carretera Mexico-Veracruz, 56130 Texcoco, Mexico
- Present Address: Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University, Jl. Meranti Kampus IPB Dramaga, Bogor, 16680 Indonesia
| | - Zerka Rashid
- Asia Regional Maize Program, International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Hyderabad, Telangana 502324 India
| | - Rayalcheruvu Usha
- Sri Padmavati Mahila Visvavidyalayam (Women’s University), Tirupati, Andhra Pradesh 517502 India
| | - Gajanan R Saykhedkar
- Asia Regional Maize Program, International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Hyderabad, Telangana 502324 India
- Present Address: Project Director, SPMESM, Dr. Hedgewar Hospital, Aurangabad, Maharashtra 431005 India
| | - Sudha K. Nair
- Asia Regional Maize Program, International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Hyderabad, Telangana 502324 India
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