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Li Y, Hu J, Lin H, Qiu D, Qu Y, Du J, Hou L, Ma L, Wu Q, Liu Z, Zhou Y, Li H. Mapping QTLs for adult-plant resistance to powdery mildew and stripe rust using a recombinant inbred line population derived from cross Qingxinmai × 041133. FRONTIERS IN PLANT SCIENCE 2024; 15:1397274. [PMID: 38779062 PMCID: PMC11109386 DOI: 10.3389/fpls.2024.1397274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
A recombinant inbred line (RIL) population derived from wheat landrace Qingxinmai and breeding line 041133 exhibited segregation in resistance to powdery mildew and stripe rust in five and three field tests, respectively. A 16K genotyping by target sequencing (GBTS) single-nucleotide polymorphism (SNP) array-based genetic linkage map was used to dissect the quantitative trait loci (QTLs) for disease resistance. Four and seven QTLs were identified for adult-plant resistance (APR) against powdery mildew and stripe rust. QPm.caas-1B and QPm.caas-5A on chromosomes 1B and 5A were responsible for the APR against powdery mildew in line 041133. QYr.caas-1B, QYr.caas-3B, QYr.caas-4B, QYr.caas-6B.1, QYr.caas-6B.2, and QYr.caas-7B detected on the five B-genome chromosomes of line 041133 conferred its APR to stripe rust. QPm.caas-1B and QYr.caas.1B were co-localized with the pleiotropic locus Lr46/Yr29/Sr58/Pm39/Ltn2. A Kompetitive Allele Specific Polymorphic (KASP) marker KASP_1B_668028290 was developed to trace QPm/Yr.caas.1B. Four lines pyramiding six major disease resistance loci, PmQ, Yr041133, QPm/Yr.caas-1B, QPm.caas-2B.1, QYr.caas-3B, and QPm.caas-6B, were developed. They displayed effective resistance against both powdery mildew and stripe rust at the seedling and adult-plant stages.
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Affiliation(s)
- Yahui Li
- College of Life and Environmental Science, Minzu University of China, Beijing, China
| | - Jinghuang Hu
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huailong Lin
- Jiushenghe Seed Industry Co. Ltd., Changji, China
| | - Dan Qiu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yunfeng Qu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Jiuyuan Du
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Lu Hou
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University/Key Laboratory of Agricultural Integrated Pest Management, Xining, China
| | - Lin Ma
- Datong Hui and Tu Autonomous County Agricultural Technology Extension Center, Xining, China
| | - Qiuhong Wu
- Institute of Biotechnology, Xianghu Laboratory, Hangzhou, China
| | - Zhiyong Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yijun Zhou
- College of Life and Environmental Science, Minzu University of China, Beijing, China
| | - Hongjie Li
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Biotechnology, Xianghu Laboratory, Hangzhou, China
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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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Sharma D, Kumari A, Sharma P, Singh A, Sharma A, Mir ZA, Kumar U, Jan S, Parthiban M, Mir RR, Bhati P, Pradhan AK, Yadav A, Mishra DC, Budhlakoti N, Yadav MC, Gaikwad KB, Singh AK, Singh GP, Kumar S. Meta-QTL analysis in wheat: progress, challenges and opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:247. [PMID: 37975911 DOI: 10.1007/s00122-023-04490-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Wheat, an important cereal crop globally, faces major challenges due to increasing global population and changing climates. The production and productivity are challenged by several biotic and abiotic stresses. There is also a pressing demand to enhance grain yield and quality/nutrition to ensure global food and nutritional security. To address these multifaceted concerns, researchers have conducted numerous meta-QTL (MQTL) studies in wheat, resulting in the identification of candidate genes that govern these complex quantitative traits. MQTL analysis has successfully unraveled the complex genetic architecture of polygenic quantitative traits in wheat. Candidate genes associated with stress adaptation have been pinpointed for abiotic and biotic traits, facilitating targeted breeding efforts to enhance stress tolerance. Furthermore, high-confidence candidate genes (CGs) and flanking markers to MQTLs will help in marker-assisted breeding programs aimed at enhancing stress tolerance, yield, quality and nutrition. Functional analysis of these CGs can enhance our understanding of intricate trait-related genetics. The discovery of orthologous MQTLs shared between wheat and other crops sheds light on common evolutionary pathways governing these traits. Breeders can leverage the most promising MQTLs and CGs associated with multiple traits to develop superior next-generation wheat cultivars with improved trait performance. This review provides a comprehensive overview of MQTL analysis in wheat, highlighting progress, challenges, validation methods and future opportunities in wheat genetics and breeding, contributing to global food security and sustainable agriculture.
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Affiliation(s)
- Divya Sharma
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Anita Kumari
- Department of Botany, University of Delhi, Delhi, India
| | - Priya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Anupma Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Anshu Sharma
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Zahoor Ahmad Mir
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Sofora Jan
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - M Parthiban
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - Reyazul Rouf Mir
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - Pradeep Bhati
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Anjan Kumar Pradhan
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Aakash Yadav
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | | | - Neeraj Budhlakoti
- ICAR- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mahesh C Yadav
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Kiran B Gaikwad
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | | | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India.
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Sethi M, Saini DK, Devi V, Kaur C, Singh MP, Singh J, Pruthi G, Kaur A, Singh A, Chaudhary DP. Unravelling the genetic framework associated with grain quality and yield-related traits in maize ( Zea mays L.). Front Genet 2023; 14:1248697. [PMID: 37609038 PMCID: PMC10440565 DOI: 10.3389/fgene.2023.1248697] [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: 06/27/2023] [Accepted: 07/26/2023] [Indexed: 08/24/2023] Open
Abstract
Maize serves as a crucial nutrient reservoir for a significant portion of the global population. However, to effectively address the growing world population's hidden hunger, it is essential to focus on two key aspects: biofortification of maize and improving its yield potential through advanced breeding techniques. Moreover, the coordination of multiple targets within a single breeding program poses a complex challenge. This study compiled mapping studies conducted over the past decade, identifying quantitative trait loci associated with grain quality and yield related traits in maize. Meta-QTL analysis of 2,974 QTLs for 169 component traits (associated with quality and yield related traits) revealed 68 MQTLs across different genetic backgrounds and environments. Most of these MQTLs were further validated using the data from genome-wide association studies (GWAS). Further, ten MQTLs, referred to as breeding-friendly MQTLs (BF-MQTLs), with a significant phenotypic variation explained over 10% and confidence interval less than 2 Mb, were shortlisted. BF-MQTLs were further used to identify potential candidate genes, including 59 genes encoding important proteins/products involved in essential metabolic pathways. Five BF-MQTLs associated with both quality and yield traits were also recommended to be utilized in future breeding programs. Synteny analysis with wheat and rice genomes revealed conserved regions across the genomes, indicating these hotspot regions as validated targets for developing biofortified, high-yielding maize varieties in future breeding programs. After validation, the identified candidate genes can also be utilized to effectively model the plant architecture and enhance desirable quality traits through various approaches such as marker-assisted breeding, genetic engineering, and genome editing.
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Affiliation(s)
- Mehak Sethi
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Veena Devi
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Charanjeet Kaur
- Department of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Mohini Prabha Singh
- Department of Floriculture and Landscaping, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Jasneet Singh
- Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, QC, Canada
| | - Gomsie Pruthi
- Department of Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Amanpreet Kaur
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Alla Singh
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Dharam Paul Chaudhary
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
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