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Cross JF, Cobo N, Drewry DT. Non-invasive diagnosis of wheat stripe rust progression using hyperspectral reflectance. FRONTIERS IN PLANT SCIENCE 2024; 15:1429879. [PMID: 39323538 PMCID: PMC11422131 DOI: 10.3389/fpls.2024.1429879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 08/12/2024] [Indexed: 09/27/2024]
Abstract
Wheat stripe rust (WSR), a fungal disease capable of inflicting severe crop loss, threatens most of global wheat production. Breeding for genetic resistance is the primary defense against stripe rust infection. Further development of rust-resistant wheat varieties depends on the ability to accurately and rapidly quantify rust resilience. In this study we demonstrate the ability of visible through shortwave infrared reflectance spectroscopy to effectively provide high-throughput classification of wheat stripe rust severity and identify important spectral regions for classification accuracy. Random forest models were developed using both leaf-level and canopy-level hyperspectral reflectance observations collected across a breeding population that was scored for WSR severity using 10 and 5 severity classes, respectively. The models were able to accurately diagnose scored disease severity class across these fine scoring scales between 45-52% of the time, which improved to 79-96% accuracy when allowing scores to be off-by-one. The canopy-level model demonstrated higher accuracy and distinct spectral characteristics relative to the leaf-level models, pointing to the use of this technology for field-scale monitoring. Leaf-level model performance was strong despite clear variation in scoring conducted between wheat growth stages. Two approaches to reduce predictor and model complexity, principal component dimensionality reduction and backward feature elimination, were applied here. Both approaches demonstrated that model classification skill could remain high while simplifying high-dimensional hyperspectral reflectance predictors, with parsimonious models having approximately 10 unique components or wavebands. Through the use of a high-resolution infection severity scoring methodology this study provides one of the most rigorous tests of the use of hyperspectral reflectance observations for WSR classification. We demonstrate that machine learning in combination with a few carefully-selected wavebands can be leveraged for precision remote monitoring and management of WSR to limit crop damage and to aid in the selection of resilient germplasm in breeding programs.
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Affiliation(s)
- James F Cross
- Department of Food, Agricultural, and Biological Engineering, Ohio State University, Columbus, OH, United States
- Environmental Sciences Graduate Program, Ohio State University, Columbus, OH, United States
| | - Nicolas Cobo
- Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco, Chile
| | - Darren T Drewry
- Department of Food, Agricultural, and Biological Engineering, Ohio State University, Columbus, OH, United States
- Environmental Sciences Graduate Program, Ohio State University, Columbus, OH, United States
- Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, United States
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, United States
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2
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Bruschi M, Bozzoli M, Ratti C, Sciara G, Goudemand E, Devaux P, Ormanbekova D, Forestan C, Corneti S, Stefanelli S, Castelletti S, Fusari E, Novi JB, Frascaroli E, Salvi S, Perovic D, Gadaleta A, Rubies-Autonell C, Sanguineti MC, Tuberosa R, Maccaferri M. Dissecting the genetic basis of resistance to Soil-borne cereal mosaic virus (SBCMV) in durum wheat by bi-parental mapping and GWAS. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:213. [PMID: 39222129 PMCID: PMC11369050 DOI: 10.1007/s00122-024-04709-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 08/04/2024] [Indexed: 09/04/2024]
Abstract
Soil-borne cereal mosaic virus (SBCMV), the causative agent of wheat mosaic, is a Furovirus challenging wheat production all over Europe. Differently from bread wheat, durum wheat shows greater susceptibility and stronger yield penalties, so identification and genetic characterization of resistance sources are major targets for durum genetics and breeding. The Sbm1 locus providing high level of resistance to SBCMV was mapped in bread wheat to the 5DL chromosome arm (Bass in Genome 49:1140-1148, 2006). This excluded the direct use of Sbm1 for durum wheat improvement. Only one major QTL has been mapped in durum wheat, namely QSbm.ubo-2B, on the 2BS chromosome region coincident with Sbm2, already known in bread wheat as reported (Bayles in HGCA Project Report, 2007). Therefore, QSbm.ubo-2B = Sbm2 is considered a pillar for growing durum in SBCMV-affected areas. Herein, we report the fine mapping of Sbm2 based on bi-parental mapping and GWAS, using the Infinium 90 K SNP array and high-throughput KASP®. Fine mapping pointed out a critical haploblock of 3.2 Mb defined by concatenated SNPs successfully converted to high-throughput KASP® markers coded as KUBO. The combination of KUBO-27, wPt-2106-ASO/HRM, KUBO-29, and KUBO-1 allows unequivocal tracing of the Sbm2-resistant haplotype. The interval harbors 52 high- and 41 low-confidence genes, encoding 17 cytochrome p450, three receptor kinases, two defensins, and three NBS-LRR genes. These results pave the way for Sbm2 positional cloning. Importantly, the development of Sbm2 haplotype tagging KASP® provides a valuable case study for improving efficacy of the European variety testing system and, ultimately, the decision-making process related to varietal characterization and choice.
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Affiliation(s)
- Martina Bruschi
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Matteo Bozzoli
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Claudio Ratti
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Giuseppe Sciara
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Ellen Goudemand
- S.A.S. Florimond-Desprez Veuve and Fils, BP41, 59242, Cappelle-en-Pévèle, France
| | - Pierre Devaux
- S.A.S. Florimond-Desprez Veuve and Fils, BP41, 59242, Cappelle-en-Pévèle, France
| | - Danara Ormanbekova
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Cristian Forestan
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Simona Corneti
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Sandra Stefanelli
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Sara Castelletti
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Elena Fusari
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Jad B Novi
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Elisabetta Frascaroli
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Dragan Perovic
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institut (JKI), Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Agata Gadaleta
- Department of Soil, Plant and Food Science (Di.S.S.P.A.), University of Bari 'Aldo Moro', 70126, Bari, Italy
| | - Concepcion Rubies-Autonell
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Maria Corinna Sanguineti
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna, 40127, Bologna, Italy.
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3
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Sirangelo TM. Molecular Investigations to Improve Fusarium Head Blight Resistance in Wheat: An Update Focusing on Multi-Omics Approaches. PLANTS (BASEL, SWITZERLAND) 2024; 13:2179. [PMID: 39204615 PMCID: PMC11359810 DOI: 10.3390/plants13162179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/24/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
Fusarium head blight (FHB) is mainly caused by Fusarium graminearum (Fg) and is a very widespread disease throughout the world, leading to severe damage to wheat with losses in both grain yield and quality. FHB also leads to mycotoxin contamination in the infected grains, being toxic to humans and animals. In spite of the continuous advancements to elucidate more and more aspects of FHB host resistance, to date, our knowledge about the molecular mechanisms underlying wheat defense response to this pathogen is not comprehensive, most likely due to the complex wheat-Fg interaction. Recently, due to climate changes, such as high temperature and heavy rainfall, FHB has become more frequent and severe worldwide, making it even more urgent to completely understand wheat defense mechanisms. In this review, after a brief description of the first wheat immune response to Fg, we discuss, for each FHB resistance type, from Type I to Type V resistances, the main molecular mechanisms involved, the major quantitative trait loci (QTLs) and candidate genes found. The focus is on multi-omics research helping discover crucial molecular pathways for each resistance type. Finally, according to the emerging examined studies and results, a wheat response model to Fg attack, showing the major interactions in the different FHB resistance types, is proposed. The aim is to establish a useful reference point for the researchers in the field interested to adopt an interdisciplinary omics approach.
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Affiliation(s)
- Tiziana M Sirangelo
- Division Biotechnologies and Agroindustry, ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development, 00123 Rome, Italy
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Peters Haugrud AR, Achilli AL, Martínez-Peña R, Klymiuk V. Future of durum wheat research and breeding: Insights from early career researchers. THE PLANT GENOME 2024:e20453. [PMID: 38760906 DOI: 10.1002/tpg2.20453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 05/20/2024]
Abstract
Durum wheat (Triticum turgidum ssp. durum) is globally cultivated for pasta, couscous, and bulgur production. With the changing climate and growing world population, the need to significantly increase durum production to meet the anticipated demand is paramount. This review summarizes recent advancements in durum research, encompassing the exploitation of existing and novel genetic diversity, exploration of potential new diversity sources, breeding for climate-resilient varieties, enhancements in production and management practices, and the utilization of modern technologies in breeding and cultivar development. In comparison to bread wheat (T. aestivum), the durum wheat community and production area are considerably smaller, often comprising many small-family farmers, notably in African and Asian countries. Public breeding programs such as the International Maize and Wheat Improvement Center (CIMMYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA) play a pivotal role in providing new and adapted cultivars for these small-scale growers. We spotlight the contributions of these and others in this review. Additionally, we offer our recommendations on key areas for the durum research community to explore in addressing the challenges posed by climate change while striving to enhance durum production and sustainability. As part of the Wheat Initiative, the Expert Working Group on Durum Wheat Genomics and Breeding recognizes the significance of collaborative efforts in advancing toward a shared objective. We hope the insights presented in this review stimulate future research and deliberations on the trajectory for durum wheat genomics and breeding.
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Affiliation(s)
- Amanda R Peters Haugrud
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, North Dakota, USA
| | - Ana Laura Achilli
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Raquel Martínez-Peña
- Regional Institute of Agri-Food and Forestry Research and Development of Castilla-La Mancha (IRIAF), Agroenvironmental Research Center El Chaparrillo, Ciudad Real, Spain
| | - Valentyna Klymiuk
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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5
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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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6
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Wang Z, Lai X, Wang C, Yang H, Liu Z, Fan Z, Li J, Zhang H, Liu M, Zhang Y. Exploring the Drought Tolerant Quantitative Trait Loci in Spring Wheat. PLANTS (BASEL, SWITZERLAND) 2024; 13:898. [PMID: 38592925 PMCID: PMC10975456 DOI: 10.3390/plants13060898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/24/2024] [Accepted: 03/01/2024] [Indexed: 04/11/2024]
Abstract
Drought-induced stress poses a significant challenge to wheat throughout its growth, underscoring the importance of identifying drought-stable quantitative trait loci (QTLs) for enhancing grain yield. Here, we evaluated 18 yield-related agronomic and physiological traits, along with their drought tolerance indices, in a recombinant inbred line population derived from the XC7 × XC21 cross. These evaluations were conducted under both non-stress and drought-stress conditions. Drought stress significantly reduced grain weight per spike and grain yield per plot. Genotyping the recombinant inbred line population using the wheat 90K single nucleotide polymorphism array resulted in the identification of 131 QTLs associated with the 18 traits. Drought stress also exerted negative impacts on grain formation and filling, directly leading to reductions in grain weight per spike and grain yield per plot. Among the identified QTLs, 43 were specifically associated with drought tolerance across the 18 traits, with 6 showing direct linkages to drought tolerance in wheat. These results provide valuable insights into the genetic mechanisms governing wheat growth and development, as well as the traits contributing to the drought tolerance index. Moreover, they serve as a theoretical foundation for the development of new wheat cultivars having exceptional drought tolerance and high yield potentials under both drought-prone and drought-free conditions.
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Affiliation(s)
- Zhong Wang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (C.W.); (Z.F.); (J.L.); (H.Z.)
- Key Laboratory of Crop Ecophysiology and Farming System in Desert Oasis Region, Ministry of Agriculture, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Crop Chemical Control Engineering Technology Research Center, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
| | - Xiangjun Lai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China;
| | - Chunsheng Wang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (C.W.); (Z.F.); (J.L.); (H.Z.)
- Key Laboratory of Crop Ecophysiology and Farming System in Desert Oasis Region, Ministry of Agriculture, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Crop Chemical Control Engineering Technology Research Center, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
| | - Hongmei Yang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
- Xinjiang Laboratory of Special Environmental Microbiology, Institute of Applied Microbiology, Urumqi 830091, China
| | - Zihui Liu
- Department of Biochemistry, Baoding University, Baoding 071000, China;
| | - Zheru Fan
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (C.W.); (Z.F.); (J.L.); (H.Z.)
- Key Laboratory of Crop Ecophysiology and Farming System in Desert Oasis Region, Ministry of Agriculture, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Crop Chemical Control Engineering Technology Research Center, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
| | - Jianfeng Li
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (C.W.); (Z.F.); (J.L.); (H.Z.)
- Key Laboratory of Crop Ecophysiology and Farming System in Desert Oasis Region, Ministry of Agriculture, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Crop Chemical Control Engineering Technology Research Center, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
| | - Hongzhi Zhang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (C.W.); (Z.F.); (J.L.); (H.Z.)
- Key Laboratory of Crop Ecophysiology and Farming System in Desert Oasis Region, Ministry of Agriculture, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Crop Chemical Control Engineering Technology Research Center, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
| | - Manshuang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China;
| | - Yueqiang Zhang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (C.W.); (Z.F.); (J.L.); (H.Z.)
- Key Laboratory of Crop Ecophysiology and Farming System in Desert Oasis Region, Ministry of Agriculture, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
- Xinjiang Crop Chemical Control Engineering Technology Research Center, Institute of Nuclear and Biological Technologies, Urumqi 830091, China
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Zhai X, Wu D, Chen C, Yang X, Cheng S, Sha L, Deng S, Cheng Y, Fan X, Kang H, Wang Y, Liu D, Zhou Y, Zhang H. A chromosome level genome assembly of Pseudoroegneria Libanotica reveals a key Kcs gene involves in the cuticular wax elongation for drought resistance. BMC Genomics 2024; 25:253. [PMID: 38448864 PMCID: PMC10916072 DOI: 10.1186/s12864-024-10140-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The genus Pseudoroegneria (Nevski) Löve (Triticeae, Poaceae), whose genome symbol was designed as "St", accounts for more than 60% of perennial Triticeae species. The diploid species Psudoroegneria libanotica (2n = 14) contains the most ancient St genome, exhibited strong drought resistance, and was morphologically covered by cuticular wax on the aerial part. Therefore, the St-genome sequencing data could provide fundamental information for studies of genome evolution and reveal its mechanisms of cuticular wax and drought resistance. RESULTS In this study, we reported the chromosome-level genome assembly for the St genome of Pse. libanotica, with a total size of 2.99 Gb. 46,369 protein-coding genes annotated and 71.62% was repeat sequences. Comparative analyses revealed that the genus Pseudoroegneria diverged during the middle and late Miocene. During this period, unique genes, gene family expansion, and contraction in Pse. libanotica were enriched in biotic and abiotic stresses, such as fatty acid biosynthesis which may greatly contribute to its drought adaption. Furthermore, we investigated genes associated with the cuticular wax formation and water deficit and found a new Kcs gene evm.TU.CTG175.54. It plays a critical role in the very long chain fatty acid (VLCFA) elongation from C18 to C26 in Pse. libanotica. The function needs more evidence to be verified. CONCLUSIONS We sequenced and assembled the St genome in Triticeae and discovered a new KCS gene that plays a role in wax extension to cope with drought. Our study lays a foundation for the genome diversification of Triticeae species and deciphers cuticular wax formation genes involved in drought resistance.
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Affiliation(s)
- Xingguang Zhai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Chen Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xunzhe Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shaobo Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Lina Sha
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shuhan Deng
- Glbizzia Biosciences Co., Ltd, Liandong U Valley, Huatuo Road 50, Daxing, Beijing, 102600, China
| | - Yiran Cheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Haiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
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Zhang H, Li Y, Liu W, Sun Y, Tang J, Che J, Yang S, Wang X, Zhang R. Genetic Analysis of Adaptive Traits in Spring Wheat in Northeast China. Life (Basel) 2024; 14:168. [PMID: 38398677 PMCID: PMC10890535 DOI: 10.3390/life14020168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 02/25/2024] Open
Abstract
The dissection of the genetic architecture and the detection of the loci for adaptive traits are important for marker-assisted selection (MAS) for breeding. A spring wheat diversity panel with 251 cultivars, mainly from China, was obtained to conduct a genome-wide association study (GWAS) to detect the new loci, including the heading date (HD), maturating date (MD), plant height (PH), and lodging resistance (LR). In total, 41 loci existing in all 21 chromosomes, except for 4A and 6B, were identified, and each explained 4.3-18.9% of the phenotypic variations existing in two or more environments. Of these, 13 loci are overlapped with the known genes or quantitative trait loci (QTLs), whereas the other 28 are likely to be novel. The 1A locus (296.9-297.7 Mb) is a multi-effect locus for LR and PH, whereas the locus on chromosome 6D (464.5-471.0 Mb) affects both the HD and MD. Furthermore, four candidate genes for adaptive traits were identified, involved in cell division, signal transduction, and plant development. Additionally, two competitive, allele-specific PCR (KASP) markers, Kasp_2D_PH for PH and Kasp_6D_HD for HD, were developed and validated in another 162 spring wheat accessions. Our study uncovered the genetic basis of adaptive traits and provided the associated SNPs and varieties with more favorable alleles for wheat MAS breeding.
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Affiliation(s)
- Hongji Zhang
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (W.L.); (Y.S.); (J.T.); (S.Y.); (X.W.)
| | - Yuyao Li
- Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
| | - Wenlin Liu
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (W.L.); (Y.S.); (J.T.); (S.Y.); (X.W.)
| | - Yan Sun
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (W.L.); (Y.S.); (J.T.); (S.Y.); (X.W.)
| | - Jingquan Tang
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (W.L.); (Y.S.); (J.T.); (S.Y.); (X.W.)
| | - Jingyu Che
- Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar 161600, China;
| | - Shuping Yang
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (W.L.); (Y.S.); (J.T.); (S.Y.); (X.W.)
| | - Xiangyu Wang
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (W.L.); (Y.S.); (J.T.); (S.Y.); (X.W.)
| | - Rui Zhang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
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9
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Marone D, Laidò G, Saccomanno A, Petruzzino G, Giaretta Azevedo CV, De Vita P, Mastrangelo AM, Gadaleta A, Ammar K, Bassi FM, Wang M, Chen X, Rubiales D, Matny O, Steffenson BJ, Pecchioni N. Genome-wide association study of common resistance to rust species in tetraploid wheat. FRONTIERS IN PLANT SCIENCE 2024; 14:1290643. [PMID: 38235202 PMCID: PMC10792004 DOI: 10.3389/fpls.2023.1290643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Rusts of the genus Puccinia are wheat pathogens. Stem (black; Sr), leaf (brown; Lr), and stripe (yellow; Yr) rust, caused by Puccinia graminis f. sp. tritici (Pgt), Puccinia triticina (Pt), and Puccinia striiformis f. sp. tritici (Pst), can occur singularly or in mixed infections and pose a threat to wheat production globally in terms of the wide dispersal of their urediniospores. The development of durable resistant cultivars is the most sustainable method for controlling them. Many resistance genes have been identified, characterized, genetically mapped, and cloned; several quantitative trait loci (QTLs) for resistance have also been described. However, few studies have considered resistance to all three rust pathogens in a given germplasm. A genome-wide association study (GWAS) was carried out to identify loci associated with resistance to the three rusts in a collection of 230 inbred lines of tetraploid wheat (128 of which were Triticum turgidum ssp. durum) genotyped with SNPs. The wheat panel was phenotyped in the field and subjected to growth chamber experiments across different countries (USA, Mexico, Morocco, Italy, and Spain); then, a mixed linear model (MLM) GWAS was performed. In total, 9, 34, and 5 QTLs were identified in the A and B genomes for resistance to Pgt, Pt, and Pst, respectively, at both the seedling and adult plant stages. Only one QTL on chromosome 4A was found to be effective against all three rusts at the seedling stage. Six QTLs conferring resistance to two rust species at the adult plant stage were mapped: three on chromosome 1B and one each on 5B, 7A, and 7B. Fifteen QTLs conferring seedling resistance to two rusts were mapped: five on chromosome 2B, three on 7B, two each on 5B and 6A, and one each on 1B, 2A, and 7A. Most of the QTLs identified were specific for a single rust species or race of a species. Candidate genes were identified within the confidence intervals of a QTL conferring resistance against at least two rust species by using the annotations of the durum (cv. 'Svevo') and wild emmer wheat ('Zavitan') reference genomes. The 22 identified loci conferring resistance to two or three rust species may be useful for breeding new and potentially durable resistant wheat cultivars.
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Affiliation(s)
- Daniela Marone
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Giovanni Laidò
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Antonietta Saccomanno
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Reggio Emilia, Italy
| | - Giuseppe Petruzzino
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Cleber V. Giaretta Azevedo
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Pasquale De Vita
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Anna Maria Mastrangelo
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Agata Gadaleta
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti (Di.S.S.P.A.), Università di Bari “Aldo Moro”, Bari, Italy
| | - Karim Ammar
- International Maize and Wheat Improvement Centre (CIMMYT), Ciudad de México, Mexico
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- Wheat Health, Genetics, and Quality Research Unit, United States Department of Agriculture - Agriculture Research Service (USDA-ARS), Pullman, WA, United States
| | - Diego Rubiales
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Nicola Pecchioni
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Reggio Emilia, Italy
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10
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Jabbour Y, Hakim MS, Al-Yossef A, Saleh MM, Shaaban ASAD, Kabbaj H, Zaïm M, Kleinerman C, Bassi FM. Genomic regions involved in the control of 1,000-kernel weight in wild relative-derived populations of durum wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1297131. [PMID: 38098797 PMCID: PMC10720367 DOI: 10.3389/fpls.2023.1297131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023]
Abstract
Terminal drought is one of the most common and devastating climatic stress factors affecting durum wheat (Triticum durum Desf.) production worldwide. The wild relatives of this crop are deemed a vast potential source of useful alleles to adapt to this stress. A nested association mapping (NAM) panel was generated using as a recurrent parent the Moroccan variety 'Nachit' derived from Triticum dicoccoides and known for its large grain size. This was recombined to three top-performing lines derived from T. dicoccoides, T. araraticum, and Aegilops speltoides, for a total of 426 inbred progenies. This NAM was evaluated across eight environments (Syria, Lebanon, and Morocco) experiencing different degrees of terminal moisture stress over two crop seasons. Our results showed that drought stress caused on average 41% loss in yield and that 1,000-kernel weight (TKW) was the most important trait for adaptation to it. Genotyping with the 25K TraitGenetics array resulted in a consensus map of 1,678 polymorphic SNPs, spanning 1,723 cM aligned to the reference 'Svevo' genome assembly. Kinship distinguished the progenies in three clades matching the parent of origin. A total of 18 stable quantitative trait loci (QTLs) were identified as controlling various traits but independent from flowering time. The most significant genomic regions were named Q.ICD.NAM-04, Q.ICD.NAM-14, and Q.ICD.NAM-16. Allelic investigation in a second germplasm panel confirmed that carrying the positive allele at all three loci produced an average TKW advantage of 25.6% when field-tested under drought conditions. The underlying SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers and successfully validated in a third germplasm set, where they explained up to 19% of phenotypic variation for TKW under moisture stress. These findings confirm the identification of critical loci for drought adaptation derived from wild relatives that can now be readily exploited via molecular breeding.
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Affiliation(s)
- Yaman Jabbour
- Field Crop Department, Faculty of Agriculture Engineering, Aleppo University, Aleppo, Syria
- General Commission for Scientific Agriculture Research (GCSAR), Field Crop Department, Aleppo, Syria
| | - Mohammad Shafik Hakim
- Field Crop Department, Faculty of Agriculture Engineering, Aleppo University, Aleppo, Syria
| | - Abdallah Al-Yossef
- General Commission for Scientific Agriculture Research (GCSAR), Field Crop Department, Aleppo, Syria
| | - Maysoun M. Saleh
- General Commission for Scientific Agriculture Research (GCSAR), Genetic Resources Department, Damascus, Syria
| | - Ahmad Shams Al-Dien Shaaban
- Biotechnology Engineering Department, Faculty of Technological Engineering, Aleppo University, Aleppo, Syria
| | - Hafssa Kabbaj
- International Center for Agricultural Research in the Dry Areas, Biodiversity and Crop Improvement, Rabat, Morocco
| | - Meryem Zaïm
- International Center for Agricultural Research in the Dry Areas, Biodiversity and Crop Improvement, Rabat, Morocco
| | - Charles Kleinerman
- International Center for Agricultural Research in the Dry Areas, Biodiversity and Crop Improvement, Rabat, Morocco
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas, Biodiversity and Crop Improvement, Rabat, Morocco
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11
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Xu YF, Ma FF, Zhang JP, Liu H, Li LH, An DG. Unraveling the genetic basis of grain number-related traits in a wheat-Agropyron cristatum introgressed line through high-resolution linkage mapping. BMC PLANT BIOLOGY 2023; 23:563. [PMID: 37964231 PMCID: PMC10647127 DOI: 10.1186/s12870-023-04547-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/19/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND Grain number per spike (GNS) is a pivotal determinant of grain yield in wheat. Pubing 3228 (PB3228), a wheat-Agropyron cristatum germplasm, exhibits a notably higher GNS. RESULTS In this study, we developed a recombinant inbred line (RIL) population derived from PB3228/Gao8901 (PG-RIL) and constructed a high-density genetic map comprising 101,136 loci, spanning 4357.3 cM using the Wheat 660 K SNP array. The genetic map demonstrated high collinearity with the wheat assembly IWGSC RefSeq v1.0. Traits related to grain number and spikelet number per spike were evaluated in seven environments for quantitative trait locus (QTL) analysis. Five environmentally stable QTLs were detected in at least three environments. Among these, two major QTLs, QGns-4A.2 and QGns-1A.1, associated with GNS, exhibited positive alleles contributed by PB3228. Further, the conditional QTL analysis revealed a predominant contribution of PB3228 to the GNS QTLs, with both grain number per spikelet (GNSL) and spikelet number per spike (SNS) contributing to the overall GNS trait. Four kompetitive allele-specific PCR (KASP) markers that linked to QGns-4A.2 and QGns-1A.1 were developed and found to be effective in verifying the QTL effect within a diversity panel. Compared to previous studies, QGns-4A.2 exhibited stability across different trials, while QGns-1A.1 represents a novel QTL. The results from unconditional and conditional QTL analyses are valuable for dissecting the genetic contribution of the component traits to GNS at the individual QTL level and for understanding the genetic basis of the superior grain number character in PB3228. The KASP markers can be utilized in marker-assisted selection for enhancing GNS. CONCLUSIONS Five environmentally stable QTLs related to grain number and spikelet number per spike were identified. PB3228 contributed to the majority of the QTLs associated with GNS.
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Affiliation(s)
- Yun-Feng Xu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Fei-Fei Ma
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Jin-Peng Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hong Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Li-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Diao-Guo An
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China.
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12
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Rabieyan E, Darvishzadeh R, Mohammadi R, Gul A, Rasheed A, Akhar FK, Abdi H, Alipour H. Genetic diversity, linkage disequilibrium, and population structure of tetraploid wheat landraces originating from Europe and Asia. BMC Genomics 2023; 24:682. [PMID: 37964224 PMCID: PMC10644499 DOI: 10.1186/s12864-023-09768-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 10/26/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND Durum wheat is one of the most important crops, especially in the Mediterranean region. Insight into the genetic diversity of germplasm can improve the breeding program management in various traits. This study was done using single nucleotide polymorphisms (SNP) markers to characterize the genetic distinctiveness and differentiation of tetraploid wheat landraces collected from nine European and Asian countries. A sum of 23,334 polymorphic SNPs was detected in 126 tetraploid wheat landraces in relation to the reference genome. RESULTS The number of identified SNPs was 11,613 and 11,721 in A and B genomes, respectively. The highest and lowest diversity was on 6B and 6 A chromosomes, respectively. Structure analysis classified the landraces into two distinct subpopulations (K = 2). Evaluating the principal coordinate analysis (PCoA) and weighted pair-group method using arithmetic averages (WPGMA) clustering results demonstrated that landraces (99.2%) are categorized into one of the two chief subpopulations. Therefore, the grouping pattern did not clearly show the presence of a clear pattern of relationships between genetic diversity and their geographical derivation. Part of this result could be due to the historical exchange between different germplasms. Although the result did not separate landraces based on their region of origin, the landraces collected from Iran were classified into the same group and cluster. Analysis of molecular variance (AMOVA) also confirmed the results of population structure. Finally, Durum wheat landraces in some countries, including Turkey, Russia, Ukraine, and Afghanistan, were highly diverse, while others, including Iran and China, were low-diversity. CONCLUSION The recent study concluded that the 126 tetraploid wheat genotypes and their GBS-SNP markers are very appropriate for quantitative trait loci (QTLs) mapping and genome-wide association studies (GWAS). The core collection comprises two distinct subpopulations. Subpopulation II genotypes are the most diverse genotypes, and if they possess desired traits, they may be used in future breeding programs. The degree of diversity in the landraces of countries can provide the ground for the improvement of new cultivars with international cooperation. linkage disequilibrium (LD) hotspot distribution across the genome was investigated, which provides useful information about the genomic regions that contain intriguing genes.
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Affiliation(s)
- Ehsan Rabieyan
- Department of Agronomy and Plant Breeding, University of Tehran, Karaj, Iran
| | - Reza Darvishzadeh
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Reza Mohammadi
- Dryland Agricultural Research Institute (DARI), AREEO, Sararood branch, Iran
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Awais Rasheed
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing, 100081, China
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Fatemeh Keykha Akhar
- Department of Plant Biotechnology, College of Agriculture, Jahrom University, Jahrom, Iran
| | - Hossein Abdi
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Hadi Alipour
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran.
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Valladares García AP, Desiderio F, Simeone R, Ravaglia S, Ciorba R, Fricano A, Guerra D, Blanco A, Cattivelli L, Mazzucotelli E. QTL mapping for kernel-related traits in a durum wheat x T. dicoccum segregating population. FRONTIERS IN PLANT SCIENCE 2023; 14:1253385. [PMID: 37849841 PMCID: PMC10577384 DOI: 10.3389/fpls.2023.1253385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/28/2023] [Indexed: 10/19/2023]
Abstract
Durum wheat breeding relies on grain yield improvement to meet its upcoming demand while coping with climate change. Kernel size and shape are the determinants of thousand kernel weight (TKW), which is a key component of grain yield, and the understanding of the genetic control behind these traits supports the progress in yield potential. The present study aimed to dissect the genetic network responsible for kernel size components (length, width, perimeter, and area) and kernel shape traits (width-to-length ratio and formcoefficient) as well as their relationships with kernel weight, plant height, and heading date in durum wheat. Quantitative Trait Locus (QTL) mapping was performed on a segregating population of 110 recombinant inbred lines, derived from a cross between the domesticated emmer wheat accession MG5323 and the durum wheat cv. Latino, evaluated in four different environments. A total of 24 QTLs stable across environments were found and further grouped in nine clusters on chromosomes 2A, 2B, 3A, 3B, 4B, 6B, and 7A. Among them, a QTL cluster on chromosome 4B was associated with kernel size traits and TKW, where the parental MG5323 contributed the favorable alleles, highlighting its potential to improve durum wheat germplasm. The physical positions of the clusters, defined by the projection on the T. durum reference genome, overlapped with already known genes (i.e., BIG GRAIN PROTEIN 1 on chromosome 4B). These results might provide genome-based guidance for the efficient exploitation of emmer wheat diversity in wheat breeding, possibly through yield-related molecular markers.
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Affiliation(s)
- Ana Paola Valladares García
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, Valencia, Spain
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Rosanna Simeone
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Bari, Italy
| | | | - Roberto Ciorba
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Rome, Italy
| | - Agostino Fricano
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Davide Guerra
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Bari, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
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14
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Orlovskaya ОA, Leonova IN, Solovey LA, Dubovets NI. Molecular cytological analysis of alien introgressions in common wheat lines created by crossing of Triticum aestivum with T. dicoccoides and T. dicoccum. Vavilovskii Zhurnal Genet Selektsii 2023; 27:553-564. [PMID: 38023811 PMCID: PMC10643109 DOI: 10.18699/vjgb-23-67] [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: 04/03/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 12/01/2023] Open
Abstract
Wild and domesticated emmer (ВВАА, 2n = 28) are of significant interest for expanding the genetic diversity of common wheat as sources of a high protein and microelement grain content, resistance to many biotic and abiotic factors. Particular interest in these species is also determined by their close relationship with Triticum aestivum L., which facilitates interspecific hybridization. The objective of this work was to analyze the nature of alien introgressions in hybrid lines from crossing common wheat varieties with T. dicoccoides and T. dicoccum, and to assess the effect of their genome fragments on the cytological stability of introgression lines. A C-banding technique and genotyping with SNP and SSR markers were used to determine localization and length of introgression fragments. Assessment of cytological stability was carried out on the basis of chromosome behavior in microsporogenesis. A molecular cytogenetic analysis of introgression wheat lines indicated that the inclusion of the genetic material of wild and domesticated emmer was carried out mainly in the form of whole arms or large fragments in the chromosomes of the B genome and less extended inserts in the A genome. At the same time, the highest frequency of introgressions of the emmer genome was observed in chromosomes 1A, 1B, 2B, and 3B. The analysis of the final stage of meiosis showed a high level of cytological stability in the vast majority of introgression wheat lines (meiotic index was 83.0-99.0 %), which ensures the formation of functional gametes in an amount sufficient for successful reproduction. These lines are of interest for the selection of promising material with agronomically valuable traits and their subsequent inclusion in the breeding process.
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Affiliation(s)
- О A Orlovskaya
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - I N Leonova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Department of Genetics and Selection, Novosibirsk State Agricultural University, Novosibirsk, Russia
| | - L A Solovey
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - N I Dubovets
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, Belarus
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15
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Szabo-Hever A, Singh G, Haugrud ARP, Running KLD, Seneviratne S, Zhang Z, Shi G, Bassi FM, Maccaferri M, Cattivelli L, Tuberosa R, Friesen TL, Liu Z, Xu SS, Faris JD. Association Mapping of Resistance to Tan Spot in the Global Durum Panel. PHYTOPATHOLOGY 2023; 113:1967-1978. [PMID: 37199466 DOI: 10.1094/phyto-02-23-0043-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Tan spot, caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr), is an important disease of durum and common wheat worldwide. Compared with common wheat, less is known about the genetics and molecular basis of tan spot resistance in durum wheat. We evaluated 510 durum lines from the Global Durum Wheat Panel (GDP) for sensitivity to the necrotrophic effectors (NEs) Ptr ToxA and Ptr ToxB and for reaction to Ptr isolates representing races 1 to 5. Overall, susceptible durum lines were most prevalent in South Asia, the Middle East, and North Africa. Genome-wide association analysis showed that the resistance locus Tsr7 was significantly associated with tan spot caused by races 2 and 3, but not races 1, 4, or 5. The NE sensitivity genes Tsc1 and Tsc2 were associated with susceptibility to Ptr ToxC- and Ptr ToxB-producing isolates, respectively, but Tsn1 was not associated with tan spot caused by Ptr ToxA-producing isolates, which further validates that the Tsn1-Ptr ToxA interaction does not play a significant role in tan spot development in durum. A unique locus on chromosome arm 2AS was associated with tan spot caused by race 4, a race once considered avirulent. A novel trait characterized by expanding chlorosis leading to increased disease severity caused by the Ptr ToxB-producing race 5 isolate DW5 was identified, and this trait was governed by a locus on chromosome 5B. We recommend that durum breeders select resistance alleles at the Tsr7, Tsc1, Tsc2, and the chromosome 2AS loci to obtain broad resistance to tan spot.
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Affiliation(s)
- Agnes Szabo-Hever
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
| | - Gurminder Singh
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102
| | - Amanda R Peters Haugrud
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
| | | | - Sudeshi Seneviratne
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102
| | - Zengcui Zhang
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
| | - Filippo M Bassi
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Institutes, Rabat 10101, Morocco
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40127, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Center for Genomics and Bioinformatics, Fiorenzuola d'Arda 29017, Italy
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna 40127, Italy
| | - Timothy L Friesen
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
| | - Steven S Xu
- U.S. Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA 94710
| | - Justin D Faris
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102
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16
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Taranto F, Esposito S, De Vita P. Genomics for Yield and Yield Components in Durum Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:2571. [PMID: 37447132 DOI: 10.3390/plants12132571] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
In recent years, many efforts have been conducted to dissect the genetic basis of yield and yield components in durum wheat thanks to linkage mapping and genome-wide association studies. In this review, starting from the analysis of the genetic bases that regulate the expression of yield for developing new durum wheat varieties, we have highlighted how, currently, the reductionist approach, i.e., dissecting the yield into its individual components, does not seem capable of ensuring significant yield increases due to diminishing resources, land loss, and ongoing climate change. However, despite the identification of genes and/or chromosomal regions, controlling the grain yield in durum wheat is still a challenge, mainly due to the polyploidy level of this species. In the review, we underline that the next-generation sequencing (NGS) technologies coupled with improved wheat genome assembly and high-throughput genotyping platforms, as well as genome editing technology, will revolutionize plant breeding by providing a great opportunity to capture genetic variation that can be used in breeding programs. To date, genomic selection provides a valuable tool for modeling optimal allelic combinations across the whole genome that maximize the phenotypic potential of an individual under a given environment.
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Affiliation(s)
- Francesca Taranto
- Institute of Biosciences and Bioresources (CNR-IBBR), 70126 Bari, Italy
| | - Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA-Council for Agricultural Research and Economics, 71122 Foggia, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA-Council for Agricultural Research and Economics, 71122 Foggia, Italy
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Ouaja M, Bahri BA, Ferjaoui S, Medini M, Sripada UM, Hamza S. Unlocking the story of resistance to Zymoseptoria tritici in Tunisian old durum wheat germplasm based on population structure analysis. BMC Genomics 2023; 24:328. [PMID: 37322410 PMCID: PMC10268414 DOI: 10.1186/s12864-023-09395-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/20/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Septoria tritici blotch (STB) remains a significant obstacle to durum wheat cultivation on a global scale. This disease remains a challenge for farmers, researchers, and breeders, who are collectively dedicated to reduce its damage and improve wheat resistance. Tunisian durum wheat landraces have been recognized as valuable genetic ressources that exhibit resistance to biotic and abiotic stresses and therefore play a crucial role in breeding program aimed at creating new wheat varieties resistant to fungal diseases as STB, as well as adapted to climate change constraints. RESULTS A total of 366 local durum wheat accessions were assessed for resistance to two virulent Tunisian isolates of Zymoseptoria tritici Tun06 and TM220 under field conditions. Population structure analysis of the durum wheat accessions, performed with 286 polymorphic SNPs (PIC > 0.3) covering the entire genome, identified three genetic subpopulations (GS1, GS2 and GS3) with 22% of admixed genotypes. Interestingly, all of the resistant genotypes were among GS2 or admixed with GS2. CONCLUSIONS This study revealed the population structure and the genetic distribution of the resistance to Z. tritici in the Tunisian durum wheat landraces. Accessions grouping pattern reflected the geographical origins of the landraces. We suggested that GS2 accessions were mostly derived from eastern Mediterranean populations, unlike GS1 and GS3 that originated from the west. Resistant GS2 accessions belonged to landraces Taganrog, Sbei glabre, Richi, Mekki, Badri, Jneh Khotifa and Azizi. Furthermore, we suggested that admixture contributed to transmit STB resistance from GS2 resistant landraces to initially susceptible landraces such as Mahmoudi (GS1), but also resulted in the loss of resistance in the case of GS2 susceptible Azizi and Jneh Khotifa accessions.
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Affiliation(s)
- Maroua Ouaja
- Department of agronomy and plant biotechnology, Laboratory of genetics and cereal breeding (LR14AGR01), The National Agronomic Institute of Tunisia (INAT), University of Carthage, 43 Avenue Charles-Nicolle, Tunis, 1082, Tunisia
| | - Bochra A Bahri
- Department of agronomy and plant biotechnology, Laboratory of genetics and cereal breeding (LR14AGR01), The National Agronomic Institute of Tunisia (INAT), University of Carthage, 43 Avenue Charles-Nicolle, Tunis, 1082, Tunisia
- Department of Plant Pathology, Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin, GA, 30223, USA
| | - Sahbi Ferjaoui
- Field Crops Laboratory, Regional Field Crops Research Center of Beja (CRRGC), P.O. Box 350, Beja, 9000, Tunisia
| | - Maher Medini
- Banque Nationale des Gènes (BNG), Boulevard du Leader Yasser Arafat Z. I Charguia 1, Tunis, 1080, Tunisie
| | - Udupa M Sripada
- International Center for Agricultural Research in the Dry Areas (ICARDA), Avenue Hafiane Cherkaoui, Rabat, Marocco
| | - Sonia Hamza
- Department of agronomy and plant biotechnology, Laboratory of genetics and cereal breeding (LR14AGR01), The National Agronomic Institute of Tunisia (INAT), University of Carthage, 43 Avenue Charles-Nicolle, Tunis, 1082, Tunisia.
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Li G, Yuan Y, Zhou J, Cheng R, Chen R, Luo X, Shi J, Wang H, Xu B, Duan Y, Zhong J, Wang X, Kong Z, Jia H, Ma Z. FHB resistance conferred by Fhb1 is under inhibitory regulation of two genetic loci in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:134. [PMID: 37217699 DOI: 10.1007/s00122-023-04380-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE Two loci inhibiting Fhb1 resistance to Fusarium head blight were identified through genome-wide association mapping and validated in biparental populations. Fhb1 confers Fusarium head blight (FHB) resistance by limiting fungal spread within spikes in wheat (type II resistance). However, not all lines with Fhb1 display the expected resistance. To identify genetic factors regulating Fhb1 effect, a genome-wide association study for type II resistance was first performed with 72 Fhb1-carrying lines using the Illumina 90 K iSelect SNP chip. Of 84 significant marker-trait associations detected, more than half were repeatedly detected in at least two environments, with the SNPs distributed in one region on chromosome 5B and one on chromosome 6A. This result was validated in a collection of 111 lines with Fhb1 and 301 lines without Fhb1. We found that these two loci caused significant resistance variations solely among lines with Fhb1 by compromising the resistance. In1, the inhibitory gene on chromosome 5B, was in close linkage with Xwgrb3860 in a recombinant inbred line population derived from Nanda2419 × Wangshuibai and a double haploid (DH) population derived from R-43 (Fhb1 near isogenic line) × Biansui7 (with Fhb1 and In1); and In2, the inhibitory gene on chromosome 6A, was mapped to the Xwgrb4113-Xwgrb4034 interval using a DH population derived from R-43 × PH8901 (with Fhb1 and In2). In1 and In2 are present in all wheat-growing areas worldwide. Their frequencies in China's modern cultivars are high but have significantly decreased in comparison with landraces. These findings are of great significance for FHB resistance breeding using Fhb1.
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Affiliation(s)
- Guoqiang Li
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China.
| | - Yang Yuan
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Jiyang Zhou
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- College of Life Science and Technology, Xinjiang University, Urumqi, 830046, Xinjiang, China
| | - Rui Cheng
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Ruitong Chen
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Xianmin Luo
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Jinxing Shi
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Heyu Wang
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Boyang Xu
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Youyu Duan
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Jinkun Zhong
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Xin Wang
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Zhongxin Kong
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Haiyan Jia
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China.
| | - Zhengqiang Ma
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China.
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Sgaramella N, Nigro D, Pasqualone A, Signorile MA, Laddomada B, Sonnante G, Blanco E, Simeone R, Blanco A. Genetic Mapping of Flavonoid Grain Pigments in Durum Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:1674. [PMID: 37111897 PMCID: PMC10142998 DOI: 10.3390/plants12081674] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
Pigmented cereal grains with high levels of flavonoid compounds have attracted the attention of nutritional science backing the development of functional foods with claimed health benefits. In this study, we report results on the genetic factors controlling grain pigmentation in durum wheat using a segregant population of recombinant inbred lines (RILs) derived from a cross between an Ethiopian purple grain accession and an Italian amber grain cultivar. The RIL population was genotyped by the wheat 25K SNP array and phenotyped for total anthocyanin content (TAC), grain color, and the L*, a*, and b* color index of wholemeal flour, based on four field trials. The mapping population showed a wide variation for the five traits in the different environments, a significant genotype x environment interaction, and high heritability. A total of 5942 SNP markers were used for constructing the genetic linkage map, with an SNP density ranging from 1.4 to 2.9 markers/cM. Two quantitative trait loci (QTL) were identified for TAC mapping on chromosome arms 2AL and 7BS in the same genomic regions of two detected QTL for purple grain. The interaction between the two QTL was indicative of an inheritance pattern of two loci having complementary effects. Moreover, two QTL for red grain color were detected on chromosome arms 3AL and 3BL. The projection of the four QTL genomic regions on the durum wheat Svevo reference genome disclosed the occurrence of the candidate genes Pp-A3, Pp-B1, R-A1, and R-B1 involved in flavonoid biosynthetic pathways and encoding of transcription factors bHLH (Myc-1) and MYB (Mpc1, Myb10), previously reported in common wheat. The present study provides a set of molecular markers associated with grain pigments useful for the selection of essential alleles for flavonoid synthesis in durum wheat breeding programs and enhancement of the health-promoting quality of derived foods.
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Affiliation(s)
- Natalia Sgaramella
- Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (N.S.); (D.N.); (A.P.); (M.A.S.)
| | - Domenica Nigro
- Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (N.S.); (D.N.); (A.P.); (M.A.S.)
| | - Antonella Pasqualone
- Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (N.S.); (D.N.); (A.P.); (M.A.S.)
| | - Massimo Antonio Signorile
- Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (N.S.); (D.N.); (A.P.); (M.A.S.)
| | - Barbara Laddomada
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Prov.le Monteroni, 73100 Lecce, Italy;
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources, National Research Council (CNR), Via Amendola 165/A, 70126 Bari, Italy; (G.S.); (E.B.)
| | - Emanuela Blanco
- Institute of Biosciences and Bioresources, National Research Council (CNR), Via Amendola 165/A, 70126 Bari, Italy; (G.S.); (E.B.)
| | - Rosanna Simeone
- Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (N.S.); (D.N.); (A.P.); (M.A.S.)
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (N.S.); (D.N.); (A.P.); (M.A.S.)
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20
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Kumar A, Saini DK, Saripalli G, Sharma PK, Balyan HS, Gupta PK. Meta-QTLs, ortho-meta QTLs and related candidate genes for yield and its component traits under water stress in wheat ( Triticum aestivum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:525-542. [PMID: 37187772 PMCID: PMC10172426 DOI: 10.1007/s12298-023-01301-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 05/17/2023]
Abstract
Meta-QTLs (MQTLs), ortho-MQTLs, and related candidate genes (CGs) for yield and its seven component traits evaluated under water deficit conditions were identified in wheat. For this purpose, a high density consensus map and 318 known QTLs were used for identification of 56 MQTLs. Confidence intervals (CIs) of the MQTLs were narrower (0.7-21 cM; mean = 5.95 cM) than the CIs of the known QTLs (0.4-66.6 cM; mean = 12.72 cM). Forty-seven MQTLs were co-located with marker trait associations reported in previous genome-wide association studies. Nine selected MQTLs were declared as 'breeders MQTLs' for use in marker-assisted breeding (MAB). Utilizing known MQTLs and synteny/collinearity among wheat, rice and maize, 12 ortho-MQTLs were also identified. A total of 1497 CGs underlying MQTLs were also identified, which were subjected to in-silico expression analysis, leading to identification of 64 differentially expressed CGs (DECGs) under normal and water deficit conditions. These DECGs encoded a variety of proteins, including the following: zinc finger, cytochrome P450, AP2/ERF domain-containing proteins, plant peroxidase, glycosyl transferase, glycoside hydrolase. The expression of 12 CGs at seedling stage (3 h stress) was validated using qRT-PCR in two wheat genotypes, namely Excalibur (drought tolerant) and PBW343 (drought sensitive). Nine of the 12 CGs were up-regulated and three down-regulated in Excalibur. The results of the present study should prove useful for MAB, for fine mapping of promising MQTLs and for cloning of genes across the three cereals studied. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01301-z.
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Affiliation(s)
- Anuj Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | | | - Gautam Saripalli
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA
| | - P. K. Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - H. S. Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - P. K. Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
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21
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Klymiuk V, Haile T, Ens J, Wiebe K, N’Diaye A, Fatiukha A, Krugman T, Ben-David R, Hübner S, Cloutier S, Pozniak CJ. Genetic architecture of rust resistance in a wheat ( Triticum turgidum) diversity panel. FRONTIERS IN PLANT SCIENCE 2023; 14:1145371. [PMID: 36998679 PMCID: PMC10043469 DOI: 10.3389/fpls.2023.1145371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/24/2023] [Indexed: 06/19/2023]
Abstract
Introduction Wheat rust diseases are widespread and affect all wheat growing areas around the globe. Breeding strategies focus on incorporating genetic disease resistance. However, pathogens can quickly evolve and overcome the resistance genes deployed in commercial cultivars, creating a constant need for identifying new sources of resistance. Methods We have assembled a diverse tetraploid wheat panel comprised of 447 accessions of three Triticum turgidum subspecies and performed a genome-wide association study (GWAS) for resistance to wheat stem, stripe, and leaf rusts. The panel was genotyped with the 90K Wheat iSelect single nucleotide polymorphism (SNP) array and subsequent filtering resulted in a set of 6,410 non-redundant SNP markers with known physical positions. Results Population structure and phylogenetic analyses revealed that the diversity panel could be divided into three subpopulations based on phylogenetic/geographic relatedness. Marker-trait associations (MTAs) were detected for two stem rust, two stripe rust and one leaf rust resistance loci. Of them, three MTAs coincide with the known rust resistance genes Sr13, Yr15 and Yr67, while the other two may harbor undescribed resistance genes. Discussion The tetraploid wheat diversity panel, developed and characterized herein, captures wide geographic origins, genetic diversity, and evolutionary history since domestication making it a useful community resource for mapping of other agronomically important traits and for conducting evolutionary studies.
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Affiliation(s)
- Valentyna Klymiuk
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Teketel Haile
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jennifer Ens
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Krystalee Wiebe
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Amidou N’Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Andrii Fatiukha
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Roi Ben-David
- Department of Vegetables and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO) – The Volcani Center, Rishon LeZion, Israel
| | - Sariel Hübner
- Galilee Research Institute (MIGAL), Tel Hai Academic College, Upper Galilee, Israel
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Curtis J. Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
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22
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Velimirović A, Jovović Z, Perović D, Lehnert H, Mikić S, Mandić D, Pržulj N, Mangini G, Finetti-Sialer MM. SNP Diversity and Genetic Structure of "Rogosija", an Old Western Balkan Durum Wheat Collection. PLANTS (BASEL, SWITZERLAND) 2023; 12:1157. [PMID: 36904017 PMCID: PMC10005349 DOI: 10.3390/plants12051157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Durum wheat landraces represent a genetic resource for the identification and isolation of new valuable genes and alleles, useful to increase the crop adaptability to climate change. Several durum wheat landraces, all denominated "Rogosija", were extensively cultivated in the Western Balkan Peninsula until the first half of the 20th century. Within the conservation program of the Montenegro Plant Gene Bank, these landraces were collected, but without being characterized. The main goal of this study was to estimate the genetic diversity of the "Rogosija collection" consisting of 89 durum accessions, using 17 morphological descriptors and the 25K Illumina single nucleotide polymorphism (SNP) array. The genetic structure analysis of the Rogosija collection showed two distinguished clusters localized in two different Montenegro eco-geographic micro-areas, characterized by continental Mediterranean climate and maritime Mediterranean climate. Data suggest that these clusters could be composed of two different Balkan durum landrace collections evolved in two different eco-geographic micro-areas. Moreover, the origin of Balkan durum landraces is discussed.
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Affiliation(s)
- Ana Velimirović
- Biotechnical Faculty Podgorica, University of Montenegro, Mihaila Lalića 15, 81000 Podgorica, Montenegro
| | - Zoran Jovović
- Biotechnical Faculty Podgorica, University of Montenegro, Mihaila Lalića 15, 81000 Podgorica, Montenegro
| | - Dragan Perović
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin-Baur-Strasse 27, 06484 Quedlinburg, Germany
| | - Heike Lehnert
- Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Julius Kuehn-Institute, Erwin-Baur-Strasse 27, 06484 Quedlinburg, Germany
| | - Sanja Mikić
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21101 Novi Sad, Serbia
| | - Dragan Mandić
- Agricultural Institute of Republika Srpska, Knjaza Miloša 17, 78000 Banja Luka, Republika Srpska, Bosnia and Herzegovina
| | - Novo Pržulj
- Faculty of Agriculture, University of Banjaluka, Bulevar vojvode P. Bojovića 1a, 78000 Banja Luka, Republika Srpska, Bosnia and Herzegovina
| | - Giacomo Mangini
- Institute of Biosciences and Bioresources, National Research Council (IBBR-CNR), Via Amendola 165/A, 70126 Bari, Italy
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23
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Guo K, Chen T, Zhang P, Liu Y, Che Z, Shahinnia F, Yang D. Meta-QTL analysis and in-silico transcriptome assessment for controlling chlorophyll traits in common wheat. THE PLANT GENOME 2023; 16:e20294. [PMID: 36636827 DOI: 10.1002/tpg2.20294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/02/2022] [Indexed: 05/10/2023]
Abstract
Chlorophyll is an important plant molecule for absorbing light and transferring electrons to produce energy for photosynthesis, which has a significant impact on crop yield. To identify quantitative trait loci (QTL) controlling chlorophyll traits in wheat (Triticum aestivum L.), a comprehensive meta-analysis of 411 original QTLs for six chlorophyll traits was performed, including the evolution of soil plant analysis development (SPAD), chlorophyll content index (CCI), chlorophyll a content (Chla), chlorophyll b content (Chlb), chlorophyll content (Chl), and ratio of chlorophyll a to b (Chla/b), derived from 41 independent experiments conducted over the past two decades. Fifty-six consensus meta-QTLs (MQTLs) were detected, unevenly distributed on chromosomes 1A, 1B, 2A, 2B, 2D, 3B, 3D, 4B, 4D, 5A, 5D, 6A, 6D, 7B, and 7D. The confidence interval (CI) of the identified MQTLs was 0.18 to 15.07 cM, with an average of 5.74 cM, and 3.17-times narrower than that of the original QTLs. A total of 30 MQTLs were aligned with marker-trait associations (MTAs) reported in genome-wide association studies (GWAS) for chlorophyll traits in wheat. Based on MQTL-flanking marker information and homology analyses combined with RNA-seq data, 136 putative candidate genes were identified in MQTL regions, involved in porphyrin metabolism, photosynthesis, terpene biosynthesis, glyoxylate and dicarboxylate metabolism, and secondary metabolites. The results of this study contribute to the understanding of the genetic basis for controlling chlorophyll traits and can be used in breeding wheat with high photosynthetic efficiency.
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Affiliation(s)
- Kaiqi Guo
- State Key Lab of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural Univ., Lanzhou, 730070, China
| | - Tao Chen
- State Key Lab of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural Univ., Lanzhou, 730070, China
| | - Peipei Zhang
- State Key Lab of Aridland Crop Science, Lanzhou, 730070, China
| | - Yuan Liu
- State Key Lab of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural Univ., Lanzhou, 730070, China
| | - Zhuo Che
- Plant Seed Master Station of Gansu Province, Lanzhou, 730000, China
| | - Fahimeh Shahinnia
- Bavarian State Research Centre for Agriculture, Institute for Crop Science and Plant Breeding, Freising, 85354, Germany
| | - Delong Yang
- State Key Lab of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural Univ., Lanzhou, 730070, China
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24
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Verma V, Kumar A, Partap M, Thakur M, Bhargava B. CRISPR-Cas: A robust technology for enhancing consumer-preferred commercial traits in crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1122940. [PMID: 36824195 PMCID: PMC9941649 DOI: 10.3389/fpls.2023.1122940] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
The acceptance of new crop varieties by consumers is contingent on the presence of consumer-preferred traits, which include sensory attributes, nutritional value, industrial products and bioactive compounds production. Recent developments in genome editing technologies provide novel insight to identify gene functions and improve the various qualitative and quantitative traits of commercial importance in plants. Various conventional as well as advanced gene-mutagenesis techniques such as physical and chemical mutagenesis, CRISPR-Cas9, Cas12 and base editors are used for the trait improvement in crops. To meet consumer demand, breakthrough biotechnologies, especially CRISPR-Cas have received a fair share of scientific and industrial interest, particularly in plant genome editing. CRISPR-Cas is a versatile tool that can be used to knock out, replace and knock-in the desired gene fragments at targeted locations in the genome, resulting in heritable mutations of interest. This review highlights the existing literature and recent developments in CRISPR-Cas technologies (base editing, prime editing, multiplex gene editing, epigenome editing, gene delivery methods) for reliable and precise gene editing in plants. This review also discusses the potential of gene editing exhibited in crops for the improvement of consumer-demanded traits such as higher nutritional value, colour, texture, aroma/flavour, and production of industrial products such as biofuel, fibre, rubber and pharmaceuticals. In addition, the bottlenecks and challenges associated with gene editing system, such as off targeting, ploidy level and the ability to edit organelle genome have also been discussed.
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Affiliation(s)
- Vipasha Verma
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Akhil Kumar
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Mahinder Partap
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Meenakshi Thakur
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Bhavya Bhargava
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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25
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Wang Y, Chen G, Zeng F, Han Z, Qiu CW, Zeng M, Yang Z, Xu F, Wu D, Deng F, Xu S, Chater C, Korol A, Shabala S, Wu F, Franks P, Nevo E, Chen ZH. Molecular evidence for adaptive evolution of drought tolerance in wild cereals. THE NEW PHYTOLOGIST 2023; 237:497-514. [PMID: 36266957 DOI: 10.1111/nph.18560] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
The considerable drought tolerance of wild cereal crop progenitors has diminished during domestication in the pursuit of higher productivity. Regaining this trait in cereal crops is essential for global food security but requires novel genetic insight. Here, we assessed the molecular evidence for natural variation of drought tolerance in wild barley (Hordeum spontaneum), wild emmer wheat (Triticum dicoccoides), and Brachypodium species collected from dry and moist habitats at Evolution Canyon, Israel (ECI). We report that prevailing moist vs dry conditions have differentially shaped the stomatal and photosynthetic traits of these wild cereals in their respective habitats. We present the genomic and transcriptomic evidence accounting for differences, including co-expression gene modules, correlated with physiological traits, and selective sweeps, driven by the xeric site conditions on the African Slope (AS) at ECI. Co-expression gene module 'circadian rhythm' was linked to significant drought-induced delay in flowering time in Brachypodium stacei genotypes. African Slope-specific differentially expressed genes are important in barley drought tolerance, verified by silencing Disease-Related Nonspecific Lipid Transfer 1 (DRN1), Nonphotochemical Quenching 4 (NPQ4), and Brassinosteroid-Responsive Ring-H1 (BRH1). Our results provide new genetic information for the breeding of resilient wheat and barley in a changing global climate with increasingly frequent drought events.
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Affiliation(s)
- Yuanyuan Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Fanrong Zeng
- Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Zhigang Han
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Cheng-Wei Qiu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Meng Zeng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, 611731, China
| | - Fei Xu
- Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Dezhi Wu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fenglin Deng
- Central Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Shengchun Xu
- Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Caspar Chater
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Mount Carmel, 34988384, Haifa, Israel
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, 7004, Australia
- School of Biological Science, University of Western Australia, Crawley, WA, 6009, Australia
| | - Feibo Wu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Peter Franks
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, 34988384, Haifa, Israel
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
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26
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Guo X, Wu C, Wang D, Wang G, Jin K, Zhao Y, Tian J, Deng Z. Conditional QTL mapping for seed germination and seedling traits under salt stress and candidate gene prediction in wheat. Sci Rep 2022; 12:21010. [PMID: 36471100 PMCID: PMC9722660 DOI: 10.1038/s41598-022-25703-3] [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: 03/03/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Breeding new wheat varieties with salt resistance is one of the best ways to solve a constraint on the sustainability and expansion of wheat cultivation. Therefore, understanding the molecular components or genes related to salt tolerance must contribute to the cultivation of salt-tolerant varieties. The present study used a recombinant inbred line (RIL) population to genetically dissect the effects of different salt stress concentrations on wheat seed germination and seedling traits using two quantitative trait locus (QTL) mapping methods. A total of 31 unconditional and 11 conditional QTLs for salt tolerance were identified on 11 chromosomes explaining phenotypic variation (PVE) ranging from 2.01 to 65.76%. Of these, 15 major QTLs were found accounting for more than 10% PVE. QTL clusters were detected on chromosomes 2A and 3B in the marker intervals 'wPt-8328 and wPt-2087' and 'wPt-666008 and wPt-3620', respectively, involving more than one salt tolerance trait. QRdw3B and QSfw3B.2 were most consistent in two or more salt stress treatments. 16 candidate genes associated with salt tolerance were predicted in wheat. These results could be useful to improve salt tolerance by marker-assisted selection (MAS) and shed new light on understanding the genetic basis of salt tolerance in wheat.
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Affiliation(s)
- Xin Guo
- grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality Breeding, Agronomy College, Shandong Agricultural University, Tai’an, Shandong People’s Republic of China ,Taiyuan Agro-Tech Extension and Service Center, 030000 Taiyuan, Shanxi People’s Republic of China
| | - Chongning Wu
- grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality Breeding, Agronomy College, Shandong Agricultural University, Tai’an, Shandong People’s Republic of China
| | - Dehua Wang
- grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality Breeding, Agronomy College, Shandong Agricultural University, Tai’an, Shandong People’s Republic of China
| | - Guanying Wang
- grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality Breeding, Agronomy College, Shandong Agricultural University, Tai’an, Shandong People’s Republic of China
| | - Kaituo Jin
- grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality Breeding, Agronomy College, Shandong Agricultural University, Tai’an, Shandong People’s Republic of China
| | - Yingjie Zhao
- grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality Breeding, Agronomy College, Shandong Agricultural University, Tai’an, Shandong People’s Republic of China
| | - Jichun Tian
- grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality Breeding, Agronomy College, Shandong Agricultural University, Tai’an, Shandong People’s Republic of China
| | - Zhiying Deng
- grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality Breeding, Agronomy College, Shandong Agricultural University, Tai’an, Shandong People’s Republic of China
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27
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Vervalle JA, Costantini L, Lorenzi S, Pindo M, Mora R, Bolognesi G, Marini M, Lashbrooke JG, Tobutt KR, Vivier MA, Roodt-Wilding R, Grando MS, Bellin D. A high-density integrated map for grapevine based on three mapping populations genotyped by the Vitis18K SNP chip. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4371-4390. [PMID: 36271055 PMCID: PMC9734222 DOI: 10.1007/s00122-022-04225-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
We present a high-density integrated map for grapevine, allowing refinement and improved understanding of the grapevine genome, while demonstrating the applicability of the Vitis18K SNP chip for linkage mapping. The improvement of grapevine through biotechnology requires identification of the molecular bases of target traits by studying marker-trait associations. The Vitis18K SNP chip provides a useful genotyping tool for genome-wide marker analysis. Most linkage maps are based on single mapping populations, but an integrated map can increase marker density and show order conservation. Here we present an integrated map based on three mapping populations. The parents consist of the well-known wine cultivars 'Cabernet Sauvignon', 'Corvina' and 'Rhine Riesling', the lesser-known wine variety 'Deckrot', and a table grape selection, G1-7720. Three high-density population maps with an average inter-locus gap ranging from 0.74 to 0.99 cM were developed. These maps show high correlations (0.9965-0.9971) with the reference assembly, containing only 93 markers with large order discrepancies compared to expected physical positions, of which a third is consistent across multiple populations. Moreover, the genetic data aid the further refinement of the grapevine genome assembly, by anchoring 104 yet unanchored scaffolds. From these population maps, an integrated map was constructed which includes 6697 molecular markers and reduces the inter-locus gap distance to 0.60 cM, resulting in the densest integrated map for grapevine thus far. A small number of discrepancies, mainly of short distance, involve 88 markers that remain conflictual across maps. The integrated map shows similar collinearity to the reference assembly (0.9974) as the single maps. This high-density map increases our understanding of the grapevine genome and provides a useful tool for its further characterization and the dissection of complex traits.
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Affiliation(s)
- Jessica A Vervalle
- Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
- ARC Infruitec-Nietvoorbij, Stellenbosch, 7599, South Africa
| | - Laura Costantini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Silvia Lorenzi
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Riccardo Mora
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Giada Bolognesi
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Martina Marini
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Justin G Lashbrooke
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Ken R Tobutt
- ARC Infruitec-Nietvoorbij, Stellenbosch, 7599, South Africa
| | - Melané A Vivier
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Rouvay Roodt-Wilding
- Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Maria Stella Grando
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Center Agriculture Food and Environment (C3A), University of Trento, San Michele all'Adige, Italy
| | - Diana Bellin
- Department of Biotechnology, University of Verona, Verona, Italy.
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Nigro D, Blanco A, Piarulli L, Signorile MA, Colasuonno P, Blanco E, Simeone R. Fine Mapping and Candidate Gene Analysis of Pm36, a Wild Emmer-Derived Powdery Mildew Resistance Locus in Durum Wheat. Int J Mol Sci 2022; 23:ijms232113659. [PMID: 36362444 PMCID: PMC9657016 DOI: 10.3390/ijms232113659] [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: 10/18/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022] Open
Abstract
Powdery mildew (PM) is an economically important foliar disease of cultivated cereals worldwide. The cultivation of disease-resistant varieties is considered the most efficient, sustainable and economical strategy for disease management. The objectives of the current study were to fine map the chromosomal region harboring the wild emmer PM resistance locus Pm36 and to identify candidate genes by exploiting the improved tetraploid wheat genomic resources. A set of backcross inbred lines (BILs) of durum wheat were genotyped with the SNP 25K chip array and comparison of the PM-resistant and susceptible lines defined a 1.5 cM region (physical interval of 1.08 Mb) harboring Pm36. The genetic map constructed with F2:3 progenies derived by crossing the PM resistant line 5BIL-42 and the durum parent Latino, restricted to 0.3 cM the genetic distance between Pm36 and the SNP marker IWB22904 (physical distance 0.515 Mb). The distribution of the marker interval including Pm36 in a tetraploid wheat collection indicated that the positive allele was largely present in the domesticated and wild emmer Triticum turgidum spp. dicoccum and ssp. dicoccoides. Ten high-confidence protein coding genes were identified in the Pm36 region of the emmer, durum and bread wheat reference genomes, while three added genes showed no homologous in the emmer genome. The tightly linked markers can be used for marker-assisted selection in wheat breeding programs, and as starting point for the Pm36 map-based cloning.
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Affiliation(s)
- Domenica Nigro
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Correspondence: ; Tel.: +39-080-5442993
| | - Luciana Piarulli
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Massimo Antonio Signorile
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Pasqualina Colasuonno
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Emanuela Blanco
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy
| | - Rosanna Simeone
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
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29
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Arriagada O, Gadaleta A, Marcotuli I, Maccaferri M, Campana M, Reveco S, Alfaro C, Matus I, Schwember AR. A comprehensive meta-QTL analysis for yield-related traits of durum wheat ( Triticum turgidum L. var. durum) grown under different water regimes. FRONTIERS IN PLANT SCIENCE 2022; 13:984269. [PMID: 36147234 PMCID: PMC9486101 DOI: 10.3389/fpls.2022.984269] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/18/2022] [Indexed: 05/13/2023]
Abstract
Abiotic stress strongly affects yield-related traits in durum wheat, in particular drought is one of the main environmental factors that have effect on grain yield and plant architecture. In order to obtain new genotypes well adapted to stress conditions, the highest number of desirable traits needs to be combined in the same genotype. In this context, hundreds of quantitative trait loci (QTL) have been identified for yield-related traits in different genetic backgrounds and environments. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies for the reliability of their location and effects. MQTL analysis is a useful method to dissect the genetic architecture of complex traits, which provide an extensive allelic coverage, a higher mapping resolution and allow the identification of putative molecular markers useful for marker-assisted selection (MAS). In the present study, a complete and comprehensive MQTL analysis was carried out to identify genomic regions associated with grain-yield related traits in durum wheat under different water regimes. A total of 724 QTL on all 14 chromosomes (genomes A and B) were collected for the 19 yield-related traits selected, of which 468 were reported under rainfed conditions, and 256 under irrigated conditions. Out of the 590 QTL projected on the consensus map, 421 were grouped into 76 MQTL associated with yield components under both irrigated and rainfed conditions, 12 genomic regions containing stable MQTL on all chromosomes except 1A, 4A, 5A, and 6B. Candidate genes associated to MQTL were identified and an in-silico expression analysis was carried out for 15 genes selected among those that were differentially expressed under drought. These results can be used to increase durum wheat grain yields under different water regimes and to obtain new genotypes adapted to climate change.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Matteo Campana
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Samantha Reveco
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christian Alfaro
- Centro Regional Rayentue, Instituto de Investigaciones Agropecuarias (INIA), Rengo, Chile
| | - Iván Matus
- Centro Regional Quilamapu, Instituto de Investigaciones Agropecuarias (INIA), Chillán, Chile
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
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30
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Marcotuli I, Soriano JM, Gadaleta A. A consensus map for quality traits in durum wheat based on genome-wide association studies and detection of ortho-meta QTL across cereal species. Front Genet 2022; 13:982418. [PMID: 36110219 PMCID: PMC9468538 DOI: 10.3389/fgene.2022.982418] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
The present work focused on the identification of durum wheat QTL hotspots from a collection of genome-wide association studies, for quality traits, such as grain protein content and composition, yellow color, fiber, grain microelement content (iron, magnesium, potassium, selenium, sulfur, calcium, cadmium), kernel vitreousness, semolina, and dough quality test. For the first time a total of 10 GWAS studies, comprising 395 marker-trait associations (MTA) on 57 quality traits, with more than 1,500 genotypes from 9 association panels, were used to investigate consensus QTL hotspots representative of a wide durum wheat genetic variation. MTA were found distributed on all the A and B genomes chromosomes with minimum number of MTA observed on chromosome 5B (15) and a maximum of 45 on chromosome 7A, with an average of 28 MTA per chromosome. The MTA were equally distributed on A (48%) and B (52%) genomes and allowed the identification of 94 QTL hotspots. Synteny maps for QTL were also performed in Zea mays, Brachypodium, and Oryza sativa, and candidate gene identification allowed the association of genes involved in biological processes playing a major role in the control of quality traits.
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Affiliation(s)
- Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
| | - Jose Miguel Soriano
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), Lleida, Spain
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
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31
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Christov NK, Tsonev S, Dragov R, Taneva K, Bozhanova V, Todorovska EG. Genetic diversity and population structure of modern Bulgarian and foreign durum wheat based on microsatellite and agronomic data. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2116999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Nikolai Kirilov Christov
- Department of Functional Genetics, Abiotic and Biotic Stress, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Stefan Tsonev
- Department of Functional Genetics, Abiotic and Biotic Stress, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Rangel Dragov
- Department of Durum Wheat Breeding, Field Crops Institute, Agricultural Academy, Chirpan, Bulgaria
| | - Krasimira Taneva
- Department of Durum Wheat Breeding, Field Crops Institute, Agricultural Academy, Chirpan, Bulgaria
| | - Violeta Bozhanova
- Department of Durum Wheat Breeding, Field Crops Institute, Agricultural Academy, Chirpan, Bulgaria
| | - Elena Georgieva Todorovska
- Department of Functional Genetics, Abiotic and Biotic Stress, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
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Genievskaya Y, Pecchioni N, Laidò G, Anuarbek S, Rsaliyev A, Chudinov V, Zatybekov A, Turuspekov Y, Abugalieva S. Genome-Wide Association Study of Leaf Rust and Stem Rust Seedling and Adult Resistances in Tetraploid Wheat Accessions Harvested in Kazakhstan. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11151904. [PMID: 35893608 PMCID: PMC9329756 DOI: 10.3390/plants11151904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/13/2022] [Accepted: 07/20/2022] [Indexed: 05/05/2023]
Abstract
Leaf rust (LR) and stem rust (SR) are diseases increasingly impacting wheat production worldwide. Fungal pathogens producing rust diseases in wheat may cause yield losses of up to 50−60%. One of the most effective methods for preventing such losses is the development of resistant cultivars with high yield potential. This goal can be achieved through complex breeding studies, including the identification of key genetic factors controlling rust disease resistance. The objective of this study was to identify sources of tetraploid wheat resistance to LR and SR races, both at the seedling growth stage in the greenhouse and at the adult plant stage in field experiments, under the conditions of the North Kazakhstan region. A panel consisting of 193 tetraploid wheat accessions was used in a genome-wide association study (GWAS) for the identification of quantitative trait loci (QTLs) associated with LR and SR resistance, using 16,425 polymorphic single-nucleotide polymorphism (SNP) markers in the seedling and adult stages of plant development. The investigated panel consisted of seven tetraploid subspecies (Triticum turgidum ssp. durum, ssp. turanicum, ssp. turgidum, ssp. polonicum, ssp. carthlicum, ssp. dicoccum, and ssp. dicoccoides). The GWAS, based on the phenotypic evaluation of the tetraploid collection’s reaction to the two rust species at the seedling (in the greenhouse) and adult (in the field) stages, revealed 38 QTLs (p < 0.001), comprising 17 for LR resistance and 21 for SR resistance. Ten QTLs were associated with the reaction to LR at the seedling stage, while six QTLs were at the adult plant stage and one QTL was at both the seedling and adult stages. Eleven QTLs were associated with SR response at the seedling stage, while nine QTLs were at the adult plant stage and one QTL was at both the seedling and adult stages. A comparison of these results with previous LR and SR studies indicated that 11 of the 38 QTLs are presumably novel loci. The QTLs identified in this work can potentially be used for marker-assisted selection of tetraploid and hexaploid wheat for the breeding of new LR- and SR-resistant cultivars.
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Affiliation(s)
- Yuliya Genievskaya
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (Y.G.); (S.A.); (A.Z.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops, 71122 Foggia, Italy; (N.P.); (G.L.)
| | - Giovanni Laidò
- Research Centre for Cereal and Industrial Crops, 71122 Foggia, Italy; (N.P.); (G.L.)
| | - Shynar Anuarbek
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (Y.G.); (S.A.); (A.Z.); (Y.T.)
| | - Aralbek Rsaliyev
- Laboratory of Phytosanitary Safety, Research Institute of Biological Safety Problems, Gvardeisky 080409, Kazakhstan;
| | - Vladimir Chudinov
- Breeding Department, Karabalyk Agricultural Experimental Station, Nauchnoe 110908, Kazakhstan;
| | - Alibek Zatybekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (Y.G.); (S.A.); (A.Z.); (Y.T.)
| | - Yerlan Turuspekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (Y.G.); (S.A.); (A.Z.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Saule Abugalieva
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (Y.G.); (S.A.); (A.Z.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Correspondence: ; Tel.: +7-727-394-8006
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Niu Y, Chen T, Zhao C, Guo C, Zhou M. Identification of QTL for Stem Traits in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:962253. [PMID: 35909739 PMCID: PMC9330363 DOI: 10.3389/fpls.2022.962253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Lodging in wheat (Triticum aestivum L.) is a complicated phenomenon that is influenced by physiological, genetics, and external factors. It causes a great yield loss and reduces grain quality and mechanical harvesting efficiency. Lodging resistance is contributed by various traits, including increased stem strength. The aim of this study was to map quantitative trait loci (QTL) controlling stem strength-related features (the number of big vascular bundles, stem diameter, stem wall thickness) using a doubled haploid (DH) population derived from a cross between Baiqimai and Neixiang 5. Field experiments were conducted during 2020-2022, and glasshouse experiments were conducted during 2021-2022. Significant genetic variations were observed for all measured traits, and they were all highly heritable. Fifteen QTL for stem strength-related traits were identified on chromosomes 2D, 3A, 3B, 3D, 4B, 5A, 6B, 7A, and 7D, respectively, and 7 QTL for grain yield-related traits were identified on chromosomes 2B, 2D, 3D, 4B, 7A, and 7B, respectively. The superior allele of the major QTL for the number of big vascular bundle (VB) was independent of plant height (PH), making it possible to improve stem strength without a trade-off of PH, thus improving lodging resistance. VB also showed positive correlations with some of the yield components. The result will be useful for molecular marker-assisted selection (MAS) for high stem strength and high yield potential.
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Affiliation(s)
- Yanan Niu
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Tianxiao Chen
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Ce Guo
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
- College of Agronomy, Shanxi Agricultural University, Taigu, China
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Mourad AMI, Draz IS, Omar GE, Börner A, Esmail SM. Genome-Wide Screening of Broad-Spectrum Resistance to Leaf Rust ( Puccinia triticina Eriks) in Spring Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:921230. [PMID: 35812968 PMCID: PMC9258335 DOI: 10.3389/fpls.2022.921230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/30/2022] [Indexed: 06/01/2023]
Abstract
Wheat leaf rust (LR) causes significant yield losses worldwide. In Egypt, resistant cultivars began to lose their efficiency in leaf rust resistance. Therefore, a diverse spring wheat panel was evaluated at the seedling stage to identify new sources of broad-spectrum seedling resistance against the Egyptian Puccinia triticina (Pt) races. In three different experiments, seedling evaluation was done using Pt spores collected from different fields and growing seasons. Highly significant differences were found among experiments confirming the presence of different races population in each experiment. Highly significant differences were found among the tested genotypes confirming the ability to select superior genotypes. Genome-wide association study (GWAS) was conducted for each experiment and a set of 87 markers located within 48 gene models were identified. The identified gene models were associated with disease resistance in wheat. Five gene models were identified to resist all Pt races in at least two experiments and could be identified as stable genes under Egyptian conditions. Ten genotypes from five different countries were stable against all the tested Pt races but showed different degrees of resistance.
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Affiliation(s)
- Amira M. I. Mourad
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Ibrahim S. Draz
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Ghady E. Omar
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Samar M. Esmail
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
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Negisho K, Shibru S, Matros A, Pillen K, Ordon F, Wehner G. Association Mapping of Drought Tolerance Indices in Ethiopian Durum Wheat ( Triticum turgidum ssp. durum). FRONTIERS IN PLANT SCIENCE 2022; 13:838088. [PMID: 35693182 PMCID: PMC9178276 DOI: 10.3389/fpls.2022.838088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Ethiopia is a major producer of durum wheat in sub-Saharan Africa. However, its production is prone to drought stress as it is fully dependent on rain, which is erratic and unpredictable. This study aimed to detect marker-trait associations (MTAs) and quantitative trait loci (QTLs) related to indices. Six drought tolerance indices, i.e., drought susceptibility index (DSI), geometric mean productivity (GMP), relative drought index (RDI), stress tolerance index (STI), tolerance index (TOL), and yield stability index (YSI) were calculated from least-square means (lsmeans) of grain yield (GY) and traits significantly (p < 0.001) correlated with grain yield (GY) under field drought stress (FDS) and field non-stress (FNS) conditions. GY, days to grain filling (DGF), soil plant analysis development (SPAD) chlorophyll meter, seeds per spike (SPS), harvest index (HI), and thousand kernel weight (TKW) were used to calculate DSI, GMP, RDI, STI, TOL, and YSI drought indices. Accessions, DW084, DW082, DZ004, C037, and DW092 were selected as the top five drought-tolerant based on DSI, RDI, TOL, and YSI combined ranking. Similarly, C010, DW033, DW080, DW124-2, and C011 were selected as stable accessions based on GMP and STI combined ranking. A total of 184 MTAs were detected linked with drought indices at -log10p ≥ 4.0,79 of which were significant at a false discovery rate (FDR) of 5%. Based on the linkage disequilibrium (LD, r 2 ≥ 0.2), six of the MTAs with a positive effect on GY-GMP were detected on chromosomes 2B, 3B, 4A, 5B, and 6B, explaining 14.72, 10.07, 26.61, 21.16, 21.91, and 22.21% of the phenotypic variance, respectively. The 184 MTAs were clustered into 102 QTLs. Chromosomes 1A, 2B, and 7A are QTL hotspots with 11 QTLs each. These chromosomes play a key role in drought tolerance and respective QTL may be exploited by marker-assisted selection for improving drought stress tolerance in wheat.
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Affiliation(s)
- Kefyalew Negisho
- National Agricultural Biotechnology Research Center, Ethiopian Institute of Agricultural Research (EIAR), Holeta, Ethiopia
| | - Surafel Shibru
- Melkassa Research Center, Ethiopian Institute of Agricultural Research (EIAR), Melkassa, Ethiopia
| | - Andrea Matros
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin Luther University, Halle, Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Gwendolin Wehner
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
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Li T, Li Q, Wang J, Yang Z, Tang Y, Su Y, Zhang J, Qiu X, Pu X, Pan Z, Zhang H, Liang J, Liu Z, Li J, Yan W, Yu M, Long H, Wei Y, Deng G. High-resolution detection of quantitative trait loci for seven important yield-related traits in wheat (Triticum aestivum L.) using a high-density SLAF-seq genetic map. BMC Genom Data 2022; 23:37. [PMID: 35562674 PMCID: PMC9107147 DOI: 10.1186/s12863-022-01050-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 04/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Yield-related traits including thousand grain weight (TGW), grain number per spike (GNS), grain width (GW), grain length (GL), plant height (PH), spike length (SL), and spikelet number per spike (SNS) are greatly associated with grain yield of wheat (Triticum aestivum L.). To detect quantitative trait loci (QTL) associated with them, 193 recombinant inbred lines derived from two elite winter wheat varieties Chuanmai42 and Chuanmai39 were employed to perform QTL mapping in six/eight environments. RESULTS A total of 30 QTLs on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 4A, 5A, 5B, 6A, 6D, 7A, 7B and 7D were identified. Among them, six major QTLs QTgw.cib-6A.1, QTgw.cib-6A.2, QGw.cib-6A, QGl.cib-3A, QGl.cib-6A, and QSl.cib-2D explaining 5.96-23.75% of the phenotypic variance were detected in multi-environments and showed strong and stable effects on corresponding traits. Three QTL clusters on chromosomes 2D and 6A containing 10 QTLs were also detected, which showed significant pleiotropic effects on multiple traits. Additionally, three Kompetitive Allele Specific PCR (KASP) markers linked with five of these major QTLs were developed. Candidate genes of QTgw.cib-6A.1/QGl.cib-6A and QGl.cib-3A were analyzed based on the spatiotemporal expression patterns, gene annotation, and orthologous search. CONCLUSIONS Six major QTLs for TGW, GL, GW and SL were detected. Three KASP markers linked with five of these major QTLs were developed. These QTLs and KASP markers will be useful for elucidating the genetic architecture of grain yield and developing new wheat varieties with high and stable yield in wheat.
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Affiliation(s)
- Tao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Qiao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Jinhui Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yanyan Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yan Su
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Juanyu Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xvebing Qiu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xi Pu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zhifen Pan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Junjun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zehou Liu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Wuyun Yan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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Mago R, Chen C, Xia X, Whan A, Forrest K, Basnet BR, Perera G, Chandramohan S, Randhawa M, Hayden M, Bansal U, Huerta-Espino J, Singh RP, Bariana H, Lagudah E. Adult plant stem rust resistance in durum wheat Glossy Huguenot: mapping, marker development and validation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1541-1550. [PMID: 35199199 DOI: 10.1007/s00122-022-04052-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/28/2022] [Indexed: 05/12/2023]
Abstract
Adult plant stem rust resistance locus, QSrGH.cs-2AL, was identified in durum wheat Glossy Huguenot and mendelised as Sr63. Markers closely linked with Sr63 were developed. An F3 population from a Glossy Huguenot (GH)/Bansi cross used in a previous Australian study was advanced to F6 for molecular mapping of adult plant stem rust resistance. Maturity differences among F6 lines confounded assessments of stem rust response. GH was crossed with a stem rust susceptible F6 recombinant inbred line (RIL), GHB14 (M14), with similar maturity and an F6:7 population was developed through single seed descent method. F7 and F8 RILs were tested along with the parents at different locations. The F6 individual plants and both parents were genotyped using the 90 K single nucleotide polymorphism (SNP) wheat array. Stem rust resistance QTL on the long arms of chromosomes 1B (QSrGH.cs-1BL) and 2A (QSrGH.cs-2AL) were detected. QSrGH.cs-1BL and QSrGH.cs-2AL were both contributed by GH and explained 22% and 18% adult plant stem rust response variation, respectively, among GH/M14 RIL population. RILs carrying combinations of these QTL reduced more than 14% stem rust severity compared to those that possessed QSrGH.cs-1BL and QSrGH.cs-2AL individually. QSrGH.cs1BL was demonstrated to be the same as Sr58/Lr46/Yr29/Pm39 through marker genotyping. Lines lacking QSrGH.cs-1BL were used to Mendelise QSrGH.cs-2AL. Based on genomic locations of previously catalogued stem rust resistance genes and the QSrGH.cs-2AL map, it appeared to represent a new APR locus and was permanently named Sr63. SNP markers associated with Sr63 were converted to kompetetive allele-specific PCR (KASP) assays and were validated on a set of durum cultivars.
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Affiliation(s)
- Rohit Mago
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia.
| | - Chunhong Chen
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Xiaodi Xia
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Alex Whan
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Kerrie Forrest
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Agribio, 5 Ring Rd, Bundoora, VIC, 3083, Australia
| | - Bhoja R Basnet
- CIMMYT, Carretera Mexico-Veracruz Km 18, El Batan, Texcoco, Estado de México, Mexico
| | - Geetha Perera
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Sutha Chandramohan
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Mandeep Randhawa
- ICRAF House, CIMMYT Kenya, United Nations Avenue, Gigiri, Village Market, P.O. Box 1041, 00621, Nairobi, Kenya
| | - Matthew Hayden
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Agribio, 5 Ring Rd, Bundoora, VIC, 3083, Australia
| | - Urmil Bansal
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Julio Huerta-Espino
- Campo Experimental Valle de México, INIFAP, Chapingo, Estado de México, Mexico
| | - Ravi P Singh
- CIMMYT, Carretera Mexico-Veracruz Km 18, El Batan, Texcoco, Estado de México, Mexico
| | - Harbans Bariana
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia.
| | - Evans Lagudah
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia.
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38
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Jambuthenne DT, Riaz A, Athiyannan N, Alahmad S, Ng WL, Ziems L, Afanasenko O, Periyannan SK, Aitken E, Platz G, Godwin I, Voss-Fels KP, Dinglasan E, Hickey LT. Mining the Vavilov wheat diversity panel for new sources of adult plant resistance to stripe rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1355-1373. [PMID: 35113190 PMCID: PMC9033734 DOI: 10.1007/s00122-022-04037-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Multi-year evaluation of the Vavilov wheat diversity panel identified new sources of adult plant resistance to stripe rust. Genome-wide association studies revealed the key genomic regions influencing resistance, including seven novel loci. Wheat stripe rust (YR) caused by Puccinia striiformis f. sp. tritici (Pst) poses a significant threat to global food security. Resistance genes commonly found in many wheat varieties have been rendered ineffective due to the rapid evolution of the pathogen. To identify novel sources of adult plant resistance (APR), 292 accessions from the N.I. Vavilov Institute of Plant Genetic Resources, Saint Petersburg, Russia, were screened for known APR genes (i.e. Yr18, Yr29, Yr46, Yr33, Yr39 and Yr59) using linked polymerase chain reaction (PCR) molecular markers. Accessions were evaluated against Pst (pathotype 134 E16 A + Yr17 + Yr27) at seedling and adult plant stages across multiple years (2014, 2015 and 2016) in Australia. Phenotypic analyses identified 132 lines that potentially carry novel sources of APR to YR. Genome-wide association studies (GWAS) identified 68 significant marker-trait associations (P < 0.001) for YR resistance, representing 47 independent quantitative trait loci (QTL) regions. Fourteen genomic regions overlapped with previously reported Yr genes, including Yr29, Yr56, Yr5, Yr43, Yr57, Yr30, Yr46, Yr47, Yr35, Yr36, Yrxy1, Yr59, Yr52 and YrYL. In total, seven QTL (positioned on chromosomes 1D, 2A, 3A, 3D, 5D, 7B and 7D) did not collocate with previously reported genes or QTL, indicating the presence of promising novel resistance factors. Overall, the Vavilov diversity panel provides a rich source of new alleles which could be used to broaden the genetic bases of YR resistance in modern wheat varieties.
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Affiliation(s)
- Dilani T Jambuthenne
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Adnan Riaz
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Naveenkumar Athiyannan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food,, Canberra, ACT, Australia
| | - Samir Alahmad
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Wei Ling Ng
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Laura Ziems
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Olga Afanasenko
- Department of Plant Resistance To Diseases, All Russian Research Institute for Plant Protection, St Petersburg, Russia, 196608
| | - Sambasivam K Periyannan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food,, Canberra, ACT, Australia
| | - Elizabeth Aitken
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Greg Platz
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, Australia
| | - Ian Godwin
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eric Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.
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Genome Wide Association Study Uncovers the QTLome for Osmotic Adjustment and Related Drought Adaptive Traits in Durum Wheat. Genes (Basel) 2022; 13:genes13020293. [PMID: 35205338 PMCID: PMC8871942 DOI: 10.3390/genes13020293] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/25/2022] [Accepted: 01/29/2022] [Indexed: 01/27/2023] Open
Abstract
Osmotic adjustment (OA) is a major component of drought resistance in crops. The genetic basis of OA in wheat and other crops remains largely unknown. In this study, 248 field-grown durum wheat elite accessions grown under well-watered conditions, underwent a progressively severe drought treatment started at heading. Leaf samples were collected at heading and 17 days later. The following traits were considered: flowering time (FT), leaf relative water content (RWC), osmotic potential (ψs), OA, chlorophyll content (SPAD), and leaf rolling (LR). The high variability (3.89-fold) in OA among drought-stressed accessions resulted in high repeatability of the trait (h2 = 72.3%). Notably, a high positive correlation (r = 0.78) between OA and RWC was found under severe drought conditions. A genome-wide association study (GWAS) revealed 15 significant QTLs (Quantitative Trait Loci) for OA (global R2 = 63.6%), as well as eight major QTL hotspots/clusters on chromosome arms 1BL, 2BL, 4AL, 5AL, 6AL, 6BL, and 7BS, where a higher OA capacity was positively associated with RWC and/or SPAD, and negatively with LR, indicating a beneficial effect of OA on the water status of the plant. The comparative analysis with the results of 15 previous field trials conducted under varying water regimes showed concurrent effects of five OA QTL cluster hotspots on normalized difference vegetation index (NDVI), thousand-kernel weight (TKW), and/or grain yield (GY). Gene content analysis of the cluster regions revealed the presence of several candidate genes, including bidirectional sugar transporter SWEET, rhomboid-like protein, and S-adenosyl-L-methionine-dependent methyltransferases superfamily protein, as well as DREB1. Our results support OA as a valuable proxy for marker-assisted selection (MAS) aimed at enhancing drought resistance in wheat.
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40
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Li Y, Tang J, Liu W, Yan W, Sun Y, Che J, Tian C, Zhang H, Yu L. The Genetic Architecture of Grain Yield in Spring Wheat Based on Genome-Wide Association Study. Front Genet 2021; 12:728472. [PMID: 34868206 PMCID: PMC8634730 DOI: 10.3389/fgene.2021.728472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/30/2021] [Indexed: 11/24/2022] Open
Abstract
Uncovering the genetic architecture for grain yield (GY)–related traits is important for wheat breeding. To detect stable loci for GY-related traits, a genome-wide association study (GWAS) was conducted in a diverse panel, which included 251 elite spring wheat accessions mainly from the Northeast of China. In total, 52,503 single nucleotide polymorphisms (SNPs) from the wheat 55 K SNP arrays were used. Thirty-eight loci for GY-related traits were detected and each explained 6.5–16.7% of the phenotypic variations among which 12 are at similar locations with the known genes or quantitative trait loci and 26 are likely to be new. Furthermore, six genes possibly involved in cell division, signal transduction, and plant development are candidate genes for GY-related traits. This study provides new insights into the genetic architecture of GY and the significantly associated SNPs and accessions with a larger number of favorable alleles could be used to further enhance GY in breeding.
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Affiliation(s)
- Yuyao Li
- Heilongjiang Bayi Agricultural University, Daqing, China.,Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jingquan Tang
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Wenlin Liu
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Wenyi Yan
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yan Sun
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jingyu Che
- Keshan Branch, Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Chao Tian
- Keshan Branch, Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Hongji Zhang
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Lihe Yu
- Heilongjiang Bayi Agricultural University, Daqing, China.,Heilongjiang Academy of Agricultural Sciences, Harbin, China
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41
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Hammond‐Kosack MC, King R, Kanyuka K, Hammond‐Kosack KE. Exploring the diversity of promoter and 5'UTR sequences in ancestral, historic and modern wheat. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2469-2487. [PMID: 34289221 PMCID: PMC8633512 DOI: 10.1111/pbi.13672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 06/15/2021] [Accepted: 07/08/2021] [Indexed: 05/25/2023]
Abstract
A data set of promoter and 5'UTR sequences of homoeo-alleles of 459 wheat genes that contribute to agriculturally important traits in 95 ancestral and commercial wheat cultivars is presented here. The high-stringency myBaits technology used made individual capture of homoeo-allele promoters possible, which is reported here for the first time. Promoters of most genes are remarkably conserved across the 83 hexaploid cultivars used with <7 haplotypes per promoter and 21% being identical to the reference Chinese Spring. InDels and many high-confidence SNPs are located within predicted plant transcription factor binding sites, potentially changing gene expression. Most haplotypes found in the Watkins landraces and a few haplotypes found in Triticum monococcum, germplasms hitherto not thought to have been used in modern wheat breeding, are already found in many commercial hexaploid wheats. The full data set which is useful for genomic and gene function studies and wheat breeding is available at https://rrescloud.rothamsted.ac.uk/index.php/s/DMCFDu5iAGTl50u/authenticate.
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Affiliation(s)
| | - Robert King
- Department of Computational and Analytical SciencesRothamsted ResearchHarpendenUK
| | - Kostya Kanyuka
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenUK
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42
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Kumar S, Singh VP, Saini DK, Sharma H, Saripalli G, Kumar S, Balyan HS, Gupta PK. Meta-QTLs, ortho-MQTLs, and candidate genes for thermotolerance in wheat ( Triticum aestivum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:69. [PMID: 37309361 PMCID: PMC10236124 DOI: 10.1007/s11032-021-01264-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
Meta-QTL analysis for thermotolerance in wheat was conducted to identify robust meta-QTLs (MQTLs). In this study, 441 QTLs related to 31 heat-responsive traits were projected on the consensus map with 50,310 markers. This exercise resulted in the identification of 85 MQTLs with confidence interval (CI) ranging from 0.11 to 34.9 cM with an average of 5.6 cM. This amounted to a 2.96-fold reduction relative to the mean CI (16.5 cM) of the QTLs used. Seventy-seven (77) of these MQTLs were also compared and verified with the results of recent genome-wide association studies (GWAS). The 85 MQTLs included seven MQTLs that are particularly useful for breeding purposes (we called them breeders' MQTLs). Seven ortho-MQTLs between wheat and rice genomes were also identified using synteny and collinearity. The MQTLs were used for the identification of 1,704 candidate genes (CGs). In silico expression analysis of these CGs permitted identification of 182 differentially expressed genes (DEGs), which included 36 high confidence CGs with known functions previously reported to be important for thermotolerance. These high confidence CGs encoded proteins belonging to the following families: protein kinase, WD40 repeat, glycosyltransferase, ribosomal protein, SNARE associated Golgi protein, GDSL lipase/esterase, SANT/Myb domain, K homology domain, etc. Thus, the present study resulted in the identification of MQTLs (including breeders' MQTLs), ortho-MQTLs, and underlying CGs, which could prove useful not only for molecular breeding for the development of thermotolerant wheat cultivars but also for future studies focused on understanding the molecular basis of thermotolerance. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01264-7.
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Affiliation(s)
- Sourabh Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Vivudh Pratap Singh
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab India
| | - Hemant Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Sachin Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
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43
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Qu P, Wang J, Wen W, Gao F, Liu J, Xia X, Peng H, Zhang L. Construction of Consensus Genetic Map With Applications in Gene Mapping of Wheat ( Triticum aestivum L.) Using 90K SNP Array. FRONTIERS IN PLANT SCIENCE 2021; 12:727077. [PMID: 34512703 PMCID: PMC8424075 DOI: 10.3389/fpls.2021.727077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/28/2021] [Indexed: 06/02/2023]
Abstract
Wheat is one of the most important cereal crops worldwide. A consensus map combines genetic information from multiple populations, providing an effective alternative to improve the genome coverage and marker density. In this study, we constructed a consensus map from three populations of recombinant inbred lines (RILs) of wheat using a 90K single nucleotide polymorphism (SNP) array. Phenotypic data on plant height (PH), spike length (SL), and thousand-kernel weight (TKW) was collected in six, four, and four environments in the three populations, and then used for quantitative trait locus (QTL) mapping. The mapping results obtained using the constructed consensus map were compared with previous results obtained using individual maps and previous studies on other populations. A simulation experiment was also conducted to assess the performance of QTL mapping with the consensus map. The constructed consensus map from the three populations spanned 4558.55 cM in length, with 25,667 SNPs, having high collinearity with physical map and individual maps. Based on the consensus map, 21, 27, and 19 stable QTLs were identified for PH, SL, and TKW, much more than those detected with individual maps. Four PH QTLs and six SL QTLs were likely to be novel. A putative gene called TraesCS4D02G076400 encoding gibberellin-regulated protein was identified to be the candidate gene for one major PH QTL located on 4DS, which may enrich genetic resources in wheat semi-dwarfing breeding. The simulation results indicated that the length of the confidence interval and standard errors of the QTLs detected using the consensus map were much smaller than those detected using individual maps. The consensus map constructed in this study provides the underlying genetic information for systematic mapping, comparison, and clustering of QTL, and gene discovery in wheat genetic study. The QTLs detected in this study had stable effects across environments and can be used to improve the wide adaptation of wheat cultivars through marker-assisted breeding.
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Affiliation(s)
- Pingping Qu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jiankang Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weie Wen
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
| | - Fengmei Gao
- Crop Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jindong Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianchun Xia
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiru Peng
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Luyan Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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44
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Mastrangelo AM, Cattivelli L. What Makes Bread and Durum Wheat Different? TRENDS IN PLANT SCIENCE 2021; 26:677-684. [PMID: 33612402 DOI: 10.1016/j.tplants.2021.01.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/24/2021] [Accepted: 01/28/2021] [Indexed: 05/18/2023]
Abstract
Durum wheat (tetraploid) and bread wheat (hexaploid) are two closely related species with potentially different adaptation capacities and only a few distinct technological properties that make durum semolina and wheat flour more suitable for pasta, or bread and bakery products, respectively. Interspecific crosses and new breeding technologies now allow researchers to develop wheat lines with durum or bread quality features in either a tetraploid or hexaploid genetic background; such lines combine any technological properties of wheat with the different adaptation capacity expressed by tetraploid and hexaploid wheat genomes. Here, we discuss what makes bread and durum wheat different, consider their environmental adaptation capacity and the major quality-related genes that explain the different end-uses of semolina and bread flour and that could be targets for future wheat breeding programs.
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Affiliation(s)
- Anna M Mastrangelo
- CREA Research Centre for Cereal and Industrial Crops, Foggia, 71122, Italy
| | - Luigi Cattivelli
- CREA Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, 29017, Italy.
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45
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Tomar V, Dhillon GS, Singh D, Singh RP, Poland J, Joshi AK, Tiwari BS, Kumar U. Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat ( Triticum aestivum L .). PeerJ 2021; 9:e11593. [PMID: 34221720 PMCID: PMC8231316 DOI: 10.7717/peerj.11593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/20/2021] [Indexed: 11/20/2022] Open
Abstract
Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon's information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.
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Affiliation(s)
- Vipin Tomar
- Borlaug Institute for South Asia, New Delhi, Delhi, India.,Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, Gandhinagar, Gujarat, India.,International Maize and Wheat Improvement Centre, New Delhi, Delhi, India
| | - Guriqbal Singh Dhillon
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
| | - Daljit Singh
- The Climate Corporation, Bayer Crop Science, Creve Coeur, MO, USA
| | - Ravi Prakash Singh
- Global Wheat Program, International Maize and Wheat Improvement Centre, Texcoco, Mexico
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia, New Delhi, Delhi, India.,International Maize and Wheat Improvement Centre, New Delhi, Delhi, India.,Global Wheat Program, International Maize and Wheat Improvement Centre, Texcoco, Mexico
| | - Budhi Sagar Tiwari
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, Gandhinagar, Gujarat, India
| | - Uttam Kumar
- Borlaug Institute for South Asia, New Delhi, Delhi, India.,International Maize and Wheat Improvement Centre, New Delhi, Delhi, India.,Global Wheat Program, International Maize and Wheat Improvement Centre, Texcoco, Mexico
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46
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Soriano JM, Colasuonno P, Marcotuli I, Gadaleta A. Meta-QTL analysis and identification of candidate genes for quality, abiotic and biotic stress in durum wheat. Sci Rep 2021; 11:11877. [PMID: 34088972 PMCID: PMC8178383 DOI: 10.1038/s41598-021-91446-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/25/2021] [Indexed: 11/15/2022] Open
Abstract
The genetic improvement of durum wheat and enhancement of plant performance often depend on the identification of stable quantitative trait loci (QTL) and closely linked molecular markers. This is essential for better understanding the genetic basis of important agronomic traits and identifying an effective method for improving selection efficiency in breeding programmes. Meta-QTL analysis is a useful approach for dissecting the genetic basis of complex traits, providing broader allelic coverage and higher mapping resolution for the identification of putative molecular markers to be used in marker-assisted selection. In the present study, extensive QTL meta-analysis was conducted on 45 traits of durum wheat, including quality and biotic and abiotic stress-related traits. A total of 368 QTL distributed on all 14 chromosomes of genomes A and B were projected: 171 corresponded to quality-related traits, 127 to abiotic stress and 71 to biotic stress, of which 318 were grouped in 85 meta-QTL (MQTL), 24 remained as single QTL and 26 were not assigned to any MQTL. The number of MQTL per chromosome ranged from 4 in chromosomes 1A and 6A to 9 in chromosome 7B; chromosomes 3A and 7A showed the highest number of individual QTL (4), and chromosome 7B the highest number of undefined QTL (4). The recently published genome sequence of durum wheat was used to search for candidate genes within the MQTL peaks. This work will facilitate cloning and pyramiding of QTL to develop new cultivars with specific quantitative traits and speed up breeding programs.
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Affiliation(s)
- Jose Miguel Soriano
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), 25198, Lleida, Spain.
| | - Pasqualina Colasuonno
- Department of Agricultural and Environmental Science, University of Bari 'Aldo Moro', Via G. Amendola 165/A, 70126, Bari, Italy
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari 'Aldo Moro', Via G. Amendola 165/A, 70126, Bari, Italy.
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari 'Aldo Moro', Via G. Amendola 165/A, 70126, Bari, Italy
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47
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Quan X, Liu J, Zhang N, Xie C, Li H, Xia X, He W, Qin Y. Genome-Wide Association Study Uncover the Genetic Architecture of Salt Tolerance-Related Traits in Common Wheat ( Triticum aestivum L.). Front Genet 2021; 12:663941. [PMID: 34093656 PMCID: PMC8172982 DOI: 10.3389/fgene.2021.663941] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/24/2021] [Indexed: 01/13/2023] Open
Abstract
Soil salinity is a serious threat to wheat yield affecting sustainable agriculture. Although salt tolerance is important for plant establishment at seedling stage, its genetic architecture remains unclear. In the present study, we have evaluated eight salt tolerance-related traits at seedling stage and identified the loci for salt tolerance by genome-wide association study (GWAS). This GWAS panel comprised 317 accessions and was genotyped with the wheat 90 K single-nucleotide polymorphism (SNP) chip. In total, 37 SNPs located at 16 unique loci were identified, and each explained 6.3 to 18.6% of the phenotypic variations. Among these, six loci were overlapped with previously reported genes or quantitative trait loci, whereas the other 10 were novel. Besides, nine loci were detected for two or more traits, indicating that the salt-tolerance genetic architecture is complex. Furthermore, five candidate genes were identified for salt tolerance-related traits, including kinase family protein, E3 ubiquitin-protein ligase-like protein, and transmembrane protein. SNPs identified in this study and the accessions with more favorable alleles could further enhance salt tolerance in wheat breeding. Our results are useful for uncovering the genetic mechanism of salt tolerance in wheat at seeding stage.
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Affiliation(s)
- Xiaoyan Quan
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Jindong Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ning Zhang
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Chunjuan Xie
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Hongmei Li
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenxing He
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Yuxiang Qin
- Department of Biological Science, School of Biological Science and Technology, University of Jinan, Jinan, China
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48
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Tuberosa R, Cattivelli L, Ceriotti A, Gadaleta A, Beres BL, Pozniak CJ. Editorial: Proceedings of FSTP3 Congress-A Sustainable Durum Wheat Chain for Food Security and Healthy Lives. FRONTIERS IN PLANT SCIENCE 2021; 12:675510. [PMID: 33897752 PMCID: PMC8063101 DOI: 10.3389/fpls.2021.675510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Roberto Tuberosa
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Aldo Ceriotti
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Rome, Italy
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science (DISAAT), University of Bari “Aldo Moro”, Bari, Italy
| | - Brian L. Beres
- Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Curtis J. Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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49
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Roncallo PF, Larsen AO, Achilli AL, Pierre CS, Gallo CA, Dreisigacker S, Echenique V. Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes. BMC Genomics 2021; 22:233. [PMID: 33820546 PMCID: PMC8022437 DOI: 10.1186/s12864-021-07519-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 03/02/2021] [Indexed: 01/04/2023] Open
Abstract
Background Durum wheat (Triticum turgidum L. ssp. durum Desf. Husn) is the main staple crop used to make pasta products worldwide. Under the current climate change scenarios, genetic variability within a crop plays a crucial role in the successful release of new varieties with high yields and wide crop adaptation. In this study we evaluated a durum wheat collection consisting of 197 genotypes that mainly comprised a historical set of Argentinian germplasm but also included worldwide accessions. Results We assessed the genetic diversity, population structure and linkage disequilibrium (LD) patterns in this collection using a 35 K SNP array. The level of polymorphism was considered, taking account of the frequent and rare allelic variants. A total of 1547 polymorphic SNPs was located within annotated genes. Genetic diversity in the germplasm collection increased slightly from 1915 to 2010. However, a reduction in genetic diversity using SNPs with rare allelic variants was observed after 1979. However, larger numbers of rare private alleles were observed in the 2000–2009 period, indicating that a high reservoir of rare alleles is still present among the recent germplasm in a very low frequency. The percentage of pairwise loci in LD in the durum genome was low (13.4%) in our collection. Overall LD and the high (r2 > 0.7) or complete (r2 = 1) LD presented different patterns in the chromosomes. The LD increased over three main breeding periods (1915–1979, 1980–1999 and 2000–2020). Conclusions Our results suggest that breeding and selection have impacted differently on the A and B genomes, particularly on chromosome 6A and 2A. The collection was structured in five sub-populations and modern Argentinian accessions (cluster Q4) which were clearly differentiated. Our study contributes to the understanding of the complexity of Argentinian durum wheat germplasm and to derive future breeding strategies enhancing the use of genetic diversity in a more efficient and targeted way. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07519-z.
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Affiliation(s)
- Pablo Federico Roncallo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Departamento de Agronomía, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Adelina Olga Larsen
- CEI Barrow, Instituto Nacional de Tecnología Agropecuaria (INTA), Tres Arroyos, Buenos Aires, Argentina
| | - Ana Laura Achilli
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Departamento de Agronomía, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Carolina Saint Pierre
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Edo. de México, Mexico
| | - Cristian Andrés Gallo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Departamento de Agronomía, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Susanne Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Edo. de México, Mexico
| | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Departamento de Agronomía, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina.
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50
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Zhou X, Zhong X, Roter J, Li X, Yao Q, Yan J, Yang S, Guo Q, Distelfeld A, Sela H, Kang Z. Genome-Wide Mapping of Loci for Adult-Plant Resistance to Stripe Rust in Durum Wheat Svevo Using the 90K SNP Array. PLANT DISEASE 2021; 105:879-888. [PMID: 33141640 DOI: 10.1094/pdis-09-20-1933-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Stripe rust is a foliar disease in wheat caused by Puccinia striiformis f. tritici. The best way to protect wheat from this disease is by growing resistant cultivars. Tetraploid wheat can serve as a good source of valuable genetic diversity for various traits. Here, we report the mapping of nine stripe rust resistance quantitative trait loci (QTL) effective against P. striiformis f. tritici in China and Israel. We used recombinant inbred lines (RILs) developed from a cross between the durum wheat cultivar Svevo and Triticum dicoccoides accession Zavitan. By genotyping the RIL population of 137 lines using the wheat 90K single-nucleotide polymorphism array, we mapped an adult-plant resistance locus QYrsv.swust-1BL.1, the most effective QTL, within a 0.75-centimorgan region in T. turgidum subsp. durum 'Svevo' on chromosome arm 1BL, corresponding to the region of 670.7 to 671.5 Mb on the Chinese Spring chromosome arm 1BL. Of the other eight minor-effect stripe rust QTL, seven were from Svevo and mapped on chromosomes 1A, 1B, 2B, 3A, 4A, and 5A, and one was from Zavitan and mapped on chromosome 2A. Several QTL with epistatic effects were identified as well. The markers linked to the resistance QTL can be useful in marker-assisted selection for incorporation of these resistance QTL into both durum and common wheat cultivars.
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Affiliation(s)
- Xinli Zhou
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, People's Republic of China
| | - Xiao Zhong
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, People's Republic of China
| | - Jonatan Roter
- The Institute for Cereal Crops Improvement Tel-Aviv University; Institute of Evolution, Department of Evolutionary and Environmental Biology, University of Haifa; Tel Aviv 6139001, Israel
| | - Xin Li
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, People's Republic of China
| | - Qiang Yao
- Key Laboratory of Agricultural Integrated Pest Management, Qinghai Province, Scientific Observing and Experimental Station of Crop Pest in Xining, Ministry of Agriculture, Academy of Agriculture and Forestry Science, Qinghai University, Xining, Qinghai 810016, People's Republic of China
| | - Jiahui Yan
- Key Laboratory of Agricultural Integrated Pest Management, Qinghai Province, Scientific Observing and Experimental Station of Crop Pest in Xining, Ministry of Agriculture, Academy of Agriculture and Forestry Science, Qinghai University, Xining, Qinghai 810016, People's Republic of China
| | - Suizhuang Yang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, People's Republic of China
| | - Qingyun Guo
- Key Laboratory of Agricultural Integrated Pest Management, Qinghai Province, Scientific Observing and Experimental Station of Crop Pest in Xining, Ministry of Agriculture, Academy of Agriculture and Forestry Science, Qinghai University, Xining, Qinghai 810016, People's Republic of China
| | - Assaf Distelfeld
- The Institute for Cereal Crops Improvement Tel-Aviv University; Institute of Evolution, Department of Evolutionary and Environmental Biology, University of Haifa; Tel Aviv 6139001, Israel
| | - Hanan Sela
- The Institute for Cereal Crops Improvement Tel-Aviv University; Institute of Evolution, Department of Evolutionary and Environmental Biology, University of Haifa; Tel Aviv 6139001, Israel
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
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