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Sthapit SR, Ruff TM, Hooker MA, Zhang B, Li X, See DR. Candidate selective sweeps in US wheat populations. THE PLANT GENOME 2024:e20513. [PMID: 39323003 DOI: 10.1002/tpg2.20513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 08/19/2024] [Accepted: 08/25/2024] [Indexed: 09/27/2024]
Abstract
Exploration of novel alleles from ex situ collection is still limited in modern plant breeding as these alleles exist in genetic backgrounds of landraces that are not adapted to modern production environments. The practice of backcross breeding results in preservation of the adapted background of elite parents but leaves little room for novel alleles from landraces to be incorporated. Selection of adaptation-associated linkage blocks instead of the entire adapted background may allow breeders to incorporate more of the landrace's genetic background and to observe and evaluate novel alleles. Important adaptation-associated linkage blocks would have been selected over multiple cycles of breeding and hence are likely to exhibit signatures of positive selection or selective sweeps. We conducted genome-wide scan for candidate selective sweeps (CSS) using Fst, Rsb, and xpEHH in state, regional, spring, winter, and market-class population pairs and reported 446 CSS in 19 population pairs over time and 1033 CSS in 44 population pairs across geography and class. Further validation of these CSS in specific breeding programs may lead to identification of sets of loci that can be selected to restore population-specific adaptation in pre-breeding germplasms.
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Affiliation(s)
- Sajal R Sthapit
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
- The Land Institute, Salina, Kansas, USA
| | - Travis M Ruff
- USDA-ARS Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman, Washington, USA
| | - Marcus A Hooker
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
- Department of Biological Sciences, College of Southern Nevada, Henderson, Nevada, USA
| | - Bosen Zhang
- Washington State University, Pullman, Washington, USA
| | - Xianran Li
- USDA-ARS Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman, Washington, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
| | - Deven R See
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
- USDA-ARS Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman, Washington, USA
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Geethanjali S, Kadirvel P, Periyannan S. Wheat improvement through advances in single nucleotide polymorphism (SNP) detection and genotyping with a special emphasis on rust resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:224. [PMID: 39283360 PMCID: PMC11405505 DOI: 10.1007/s00122-024-04730-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 08/24/2024] [Indexed: 09/22/2024]
Abstract
KEY MESSAGE Single nucleotide polymorphism (SNP) markers in wheat and their prospects in breeding with special reference to rust resistance. Single nucleotide polymorphism (SNP)-based markers are increasingly gaining momentum for screening and utilizing vital agronomic traits in wheat. To date, more than 260 million SNPs have been detected in modern cultivars and landraces of wheat. This rapid SNP discovery was made possible through the release of near-complete reference and pan-genome assemblies of wheat and its wild relatives, coupled with whole genome sequencing (WGS) of thousands of wheat accessions. Further, genotyping customized SNP sites were facilitated by a series of arrays (9 to 820Ks), a cost effective substitute WGS. Lately, germplasm-specific SNP arrays have been introduced to characterize novel traits and detect closely linked SNPs for marker-assisted breeding. Subsequently, the kompetitive allele-specific PCR (KASP) assay was introduced for rapid and large-scale screening of specific SNP markers. Moreover, with the advances and reduction in sequencing costs, ample opportunities arise for generating SNPs artificially through mutations and in combination with next-generation sequencing and comparative genomic analyses. In this review, we provide historical developments and prospects of SNP markers in wheat breeding with special reference to rust resistance where over 50 genetic loci have been characterized through SNP markers. Rust resistance is one of the most essential traits for wheat breeding as new strains of the Puccinia fungus, responsible for rust diseases, evolve frequently and globally.
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Affiliation(s)
- Subramaniam Geethanjali
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland, 4350, Australia
| | - Palchamy Kadirvel
- Crop Improvement Section, Indian Council of Agricultural Research-Indian Institute of Oilseeds Research, Hyderabad, Telangana, 500030, India
| | - Sambasivam Periyannan
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland, 4350, Australia.
- School of Agriculture and Environmental Science, University of Southern Queensland, Toowoomba, Queensland, 4350, Australia.
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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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Mokhtari N, Majidi MM, Mirlohi A. Physiological and antioxidant responses of synthetic hexaploid wheat germplasm under drought. BMC PLANT BIOLOGY 2024; 24:747. [PMID: 39098916 PMCID: PMC11299349 DOI: 10.1186/s12870-024-05445-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/22/2024] [Indexed: 08/06/2024]
Abstract
BACKGROUND As a result of the world population and climate change impact increases (especially in arid environments), there is a critical need for high-yield, drought-tolerant wheat. Synthetic hexaploid wheat derived lines (SHW-DL), were created artificially by crossing different durum wheat cultivars (AABB) with accessions of Aegilops tauschii (DD), a beneficial source of new genes for common bread wheat (Triticum aestivum L). Here, we studied the response of a panel of 91 SHW-DL for drought tolerance based on physiological, antioxidant enzyme activities, and drought tolerance indices. RESULTS A wide range of variation and high values of heritability observed for grain yield, physiological and antioxidant traits indicating that the SHW-DL panel constitutes a valuable gene source for drought tolerance improvement of wheat. Despite decreases in grain yield (YLD), leaf area index (LAI), and relative water content (RWC) an increase in the content of malondialdehyde (MDA) was observed. Moreover, drought streass increased the antioxidant enzyme activities of ascorbate peroxidase (APX), catalase (CAT) and peroxidase (POD), and also photosynthetic pigments, proline (Pro), and MDA content. With higher values of grain yield, physiological and biochemical traits such as photosynthetic pigments, and RWC, and lower content of MDA, and peroxidase (H2O2) activity, SHW-DL performed better compared to common wheat lines under water stress conditions. CONCLUSIONS Different responses to water stress within the germplasm and between synthetic and common wheat suggest that selection for adaptive and suitable genotypes is possible for drought tolerance in synthetic wheat germplasm. Genotypes 54, 98, 102, 105, 122, 124, 143, 159, 196, and 198 were identified to be directly used in breeding programs or indirectly by crossing them with other wheat germplasm collections.
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Affiliation(s)
- Niloofar Mokhtari
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 8415683111, Iran
| | - Mohammad Mahdi Majidi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 8415683111, Iran.
| | - Aghafakhr Mirlohi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 8415683111, Iran
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Lhamo D, Li G, Song G, Li X, Sen TZ, Gu YQ, Xu X, Xu SS. Genome-wide association studies on resistance to powdery mildew in cultivated emmer wheat. THE PLANT GENOME 2024:e20493. [PMID: 39073025 DOI: 10.1002/tpg2.20493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/01/2024] [Accepted: 06/30/2024] [Indexed: 07/30/2024]
Abstract
Powdery mildew, caused by the fungal pathogen Blumeria graminis (DC.) E. O. Speer f. sp. tritici Em. Marchal (Bgt), is a constant threat to global wheat (Triticum aestivum L.) production. Although ∼100 powdery mildew (Pm) resistance genes and alleles have been identified in wheat and its relatives, more is needed to minimize Bgt's fast evolving virulence. In tetraploid wheat (Triticum turgidum L.), wild emmer wheat [T. turgidum ssp. dicoccoides (Körn. ex Asch. & Graebn.) Thell.] accessions from Israel have contributed many Pm resistance genes. However, the diverse genetic reservoirs of cultivated emmer wheat [T. turgidum ssp. dicoccum (Schrank ex Schübl.) Thell.] have not been fully exploited. In the present study, we evaluated a diverse panel of 174 cultivated emmer accessions for their reaction to Bgt isolate OKS(14)-B-3-1 and found that 66% of accessions, particularly those of Ethiopian (30.5%) and Indian (6.3%) origins, exhibited high resistance. To determine the genetic basis of Bgt resistance in the panel, genome-wide association studies were performed using 46,383 single nucleotide polymorphisms (SNPs) from genotype-by-sequencing and 4331 SNPs from the 9K SNP Infinium array. Twenty-five significant SNP markers were identified to be associated with Bgt resistance, of which 21 SNPs are likely novel loci, whereas four possibly represent emmer derived Pm4a, Pm5a, PmG16, and Pm64. Most novel loci exhibited minor effects, whereas three novel loci on chromosome arms 2AS, 3BS, and 5AL had major effect on the phenotypic variance. This study demonstrates cultivated emmer as a rich source of powdery mildew resistance, and the resistant accessions and novel loci found herein can be utilized in wheat breeding programs to enhance Bgt resistance in wheat.
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Affiliation(s)
- Dhondup Lhamo
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, California, USA
| | - Genqiao Li
- USDA-ARS Peanut and Small Grains Research Unit, Stillwater, Oklahoma, USA
| | - George Song
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, California, USA
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Taner Z Sen
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, California, USA
| | - Yong-Qiang Gu
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, California, USA
| | - Xiangyang Xu
- USDA-ARS Peanut and Small Grains Research Unit, Stillwater, Oklahoma, USA
| | - Steven S Xu
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, California, USA
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Metakovsky E, Melnik VA, Pascual L, Wrigley CW. How Important Are Genetic Diversity and Cultivar Uniformity in Wheat? The Case of Gliadins. Genes (Basel) 2024; 15:927. [PMID: 39062706 PMCID: PMC11276297 DOI: 10.3390/genes15070927] [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: 04/18/2024] [Revised: 07/11/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Improvements in self-pollinated crops rely on crosses between different genotypes. It has been suggested that the repeated use of "the best" genotypes may lead to the restriction of the genetic diversity of the crop. In wheat, the analysis of gliadin (storage protein) polymorphism has provided evidence that genetic diversity was high and stable throughout the 20th century. Moreover, a worldwide analysis of gliadin polymorphism shows that genetic diversity is structured spatially across countries and their regions. Therefore, the analysis of gliadin genotypes in a given grain sample can provide reliable information about the origin of grains in this sample. An unexpected finding is that many registered common wheat cultivars are genetically non-uniform and composed of authentic biotypes (genotypically related lines originated from the initial cross) in spite of current crop-registration rules that include a strict demand for each new cultivar to be genetically uniform (DUS rules). In summary, the results suggest that each cultivar is the fruit of joint effects of a breeder and of a region's environmental factors. We believe this finding will not be restricted to wheat and suggest there may be a need to re-evaluate relevant rules of cultivar registration for crop species in general.
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Affiliation(s)
- Eugene Metakovsky
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Viktor A. Melnik
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Laura Pascual
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Colin W. Wrigley
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, Brisbane, QLD 4072, Australia
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Singh D, Kankwatsa P, Sandhu KS, Bansal UK, Forrest KL, Park RF. Mapping of Leaf Rust Resistance Loci in Two Kenyan Wheats and Development of Linked Markers. Genes (Basel) 2024; 15:583. [PMID: 38790212 PMCID: PMC11121149 DOI: 10.3390/genes15050583] [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: 04/09/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Leaf rust caused by the pathogen Puccinia triticina (Pt) is a destructive fungal disease of wheat that occurs in almost all wheat-growing areas across the globe. Genetic resistance has proven to be the best solution to mitigate the disease. Wheat breeders are continuously seeking new diversified and durable sources of resistance to use in developing new varieties. We developed recombinant inbred line (RIL) populations from two leaf rust-resistant genotypes (Kenya Kudu and AUS12568) introduced from Kenya to identify and characterize resistance to Pt and to develop markers linked closely to the resistance that was found. Our studies detected four QTL conferring adult plant resistance (APR) to leaf rust. Two of these loci are associated with known genes, Lr46 and Lr68, residing on chromosomes 1B and 7B, respectively. The remaining two, QLrKK_2B and QLrAus12568_5A, contributed by Kenya Kudu and AUS12568 respectively, are putatively new loci for Pt resistance. Both QLrKK_2B and QLrAus12568_5A were found to interact additively with Lr46 in significantly reducing the disease severity at adult plant growth stages in the field. We further developed a suite of six closely linked markers within the QLrAus12568_5A locus and four within the QLrKK_2B region. Among these, markers sunKASP_522 and sunKASP_524, flanking QLrAus12568_5A, and sunKASP_536, distal to QLrKK_2B, were identified as the most closely linked and reliable for marker-assisted selection. The markers were validated on a selection of 64 Australian wheat varieties and found to be polymorphic and robust, allowing for clear allelic discrimination. The identified new loci and linked molecular markers will enable rapid adoption by breeders in developing wheat varieties carrying diversified and durable resistance to leaf rust.
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Affiliation(s)
- Davinder Singh
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW 2567, Australia; (K.S.S.); (U.K.B.); (R.F.P.)
| | - Peace Kankwatsa
- National Agricultural Research Organization, MbaZARDI, Mbarara City P.O. Box 389, Uganda;
| | - Karanjeet S. Sandhu
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW 2567, Australia; (K.S.S.); (U.K.B.); (R.F.P.)
| | - Urmil K. Bansal
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW 2567, Australia; (K.S.S.); (U.K.B.); (R.F.P.)
| | - Kerrie L. Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia;
| | - Robert F. Park
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW 2567, Australia; (K.S.S.); (U.K.B.); (R.F.P.)
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Li Y, Wang M, Hu X, Chen X. Identification of a Locus for High-Temperature Adult-Plant Resistance to Stripe Rust in the Wheat Yr8 Near-Isogenic Line Through Mutagenesis and Molecular Mapping. PLANT DISEASE 2024; 108:1261-1269. [PMID: 37938905 DOI: 10.1094/pdis-10-23-2037-re] [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: 11/10/2023]
Abstract
Aegilops species are wheat relatives that harbor valuable disease resistance genes for wheat breeding. The wheat Yr8 near-isogenic line AvSYr8NIL has long been believed to carry only Yr8 for race-specific all-stage resistance to stripe rust, caused by Puccinia striiformis f. sp. tritici, derived from Aegilops comosa. However, AvSYr8NIL has been found to have high-temperature adult-plant (HTAP) resistance in our field and greenhouse tests. To confirm both HTAP and Yr8 resistance, seeds from AvSYr8NIL were treated with ethyl methanesulfonate to generate mutant lines. The mutant lines with only Yr8 (M641) and only HTAP resistance (M488) were crossed with the susceptible recurrent parent Avocet S (AvS). The F1 and F4 lines of AvS/M641 were phenotyped with Yr8-avirulent races in the seedling stage at the low-temperature (4 to 20°C) profile, while the F1, F2, F4, and F5 lines of AvS/M488 were phenotyped with Yr8-virulent races in the adult-plant stage at the high-temperature (10 to 30°C) profile. Both Yr8 and the HTAP resistance gene (YrM488) were recessive. The F4 populations of AvS/M641 and AvS/M488 were genotyped using polymorphic Kompetitive allele-specific PCR markers converted from single-nucleotide polymorphisms. Yr8 was mapped to a 0.66-cM fragment, and YrM488 was mapped to a 1.22-cM interval on chromosome 2D. The physical distance between the two resistance genes was estimated to be more than 500 Mb, indicating their distinct loci. The mutant lines with separated resistance genes would be useful in enhancing our understanding of different types of resistance and in further studying the interactions between wheat and the stripe rust pathogen.
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Affiliation(s)
- Yuxiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, U.S.A
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, U.S.A
| | - Xiaoping Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, U.S.A
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164, U.S.A
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9
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Hong MJ, Ko CS, Kim DY. Genome-Wide Association Study to Identify Marker-Trait Associations for Seed Color in Colored Wheat ( Triticum aestivum L.). Int J Mol Sci 2024; 25:3600. [PMID: 38612412 PMCID: PMC11011601 DOI: 10.3390/ijms25073600] [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: 02/29/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
This study conducted phenotypic evaluations on a wheat F3 population derived from 155 F2 plants. Traits related to seed color, including chlorophyll a, chlorophyll b, carotenoid, anthocyanin, L*, a*, and b*, were assessed, revealing highly significant correlations among various traits. Genotyping using 81,587 SNP markers resulted in 3969 high-quality markers, revealing a genome-wide distribution with varying densities across chromosomes. A genome-wide association study using fixed and random model circulating probability unification (FarmCPU) and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) identified 11 significant marker-trait associations (MTAs) associated with L*, a*, and b*, and chromosomal distribution patterns revealed predominant locations on chromosomes 2A, 2B, and 4B. A comprehensive annotation uncovered 69 genes within the genomic vicinity of each MTA, providing potential functional insights. Gene expression analysis during seed development identified greater than 2-fold increases or decreases in expression in colored wheat for 16 of 69 genes. Among these, eight genes, including transcription factors and genes related to flavonoid and ubiquitination pathways, exhibited distinct expression patterns during seed development, providing further approaches for exploring seed coloration. This comprehensive exploration expands our understanding of the genetic basis of seed color and paves the way for informed discussions on the molecular intricacies contributing to this phenotypic trait.
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Affiliation(s)
- Min Jeong Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu, Jeongeup 56212, Republic of Korea; (M.J.H.); (C.S.K.)
| | - Chan Seop Ko
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu, Jeongeup 56212, Republic of Korea; (M.J.H.); (C.S.K.)
| | - Dae Yeon Kim
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, 54 Daehak-ro, Yesan-eup 32439, Republic of Korea
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Deng P, Du X, Wang Y, Yang X, Cheng X, Huang C, Li T, Li T, Chen C, Zhao J, Wang C, Liu X, Tian Z, Ji W. GenoBaits®WheatplusEE: a targeted capture sequencing panel for quick and accurate identification of wheat-Thinopyrum derivatives. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:36. [PMID: 38291310 DOI: 10.1007/s00122-023-04538-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024]
Abstract
KEY MESSAGE A total of 90,000 capture probes derived from wheat and Thinopyrum elongatum were integrated into one chip, which served as an economical genotype for explorating Thinopyrumspecies and their derivatives. Thinopyrum species play a crucial role as a source of new genetic variations for enhancing wheat traits, including resistance to both abiotic and biotic factors. Accurate identification of exogenous chromosome(s) or chromosome segments or genes is essential following the introduction of alien genetic material into wheat, but this task remains challenging. This study aimed to develop a high-resolution wheat-Thinopyrum elongatum array, named GenoBaits®WheatplusEE, to trace alien genetic information by genotyping using a target sequencing system. This GenoBaits®WheatplusEE array included 90,000 capture probes derived from two species and integrated into one chip, with 10,000 and 80,000 originating from wheat and Th. elongatum, respectively. The capture probes were strategically positioned in genes and evenly distributed across the genome, facilitating the development of a roadmap for identifying each alien gene. The array was applied to the high-throughput identification of the alien chromosomes or segments in Thinopyrum and distantly related species and their derivatives. Our results demonstrated that the GenoBaits®WheatplusEE array could be used for direct identification of the breakpoint of alien segments, determine copy number of alien chromosomes, and reveal variations in wheat chromosomes by a single round of target sequencing of the sample. Additionally, we could efficiently and cost-effectively genotype, supporting the exploration of subgenome composition, phylogenetic relationships, and polymorphisms in essential genes (e.g., Fhb7 gene) among Thinopyrum species and their derivatives. We hope that GenoBaits®WheatplusEE will become a widely adopted tool for exporting wild germplasm for wheat improvement in the future.
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Affiliation(s)
- Pingchuan Deng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xin Du
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yanzhen Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, Shanxi, China
| | - Xiaoying Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaofang Cheng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chenxi Huang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Tingting Li
- College of Bioengineering, Yangling Vocational Technical College, Yangling, 712100, Shaanxi, China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jixin Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xinlun Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zengrong Tian
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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11
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Montesinos-López A, Gutiérrez-Pulido H, Ramos-Pulido S, Montesinos-López JC, Montesinos-López OA, Crossa J. Bayesian discrete lognormal regression model for genomic prediction. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:21. [PMID: 38221602 DOI: 10.1007/s00122-023-04526-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 12/11/2023] [Indexed: 01/16/2024]
Abstract
KEY MESSAGE Genomic prediction models for quantitative traits assume continuous and normally distributed phenotypes. In this research, we proposed a novel Bayesian discrete lognormal regression model. Genomic selection is a powerful tool in modern breeding programs that uses genomic information to predict the performance of individuals and select those with desirable traits. It has revolutionized animal and plant breeding, as it allows breeders to identify the best candidates without labor-intensive and time-consuming phenotypic evaluations. While several statistical models have been developed, most of them have been for quantitative continuous traits and only a few for count responses. In this paper, we propose a discrete lognormal regression model in the Bayesian context, that with a Gibbs sampler to explore the corresponding posterior distribution and make the predictions. Two datasets of resistance disease is used in the wheat crop and are then evaluated against the traditional Gaussian model and a lognormal model. The results indicate the proposed model is a competitive and natural model for predicting count genomic traits.
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Affiliation(s)
- Abelardo Montesinos-López
- Departamento de Matemáticas, Centro Universitario de Ciencias Exactas e Ingenierías (CUCEI), Universidad de Guadalajara, C. P. 44430, Guadalajara, Jalisco, México
| | - Humberto Gutiérrez-Pulido
- Departamento de Matemáticas, Centro Universitario de Ciencias Exactas e Ingenierías (CUCEI), Universidad de Guadalajara, C. P. 44430, Guadalajara, Jalisco, México
| | - Sofía Ramos-Pulido
- Departamento de Matemáticas, Centro Universitario de Ciencias Exactas e Ingenierías (CUCEI), Universidad de Guadalajara, C. P. 44430, Guadalajara, Jalisco, México
| | | | | | - José Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, C. P. 56237, Texcoco, Edo. de México, México.
- Colegio de Postgraduados, C. P. 56230, Montecillos, Edo. de México, México.
- Centre for Crop & Food Innovation, Food Futures Institute, Murdoch University, Murdoch, 6150, Australia.
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12
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Yang J, Wang J. Genome-Wide Association Study of Preharvest Sprouting in Wheat. Methods Mol Biol 2024; 2830:121-129. [PMID: 38977573 DOI: 10.1007/978-1-0716-3965-8_11] [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] [Indexed: 07/10/2024]
Abstract
Genome-wide association study (GWAS) is widely used to characterize genes or quantitative trait loci (QTLs) associated with preharvest sprouting and seed dormancy. GWAS can identify both previously discovered and novel QTLs across diverse genetic panels. The high-throughput SNP arrays or next-generation sequencing technologies have facilitated the identification of numerous genetic markers, thereby significantly enhancing the resolution of GWAS. Although various methods have been developed, the fundamental principles underlying these techniques remain constant. Here, we provide a basic technological flow to perform seed dormancy assay, followed by GWAS using population structure control, and compared it with previous identified QTLs and genes.
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Affiliation(s)
- Jian Yang
- Institute of Wheat, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
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Niu J, Ma S, Zheng S, Zhang C, Lu Y, Si Y, Tian S, Shi X, Liu X, Naeem MK, Sun H, Hu Y, Wu H, Cui Y, Chen C, Long W, Zhang Y, Gu M, Cui M, Lu Q, Zhou W, Peng J, Akhunov E, He F, Zhao S, Ling HQ. Whole-genome sequencing of diverse wheat accessions uncovers genetic changes during modern breeding in China and the United States. THE PLANT CELL 2023; 35:4199-4216. [PMID: 37647532 PMCID: PMC10689146 DOI: 10.1093/plcell/koad229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/25/2023] [Accepted: 08/08/2023] [Indexed: 09/01/2023]
Abstract
Breeding has dramatically changed the plant architecture of wheat (Triticum aestivum), resulting in the development of high-yielding varieties adapted to modern farming systems. However, how wheat breeding shaped the genomic architecture of this crop remains poorly understood. Here, we performed a comprehensive comparative analysis of a whole-genome resequencing panel of 355 common wheat accessions (representing diverse landraces and modern cultivars from China and the United States) at the phenotypic and genomic levels. The genetic diversity of modern wheat cultivars was clearly reduced compared to landraces. Consistent with these genetic changes, most phenotypes of cultivars from China and the United States were significantly altered. Of the 21 agronomic traits investigated, 8 showed convergent changes between the 2 countries. Moreover, of the 207 loci associated with these 21 traits, more than half overlapped with genomic regions that showed evidence of selection. The distribution of selected loci between the Chinese and American cultivars suggests that breeding for increased productivity in these 2 regions was accomplished by pyramiding both shared and region-specific variants. This work provides a framework to understand the genetic architecture of the adaptation of wheat to diverse agricultural production environments, as well as guidelines for optimizing breeding strategies to design better wheat varieties.
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Affiliation(s)
- Jianqing Niu
- Hainan Yazhou Bay Seed Laboratory, Hainan, Sanya 572024, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengwei Ma
- Hainan Yazhou Bay Seed Laboratory, Hainan, Sanya 572024, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yaru Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaoqi Si
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuiquan Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoli Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaolin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Muhammad Kashif Naeem
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yafei Hu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Huilan Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Cui
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunlin Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenbo Long
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yue Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mengjun Gu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Man Cui
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiao Lu
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjuan Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Junhua Peng
- Huazhi Bio-tech Company Ltd., Changsha, Hunan 410125, China
| | - Eduard Akhunov
- Wheat Genetic Resources Center, Kansas State University, Manhattan, KS 66506, USA
| | - Fei He
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shancen Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Hong-Qing Ling
- Hainan Yazhou Bay Seed Laboratory, Hainan, Sanya 572024, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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14
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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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15
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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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16
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Ritzinger M, Sallam AH, Smith KP, Case AJ, Wodarek J, Curland RD, Dill-Macky R, Steffenson BJ. Genome-Wide Association Mapping of Bacterial Leaf Streak Resistance in Two Elite Barley Breeding Panels. PHYTOPATHOLOGY 2023; 113:2119-2126. [PMID: 37069124 DOI: 10.1094/phyto-10-22-0402-sa] [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: 06/19/2023]
Abstract
Bacterial leaf streak (BLS), caused chiefly by the pathogen Xanthomonas translucens pv. translucens, is becoming an increasingly important foliar disease of barley in the Upper Midwest. The deployment of resistant cultivars is the most economical and practical method of control. To identify sources of BLS resistance, we evaluated two panels of breeding lines from the University of Minnesota (UMN) and Anheuser-Busch InBev (ABI) barley improvement programs for reaction to strain CIX95 in the field at St. Paul and Crookston, MN, in 2020 and 2021. The percentage of resistant lines in the UMN and ABI panels with mid-season maturity was 1.8% (6 of 333 lines) and 5.2% (13 of 251 lines), respectively. Both panels were genotyped with the barley 50K iSelect SNP array, and then a genome-wide association study was performed. A single, highly significant association was identified for BLS resistance on chromosome 6H in the UMN panel. This association was also identified in the ABI panel. Seven other significant associations were detected in the ABI panel: two each on chromosomes 1H, 2H, and 3H and one on chromosome 5H. Of the eight associations identified in the panels, five were novel. The discovery of resistance in elite breeding lines will hasten the time needed to develop and release a BLS-resistant cultivar.
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Affiliation(s)
- Mitch Ritzinger
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Ahmad H Sallam
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Kevin P Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
| | | | - Joseph Wodarek
- University of Minnesota, Northwest Research and Outreach Center, Crookston, MN 56716
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
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Feng J, Yao F, Wang M, See DR, Chen X. Molecular Mapping of Yr85 and Comparison with Other Genes for Resistance to Stripe Rust on Wheat Chromosome 1B. PLANT DISEASE 2023; 107:3585-3591. [PMID: 37221244 DOI: 10.1094/pdis-11-22-2600-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most serious plant diseases worldwide. Resistant cultivars are the most effective way to control the disease. YrTr1 is an important stripe rust resistance gene that has been used in wheat breeding programs and is represented in the host differential set to identify P. striiformis f. sp. tritici races in the United States. To map YrTr1, AvSYrTr1NIL was backcrossed to its recurrent parent Avocet S (AvS). Seedlings of BC7F2, BC7F3, and BC8F1 populations were tested with YrTr1-avirulent races under controlled conditions, and BC7F2 plants were genotyped using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. YrTr1 was mapped to the short arm of chromosome 1B using four SSR and seven SNP markers. The genetic distances of YrTr1 from the nearest flanking markers IWA2583 and IWA7480 were 1.8 and 1.3 centimorgans (cM), respectively. DNA amplification of a set of 21 Chinese Spring (CS) nulli-tetrasomic lines and seven CS 1B deletion lines with three SSR markers confirmed the chromosome arm location and further placed the gene in chromosomal bin region 1BS18 (0.5). The gene was determined to be about 7.4 cM proximal to Yr10. Based on multirace response array and chromosomal location, YrTr1 was determined to be different from other permanently named stripe rust resistance genes in chromosome arm 1BS and was named Yr85.
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Affiliation(s)
- Junyan Feng
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610061, China
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Fangjie Yao
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610061, China
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Deven R See
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
- Wheat Health, Genetics, and Quality Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Pullman, WA 99164-6430, U.S.A
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
- Wheat Health, Genetics, and Quality Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Pullman, WA 99164-6430, U.S.A
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18
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Xu X, Sun D, Ni Z, Zou X, Xu X, Sun M, Cao Q, Tong J, Ding F, Zhang Y, Wang F, Dong Y, Zhang L, Wang J, Xia X, He Z, Hao Y. Molecular identification and validation of four stable QTL for adult-plant resistance to powdery mildew in Chinese wheat cultivar Bainong 64. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:232. [PMID: 37875655 DOI: 10.1007/s00122-023-04481-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023]
Abstract
KEY MESSAGE Four stable QTL for adult-plant resistance (APR) to powdery mildew were identified on chromosome arms 1DL, 2BS, 2DL, and 6BL in the widely grown Chinese wheat cultivar Bainong 64. These QTL had no effect on response to stripe rust or leaf rust. Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a devastating fungal disease. Seedlings of Chinese wheat Bainong 64 are susceptible to Bgt, but adult plants have maintained resistance since it was released in 1996. A population of 171 recombinant inbred lines (RILs) developed from cross Jingshuang 16/Bainong 64 (JS16/BN64) was used to dissect genetic components of powdery mildew resistance. A genetic map comprising 5383 polymorphic markers was constructed using the 15 K SNP chip and kompetitive allele-specific PCR (KASP) markers. Composite interval mapping identified four stable QTL with favorable alleles all from BN64 on chromosome arms 1DL, 2BS, 2DL, and 6BL in at least four environments. They accounted for 8.3%, 13.8%, 14.4%, and 9.0% of the total phenotypic variation explained (PVE) in maximum, respectively. QPmjbr.caas-1DL, situated about 22 Mb from centromere, is probably a new QTL. QPmjbr.caas-2DL located near the end of arm 2DL and explained the largest PVE. Using genetic maps populated with KASP markers, QPmjbr.caas-2BS and QPmjbr.caas-6BL were fine mapped to a 1.8 cM genetic intervals spanning 13.6 Mb (76.0-89.6 Mb) and 1.7 cM and 4.9 Mb (659.9-664.8 Mb), respectively. The four QTL independent of stripe rust and leaf rust resistance were validated for powdery mildew resistance in another RIL population related to BN64 and a cultivar panel using representative KASP markers. Since BN64 has been a leading cultivar and an important breeding parent in China, the QTL and markers reported in this study will be useful for marker-assisted selection of APR.
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Affiliation(s)
- Xiaowan Xu
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Daojie Sun
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Zhongqiu Ni
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xinyu Zou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xiaoting Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Mengjing Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Qiang Cao
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Fugong Ding
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yelun Zhang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/The Key Laboratory of Crop Genetics and Breeding of Hebei Province, Shijiazhuang, 050035, Hebei, China
| | - Fengju Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yachao Dong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Luyan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jiankang Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
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Tyrka M, Krajewski P, Bednarek PT, Rączka K, Drzazga T, Matysik P, Martofel R, Woźna-Pawlak U, Jasińska D, Niewińska M, Ługowska B, Ratajczak D, Sikora T, Witkowski E, Dorczyk A, Tyrka D. Genome-wide association mapping in elite winter wheat breeding for yield improvement. J Appl Genet 2023; 64:377-391. [PMID: 37120451 PMCID: PMC10457411 DOI: 10.1007/s13353-023-00758-8] [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: 12/11/2022] [Revised: 03/19/2023] [Accepted: 04/03/2023] [Indexed: 05/01/2023]
Abstract
Increased grain yield (GY) is the primary breeding target of wheat breeders. We performed the genome-wide association study (GWAS) on 168 elite winter wheat lines from an ongoing breeding program to identify the main determinants of grain yield. Sequencing of Diversity Array Technology fragments (DArTseq) resulted in 19,350 single-nucleotide polymorphism (SNP) and presence-absence variation (PAV) markers. We identified 15 main genomic regions located in ten wheat chromosomes (1B, 2B, 2D, 3A, 3D, 5A, 5B, 6A, 6B, and 7B) that explained from 7.9 to 20.3% of the variation in grain yield and 13.3% of the yield stability. Loci identified in the reduced genepool are important for wheat improvement using marker-assisted selection. We found marker-trait associations between three genes involved in starch biosynthesis and grain yield. Two starch synthase genes (TraesCS2B03G1238800 and TraesCS2D03G1048800) and a sucrose synthase gene (TraesCS3D03G0024300) were found in regions of QGy.rut-2B.2, QGy.rut-2D.1, and QGy.rut-3D, respectively. These loci and other significantly associated SNP markers found in this study can be used for pyramiding favorable alleles in high-yielding varieties or to improve the accuracy of prediction in genomic selection.
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Affiliation(s)
- Mirosław Tyrka
- Department of Biotechnology and Bioinformatics, Rzeszow University of Technology, Powstańców Warszawy 6, 35-959, Rzeszów, Poland.
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Piotr Tomasz Bednarek
- Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, 05-870, Błonie, Poland
| | - Kinga Rączka
- Department of Biotechnology and Bioinformatics, Rzeszow University of Technology, Powstańców Warszawy 6, 35-959, Rzeszów, Poland
| | - Tadeusz Drzazga
- Małopolska Plant Breeding Ltd, Sportowa 21, 55-040, Kobierzyce, Poland
| | - Przemysław Matysik
- Plant Breeding Strzelce Group IHAR Ltd, Główna 20, 99-307, Strzelce, Poland
| | - Róża Martofel
- Poznań Plant Breeding Ltd, Kasztanowa 5, 63-004, Tulce, Poland
| | | | - Dorota Jasińska
- Poznań Plant Breeding Ltd, Kasztanowa 5, 63-004, Tulce, Poland
| | | | | | | | - Teresa Sikora
- DANKO Plant Breeders Ltd, Ks. Strzybnego 23, 47-411, Rudnik, Poland
| | - Edward Witkowski
- Plant Breeding Smolice Ltd, Smolice 146, 63-740, Kobylin, Poland
| | - Ada Dorczyk
- Plant Breeding Smolice Ltd, Smolice 146, 63-740, Kobylin, Poland
| | - Dorota Tyrka
- Department of Biotechnology and Bioinformatics, Rzeszow University of Technology, Powstańców Warszawy 6, 35-959, Rzeszów, Poland
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20
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Yan Q, Jia G, Tan W, Tian R, Zheng X, Feng J, Luo X, Si B, Li X, Huang K, Wang M, Chen X, Ren Y, Yang S, Zhou X. Genome-wide QTL mapping for stripe rust resistance in spring wheat line PI 660122 using the Wheat 15K SNP array. FRONTIERS IN PLANT SCIENCE 2023; 14:1232897. [PMID: 37701804 PMCID: PMC10493333 DOI: 10.3389/fpls.2023.1232897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/31/2023] [Indexed: 09/14/2023]
Abstract
Introduction Stripe rust is a global disease of wheat. Identification of new resistance genes is key to developing and growing resistant varieties for control of the disease. Wheat line PI 660122 has exhibited a high level of stripe rust resistance for over a decade. However, the genetics of stripe rust resistance in this line has not been studied. A set of 239 recombinant inbred lines (RILs) was developed from a cross between PI 660122 and an elite Chinese cultivar Zhengmai 9023. Methods The RIL population was phenotyped for stripe rust response in three field environments and genotyped with the Wheat 15K single-nucleotide polymorphism (SNP) array. Results A total of nine quantitative trait loci (QTLs) for stripe rust resistance were mapped to chromosomes 1B (one QTL), 2B (one QTL), 4B (two QTLs), 4D (two QTLs), 6A (one QTL), 6D (one QTL), and 7D (one QTL), of which seven QTLs were stable and designated as QYrPI660122.swust-4BS, QYrPI660122.swust-4BL, QYrPI660122.swust-4DS, QYrPI660122.swust-4DL, QYrZM9023.swust-6AS, QYrZM9023.swust-6DS, and QYrPI660122.swust-7DS. QYrPI660122.swust-4DS was a major all-stage resistance QTL explaining the highest percentage (10.67%-20.97%) of the total phenotypic variation and was mapped to a 12.15-cM interval flanked by SNP markers AX-110046962 and AX-111093894 on chromosome 4DS. Discussion The QTL and their linked SNP markers in this study can be used in wheat breeding to improve resistance to stripe rust. In addition, 26 lines were selected based on stripe rust resistance and agronomic traits in the field for further selection and release of new cultivars.
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Affiliation(s)
- Qiong Yan
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Guoyun Jia
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Wenjing Tan
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Ran Tian
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Xiaochen Zheng
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Junming Feng
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Xiaoqin Luo
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Binfan Si
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Xin Li
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Kebing Huang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - 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, US Department of Agriculture-Agricultural Research Service (USDA-ARS), Pullman, WA, United States
| | - Yong Ren
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang Institute of Agricultural Science, Mianyang, Sichuan, China
| | - Suizhuang Yang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Xinli Zhou
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
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21
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Khan N, Zhang J, Islam S, Appels R, Dell B. Wheat Water-Soluble Carbohydrate Remobilisation under Water Deficit by 1-FEH w3. Curr Issues Mol Biol 2023; 45:6634-6650. [PMID: 37623238 PMCID: PMC10453044 DOI: 10.3390/cimb45080419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
Fructan 1-exohydrolase (1-FEH) is one of the major enzymes in water-soluble carbohydrate (WSC) remobilisation for grains in wheat. We investigated the functional role of 1-FEH w1, w2, and w3 isoforms in WSC remobilisation under post-anthesis water deficit using mutation lines derived from the Australian wheat variety Chara. F1 seeds, developed by backcrossing the 1-FEH w1, w2, and w3 mutation lines with Chara, were genotyped using the Infinium 90K SNP iSelect platform to characterise the mutated region. Putative deletions were identified in FEH mutation lines encompassing the FEH genomic regions. Mapping analysis demonstrated that mutations affected significantly longer regions than the target FEH gene regions. Functional roles of the non-target genes were carried out utilising bioinformatics and confirmed that the non-target genes were unlikely to confound the effects considered to be due to the influence of 1-FEH gene functions. Glasshouse experiments revealed that the 1-FEH w3 mutation line had a slower degradation and remobilisation of fructans than the 1-FEH w2 and w1 mutation lines and Chara, which reduced grain filling and grain yield. Thus, 1-FEH w3 plays a vital role in reducing yield loss under drought. This insight into the distinct role of the 1-FEH isoforms provides new gene targets for water-deficit-tolerant wheat breeding.
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Affiliation(s)
- Nusrat Khan
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6163, Australia; (N.K.); (J.Z.); (S.I.)
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Jingjuan Zhang
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6163, Australia; (N.K.); (J.Z.); (S.I.)
| | - Shahidul Islam
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6163, Australia; (N.K.); (J.Z.); (S.I.)
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Rudi Appels
- Faculty of Science, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Bernard Dell
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6163, Australia; (N.K.); (J.Z.); (S.I.)
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22
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Mulugeta B, Ortiz R, Geleta M, Hailesilassie T, Hammenhag C, Hailu F, Tesfaye K. Harnessing genome-wide genetic diversity, population structure and linkage disequilibrium in Ethiopian durum wheat gene pool. FRONTIERS IN PLANT SCIENCE 2023; 14:1192356. [PMID: 37546270 PMCID: PMC10400094 DOI: 10.3389/fpls.2023.1192356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 08/08/2023]
Abstract
Yanyang Liu, Henan Academy of Agricultural Sciences (HNAAS), China; Landraces are an important genetic source for transferring valuable novel genes and alleles required to enhance genetic variation. Therefore, information on the gene pool's genetic diversity and population structure is essential for the conservation and sustainable use of durum wheat genetic resources. Hence, the aim of this study was to assess genetic diversity, population structure, and linkage disequilibrium, as well as to identify regions with selection signature. Five hundred (500) individuals representing 46 landraces, along with 28 cultivars were evaluated using the Illumina Infinium 25K wheat SNP array, resulting in 8,178 SNPs for further analysis. Gene diversity (GD) and the polymorphic information content (PIC) ranged from 0.13-0.50 and 0.12-0.38, with mean GD and PIC values of 0.34 and 0.27, respectively. Linkage disequilibrium (LD) revealed 353,600 pairs of significant SNPs at a cut-off (r2 > 0.20, P < 0.01), with an average r2 of 0.21 for marker pairs. The nucleotide diversity (π) and Tajima's D (TD) per chromosome for the populations ranged from 0.29-0.36 and 3.46-5.06, respectively, with genome level, mean π values of 0.33 and TD values of 4.43. Genomic scan using the Fst outlier test revealed 85 loci under selection signatures, with 65 loci under balancing selection and 17 under directional selection. Putative candidate genes co-localized with regions exhibiting strong selection signatures were associated with grain yield, plant height, host plant resistance to pathogens, heading date, grain quality, and phenolic content. The Bayesian Model (STRUCTURE) and distance-based (principal coordinate analysis, PCoA, and unweighted pair group method with arithmetic mean, UPGMA) methods grouped the genotypes into five subpopulations, where landraces from geographically non-adjoining environments were clustered in the same cluster. This research provides further insights into population structure and genetic relationships in a diverse set of durum wheat germplasm, which could be further used in wheat breeding programs to address production challenges sustainably.
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Affiliation(s)
- Behailu Mulugeta
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
- Sinana Agricultural Research Center, Oromia Agricultural Research Institute, Bale-Robe, Ethiopia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Faris Hailu
- Bio and Emerging Technology Institute, Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Biology and Biotechnology, Wollo University, Dessie, Ethiopia
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23
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Emebiri L, Hildebrand S. Natural variation and genetic loci underlying resistance to grain shattering in standing crop of modern wheat. Mol Genet Genomics 2023:10.1007/s00438-023-02051-z. [PMID: 37410105 PMCID: PMC10363068 DOI: 10.1007/s00438-023-02051-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 06/25/2023] [Indexed: 07/07/2023]
Abstract
Modern wheat (Triticum aestivum L.) cultivars have a free-threshing habit, which allows for easy manual or mechanical threshing. However, when harvesting is delayed or extreme weather events occur at harvest time, grain shattering can cause severe loss of harvestable yield. In the past, grain size was considered a predisposing factor as large, plump kernels can lead to buckling and breaking of the outer glume, but the correlation between glume strength and shattering is not strong in modern wheat, and it is hypothesised that there may be other genetic mechanisms. Data from two bi-parent populations and a wheat diversity panel were analyzed to explore the underlying genetic basis for grain shattering observed in multiple field experiments through quantitative trait loci (QTL) analysis. Grain shattering had a significant and negative association with grain yield, irrespective of populations and environments. The correlation with plant height was positive in all populations, but correlations with phenology were population specific, being negative in the diversity panel and the Drysdale × Waagan population, and positive in the Crusader × RT812 population. In the wheat diversity panel, allelic variations at well-known major genes (Rht-B1, Rht-D1 and Ppd-D1) showed minimal association with grain shattering. Instead, the genome-wide analysis identified a single locus on chromosome 2DS, which explained 50% of the phenotypic variation, and mapping to ~ 10 Mb from Tenacious glume (Tg) gene. In the Drysdale × Waagan cross, however, the reduced height (Rht) genes showed major effects on grain shattering. At the Rht-B1 locus, the Rht-B1b allele was associated with 10.4 cm shorter plant height, and 18% decreased grain shattering, whereas Rht-D1b reduced plant height by 11.4 cm and reduced grain shattering by 20%. Ten QTL were detected in the Crusader × RT812, including a major locus detected on the long arm of chromosome 5A. All the QTL identified in this population were non-pleiotropic, as they were still significant even after removing the influence of plant height. In conclusion, these results indicated a complex genetic system for grain shattering in modern wheat, which varied with genetic background, involved pleiotropic as well as independent gene actions, and which might be different from shattering in wild wheat species caused by major domestication genes. The influence of Rht genes was confirmed, and this provides valuable information in breeding crops of the future. Further, the SNP marker close to Tg on chromosome 2DS should be considered for utility in marker-assisted selection.
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Affiliation(s)
- Livinus Emebiri
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia.
| | - Shane Hildebrand
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
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24
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Kang Y, Choi C, Kim JY, Min KD, Kim C. Optimizing genomic selection of agricultural traits using K-wheat core collection. FRONTIERS IN PLANT SCIENCE 2023; 14:1112297. [PMID: 37389296 PMCID: PMC10303932 DOI: 10.3389/fpls.2023.1112297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/02/2023] [Indexed: 07/01/2023]
Abstract
The agricultural traits that constitute basic plant breeding information are usually quantitative or complex in nature. This quantitative and complex combination of traits complicates the process of selection in breeding. This study examined the potential of genome-wide association studies (GWAS) and genomewide selection (GS) for breeding ten agricultural traits by using genome-wide SNPs. As a first step, a trait-associated candidate marker was identified by GWAS using a genetically diverse 567 Korean (K)-wheat core collection. The accessions were genotyped using an Axiom® 35K wheat DNA chip, and ten agricultural traits were determined (awn color, awn length, culm color, culm length, ear color, ear length, days to heading, days to maturity, leaf length, and leaf width). It is essential to sustain global wheat production by utilizing accessions in wheat breeding. Among the traits associated with awn color and ear color that showed a high positive correlation, a SNP located on chr1B was significantly associated with both traits. Next, GS evaluated the prediction accuracy using six predictive models (G-BLUP, LASSO, BayseA, reproducing kernel Hilbert space, support vector machine (SVM), and random forest) and various training populations (TPs). With the exception of the SVM, all statistical models demonstrated a prediction accuracy of 0.4 or better. For the optimization of the TP, the number of TPs was randomly selected (10%, 30%, 50% and 70%) or divided into three subgroups (CC-sub 1, CC-sub 2 and CC-sub 3) based on the subpopulation structure. Based on subgroup-based TPs, better prediction accuracy was found for awn color, culm color, culm length, ear color, ear length, and leaf width. A variety of Korean wheat cultivars were used for validation to evaluate the prediction ability of populations. Seven out of ten cultivars showed phenotype-consistent results based on genomics-evaluated breeding values (GEBVs) calculated by the reproducing kernel Hilbert space (RKHS) predictive model. Our research provides a basis for improving complex traits in wheat breeding programs through genomics assisted breeding. The results of our research can be used as a basis for improving wheat breeding programs by using genomics-assisted breeding.
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Affiliation(s)
- Yuna Kang
- Department of Crop Science, Chungnam National University, Daejeon, Republic of Korea
| | - Changhyun Choi
- Wheat Research Team, National Institution Crop Sciences, Wanju-gun, Republic of Korea
| | - Jae Yoon Kim
- Department of Plant Resources, Kongju National University, Yesan, Republic of Korea
| | - Kyeong Do Min
- Department of Plant Resources, Kongju National University, Yesan, Republic of Korea
| | - Changsoo Kim
- Department of Crop Science, Chungnam National University, Daejeon, Republic of Korea
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon, Republic of Korea
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25
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Pradhan AK, Budhlakoti N, Chandra Mishra D, Prasad P, Bhardwaj SC, Sareen S, Sivasamy M, Jayaprakash P, Geetha M, Nisha R, Shajitha P, Peter J, Kaur A, Kaur S, Vikas VK, Singh K, Kumar S. Identification of Novel QTLs/Defense Genes in Spring Wheat Germplasm Panel for Seedling and Adult Plant Resistance to Stem Rust and Their Validation Through KASP Marker Assays. PLANT DISEASE 2023:PDIS09222242RE. [PMID: 37311158 DOI: 10.1094/pdis-09-22-2242-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Stem rust is one of the major diseases threatening wheat production globally. To identify novel resistance quantitative trait loci (QTLs), we performed 35K Axiom Array SNP genotyping assays on an association mapping panel of 400 germplasm accessions, including Indian landraces, in conjunction with phenotyping for stem rust at seedling and adult plant stages. Association analyses using three genome wide association study (GWAS) models (CMLM, MLMM, and FarmCPU) revealed 20 reliable QTLs for seedling and adult plant resistance. Among these 20 QTLs, five QTLs were found consistent with three models, i.e., four QTLs on chromosome 2AL, 2BL, 2DL, and 3BL for seedling resistance and one QTL on chromosome 7DS for adult plant resistance. Further, we identified a total of 21 potential candidate genes underlying QTLs using gene ontology analysis, including a leucine rich repeat receptor (LRR) and P-loop nucleoside triphosphate hydrolase, which have a role in pathogen recognition and disease resistance. Furthermore, four QTLs (Qsr.nbpgr-3B_11, QSr.nbpgr-6AS_11, QSr.nbpgr-2AL_117-6, and QSr.nbpgr-7BS_APR) were validated through KASP located on chromosomes 3B, 6A, 2A, and 7B. Out of these QTLs, QSr.nbpgr-7BS_APR was identified as a novel QTL for stem rust resistance which has been found effective in both seedling as well as the adult plant stages. Identified novel genomic regions and validated QTLs have the potential to be deployed in wheat improvement programs to develop disease resistant varieties for stem rust and can diversify the genetic basis of resistance.
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Affiliation(s)
| | - Neeraj Budhlakoti
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | | | - Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal Pradesh 171002, India
| | - S C Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal Pradesh 171002, India
| | - Sindhu Sareen
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | - M Sivasamy
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - P Jayaprakash
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - M Geetha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - R Nisha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - P Shajitha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - John Peter
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - Amandeep Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, India
| | - V K Vikas
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - Kuldeep Singh
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana 502324, India
| | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
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Amalova A, Yermekbayev K, Griffiths S, Winfield MO, Morgounov A, Abugalieva S, Turuspekov Y. Population Structure of Modern Winter Wheat Accessions from Central Asia. PLANTS (BASEL, SWITZERLAND) 2023; 12:2233. [PMID: 37375859 DOI: 10.3390/plants12122233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
Despite the importance of winter wheat in Central Asian countries, there are limited reports describing their diversity within this region. In this study, the population structures of 115 modern winter wheat cultivars from four Central Asian countries were compared to germplasms from six other geographic origins using 10,746 polymorphic single-nucleotide polymorphism (SNP) markers. After applying the STRUCTURE package, we found that in terms of the most optimal K steps, samples from Kazakhstan and Kyrgyzstan were grouped together with samples from Russia, while samples from Tajikistan and Uzbekistan were grouped with samples from Afghanistan. The mean value of Nei's genetic diversity index for the germplasm from four groups from Central Asia was 0.261, which is comparable to that of the six other groups studied: Europe, Australia, the USA, Afghanistan, Turkey, and Russia. The Principal Coordinate Analysis (PCoA) showed that samples from Kyrgyzstan, Tajikistan, and Uzbekistan were close to samples from Turkey, while Kazakh accessions were located near samples from Russia. The evaluation of 10,746 SNPs in Central Asian wheat suggested that 1006 markers had opposing allele frequencies. Further assessment of the physical positions of these 1006 SNPs in the Wheat Ensembl database indicated that most of these markers are constituents of genes associated with plant stress tolerance and adaptability. Therefore, the SNP markers identified can be effectively used in regional winter wheat breeding projects for facilitating plant adaptation and stress resistance.
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Affiliation(s)
- Akerke Amalova
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
| | - Kanat Yermekbayev
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
- Crop Genetics Department, John Innes Centre, Norwich NR4 7UH, UK
| | - Simon Griffiths
- Crop Genetics Department, John Innes Centre, Norwich NR4 7UH, UK
| | | | - Alexey Morgounov
- Science Department, S. Seifullin Kazakh Agrotechnical University, Astana 010011, Kazakhstan
| | - Saule Abugalieva
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Yerlan Turuspekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
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Patwa N, Penning BW. Genetics of a diverse soft winter wheat population for pre-harvest sprouting, agronomic, and flour quality traits. FRONTIERS IN PLANT SCIENCE 2023; 14:1137808. [PMID: 37346135 PMCID: PMC10280069 DOI: 10.3389/fpls.2023.1137808] [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: 01/04/2023] [Accepted: 05/02/2023] [Indexed: 06/23/2023]
Abstract
Soft winter wheat has been adapted to the north-central, north-western, and south-central United States over hundreds of years for optimal yield, height, heading date, and pathogen and pest resistance. Environmental factors like weather affect abiotic traits such as pre-harvest sprouting resistance. However, pre-harvest sprouting has rarely been a target for breeding. Owing to changing weather patterns from climate change, pre-harvest sprouting resistance is needed to prevent significant crop losses not only in the United States, but worldwide. Twenty-two traits including age of breeding line as well as agronomic, flour quality, and pre-harvest sprouting traits were studied in a population of 188 lines representing genetic diversity over 200 years of soft winter wheat breeding. Some traits were correlated with one another by principal components analysis and Pearson's correlations. A genome-wide association study using 1,978 markers uncovered a total of 102 regions encompassing 226 quantitative trait nucleotides. Twenty-six regions overlapped multiple traits with common significant markers. Many of these traits were also found to be correlated by Pearson's correlation and principal components analyses. Most pre-harvest sprouting regions were not co-located with agronomic traits and thus useful for crop improvement against climate change without affecting crop performance. Six different genome-wide association statistical models (GLM, MLM, MLMM, FarmCPU, BLINK, and SUPER) were utilized to search for reasonable models to analyze soft winter wheat populations with increased markers and/or breeding lines going forward. Some flour quality and agronomic traits seem to have been selected over time, but not pre-harvest sprouting. It appears possible to select for pre-harvest sprouting resistance without impacting flour quality or the agronomic value of soft winter wheat.
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Arca M, Gouesnard B, Mary-Huard T, Le Paslier MC, Bauland C, Combes V, Madur D, Charcosset A, Nicolas SD. Genotyping of DNA pools identifies untapped landraces and genomic regions to develop next-generation varieties. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1123-1139. [PMID: 36740649 DOI: 10.1111/pbi.14022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 01/18/2023] [Indexed: 05/27/2023]
Abstract
Landraces, that is, traditional varieties, have a large diversity that is underexploited in modern breeding. A novel DNA pooling strategy was implemented to identify promising landraces and genomic regions to enlarge the genetic diversity of modern varieties. As proof of concept, DNA pools from 156 American and European maize landraces representing 2340 individuals were genotyped with an SNP array to assess their genome-wide diversity. They were compared to elite cultivars produced across the 20th century, represented by 327 inbred lines. Detection of selective footprints between landraces of different geographic origin identified genes involved in environmental adaptation (flowering times, growth) and tolerance to abiotic and biotic stress (drought, cold, salinity). Promising landraces were identified by developing two novel indicators that estimate their contribution to the genome of inbred lines: (i) a modified Roger's distance standardized by gene diversity and (ii) the assignation of lines to landraces using supervised analysis. It showed that most landraces do not have closely related lines and that only 10 landraces, including famous landraces as Reid's Yellow Dent, Lancaster Surecrop and Lacaune, cumulated half of the total contribution to inbred lines. Comparison of ancestral lines directly derived from landraces with lines from more advanced breeding cycles showed a decrease in the number of landraces with a large contribution. New inbred lines derived from landraces with limited contributions enriched more the haplotype diversity of reference inbred lines than those with a high contribution. Our approach opens an avenue for the identification of promising landraces for pre-breeding.
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Affiliation(s)
- Mariangela Arca
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Brigitte Gouesnard
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Tristan Mary-Huard
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Cyril Bauland
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Valérie Combes
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Delphine Madur
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alain Charcosset
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Stéphane D Nicolas
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
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29
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Sertse D, You FM, Klymiuk V, Haile JK, N'Diaye A, Pozniak CJ, Cloutier S, Kagale S. Historical Selection, Adaptation Signatures, and Ambiguity of Introgressions in Wheat. Int J Mol Sci 2023; 24:ijms24098390. [PMID: 37176097 PMCID: PMC10179502 DOI: 10.3390/ijms24098390] [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: 04/08/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Wheat was one of the crops domesticated in the Fertile Crescent region approximately 10,000 years ago. Despite undergoing recent polyploidization, hull-to-free-thresh transition events, and domestication bottlenecks, wheat is now grown in over 130 countries and accounts for a quarter of the world's cereal production. The main reason for its widespread success is its broad genetic diversity that allows it to thrive in different environments. To trace historical selection and hybridization signatures, genome scans were performed on two datasets: approximately 113K SNPs from 921 predominantly bread wheat accessions and approximately 110K SNPs from about 400 wheat accessions representing all ploidy levels. To identify environmental factors associated with the loci, a genome-environment association (GEA) was also performed. The genome scans on both datasets identified a highly differentiated region on chromosome 4A where accessions in the first dataset were dichotomized into a group (n = 691), comprising nearly all cultivars, wild emmer, and most landraces, and a second group (n = 230), dominated by landraces and spelt accessions. The grouping of cultivars is likely linked to their potential ancestor, bread wheat cv. Norin-10. The 4A region harbored important genes involved in adaptations to environmental conditions. The GEA detected loci associated with latitude and temperature. The genetic signatures detected in this study provide insight into the historical selection and hybridization events in the wheat genome that shaped its current genetic structure and facilitated its success in a wide spectrum of environmental conditions. The genome scans and GEA approaches applied in this study can help in screening the germplasm housed in gene banks for breeding, and for conservation purposes.
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Affiliation(s)
- Demissew Sertse
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK S7N 0W9, Canada
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Valentyna Klymiuk
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Jemanesh K Haile
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Amidou N'Diaye
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Curtis J Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK S7N 0W9, Canada
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Li Y, Tao F, Hao Y, Tong J, Xiao Y, He Z, Reynolds M. Variations in phenological, physiological, plant architectural and yield-related traits, their associations with grain yield and genetic basis. ANNALS OF BOTANY 2023; 131:503-519. [PMID: 36655618 PMCID: PMC10072080 DOI: 10.1093/aob/mcad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND AIMS Physiological and morphological traits play essential roles in wheat (Triticum aestivum) growth and development. In particular, photosynthesis is a limitation to yield. Increasing photosynthesis in wheat has been identified as an important strategy to increase yield. However, the genotypic variations and the genomic regions governing morphological, architectural and photosynthesis traits remain unexplored. METHODS Here, we conducted a large-scale investigation of the phenological, physiological, plant architectural and yield-related traits, involving 32 traits for 166 wheat lines during 2018-2020 in four environments, and performed a genome-wide association study with wheat 90K and 660K single nucleotide polymorphism (SNP) arrays. KEY RESULTS These traits exhibited considerable genotypic variations in the wheat diversity panel. Higher yield was associated with higher net photosynthetic rate (r = 0.41, P < 0.01), thousand-grain weight (r = 0.36, P < 0.01) and truncated and lanceolate shape, but shorter plant height (r = -0.63, P < 0.01), flag leaf angle (r = -0.49, P < 0.01) and spike number per square metre (r = -0.22, P < 0.01). Genome-wide association mapping discovered 1236 significant stable loci detected in the four environments among the 32 traits using SNP markers. Trait values have a cumulative effect as the number of the favourable alleles increases, and significant progress has been made in determining phenotypic values and favourable alleles over the years. Eleven elite cultivars and 14 traits associated with grain yield per plot (GY) were identified as potential parental lines and as target traits to develop high-yielding cultivars. CONCLUSIONS This study provides new insights into the phenotypic and genetic elucidation of physiological and morphological traits in wheat and their associations with GY, paving the way for discovering their underlying gene control and for developing enhanced ideotypes in wheat breeding.
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Affiliation(s)
- Yibo Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yonggui Xiao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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31
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Alemu A, Batista L, Singh PK, Ceplitis A, Chawade A. Haplotype-tagged SNPs improve genomic prediction accuracy for Fusarium head blight resistance and yield-related traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:92. [PMID: 37009920 PMCID: PMC10068637 DOI: 10.1007/s00122-023-04352-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Linkage disequilibrium (LD)-based haplotyping with subsequent SNP tagging improved the genomic prediction accuracy up to 0.07 and 0.092 for Fusarium head blight resistance and spike width, respectively, across six different models. Genomic prediction is a powerful tool to enhance genetic gain in plant breeding. However, the method is accompanied by various complications leading to low prediction accuracy. One of the major challenges arises from the complex dimensionality of marker data. To overcome this issue, we applied two pre-selection methods for SNP markers viz. LD-based haplotype-tagging and GWAS-based trait-linked marker identification. Six different models were tested with preselected SNPs to predict the genomic estimated breeding values (GEBVs) of four traits measured in 419 winter wheat genotypes. Ten different sets of haplotype-tagged SNPs were selected by adjusting the level of LD thresholds. In addition, various sets of trait-linked SNPs were identified with different scenarios from the training-test combined and only from the training populations. The BRR and RR-BLUP models developed from haplotype-tagged SNPs had a higher prediction accuracy for FHB and SPW by 0.07 and 0.092, respectively, compared to the corresponding models developed without marker pre-selection. The highest prediction accuracy for SPW and FHB was achieved with tagged SNPs pruned at weak LD thresholds (r2 < 0.5), while stringent LD was required for spike length (SPL) and flag leaf area (FLA). Trait-linked SNPs identified only from training populations failed to improve the prediction accuracy of the four studied traits. Pre-selection of SNPs via LD-based haplotype-tagging could play a vital role in optimizing genomic selection and reducing genotyping costs. Furthermore, the method could pave the way for developing low-cost genotyping methods through customized genotyping platforms targeting key SNP markers tagged to essential haplotype blocks.
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Affiliation(s)
- Admas Alemu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Pawan K Singh
- International Maize and Wheat Improvement Center, Texcoco, Mexico
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
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Koroluk A, Sowa S, Boczkowska M, Paczos-Grzęda E. Utilizing Genomics to Characterize the Common Oat Gene Pool—The Story of More than a Century of Polish Breeding. Int J Mol Sci 2023; 24:ijms24076547. [PMID: 37047519 PMCID: PMC10094864 DOI: 10.3390/ijms24076547] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
This study was undertaken to investigate the diversity and population structure of 487 oat accessions, including breeding lines from the ongoing programs of the three largest Polish breeding companies, along with modern and historical Polish and foreign cultivars. The analysis was based on 7411 DArTseq-derived SNPs distributed among three sub-genomes (A, C, and D). The heterogeneity of the studied material was very low, as only cultivars and advanced breeding lines were examined. Principal component analysis (PCA), principal coordinate analysis (PCoA), and cluster and STRUCTURE analyses found congruent results, which show that most of the examined cultivars and materials from Polish breeding programs formed major gene pools, that only some accessions derived from Strzelce Plant Breeding, and that foreign cultivars were outside of the main group. During the 120 year oat breeding process, only 67 alleles from the old gene pool were lost and replaced by 67 new alleles. The obtained results indicate that no erosion of genetic diversity was observed within the Polish native oat gene pool. Moreover, current oat breeding programs have introduced 673 new alleles into the gene pool relative to historical cultivars. The analysis also showed that most of the changes in relation to historical cultivars occurred within the A sub-genome with emphasis on chromosome 6A. The targeted changes were the rarest in the C sub-genome. This study showed that Polish oat breeding based mainly on traditional breeding methods—although focused on improving traits typical to this crop, i.e., enhancing the grain yield and quality and improving adaptability—did not significantly narrow the oat gene pool and in fact produced cultivars that are not only competitive in the European market but are also reservoirs of new alleles that were not found in the analyzed foreign materials.
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Wang S, Wang T, Xuan Q, Qu X, Xu Q, Jiang Q, Pu Z, Li Y, Jiang Y, Chen G, Deng M, Liu Y, Tang H, Chen G, He Y, Gou L, Wei Y, Zheng Y, Ma J. Major and stably expressed QTL for traits related to the mature wheat embryo independent of kernel size. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:90. [PMID: 37000252 DOI: 10.1007/s00122-023-04346-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Two major and stably expressed QTL for traits related to mature wheat embryo independent of kernel size were identified and validated in a natural population that contained 171 Sichuan wheat accessions and 49 Sichuan wheat landraces. As the juvenile of a highly differentiated plant, mature wheat (Triticum aestivum L.) embryos are highly significant to agricultural production. To understand the genetic basis of traits related to wheat embryo size, the embryo of mature kernels in a recombination inbred line that contained 126 lines from four environments was measured. The genetic loci of embryo size, including embryo length (EL), embryo width (EW), embryo area (EA), embryo length/kernel length (EL/KL), embryo width/kernel width (EW/KW), and EL/EW, were identified based on a genetic linkage map constructed based on PCR markers and the Wheat 55 K single nucleotide polymorphism (SNP) array. A total of 50 quantitative trait loci (QTL) for traits related to wheat embryo size were detected. Among them, QEL.sicau-2SY-4A for EL and QEW.sicau-2SY-7B for EW were major and stably expressed and were genetically independent of KL and KW, respectively. Their effects were further verified in a natural population that contained 171 Sichuan wheat accessions and 49 Sichuan wheat landraces. Further analysis showed that TraesCS4A02G343300 and TraesCS7B02G006800 could be candidate genes for QEL.sicau-2SY-4A and QEW.sicau-2SY-7B, respectively. In addition, significant positive correlations between EL and kernel-related traits and the 1,000-grain weight were detected. Collectively, this study broadens our understanding of the genetic basis of wheat embryo size and will be helpful for the further fine-mapping of interesting loci in the future.
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Affiliation(s)
- Surong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tianyu Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qijing Xuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiangru Qu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yanling Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuanjiang He
- Mianyang Academy of Agricultural Science/Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, 621000, China
| | - Lulu Gou
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Wang L, Xu J, Wang H, Chen T, You E, Bian H, Chen W, Zhang B, Shen Y. Population structure analysis and genome-wide association study of a hexaploid oat landrace and cultivar collection. FRONTIERS IN PLANT SCIENCE 2023; 14:1131751. [PMID: 37025134 PMCID: PMC10070682 DOI: 10.3389/fpls.2023.1131751] [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: 12/26/2022] [Accepted: 02/22/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Oat (Avena sativa L.) is an important cereal crop grown worldwide for grain and forage, owing to its high adaptability to diverse environments. However, the genetic and genomics research of oat is lagging behind that of other staple cereal crops. METHODS In this study, a collection of 288 oat lines originating worldwide was evaluated using 2,213 single nucleotide polymorphism (SNP) markers obtained from an oat iSelect 6K-beadchip array to study its genetic diversity, population structure, and linkage disequilibrium (LD) as well as the genotype-phenotype association for hullessness and lemma color. RESULTS The average gene diversity and polymorphic information content (PIC) were 0.324 and 0.262, respectively. The first three principal components (PCs) accounted for 30.33% of the genetic variation, indicating that the population structure of this panel of oat lines was stronger than that reported in most previous studies. In addition, accessions could be classified into two subpopulations using a Bayesian clustering approach, and the clustering pattern of accessions was closely associated with their region of origin. Additionally, evaluation of LD decay using 2,143 mapped markers revealed that the intrachromosomal whole-genome LD decayed rapidly to a critical r2 value of 0.156 for marker pairs separated by a genetic distance of 1.41 cM. Genome-wide association study (GWAS) detected six significant associations with the hullessness trait. Four of these six markers were located on the Mrg21 linkage group between 194.0 and 205.7 cM, while the other two significant markers mapped to Mrg05 and Mrg09. Three significant SNPs, showing strong association with lemma color, were located on linkage groups Mrg17, Mrg18, and Mrg20. DISCUSSION Our results discerned relevant patterns of genetic diversity, population structure, and LD among members of a worldwide collection of oat landraces and cultivars proposed to be 'typical' of the Qinghai-Tibetan Plateau. These results have important implications for further studies on association mapping and practical breeding in high-altitude oat.
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Affiliation(s)
- Lei Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Jinqing Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Handong Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Tongrui Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - En You
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haiyan Bian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Wenjie Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, China
| | - Bo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, China
| | - Yuhu Shen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, China
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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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Niu J, Si Y, Tian S, Liu X, Shi X, Ma S, Yu Z, Ling HQ, Zheng S. A Wheat 660 K SNP array-based high-density genetic map facilitates QTL mapping of flag leaf-related traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:51. [PMID: 36913011 DOI: 10.1007/s00122-023-04248-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 11/26/2022] [Indexed: 06/18/2023]
Abstract
A high-density genetic map containing 122,620 SNP markers was constructed, which facilitated the identification of eight major flag leaf-related QTL in relatively narrow intervals. The flag leaf plays an important role in photosynthetic capacity and yield potential in wheat. In this study, we used a recombinant inbred line population containing 188 lines derived from a cross between 'Lankao86' (LK86) and 'Ermangmai' to construct a genetic map using the Wheat 660 K single-nucleotide polymorphism (SNP) array. The high-density genetic map contains 122,620 SNP markers spanning 5185.06 cM. It shows good collinearity with the physical map of Chinese Spring and anchors multiple sequences of previously unplaced scaffolds onto chromosomes. Based on the high-density genetic map, we identified seven, twelve, and eight quantitative trait loci (QTL) for flag leaf length (FLL), width (FLW), and area (FLA) across eight environments, respectively. Among them, three, one, and four QTL for FLL, FLW, and FLA are major and stably express in more than four environments. The physical distance between the flanking markers for QFll.igdb-3B/QFlw.igdb-3B/QFla.igdb-3B is only 444 kb containing eight high confidence genes. These results suggested that we could directly map the candidate genes in a relatively small region by the high-density genetic map constructed with the Wheat 660 K array. Furthermore, the identification of environmentally stable QTL for flag leaf morphology laid a foundation for the following gene cloning and flag leaf morphology improvement.
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Affiliation(s)
- Jianqing Niu
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yaoqi Si
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shuiquan Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shengwei Ma
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zhongqing Yu
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Hong-Qing Ling
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
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Halder J, Gill HS, Zhang J, Altameemi R, Olson E, Turnipseed B, Sehgal SK. Genome-wide association analysis of spike and kernel traits in the U.S. hard winter wheat. THE PLANT GENOME 2023; 16:e20300. [PMID: 36636831 DOI: 10.1002/tpg2.20300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/20/2022] [Indexed: 05/10/2023]
Abstract
A better understanding of the genetic control of spike and kernel traits that have higher heritability can help in the development of high-yielding wheat varieties. Here, we identified the marker-trait associations (MTAs) for various spike- and kernel-related traits in winter wheat (Triticum aestivum L.) through genome-wide association studies (GWAS). An association mapping panel comprising 297 hard winter wheat accessions from the U.S. Great Plains was evaluated for eight spike- and kernel-related traits in three different environments. A GWAS using 15,590 single-nucleotide polymorphisms (SNPs) identified a total of 53 MTAs for seven spike- and kernel-related traits, where the highest number of MTAs were identified for spike length (16) followed by the number of spikelets per spike (15) and spikelet density (11). Out of 53 MTAs, 14 were considered to represent stable quantitative trait loci (QTL) as they were identified in multiple environments. Five multi-trait MTAs were identified for various traits including the number of spikelets per spike (NSPS), spikelet density (SD), kernel width (KW), and kernel area (KA) that could facilitate the pyramiding of yield-contributing traits. Further, a significant additive effect of accumulated favorable alleles on the phenotype of four spike-related traits suggested that breeding lines and cultivars with a higher number of favorable alleles could be a valuable resource for breeders to improve yield-related traits. This study improves the understanding of the genetic basis of yield-related traits in hard winter wheat and provides reliable molecular markers that will facilitate marker-assisted selection (MAS) in wheat breeding programs.
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Affiliation(s)
- Jyotirmoy Halder
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
| | - Harsimardeep S Gill
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
| | - Jinfeng Zhang
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
| | - Rami Altameemi
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
| | - Eric Olson
- Dep. of Plant, Soil and Microbial Sciences, Michigan State Univ., East Lansing, MI, 48824, USA
| | - Brent Turnipseed
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
| | - Sunish K Sehgal
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
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Li C, Zhuang L, Li T, Hou J, Liu H, Jian C, Li H, Zhao J, Liu Y, Xi W, Hao P, Liu S, Si X, Wang X, Zhang X, Hao C. Conservatively transmitted alleles of key agronomic genes provide insights into the genetic basis of founder parents in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2023; 23:100. [PMID: 36805674 PMCID: PMC9938602 DOI: 10.1186/s12870-023-04098-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Founder parents play extremely important roles in wheat breeding. Studies into the genetic basis of founder parents and the transmission rules of favorable alleles are of great significance in improving agronomically important traits in wheat. RESULTS Here, a total of 366 founder parents, widely grown cultivars, and derivatives of four representative founder parents were genotyped based on efficient kompetitive allele-specific PCR (KASP) markers in 87 agronomically important genes controlling yield, quality, adaptability, and stress resistance. Genetic composition analysis of founder parents and widely grown cultivars showed a consistently high frequency of favorable alleles for yield-related genes. This analysis further showed that other alleles favorable for resistance, strong gluten, dwarf size, and early heading date were also subject to selective pressure over time. By comparing the transmission of alleles from four representative founder parents to their derivatives during different breeding periods, it was found that the genetic composition of the representative founder parents was optimized as breeding progressed over time, with the number and types of favorable alleles carried gradually increasing and becoming enriched. There are still a large number of favorable alleles in wheat founder parents that have not been fully utilized in breeding selection. Eighty-seven agronomically important genes were used to construct an enrichment map that shows favorable alleles of four founder parents, providing an important theoretical foundation for future identification of candidate wheat founder parents. CONCLUSIONS These results reveal the genetic basis of founder parents and allele transmission for 87 agronomically important genes and shed light on breeding strategies for the next generation of elite founder parents in wheat.
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Affiliation(s)
- Chang Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lei Zhuang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hongxia Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Chao Jian
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Huifang Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jing Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yunchuan Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Wei Xi
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Pingan Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shujuan Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xuemei Si
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiaolu Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Li Y, Liu L, Wang M, Ruff T, See DR, Hu X, Chen X. Characterization and Molecular Mapping of a Gene Conferring High-Temperature Adult-Plant Resistance to Stripe Rust Originally from Aegilops ventricosa. PLANT DISEASE 2023; 107:431-442. [PMID: 35852900 DOI: 10.1094/pdis-06-22-1419-re] [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: 06/15/2023]
Abstract
Wheat near-isogenic line AvSYr17NIL carrying Yr17, originally from Aegilops ventricosa for all-stage resistance to Puccinia striiformis f. sp. tritici, also shows nonrace-specific, high-temperature adult-plant (HTAP) resistance to the stripe rust pathogen. To separate and identify the HTAP resistance gene, seeds of AvSYr17NIL were treated with ethyl methanesulfonate. Mutant lines with only HTAP resistance were obtained, and one of the lines, M1225, was crossed with the susceptible recurrent parent Avocet S (AvS). Field responses of the F2 plants and F3 lines, together with the parents, were recorded at the adult-plant stage in Pullman and Mount Vernon, WA under natural P. striiformis f. sp. tritici infection. The parents and the F4 population were phenotyped with a Yr17-virulent P. striiformis f. sp. tritici race in the adult-plant stage under the high-temperature profile in the greenhouse. The phenotypic results were confirmed by testing the F5 population in the field under natural P. striiformis f. sp. tritici infection. The F2 data indicated a single recessive gene, temporarily named YrM1225, for HTAP resistance. The F4 lines were genotyped with Kompetitive allele-specific PCR markers converted from single-nucleotide polymorphism markers polymorphic between M1225 and AvS. The HTAP resistance gene was mapped on the short arm of chromosome 2A in an interval of 7.5 centimorgans using both linkage and quantitative trait locus mapping approaches. The separation of the HTAP resistance gene from Yr17 should improve the understanding and utilization of the different types of resistance.
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Affiliation(s)
- Yuxiang Li
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Lu Liu
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Travis Ruff
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Deven R See
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
- United States Department of Agriculture Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430, U.S.A
| | - Xiaoping Hu
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
- United States Department of Agriculture Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430, U.S.A
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Xiang M, Liu S, Wang X, Zhang M, Yan W, Wu J, Wang Q, Li C, Zheng W, He Y, Ge Y, Wang C, Kang Z, Han D, Zeng Q. Development of breeder chip for gene detection and molecular-assisted selection by target sequencing in wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:13. [PMID: 37313130 PMCID: PMC10248658 DOI: 10.1007/s11032-023-01359-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/03/2023] [Indexed: 06/15/2023]
Abstract
Wheat is an essential food crop and its high and stable yield is suffering from great challenges due to the limitations of current breeding technology and various stresses. Accelerating molecularly assisted stress-resistance breeding is critical. Through a meta-analysis of published loci in wheat over the last two decades, we selected 60 loci with main breeding objectives, high heritability, and reliable genotyping, such as stress resistance, yield, plant height, and resistance to spike germination. Then, using genotyping by target sequencing (GBTS) technology, we developed a liquid phase chip based on 101 functional or closely linked markers. The genotyping of 42 loci was confirmed in an extensive collection of Chinese wheat cultivars, indicating that the chip can be used in molecular-assisted selection (MAS) for target breeding goals. Besides, we can perform the preliminary parentage analysis with the genotype data. The most significant contribution of this work lies in translating a large number of molecular markers into a viable chip and providing reliable genotypes. Breeders can quickly screen germplasm resources, parental breeding materials, and intermediate materials for the presence of excellent allelic variants using the genotyping data by this chip, which is high throughput, convenient, reliable, and cost-efficient. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01359-3.
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Affiliation(s)
- Mingjie Xiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xiaoting Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Mingming Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Weiyi Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Chunlian Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Weijun Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yilin He
- MolBreeding Biotechnology Co., Ltd., Shijiazhuang, 050035 Hebei China
| | - Yunxia Ge
- MolBreeding Biotechnology Co., Ltd., Shijiazhuang, 050035 Hebei China
| | - Changfa Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi China
- Yangling Seed Industry Innovation Center, Yangling, 712100 Shaanxi China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi China
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Broccanello C, Bellin D, DalCorso G, Furini A, Taranto F. Genetic approaches to exploit landraces for improvement of Triticum turgidum ssp. durum in the age of climate change. FRONTIERS IN PLANT SCIENCE 2023; 14:1101271. [PMID: 36778704 PMCID: PMC9911883 DOI: 10.3389/fpls.2023.1101271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Addressing the challenges of climate change and durum wheat production is becoming an important driver for food and nutrition security in the Mediterranean area, where are located the major producing countries (Italy, Spain, France, Greece, Morocco, Algeria, Tunisia, Turkey, and Syria). One of the emergent strategies, to cope with durum wheat adaptation, is the exploration and exploitation of the existing genetic variability in landrace populations. In this context, this review aims to highlight the important role of durum wheat landraces as a useful genetic resource to improve the sustainability of Mediterranean agroecosystems, with a focus on adaptation to environmental stresses. We described the most recent molecular techniques and statistical approaches suitable for the identification of beneficial genes/alleles related to the most important traits in landraces and the development of molecular markers for marker-assisted selection. Finally, we outline the state of the art about landraces genetic diversity and signature of selection, already identified from these accessions, for adaptability to the environment.
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Affiliation(s)
| | - Diana Bellin
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Antonella Furini
- Department of Biotechnology, University of Verona, Verona, Italy
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Sehgal D, Dhakate P, Ambreen H, Shaik KHB, Rathan ND, Anusha NM, Deshmukh R, Vikram P. Wheat Omics: Advancements and Opportunities. PLANTS (BASEL, SWITZERLAND) 2023; 12:426. [PMID: 36771512 PMCID: PMC9919419 DOI: 10.3390/plants12030426] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
Plant omics, which includes genomics, transcriptomics, metabolomics and proteomics, has played a remarkable role in the discovery of new genes and biomolecules that can be deployed for crop improvement. In wheat, great insights have been gleaned from the utilization of diverse omics approaches for both qualitative and quantitative traits. Especially, a combination of omics approaches has led to significant advances in gene discovery and pathway investigations and in deciphering the essential components of stress responses and yields. Recently, a Wheat Omics database has been developed for wheat which could be used by scientists for further accelerating functional genomics studies. In this review, we have discussed various omics technologies and platforms that have been used in wheat to enhance the understanding of the stress biology of the crop and the molecular mechanisms underlying stress tolerance.
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Affiliation(s)
- Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco 56237, Mexico
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Priyanka Dhakate
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110076, India
| | - Heena Ambreen
- School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK
| | - Khasim Hussain Baji Shaik
- Faculty of Agriculture Sciences, Georg-August-Universität, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Nagenahalli Dharmegowda Rathan
- Indian Agricultural Research Institute (ICAR-IARI), New Delhi 110012, India
- Corteva Agriscience, Hyderabad 502336, Telangana, India
| | | | - Rupesh Deshmukh
- Department of Biotechnology, Central University of Haryana, Mahendragarh 123031, Haryana, India
| | - Prashant Vikram
- Bioseed Research India Ltd., Hyderabad 5023324, Telangana, India
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Discovering Loci for Breeding Prospective and Phenology in Wheat Mediterranean Landraces by Environmental and eigenGWAS. Int J Mol Sci 2023; 24:ijms24021700. [PMID: 36675215 PMCID: PMC9863576 DOI: 10.3390/ijms24021700] [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: 11/30/2022] [Revised: 12/27/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
Knowledge of the genetic basis of traits controlling phenology, differentiation patterns, and environmental adaptation is essential to develop new cultivars under climate change conditions. Landrace collections are an appropriate platform to study the hidden variation caused by crop breeding. The use of genome-wide association analysis for phenology, climatic data and differentiation among Mediterranean landraces led to the identification of 651 marker-trait associations that could be grouped in 46 QTL hotspots. A candidate gene analysis using the annotation of the genome sequence of the wheat cultivar 'Chinese Spring' detected 1097 gene models within 33 selected QTL hotspots. From all the gene models, 42 were shown to be differentially expressed (upregulated) under abiotic stress conditions, and 9 were selected based on their levels of expression. Different gene families previously reported for their involvement in different stress responses were found (protein kinases, ras-like GTP binding proteins and ethylene-responsive transcription factors). Finally, the synteny analysis in the QTL hotspots regions among the genomes of wheat and other cereal species identified 23, 21 and 7 ortho-QTLs for Brachypodium, rice and maize, respectively, confirming the importance of these loci.
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Benaouda S, Stöcker T, Schoof H, Léon J, Ballvora A. Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat. BMC PLANT BIOLOGY 2023; 23:25. [PMID: 36631761 PMCID: PMC9835304 DOI: 10.1186/s12870-022-03986-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The transition from vegetative to floral phase is the result of complex crosstalk of exogenous and endogenous floral integrators. This critical physiological event is the response to environmental interaction, which causes biochemical cascades of reactions at different internal tissues, organs, and releases signals that make the plant moves from vegetative status to a reproductive phase. This network controlling flowering time is not deciphered largely in bread wheat. In this study, a comparative transcriptome analysis at a transition time in combination with genetic mapping was used to identify responsible genes in a stage and tissue-specific manner. For this reason, two winter cultivars that have been bred in Germany showing contrasting and stable heading time in different environments were selected for the analysis. RESULTS In total, 670 and 1075 differentially expressed genes in the shoot apical meristem and leaf tissue, respectively, could be identified in 23 QTL intervals for the heading date. In the transition apex, Histone methylation H3-K36 and regulation of circadian rhythm are both controlled by the same homoeolog genes mapped in QTL TaHd112, TaHd124, and TaHd137. TaAGL14 gene that identifies the floral meristem was mapped in TaHd054 in the double ridge. In the same stage, the homoeolog located on chromosome 7D of FLOWERING TIME LOCUS T mapped on chr 7B, which evolved an antagonist function and acts as a flowering repressor was uncovered. The wheat orthologue of transcription factor ASYMMETRIC LEAVES 1 (AS1) was identified in the late reproductive stage and was mapped in TaHd102, which is strongly associated with heading date. Deletion of eight nucleotides in the AS1 promoter could be identified in the binding site of the SUPPRESSOR OF CONSTANS OVEREXPRESSION 1 (SOC1) gene in the late flowering cultivar. Both proteins AS1 and SOC1 are inducing flowering time in response to gibberellin biosynthesis. CONCLUSION The global transcriptomic at the transition phase uncovered stage and tissue-specific genes mapped in QTL of heading date in winter wheat. In response to Gibberellin signaling, wheat orthologous transcription factor AS1 is expressed in the late reproductive phase of the floral transition. The locus harboring this gene is the strongest QTL associated with the heading date trait in the German cultivars. Consequently, we conclude that this is another indication of the Gibberellin biosynthesis as the mechanism behind the heading variation in wheat.
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Affiliation(s)
- Salma Benaouda
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
| | - Tyll Stöcker
- Institute for Crop Science and Resource Conservation, Chair of Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Heiko Schoof
- Institute for Crop Science and Resource Conservation, Chair of Crop Bioinformatics, University of Bonn, Bonn, Germany
| | - Jens Léon
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
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Schulthess AW, Kale SM, Zhao Y, Gogna A, Rembe M, Philipp N, Liu F, Beukert U, Serfling A, Himmelbach A, Oppermann M, Weise S, Boeven PHG, Schacht J, Longin CFH, Kollers S, Pfeiffer N, Korzun V, Fiebig A, Schüler D, Lange M, Scholz U, Stein N, Mascher M, Reif JC. Large-scale genotyping and phenotyping of a worldwide winter wheat genebank for its use in pre-breeding. Sci Data 2022; 9:784. [PMID: 36572688 PMCID: PMC9792552 DOI: 10.1038/s41597-022-01891-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/07/2022] [Indexed: 12/27/2022] Open
Abstract
Plant genetic resources (PGR) stored at genebanks are humanity's crop diversity savings for the future. Information on PGR contrasted with modern cultivars is key to select PGR parents for pre-breeding. Genotyping-by-sequencing was performed for 7,745 winter wheat PGR samples from the German Federal ex situ genebank at IPK Gatersleben and for 325 modern cultivars. Whole-genome shotgun sequencing was carried out for 446 diverse PGR samples and 322 modern cultivars and lines. In 19 field trials, 7,683 PGR and 232 elite cultivars were characterized for resistance to yellow rust - one of the major threats to wheat worldwide. Yield breeding values of 707 PGR were estimated using hybrid crosses with 36 cultivars - an approach that reduces the lack of agronomic adaptation of PGR and provides better estimates of their contribution to yield breeding. Cross-validations support the interoperability between genomic and phenotypic data. The here presented data are a stepping stone to unlock the functional variation of PGR for European pre-breeding and are the basis for future breeding and research activities.
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Affiliation(s)
- Albert W Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sandip M Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Abhishek Gogna
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Maximilian Rembe
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Norman Philipp
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Fang Liu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Ulrike Beukert
- Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Albrecht Serfling
- Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Markus Oppermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Stephan Weise
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | | | | | | | | | | | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Danuta Schüler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
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Abstract
Semidwarfing genes have greatly increased wheat yields globally, yet the widely used gibberellin (GA)-insensitive genes Rht-B1b and Rht-D1b have disadvantages for seedling emergence. Use of the GA-sensitive semidwarfing gene Rht13 avoids this pleiotropic effect. Here, we show that Rht13 encodes a nucleotide-binding site/leucine-rich repeat (NB-LRR) gene. A point mutation in the semidwarf Rht-B13b allele autoactivates the NB-LRR gene and causes a height reduction comparable with Rht-B1b and Rht-D1b in diverse genetic backgrounds. The autoactive Rht-B13b allele leads to transcriptional up-regulation of pathogenesis-related genes including class III peroxidases associated with cell wall remodeling. Rht13 represents a new class of reduced height (Rht) gene, unlike other Rht genes, which encode components of the GA signaling or metabolic pathways. This discovery opens avenues to use autoactive NB-LRR genes as semidwarfing genes in a range of crop species, and to apply Rht13 in wheat breeding programs using a perfect genetic marker.
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Potentials of synthetic hexaploid wheats to improve drought tolerance. Sci Rep 2022; 12:20482. [PMID: 36443382 PMCID: PMC9705419 DOI: 10.1038/s41598-022-24678-5] [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: 03/02/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
Synthetic hexaploid wheat-derived lines (SHW-DL) offers new hope for breeders to restore genes lost during the evolutionary bottleneck. The study of adaptability, variation, and the possibility of selection in SHW-DL for drought tolerance is poorly understood in arid environments. The potential of 184 SHW-DL and their variation for agro-morphological traits were assessed under normal and water stress conditions for 2 years. The mean values of grain yield (YLD) varied from 683.9 g/m2 (water stress) to 992.1 g/m2 (normal conditions). Grain yield decreased by 64 and 71% under water stress in the two growing seasons. High genotypic variation was found for measured traits and drought tolerance. Heritability ranged from 19 (harvest index) to 47% (spike length), whereas grain yield indicated a moderate heritability (32%). Using the assessment of the interrelationship of traits, hectoliter (a quality trait) was correlated with drought tolerance and stability indices. Therefore, it can be considered as an important trait to select drought tolerant genotypes. In the following, the priority of yield components entering the regression model was different in two moisture conditions suggesting different strategies in indirect selection programs to improve yield. Spike m-2 and grain spike-1 indirectly and negatively affected yield through thousand-grain weight (TGW) under normal and water stress conditions, respectively. Furthermore, SHW-DL compared to ordinary wheat were significantly superior in terms of early maturity, dwarfing, yield, TGW, stem diameter, and harvest index. Overall, our findings suggest that SHW-DL are a valuable source for improving wheat yield and drought tolerance, and indirect selection might be possible to improve these complex traits.
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Lehnert H, Berner T, Lang D, Beier S, Stein N, Himmelbach A, Kilian B, Keilwagen J. Insights into breeding history, hotspot regions of selection, and untapped allelic diversity for bread wheat breeding. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:897-918. [PMID: 36073999 DOI: 10.1111/tpj.15952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Breeding has increasingly altered the genetics of crop plants since the domestication of their wild progenitors. It is postulated that the genetic diversity of elite wheat breeding pools is too narrow to cope with future challenges. In contrast, plant genetic resources (PGRs) of wheat stored in genebanks are valuable sources of unexploited genetic diversity. Therefore, to ensure breeding progress in the future, it is of prime importance to identify the useful allelic diversity available in PGRs and to transfer it into elite breeding pools. Here, a diverse collection consisting of modern winter wheat cultivars and genebank accessions was investigated based on reduced-representation genomic sequencing and an iSelect single nucleotide polymorphism (SNP) chip array. Analyses of these datasets provided detailed insights into population structure, levels of genetic diversity, sources of new allelic diversity, and genomic regions affected by breeding activities. We identified 57 regions representing genomic signatures of selection and 827 regions representing private alleles associated exclusively with genebank accessions. The presence of known functional wheat genes, quantitative trait loci, and large chromosomal modifications, i.e., introgressions from wheat wild relatives, provided initial evidence for putative traits associated within these identified regions. These findings were supported by the results of ontology enrichment analyses. The results reported here will stimulate further research and promote breeding in the future by allowing for the targeted introduction of novel allelic diversity into elite wheat breeding pools.
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Affiliation(s)
- Heike Lehnert
- Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, Germany
| | - Thomas Berner
- Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, Germany
| | - Daniel Lang
- PGSB, Helmholtz Center Munich, German Research Center for Environmental Health, Plant Genome and Systems Biology, Neuherberg, Germany
| | - Sebastian Beier
- Research Group Bioinformatics and Information Technology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nils Stein
- Research Group Genomics of Genetic Resources, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Center of integrated Breeding Research (CiBreed), Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Axel Himmelbach
- Research Group Genomics of Genetic Resources, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, Germany
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49
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Yang N, Ovenden B, Baxter B, McDonald MC, Solomon PS, Milgate A. Multi-stage resistance to Zymoseptoria tritici revealed by GWAS in an Australian bread wheat diversity panel. FRONTIERS IN PLANT SCIENCE 2022; 13:990915. [PMID: 36352863 PMCID: PMC9637935 DOI: 10.3389/fpls.2022.990915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Septoria tritici blotch (STB) has been ranked the third most important wheat disease in the world, threatening a large area of wheat production. Although major genes play an important role in the protection against Zymoseptoria tritici infection, the lifespan of their resistance unfortunately is very short in modern wheat production systems. Combinations of quantitative resistance with minor effects, therefore, are believed to have prolonged and more durable resistance to Z. tritici. In this study, new quantitative trait loci (QTLs) were identified that are responsible for seedling-stage resistance and adult-plant stage resistance (APR). More importantly was the characterisation of a previously unidentified QTL that can provide resistance during different stages of plant growth or multi-stage resistance (MSR). At the seedling stage, we discovered a new isolate-specific QTL, QSt.wai.1A.1. At the adult-plant stage, the new QTL QStb.wai.6A.2 provided stable and consistent APR in multiple sites and years, while the QTL QStb.wai.7A.2 was highlighted to have MSR. The stacking of multiple favourable MSR alleles was found to improve resistance to Z. tritici by up to 40%.
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Affiliation(s)
- Nannan Yang
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Ben Ovenden
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Brad Baxter
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Megan C. McDonald
- University of Birmingham, School of Biosciences, Birmingham, West Midlands, United Kingdom
| | - Peter S. Solomon
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Andrew Milgate
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
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50
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Du B, Wu J, Islam MS, Sun C, Lu B, Wei P, Liu D, Chen C. Genome-wide meta-analysis of QTL for morphological related traits of flag leaf in bread wheat. PLoS One 2022; 17:e0276602. [PMID: 36279291 PMCID: PMC9591062 DOI: 10.1371/journal.pone.0276602] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Flag leaf is an important organ for photosynthesis of wheat plants, and a key factor affecting wheat yield. In this study, quantitative trait loci (QTL) for flag leaf morphological traits in wheat reported since 2010 were collected to investigate the genetic mechanism of these traits. Integration of 304 QTLs from various mapping populations into a high-density consensus map composed of various types of molecular markers as well as QTL meta-analysis discovered 55 meta-QTLs (MQTL) controlling morphological traits of flag leaves, of which 10 MQTLs were confirmed by GWAS. Four high-confidence MQTLs (MQTL-1, MQTL-11, MQTL-13, and MQTL-52) were screened out from 55 MQTLs, with an average confidence interval of 0.82 cM and a physical distance of 9.4 Mb, according to the definition of hcMQTL. Ten wheat orthologs from rice (7) and Arabidopsis (3) that regulated leaf angle, development and morphogenesis traits were identified in the hcMQTL region using comparative genomics, and were speculated to be potential candidate genes regulating flag leaf morphological traits in wheat. The results from this study provides valuable information for fine mapping and molecular markers assisted selection to improve morphological characters in wheat flag leaf.
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Affiliation(s)
- Binbin Du
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Jia Wu
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Md. Samiul Islam
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Chaoyue Sun
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Baowei Lu
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Peipei Wei
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Dong Liu
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Cunwu Chen
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
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