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Amalova A, Babkenov A, Philp C, Griffiths S, Abugalieva S, Turuspekov Y. Identification of Quantitative Trait Loci Associated with Plant Adaptation Traits Using Nested Association Mapping Population. PLANTS (BASEL, SWITZERLAND) 2024; 13:2623. [PMID: 39339597 PMCID: PMC11435412 DOI: 10.3390/plants13182623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 09/10/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024]
Abstract
This study evaluated 290 recombinant inbred lines (RILs) of the nested association mapping (NAM) population from the UK. The population derived from 24 families, where a common parent was "Paragon," one of the UK's spring wheat cultivar standards. All genotypes were tested in two regions of Kazakhstan at the Kazakh Research Institute of Agriculture and Plant Industry (KRIAPI, Almaty region, Southeast Kazakhstan, 2019-2022 years) and Alexandr Barayev Scientific-Production Center for Grain Farming (SPCGF, Shortandy, Akmola region, Northern Kazakhstan, 2019-2022 years). The studied traits consisted of plant adaptation-related traits, including heading date (HD, days), seed maturation date (SMD, days), plant height (PH, cm), and peduncle length (PL, cm). In addition, the yield per m2 was analyzed in both regions. Based on a field evaluation of the population in northern and southeastern Kazakhstan and using 10,448 polymorphic SNP (single-nucleotide polymorphism) markers, the genome-wide association study (GWAS) allowed for detecting 74 QTLs in four studied agronomic traits (HD, SMD, PH, and PL). The literature survey suggested that 16 of the 74 QTLs identified in our study had also been detected in previous QTL mapping studies and GWASs for all studied traits. The results will be used for further studies related to the adaptation and productivity of wheat in breeding projects for higher grain productivity.
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Affiliation(s)
- Akerke Amalova
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
| | - Adylkhan Babkenov
- Alexandr Barayev Scientific-Production Center for Grain Farming, Shortandy 021600, Kazakhstan
| | | | | | - Saule Abugalieva
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Yerlan Turuspekov
- 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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2
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Sigalas PP, Shewry PR, Riche A, Wingen L, Feng C, Siluveru A, Chayut N, Burridge A, Uauy C, Castle M, Parmar S, Philp C, Steele D, Orford S, Leverington-Waite M, Cheng S, Griffiths S, Hawkesford MJ. Improving wheat grain composition for human health by constructing a QTL atlas for essential minerals. Commun Biol 2024; 7:1001. [PMID: 39147896 PMCID: PMC11327371 DOI: 10.1038/s42003-024-06692-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 08/06/2024] [Indexed: 08/17/2024] Open
Abstract
Wheat is an important source of minerals for human nutrition and increasing grain mineral content can contribute to reducing mineral deficiencies. Here, we identify QTLs for mineral micronutrients in grain of wheat by determining the contents of six minerals in a total of eleven sample sets of three biparental populations from crosses between A.E. Watkins landraces and cv. Paragon. Twenty-three of the QTLs are mapped in two or more sample sets, with LOD scores above five in at least one set with the increasing alleles for sixteen of the QTLs being present in the landraces and seven in Paragon. Of these QTLs, the number for each mineral varies between three and five and they are located on 14 of the 21 chromosomes, with clusters on chromosomes 5A (four), 6A (three), and 7A (three). The gene content within 5 megabases of DNA on either side of the marker for the QTL with the highest LOD score is determined and the gene responsible for the strongest QTL (chromosome 5A for Ca) identified as an ATPase transporter gene (TraesCS5A02G543300) using mutagenesis. The identification of these QTLs, together with associated SNP markers and candidate genes, will facilitate the improvement of grain nutritional quality.
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Affiliation(s)
| | - Peter R Shewry
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Andrew Riche
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Luzie Wingen
- John Innes Centre, Norwich, Norfolk, NR4 7UH, UK
| | - Cong Feng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | | | - Noam Chayut
- John Innes Centre, Norwich, Norfolk, NR4 7UH, UK
| | - Amanda Burridge
- School of Biological Sciences, University of Bristol, Bristol, BS8 1UD, UK
| | | | - March Castle
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Saroj Parmar
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | | | - David Steele
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Simon Orford
- John Innes Centre, Norwich, Norfolk, NR4 7UH, UK
| | | | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
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3
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Cheng S, Feng C, Wingen LU, Cheng H, Riche AB, Jiang M, Leverington-Waite M, Huang Z, Collier S, Orford S, Wang X, Awal R, Barker G, O'Hara T, Lister C, Siluveru A, Quiroz-Chávez J, Ramírez-González RH, Bryant R, Berry S, Bansal U, Bariana HS, Bennett MJ, Bicego B, Bilham L, Brown JKM, Burridge A, Burt C, Buurman M, Castle M, Chartrain L, Chen B, Denbel W, Elkot AF, Fenwick P, Feuerhelm D, Foulkes J, Gaju O, Gauley A, Gaurav K, Hafeez AN, Han R, Horler R, Hou J, Iqbal MS, Kerton M, Kondic-Spica A, Kowalski A, Lage J, Li X, Liu H, Liu S, Lovegrove A, Ma L, Mumford C, Parmar S, Philp C, Playford D, Przewieslik-Allen AM, Sarfraz Z, Schafer D, Shewry PR, Shi Y, Slafer GA, Song B, Song B, Steele D, Steuernagel B, Tailby P, Tyrrell S, Waheed A, Wamalwa MN, Wang X, Wei Y, Winfield M, Wu S, Wu Y, Wulff BBH, Xian W, Xu Y, Xu Y, Yuan Q, Zhang X, Edwards KJ, Dixon L, Nicholson P, Chayut N, Hawkesford MJ, Uauy C, Sanders D, Huang S, Griffiths S. Harnessing landrace diversity empowers wheat breeding. Nature 2024; 632:823-831. [PMID: 38885696 PMCID: PMC11338829 DOI: 10.1038/s41586-024-07682-9] [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: 09/18/2023] [Accepted: 06/06/2024] [Indexed: 06/20/2024]
Abstract
Harnessing genetic diversity in major staple crops through the development of new breeding capabilities is essential to ensure food security1. Here we examined the genetic and phenotypic diversity of the A. E. Watkins landrace collection2 of bread wheat (Triticum aestivum), a major global cereal, by whole-genome re-sequencing of 827 Watkins landraces and 208 modern cultivars and in-depth field evaluation spanning a decade. We found that modern cultivars are derived from two of the seven ancestral groups of wheat and maintain very long-range haplotype integrity. The remaining five groups represent untapped genetic sources, providing access to landrace-specific alleles and haplotypes for breeding. Linkage disequilibrium-based haplotypes and association genetics analyses link Watkins genomes to the thousands of identified high-resolution quantitative trait loci and significant marker-trait associations. Using these structured germplasm, genotyping and informatics resources, we revealed many Watkins-unique beneficial haplotypes that can confer superior traits in modern wheat. Furthermore, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritized quantitative trait loci in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilizing genetic diversity in crop improvement to achieve sustainable food security.
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Affiliation(s)
- Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Cong Feng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | | | - Hong Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | | | - Mei Jiang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | | | - Zejian Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | | | | | - Xiaoming Wang
- John Innes Centre, Norwich, UK
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | | | - Gary Barker
- Functional Genomics, School of Biological Sciences, University of Bristol, Bristol, UK
| | | | | | | | | | | | | | | | - Urmil Bansal
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, Cobbitty, New South Wales, Australia
| | - Harbans S Bariana
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, Cobbitty, New South Wales, Australia
- Western Sydney University, Richmond, New South Wales, Australia
| | - Malcolm J Bennett
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Breno Bicego
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida-AGROTECNIO-CERCA Center, Lleida, Spain
| | | | | | - Amanda Burridge
- Functional Genomics, School of Biological Sciences, University of Bristol, Bristol, UK
| | | | | | | | | | - Baizhi Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Worku Denbel
- Debre Zeit Agricultural Research Center, Ethiopian Institute of Agricultural Research, Debre Zeit, Ethiopia
| | - Ahmed F Elkot
- Wheat Research Department, Field Crops Research Institute, Agricultural Research Center, Giza, Egypt
| | | | | | - John Foulkes
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Oorbessy Gaju
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Adam Gauley
- School of Biology, University of Leeds, Leeds, UK
- Agri-Food and Biosciences Institute, Belfast, UK
| | | | | | - Ruirui Han
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Qingdao Agricultural University, Qingdao, China
| | | | - Junliang Hou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Muhammad S Iqbal
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | | | - Ankica Kondic-Spica
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Novi Sad, Republic of Serbia
| | | | | | - Xiaolong Li
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Hongbing Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shiyan Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | | | - Lingling Ma
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | | | | | | | | | | | - Zareen Sarfraz
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | | | | | - Yan Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Gustavo A Slafer
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida-AGROTECNIO-CERCA Center, Lleida, Spain
- ICREA, Catalonian Institution for Research and Advanced Studies, Barcelona, Spain
| | - Baoxing Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Bo Song
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | | | | | | | | | - Abdul Waheed
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | | | - Xingwei Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yanping Wei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Mark Winfield
- Functional Genomics, School of Biological Sciences, University of Bristol, Bristol, UK
| | - Shishi Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yubing Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Huazhong Agricultural University, Wuhan, China
| | - Brande B H Wulff
- John Innes Centre, Norwich, UK
- Center for Desert Agriculture, Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Wenfei Xian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Yawen Xu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Huazhong Agricultural University, Wuhan, China
| | - Yunfeng Xu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Quan Yuan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xin Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Huazhong Agricultural University, Wuhan, China
| | - Keith J Edwards
- Functional Genomics, School of Biological Sciences, University of Bristol, Bristol, UK
| | - Laura Dixon
- School of Biology, University of Leeds, Leeds, UK
| | | | | | | | | | | | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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4
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Liu Y, Fu B, Zhang Q, Cai J, Guo W, Zhai W, Wu J. Genetic diversity and population structure of wheat landraces in Southern Winter Wheat Region of China. BMC Genomics 2024; 25:664. [PMID: 38961357 PMCID: PMC11223385 DOI: 10.1186/s12864-024-10564-z] [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: 02/06/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Wheat landraces are considered a valuable source of genetic diversity for breeding programs. It is useful to evaluate the genetic diversity in breeding studies such as marker-assisted selection (MAS), genome-wide association studies (GWAS), and genomic selection. In addition, constructing a core germplasm set that represents the genetic diversity of the entire variety set is of great significance for the efficient conservation and utilization of wheat landrace germplasms. RESULTS To understand the genetic diversity in wheat landrace, 2,023 accessions in the Jiangsu Provincial Crop Germplasm Resource Bank were used to explore the molecular diversity and population structure using the Illumina 15 K single nucleotide polymorphism (SNP) chip. These accessions were divided into five subpopulations based on population structure, principal coordinate and kinship analysis. A significant variation was found within and among the subpopulations based on the molecular variance analysis (AMOVA). Subpopulation 3 showed more genetic variability based on the different allelic patterns (Na, Ne and I). The M strategy as implemented in MStratv 4.1 software was used to construct the representative core collection. A core collection with a total of 311 accessions (15.37%) was selected from the entire landrace germplasm based on genotype and 12 different phenotypic traits. Compared to the initial landrace collections, the core collection displayed higher gene diversity (0.31) and polymorphism information content (PIC) (0.25), and represented almost all phenotypic variation. CONCLUSIONS A core collection comprising 311 accessions containing 100% of the genetic variation in the initial population was developed. This collection provides a germplasm base for effective management, conservation, and utilization of the variation in the original set.
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Affiliation(s)
- Ying Liu
- Institute of Germplasm Resources and Biotechnology/Jiangsu Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Bisheng Fu
- Institute of Germplasm Resources and Biotechnology/Jiangsu Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu, 210014, China
| | - Qiaofeng Zhang
- Institute of Germplasm Resources and Biotechnology/Jiangsu Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Jin Cai
- Institute of Germplasm Resources and Biotechnology/Jiangsu Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu, 210014, China
| | - Wei Guo
- Institute of Germplasm Resources and Biotechnology/Jiangsu Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu, 210014, China
| | - Wenling Zhai
- Institute of Germplasm Resources and Biotechnology/Jiangsu Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Jizhong Wu
- Institute of Germplasm Resources and Biotechnology/Jiangsu Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China.
- Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu, 210014, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
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Wright TIC, Horsnell R, Love B, Burridge AJ, Gardner KA, Jackson R, Leigh FJ, Ligeza A, Heuer S, Bentley AR, Howell P. A new winter wheat genetic resource harbors untapped diversity from synthetic hexaploid wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:73. [PMID: 38451354 PMCID: PMC10920491 DOI: 10.1007/s00122-024-04577-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
KEY MESSAGE The NIAB_WW_SHW_NAM population, a large nested association mapping panel, is a useful resource for mapping QTL from synthetic hexaploid wheat that can improve modern elite wheat cultivars. The allelic richness harbored in progenitors of hexaploid bread wheat (Triticum aestivum L.) is a useful resource for addressing the genetic diversity bottleneck in modern cultivars. Synthetic hexaploid wheat (SHW) is created through resynthesis of the hybridisation events between the tetraploid (Triticum turgidum subsp. durum Desf.) and diploid (Aegilops tauschii Coss.) bread wheat progenitors. We developed a large and diverse winter wheat nested association mapping (NAM) population (termed the NIAB_WW_SHW_NAM) consisting of 3241 genotypes derived from 54 nested back-cross 1 (BC1) populations, each formed via back-crossing a different primary SHW into the UK winter wheat cultivar 'Robigus'. The primary SHW lines were created using 15 T. durum donors and 47 Ae. tauschii accessions that spanned the lineages and geographical range of the species. Primary SHW parents were typically earlier flowering, taller and showed better resistance to yellow rust infection (Yr) than 'Robigus'. The NIAB_WW_SHW_NAM population was genotyped using a single nucleotide polymorphism (SNP) array and 27 quantitative trait loci (QTLs) were detected for flowering time, plant height and Yr resistance. Across multiple field trials, a QTL for Yr resistance was found on chromosome 4D that corresponded to the Yr28 resistance gene previously reported in other SHW lines. These results demonstrate the value of the NIAB_WW_SHW_NAM population for genetic mapping and provide the first evidence of Yr28 working in current UK environments and genetic backgrounds. These examples, coupled with the evidence of commercial wheat breeders selecting promising genotypes, highlight the potential value of the NIAB_WW_SHW_NAM to variety improvement.
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Affiliation(s)
- Tally I C Wright
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
| | - Richard Horsnell
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Bethany Love
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | | | - Keith A Gardner
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
| | - Robert Jackson
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Fiona J Leigh
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Aleksander Ligeza
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
- Processors and Growers Research Organization (PGRO), The Research Station, Thornhaugh, Peterborough, PE8 6HJ, UK
| | - Sigrid Heuer
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Alison R Bentley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Philip Howell
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
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6
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Horsnell R, Leigh FJ, Wright TIC, Burridge AJ, Ligeza A, Przewieslik-Allen AM, Howell P, Uauy C, Edwards KJ, Bentley AR. A wheat chromosome segment substitution line series supports characterization and use of progenitor genetic variation. THE PLANT GENOME 2024; 17:e20288. [PMID: 36718796 DOI: 10.1002/tpg2.20288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/20/2022] [Indexed: 06/18/2023]
Abstract
Genome-wide introgression and substitution lines have been developed in many plant species, enhancing mapping precision, gene discovery, and the identification and exploitation of variation from wild relatives. Created over multiple generations of crossing and/or backcrossing accompanied by marker-assisted selection, the resulting introgression lines are a fixed genetic resource. In this study we report the development of spring wheat (Triticum aestivum L.) chromosome segment substitution lines (CSSLs) generated to systematically capture genetic variation from tetraploid (T. turgidum ssp. dicoccoides) and diploid (Aegilops tauschii) progenitor species. Generated in a common genetic background over four generations of backcrossing, this is a base resource for the mapping and characterization of wheat progenitor variation. To facilitate further exploitation the final population was genetically characterized using a high-density genotyping array and a range of agronomic and grain traits assessed to demonstrate the potential use of the populations for trait localization in wheat.
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Affiliation(s)
- Richard Horsnell
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | - Fiona J Leigh
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | - Tally I C Wright
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | | | - Aleksander Ligeza
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | | | - Philip Howell
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Alison R Bentley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
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7
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Korpetis E, Ninou E, Mylonas I, Ouzounidou G, Xynias IN, Mavromatis AG. Bread Wheat Landraces Adaptability to Low-Input Agriculture. PLANTS (BASEL, SWITZERLAND) 2023; 12:2561. [PMID: 37447122 DOI: 10.3390/plants12132561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
Bread wheat landraces were an important source of biodiversity used in agriculture before the widespread adoption of high-yielding commercial cultivars adapted to high inputs. Could future agriculture exploit these landraces in different cropping systems in organic or lower-input environments? A two-year field trial was conducted to evaluate grain yield, agronomic performance, and grain quality of bread wheat landraces under different cropping systems, including low-input/organic/conventional environments. Significant variability was found for almost all characteristics among landraces, which makes landraces valuable sources of genetic variation for breeding programs aimed at achieving high and consistent production as well as high-quality products in low-input/organic environments. Additionally, landraces play a crucial role in expanding the genetic diversity of cultivated bread wheat and mitigating biodiversity erosion, thereby enabling crops to better withstand the challenges of low-input/organic agriculture. The landrace "Xilokastro Lamias" had the highest yield among the landraces evaluated in the first growing season (2.65 t·ha-1) and one of the highest yields (2.52 t·ha-1) of all genotypes in the second growing season, which shows promising potential as a starting material in breeding programs targeting high and stable yields. GGE biplot analysis identified the landrace "Xilokastro Lamias", along with commercial cultivars "Yecora E" and "Panifor", as suitable candidates for direct use in low-input/organic wheat farming systems to achieve enhanced productivity. In the conventional environment (C2-IPGRB), commercial cultivars showed the highest values (3.09 to 3.41 ton·ha-1). Of the landraces, only the X4 showed a high GY (3.10 ton·ha-1) while the other landraces had ~33-85% lower yield. In the organic environment (O2-IPGRB), the highest productivity was found in the commercial cultivar X5 and the landrace X4. Commercial cultivars X8 and X7 showed ~68% reduction in GY in the organic environment compared to the conventional, while this reduction was half for the landraces. Finally, the reduction in grain yield between conventional and organic environments was observed to be 45% for commercial cultivars, while it was only half for landraces. This finding confirms the adaptability of landraces to organic agriculture.
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Affiliation(s)
- Evangelos Korpetis
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DIMITRA, 57001 Thessaloniki, Greece
| | - Elissavet Ninou
- Department of Agriculture, International Hellenic University, Sindos, 57400 Thessaloniki, Greece
| | - Ioannis Mylonas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DIMITRA, 57001 Thessaloniki, Greece
| | - Georgia Ouzounidou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization DIMITRA, S. Venizelou 1, Lycovrissi, 141 23 Attika, Greece
| | - Ioannis N Xynias
- School of Agricultural Technol. & Food Technol. and Nutrition, University of Western Macedonia, 53100 Florina, Greece
| | - Athanasios G Mavromatis
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Jiao C, Hao C, Li T, Bohra A, Wang L, Hou J, Liu H, Liu H, Zhao J, Wang Y, Liu Y, Wang Z, Jing X, Wang X, Varshney RK, Fu J, Zhang X. Fast integration and accumulation of beneficial breeding alleles through an AB-NAMIC strategy in wheat. PLANT COMMUNICATIONS 2023; 4:100549. [PMID: 36642955 DOI: 10.1016/j.xplc.2023.100549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/26/2022] [Accepted: 01/11/2023] [Indexed: 05/11/2023]
Abstract
Wheat (Triticum aestivum) is among the most important staple crops for safeguarding the food security of the growing world population. To bridge the gap between genebank diversity and breeding programs, we developed an advanced backcross-nested association mapping plus inter-crossed population (AB-NAMIC) by crossing three popular wheat cultivars as recurrent founders to 20 germplasm lines from a mini core collection. Selective backcrossing combined with selection against undesirable traits and extensive crossing within and between sub-populations created new opportunities to detect unknown genes and increase the frequency of beneficial alleles in the AB-NAMIC population. We performed phenotyping of 590 AB-NAMIC lines and a natural panel of 476 cultivars for six consecutive growing seasons and genotyped these 1066 lines with a 660K SNP array. Genome-wide association studies of both panels for plant development and yield traits demonstrated improved power to detect rare alleles and loci with medium genetic effects in AB-NAMIC. Notably, genome-wide association studies in AB-NAMIC detected the candidate gene TaSWEET6-7B (TraesCS7B03G1216700), which has high homology to the rice SWEET6b gene and exerts strong effects on adaptation and yield traits. The commercial release of two derived AB-NAMIC lines attests to its direct applicability in wheat improvement. Valuable information on genome-wide association study mapping, candidate genes, and their haplotypes for breeding traits are available through WheatGAB. Our research provides an excellent framework for fast-tracking exploration and accumulation of beneficial alleles stored in genebanks.
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Affiliation(s)
- Chengzhi Jiao
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Chenyang Hao
- 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
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Abhishek Bohra
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia
| | - Lanfen Wang
- 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
- 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
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hong Liu
- 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
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yamei Wang
- 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
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiwei Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Jing
- Smartgenomics Technology Institute, Tianjin 301700, China
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Rajeev K Varshney
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia.
| | - Junjie Fu
- 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
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
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Sharma S, Kumar T, Foulkes MJ, Orford S, Singh AM, Wingen LU, Karnam V, Nair LS, Mandal PK, Griffiths S, Hawkesford MJ, Shewry PR, Bentley AR, Pandey R. Nitrogen uptake and remobilization from pre- and post-anthesis stages contribute towards grain yield and grain protein concentration in wheat grown in limited nitrogen conditions. CABI AGRICULTURE AND BIOSCIENCE 2023; 4:12. [PMID: 38800116 PMCID: PMC11116178 DOI: 10.1186/s43170-023-00153-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 04/24/2023] [Indexed: 05/29/2024]
Abstract
Background In wheat, nitrogen (N) remobilization from vegetative tissues to developing grains largely depends on genetic and environmental factors. The evaluation of genetic potential of crops under limited resource inputs such as limited N supply would provide an opportunity to identify N-efficient lines with improved N utilisation efficiency and yield potential. We assessed the genetic variation in wheat recombinant inbred lines (RILs) for uptake, partitioning, and remobilization of N towards grain, its association with grain protein concentration (GPC) and grain yield. Methods We used the nested association mapping (NAM) population (195 lines) derived by crossing Paragon (P) with CIMMYT core germplasm (P × Cim), Baj (P × Baj), Watkins (P × Wat), and Wyalkatchem (P × Wya). These lines were evaluated in the field for two seasons under limited N supply. The plant sampling was done at anthesis and physiological maturity stages. Various physiological traits were recorded and total N uptake and other N related indices were calculated. The grain protein deviation (GPD) was calculated from the regression of grain yield on GPC. These lines were grouped into different clusters by hierarchical cluster analysis based on grain yield and N-remobilization efficiency (NRE). Results The genetic variation in accumulation of biomass at both pre- and post-anthesis stages were correlated with grain-yield. The NRE significantly correlated with aboveground N uptake at anthesis (AGNa) and grain yield but negatively associated with AGN at post-anthesis (AGNpa) suggesting higher N uptake till anthesis favours high N remobilization during grain filling. Hierarchical cluster analysis of these RILs based on NRE and yield resulted in four clusters, efficient (31), moderately efficient (59), moderately inefficient (58), and inefficient (47). In the N-efficient lines, AGNa contributed to 77% of total N accumulated in grains, while it was 63% in N-inefficient lines. Several N-efficient lines also exhibited positive grain protein deviation (GPD), combining high grain yield and GPC. Among crosses, the P × Cim were superior and N-efficient, while P × Wya responded poorly to low N input. Conclusions We propose that traits favouring pre- or post-anthesis biomass accumulation and pre-anthesis N uptake may be targeted for breeding to improve grain-yield under limited N. The lines with positive GPD, a first report of genotype-dependent GPD associated with both AGNpa and AGNa in wheat, may be used as varieties or genetic resources to improve grain yield with high GPC for sustainable development under limited N conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s43170-023-00153-7.
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Affiliation(s)
- Sandeep Sharma
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Tarun Kumar
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - M. John Foulkes
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Leicestershire, LE12 5RD UK
| | - Simon Orford
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Anju Mahendru Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Luzie U. Wingen
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Venkatesh Karnam
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana India
| | - Lekshmy S. Nair
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Pranab Kumar Mandal
- National Institute of Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Simon Griffiths
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | | | - Peter R. Shewry
- Plant Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ UK
| | - Alison R. Bentley
- National Institute for Agricultural Botany, Cambridge, CB3 0LE UK
- Present Address: International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Mexico
| | - Renu Pandey
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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10
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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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11
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Zafeiriou P, Savva GM, Ahn-Jarvis JH, Warren FJ, Pasquariello M, Griffiths S, Seung D, Hazard BA. Mining the A.E. Watkins Wheat Landrace Collection for Variation in Starch Digestibility Using a New High-Throughput Assay. Foods 2023; 12:266. [PMID: 36673358 PMCID: PMC9858048 DOI: 10.3390/foods12020266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/11/2023] Open
Abstract
Breeding for less digestible starch in wheat can improve the health impact of bread and other wheat foods. The application of forward genetic approaches has lately opened opportunities for the discovery of new genes that influence the digestibility of starch, without the burden of detrimental effects on yield or on pasta and bread-making quality. In this study we developed a high-throughput in vitro starch digestibility assay (HTA) for use in forward genetic approaches to screen wheat germplasm. The HTA was validated using standard maize and wheat starches. Using the HTA we measured starch digestibility in hydrothermally processed flour samples and found wide variation among 118 wheat landraces from the A. E. Watkins collection and among eight elite UK varieties (23.5 to 39.9% and 31.2 to 43.5% starch digested after 90 min, respectively). We further investigated starch digestibility in fractions of sieved wholemeal flour and purified starch in a subset of the Watkins lines and elite varieties and found that the matrix properties of flour rather than the intrinsic properties of starch granules conferred lower starch digestibility.
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12
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Luo G, Najafi J, Correia PMP, Trinh MDL, Chapman EA, Østerberg JT, Thomsen HC, Pedas PR, Larson S, Gao C, Poland J, Knudsen S, DeHaan L, Palmgren M. Accelerated Domestication of New Crops: Yield is Key. PLANT & CELL PHYSIOLOGY 2022; 63:1624-1640. [PMID: 35583202 PMCID: PMC9680862 DOI: 10.1093/pcp/pcac065] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/17/2022] [Accepted: 05/17/2022] [Indexed: 05/05/2023]
Abstract
Sustainable agriculture in the future will depend on crops that are tolerant to biotic and abiotic stresses, require minimal input of water and nutrients and can be cultivated with a minimal carbon footprint. Wild plants that fulfill these requirements abound in nature but are typically low yielding. Thus, replacing current high-yielding crops with less productive but resilient species will require the intractable trade-off of increasing land area under cultivation to produce the same yield. Cultivating more land reduces natural resources, reduces biodiversity and increases our carbon footprint. Sustainable intensification can be achieved by increasing the yield of underutilized or wild plant species that are already resilient, but achieving this goal by conventional breeding programs may be a long-term prospect. De novo domestication of orphan or crop wild relatives using mutagenesis is an alternative and fast approach to achieve resilient crops with high yields. With new precise molecular techniques, it should be possible to reach economically sustainable yields in a much shorter period of time than ever before in the history of agriculture.
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Affiliation(s)
- Guangbin Luo
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C DK-1871, Denmark
| | - Javad Najafi
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C DK-1871, Denmark
| | - Pedro M P Correia
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C DK-1871, Denmark
| | - Mai Duy Luu Trinh
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C DK-1871, Denmark
| | - Elizabeth A Chapman
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V DK-1799, Denmark
| | | | | | - Pai Rosager Pedas
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V DK-1799, Denmark
| | - Steve Larson
- US Department of Agriculture (USDA), USDA–ARS Forage & Range Research Lab, Utah State University Logan, Logan, UT 84322, USA
| | - Caixia Gao
- Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jesse Poland
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Makkah 23955, Saudi Arabia
| | - Søren Knudsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V DK-1799, Denmark
| | - Lee DeHaan
- The Land Institute, Salina, KS 67401, USA
| | - Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C DK-1871, Denmark
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13
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Niu Y, Chen T, Zhao C, Guo C, Zhou M. Identification of QTL for Stem Traits in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:962253. [PMID: 35909739 PMCID: PMC9330363 DOI: 10.3389/fpls.2022.962253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Lodging in wheat (Triticum aestivum L.) is a complicated phenomenon that is influenced by physiological, genetics, and external factors. It causes a great yield loss and reduces grain quality and mechanical harvesting efficiency. Lodging resistance is contributed by various traits, including increased stem strength. The aim of this study was to map quantitative trait loci (QTL) controlling stem strength-related features (the number of big vascular bundles, stem diameter, stem wall thickness) using a doubled haploid (DH) population derived from a cross between Baiqimai and Neixiang 5. Field experiments were conducted during 2020-2022, and glasshouse experiments were conducted during 2021-2022. Significant genetic variations were observed for all measured traits, and they were all highly heritable. Fifteen QTL for stem strength-related traits were identified on chromosomes 2D, 3A, 3B, 3D, 4B, 5A, 6B, 7A, and 7D, respectively, and 7 QTL for grain yield-related traits were identified on chromosomes 2B, 2D, 3D, 4B, 7A, and 7B, respectively. The superior allele of the major QTL for the number of big vascular bundle (VB) was independent of plant height (PH), making it possible to improve stem strength without a trade-off of PH, thus improving lodging resistance. VB also showed positive correlations with some of the yield components. The result will be useful for molecular marker-assisted selection (MAS) for high stem strength and high yield potential.
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Affiliation(s)
- Yanan Niu
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Tianxiao Chen
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Ce Guo
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
- College of Agronomy, Shanxi Agricultural University, Taigu, China
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14
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Yang M, Yang Z, Yang W, Yang E. Genetic Diversity Assessment of the International Maize and Wheat Improvement Center and Chinese Wheat Core Germplasms by Non-Denaturing Fluorescence In Situ Hybridization. PLANTS (BASEL, SWITZERLAND) 2022; 11:1403. [PMID: 35684176 PMCID: PMC9183173 DOI: 10.3390/plants11111403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Germplasm is the material basis for crop genetic improvement and related basic research. Knowledge of genetic diversity present in wheat is the prerequisite for wheat breeding and improvement. Non-denaturing fluorescence in situ hybridization (ND-FISH) is a powerful tool to distinguish chromosomal polymorphisms and evaluate genetic diversity in wheat. In this study, ND-FISH using Oligo-pSc119.2-1, Oligo-pTa535-1, and Oligo-(GAA)7 as probes were used to analyze the genetic diversity among 60 International Maize and Wheat Improvement Center (CIMMYT) derived wheat lines, and 93 cultivated wheat and landraces from the Chinese wheat core germplasm. A total of 137 polymorphic FISH patterns were obtained, in which 41, 65, and 31 were from A-, B-, and D-genome chromosomes, respectively, indicating polymorphism of B-genome > A-genome > D-genome. In addition, 22 and 51 specific FISH types were observed in the two germplasm resource lines. Twelve types of rearrangements, including seven new translocations, were detected in all 153 wheat lines. Genetic relationships among 153 wheat lines were clustered into six groups. Our research provides cytological information for rational utilization of wheat germplasm resources.
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Affiliation(s)
- Manyu Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (M.Y.); (W.Y.)
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Chengdu 610066, China
- Environment-friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China;
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (M.Y.); (W.Y.)
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Chengdu 610066, China
- Environment-friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Ennian Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (M.Y.); (W.Y.)
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Chengdu 610066, China
- Environment-friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
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15
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Shewry PR, Lovegrove A, Wingen LU, Griffiths S. Opinion Exploiting genomics to improve the benefits of wheat: Prospects and limitations. J Cereal Sci 2022; 105:103444. [PMID: 35712025 PMCID: PMC9106566 DOI: 10.1016/j.jcs.2022.103444] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/14/2022] [Accepted: 02/25/2022] [Indexed: 11/17/2022]
Abstract
Image 1.
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Affiliation(s)
| | | | - Luzie U. Wingen
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Simon Griffiths
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
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16
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Leigh FJ, Wright TIC, Horsnell RA, Dyer S, Bentley AR. Progenitor species hold untapped diversity for potential climate-responsive traits for use in wheat breeding and crop improvement. Heredity (Edinb) 2022; 128:291-303. [PMID: 35383318 PMCID: PMC9076643 DOI: 10.1038/s41437-022-00527-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/13/2022] [Accepted: 03/15/2022] [Indexed: 01/07/2023] Open
Abstract
Climate change will have numerous impacts on crop production worldwide necessitating a broadening of the germplasm base required to source and incorporate novel traits. Major variation exists in crop progenitor species for seasonal adaptation, photosynthetic characteristics, and root system architecture. Wheat is crucial for securing future food and nutrition security and its evolutionary history and progenitor diversity offer opportunities to mine favourable functional variation in the primary gene pool. Here we provide a review of the status of characterisation of wheat progenitor variation and the potential to use this knowledge to inform the use of variation in other cereal crops. Although significant knowledge of progenitor variation has been generated, we make recommendations for further work required to systematically characterise underlying genetics and physiological mechanisms and propose steps for effective use in breeding. This will enable targeted exploitation of useful variation, supported by the growing portfolio of genomics and accelerated breeding approaches. The knowledge and approaches generated are also likely to be useful across wider crop improvement.
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Affiliation(s)
- Fiona J Leigh
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Tally I C Wright
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Richard A Horsnell
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Sarah Dyer
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Alison R Bentley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
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Javed T, I I, Singhal RK, Shabbir R, Shah AN, Kumar P, Jinger D, Dharmappa PM, Shad MA, Saha D, Anuragi H, Adamski R, Siuta D. Recent Advances in Agronomic and Physio-Molecular Approaches for Improving Nitrogen Use Efficiency in Crop Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:877544. [PMID: 35574130 PMCID: PMC9106419 DOI: 10.3389/fpls.2022.877544] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/11/2022] [Indexed: 05/05/2023]
Abstract
The efficiency with which plants use nutrients to create biomass and/or grain is determined by the interaction of environmental and plant intrinsic factors. The major macronutrients, especially nitrogen (N), limit plant growth and development (1.5-2% of dry biomass) and have a direct impact on global food supply, fertilizer demand, and concern with environmental health. In the present time, the global consumption of N fertilizer is nearly 120 MT (million tons), and the N efficiency ranges from 25 to 50% of applied N. The dynamic range of ideal internal N concentrations is extremely large, necessitating stringent management to ensure that its requirements are met across various categories of developmental and environmental situations. Furthermore, approximately 60 percent of arable land is mineral deficient and/or mineral toxic around the world. The use of chemical fertilizers adds to the cost of production for the farmers and also increases environmental pollution. Therefore, the present study focused on the advancement in fertilizer approaches, comprising the use of biochar, zeolite, and customized nano and bio-fertilizers which had shown to be effective in improving nitrogen use efficiency (NUE) with lower soil degradation. Consequently, adopting precision farming, crop modeling, and the use of remote sensing technologies such as chlorophyll meters, leaf color charts, etc. assist in reducing the application of N fertilizer. This study also discussed the role of crucial plant attributes such as root structure architecture in improving the uptake and transport of N efficiency. The crosstalk of N with other soil nutrients plays a crucial role in nutrient homeostasis, which is also discussed thoroughly in this analysis. At the end, this review highlights the more efficient and accurate molecular strategies and techniques such as N transporters, transgenes, and omics, which are opening up intriguing possibilities for the detailed investigation of the molecular components that contribute to nitrogen utilization efficiency, thus expanding our knowledge of plant nutrition for future global food security.
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Affiliation(s)
- Talha Javed
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Indu I
- Indian Council of Agricultural Research (ICAR)-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Rajesh Kumar Singhal
- Indian Council of Agricultural Research (ICAR)-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Rubab Shabbir
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Plant Breeding and Genetics, Seed Science and Technology, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Pawan Kumar
- Indian Council of Agricultural Research (ICAR)-Central Institute for Arid Horticulture, Bikaner, India
| | - Dinesh Jinger
- Research Centre, Indian Council of Agricultural Research (ICAR)-Indian Institute of Soil and Water Conservation, Anand, India
| | - Prathibha M. Dharmappa
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Horticultural Research, Bengaluru, India
| | - Munsif Ali Shad
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene, Hubei Hongshan Laboratory, Wuhan, China
| | - Debanjana Saha
- Centurion University of Technology and Management, Jatni, India
| | - Hirdayesh Anuragi
- Indian Council of Agricultural Research (ICAR)- Central Agroforestry Research Institute, Jhansi, India
| | - Robert Adamski
- Faculty of Process and Environmental Engineering, Łódź University of Technology, Łódź, Poland
| | - Dorota Siuta
- Faculty of Process and Environmental Engineering, Łódź University of Technology, Łódź, Poland
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18
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Huang Z, Qiao F, Yang B, Liu J, Liu Y, Wulff BBH, Hu P, Lv Z, Zhang R, Chen P, Xing L, Cao A. Genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq. BMC Genomics 2022; 23:118. [PMID: 35144544 PMCID: PMC8832786 DOI: 10.1186/s12864-022-08334-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 01/24/2022] [Indexed: 01/19/2023] Open
Abstract
Background Nucleotide-binding and leucine-rich repeat (NLR) genes have attracted wide attention due to their crucial role in protecting plants from pathogens. SMRT-RenSeq, combining PacBio sequencing after resistance gene enrichment sequencing (RenSeq), is a powerful method for selectively capturing and sequencing full-length NLRs. Haynaldia villosa, a wild grass species with a proven potential for wheat improvement, confers resistance to multiple diseases. So, genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq can facilitate disease resistance genes exploration. Results In this study, SMRT-RenSeq was performed to identify the genome-wide NLR complement of H. villosa. In total, 1320 NLRs were annotated in 1169 contigs, including 772 complete NLRs. All the complete NLRs were phylogenetically analyzed and 11 main clades with special characteristics were derived. NLRs could be captured with high efficiency when aligned with cloned R genes, and cluster expansion in some specific gene loci was observed. The physical location of NLRs to individual chromosomes in H. villosa showed a perfect homoeologous relationship with group 1, 2, 3, 5 and 6 of other Triticeae species, however, NLRs physically located on 4VL were largely in silico predicted to be located on the homoeologous group 7. Fifteen types of integrated domains (IDs) were integrated in 52 NLRs, and Kelch and B3 NLR-IDs were found to have expanded in H. villosa, while DUF948, NAM-associated and PRT_C were detected as unique integrated domains implying the new emergence of NLR-IDs after H. villosa diverged from other species. Conclusion SMRT-RenSeq is a powerful tool to identify NLR genes from wild species using the baits of the evolutionary related species with reference sequences. The availability of the NLRs from H. villosa provide a valuable library for R gene mining and transfer of disease resistance into wheat. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08334-w.
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Affiliation(s)
- Zhenpu Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Fangyuan Qiao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Boming Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Jiaqian Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Yangqi Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Brande B H Wulff
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Ping Hu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Zengshuai Lv
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Ruiqi Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Peidu Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Liping Xing
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China.
| | - Aizhong Cao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China.
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19
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Yang Z, Mu Y, Wang Y, He F, Shi L, Fang Z, Zhang J, Zhang Q, Geng G, Zhang S. Characterization of a Novel TtLEA2 Gene From Tritipyrum and Its Transformation in Wheat to Enhance Salt Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:830848. [PMID: 35444677 PMCID: PMC9014267 DOI: 10.3389/fpls.2022.830848] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/11/2022] [Indexed: 05/12/2023]
Abstract
Late embryogenesis-abundant (LEA) proteins are critical in helping plants cope with salt stress. "Y1805" is a salt-tolerant Tritipyrum. We identified a "Y1805"-specific LEA gene that was expressed highly and sensitively under salt stress using transcriptome analysis. The novel group 2 LEA gene (TtLEA2-1) was cloned from "Y1805." TtLEA2-1 contained a 453 bp open reading frame encoding an 151-amino-acid protein that showed maximum sequence identity (77.00%) with Thinopyrum elongatum by phylogenetic analysis. It was mainly found to be expressed highly in the roots by qRT-PCR analysis and was located in the whole cell. Forty-eight candidate proteins believed to interact with TtLEA2-1 were confirmed by yeast two-hybrid analysis. These interacting proteins were mainly enriched in "environmental information processing," "glycan biosynthesis and metabolism," and "carbohydrate metabolism." Protein-protein interaction analysis indicated that the translation-related 40S ribosomal protein SA was the central node. An efficient wheat transformation system has been established. A coleoptile length of 2 cm, an Agrobacteria cell density of 0.55-0.60 OD600, and 15 KPa vacuum pressure were ideal for common wheat transformation, with an efficiency of up to 43.15%. Overexpression of TaLEA2-1 in wheat "1718" led to greater height, stronger roots, and higher catalase activity than in wild type seedlings. TaLEA2-1 conferred enhanced salt tolerance in transgenic wheat and may be a valuable gene for genetic modification in crops.
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Affiliation(s)
- Zhifen Yang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Yuanhang Mu
- College of Agriculture, Guizhou University, Guiyang, China
| | - Yiqin Wang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Fang He
- College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Subcenter of National Wheat Improvement Center, Guiyang, China
| | - Luxi Shi
- College of Agriculture, Guizhou University, Guiyang, China
| | - Zhongming Fang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Jun Zhang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Qingqin Zhang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Guangdong Geng
- College of Agriculture, Guizhou University, Guiyang, China
- *Correspondence: Guangdong Geng,
| | - Suqin Zhang
- College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Subcenter of National Wheat Improvement Center, Guiyang, China
- Suqin Zhang,
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20
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Winfield M, Wilkinson P, Burridge A, Allen A, Coghill J, Waterfall C, Edwards K, Barker G. CerealsDB: A Whistle-Stop Tour of an Open Access SNP Resource. Methods Mol Biol 2022; 2443:133-146. [PMID: 35037203 DOI: 10.1007/978-1-0716-2067-0_6] [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] [Indexed: 06/14/2023]
Abstract
The CerealsDB website, created by members of the Functional Genomics Group at the University of Bristol, provides access to a database containing SNP and genotyping data for hexaploid wheat and, to a lesser extent, its progenitors and several of its relatives. The site is principally aimed at plant breeders and research scientists who wish to obtain information regarding SNP markers; for example, obtain primers used for their identification or the sequences upon which they are based. The database underpinning the website contains circa one million putative varietal SNPs of which several hundreds of thousands have been experimentally validated on a range of common genotyping platforms. For each SNP marker, the site also hosts the allelic scores for thousands of elite wheat varieties, landrace cultivars, and wheat relatives. Tools are available to help negotiate and visualize the datasets. The website has been designed to be simple and straightforward to use and is completely open access.
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Affiliation(s)
- Mark Winfield
- School of Biological Sciences, University of Bristol, Bristol, UK.
| | - Paul Wilkinson
- Department of Functional and Comparative Genomics, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Amanda Burridge
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Alexandra Allen
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Jane Coghill
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Keith Edwards
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Gary Barker
- School of Biological Sciences, University of Bristol, Bristol, UK
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21
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Zhang S, Du P, Lu X, Fang J, Wang J, Chen X, Chen J, Wu H, Yang Y, Tsujimoto H, Chu C, Qi Z. Frequent numerical and structural chromosome changes in early generations of synthetic hexaploid wheat. Genome 2021; 65:205-217. [PMID: 34914567 DOI: 10.1139/gen-2021-0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Modern hexaploid wheat (Triticum aestivum L.; AABBDD) evolved from a hybrid of tetraploid wheat (closely related to Triticum turgidum L. ssp. durum (Desf.) Husn., AABB) and goatgrass (Aegilops tauschii Coss., DD). Variations in chromosome structure and ploidy played important roles in wheat evolution. How these variations occurred and their role in expanding the genetic diversity in modern wheat is mostly unknown. Synthetic hexaploid wheat (SHW) can be used to investigate chromosome variation that occurs during the early generations of existence. SHW lines derived by crossing durum wheat 'Langdon' with twelve Ae. tauschii accessions were analyzed using oligonucelotide probe multiplex fluorescence in situ hybridization (FISH) to metaphase chromosomes and SNP markers. Cluster analysis based on SNP markers categorized them into three groups. Among 702 plants from the S8 and S9 generations, 415 (59.12%) carried chromosome variations involving all 21 chromosomes but with different frequencies for each chromosome and sub-genome. Total chromosome variation frequencies varied between lines, but there was no significant difference among the three groups. The non-random chromosome variations in SHW lines detected in this research may be an indication that similar variations occurred in the early stages of wheat polyploidization and played important roles in wheat evolution.
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Affiliation(s)
- Siyu Zhang
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Pei Du
- Henan Academy of Agricultural Sciences, 74728, Henan Academy of Crop Molecular Breeding, Zhengzhou, Henan, China;
| | - Xueying Lu
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Jiaxin Fang
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Jiaqi Wang
- Nanjing Agricultural University, 70578, Weigang No.1, Nanjing, Jiangsu, China, 210095;
| | - Xuejun Chen
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Jianyong Chen
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Hao Wu
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Yang Yang
- Zaozhuang University, 372543, Zaozhuang, Shandong, China;
| | - Hisashi Tsujimoto
- Tottori University, 13114, Arid Land Research Center, Hamasaka, Tottori, Japan;
| | - Chenggen Chu
- USDA ARS, 17123, Fargo, North Dakota, United States;
| | - Zengjun Qi
- Nanjing Agricultural University, 70578, Weigang 1,Nanjing, Nanjing, China, 210095;
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22
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Dyda M, Tyrka M, Gołębiowska G, Rapacz M, Wędzony M. Genetic mapping of adult-plant resistance genes to powdery mildew in triticale. J Appl Genet 2021; 63:73-86. [PMID: 34561842 PMCID: PMC8755695 DOI: 10.1007/s13353-021-00664-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 11/21/2022]
Abstract
Triticale is a cereal of high economic importance; however, along with the increase in the area of this cereal, it is more often infected by the fungal pathogen Blumeria graminis, which causes powdery mildew. The rapid development of molecular biology techniques, in particular methods based on molecular markers may be an important tool used in modern plant breeding. Development of genetic maps, location of the QTLs defining the region of the genome associated with resistance and selection of markers linked to particular trait can be used to select resistant genotypes as well as to pyramidize several resistance genes in one variety. In this paper, we present a new, high-density genetic map of triticale doubled haploids (DH) population “Grenado” × “Zorro” composed of DArT, silicoDArT, and SNP markers. Composite interval mapping method was used to detect eight QTL regions associated with the area under disease progress curve (AUDPC) and 15 regions with the average value of powdery mildew infection (avPM) based on observation conducted in 3-year period in three different locations across the Poland. Two regions on rye chromosome 4R, and single loci on 5R and 6R were reported for the first time as regions associated with powdery mildew resistance. Among all QTLs, 14 candidate genes were identified coded cyclin-dependent kinase, serine/threonine-protein kinase-like protein as well as AMEIOTIC 1 homolog DYAD-like protein, DETOXIFICATION 16-like protein, and putative disease resistance protein RGA3. Three of identified candidate genes were found among newly described QTL regions associated with powdery mildew resistance in triticale.
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Affiliation(s)
- Mateusz Dyda
- Chair of Genetics, Institute of Biology, Pedagogical University of Cracow, Podchorążych 2, 30-084, Kraków, Poland.
| | - Mirosław Tyrka
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszów University of Technology, Rzeszów, Poland
| | - Gabriela Gołębiowska
- Chair of Genetics, Institute of Biology, Pedagogical University of Cracow, Podchorążych 2, 30-084, Kraków, Poland
| | - Marcin Rapacz
- Department of Plant Breeding, Physiology and Seed Science, University of Agriculture in Kraków, Podłużna 3, 30-239, Krakow, Poland
| | - Maria Wędzony
- Chair of Genetics, Institute of Biology, Pedagogical University of Cracow, Podchorążych 2, 30-084, Kraków, Poland
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23
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Qu P, Wang J, Wen W, Gao F, Liu J, Xia X, Peng H, Zhang L. Construction of Consensus Genetic Map With Applications in Gene Mapping of Wheat ( Triticum aestivum L.) Using 90K SNP Array. FRONTIERS IN PLANT SCIENCE 2021; 12:727077. [PMID: 34512703 PMCID: PMC8424075 DOI: 10.3389/fpls.2021.727077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/28/2021] [Indexed: 06/02/2023]
Abstract
Wheat is one of the most important cereal crops worldwide. A consensus map combines genetic information from multiple populations, providing an effective alternative to improve the genome coverage and marker density. In this study, we constructed a consensus map from three populations of recombinant inbred lines (RILs) of wheat using a 90K single nucleotide polymorphism (SNP) array. Phenotypic data on plant height (PH), spike length (SL), and thousand-kernel weight (TKW) was collected in six, four, and four environments in the three populations, and then used for quantitative trait locus (QTL) mapping. The mapping results obtained using the constructed consensus map were compared with previous results obtained using individual maps and previous studies on other populations. A simulation experiment was also conducted to assess the performance of QTL mapping with the consensus map. The constructed consensus map from the three populations spanned 4558.55 cM in length, with 25,667 SNPs, having high collinearity with physical map and individual maps. Based on the consensus map, 21, 27, and 19 stable QTLs were identified for PH, SL, and TKW, much more than those detected with individual maps. Four PH QTLs and six SL QTLs were likely to be novel. A putative gene called TraesCS4D02G076400 encoding gibberellin-regulated protein was identified to be the candidate gene for one major PH QTL located on 4DS, which may enrich genetic resources in wheat semi-dwarfing breeding. The simulation results indicated that the length of the confidence interval and standard errors of the QTLs detected using the consensus map were much smaller than those detected using individual maps. The consensus map constructed in this study provides the underlying genetic information for systematic mapping, comparison, and clustering of QTL, and gene discovery in wheat genetic study. The QTLs detected in this study had stable effects across environments and can be used to improve the wide adaptation of wheat cultivars through marker-assisted breeding.
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Affiliation(s)
- Pingping Qu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jiankang Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weie Wen
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
| | - Fengmei Gao
- Crop Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jindong Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianchun Xia
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiru Peng
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Luyan Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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24
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Alabdullah AK, Moore G, Martín AC. A Duplicated Copy of the Meiotic Gene ZIP4 Preserves up to 50% Pollen Viability and Grain Number in Polyploid Wheat. BIOLOGY 2021; 10:290. [PMID: 33918149 PMCID: PMC8065865 DOI: 10.3390/biology10040290] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 12/20/2022]
Abstract
Although most flowering plants are polyploid, little is known of how the meiotic process evolves after polyploidisation to stabilise and preserve fertility. On wheat polyploidisation, the major meiotic gene ZIP4 on chromosome 3B duplicated onto 5B and diverged (TaZIP4-B2). TaZIP4-B2 was recently shown to promote homologous pairing, synapsis and crossover, and suppress homoeologous crossover. We therefore suspected that these meiotic stabilising effects could be important for preserving wheat fertility. A CRISPR Tazip4-B2 mutant was exploited to assess the contribution of the 5B duplicated ZIP4 copy in maintaining pollen viability and grain setting. Analysis demonstrated abnormalities in 56% of meiocytes in the Tazip4-B2 mutant, with micronuclei in 50% of tetrads, reduced size in 48% of pollen grains and a near 50% reduction in grain number. Further studies showed that most of the reduced grain number occurred when Tazip4-B2 mutant plants were pollinated with the less viable Tazip4-B2 mutant pollen rather than with wild type pollen, suggesting that the stabilising effect of TaZIP4-B2 on meiosis has a greater consequence in subsequent male, rather than female gametogenesis. These studies reveal the extraordinary value of the wheat chromosome 5B TaZIP4-B2 duplication to agriculture and human nutrition. Future studies should further investigate the role of TaZIP4-B2 on female fertility and assess whether different TaZIP4-B2 alleles exhibit variable effects on meiotic stabilisation and/or resistance to temperature change.
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Affiliation(s)
| | - Graham Moore
- Crop Genetics Department, John Innes Centre, Colney, Norwich NR4 7UH, UK; (A.K.A.); (A.C.M.)
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25
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Wheat Developmental Traits as Affected by the Interaction between Eps-7D and Temperature under Contrasting Photoperiods with Insensitive Ppd-D1 Background. PLANTS 2021; 10:plants10030547. [PMID: 33805828 PMCID: PMC7999118 DOI: 10.3390/plants10030547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/01/2021] [Accepted: 03/09/2021] [Indexed: 01/14/2023]
Abstract
Earliness per se (Eps) genes are important to fine tune adaptation, and studying their probable pleiotropic effect on wheat yield traits is worthwhile. In addition, it has been shown that some Eps genes interact with temperature and therefore determining the likely Eps × temperature interaction is needed for each newly identified Eps gene. We studied two NILs differing in the newly identified Eps-7D (carrying insensitive Ppd-D1 in the background) under three temperature regimes (9, 15 and 18 °C) and two photoperiods (12 and 24 h). Eps-7D affected time to anthesis as expected and the Eps-7D-late allele extended both the period before and after terminal spikelet. The interaction effect of Eps-7D × temperature was significant but not cross-over: the magnitude and level of significance of the difference between NILs with the late or early allele was affected by the growing temperature (i.e., difference was least at 18 °C and largest at 9 °C), and the differences caused due to temperature sensitivity were influenced by photoperiod. The rate of leaf initiation was faster in NIL with Eps-7D-early than with the late allele which compensated for the shorter duration of leaf initiation resulting in similar final leaf number between two NILs. Eps-7D-late consistently increased spike fertility through improving floret primordia survival as a consequence of extending the late reproductive phase.
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Hayta S, Smedley MA, Clarke M, Forner M, Harwood WA. An Efficient Agrobacterium-Mediated Transformation Protocol for Hexaploid and Tetraploid Wheat. Curr Protoc 2021; 1:e58. [PMID: 33656289 DOI: 10.1002/cpz1.58] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Wheat, though a key crop plant with considerable influence on world food security, has nonetheless trailed behind other major cereals in the advancement of gene transformation technology for its improvement. New breeding technologies such as genome editing allow precise DNA manipulation, but their potential is limited by low regeneration efficiencies in tissue culture and the lack of transformable genotypes. We developed, in the hexaploid spring wheat cultivar "Fielder," a robust, reproducible Agrobacterium tumefaciens-mediated transformation system with transformation efficiencies of up to 33%. The system requires immature embryos as starting material and includes a centrifugation pretreatment before the inoculation with Agrobacterium. This high-throughput, highly efficient, and repeatable transformation system has been used effectively to introduce genes of interest for overexpression, RNA interference, and CRISPR-Cas-based genome editing. With slight modifications reported here, the standard protocol can be applied to the hexaploid wheat "Cadenza" and the tetraploid durum wheat "Kronos" with efficiencies of up to 4% and 10%, respectively. The system has also been employed to assess the developmental gene fusion GRF-GIF with outstanding results. In our hands, this technology combined with our transformation system improved transformation efficiency to 77.5% in Fielder. This combination should help alleviate the genotype dependence of wheat transformation, allowing new genome-editing tools to be used directly in more elite wheat varieties. © 2021 The Authors. Basic Protocol 1: Growing of donor plants Basic Protocol 2: Transformation of Agrobacterium with vector by electroporation Basic Protocol 3: Starting material collection, sterilization, and embryo inoculation Basic Protocol 4: Selection, regeneration, rooting, and acclimatization of transformants.
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Affiliation(s)
- Sadiye Hayta
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, Norfolk, UK
| | - Mark A Smedley
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, Norfolk, UK
| | - Martha Clarke
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, Norfolk, UK
| | - Macarena Forner
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, Norfolk, UK
| | - Wendy A Harwood
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, Norfolk, UK
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Basavaraddi PA, Savin R, Wingen LU, Bencivenga S, Przewieslik-Allen AM, Griffiths S, Slafer GA. Interactions between two QTLs for time to anthesis on spike development and fertility in wheat. Sci Rep 2021; 11:2451. [PMID: 33510240 PMCID: PMC7843729 DOI: 10.1038/s41598-021-81857-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/12/2021] [Indexed: 01/30/2023] Open
Abstract
Earliness per se (Eps) genes are reported to be important in fine-tuning flowering time in wheat independently of photoperiod (Ppd) and vernalisation (Vrn). Unlike Ppd and Vrn genes, Eps have relatively small effects and their physiological effect along with chromosomal position are not well defined. We evaluated eight lines derived from crossing two vernalisation insensitive lines, Paragon and Baj (late and early flowering respectively), to study the detailed effects of two newly identified QTLs, Eps-7D and Eps-2B and their interactions under field conditions. The effect of both QTLs was minor and was affected by the allelic status of the other. While the magnitude of effect of these QTLs on anthesis was similar, they are associated with very different profiles of pre-anthesis development which also depends on their interaction. Eps-7D affected both duration before and after terminal spikelet while not affecting final leaf number (FLN) so Eps-7D-early had a faster rate of leaf appearance. Eps-2B acted more specifically in the early reproductive phase and slightly altered FLN without affecting the leaf appearance rate. Both QTLs affected the spike fertility by altering the rate of floret development and mortality. The effect of Eps-2B was very small but consistent in that -late allele tended to produce more fertile florets.
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Affiliation(s)
- Priyanka A. Basavaraddi
- grid.15043.330000 0001 2163 1432Department of Crop and Forest Sciences, University of Lleida-AGROTECNIO Center, Av. R. Roure 191, 25198 Lleida, Spain
| | - Roxana Savin
- grid.15043.330000 0001 2163 1432Department of Crop and Forest Sciences, University of Lleida-AGROTECNIO Center, Av. R. Roure 191, 25198 Lleida, Spain
| | - Luzie U. Wingen
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Stefano Bencivenga
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | | | - Simon Griffiths
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Gustavo A. Slafer
- grid.15043.330000 0001 2163 1432Department of Crop and Forest Sciences, University of Lleida-AGROTECNIO Center, Av. R. Roure 191, 25198 Lleida, Spain ,grid.425902.80000 0000 9601 989XICREA, Catalonian Institution for Research and Advanced Studies, Barcelona, Spain
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Tyrka M, Mokrzycka M, Bakera B, Tyrka D, Szeliga M, Stojałowski S, Matysik P, Rokicki M, Rakoczy-Trojanowska M, Krajewski P. Evaluation of genetic structure in European wheat cultivars and advanced breeding lines using high-density genotyping-by-sequencing approach. BMC Genomics 2021; 22:81. [PMID: 33509072 PMCID: PMC7842024 DOI: 10.1186/s12864-020-07351-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/27/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The genetic diversity and gene pool characteristics must be clarified for efficient genome-wide association studies, genomic selection, and hybrid breeding. The aim of this study was to evaluate the genetic structure of 509 wheat accessions representing registered varieties and advanced breeding lines via the high-density genotyping-by-sequencing approach. RESULTS More than 30% of 13,499 SNP markers representing 2162 clusters were mapped to genes, whereas 22.50% of 26,369 silicoDArT markers overlapped with coding sequences and were linked in 3527 blocks. Regarding hexaploidy, perfect sequence matches following BLAST searches were not sufficient for the unequivocal mapping to unique loci. Moreover, allelic variations in homeologous loci interfered with heterozygosity calculations for some markers. Analyses of the major genetic changes over the last 27 years revealed the selection pressure on orthologs of the gibberellin biosynthesis-related GA2 gene and the senescence-associated SAG12 gene. A core collection representing the wheat population was generated for preserving germplasm and optimizing breeding programs. CONCLUSIONS Our results confirmed considerable differences among wheat subgenomes A, B and D, with D characterized by the lowest diversity but the highest LD. They revealed genomic regions that have been targeted by breeding.
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Affiliation(s)
- Mirosław Tyrka
- Rzeszow University of Technology, Powstańców Warszawy 12, 35-959, Rzeszów, Poland
| | - Monika Mokrzycka
- Institute of Plant Genetics, Polish Academy of Science, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Beata Bakera
- Warsaw University of Life Sciences, Nowoursynowska 166, 02-787, Warszawa, Poland
| | - Dorota Tyrka
- Rzeszow University of Technology, Powstańców Warszawy 12, 35-959, Rzeszów, Poland
| | - Magdalena Szeliga
- Rzeszow University of Technology, Powstańców Warszawy 12, 35-959, Rzeszów, Poland
| | - Stefan Stojałowski
- West Pomeranian University of Technology Szczecin, Słowackiego 17, 71-434, Szczecin, Poland
| | - Przemysław Matysik
- Plant Breeding Strzelce Group IHAR Ltd., Kasztanowa 5, 63-004, Tulce, Poland
| | - Michał Rokicki
- Poznań Plant Breeding Ltd., Główna 20, 99-307, Strzelce, Poland
| | | | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Science, Strzeszyńska 34, 60-479, Poznań, Poland.
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Scott MF, Ladejobi O, Amer S, Bentley AR, Biernaskie J, Boden SA, Clark M, Dell'Acqua M, Dixon LE, Filippi CV, Fradgley N, Gardner KA, Mackay IJ, O'Sullivan D, Percival-Alwyn L, Roorkiwal M, Singh RK, Thudi M, Varshney RK, Venturini L, Whan A, Cockram J, Mott R. Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding. Heredity (Edinb) 2020; 125:396-416. [PMID: 32616877 PMCID: PMC7784848 DOI: 10.1038/s41437-020-0336-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 11/21/2022] Open
Abstract
Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm 'package' that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding.
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Affiliation(s)
| | | | - Samer Amer
- University of Reading, Reading, RG6 6AH, UK
- Faculty of Agriculture, Alexandria University, Alexandria, 23714, Egypt
| | - Alison R Bentley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Jay Biernaskie
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Scott A Boden
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | | | | | - Laura E Dixon
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Carla V Filippi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Nicolas Repetto y Los Reseros s/n, 1686, Hurlingham, Buenos Aires, Argentina
| | - Nick Fradgley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Keith A Gardner
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Ian J Mackay
- SRUC, West Mains Road, Kings Buildings, Edinburgh, EH9 3JG, UK
| | | | | | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rakesh Kumar Singh
- International Center for Biosaline Agriculture, Academic City, Dubai, United Arab Emirates
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev Kumar Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Alex Whan
- CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - James Cockram
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Richard Mott
- UCL Genetics Institute, Gower Street, London, WC1E 6BT, UK
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A haplotype-led approach to increase the precision of wheat breeding. Commun Biol 2020; 3:712. [PMID: 33239669 PMCID: PMC7689427 DOI: 10.1038/s42003-020-01413-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
Crop productivity must increase at unprecedented rates to meet the needs of the growing worldwide population. Exploiting natural variation for the genetic improvement of crops plays a central role in increasing productivity. Although current genomic technologies can be used for high-throughput identification of genetic variation, methods for efficiently exploiting this genetic potential in a targeted, systematic manner are lacking. Here, we developed a haplotype-based approach to identify genetic diversity for crop improvement using genome assemblies from 15 bread wheat (Triticum aestivum) cultivars. We used stringent criteria to identify identical-by-state haplotypes and distinguish these from near-identical sequences (~99.95% identity). We showed that each cultivar shares ~59 % of its genome with other sequenced cultivars and we detected the presence of extended haplotype blocks containing hundreds to thousands of genes across all wheat chromosomes. We found that genic sequence alone was insufficient to fully differentiate between haplotypes, as were commonly used array-based genotyping chips due to their gene centric design. We successfully used this approach for focused discovery of novel haplotypes from a landrace collection and documented their potential for trait improvement in modern bread wheat. This study provides a framework for defining and exploiting haplotypes to increase the efficiency and precision of wheat breeding towards optimising the agronomic performance of this crucial crop. Brinton, Uauy and colleagues utilize genomic data from the 10+ Wheat Genome Project to develop a useful tool for studying and generating new wheat cultivars. This framework uses advanced exploitation of wheat haplotypes to bring newfound precision and efficiency to wheat breeding.
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Khadka K, Torkamaneh D, Kaviani M, Belzile F, Raizada MN, Navabi A. Population structure of Nepali spring wheat (Triticum aestivum L.) germplasm. BMC PLANT BIOLOGY 2020; 20:530. [PMID: 33225886 PMCID: PMC7682013 DOI: 10.1186/s12870-020-02722-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 10/26/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Appropriate information about genetic diversity and population structure of germplasm improves the efficiency of plant breeding. The low productivity of Nepali bread wheat (Triticum aestivum L.) is a major concern particularly since Nepal is ranked the 4th most vulnerable nation globally to climate change. The genetic diversity and population structure of Nepali spring wheat have not been reported. This study aims to improve the exploitation of more diverse and under-utilized genetic resources to contribute to current and future breeding efforts for global food security. RESULTS We used genotyping-by-sequencing (GBS) to characterize a panel of 318 spring wheat accessions from Nepal including 166 landraces, 115 CIMMYT advanced lines, and 34 Nepali released varieties. We identified 95 K high-quality SNPs. The greatest genetic diversity was observed among the landraces, followed by CIMMYT lines, and released varieties. Though we expected only 3 groupings corresponding to these 3 seed origins, the population structure revealed two large, distinct subpopulations along with two smaller and scattered subpopulations in between, with significant admixture. This result was confirmed by principal component analysis (PCA) and UPGMA distance-based clustering. The pattern of LD decay differed between subpopulations, ranging from 60 to 150 Kb. We discuss the possibility that germplasm explorations during the 1970s-1990s may have mistakenly collected exotic germplasm instead of local landraces and/or collected materials that had already cross-hybridized since exotic germplasm was introduced starting in the 1950s. CONCLUSION We suggest that only a subset of wheat "landraces" in Nepal are authentic which this study has identified. Targeting these authentic landraces may accelerate local breeding programs to improve the food security of this climate-vulnerable nation. Overall, this study provides a novel understanding of the genetic diversity of wheat in Nepal and this may contribute to global wheat breeding initiatives.
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Affiliation(s)
- Kamal Khadka
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
| | - Davoud Torkamaneh
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
- Département de Phytologie, Université Laval, Québec City, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
| | - Mina Kaviani
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Francois Belzile
- Département de Phytologie, Université Laval, Québec City, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
| | - Manish N Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Alireza Navabi
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Eller F, Hyldgaard B, Driever SM, Ottosen CO. Inherent trait differences explain wheat cultivar responses to climate factor interactions: New insights for more robust crop modelling. GLOBAL CHANGE BIOLOGY 2020; 26:5965-5978. [PMID: 32677162 DOI: 10.1111/gcb.15278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Climate change predictions foresee a combination of rising CO2 , temperature and altered precipitation. Effects of single climatic variables are well defined, but the importance of combined variables and genotypic effects is less known, although pivotal for assessing climate change impacts, for example, with crop growth models. This study provides developmental and physiological data from combined climatic factors for two distinct wheat cultivars (Paragon and Gladius), as a basis to improve predictions for climate change scenarios. The two cultivars were grown in controlled climate chambers in a fully factorial setup of atmospheric CO2 concentration, growth temperature and watering regime. The cultivars differed considerably in their developmental rate, response pattern and the parameters responsible for most of their variation. The growth of Paragon was linked to climatic effects on photosynthesis and mainly affected by temperature. Paragon was overall more negatively affected by all treatment combinations compared to Gladius. Gladius was mostly affected by watering regime. The cultivars' acclimation strategies to climate factors varied significantly. Thus, considering a single factor is an oversimplification very likely impacting the accuracy of crop growth models. Intraspecific crop variation could help understanding genotype by environment variation. Cultivars with high phenotypic plasticity may have greater resilience against climatic variability.
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Affiliation(s)
| | - Benita Hyldgaard
- Department of Biology, Aarhus University, Aarhus C, Denmark
- Department of Food Science, Aarhus University, Aarhus N, Denmark
| | - Steven M Driever
- Centre for Crop Systems Analysis, Wageningen University, Wageningen, The Netherlands
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Yermekbayev K, Griffiths S, Chhetry M, Leverington-Waite M, Orford S, Amalova A, Abugalieva S, Turuspekov Y. Construction of a Genetic Map of RILs Derived from Wheat (T. aestivum L.) Varieties Pamyati Azieva × Paragon Using High-Throughput SNP Genotyping Platform KASP—Kompetitive Allele Specific PCR. RUSS J GENET+ 2020. [DOI: 10.1134/s102279542009015x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Bánfalvi Á, Németh R, Bagdi A, Gergely S, Rakszegi M, Bedő Z, Láng L, Vida G, Tömösközi S. A novel approach to the characterization of old wheat (Triticum aestivum L.) varieties by complex rheological analysis. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:4409-4417. [PMID: 32388854 DOI: 10.1002/jsfa.10479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 04/14/2020] [Accepted: 05/09/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Lines of the internationally recognized old Hungarian Bánkúti 1201 variety are important genetic resources for breeding programmes. Their protein composition and gluten dependent technological traits have been comprehensively studied, however, little information is available about their carbohydrate dependent viscous properties. The aim of this work was to obtain comprehensive rheological characterization of all sublines of Bánkúti 1201 maintained at Martonvásár and to investigate their variability if the carbohydrate dependent viscous behaviour was also included in the analyses. RESULTS The majority of the lines reflected the famously good mixing quality of Bánkúti, however, much higher diversity of pasting behaviour was detected. Cluster analysis of the Mixolab data was performed resulting in four sample groups. Since several lines of similar mixing properties had significantly different pasting characteristics, it was assumed that classification was mainly based on the viscous properties. From each cluster two to three representative samples were selected for wider examination using conventional testing methods. These results also supported the higher variability of pasting behaviour of the lines, which can be critical for end product quality. The members of the second cluster can be highlighted due to their waxy wheat like behaviour. CONCLUSIONS Possible reasons for the great variability of pasting behaviour could be the compositional and structural differences of starch and other carbohydrates (e.g. arabinoxylans). Complex rheological characterization and study of molecular background can provide information about important traits from the point of view of technology and product development, which are unknown in the case of old wheat varieties and landraces. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Ágnes Bánfalvi
- Research Group of Cereal Science and Food Quality, Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics (BME), Budapest, Hungary
| | - Renáta Németh
- Research Group of Cereal Science and Food Quality, Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics (BME), Budapest, Hungary
| | - Attila Bagdi
- Research Group of Cereal Science and Food Quality, Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics (BME), Budapest, Hungary
| | - Szilveszter Gergely
- Research Group of Cereal Science and Food Quality, Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics (BME), Budapest, Hungary
| | - Marianna Rakszegi
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Zoltán Bedő
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - László Láng
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Gyula Vida
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Sándor Tömösközi
- Research Group of Cereal Science and Food Quality, Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics (BME), Budapest, Hungary
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Hazard B, Trafford K, Lovegrove A, Griffiths S, Uauy C, Shewry P. Strategies to improve wheat for human health. NATURE FOOD 2020; 1:475-480. [PMID: 37128081 DOI: 10.1038/s43016-020-0134-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 07/17/2020] [Indexed: 05/03/2023]
Abstract
Despite their economic importance and growing demand, concerns are emerging around wheat-based foods and human health. Most wheat-based foods are made from refined white flour rather than wholemeal flour, and the overconsumption of these products may contribute to the increasing global prevalence of chronic diseases, particularly type 2 diabetes and obesity. Here, we review how the amount, composition and interactions of starch and cell wall polysaccharides, the major carbohydrate components in refined wheat products, impact human health. We discuss strategies and challenges to manipulate these components for improved diet and health using newly developed wheat genomics tools and resources. Commercial foods developed from these novel approaches must be produced without adverse effects on cost, consumer acceptability and processing properties.
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36
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Gage JL, Monier B, Giri A, Buckler ES. Ten Years of the Maize Nested Association Mapping Population: Impact, Limitations, and Future Directions. THE PLANT CELL 2020; 32:2083-2093. [PMID: 32398275 PMCID: PMC7346555 DOI: 10.1105/tpc.19.00951] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 04/02/2020] [Accepted: 05/11/2020] [Indexed: 05/21/2023]
Abstract
It has been just over a decade since the release of the maize (Zea mays) Nested Association Mapping (NAM) population. The NAM population has been and continues to be an invaluable resource for the maize genetics community and has yielded insights into the genetic architecture of complex traits. The parental lines have become some of the most well-characterized maize germplasm, and their de novo assemblies were recently made publicly available. As we enter an exciting new stage in maize genomics, this retrospective will summarize the design and intentions behind the NAM population; its application, the discoveries it has enabled, and its influence in other systems; and use the past decade of hindsight to consider whether and how it will remain useful in a new age of genomics.
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Affiliation(s)
- Joseph L Gage
- U.S. Department of Agriculture-Agricultural Research Service, Ithaca, New York 14853
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
| | - Brandon Monier
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
| | - Anju Giri
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
| | - Edward S Buckler
- U.S. Department of Agriculture-Agricultural Research Service, Ithaca, New York 14853
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
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Khazan S, Minz-Dub A, Sela H, Manisterski J, Ben-Yehuda P, Sharon A, Millet E. Reducing the size of an alien segment carrying leaf rust and stripe rust resistance in wheat. BMC PLANT BIOLOGY 2020; 20:153. [PMID: 32272895 PMCID: PMC7147030 DOI: 10.1186/s12870-020-2306-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/24/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Leaf and stripe rusts are two major wheat diseases, causing significant yield losses. The preferred way for protecting wheat from rust pathogens is by introgression of rust resistance traits from wheat-related wild species. To avoid genetic drag due to replacement of large wheat chromosomal segments by the alien chromatin, it is necessary to shorten the alien chromosome segment in primary recombinants. RESULTS Here we report on shortening of an alien chromosome segment in wheat that carries leaf and stripe rust resistance from Sharon goatgrass (Aegilops sharonensis). Rust resistant wheat introgression lines were selected and the alien region was mapped using genotyping by sequencing. Single polymorphic nucleotides (SNP) were identified and used to generate diagnostic PCR markers. Shortening of the alien fragment was achieved by induced homoeologous pairing and lines with shortened alien chromosome were identified using the PCR markers. Further reduction of the segment was achieved in tertiary recombinants without losing the rust resistance. CONCLUSIONS Alien chromatin in wheat with novel rust resistance genes was characterized by SNP markers and shortened by homoeologous recombination to avoid deleterious traits. The resulting wheat lines are resistant to highly virulent races of leaf and stripe rust pathogens and can be used as both resistant wheat in the field and source for gene transfer to other wheat lines/species.
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Affiliation(s)
- Sofia Khazan
- Institute for Cereal Crops Improvement, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Anna Minz-Dub
- Institute for Cereal Crops Improvement, Tel Aviv University, 69978, Tel Aviv, Israel.
| | - Hanan Sela
- Institute for Cereal Crops Improvement, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Jacob Manisterski
- Institute for Cereal Crops Improvement, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Pnina Ben-Yehuda
- Institute for Cereal Crops Improvement, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Amir Sharon
- Institute for Cereal Crops Improvement, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Eitan Millet
- Institute for Cereal Crops Improvement, Tel Aviv University, 69978, Tel Aviv, Israel
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Lyra DH, Virlet N, Sadeghi-Tehran P, Hassall KL, Wingen LU, Orford S, Griffiths S, Hawkesford MJ, Slavov GT. Functional QTL mapping and genomic prediction of canopy height in wheat measured using a robotic field phenotyping platform. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1885-1898. [PMID: 32097472 PMCID: PMC7094083 DOI: 10.1093/jxb/erz545] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 02/19/2020] [Indexed: 05/08/2023]
Abstract
Genetic studies increasingly rely on high-throughput phenotyping, but the resulting longitudinal data pose analytical challenges. We used canopy height data from an automated field phenotyping platform to compare several approaches to scanning for quantitative trait loci (QTLs) and performing genomic prediction in a wheat recombinant inbred line mapping population based on up to 26 sampled time points (TPs). We detected four persistent QTLs (i.e. expressed for most of the growing season), with both empirical and simulation analyses demonstrating superior statistical power of detecting such QTLs through functional mapping approaches compared with conventional individual TP analyses. In contrast, even very simple individual TP approaches (e.g. interval mapping) had superior detection power for transient QTLs (i.e. expressed during very short periods). Using spline-smoothed phenotypic data resulted in improved genomic predictive abilities (5-8% higher than individual TP prediction), while the effect of including significant QTLs in prediction models was relatively minor (<1-4% improvement). Finally, although QTL detection power and predictive ability generally increased with the number of TPs analysed, gains beyond five or 10 TPs chosen based on phenological information had little practical significance. These results will inform the development of an integrated, semi-automated analytical pipeline, which will be more broadly applicable to similar data sets in wheat and other crops.
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Affiliation(s)
- Danilo H Lyra
- Department of Computational & Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Nicolas Virlet
- Department of Plant Sciences, Rothamsted Research, Harpenden, UK
| | | | - Kirsty L Hassall
- Department of Computational & Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Luzie U Wingen
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | - Simon Orford
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | - Simon Griffiths
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | | | - Gancho T Slavov
- Department of Computational & Analytical Sciences, Rothamsted Research, Harpenden, UK
- Scion, Rotorua, New Zealand
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Lyra DH, Virlet N, Sadeghi-Tehran P, Hassall KL, Wingen LU, Orford S, Griffiths S, Hawkesford MJ, Slavov GT. Functional QTL mapping and genomic prediction of canopy height in wheat measured using a robotic field phenotyping platform. JOURNAL OF EXPERIMENTAL BOTANY 2020. [PMID: 32097472 DOI: 10.17632/pkxpkw6j43.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Genetic studies increasingly rely on high-throughput phenotyping, but the resulting longitudinal data pose analytical challenges. We used canopy height data from an automated field phenotyping platform to compare several approaches to scanning for quantitative trait loci (QTLs) and performing genomic prediction in a wheat recombinant inbred line mapping population based on up to 26 sampled time points (TPs). We detected four persistent QTLs (i.e. expressed for most of the growing season), with both empirical and simulation analyses demonstrating superior statistical power of detecting such QTLs through functional mapping approaches compared with conventional individual TP analyses. In contrast, even very simple individual TP approaches (e.g. interval mapping) had superior detection power for transient QTLs (i.e. expressed during very short periods). Using spline-smoothed phenotypic data resulted in improved genomic predictive abilities (5-8% higher than individual TP prediction), while the effect of including significant QTLs in prediction models was relatively minor (<1-4% improvement). Finally, although QTL detection power and predictive ability generally increased with the number of TPs analysed, gains beyond five or 10 TPs chosen based on phenological information had little practical significance. These results will inform the development of an integrated, semi-automated analytical pipeline, which will be more broadly applicable to similar data sets in wheat and other crops.
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Affiliation(s)
- Danilo H Lyra
- Department of Computational & Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Nicolas Virlet
- Department of Plant Sciences, Rothamsted Research, Harpenden, UK
| | | | - Kirsty L Hassall
- Department of Computational & Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Luzie U Wingen
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | - Simon Orford
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | - Simon Griffiths
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | | | - Gancho T Slavov
- Department of Computational & Analytical Sciences, Rothamsted Research, Harpenden, UK
- Scion, Rotorua, New Zealand
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Adamski NM, Borrill P, Brinton J, Harrington SA, Marchal C, Bentley AR, Bovill WD, Cattivelli L, Cockram J, Contreras-Moreira B, Ford B, Ghosh S, Harwood W, Hassani-Pak K, Hayta S, Hickey LT, Kanyuka K, King J, Maccaferrri M, Naamati G, Pozniak CJ, Ramirez-Gonzalez RH, Sansaloni C, Trevaskis B, Wingen LU, Wulff BBH, Uauy C. A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat. eLife 2020; 9:e55646. [PMID: 32208137 PMCID: PMC7093151 DOI: 10.7554/elife.55646] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/12/2020] [Indexed: 02/04/2023] Open
Abstract
Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite their importance, a lack of genomic information and resources has hindered the functional characterisation of genes in major crops. The recent release of high-quality reference sequences for these crops underpins a suite of genetic and genomic resources that support basic research and breeding. For wheat, these include gene model annotations, expression atlases and gene networks that provide information about putative function. Sequenced mutant populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources. This review provides a helpful guide for plant scientists, especially those expanding into crop research, to capitalise on the discoveries made in Arabidopsis and other plants. This will accelerate the improvement of crops of vital importance for food and nutrition security.
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Affiliation(s)
| | - Philippa Borrill
- School of Biosciences, University of BirminghamBirminghamUnited Kingdom
| | - Jemima Brinton
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | | | | | | | - William D Bovill
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and BioinformaticsFiorenzuola d'ArdaItaly
| | | | - Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Brett Ford
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Sreya Ghosh
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Wendy Harwood
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | | | - Sadiye Hayta
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of QueenslandSt LuciaAustralia
| | | | - Julie King
- Division of Plant and Crop Sciences, The University of Nottingham, Sutton Bonington CampusLoughboroughUnited Kingdom
| | - Marco Maccaferrri
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna (University of Bologna)BolognaItaly
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Curtis J Pozniak
- Crop Development Centre, University of SaskatchewanSaskatoonCanada
| | | | | | - Ben Trevaskis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Luzie U Wingen
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Brande BH Wulff
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
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Khokhar JS, King J, King IP, Young SD, Foulkes MJ, De Silva J, Weerasinghe M, Mossa A, Griffiths S, Riche AB, Hawkesford M, Shewry P, Broadley MR. Novel sources of variation in grain Zinc (Zn) concentration in bread wheat germplasm derived from Watkins landraces. PLoS One 2020; 15:e0229107. [PMID: 32109944 PMCID: PMC7048275 DOI: 10.1371/journal.pone.0229107] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/29/2020] [Indexed: 11/19/2022] Open
Abstract
A diverse panel of 245 wheat genotypes, derived from crosses between landraces from the Watkins collection representing global diversity in the early 20th century and the modern wheat cultivar Paragon, was grown at two field sites in the UK in 2015-16 and the concentrations of zinc and iron determined in wholegrain using inductively coupled plasma-mass spectrometry (ICP-MS). Zinc concentrations in wholegrain varied from 24-49 mg kg-1 and were correlated with iron concentration (r = 0.64) and grain protein content (r = 0.14). However, the correlation with yield was low (r = -0.16) indicating little yield dilution. A sub-set of 24 wheat lines were selected from 245 wheat genotypes and characterised for Zn and Fe concentrations in wholegrain and white flour over two sites and years. White flours from 24 selected lines contained 8-15 mg kg-1 of zinc, which was positively correlated with the wholegrain Zn concentration (r = 0.79, averaged across sites and years). This demonstrates the potential to exploit the diversity in landraces to increase the concentration of Zn in wholegrain and flour of modern high yielding bread wheat cultivars.
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Affiliation(s)
- Jaswant S. Khokhar
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
- * E-mail:
| | - Julie King
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Ian P. King
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Scott D. Young
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Michael J. Foulkes
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Jayalath De Silva
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Minuka Weerasinghe
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Abdul Mossa
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | | | - Andrew B. Riche
- Plant Sciences, Rothamsted Research, Harpenden, United Kingdom
| | | | - Peter Shewry
- Plant Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Martin R. Broadley
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
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Coulton A, Przewieslik-Allen AM, Burridge AJ, Shaw DS, Edwards KJ, Barker GLA. Segregation distortion: Utilizing simulated genotyping data to evaluate statistical methods. PLoS One 2020; 15:e0228951. [PMID: 32074141 PMCID: PMC7029859 DOI: 10.1371/journal.pone.0228951] [Citation(s) in RCA: 8] [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: 11/08/2019] [Accepted: 01/26/2020] [Indexed: 11/18/2022] Open
Abstract
Segregation distortion is the phenomenon in which genotypes deviate from expected Mendelian ratios in the progeny of a cross between two varieties or species. There is not currently a widely used consensus for the appropriate statistical test, or more specifically the multiple testing correction procedure, used to detect segregation distortion for high-density single-nucleotide polymorphism (SNP) data. Here we examine the efficacy of various multiple testing procedures, including chi-square test with no correction for multiple testing, false-discovery rate correction and Bonferroni correction using an in-silico simulation of a biparental mapping population. We find that the false discovery rate correction best approximates the traditional p-value threshold of 0.05 for high-density marker data. We also utilize this simulation to test the effect of segregation distortion on the genetic mapping process, specifically on the formation of linkage groups during marker clustering. Only extreme segregation distortion was found to effect genetic mapping. In addition, we utilize replicate empirical mapping populations of wheat varieties Avalon and Cadenza to assess how often segregation distortion conforms to the same pattern between closely related wheat varieties.
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Affiliation(s)
- Alexander Coulton
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom
- * E-mail:
| | | | - Amanda J. Burridge
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom
| | - Daniel S. Shaw
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom
| | - Keith J. Edwards
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom
| | - Gary L. A. Barker
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom
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Identification of a major QTL and associated molecular marker for high arabinoxylan fibre in white wheat flour. PLoS One 2020; 15:e0227826. [PMID: 32023285 PMCID: PMC7001892 DOI: 10.1371/journal.pone.0227826] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/29/2019] [Indexed: 12/18/2022] Open
Abstract
Dietary fibre (DF) has multiple health benefits and wheat grains are major sources of DF for human health. However, DF is depleted in white wheat flour which is more widely consumed than wholegrain. The major DF component in white flour is the cell wall polysaccharide arabinoxylan (AX). We have identified the Chinese wheat cultivar Yumai 34 as having unusually high contents of AX in both water-soluble and insoluble forms. We have therefore used populations generated from crosses between Yumai 34 and four other wheat cultivars, three with average contents of AX (Ukrainka, Altigo and Claire) and one also having unusually high AX (Valoris), in order to map QTLs for soluble AX (determined as relative viscosity of aqueous extracts of wholemeal flours) and total AX (determined by enzyme fingerprinting of white flour). A number of QTL were mapped, but most were only detected in one or two crosses. However, all four crosses showed strong QTLs for high RV/total AX on chromosome 1B, with Yumai 34 being the increasing parent, and a KASP marker for the Yumai 34 high AX allele was validated by analysis of high AX lines derived from Yumai 34 but selected by biochemical analysis. A QTL for RV was also mapped on chromosome 6B in Yumai 34 x Valoris, with Valoris being the increasing allele, which is consistent with the observation of transgressive segregation for this population. Association studies in an independent germplasm panel identified marker trait associations for relative viscosity in these same locations while direct selection for fibre content in breeding resulted in high levels of enrichment for the Yumai 34 1B allele. The data therefore indicate that marker-assisted breeding can be used to develop wheat with high AX fibre in white flour.
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Wilkinson PA, Allen AM, Tyrrell S, Wingen LU, Bian X, Winfield MO, Burridge A, Shaw DS, Zaucha J, Griffiths S, Davey RP, Edwards KJ, Barker GLA. CerealsDB-new tools for the analysis of the wheat genome: update 2020. Database (Oxford) 2020; 2020:baaa060. [PMID: 32754757 PMCID: PMC7402920 DOI: 10.1093/database/baaa060] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/08/2020] [Accepted: 07/07/2020] [Indexed: 11/24/2022]
Abstract
CerealsDB (www.cerealsdb.uk.net) is an online repository of mainly hexaploid wheat (Triticum aestivum) single nucleotide polymorphisms (SNPs) and genotyping data. The CerealsDB website has been designed to enable wheat breeders and scientists to select the appropriate markers for research breeding tasks, such as marker-assisted selection. We report a large update of genotyping information for over 6000 wheat accessions and describe new webtools for exploring and visualizing the data. We also describe a new database of quantitative trait loci that links phenotypic traits to CerealsDB SNP markers and allelic scores for each of those markers. CerealsDB is an open-access website that hosts information on wheat SNPs considered useful for both plant breeders and research scientists. The latest CerealsDB database is available at https://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php.
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Affiliation(s)
- Paul A Wilkinson
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
- Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, BioSciences Building, Crown Street, Liverpool, L69 7ZB, UK
| | - Alexandra M Allen
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Simon Tyrrell
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Luzie U Wingen
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Xingdong Bian
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Mark O Winfield
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Amanda Burridge
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Daniel S Shaw
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Jan Zaucha
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Simon Griffiths
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Robert P Davey
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Keith J Edwards
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Gary L A Barker
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
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Halder J, Zhang J, Ali S, Sidhu JS, Gill HS, Talukder SK, Kleinjan J, Turnipseed B, Sehgal SK. Mining and genomic characterization of resistance to tan spot, Stagonospora nodorum blotch (SNB), and Fusarium head blight in Watkins core collection of wheat landraces. BMC PLANT BIOLOGY 2019; 19:480. [PMID: 31703626 PMCID: PMC6839225 DOI: 10.1186/s12870-019-2093-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/21/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND In the late 1920s, A. E. Watkins collected about 7000 landrace cultivars (LCs) of bread wheat (Triticum aestivum L.) from 32 different countries around the world. Among which 826 LCs remain viable and could be a valuable source of superior/favorable alleles to enhance disease resistance in wheat. In the present study, a core set of 121 LCs, which captures the majority of the genetic diversity of Watkins collection, was evaluated for identifying novel sources of resistance against tan spot, Stagonospora nodorum blotch (SNB), and Fusarium Head Blight (FHB). RESULTS A diverse response was observed in 121 LCs for all three diseases. The majority of LCs were moderately susceptible to susceptible to tan spot Ptr race 1 (84%) and FHB (96%) whereas a large number of LCs were resistant or moderately resistant against tan spot Ptr race 5 (95%) and SNB (54%). Thirteen LCs were identified in this study could be a valuable source for multiple resistance to tan spot Ptr races 1 and 5, and SNB, and another five LCs could be a potential source for FHB resistance. GWAS analysis was carried out using disease phenotyping score and 8807 SNPs data of 118 LCs, which identified 30 significant marker-trait associations (MTAs) with -log10 (p-value) > 3.0. Ten, five, and five genomic regions were found to be associated with resistance to tan spot Ptr race 1, race 5, and SNB, respectively in this study. In addition to Tsn1, several novel genomic regions Q.Ts1.sdsu-4BS and Q.Ts1.sdsu-5BS (tan spot Ptr race 1) and Q.Ts5.sdsu-1BL, Q.Ts5.sdsu-2DL, Q.Ts5.sdsu-3AL, and Q.Ts5.sdsu-6BL (tan spot Ptr race 5) were also identified. Our results indicate that these putative genomic regions contain several genes that play an important role in plant defense mechanisms. CONCLUSION Our results suggest the existence of valuable resistant alleles against leaf spot diseases in Watkins LCs. The single-nucleotide polymorphism (SNP) markers linked to the quantitative trait loci (QTLs) for tan spot and SNB resistance along with LCs harboring multiple disease resistance could be useful for future wheat breeding.
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Affiliation(s)
- Jyotirmoy Halder
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Jinfeng Zhang
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Shaukat Ali
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Jagdeep S Sidhu
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Harsimardeep S Gill
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Shyamal K Talukder
- California Cooperative Rice Research Foundation, Inc., Rice Experiment Station, Biggs, CA, 95917, USA
| | - Jonathan Kleinjan
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Brent Turnipseed
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA.
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Fan C, Luo J, Zhang S, Liu M, Li Q, Li Y, Huang L, Chen X, Ning S, Yuan Z, Zhang L, Wang J, Zheng Y, Liu D, Hao M. Genetic mapping of a major QTL promoting homoeologous chromosome pairing in a wheat landrace. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2155-2166. [PMID: 31016346 DOI: 10.1007/s00122-019-03344-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Common wheat landrace Kaixian-luohanmai carries a gene(s) that promotes homoeologous chromosome pairing. A major QTL responsible for this effect was mapped to chromosome arm 3AL. Polyhaploid hybrids of a Chinese common wheat landrace Kaixian-luohanmai (KL) and related species show increased levels of chromosome pairing. Over 90% of that pairing is between homoeologous arms of wheat chromosomes, with a very strong preference for pairing between homoeologs from genomes A and D. Wheat-rye pairing was also observed at low frequency. Two mapping populations were created from the hybrids of KL with two wheat genotypes top crossed to rye. Mean chiasmata numbers per plant were used as phenotypic data. Wheat 660 K and 15 K SNP arrays, DArT markers and SSR markers were used for genotyping of the top-cross ABDR hybrids. One major QTL, named QPh.sicau-3A, for increased homoeologous pairing was detected on chromosome arm 3AL, and it was responsible for ca. 16% of the total variation. This QTL was located in the interval 696-725 Mb in the Chinese Spring reference genome. SNP markers closely linked with QPh.sicau-3A were converted to KASP markers and validated for marker-assisted selection.
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Affiliation(s)
- Chaolan Fan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu Campus, Wenjiang, 611130, Sichuan, China
| | - Jiangtao Luo
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu, 610066, Sichuan, China
| | - Shujie Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu Campus, Wenjiang, 611130, Sichuan, China
| | - Meng Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu Campus, Wenjiang, 611130, Sichuan, China
| | - Qingcheng Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu Campus, Wenjiang, 611130, Sichuan, China
| | - Yazhou Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu Campus, Wenjiang, 611130, Sichuan, China
| | - Lei Huang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu Campus, Wenjiang, 611130, Sichuan, China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu Campus, Wenjiang, 611130, Sichuan, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu Campus, Wenjiang, 611130, Sichuan, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu Campus, Wenjiang, 611130, Sichuan, China
| | - Lianquan Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu Campus, Wenjiang, 611130, Sichuan, China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu Campus, Wenjiang, 611130, Sichuan, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu Campus, Wenjiang, 611130, Sichuan, China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu Campus, Wenjiang, 611130, Sichuan, China.
- Joint International Research Laboratory of Crop Resources and Genetic Improvement, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China.
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu Campus, Wenjiang, 611130, Sichuan, China.
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Genome-Wide Analyses Reveal Footprints of Divergent Selection and Drought Adaptive Traits in Synthetic-Derived Wheats. G3-GENES GENOMES GENETICS 2019; 9:1957-1973. [PMID: 31018942 PMCID: PMC6553533 DOI: 10.1534/g3.119.400010] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Crop-wild introgressions have long been exploited without knowing the favorable recombination points. Synthetic hexaploid wheats are one of the most exploited genetic resources for bread wheat improvement. However, despite some QTL with major effects, much less is known about genome-wide patterns of introgressions and their effects on phenotypes. We used two genome-wide association approaches: SNP-GWAS and haplotype-GWAS to identify SNPs and haplotypes associated with productivity under water-limited conditions in a synthetic-derived wheat (SYN-DER) population. Haplotype-GWAS further enriched and identified 20 more genomic regions associated with drought adaptability that did not overlap with SNP-GWAS. Since GWAS is biased to the phenotypes in the study and may fail to detect important genetic diversity during breeding, we used five complementary analytical approaches (t-test, Tajima’s D, nucleotide diversity (π), Fst, and EigenGWAS) to identify divergent selections in SYN-DER compared to modern bread wheat. These approaches consistently pinpointed 89 ‘selective sweeps’, out of which 30 selection loci were identified on D-genome. These key selections co-localized with important functional genes of adaptive traits such as TaElf3-D1 (1D) for earliness per se (Eps), TaCKX-D1 (3D), TaGS1a (6D) and TaGS-D1 (7D) for grain size, weight and morphology, TaCwi-D1 (5D) influencing drought tolerance, and Vrn-D3 (7D) for vernalization. Furthermore, 55 SNPs and 23 haplotypes of agronomic and physiological importance such as grain yield, relative water content and thousand grain weight in SYN-DER, were among the top 5% of divergent selections contributed by synthetic hexaploid wheats. These divergent selections associated with improved agronomic performance carry new alleles that have been introduced to wheat. Our results demonstrated that GWAS and selection sweep analyses are powerful approaches for investigating favorable introgressions under strong selection pressure and the use of crop-wild hybridization to assist the improvement of wheat yield and productivity under moisture limiting environments.
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Hawkesford MJ, Griffiths S. Exploiting genetic variation in nitrogen use efficiency for cereal crop improvement. CURRENT OPINION IN PLANT BIOLOGY 2019; 49:35-42. [PMID: 31176099 PMCID: PMC6692496 DOI: 10.1016/j.pbi.2019.05.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 05/18/2023]
Abstract
Cereals are the most important sources of calories and nutrition for the human population, and are an essential animal feed. Food security depends on adequate production and demands are predicted to rise as the global population rises. The need for increased yields will have to be coupled to the efficient use of resources including fertilisers such as nitrogen to underpin the sustainability of food production. Although optimally performing crops with high yields require a balanced mineral nutrition, nitrogen fundamentally drives growth and yield as well as requirements for other nutrients. It is estimated that globally only 33% of applied nitrogen fertiliser is recovered in the harvested grain, indicative of a huge waste of resource and potential major pollutant and is thus a major target for crop improvement. Both agronomy and breeding will contribute to improved nitrogen use efficiency (NUE) and an important component of the latter is harnessing germplasm variation. This review will consider the key traits involved in NUE, the potential to exploit genetic variation for these specific traits, and the approaches to be utilised.
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Gardiner LJ, Wingen LU, Bailey P, Joynson R, Brabbs T, Wright J, Higgins JD, Hall N, Griffiths S, Clavijo BJ, Hall A. Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency. Genome Biol 2019; 20:69. [PMID: 30982471 PMCID: PMC6463664 DOI: 10.1186/s13059-019-1675-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 03/13/2019] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. A lack of recombination limits breeding efforts in crops; therefore, increasing recombination rates can reduce linkage drag and generate new genetic combinations. RESULTS We use computational analysis of 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat (Triticum aestivum). We observe that high-frequency crossover sites are shared between populations and that closely related parents lead to populations with more similar crossover patterns. We demonstrate that gene conversion is more prevalent and covers more of the genome in wheat than in other plants, making it a critical process in the generation of new haplotypes, particularly in centromeric regions where crossovers are rare. We identify quantitative trait loci for altered gene conversion and crossover frequency and confirm functionality for a novel RecQ helicase gene that belongs to an ancient clade that is missing in some plant lineages including Arabidopsis. CONCLUSIONS This is the first gene to be demonstrated to be involved in gene conversion in wheat. Harnessing the RecQ helicase has the potential to break linkage drag utilizing widespread gene conversions.
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Affiliation(s)
| | | | | | | | | | | | - James D. Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH UK
| | - Neil Hall
- Earlham Institute, Norwich, NR4 7UZ UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| | | | | | - Anthony Hall
- Earlham Institute, Norwich, NR4 7UZ UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK
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Brinton J, Uauy C. A reductionist approach to dissecting grain weight and yield in wheat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:337-358. [PMID: 30421518 PMCID: PMC6492019 DOI: 10.1111/jipb.12741] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/07/2018] [Indexed: 05/20/2023]
Abstract
Grain yield is a highly polygenic trait that is influenced by the environment and integrates events throughout the life cycle of a plant. In wheat, the major grain yield components often present compensatory effects among them, which alongside the polyploid nature of wheat, makes their genetic and physiological study challenging. We propose a reductionist and systematic approach as an initial step to understand the gene networks regulating each individual yield component. Here, we focus on grain weight and discuss the importance of examining individual sub-components, not only to help in their genetic dissection, but also to inform our mechanistic understanding of how they interrelate. This knowledge should allow the development of novel combinations, across homoeologs and between complementary modes of action, thereby advancing towards a more integrated strategy for yield improvement. We argue that this will break barriers in terms of phenotypic variation, enhance our understanding of the physiology of yield, and potentially deliver improved on-farm yield.
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Affiliation(s)
- Jemima Brinton
- John Innes CentreNorwich Research ParkNorwich NR4 7UHUnited Kingdom
| | - Cristobal Uauy
- John Innes CentreNorwich Research ParkNorwich NR4 7UHUnited Kingdom
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