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Hansson M, Youssef HM, Zakhrabekova S, Stuart D, Svensson JT, Dockter C, Stein N, Waugh R, Lundqvist U, Franckowiak J. A guide to barley mutants. Hereditas 2024; 161:11. [PMID: 38454479 PMCID: PMC10921644 DOI: 10.1186/s41065-023-00304-w] [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: 11/06/2023] [Accepted: 11/24/2023] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Mutants have had a fundamental impact upon scientific and applied genetics. They have paved the way for the molecular and genomic era, and most of today's crop plants are derived from breeding programs involving mutagenic treatments. RESULTS Barley (Hordeum vulgare L.) is one of the most widely grown cereals in the world and has a long history as a crop plant. Barley breeding started more than 100 years ago and large breeding programs have collected and generated a wide range of natural and induced mutants, which often were deposited in genebanks around the world. In recent years, an increased interest in genetic diversity has brought many historic mutants into focus because the collections are regarded as valuable resources for understanding the genetic control of barley biology and barley breeding. The increased interest has been fueled also by recent advances in genomic research, which provided new tools and possibilities to analyze and reveal the genetic diversity of mutant collections. CONCLUSION Since detailed knowledge about phenotypic characters of the mutants is the key to success of genetic and genomic studies, we here provide a comprehensive description of mostly morphological barley mutants. The review is closely linked to the International Database for Barley Genes and Barley Genetic Stocks ( bgs.nordgen.org ) where further details and additional images of each mutant described in this review can be found.
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Affiliation(s)
- Mats Hansson
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden.
| | - Helmy M Youssef
- Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle, 06120, Germany
| | | | - David Stuart
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden
| | - Jan T Svensson
- Nordic Genetic Resource Center (NordGen), Växthusvägen 12, 23456, Alnarp, Sweden
| | - Christoph Dockter
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, E06466, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, University of Dundee, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- School of Agriculture Food and Wine, Waite Campus, The University of Adelaide, Urrbrae, 5064, Australia
| | - Udda Lundqvist
- Nordic Genetic Resource Center (NordGen), Växthusvägen 12, 23456, Alnarp, Sweden
| | - Jerome Franckowiak
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, 411 Borlaug Hall, 1991 Upper Buford Circle, St Paul, MN, 55108, USA
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Haq SAU, Bashir T, Roberts TH, Husaini AM. Ameliorating the effects of multiple stresses on agronomic traits in crops: modern biotechnological and omics approaches. Mol Biol Rep 2023; 51:41. [PMID: 38158512 DOI: 10.1007/s11033-023-09042-8] [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: 12/15/2022] [Accepted: 10/13/2023] [Indexed: 01/03/2024]
Abstract
While global climate change poses a significant environmental threat to agriculture, the increasing population is another big challenge to food security. To address this, developing crop varieties with increased productivity and tolerance to biotic and abiotic stresses is crucial. Breeders must identify traits to ensure higher and consistent yields under inconsistent environmental challenges, possess resilience against emerging biotic and abiotic stresses and satisfy customer demands for safer and more nutritious meals. With the advent of omics-based technologies, molecular tools are now integrated with breeding to understand the molecular genetics of genotype-based traits and develop better climate-smart crops. The rapid development of omics technologies offers an opportunity to generate novel datasets for crop species. Identifying genes and pathways responsible for significant agronomic traits has been made possible by integrating omics data with genetic and phenotypic information. This paper discusses the importance and use of omics-based strategies, including genomics, transcriptomics, proteomics and phenomics, for agricultural and horticultural crop improvement, which aligns with developing better adaptability in these crop species to the changing climate conditions.
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Affiliation(s)
- Syed Anam Ul Haq
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Tanzeel Bashir
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Thomas H Roberts
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, Sydney Institute of Agriculture, The University of Sydney, Eveleigh, Australia
| | - Amjad M Husaini
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, 190025, India.
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Qin D, Liu G, Liu R, Wang C, Xu F, Xu Q, Ling Y, Dong G, Peng Y, Ge S, Guo G, Dong J, Li C. Positional cloning identified HvTUBULIN8 as the candidate gene for round lateral spikelet (RLS) in barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:7. [PMID: 36656367 PMCID: PMC9852219 DOI: 10.1007/s00122-023-04272-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
Map-based cloning, subcellular localization, virus-induced-gene-silencing and transcriptomic analysis reveal HvTUB8 as a candidate gene with pleiotropic effects on barley spike and leaf development via ethylene and chlorophyll metabolism. Barley lateral spikelet morphology and grain shape play key roles in grain physical quality and yield. Several genes and QTLs for these traits have been cloned or fine mapped previously. Here, we report the phenotypic and genotypic analysis of a barley mutant with round lateral spikelet (rls) from cv. Edamai 934. rls had round lateral spikelet, short but round grain, shortened awn, thick glume and dark green leaves. Histocytologic and ultrastructural analysis revealed that the difference of grain shape of rls was caused by change of cell arrangement in glume, and the dark leaf color resulted from enlarged chloroplast. HvTUBULIN8 (HvTUB8) was identified as the candidate gene for rls by combination of RNA-Seq, map-based-cloning, virus-induced-gene-silencing (VIGS) and protein subcellular location. A single G-A substitution at the third exon of HvTUB8 resulted in change of Cysteine 354 to tyrosine. Furthermore, the mutant isoform Hvtub8 could be detected in both nucleus and cytoplasm, whereas the wild-type protein was only in cytoplasm and granular organelles of wheat protoplasts. Being consistent with the rare phenotype, the "A" allele of HvTUB8 was only detected in rls, but not in a worldwide barley germplasm panel with 400 accessions. VIGS confirmed that HvTUB8 was essential to maintain spike integrity. RNA-Seq results suggested that HvTUB8 may control spike morphogenesis via ethylene homeostasis and signaling, and control leaf color through chlorophyll metabolism. Collectively, our results support HvTUB8 as a candidate gene for barley spike and leaf morphology and provide insight of a novel mechanism of it in barley development.
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Affiliation(s)
- Dandan Qin
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Gang Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Rui Liu
- Wuhan Polytechnic University, Wuhan, 430023, Hubei, China
| | - Chunchao Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fuchao Xu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Qing Xu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, China
| | - Guoqing Dong
- Wuhan Polytechnic University, Wuhan, 430023, Hubei, China
| | - Yanchun Peng
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Shuangtao Ge
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Ganggang Guo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing Dong
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Chengdao Li
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Western Australia, WA, 6150, Australia.
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Developing Genetic Engineering Techniques for Control of Seed Size and Yield. Int J Mol Sci 2022; 23:ijms232113256. [PMID: 36362043 PMCID: PMC9655546 DOI: 10.3390/ijms232113256] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/15/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022] Open
Abstract
Many signaling pathways regulate seed size through the development of endosperm and maternal tissues, which ultimately results in a range of variations in seed size or weight. Seed size can be determined through the development of zygotic tissues (endosperm and embryo) and maternal ovules. In addition, in some species such as rice, seed size is largely determined by husk growth. Transcription regulator factors are responsible for enhancing cell growth in the maternal ovule, resulting in seed growth. Phytohormones induce significant effects on entire features of growth and development of plants and also regulate seed size. Moreover, the vegetative parts are the major source of nutrients, including the majority of carbon and nitrogen-containing molecules for the reproductive part to control seed size. There is a need to increase the size of seeds without affecting the number of seeds in plants through conventional breeding programs to improve grain yield. In the past decades, many important genetic factors affecting seed size and yield have been identified and studied. These important factors constitute dynamic regulatory networks governing the seed size in response to environmental stimuli. In this review, we summarized recent advances regarding the molecular factors regulating seed size in Arabidopsis and other crops, followed by discussions on strategies to comprehend crops' genetic and molecular aspects in balancing seed size and yield.
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Li W, Boer MP, van Rossum BJ, Zheng C, Joosen RVL, van Eeuwijk FA. statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations. Bioinformatics 2022; 38:5134-5136. [PMID: 36193999 PMCID: PMC9665859 DOI: 10.1093/bioinformatics/btac662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/23/2022] [Accepted: 10/03/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Multi-parent populations (MPPs) are popular for QTL mapping because they combine wide genetic diversity in parents with easy control of population structure, but a limited number of software tools for QTL mapping are specifically developed for general MPP designs. RESULTS We developed an R package called statgenMPP, adopting a unified identity-by-descent (IBD)-based mixed model approach for QTL analysis in MPPs. The package offers easy-to-use functionalities of IBD calculations, mixed model solutions and visualizations for QTL mapping in a wide range of MPP designs, including diallele, nested-association mapping populations, multi-parent advanced genetic inter-cross populations and other complicated MPPs with known crossing schemes. AVAILABILITY AND IMPLEMENTATION The R package statgenMPP is open-source and freely available on CRAN at https://CRAN.R-project.org/package=statgenMPP. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wenhao Li
- Biometris, Wageningen University and Research Center, Wageningen, 6700 AC, The Netherlands
| | | | - Bart-Jan van Rossum
- Biometris, Wageningen University and Research Center, Wageningen, 6700 AC, The Netherlands
| | - Chaozhi Zheng
- Biometris, Wageningen University and Research Center, Wageningen, 6700 AC, The Netherlands
| | | | - Fred A van Eeuwijk
- Biometris, Wageningen University and Research Center, Wageningen, 6700 AC, The Netherlands
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Dang VH, Hill CB, Zhang XQ, Angessa TT, McFawn LA, Li C. Multi-locus genome-wide association studies reveal novel alleles for flowering time under vernalisation and extended photoperiod in a barley MAGIC population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3087-3102. [PMID: 35879467 PMCID: PMC9482607 DOI: 10.1007/s00122-022-04169-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Key genes controlling flowering and interactions of different photoperiod alleles with various environments were identified in a barley MAGIC population. A new candidate gene for vernalisation requirements was also detected. Optimal flowering time has a major impact on grain yield in crop species, including the globally important temperate cereal crop barley (Hordeum vulgare L.). Understanding the genetics of flowering is a key avenue to enhancing yield potential. Although bi-parental populations were used intensively to map genes controlling flowering, their lack of genetic diversity requires additional work to obtain desired gene combinations in the selected lines, especially when the two parental cultivars did not carry the genes. Multi-parent mapping populations, which use a combination of four or eight parental cultivars, have higher genetic and phenotypic diversity and can provide novel genetic combinations that cannot be achieved using bi-parental populations. This study uses a Multi-parent advanced generation intercross (MAGIC) population from four commercial barley cultivars to identify genes controlling flowering time in different environmental conditions. Genome-wide association studies (GWAS) were performed using 5,112 high-quality markers from Diversity Arrays Technology sequencing (DArT-seq), and Kompetitive allele-specific polymerase chain reaction (KASP) genetic markers were developed. Phenotypic data were collected from fifteen different field trials for three consecutive years. Planting was conducted at various sowing times, and plants were grown with/without additional vernalisation and extended photoperiod treatments. This study detected fourteen stable regions associated with flowering time across multiple environments. GWAS combined with pangenome data highlighted the role of CEN gene in flowering and enabled the prediction of different CEN alleles from parental lines. As the founder lines of the multi-parental population are elite germplasm, the favourable alleles identified in this study are directly relevant to breeding, increasing the efficiency of subsequent breeding strategies and offering better grain yield and adaptation to growing conditions.
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Affiliation(s)
- Viet Hoang Dang
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Perth, WA, Australia
- Department of Primary Industries and Regional Development, Perth, WA, Australia
| | - Camilla Beate Hill
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Perth, WA, Australia
| | - Xiao-Qi Zhang
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Perth, WA, Australia
| | - Tefera Tolera Angessa
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Perth, WA, Australia
| | - Lee-Anne McFawn
- Department of Primary Industries and Regional Development, Perth, WA, Australia
| | - Chengdao Li
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Perth, WA, Australia.
- Department of Primary Industries and Regional Development, Perth, WA, Australia.
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Petersen KB, Kellogg EA. Diverse ecological functions and the convergent evolution of grass awns. AMERICAN JOURNAL OF BOTANY 2022; 109:1331-1345. [PMID: 36048829 PMCID: PMC9828495 DOI: 10.1002/ajb2.16060] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
The awn of grasses is a long, conspicuous outgrowth of the floral bracts in a grass spikelet. It is known to impact agricultural yield, but we know little about its broader ecological function, nor the selective forces that lead to its evolution. Grass awns are phenotypically diverse across the extant ~12,000 species of Poaceae. Awns have been lost and gained repeatedly over evolutionary time, between and within lineages, suggesting that they could be under selection and might provide adaptive benefit in some environments. Despite the phylogenetic context, we know of no studies that have tested whether the origin of awns correlates with putative selective forces on their form and function. Presence or absence of awns is not plastic; rather, heritability is high. The awns of grasses often are suggested as adaptations for dispersal, and most experimental work has been aimed at testing this hypothesis. Proposed dispersal functions include soil burial, epizoochory, and aerial orientation. Awns may also protect the seed from drought, herbivores, or fire by helping it become buried in soil. We do not fully understand the fitness or nutrient costs of awn production, but in some species awns function in photosynthesis, providing carbon to the seed. Here we show that awns likely provide an adaptive advantage, but argue that studies on awn function have lacked critical phylogenetic information to demonstrate adaptive convergent evolution, are taxonomically biased, and often lack clear alternative hypotheses.
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Phenotype and Genotype Interaction Underlying Distributive Characteristic for Awn Development in Rice. PLANTS 2022; 11:plants11070851. [PMID: 35406831 PMCID: PMC9002577 DOI: 10.3390/plants11070851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 11/26/2022]
Abstract
As a wild ancestor of cultivated rice, Oryza rufipogon is domesticated into cultivated rice Oryza sativa, many agricultural traits are newly created or disappear. In particular, in wild rice, awn protects from predators and is easily blown by the wind and used as a means of propagation. However, awns gradually disappeared as they were breeding from wild rice to cultivated rice. Since awn development is disadvantageous to rice yield, it is important to understand the genetic basis related to awn development. In addition, characterization of the genes associated with awn development is helpful in analyzing the genetic relationships of rice from ancient times to the present for the regulatory mechanisms of awn formation. QTL analysis identified RM14330-RM218 on chromosome 3 using a 120 Cheongcheong/Nagdong double haploid population. Through screening of genes related to awn development in RM-14330-RM218, it is indicated that OsDRPq3 is a causal gene that can be involved in awn development. OsDRPq3 transcription level is maintained high in long awn and less yield populations during the panicle formation stage, the period during awn development. Moreover, the sequence of OsDRPq3 has high homology with the drooping protein leaf. This study provides a new resource for phylogenetic research of rice and exploration of awn development.
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Huang B, Wu W, Hong Z. Genetic Loci Underlying Awn Morphology in Barley. Genes (Basel) 2021; 12:genes12101613. [PMID: 34681007 PMCID: PMC8535194 DOI: 10.3390/genes12101613] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/03/2021] [Accepted: 10/09/2021] [Indexed: 11/28/2022] Open
Abstract
Barley awns are highly active in photosynthesis and account for 30–50% of grain weight in barley. They are diverse in length, ranging from long to awnless, and in shape from straight to hooded or crooked. Their diversity and importance have intrigued geneticists for several decades. A large collection of awnness mutants are available—over a dozen of them have been mapped on chromosomes and a few recently cloned. Different awnness genes interact with each other to produce diverse awn phenotypes. With the availability of the sequenced barley genome and application of new mapping and gene cloning strategies, it will now be possible to identify and clone more awnness genes. A better understanding of the genetic basis of awn diversity will greatly facilitate development of new barley cultivars with improved yield, adaptability and sustainability.
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Affiliation(s)
- Biguang Huang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Fujian Collegiate Key Laboratory of Applied Plant Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Weiren Wu
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.W.); (Z.H.)
| | - Zonglie Hong
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
- Correspondence: (W.W.); (Z.H.)
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Kaur B, Sandhu KS, Kamal R, Kaur K, Singh J, Röder MS, Muqaddasi QH. Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects. PLANTS 2021; 10:plants10101989. [PMID: 34685799 PMCID: PMC8541486 DOI: 10.3390/plants10101989] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 12/22/2022]
Abstract
Omics technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal crop breeding program, as they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in omics assure time efficiency and cost benefits to improve cereal crops. This review provides a comprehensive overview of the established omics methods in five major cereals, namely rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants; (2) high-density transcriptomics data to study gene expression patterns; (3) global and targeted proteome profiling to study protein structure and interaction; (4) metabolomic profiling to quantify organ-level, small-density metabolites, and their composition; and (5) high-resolution, high-throughput, image-based phenomics approaches are surveyed in this review.
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Affiliation(s)
- Balwinder Kaur
- Everglades Research and Education Center, University of Florida, 3200 E. Palm Beach Rd., Belle Glade, FL 33430, USA;
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA;
| | - Roop Kamal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Kawalpreet Kaur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Jagmohan Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Quddoos H. Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
- Correspondence: or
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Maity A, Singh V, Jessup R, Bagavathiannan M. Seed traits correlate with herbicide resistance in Italian ryegrass (Lolium perenne ssp. multiflorum). PEST MANAGEMENT SCIENCE 2021; 77:2756-2765. [PMID: 33506986 DOI: 10.1002/ps.6304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/23/2021] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Italian ryegrass (Lolium perenne ssp. multiflorum) is one of the major winter annual weeds worldwide. In this research, diversity for seed morpho-physiological traits such as seed weight, seed size, awnedness, dormancy, speed of germination, and seed vigor among Italian ryegrass populations collected from the Texas Blacklands region were assessed, and potential association with herbicide resistance was investigated. RESULTS A high degree of diversity was observed among the populations for 100-seed weight (125-256 mg), seed length (4.8-6.6 mm), awn length (0-6 mm), and total seedling length (9-14 cm at 21 days after seed germination). Inter-population range for seed dormancy was higher in the freshly harvested seed (31-85%), which reduced to 18 to 62% at 9 months after harvest. Populations with high initial seed dormancy (> 70% dormancy) released dormancy at a faster rate than the low dormancy group (< 40%). Percent survival status to multiple postemergence herbicides was positively correlated with 100-seed weight and fresh or initial seed dormancy. CONCLUSION Early emerging cohorts are easily controlled by pre-plant tillage and preemergence herbicides, whereas late emerging cohorts (facilitated by seed dormancy) are exposed to postemergence herbicides wherein greater opportunities exist for resistance evolution, likely explaining the occurrence of high seed dormancy in Italian ryegrass populations resistant to postemergence herbicides. High seed weights can further allow seedling emergence from greater burial depth, thereby exposing more seedlings to postemergence herbicides and increasing the likelihood of resistance evolution. Results provide unique insights into the association between seed traits and herbicide resistance in this species. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Aniruddha Maity
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
- Division of Seed Technology, ICAR - Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Vijay Singh
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
- Eastern Shore Agricultural Research and Extension Center, Virginia Tech, Painter, VA, USA
| | - Russell Jessup
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
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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: 68] [Impact Index Per Article: 17.0] [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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Ntakirutimana F, Xie W. Unveiling the Actual Functions of Awns in Grasses: From Yield Potential to Quality Traits. Int J Mol Sci 2020; 21:ijms21207593. [PMID: 33066600 PMCID: PMC7589186 DOI: 10.3390/ijms21207593] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 12/25/2022] Open
Abstract
Awns, which are either bristles or hair-like outgrowths of lemmas in the florets, are one of the typical morphological characteristics of grass species. These stiff structures contribute to grain dispersal and burial and fend off animal predators. However, their phenotypic and genetic associations with traits deciding potential yield and quality are not fully understood. Awns appear to improve photosynthesis, provide assimilates for grain filling, thus contributing to the final grain yield, especially under temperature- and water-stress conditions. Long awns, however, represent a competing sink with developing kernels for photosynthates, which can reduce grain yield under favorable conditions. In addition, long awns can hamper postharvest handling, storage, and processing activities. Overall, little is known about the elusive role of awns, thus, this review summarizes what is known about the effect of awns on grain yield and biomass yield, grain nutritional value, and forage-quality attributes. The influence of awns on the agronomic performance of grasses seems to be associated with environmental and genetic factors and varies in different stages of plant development. The contribution of awns to yield traits and quality features previously documented in major cereal crops, such as rice, barley, and wheat, emphasizes that awns can be targeted for yield and quality improvement and may advance research aimed at identifying the phenotypic effects of morphological traits in grasses.
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Yu K, Wang J, Sun C, Liu X, Xu H, Yang Y, Dong L, Zhang D. High-density QTL mapping of leaf-related traits and chlorophyll content in three soybean RIL populations. BMC PLANT BIOLOGY 2020; 20:470. [PMID: 33050902 PMCID: PMC7556954 DOI: 10.1186/s12870-020-02684-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Leaf size and shape, which affect light capture, and chlorophyll content are important factors affecting photosynthetic efficiency. Genetic variation of these components significantly affects yield potential and seed quality. Identification of the genetic basis for these traits and the relationship between them is of great practical significance for achieving ideal plant architecture and high photosynthetic efficiency for improved yield. RESULTS Here, we undertook a large-scale linkage mapping study using three mapping populations to determine the genetic interplay between soybean leaf-related traits and chlorophyll content across two environments. Correlation analysis revealed a significant negative correlation between leaf size and shape, while both traits were positively correlated with chlorophyll content. This phenotypic relationship was verified across the three mapping populations as determined by principal component analysis, suggesting that these traits are under the control of complex and interrelated genetic components. The QTLs for leaf-related traits and chlorophyll are partly shared, which further supports the close genetic relationship between the two traits. The largest-effect major loci, q20, was stably identified across all population and environments and harbored the narrow leaflet gene Gm-JAG1 (Ln/ln), which is a key regulator of leaflet shape in soybean. CONCLUSION Our results uncover several major QTLs (q4-1, q4-2, q11, q13, q18 and q20) and its candidate genes specific or common to leaf-related traits and chlorophyll, and also show a complex epistatic interaction between the two traits. The SNP markers closely linked to these valuable QTLs could be used for molecular design breeding with improved plant architecture, photosynthetic capacity and even yield.
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Affiliation(s)
- Kaiye Yu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Jinshe Wang
- Zhengzhou National Subcenter for Soybean Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Chongyuan Sun
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Xiaoqian Liu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Huanqing Xu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Yuming Yang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Lidong Dong
- School of Life Sciences, Guangzhou University, Guangzhou, 510006 Guangdong China
| | - Dan Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou, 450002 Henan China
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Niu J, Zheng S, Shi X, Si Y, Tian S, He Y, Ling HQ. Fine mapping and characterization of the awn inhibitor B1 locus in common wheat (Triticum aestivum L.). ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.cj.2019.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Huang B, Huang D, Hong Z, Owie SO, Wu W. Genetic analysis reveals four interacting loci underlying awn trait diversity in barley (Hordeum vulgare). Sci Rep 2020; 10:12535. [PMID: 32719425 PMCID: PMC7385259 DOI: 10.1038/s41598-020-69335-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/10/2020] [Indexed: 11/09/2022] Open
Abstract
Barley (Hordeum vulgare) awns contribute to grain yield, but the genetic basis of awn development remains largely unclear. Five barley lines differing in awn traits and row types were used to create four F2 populations. Genetic analyses revealed that four pairs of genes were involved in awn development: A/a (awnless/awned), B/b (awnless/awned), H/h (hooded/straight), and L/l (long/short). Of these four loci, A, H and L functioned on both central rows (CR) and lateral rows (LR) of the barley spikes, while B exhibited effect only on LR. A and B had duplicate effects on LR, and both showed dominant epistasis to loci H and L, whereas H was epistatic to L. Meanwhile, A and B were found to be genetically linked, with a row-type locus V located between them. The genetic distances of A-V and B-V were estimated to be 9.6 and 7.7 cM, respectively. Literature search suggested that A, H and V may correspond to the reported Lks1, Kap1 and Vrs1, respectively, whereas B is a novel gene specifically controlling awn development on LR, designated as Lsa1 for lateral spikelet awnless 1. The only barley homolog of wheat awn inhibitor gene B1, HORVU2Hr1G077570, is a potential candidate of Lsa1.
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Affiliation(s)
- Biguang Huang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. .,Fujian Collegiate Key Laboratory of Applied Plant Genetics, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. .,Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA.
| | - Daiqing Huang
- Aquatic and Crop Resource Development, National Research Council of Canada, Saskatoon, SK, S7N 0W9, Canada
| | - Zonglie Hong
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Swithin Omosuwa Owie
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Fujian Collegiate Key Laboratory of Applied Plant Genetics, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Weiren Wu
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. .,Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Jaganathan D, Bohra A, Thudi M, Varshney RK. Fine mapping and gene cloning in the post-NGS era: advances and prospects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1791-1810. [PMID: 32040676 PMCID: PMC7214393 DOI: 10.1007/s00122-020-03560-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/29/2020] [Indexed: 05/18/2023]
Abstract
Improvement in traits of agronomic importance is the top breeding priority of crop improvement programs. Majority of these agronomic traits show complex quantitative inheritance. Identification of quantitative trait loci (QTLs) followed by fine mapping QTLs and cloning of candidate genes/QTLs is central to trait analysis. Advances in genomic technologies revolutionized our understanding of genetics of complex traits, and genomic regions associated with traits were employed in marker-assisted breeding or cloning of QTLs/genes. Next-generation sequencing (NGS) technologies have enabled genome-wide methodologies for the development of ultra-high-density genetic linkage maps in different crops, thus allowing placement of candidate loci within few kbs in genomes. In this review, we compare the marker systems used for fine mapping and QTL cloning in the pre- and post-NGS era. We then discuss how different NGS platforms in combination with advanced experimental designs have improved trait analysis and fine mapping. We opine that efficient genotyping/sequencing assays may circumvent the need for cumbersome procedures that were earlier used for fine mapping. A deeper understanding of the trait architectures of agricultural significance will be crucial to accelerate crop improvement.
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Affiliation(s)
- Deepa Jaganathan
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - Abhishek Bohra
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
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Alqudah AM, Sallam A, Stephen Baenziger P, Börner A. GWAS: Fast-forwarding gene identification and characterization in temperate Cereals: lessons from Barley - A review. J Adv Res 2020; 22:119-135. [PMID: 31956447 PMCID: PMC6961222 DOI: 10.1016/j.jare.2019.10.013] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/07/2019] [Accepted: 10/31/2019] [Indexed: 11/28/2022] Open
Abstract
Understanding the genetic complexity of traits is an important objective of small grain temperate cereals yield and adaptation improvements. Bi-parental quantitative trait loci (QTL) linkage mapping is a powerful method to identify genetic regions that co-segregate in the trait of interest within the research population. However, recently, association or linkage disequilibrium (LD) mapping using a genome-wide association study (GWAS) became an approach for unraveling the molecular genetic basis underlying the natural phenotypic variation. Many causative allele(s)/loci have been identified using the power of this approach which had not been detected in QTL mapping populations. In barley (Hordeum vulgare L.), GWAS has been successfully applied to define the causative allele(s)/loci which can be used in the breeding crop for adaptation and yield improvement. This promising approach represents a tremendous step forward in genetic analysis and undoubtedly proved it is a valuable tool in the identification of candidate genes. In this review, we describe the recently used approach for genetic analyses (linkage mapping or association mapping), and then provide the basic genetic and statistical concepts of GWAS, and subsequently highlight the genetic discoveries using GWAS. The review explained how the candidate gene(s) can be detected using state-of-art bioinformatic tools.
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Affiliation(s)
- Ahmad M. Alqudah
- Resources Genetics and Reproduction, Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, 71526- Assiut, Egypt
| | - P. Stephen Baenziger
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, 68583-Lincoln, NE, USA
| | - Andreas Börner
- Resources Genetics and Reproduction, Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
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Ntakirutimana F, Xiao B, Xie W, Zhang J, Zhang Z, Wang N, Yan J. Potential Effects of Awn Length Variation on Seed Yield and Components, Seed Dispersal and Germination Performance in Siberian Wildrye ( Elymus sibiricus L.). PLANTS 2019; 8:plants8120561. [PMID: 31805733 PMCID: PMC6963408 DOI: 10.3390/plants8120561] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/23/2019] [Accepted: 11/27/2019] [Indexed: 11/16/2022]
Abstract
: Awns, needle-like structures formed on the distal of the lemmas in the florets, are of interest because of their essential roles in seed dispersal, germination and photosynthesis. Previous research has reported the potential benefits of awns in major cereal grasses, yet reports on the agronomic and economic implications of awn length variation in forage grasses remain scarce. This study investigated the variation of awn length among 20 Siberian wildrye populations and the effect of awn length on seed yield and yield components. This work then studied the impact of awn length on seed dispersal and germination. The analyses indicated a high level of awn length variation among populations. Awn length showed a significant influence on harvested seed yield per plant (p < 0.05) mostly driven by interactions between awn length and the majority of seed yield components. Principal component analysis clearly revealed that the final impact of awn length on seed yield depends on the balance of its positive and negative effects on traits determining seed yield. Furthermore, awn length tended to increase seed dispersal distance, although little diversity in the nature of this progression was observed in some populations. Awn length exhibited a significant relationship (p < 0.05) with germination percentage. It also tended to shorten germination duration, although this interaction was not statistically significant. Collectively, these results provide vital information for breeding and agronomic programs aiming to maintain yield in grasses. This is the first report to demonstrate in Siberian wildrye the agronomic impacts of awn length variation.
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Affiliation(s)
- Fabrice Ntakirutimana
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (F.N.); (B.X.); (J.Z.); (Z.Z.); (N.W.)
| | - Bowen Xiao
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (F.N.); (B.X.); (J.Z.); (Z.Z.); (N.W.)
| | - Wengang Xie
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (F.N.); (B.X.); (J.Z.); (Z.Z.); (N.W.)
- Correspondence: ; Tel.: +86-931-891-3014
| | - Junchao Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (F.N.); (B.X.); (J.Z.); (Z.Z.); (N.W.)
| | - Zongyu Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (F.N.); (B.X.); (J.Z.); (Z.Z.); (N.W.)
| | - Na Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (F.N.); (B.X.); (J.Z.); (Z.Z.); (N.W.)
| | - Jiajun Yan
- Sichuan Academy of Grassland Science, Chengdu 611731, China;
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Bresadola L, Caseys C, Castiglione S, Buerkle CA, Wegmann D, Lexer C. Admixture mapping in interspecific Populus hybrids identifies classes of genomic architectures for phytochemical, morphological and growth traits. THE NEW PHYTOLOGIST 2019; 223:2076-2089. [PMID: 31104343 PMCID: PMC6771622 DOI: 10.1111/nph.15930] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 05/06/2019] [Indexed: 05/03/2023]
Abstract
The genomic architecture of functionally important traits is key to understanding the maintenance of reproductive barriers and trait differences when divergent populations or species hybridize. We conducted a genome-wide association study (GWAS) to study trait architecture in natural hybrids of two ecologically divergent Populus species. We genotyped 472 seedlings from a natural hybrid zone of Populus alba and Populus tremula for genome-wide markers from reduced representation sequencing, phenotyped the plants in common gardens for 46 phytochemical (phenylpropanoid), morphological and growth traits, and used a Bayesian polygenic model for mapping. We detected three classes of genomic architectures: traits with finite, detectable associations of genetic loci with phenotypic variation in addition to highly polygenic heritability; traits with indications for polygenic heritability only; and traits with no detectable heritability. For the first class, we identified genome regions with plausible candidate genes for phenylpropanoid biosynthesis or its regulation, including MYB transcription factors and glycosyl transferases. GWAS in natural, recombinant hybrids represent a promising step towards resolving the genomic architecture of phenotypic traits in long-lived species. This facilitates the fine-mapping and subsequent functional characterization of genes and networks causing differences in hybrid performance and fitness.
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Affiliation(s)
- Luisa Bresadola
- Department of BiologyUniversity of FribourgChemin du Musée 101700FribourgSwitzerland
| | - Céline Caseys
- Department of BiologyUniversity of FribourgChemin du Musée 101700FribourgSwitzerland
- Department of Plant SciencesUniversity of California DavisOne Shields AvenueDavisCA95616USA
| | - Stefano Castiglione
- Department of Chemistry and Biology ‘A. Zambelli’University of SalernoVia Giovanni Paolo II 13284084Fisciano, SalernoItaly
| | - C. Alex Buerkle
- Department of BotanyUniversity of Wyoming1000 E. University Ave.LaramieWY82071USA
| | - Daniel Wegmann
- Department of BiologyUniversity of FribourgChemin du Musée 101700FribourgSwitzerland
- Swiss Institute of Bioinformatics1700FribourgSwitzerland
| | - Christian Lexer
- Department of BiologyUniversity of FribourgChemin du Musée 101700FribourgSwitzerland
- Department of Botany and Biodiversity ResearchFaculty of Life SciencesUniversity of ViennaRennweg 12A‐1030ViennaAustria
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Zheng C, Boer MP, van Eeuwijk FA. Construction of Genetic Linkage Maps in Multiparental Populations. Genetics 2019; 212:1031-1044. [PMID: 31182487 PMCID: PMC6707453 DOI: 10.1534/genetics.119.302229] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/04/2019] [Indexed: 11/18/2022] Open
Abstract
Construction of genetic linkage maps has become a routine step for mapping quantitative trait loci (QTL), particularly in animal and plant breeding populations. Many multiparental populations have recently been produced to increase genetic diversity and QTL mapping resolution. However, few software packages are available for map construction in these populations. In this paper, we build a general framework for the construction of genetic linkage maps from genotypic data in diploid populations, including bi- and multiparental populations, cross-pollinated (CP) populations, and breeding pedigrees. The framework is implemented as an automatic pipeline called magicMap, where the maximum multilocus likelihood approach utilizes genotypic information efficiently. We evaluate magicMap by extensive simulations and eight real datasets: one biparental, one CP, four multiparent advanced generation intercross (MAGIC), and two nested association mapping (NAM) populations, the number of markers ranging from a few hundred to tens of thousands. Not only is magicMap the only software capable of accommodating all of these designs, it is more accurate and robust to missing genotypes and genotyping errors than commonly used packages.
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Affiliation(s)
- Chaozhi Zheng
- Biometris, Wageningen University and Research, 6700 AA, The Netherlands
| | - Martin P Boer
- Biometris, Wageningen University and Research, 6700 AA, The Netherlands
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Ntakirutimana F, Xie W. Morphological and Genetic Mechanisms Underlying Awn Development in Monocotyledonous Grasses. Genes (Basel) 2019; 10:E573. [PMID: 31366144 PMCID: PMC6723108 DOI: 10.3390/genes10080573] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/26/2019] [Accepted: 07/28/2019] [Indexed: 01/01/2023] Open
Abstract
The identification of biological mechanisms underlying the development of complex quantitative traits, including those that contribute to plant architecture, yield and quality potential, and seed dispersal, is a major focus in the evolutionary biology and plant breeding. The awn, a bristle-like extension from the lemma in the floret, is one of the distinct morphological and physiological traits in grass species. Awns are taught as an evolutionary trait assisting seed dispersal and germination and increasing photosynthesis. Awn development seems to be complex process, involving dramatic phenotypic and molecular changes. Although recent advances investigated the underlying morphological and molecular genetic factors of awn development, there is little agreement about how these factors interact during awn formation and how this interaction affects variation of awn morphology. Consequently, the developmental sequence of the awn is not yet well understood. Here, we review awn morphological and histological features, awn development pathways, and molecular processes of awn development. We argue that morphological and molecular genetic mechanisms of awn development previously studied in major cereal crops, such as barley, wheat, and rice, offered intriguing insights helping to characterize this process in a comparative approach. Applying such an approach will aid to deeply understand factors involved in awn development in grass species.
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Affiliation(s)
- Fabrice Ntakirutimana
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Wengang Xie
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
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Haas M, Schreiber M, Mascher M. Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:204-225. [PMID: 30414305 DOI: 10.1111/jipb.12737] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/27/2018] [Indexed: 05/02/2023]
Abstract
Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms. Knowledge about the geographical origins of these crops and the genes responsible for domestication traits largely pre-dates the era of next-generation sequencing, although sequencing will lead to new insights. Molecular markers were initially used to calculate distance (relatedness), genetic diversity and to generate genetic maps which were useful in cloning major domestication genes. Both crops are characterized by large, complex genomes which were long thought to be beyond the scope of whole-genome sequencing. However, advances in sequencing technologies have improved the state of genomic resources for both wheat and barley. The availability of reference genomes for wheat and some of its progenitors, as well as for barley, sets the stage for answering unresolved questions in domestication genomics of wheat and barley.
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Affiliation(s)
- Matthew Haas
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
| | - Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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24
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Girma G, Nida H, Seyoum A, Mekonen M, Nega A, Lule D, Dessalegn K, Bekele A, Gebreyohannes A, Adeyanju A, Tirfessa A, Ayana G, Taddese T, Mekbib F, Belete K, Tesso T, Ejeta G, Mengiste T. A Large-Scale Genome-Wide Association Analyses of Ethiopian Sorghum Landrace Collection Reveal Loci Associated With Important Traits. FRONTIERS IN PLANT SCIENCE 2019; 10:691. [PMID: 31191590 PMCID: PMC6549537 DOI: 10.3389/fpls.2019.00691] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/08/2019] [Indexed: 05/20/2023]
Abstract
The eastern Africa region, Ethiopia and its surroundings, is considered as the center of origin and diversity for sorghum, and has contributed to global sorghum genetic improvement. The germplasm from this region harbors enormous genetic variation for various traits but little is known regarding the genetic architecture of most traits. Here, 1425 Ethiopian landrace accessions were phenotyped under field conditions for presence or absence of awns, panicle compactness and shape, panicle exsertion, pericarp color, glume cover, plant height and smut resistance under diverse environmental conditions in Ethiopia. In addition, F1 hybrids obtained from a subset of 1341 accessions crossed to an A1 cytoplasmic male sterile line, ATx623, were scored for fertility/sterility reactions. Subsequently, genotyping-by-sequencing generated a total of 879,407 SNPs from which 72,190 robust SNP markers were selected after stringent quality control (QC). Pairwise distance-based hierarchical clustering identified 11 distinct groups. Of the genotypes assigned to either one of the 11 sub-populations, 65% had high ancestry membership coefficient with the likelihood of more than 0.60 and the remaining 35% represented highly admixed accessions. A genome-wide association study (GWAS) identified loci and SNPs associated with aforementioned traits. GWAS based on compressed mixed linear model (CMLM) identified SNPs with significant association (FDR ≤ 0.05) to the different traits studied. The percentage of total phenotypic variation explained with significant SNPs across traits ranged from 2 to 43%. Candidate genes showing significant association with different traits were identified. The sorghum bHLH transcription factor, ABORTED MICROSPORES was identified as a strong candidate gene conditioning male fertility. Notably, sorghum CLAVATA1 receptor like kinase, known for regulation of plant growth, and the ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR gene RAP2-7, known to suppress transition to flowering, were significantly associated with plant height. In addition, the YELLOW SEED1 like MYB transcription factor and TANNIN1 showed strong association with pericarp color validating previous observations. Overall, the genetic architecture of natural variation representing the complex Ethiopian sorghum germplasm was established. The study contributes to the characterization of genes and alleles controlling agronomic traits, and will serve as a source of markers for molecular breeding.
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Affiliation(s)
- Gezahegn Girma
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Habte Nida
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Amare Seyoum
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Moges Mekonen
- Chiro Agricultural Research Center, Ethiopian Institute of Agricultural Research, Chiro, Ethiopia
| | - Amare Nega
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Dagnachew Lule
- Bako Agricultural Research Center, Oromia Agricultural Research Institute, Bako, Ethiopia
| | - Kebede Dessalegn
- Bako Agricultural Research Center, Oromia Agricultural Research Institute, Bako, Ethiopia
| | - Alemnesh Bekele
- School of Plant Sciences, Haramaya University, Dire Dawa, Ethiopia
| | - Adane Gebreyohannes
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Adedayo Adeyanju
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Alemu Tirfessa
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Getachew Ayana
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Taye Taddese
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Firew Mekbib
- School of Plant Sciences, Haramaya University, Dire Dawa, Ethiopia
| | - Ketema Belete
- School of Plant Sciences, Haramaya University, Dire Dawa, Ethiopia
| | - Tesfaye Tesso
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Gebisa Ejeta
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
- *Correspondence: Gebisa Ejeta,
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Tesfaye Mengiste,
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25
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Milner SG, Jost M, Taketa S, Mazón ER, Himmelbach A, Oppermann M, Weise S, Knüpffer H, Basterrechea M, König P, Schüler D, Sharma R, Pasam RK, Rutten T, Guo G, Xu D, Zhang J, Herren G, Müller T, Krattinger SG, Keller B, Jiang Y, González MY, Zhao Y, Habekuß A, Färber S, Ordon F, Lange M, Börner A, Graner A, Reif JC, Scholz U, Mascher M, Stein N. Genebank genomics highlights the diversity of a global barley collection. Nat Genet 2018; 51:319-326. [PMID: 30420647 DOI: 10.1038/s41588-018-0266-x] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/26/2018] [Indexed: 01/22/2023]
Abstract
Genebanks hold comprehensive collections of cultivars, landraces and crop wild relatives of all major food crops, but their detailed characterization has so far been limited to sparse core sets. The analysis of genome-wide genotyping-by-sequencing data for almost all barley accessions of the German ex situ genebank provides insights into the global population structure of domesticated barley and points out redundancies and coverage gaps in one of the world's major genebanks. Our large sample size and dense marker data afford great power for genome-wide association scans. We detect known and novel loci underlying morphological traits differentiating barley genepools, find evidence for convergent selection for barbless awns in barley and rice and show that a major-effect resistance locus conferring resistance to bymovirus infection has been favored by traditional farmers. This study outlines future directions for genomics-assisted genebank management and the utilization of germplasm collections for linking natural variation to human selection during crop evolution.
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Affiliation(s)
- Sara G Milner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Matthias Jost
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,Agriculture and Food, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australia
| | - Shin Taketa
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Elena Rey Mazón
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Markus Oppermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Stephan Weise
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Helmut Knüpffer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Martín Basterrechea
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Patrick König
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Danuta Schüler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Rajiv Sharma
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,University of Dundee at the James Hutton Institute, Invergowrie, UK
| | - Raj K Pasam
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,Department of Economic Development, Jobs, Transport and Resources, Centre for AgriBioscience, Agriculture Victoria Research, Bundoora, Victoria, Australia
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Ganggang Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dongdong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gerhard Herren
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Thomas Müller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Simon G Krattinger
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Maria Y González
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Antje Habekuß
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Sandra Färber
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany. .,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany. .,Center for Integrated Breeding Research, Georg-August-Universität Göttingen, Göttingen, Germany.
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26
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Recursive Algorithms for Modeling Genomic Ancestral Origins in a Fixed Pedigree. G3-GENES GENOMES GENETICS 2018; 8:3231-3245. [PMID: 30068523 PMCID: PMC6169389 DOI: 10.1534/g3.118.200340] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The study of gene flow in pedigrees is of strong interest for the development of quantitative trait loci (QTL) mapping methods in multiparental populations. We developed a Markovian framework for modeling ancestral origins along two homologous chromosomes within individuals in fixed pedigrees. A highly beneficial property of our method is that the size of state space depends linearly or quadratically on the number of pedigree founders, whereas this increases exponentially with pedigree size in alternative methods. To calculate the parameter values of the Markov process, we describe two novel recursive algorithms that differ with respect to the pedigree founders being assumed to be exchangeable or not. Our algorithms apply equally to autosomes and sex chromosomes, another desirable feature of our approach. We tested the accuracy of the algorithms by a million simulations on a pedigree. We demonstrated two applications of the recursive algorithms in multiparental populations: design a breeding scheme for maximizing the overall density of recombination breakpoints and thus the QTL mapping resolution, and incorporate pedigree information into hidden Markov models in ancestral inference from genotypic data; the conditional probabilities and the recombination breakpoint data resulting from ancestral inference can facilitate follow-up QTL mapping. The results show that the generality of the recursive algorithms can greatly increase the application range of genetic analysis such as ancestral inference in multiparental populations.
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27
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Savadi S. Molecular regulation of seed development and strategies for engineering seed size in crop plants. PLANT GROWTH REGULATION 2018; 84:401-422. [PMID: 0 DOI: 10.1007/s10725-017-0355-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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28
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Ogawa D, Yamamoto E, Ohtani T, Kanno N, Tsunematsu H, Nonoue Y, Yano M, Yamamoto T, Yonemaru JI. Haplotype-based allele mining in the Japan-MAGIC rice population. Sci Rep 2018. [PMID: 29531264 PMCID: PMC5847589 DOI: 10.1038/s41598-018-22657-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Multi-parent advanced generation inter-cross (MAGIC) lines have broader genetic variation than bi-parental recombinant inbred lines. Genome-wide association study (GWAS) using high number of DNA polymorphisms such as single-nucleotide polymorphisms (SNPs) is a popular tool for allele mining in MAGIC populations, in which the associations of phenotypes with SNPs are investigated; however, the effects of haplotypes from multiple founders on phenotypes are not considered. Here, we describe an improved method of allele mining using the newly developed Japan-MAGIC (JAM) population, which is derived from eight high-yielding rice cultivars in Japan. To obtain information on the haplotypes in the JAM lines, we predicted the haplotype blocks in the whole chromosomes using 16,345 SNPs identified via genotyping-by-sequencing analysis. Using haplotype-based GWAS, we clearly detected the loci controlling the glutinous endosperm and culm length traits. Information on the alleles of the eight founders, which was based on the effects of mutations revealed by the analysis of next-generation sequencing data, was used to narrow down the candidate genes and reveal the associations between alleles and phenotypes. The haplotype-based allele mining (HAM) proposed in this study is a promising approach to the detection of allelic variation in genes controlling agronomic traits in MAGIC populations.
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Affiliation(s)
- Daisuke Ogawa
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan.,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Eiji Yamamoto
- Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Toshikazu Ohtani
- Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Noriko Kanno
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan.,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Hiroshi Tsunematsu
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Yasunori Nonoue
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Masahiro Yano
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan.,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Toshio Yamamoto
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan. .,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan.
| | - Jun-Ichi Yonemaru
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan. .,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan.
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29
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30
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Nishijima R, Ikeda TM, Takumi S. Genetic mapping reveals a dominant awn-inhibiting gene related to differentiation of the variety anathera in the wild diploid wheat Aegilops tauschii. Genetica 2017; 146:75-84. [PMID: 29101627 DOI: 10.1007/s10709-017-9998-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/30/2017] [Indexed: 11/24/2022]
Abstract
Aegilops tauschii, a wild wheat relative, is the D-genome donor of common wheat. Subspecies and varieties of Ae. tauschii are traditionally classified based on differences in their inflorescence architecture. However, the genetic information for their diversification has been quite limited in the wild wheat relatives. The variety anathera has no awn on the lemma, but the genetic basis for this diagnostic character is unknown. Wide variations in awn length traits at the top and middle spikes were found in the Ae. tauschii core collection, and the awn length at the middle spike was significantly smaller in the eastward-dispersed sublineage than in those in other sublineages. To clarify loci controlling the awnless phenotype of var. anathera, we measured awn length of an intervariety F2 mapping population, and found that the F2 individuals could be divided into two groups mainly based on the awn length at the middle of spike, namely short and long awn groups, significantly fitting a 3:1 segregation ratio, which indicated that a single locus controls the awnless phenotype. The awnless locus, Anathera (Antr), was assigned to the distal region of the short arm of chromosome 5D. Quantitative trait locus analysis using the awn length data of each F2 individual showed that only one major locus was at the same chromosomal position as Antr. These results suggest that a single dominant allele determines the awnless diagnostic character in the variety anathera. The Antr dominant allele is a novel gene inhibiting awn elongation in wheat and its relatives.
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Affiliation(s)
- Ryo Nishijima
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, 657-8501, Japan
| | - Tatsuya M Ikeda
- Western Region Agricultural Research Center of the National Agriculture and Food Research Organization, 6-12-1 Nishi-fukatsucho, Fukuyama, Hiroshima, 721-8514, Japan
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, 657-8501, Japan.
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31
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van Esse GW, Walla A, Finke A, Koornneef M, Pecinka A, von Korff M. Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley. PLANT PHYSIOLOGY 2017; 174:2397-2408. [PMID: 28655778 PMCID: PMC5543938 DOI: 10.1104/pp.17.00108] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 06/25/2017] [Indexed: 05/17/2023]
Abstract
The complex nature of crop genomes has long prohibited the efficient isolation of agronomically relevant genes. However, recent advances in next-generation sequencing technologies provide new ways to accelerate fine-mapping and gene isolation in crops. We used RNA sequencing of allelic six-rowed spike3 (vrs3) mutants with altered spikelet development for gene identification and functional analysis in barley (Hordeum vulgare). Variant calling in two allelic vrs3 mutants revealed that VRS3 encodes a putative histone Lys demethylase with a conserved zinc finger and Jumonji C and N domain. Sanger sequencing of this candidate gene in independent allelic vrs3 mutants revealed a series of mutations in conserved domains, thus confirming our candidate as the VRS3 gene and suggesting that the row type in barley is determined epigenetically. Global transcriptional profiling in developing shoot apical meristems of vrs3 suggested that VRS3 acts as a transcriptional activator of the row-type genes VRS1 (Hv.HOMEOBOX1) and INTERMEDIUM-C (INT-C; Hv.TEOSINTE BRANCHED1). Comparative transcriptome analysis of the row-type mutants vrs3, vrs4 (Hv.RAMOSA2), and int-c confirmed that all three genes act as transcriptional activators of VRS1 and quantitative variation in the expression levels of VRS1 in these mutants correlated with differences in the number of developed lateral spikelets. The identification of genes and pathways affecting seed number in small grain cereals will enable to further unravel the transcriptional networks controlling this important yield component.
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Affiliation(s)
- G Wilma van Esse
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Institute for Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Cluster of Excellence in Plant Sciences, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
| | - Agatha Walla
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Institute for Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Cluster of Excellence in Plant Sciences, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
| | - Andreas Finke
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Maarten Koornneef
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Maria von Korff
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Institute for Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Cluster of Excellence in Plant Sciences, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
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