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Mohammadi M, Mohammadi R. Potential of tetraploid wheats in plant breeding: A review. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112155. [PMID: 38885883 DOI: 10.1016/j.plantsci.2024.112155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/05/2024] [Accepted: 06/08/2024] [Indexed: 06/20/2024]
Abstract
Domestication syndrome, selection pressure, and modern plant breeding programs have reduced the genetic diversity of the wheat germplasm. For the genetic gains of breeding programs to be sustainable, plant breeders require a diverse gene pool to select genes for resistance to biotic stress factors, tolerance to abiotic stress factors, and improved quality and yield components. Thus, old landraces, subspecies and wild ancestors are rich sources of genetic diversity that have not yet been fully exploited, and it is possible to utilize this diversity. Compared with durum wheat, tetraploid wheat subspecies have retained much greater genetic diversity despite genetic drift and various environmental influences, and the identification and utilization of this diversity can make a greater contribution to the genetic enrichment of wheat. In addition, using the pre-breeding method, the valuable left-behind alleles in the wheat gene pool can be re-introduced through hybridization and introgressive gene flow to create a sustainable opportunity for the genetic gain of wheat. This review provides some insights about the potential of tetraploid wheats in plant breeding and the genetic gains made by them in plant breeding across past decades, and gathers the known functional information on genes/QTLs, metabolites, traits and their direct involvement in wheat resistance/tolerance to biotic/abiotic stresses.
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Affiliation(s)
- Majid Mohammadi
- Dryland Agricultural Research Institute (DARI), Sararood branch, AREEO, Kermanshah, Iran.
| | - Reza Mohammadi
- Dryland Agricultural Research Institute (DARI), Sararood branch, AREEO, Kermanshah, Iran.
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2
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A Y K, E M, R B, E M, M D, L C, F D. Independent genetic factors control floret number and spikelet number in Triticum turgidum ssp. FRONTIERS IN PLANT SCIENCE 2024; 15:1390401. [PMID: 39253571 PMCID: PMC11381284 DOI: 10.3389/fpls.2024.1390401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 08/02/2024] [Indexed: 09/11/2024]
Abstract
Wheat grain yield is a complex trait resulting from a trade-off among many distinct components. During wheat evolution, domestication events and then modern breeding have strongly increased the yield potential of wheat plants, by enhancing spike fertility. To address the genetic bases of spike fertility in terms of spikelet number per spike and floret number per spikelet, a population of 110 recombinant inbred lines (RILS) obtained crossing a Triticum turgidum ssp. durum cultivar (Latino) and a T. dicoccum accession (MG5323) was exploited. Being a modern durum and a semi-domesticated genotype, respectively, the two parents differ for spike architecture and fertility, and thus the corresponding RIL population is the ideal genetic material to dissect genetic bases of yield components. The RIL population was phenotyped in four environments. Using a high-density SNP genetic map and taking advantage of several genome sequencing available for Triticeae, a total of 94 QTLs were identified for the eight traits considered; these QTLs were further reduced to 17 groups, based on their genetic and physical co-location. QTLs controlling floret number per spikelet and spikelet number per spike mapped in non-overlapping chromosomal regions, suggesting that independent genetic factors determine these fertility-related traits. The physical intervals of QTL groups were considered for possible co-location with known genes functionally involved in spike fertility traits and with yield-related QTLs previously mapped in tetraploid wheat. The most interesting result concerns a QTL group on chromosome 5B, associated with spikelet number per spike, since it could host genes still uncharacterized for their association to spike fertility. Finally, we identified two different regions where the trade-off between fertility related traits and kernel weight is overcome. Further analyses of these regions could pave the way for a future identification of new genetic loci contributing to fertility traits essential for yield improvement in durum wheat.
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Affiliation(s)
- Kiros A Y
- Center of Plant Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Mica E
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica, Università del Piemonte Orientale, Vercelli, Italy
| | - Battaglia R
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Mazzucotelli E
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Dell'Acqua M
- Center of Plant Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Cattivelli L
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Desiderio F
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
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3
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Wang Z, Miao L, Chen Y, Peng H, Ni Z, Sun Q, Guo W. Deciphering the evolution and complexity of wheat germplasm from a genomic perspective. J Genet Genomics 2023; 50:846-860. [PMID: 37611848 DOI: 10.1016/j.jgg.2023.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023]
Abstract
Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research. Here, we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome. New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress, genomic variations at multiple scales contributing to the diversity of wheat germplasm, and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat. Genomics databases and bioinformatics tools meeting the urgent needs of wheat genomics research are also summarized. The ever-increasing omics data, along with advanced tools and well-structured databases, are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.
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Affiliation(s)
- Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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4
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Valladares García AP, Desiderio F, Simeone R, Ravaglia S, Ciorba R, Fricano A, Guerra D, Blanco A, Cattivelli L, Mazzucotelli E. QTL mapping for kernel-related traits in a durum wheat x T. dicoccum segregating population. FRONTIERS IN PLANT SCIENCE 2023; 14:1253385. [PMID: 37849841 PMCID: PMC10577384 DOI: 10.3389/fpls.2023.1253385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/28/2023] [Indexed: 10/19/2023]
Abstract
Durum wheat breeding relies on grain yield improvement to meet its upcoming demand while coping with climate change. Kernel size and shape are the determinants of thousand kernel weight (TKW), which is a key component of grain yield, and the understanding of the genetic control behind these traits supports the progress in yield potential. The present study aimed to dissect the genetic network responsible for kernel size components (length, width, perimeter, and area) and kernel shape traits (width-to-length ratio and formcoefficient) as well as their relationships with kernel weight, plant height, and heading date in durum wheat. Quantitative Trait Locus (QTL) mapping was performed on a segregating population of 110 recombinant inbred lines, derived from a cross between the domesticated emmer wheat accession MG5323 and the durum wheat cv. Latino, evaluated in four different environments. A total of 24 QTLs stable across environments were found and further grouped in nine clusters on chromosomes 2A, 2B, 3A, 3B, 4B, 6B, and 7A. Among them, a QTL cluster on chromosome 4B was associated with kernel size traits and TKW, where the parental MG5323 contributed the favorable alleles, highlighting its potential to improve durum wheat germplasm. The physical positions of the clusters, defined by the projection on the T. durum reference genome, overlapped with already known genes (i.e., BIG GRAIN PROTEIN 1 on chromosome 4B). These results might provide genome-based guidance for the efficient exploitation of emmer wheat diversity in wheat breeding, possibly through yield-related molecular markers.
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Affiliation(s)
- Ana Paola Valladares García
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, Valencia, Spain
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Rosanna Simeone
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Bari, Italy
| | | | - Roberto Ciorba
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Rome, Italy
| | - Agostino Fricano
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Davide Guerra
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Bari, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
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5
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Wang Z, Wang W, Xie X, Wang Y, Yang Z, Peng H, Xin M, Yao Y, Hu Z, Liu J, Su Z, Xie C, Li B, Ni Z, Sun Q, Guo W. Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference. Nat Commun 2022; 13:3891. [PMID: 35794156 PMCID: PMC9259585 DOI: 10.1038/s41467-022-31581-0] [Citation(s) in RCA: 29] [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: 11/25/2021] [Accepted: 06/23/2022] [Indexed: 12/15/2022] Open
Abstract
Major crops are all survivors of domestication bottlenecks. Studies have focused on the genetic loci related to the domestication syndrome, while the contribution of ancient haplotypes remains largely unknown. Here, an ancestral genomic haploblock dissection method is developed and applied to a resequencing dataset of 386 tetraploid/hexaploid wheat accessions, generating a pan-ancestry haploblock map. Together with cytoplastic evidences, we reveal that domesticated polyploid wheat emerged from the admixture of six founder wild emmer lineages, which contributed the foundation of ancestral mosaics. The key domestication-related loci, originated over a wide geographical range, were gradually pyramided through a protracted process. Diverse stable-inheritance ancestral haplotype groups of the chromosome central zone are identified, revealing the expanding routes of wheat and the trends of modern wheat breeding. Finally, an evolution model of polyploid wheat is proposed, highlighting the key role of wild-to-crop and interploidy introgression, that increased genomic diversity following bottlenecks introduced by domestication and polyploidization.
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Affiliation(s)
- Zihao Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Wenxi Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xiaoming Xie
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yongfa Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhengzhao Yang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Jie Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhenqi Su
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Chaojie Xie
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Baoyun Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China.
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China.
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6
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Levy AA, Feldman M. Evolution and origin of bread wheat. THE PLANT CELL 2022; 34:2549-2567. [PMID: 35512194 PMCID: PMC9252504 DOI: 10.1093/plcell/koac130] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/18/2022] [Indexed: 05/12/2023]
Abstract
Bread wheat (Triticum aestivum, genome BBAADD) is a young hexaploid species formed only 8,500-9,000 years ago through hybridization between a domesticated free-threshing tetraploid progenitor, genome BBAA, and Aegilops tauschii, the diploid donor of the D subgenome. Very soon after its formation, it spread globally from its cradle in the fertile crescent into new habitats and climates, to become a staple food of humanity. This extraordinary global expansion was probably enabled by allopolyploidy that accelerated genetic novelty through the acquisition of new traits, new intergenomic interactions, and buffering of mutations, and by the attractiveness of bread wheat's large, tasty, and nutritious grain with high baking quality. New genome sequences suggest that the elusive donor of the B subgenome is a distinct (unknown or extinct) species rather than a mosaic genome. We discuss the origin of the diploid and tetraploid progenitors of bread wheat and the conflicting genetic and archaeological evidence on where it was formed and which species was its free-threshing tetraploid progenitor. Wheat experienced many environmental changes throughout its evolution, therefore, while it might adapt to current climatic changes, efforts are needed to better use and conserve the vast gene pool of wheat biodiversity on which our food security depends.
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Affiliation(s)
- Avraham A Levy
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Moshe Feldman
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100 Israel
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Xie P, Tang S, Chen C, Zhang H, Yu F, Li C, Wei H, Sui Y, Wu C, Diao X, Wu Y, Xie Q. Natural variation in Glume Coverage 1 causes naked grains in sorghum. Nat Commun 2022; 13:1068. [PMID: 35217660 PMCID: PMC8881591 DOI: 10.1038/s41467-022-28680-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/07/2022] [Indexed: 12/30/2022] Open
Abstract
One of the most critical steps in cereal threshing is the ease with which seeds are detached from sticky glumes. Naked grains with low glume coverage have dramatically increased threshing efficiency and seed quality. Here, we demonstrate that GC1 (Glume Coverage 1), encoding an atypical G protein γ subunit, negatively regulates sorghum glume coverage. Naturally truncated variations of GC1 C-terminus accumulate at higher protein levels and affect the stability of a patatin-related phospholipase SbpPLAII-1. A strong positive selection signature around the GC1 genic region is found in the naked sorghum cultivars. Our findings reveal a crucial event during sorghum domestication through a subtle regulation of glume development by GC1 C-terminus variation, and establish a strategy for future breeding of naked grains. Low glume coverage is the preferred for easy threshing in grain production, but the genetic basis remains unclear. Here, the authors report the gene GC1, which encodes an atypical G protein γ subunit, negatively regulates sorghum glume coverage and the naturally truncated alleles can be useful in the naked grain breeding.
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Affiliation(s)
- Peng Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China. .,University of Chinese Academy of Sciences, 100049, Beijing, P. R. China.
| | - Sanyuan Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Chengxuan Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China.,University of Chinese Academy of Sciences, 100049, Beijing, P. R. China
| | - Huili Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Feifei Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Chao Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Huimin Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China.,University of Chinese Academy of Sciences, 100049, Beijing, P. R. China
| | - Yi Sui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, P. R. China
| | - Chuanyin Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, P. R. China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, P. R. China
| | - Yaorong Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China.
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China. .,University of Chinese Academy of Sciences, 100049, Beijing, P. R. China.
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8
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Improvement and Re-Evolution of Tetraploid Wheat for Global Environmental Challenge and Diversity Consumption Demand. Int J Mol Sci 2022; 23:ijms23042206. [PMID: 35216323 PMCID: PMC8878472 DOI: 10.3390/ijms23042206] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 02/01/2023] Open
Abstract
Allotetraploid durum wheat is the second most widely cultivated wheat, following hexaploid bread wheat, and is one of the major protein and calorie sources of the human diet. However, durum wheat is encountered with a severe grain yield bottleneck due to the erosion of genetic diversity stemming from long-term domestication and especially modern breeding programs. The improvement of yield and grain quality of durum wheat is crucial when confronted with the increasing global population, changing climate environments, and the non-ignorable increasing incidence of wheat-related disorders. This review summarized the domestication and evolution process and discussed the durum wheat re-evolution attempts performed by global researchers using diploid einkorn, tetraploid emmer wheat, hexaploid wheat (particularly the D-subgenome), etc. In addition, the re-evolution of durum wheat would be promoted by the genetic enrichment process, which could diversify allelic combinations through enhancing chromosome recombination (pentaploid hybridization or pairing of homologous chromosomes gene Ph mutant line induced homoeologous recombination) and environmental adaptability via alien introgressive genes (wide cross or distant hybridization followed by embryo rescue), and modifying target genes or traits by molecular approaches, such as CRISPR/Cas9 or RNA interference (RNAi). A brief discussion of the future perspectives for exploring germplasm for the modern improvement and re-evolution of durum wheat is included.
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9
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He G, Zhang Y, Liu P, Jing Y, Zhang L, Zhu Y, Kong X, Zhao H, Zhou Y, Sun J. The transcription factor TaLAX1 interacts with Q to antagonistically regulate grain threshability and spike morphogenesis in bread wheat. THE NEW PHYTOLOGIST 2021; 230:988-1002. [PMID: 33521967 DOI: 10.1111/nph.17235] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
The domestication gene Q is largely responsible for the widespread cultivation of wheat because it confers multiple domestication traits. However, the underlying molecular mechanisms of how Q regulates these domestication traits remain unclear. In this study, we identify a Q-interacting protein TaLAX1, a basic helix-loop-helix transcription factor, through yeast two-hybrid assays. Using biochemical and genetic approaches, we explore the roles of TaLAX1 in regulating wheat domestication traits. Overexpression of TaLAX1 produces phenotypes, reminiscent of the q allele; loss-of-function Talax1 mutations confer compact spikes, largely similar to the Q-overexpression wheat lines. The two transcription factors TaLAX1 and Q disturb each other's activity to antagonistically regulate the expression of the lignin biosynthesis-related gene TaKNAT7-4D. More interestingly, a natural variation (InDel, +/- TATA), which occurs in the promoter of TaLAX1, is associated with the promoter activity difference between the D subgenome of bread wheat and its ancestor Aegilops tauschii accession T093. This study reveals that the transcription factor TaLAX1 physically interacts with Q to antagonistically regulate wheat domestication traits and a natural variation (InDel, +/- TATA) is associated with the diversification of TaLAX1 promoter activity.
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Affiliation(s)
- Guanhua He
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yunwei Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pan Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yexing Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lichao Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Xiuying Kong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huixian Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yun Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Jiaqiang Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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10
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Okada T, Jayasinghe JEARM, Eckermann P, Watson-Haigh NS, Warner P, Williams ME, Albertsen MC, Baumann U, Whitford R. Genetic factors associated with favourable pollinator traits in the wheat cultivar Piko. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:434-447. [PMID: 33332999 DOI: 10.1071/fp20181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Hybrid breeding in wheat has the potential to boost yields. An efficient hybrid seed production system requires elite pollinators; however, such germplasm is limited among modern cultivars. Piko, a winter wheat (Triticum aestivum L.) cultivar, has been identified as a superior pollinator and has been used in Europe. Piko has favourable pollinator traits for anther extrusion, anther length, pollen mass and hybrid seed set. However, the genetic factors responsible for Piko's favourable traits are largely unknown. Here, we report on the genetic analysis of a Piko-derived F2 mapping population. We confirmed that Piko's Rht-D1a allele for tall stature is associated with large anthers and high anther extrusion. However, Rht-D1 was not found to be associated with anther filament length, confirmed by near isogenic lines. Piko's photoperiod sensitive Ppd-B1b allele shows an association with increased spike length, more spikelets and spike architecture traits, while the insensitive Ppd-B1a allele is linked with high anther extrusion and larger anthers. We identified an anther extrusion quantitative trait locus (QTL) on chromosome 6A that showed significantly biased transmission of the favourable Piko allele amongst F2 progenies. The Piko allele is completely absent in the distal 6AS region and the central 6A region revealed a significantly lower ratio (<8%) of F2 with homozygous Piko alleles. Our study provided further evidence for the effects of Rht-D1 and Ppd-B1 loci on multiple pollinator traits and a novel anther extrusion QTL that exhibits segregation distortion.
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Affiliation(s)
- Takashi Okada
- School of Agriculture, Food and Wine, University of Adelaide, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia; and Present address: The Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide Health and Medical Science Building, North Terrace, Adelaide, SA 5000, Australia; and Corresponding author.
| | - J E A Ridma M Jayasinghe
- School of Agriculture, Food and Wine, University of Adelaide, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Paul Eckermann
- School of Agriculture, Food and Wine, University of Adelaide, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Nathan S Watson-Haigh
- School of Agriculture, Food and Wine, University of Adelaide, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Patricia Warner
- School of Agriculture, Food and Wine, University of Adelaide, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Mark E Williams
- Corteva Agriscience, 7250 NW 62nd Avenue, Johnston, IA 50131-1004, USA
| | - Marc C Albertsen
- Corteva Agriscience, 7250 NW 62nd Avenue, Johnston, IA 50131-1004, USA
| | - Ute Baumann
- School of Agriculture, Food and Wine, University of Adelaide, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Ryan Whitford
- School of Agriculture, Food and Wine, University of Adelaide, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia
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11
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Song L, Zhao H, Zhang Z, Zhang S, Liu J, Zhang W, Zhang N, Ji J, Li L, Li J. Molecular Cytogenetic Identification of Wheat- Aegilops Biuncialis 5M b Disomic Addition Line with Tenacious and Black Glumes. Int J Mol Sci 2020; 21:E4053. [PMID: 32517065 PMCID: PMC7312955 DOI: 10.3390/ijms21114053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 05/23/2020] [Accepted: 06/03/2020] [Indexed: 12/02/2022] Open
Abstract
Production of wheat-alien disomic addition lines is of great value to the exploitation and utilization of elite genes originated from related species to wheat. In this study, a novel wheat-Aegilops biuncialis 5Mb disomic addition line WA317 was characterized by in situ hybridization (ISH) and specific-locus amplified fragment sequencing (SLAF-seq) markers. Compared to its parent Chinese Spring (CS), the glumes of WA317 had black color and were difficult to remove after harvesting, suggesting chromosome 5Mb carried gene(s) related to glume development and Triticeae domestication process. A total of 242 Ae. biuncialis SLAF-based markers (298 amplified patterns) were developed and further divided into four categories by Ae. biuncialis Y17, Ae. umbellulata Y139 and Ae. comosa Y258, including 172 markers amplifying the same bands of U and M genome, six and 102 markers amplifying U-specific and M-specific bands, respectively and eighteen markers amplifying specific bands in Y17. Among them, 45 markers had the specific amplifications in WA317 and were 5Mb specific markers. Taken together, line WA317 with tenacious and black glumes should serve as the foundation for understanding of the Triticeae domestication process and further exploitation of primitive alleles for wheat improvement. Ae. biuncialis SLAF-based markers can be used for studying syntenic relationships between U and M genomes as well as rapid tracking of U and M chromosomal segments in wheat background.
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Affiliation(s)
- Liqiang Song
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang 050022, China; (L.S.); (S.Z.); (J.L.); (W.Z.); (N.Z.); (J.J.)
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing 100101, China
| | - Hui Zhao
- College of Bioscience and Bioengineering, Hebei University of Science and Technology, Shijiazhuang 050018, China;
| | - Zhi Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.Z.); (L.L.)
| | - Shuai Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang 050022, China; (L.S.); (S.Z.); (J.L.); (W.Z.); (N.Z.); (J.J.)
| | - Jiajia Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang 050022, China; (L.S.); (S.Z.); (J.L.); (W.Z.); (N.Z.); (J.J.)
| | - Wei Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang 050022, China; (L.S.); (S.Z.); (J.L.); (W.Z.); (N.Z.); (J.J.)
| | - Na Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang 050022, China; (L.S.); (S.Z.); (J.L.); (W.Z.); (N.Z.); (J.J.)
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Ji
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang 050022, China; (L.S.); (S.Z.); (J.L.); (W.Z.); (N.Z.); (J.J.)
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing 100101, China
| | - Lihui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.Z.); (L.L.)
| | - Junming Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang 050022, China; (L.S.); (S.Z.); (J.L.); (W.Z.); (N.Z.); (J.J.)
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing 100101, China
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12
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Durum wheat genome highlights past domestication signatures and future improvement targets. Nat Genet 2019; 51:885-895. [PMID: 30962619 DOI: 10.1038/s41588-019-0381-3] [Citation(s) in RCA: 369] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/22/2019] [Indexed: 12/13/2022]
Abstract
The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. The assembly enabled genome-wide genetic diversity analyses revealing the changes imposed by thousands of years of empirical selection and breeding. Regions exhibiting strong signatures of genetic divergence associated with domestication and breeding were widespread in the genome with several major diversity losses in the pericentromeric regions. A locus on chromosome 5B carries a gene encoding a metal transporter (TdHMA3-B1) with a non-functional variant causing high accumulation of cadmium in grain. The high-cadmium allele, widespread among durum cultivars but undetected in wild emmer accessions, increased in frequency from domesticated emmer to modern durum wheat. The rapid cloning of TdHMA3-B1 rescues a wild beneficial allele and demonstrates the practical use of the Svevo genome for wheat improvement.
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13
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Sharma JS, Running KLD, Xu SS, Zhang Q, Peters Haugrud AR, Sharma S, McClean PE, Faris JD. Genetic analysis of threshability and other spike traits in the evolution of cultivated emmer to fully domesticated durum wheat. Mol Genet Genomics 2019; 294:757-771. [PMID: 30887143 DOI: 10.1007/s00438-019-01544-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 02/27/2019] [Indexed: 12/11/2022]
Abstract
Genetic mutations in genes governing wheat threshability were critical for domestication. Knowing when these genes mutated during wheat evolution will provide more insight into the domestication process and lead to further exploitation of primitive alleles for wheat improvement. We evaluated a population of recombinant inbred lines derived from a cross between the durum variety Rusty and the cultivated emmer accession PI 193883 for threshability, rachis fragility, and other spike-related traits. Quantitative trait loci (QTL) associated with spike length, spikelets per spike, and spike compactness were primarily associated with known genes such as the pleiotropic domestication gene Q. Interestingly, rachis fragility was not associated with the Q locus, suggesting that this trait, usually a pleiotropic effect of the q allele, can be influenced by the genetic background. Threshability QTL were identified on chromosome arms 2AS, 2BS, and 5AL corresponding to the tenacious glume genes Tg2A and Tg2B as well as the Q gene, respectively, further demonstrating that cultivated emmer harbors the primitive non-free-threshing alleles at all three loci. Genetic analysis indicated that the effects of the three genes are mostly additive, with Q having the most profound effects on threshability, and that free-threshing alleles are necessary at all three loci to attain a completely free-threshing phenotype. These findings provide further insight into the timeline and possible pathways of wheat domestication and evolution that led to the formation of modern day domesticated wheats.
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Affiliation(s)
- Jyoti S Sharma
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB, R6M 1Y5, Canada
| | | | - Steven S Xu
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Northern Crop Science Laboratory, 1605 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA
| | - Qijun Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | | | - Sapna Sharma
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Phillip E McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Justin D Faris
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Northern Crop Science Laboratory, 1605 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA.
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14
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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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15
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Niu Z, Chao S, Cai X, Whetten RB, Breiland M, Cowger C, Chen X, Friebe B, Gill BS, Rasmussen JB, Klindworth DL, Xu SS. Molecular and Cytogenetic Characterization of Six Wheat- Aegilops markgrafii Disomic Addition Lines and Their Resistance to Rusts and Powdery Mildew. FRONTIERS IN PLANT SCIENCE 2018; 9:1616. [PMID: 30467511 PMCID: PMC6236143 DOI: 10.3389/fpls.2018.01616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/18/2018] [Indexed: 05/07/2023]
Abstract
Aegilops markgrafii (Greuter) Hammer is an important source of genes for resistance to abiotic stresses and diseases in wheat (Triticum aestivum L.). A series of six wheat 'Alcedo'-Ae. markgrafii chromosome disomic addition lines, designated as AI(B), AII(C), AIII(D), AV(E), AIV(F), and AVIII(G) carrying the Ae. markgrafii chromosomes B, C, D, E, F, and G, respectively, were tested with SSR markers to establish homoeologous relationships to wheat and identify markers useful in chromosome engineering. The addition lines were evaluated for resistance to rust and powdery mildew diseases. The parents Alcedo and Ae. markgrafii accession 'S740-69' were tested with 1500 SSR primer pairs and 935 polymorphic markers were identified. After selecting for robust markers and confirming the polymorphisms on the addition lines, 132 markers were considered useful for engineering and establishing homoeologous relationships. Based on the marker analysis, we concluded that the chromosomes B, C, D, E, F, and G belong to wheat homoeologous groups 2, 5, 6, 7, 3, and 4, respectively. Also, we observed chromosomal rearrangements in several addition lines. When tested with 20 isolates of powdery mildew pathogen (Blumeria graminis f. sp. tritici) from five geographic regions of the United States, four addition lines [AIII(D), AV(E), AIV(F), and AVIII(G)] showed resistance to some isolates, with addition line AV(E) being resistant to 19 of 20 isolates. The addition lines were tested with two races (TDBJ and TNBJ) of the leaf rust pathogen (Puccinia triticina), and only addition line AI(B) exhibited resistance at a level comparable to the Ae. markgrafii parent. Addition lines AII(C) and AIII(D) had been previously identified as resistant to the Ug99 race group of the stem rust pathogen (Puccinia graminis f. sp. tritici). The addition lines were also tested for resistance to six United States races (PSTv-4, PSTv-14, PSTv-37, PSTv-40, PSTv-51, and PSTv-198) of the stripe rust pathogen (Puccinia striiformis f. sp. tritici); we found no resistance either in Alcedo or any of the addition lines. The homoeologous relationships of the chromosomes in the addition lines, molecular markers located on each chromosome, and disease resistance associated with each chromosome will allow for chromosome engineering of the resistance genes.
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Affiliation(s)
- Zhixia Niu
- Cereal Crops Research Unit, Red River Valley Agricultural Research Center, United States Department of Agriculture–Agricultural Research Service, Fargo, ND, United States
| | - Shiaoman Chao
- Cereal Crops Research Unit, Red River Valley Agricultural Research Center, United States Department of Agriculture–Agricultural Research Service, Fargo, ND, United States
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Rebecca B. Whetten
- Plant Science Research Unit, United States Department of Agriculture–Agricultural Research Service, Raleigh, NC, United States
| | - Matthew Breiland
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Christina Cowger
- Plant Science Research Unit, United States Department of Agriculture–Agricultural Research Service, Raleigh, NC, United States
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, United States Department of Agriculture–Agricultural Research Service, Pullman, WA, United States
| | - Bernd Friebe
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Bikram S. Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Jack B. Rasmussen
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Daryl L. Klindworth
- Cereal Crops Research Unit, Red River Valley Agricultural Research Center, United States Department of Agriculture–Agricultural Research Service, Fargo, ND, United States
| | - Steven S. Xu
- Cereal Crops Research Unit, Red River Valley Agricultural Research Center, United States Department of Agriculture–Agricultural Research Service, Fargo, ND, United States
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16
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Cao D, Chen W, Wang H, Liu D, Zhang B, Liu B, Zhang H. The transfer to and functional annotation of alien alleles in advanced wheat lines derived from synthetic hexaploid wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 130:89-93. [PMID: 29980097 DOI: 10.1016/j.plaphy.2018.06.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/26/2018] [Accepted: 06/26/2018] [Indexed: 06/08/2023]
Abstract
The abundant genetic diversity in synthetic hexaploid wheat (SHW) can achieve breakthroughs in wheat genetic improvement, but little is known of the genetic mechanisms involved. In this study, three populations of advanced lines (totaling 284 individuals), derived from three top-crosses of SHW-L1 with different common wheat cultivars, followed by ten generations of artificial selection, were used to evaluate the transfer of alien alleles with 24872 Diversity Arrays Technology (DArT) markers. Only 1824, 1786 and 1514 DArT markers were needed to distinguish the alleles from SHW-L1 and the other common wheat parent in the populations SCPD, SS7M and SSYZ, respectively. The data clearly showed that all the advanced lines contained alien alleles from SHW-L1. The lowest percentage of alien alleles was 6.97% in an advanced line in population SSYZ, while the biggest was 30.41% in a SCPD advanced lines. The percentages of alien alleles at each locus ranged from 0% to 100% in all three populations. Forty-four alien alleles did not exist in all advanced lines, while two alien alleles were present in all advanced lines. Two of the 100% alien alleles were associated with thousand-grain weight and leaf rust resistance. Thirteen alien alleles were associated with grain yield, grain thickness and width, thousand-grain weight, grain weight/ear, plant height, grain weight, grain number, powdery mildew resistance, spikelet number per spike or yellow rust resistance. The research provided direct evidence of the existence of alien alleles in advanced lines and detected a number of valuable alleles related to wheat yield or disease resistance. More research is needed to analyze the functional mechanisms of these alleles, and to use these materials and alleles in wheat improvement.
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Affiliation(s)
- Dong Cao
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, 810008, China; Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjie Chen
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, 810008, China; Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, China
| | - Hongxia Wang
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, 810008, China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Bo Zhang
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, 810008, China; Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, China
| | - Baolong Liu
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, 810008, China; Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Huaigang Zhang
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, 810008, China; Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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17
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Lundström M, Leino MW, Hagenblad J. Evolutionary history of the NAM-B1 gene in wild and domesticated tetraploid wheat. BMC Genet 2017; 18:118. [PMID: 29262777 PMCID: PMC5738170 DOI: 10.1186/s12863-017-0566-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/09/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The NAM-B1 gene in wheat has for almost three decades been extensively studied and utilized in breeding programs because of its significant impact on grain protein and mineral content and pleiotropic effects on senescence rate and grain size. First detected in wild emmer wheat, the wild-type allele of the gene has been introgressed into durum and bread wheat. Later studies have, however, also found the presence of the wild-type allele in some domesticated subspecies. In this study we trace the evolutionary history of the NAM-B1 in tetraploid wheat species and evaluate it as a putative domestication gene. RESULTS Genotyping of wild and landrace tetraploid accessions showed presence of only null alleles in durum. Domesticated emmer wheats contained both null alleles and the wild-type allele while wild emmers, with one exception, only carried the wild-type allele. One of the null alleles consists of a deletion that covers several 100 kb. The other null-allele, a one-basepair frame-shift insertion, likely arose among wild emmer. This allele was the target of a selective sweep, extending over several 100 kb. CONCLUSIONS The NAM-B1 gene fulfils some criteria for being a domestication gene by encoding a trait of domestication relevance (seed size) and is here shown to have been under positive selection. The presence of both wild-type and null alleles in domesticated emmer does, however, suggest the gene to be a diversification gene in this species. Further studies of genotype-environment interactions are needed to find out under what conditions selection on different NAM-B1 alleles have been beneficial.
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Affiliation(s)
- Maria Lundström
- Linköping University, IFM Biology, SE-581 83, Linköping, Sweden
| | - Matti W Leino
- Linköping University, IFM Biology, SE-581 83, Linköping, Sweden.,Nordiska museet, Swedish Museum of Cultural History, Box 27820, SE-115 93, Stockholm, Sweden.,The Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Jenny Hagenblad
- Linköping University, IFM Biology, SE-581 83, Linköping, Sweden.
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18
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Boukid F, Folloni S, Sforza S, Vittadini E, Prandi B. Current Trends in Ancient Grains-Based Foodstuffs: Insights into Nutritional Aspects and Technological Applications. Compr Rev Food Sci Food Saf 2017; 17:123-136. [PMID: 33350067 DOI: 10.1111/1541-4337.12315] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/15/2017] [Accepted: 09/22/2017] [Indexed: 12/18/2022]
Abstract
For centuries, ancient grains fed populations, but due to their low yield, they were abandoned and replaced by high-yielding species. However, currently, there is a renewed interest in ancient wheat and pseudocereal grains from consumers, farmers, and manufacturers. Ancient wheat such as einkorn, emmer, spelt, and Kamut®, are being reintegrated because of their low fertilizer input, high adaptability and important genetic diversity. New trends in pseudocereal products are also emerging, and they are mostly appreciated for their nutritional outcomes, particularly by the gluten-free market. Toward healthier lifestyle, ancient grains-based foodstuffs are a growing business and their industrialization is taking 2 pathways, either as a raw ingredient or a functional ingredient. This paper deals with these grain characteristics by focusing on the compositional profile and the technological potential.
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Affiliation(s)
- Fatma Boukid
- Food and Drug Dept., Univ. of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | | | - Stefano Sforza
- Food and Drug Dept., Univ. of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Elena Vittadini
- Food and Drug Dept., Univ. of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Barbara Prandi
- Food and Drug Dept., Univ. of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
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19
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Jorgensen C, Luo MC, Ramasamy R, Dawson M, Gill BS, Korol AB, Distelfeld A, Dvorak J. A High-Density Genetic Map of Wild Emmer Wheat from the Karaca Dağ Region Provides New Evidence on the Structure and Evolution of Wheat Chromosomes. FRONTIERS IN PLANT SCIENCE 2017; 8:1798. [PMID: 29104581 PMCID: PMC5655018 DOI: 10.3389/fpls.2017.01798] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 10/03/2017] [Indexed: 05/05/2023]
Abstract
Wild emmer (Triticum turgidum ssp. dicoccoides) is a progenitor of all cultivated wheat grown today. It has been hypothesized that emmer was domesticated in the Karaca Dağ region in southeastern Turkey. A total of 445 recombinant inbred lines of T. turgidum ssp. durum cv. 'Langdon' x wild emmer accession PI 428082 from this region was developed and genotyped with the Illumina 90K single nucleotide polymorphism Infinium assay. A genetic map comprising 2,650 segregating markers was constructed. The order of the segregating markers and an additional 8,264 co-segregating markers in the Aegilops tauschii reference genome sequence was used to compare synteny of the tetraploid wheat with the Brachypodium distachyon, rice, and sorghum. These comparisons revealed the presence of 15 structural chromosome rearrangements, in addition to the already known 4A-5A-7B rearrangements. The most common type was an intra-chromosomal translocation in which the translocated segment was short and was translocated only a short distance along the chromosome. A large reciprocal translocation, one small non-reciprocal translocation, and three large and one small paracentric inversions were also discovered. The use of inversions for a phylogeny reconstruction in the Triticum-Aegilops alliance was illustrated. The genetic map was inconsistent with the current model of evolution of the rearranged chromosomes 4A-5A-7B. Genetic diversity in the rearranged chromosome 4A showed that the rearrangements might have been contemporary with wild emmer speciation. A selective sweep was found in the centromeric region of chromosome 4A in Karaca Dağ wild emmer but not in 4A of T. aestivum. The absence of diversity from a large portion of chromosome 4A of wild emmer, believed to be ancestral to all domesticated wheat, is puzzling.
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Affiliation(s)
- Chad Jorgensen
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Ramesh Ramasamy
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Mathew Dawson
- Department of Statistics, University of California, Davis, Davis, CA, United States
| | - Bikram S. Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | | | - Assaf Distelfeld
- Institute for Cereal Crops Improvement, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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Virdi SK, Liu Z, Overlander ME, Zhang Z, Xu SS, Friesen TL, Faris JD. New Insights into the Roles of Host Gene-Necrotrophic Effector Interactions in Governing Susceptibility of Durum Wheat to Tan Spot and Septoria nodorum Blotch. G3 (BETHESDA, MD.) 2016; 6:4139-4150. [PMID: 27777262 PMCID: PMC5144982 DOI: 10.1534/g3.116.036525] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/14/2016] [Indexed: 01/09/2023]
Abstract
Tan spot and Septoria nodorum blotch (SNB) are important diseases of wheat caused by the necrotrophic fungi Pyrenophora tritici-repentis and Parastagonospora nodorum, respectively. The P. tritici-repentis necrotrophic effector (NE) Ptr ToxB causes tan spot when recognized by the Tsc2 gene. The NE ToxA is produced by both pathogens and has been associated with the development of both tan spot and SNB when recognized by the wheat Tsn1 gene. Most work to study these interactions has been conducted in common wheat, but little has been done in durum wheat. Here, quantitative trait loci (QTL) analysis of a segregating biparental population indicated that the Tsc2-Ptr ToxB interaction plays a prominent role in the development of tan spot in durum. However, analysis of two biparental populations indicated that the Tsn1-ToxA interaction was not associated with the development of tan spot, but was strongly associated with the development of SNB. Pa. nodorum expressed ToxA at high levels in infected Tsn1 plants, whereas ToxA expression in P. tritici-repentis was barely detectable, suggesting that the differences in disease levels associated with the Tsn1-ToxA interaction were due to differences in pathogen expression of ToxA These and previous results together indicate that: (1) the effects of Tsn1-ToxA on tan spot in common wheat can range from nonsignificant to highly significant depending on the host genetic background; (2) Tsn1-ToxA is not a significant factor for tan spot development in durum wheat; and (3) Tsn1-ToxA plays a major role in SNB development in both common and durum wheat. Durum and common wheat breeders alike should strive to remove both Tsc2 and Tsn1 from their materials to achieve disease resistance.
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Affiliation(s)
- Simerjot K Virdi
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58108
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota 58108
| | - Megan E Overlander
- United States Department of Agriculture-Agricultural Research Service, Cereal Cops Research Unit, Northern Crop Science Laboratory, Fargo, North Dakota 58102
| | - Zengcui Zhang
- United States Department of Agriculture-Agricultural Research Service, Cereal Cops Research Unit, Northern Crop Science Laboratory, Fargo, North Dakota 58102
| | - Steven S Xu
- United States Department of Agriculture-Agricultural Research Service, Cereal Cops Research Unit, Northern Crop Science Laboratory, Fargo, North Dakota 58102
| | - Timothy L Friesen
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota 58108
- United States Department of Agriculture-Agricultural Research Service, Cereal Cops Research Unit, Northern Crop Science Laboratory, Fargo, North Dakota 58102
| | - Justin D Faris
- United States Department of Agriculture-Agricultural Research Service, Cereal Cops Research Unit, Northern Crop Science Laboratory, Fargo, North Dakota 58102
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Li LF, Olsen KM. To Have and to Hold: Selection for Seed and Fruit Retention During Crop Domestication. Curr Top Dev Biol 2016; 119:63-109. [PMID: 27282024 DOI: 10.1016/bs.ctdb.2016.02.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Crop domestication provides a useful model system to characterize the molecular and developmental bases of morphological variation in plants. Among the most universal changes resulting from selection during crop domestication is the loss of seed and fruit dispersal mechanisms, which greatly facilitates harvesting efficiency. In this review, we consider the molecular genetic and developmental bases of the loss of seed shattering and fruit dispersal in six major crop plant families, three of which are primarily associated with seed crops (Poaceae, Brassicaceae, Fabaceae) and three of which are associated with fleshy-fruited crops (Solanaceae, Rosaceae, Rutaceae). We find that the developmental basis of the loss of seed/fruit dispersal is conserved in a number of independently domesticated crops, indicating the widespread occurrence of developmentally convergent evolution in response to human selection. With regard to the molecular genetic approaches used to characterize the basis of this trait, traditional biparental quantitative trait loci mapping remains the most commonly used strategy; however, recent advances in next-generation sequencing technologies are now providing new avenues to map and characterize loss of shattering/dispersal alleles. We anticipate that continued application of these approaches, together with candidate gene analyses informed by known shattering candidate genes from other crops, will lead to a rapid expansion of our understanding of this critical domestication trait.
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Affiliation(s)
- L-F Li
- Washington University in St. Louis, St. Louis, MO, United States; Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, PR China.
| | - K M Olsen
- Washington University in St. Louis, St. Louis, MO, United States.
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22
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Zou H, Tzarfati R, Hübner S, Krugman T, Fahima T, Abbo S, Saranga Y, Korol AB. Transcriptome profiling of wheat glumes in wild emmer, hulled landraces and modern cultivars. BMC Genomics 2015; 16:777. [PMID: 26462652 PMCID: PMC4603339 DOI: 10.1186/s12864-015-1996-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/03/2015] [Indexed: 12/02/2022] Open
Abstract
Background Wheat domestication is considered as one of the most important events in the development of human civilization. Wheat spikelets have undergone significant changes during evolution under domestication, resulting in soft glumes and larger kernels that are released easily upon threshing. Our main goal was to explore changes in transcriptome expression in glumes that accompanied wheat evolution under domestication. Methods A total of six tetraploid wheat accessions were selected for transcriptome profiling based on their rachis brittleness and glumes toughness. RNA pools from glumes of the central spikelet at heading time were used to construct cDNA libraries for sequencing. The trimmed reads from each library were separately aligned to the reference sub-genomes A and B, which were extracted from wheat survey sequence. Differentially expression analysis and functional annotation were performed between wild and domesticated wheat, to identity candidate genes associated with evolution under domestication. Selected candidate genes were validated using real time PCR. Results Transcriptome profiles of wild emmer wheat, wheat landraces, and wheat cultivars were compared using next generation sequencing (RNA-seq). We have found a total of 194,893 transcripts, of which 73,150 were shared between wild, landraces, and cultivars. From 781 differentially expressed genes (DEGs), 336 were down-regulated and 445 were up-regulated in the domesticated compared to wild wheat genotypes. Gene Ontology (GO) annotation assigned 293 DEGs (37.5 %) to GO term groups, of which 134 (17.1 %) were down-regulated and 159 (20.4 %) up-regulated in the domesticated wheat. Some of the down-regulated DEGs in domesticated wheat are related to the biosynthetic pathways that eventually define the mechanical strength of the glumes, such as cell wall, lignin, pectin and wax biosynthesis. The reduction in gene expression of such genes, may explain the softness of the glumes in the domesticated forms. In addition, we have identified genes involved in nutrient remobilization that may affect grain size and other agronomic traits evolved under domestication. Conclusions The comparison of RNA-seq profiles between glumes of wheat groups differing in glumes toughness and rachis brittleness revealed a few DEGs that may be involved in glumes toughness and nutrient remobilization. These genes may be involved in processes of wheat improvement under domestication. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1996-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongda Zou
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Raanan Tzarfati
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Sariel Hübner
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Tamar Krugman
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Shahal Abbo
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| | - Yehoshua Saranga
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| | - Abraham B Korol
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, 31905, Israel.
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23
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Jordan KW, Wang S, Lun Y, Gardiner LJ, MacLachlan R, Hucl P, Wiebe K, Wong D, Forrest KL, Sharpe AG, Sidebottom CH, Hall N, Toomajian C, Close T, Dubcovsky J, Akhunova A, Talbert L, Bansal UK, Bariana HS, Hayden MJ, Pozniak C, Jeddeloh JA, Hall A, Akhunov E. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol 2015; 16:48. [PMID: 25886949 PMCID: PMC4389885 DOI: 10.1186/s13059-015-0606-4] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/04/2015] [Indexed: 12/21/2022] Open
Abstract
Background Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. Results A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies. Conclusions Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0606-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katherine W Jordan
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Shichen Wang
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Yanni Lun
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. .,Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA.
| | - Laura-Jayne Gardiner
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Ron MacLachlan
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Pierre Hucl
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Krysta Wiebe
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Debbie Wong
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | - Kerrie L Forrest
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | | | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0 W9, Canada.
| | | | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | | | - Timothy Close
- Department Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA.
| | - Jorge Dubcovsky
- Department Plant Sciences, University of California, Davis, CA, 95616, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| | - Alina Akhunova
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. .,Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA.
| | - Luther Talbert
- Department Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717, USA.
| | - Urmil K Bansal
- Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia.
| | - Harbans S Bariana
- Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia.
| | - Matthew J Hayden
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | - Curtis Pozniak
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | | | - Anthony Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Eduard Akhunov
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
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24
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Genome-wide quantitative trait locus mapping identifies multiple major loci for brittle rachis and threshability in Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum Shao). PLoS One 2014; 9:e114066. [PMID: 25474652 PMCID: PMC4256410 DOI: 10.1371/journal.pone.0114066] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/21/2014] [Indexed: 11/19/2022] Open
Abstract
Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum Shao) is a semi-wild hexaploid wheat resource that is only naturally distributed in the Qinghai-Tibet Plateau. Brittle rachis and hard threshing are two important characters of Tibetan semi-wild wheat. A whole-genome linkage map of T. aestivum ssp. tibetanum was constructed using a recombinant inbred line population (Q1028×ZM9023) with 186 lines, 564 diversity array technology markers, and 117 simple sequence repeat markers. Phenotypic data on brittle rachis and threshability, as two quantitative traits, were evaluated on the basis of the number of average spike rachis fragments per spike and percent threshability in 2012 and 2013, respectively. Quantitative trait locus (QTL) mapping performed using inclusive composite interval mapping analysis clearly identified four QTLs for brittle rachis and three QTLs for threshability. However, three loci on 2DS, 2DL, and 5AL showed pleiotropism for brittle rachis and threshability; they respectively explained 5.3%, 18.6%, and 18.6% of phenotypic variation for brittle rachis and 17.4%, 13.2%, and 35.2% of phenotypic variation for threshability. A locus on 3DS showed an independent effect on brittle rachis, which explained 38.7% of the phenotypic variation. The loci on 2DS and 3DS probably represented the effect of Tg and Br1, respectively. The locus on 5AL was in very close proximity to the Q gene, but was different from the predicted q in Tibetan semi-wild wheat. To our knowledge, the locus on 2DL has never been reported in common wheat but was prominent in T. aestivum ssp. tibetanum accession Q1028. It remarkably interacted with the locus on 5AL to affect brittle rachis. Several major loci for brittle rachis and threshability were identified in Tibetan semi-wild wheat, improving the understanding of these two characters and suggesting the occurrence of special evolution in Tibetan semi-wild wheat.
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25
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Faris JD, Zhang Q, Chao S, Zhang Z, Xu SS. Analysis of agronomic and domestication traits in a durum × cultivated emmer wheat population using a high-density single nucleotide polymorphism-based linkage map. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2333-48. [PMID: 25186168 DOI: 10.1007/s00122-014-2380-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 08/15/2014] [Indexed: 05/21/2023]
Abstract
Development of a high-density SNP map and evaluation of QTL shed light on domestication events in tetraploid wheat and the potential utility of cultivated emmer wheat for durum wheat improvement. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum) is tetraploid and considered as one of the eight founder crops that spawned the Agricultural Revolution about 10,000 years ago. Cultivated emmer has non-free-threshing seed and a somewhat fragile rachis, but mutations in genes governing these and other agronomic traits occurred that led to the formation of today's fully domesticated durum wheat (T. turgidum ssp. durum). Here, we evaluated a population of recombinant inbred lines (RILs) derived from a cross between a cultivated emmer accession and a durum wheat variety. A high-density single nucleotide polymorphism (SNP)-based genetic linkage map consisting of 2,593 markers was developed for the identification of quantitative trait loci. The major domestication gene Q had profound effects on spike length and compactness, rachis fragility, and threshability as expected. The cultivated emmer parent contributed increased spikelets per spike, and the durum parent contributed higher kernel weight, which led to the identification of some RILs that had significantly higher grain weight per spike than either parent. Threshability was governed not only by the Q locus, but other loci as well including Tg-B1 on chromosome 2B and a putative Tg-A1 locus on chromosome 2A indicating that mutations in the Tg loci occurred during the transition of cultivated emmer to the fully domesticated tetraploid. These results not only shed light on the events that shaped wheat domestication, but also demonstrate that cultivated emmer is a useful source of genetic variation for the enhancement of durum varieties.
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Affiliation(s)
- Justin D Faris
- USDA-Agricultural Research Service, Cereal Crops Research Unit, Red River Valley Agricultural Research Unit, Fargo, ND, 58102, USA,
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