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Wolde GM, Schnurbusch T. Inferring vascular architecture of the wheat spikelet based on resource allocation in the branched head t (bh t-A1) near isogenic lines. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:1023-1035. [PMID: 32172750 DOI: 10.1071/fp19041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 06/21/2019] [Indexed: 06/10/2023]
Abstract
Substantial genetic and physiological efforts were made to understand the causal factors of floral abortion and grain filling problem in wheat. However, the vascular architecture during wheat spikelet development is surprisingly under-researched. We used the branched headt near-isogenic lines, FL-bht-A1-NILs, to visualise the dynamics of spikelet fertility and dry matter accumulation in spikelets sharing the same rachis node (henceforth Primary Spikelet, PSt, and Secondary Spikelet, SSt). The experiment was conducted after grouping FL-bht-A1-NILs into two groups, where tillers were consistently removed from one group. Our results show differential spikelet fertility and dry matter accumulation between the PSt and SSt, but also showed a concomitant improvement after de-tillering. This suggests a tight regulation of assimilate supply and dry matter accumulation in wheat spikelets. Since PSt and SSt share the same rachis node, the main vascular bundle in the rachis/rachilla is expected to bifurcate to connect each spikelet/floret to the vascular system. We postulate that the vascular structure in the wheat spikelet might even follow Murray's law, where the wide conduits assigned at the base of the spikelet feed the narrower conduits of the distal florets. We discuss our results based on the two modalities of the vascular network systems in plants.
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Affiliation(s)
- Gizaw M Wolde
- Independent HEISENBERG-Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Seeland, Germany; and Present address: Department of Plant Sciences, University of California, Davis, CA 95616, USA; and Corresponding authors. Emails: ;
| | - Thorsten Schnurbusch
- Independent HEISENBERG-Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Seeland, Germany; and Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; and Corresponding authors. Emails: ;
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TaAPO-A1, an ortholog of rice ABERRANT PANICLE ORGANIZATION 1, is associated with total spikelet number per spike in elite European hexaploid winter wheat (Triticum aestivum L.) varieties. Sci Rep 2019; 9:13853. [PMID: 31554871 PMCID: PMC6761172 DOI: 10.1038/s41598-019-50331-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/11/2019] [Indexed: 12/16/2022] Open
Abstract
We dissected the genetic basis of total spikelet number (TSN) along with other traits, viz. spike length (SL) and flowering time (FT) in a panel of 518 elite European winter wheat varieties. Genome-wide association studies (GWAS) based on 39,908 SNP markers revealed highly significant quantitative trait loci (QTL) for TSN on chromosomes 2D, 7A, and 7B, for SL on 5A, and FT on 2D, with 2D-QTL being the functional marker for the gene Ppd-D1. The physical region of the 7A-QTL for TSN revealed the presence of a wheat ortholog (TaAPO-A1) to APO1–a rice gene that positively controls the spikelet number on the panicles. Interspecific analyses of the TaAPO-A1 orthologs showed that it is a highly conserved gene important for floral development and present in a wide range of terrestrial plants. Intraspecific studies of the TaAPO-A1 across wheat genotypes revealed a polymorphism in the conserved F-box domain, defining two haplotypes. A KASP marker developed on the polymorphic site showed a highly significant association of TaAPO-A1 with TSN, explaining 23.2% of the total genotypic variance. Also, the TaAPO-A1 alleles showed weak but significant differences for SL and grain yield. Our results demonstrate the importance of wheat sequence resources to identify candidate genes for important traits based on genetic analyses.
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Ye X, Li J, Cheng Y, Yao F, Long L, Wang Y, Wu Y, Li J, Wang J, Jiang Q, Kang H, Li W, Qi P, Lan X, Ma J, Liu Y, Jiang Y, Wei Y, Chen X, Liu C, Zheng Y, Chen G. Genome-wide association study reveals new loci for yield-related traits in Sichuan wheat germplasm under stripe rust stress. BMC Genomics 2019; 20:640. [PMID: 31395029 PMCID: PMC6688255 DOI: 10.1186/s12864-019-6005-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 07/29/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As one of the most important food crops in the world, increasing wheat (Triticum aestivum L.) yield is an urgent task for global food security under the continuous threat of stripe rust (caused by Puccinia striiformis f. sp. tritici) in many regions of the world. Molecular marker-assisted breeding is one of the most efficient ways to increase yield. Here, we identified loci associated to multi-environmental yield-related traits under stripe rust stress in 244 wheat accessions from Sichuan Province through genome-wide association study (GWAS) using 44,059 polymorphic markers from the 55 K single nucleotide polymorphism (SNP) chip. RESULTS A total of 13 stable quantitative trait loci (QTLs) were found to be highly associating to yield-related traits, including 6 for spike length (SL), 3 for thousand-kernel weight (TKW), 2 for kernel weight per spike (KWPS), and 2 for both TKW and KWPS, in at least two test environments under stripe rust stress conditions. Of them, ten QTLs were overlapped or very close to the reported QTLs, three QTLs, QSL.sicau-1AL, QTKW.sicau-4AL, and QKWPS.sicau-4AL.1, were potentially novel through the physical location comparison with previous QTLs. Further, 21 candidate genes within three potentially novel QTLs were identified, they were mainly involved in the regulation of phytohormone, cell division and proliferation, meristem development, plant or organ development, and carbohydrate transport. CONCLUSIONS QTLs and candidate genes detected in our study for yield-related traits under stripe rust stress will facilitate elucidating genetic basis of yield-related trait and could be used in marker-assisted selection in wheat yield breeding.
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Affiliation(s)
- Xueling Ye
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jian Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yukun Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Fangjie Yao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Li Long
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yuqi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yu Wu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jing Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Houyang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Pengfei Qi
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Xiujin Lan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yunfeng Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Xianming Chen
- US Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit; and Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Chunji Liu
- CSIRO Agriculture and Food, St Lucia, Queensland, 4067, Australia
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China.
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China.
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Golan G, Ayalon I, Perry A, Zimran G, Ade-Ajayi T, Mosquna A, Distelfeld A, Peleg Z. GNI-A1 mediates trade-off between grain number and grain weight in tetraploid wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2353-2365. [PMID: 31079164 DOI: 10.1007/s00122-019-03358-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/02/2019] [Indexed: 05/19/2023]
Abstract
Wild emmer allele of GNI-A1 ease competition among developing grains through the suppression of floret fertility and increase grain weight in tetraploid wheat. Grain yield is a highly polygenic trait determined by the number of grains per unit area, as well as by grain weight. In wheat, grain number and grain weight are usually negatively correlated. Yet, the genetic basis underlying trade-off between the two is mostly unknown. Here, we fine-mapped a grain weight QTL using wild emmer introgressions in a durum wheat background and showed that grain weight is associated with the GNI-A1 gene, a regulator of floret fertility. In-depth characterization of grain number and grain weight indicated that suppression of distal florets by the wild emmer GNI-A1 allele increases weight of proximal grains in basal and central spikelets due to alteration in assimilate distribution. Re-sequencing of GNI-A1 in tetraploid wheat demonstrated the rich allelic repertoire of the wild emmer gene pool, including a rare allele which was present in two gene copies and contained a nonsynonymous mutation in the C-terminus of the protein. Using an F2 population generated from a cross between wild emmer accessions Zavitan, which carries the rare allele, and TTD140, we demonstrated that this unique polymorphism is associated with grain weight, independent of grain number. Moreover, we showed, for the first time, that GNI-A1 proteins are transcriptional activators and that selection targeted compromised activity of the protein. Our findings expand the knowledge of the genetic basis underlying trade-off between key yield components and may contribute to breeding efforts for enhanced grain yield.
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Affiliation(s)
- Guy Golan
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, 7610001, Rehovot, Israel
| | - Idan Ayalon
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, 7610001, Rehovot, Israel
| | - Aviad Perry
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, 7610001, Rehovot, Israel
| | - Gil Zimran
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, 7610001, Rehovot, Israel
| | - Toluwanimi Ade-Ajayi
- School of Plant Sciences and Food Security, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Assaf Mosquna
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, 7610001, Rehovot, Israel
| | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, 7610001, Rehovot, Israel.
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Wolde GM, Trautewig C, Mascher M, Schnurbusch T. Genetic insights into morphometric inflorescence traits of wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1661-1676. [PMID: 30762083 PMCID: PMC6531419 DOI: 10.1007/s00122-019-03305-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 02/05/2019] [Indexed: 05/02/2023]
Abstract
KEY MESSAGE Modifying morphometric inflorescence traits is important for increasing grain yield in wheat. Mapping revealed nine QTL, including new QTL and a new allele for the q locus, controlling wheat spike morphometric traits. To identify loci controlling spike morphometric traits, namely spike length (SL), internode length (IL), node number per spike (NPS), and node density (ND), we studied 146 Recombinant Inbred Lines of tetraploid wheat (Triticum turgidum L.) derived from standard spike and spike-branching mutant parents. Phenotypic analyses of spike morphometric traits showed low genetic coefficients of variation, resulting in high heritabilities. The phenotypic correlation between NPS with growing degree days (GDD) suggested the importance of GDD in the determination of node number in wheat. The major effect QTL for GDD or heading date was mapped to chromosome 7BS carrying the flowering time gene, Vrn3-B1. Mapping also identified nine QTL controlling spike morphometric traits. Most of these loci controlled more than a single trait, suggesting a close genetic interrelationship among spike morphometric traits. For example, this study identified a new QTL, QND.ipk-4AL, controlling ND (up to 17.6% of the phenotypic variance), IL (up to 11% of the phenotypic variance), and SL (up to 20.8% of the phenotypic variance). Similarly, the major effect QTL for IL was mapped to the q locus. Sequencing of the Q/q gene further revealed a new q allele, qdel-5A, in spike-branching accessions possessing a six base pair deletion close to the miR172 target site. The identification of qdel-5A suggested that the spike-branching tetraploid wheats are double mutants for the spikelet meristem (SM) identity gene, i.e., branched headt (TtBHt), and the q gene, which is believed to be involved in the SM indeterminacy complex in wheat.
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Affiliation(s)
- Gizaw M Wolde
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3 OT Gatersleben, 06466, Seeland, Germany
- Department of Plant Sciences, University of California, Davis, USA
| | - Corinna Trautewig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3 OT Gatersleben, 06466, Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3 OT Gatersleben, 06466, Seeland, Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3 OT Gatersleben, 06466, Seeland, Germany.
- Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin-Luther-University, Halle-Wittenberg, 06120, Halle, Germany.
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Venske E, dos Santos RS, Busanello C, Gustafson P, Costa de Oliveira A. Bread wheat: a role model for plant domestication and breeding. Hereditas 2019; 156:16. [PMID: 31160891 PMCID: PMC6542105 DOI: 10.1186/s41065-019-0093-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/20/2019] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Bread wheat is one of the most important crops in the world. Its domestication coincides with the beginning of agriculture and since then, it has been constantly under selection by humans. Its breeding has followed millennia of cultivation, sometimes with unintended selection on adaptive traits, and later by applying intentional but empirical selective pressures. For more than one century, wheat breeding has been based on science, and has been constantly evolving due to on farm agronomy and breeding program improvements. The aim of this work is to briefly review wheat breeding, with emphasis on the current advances. DISCUSSION Improving yield potential, resistance/tolerance to biotic and abiotic stresses, and baking quality, have been priorities for breeding this cereal, however, new objectives are arising, such as biofortification enhancement. The narrow genetic diversity and complexity of its genome have hampered the breeding progress and the application of biotechnology. Old approaches, such as the introgression from relative species, mutagenesis, and hybrid breeding are strongly reappearing, motivated by an accumulation of knowledge and new technologies. A revolution has taken place regarding the use of molecular markers whereby thousands of plants can be routinely genotyped for thousands of loci. After 13 years, the wheat reference genome sequence and annotation has finally been completed, and is currently available to the scientific community. Transgenics, an unusual approach for wheat improvement, still represents a potential tool, however it is being replaced by gene editing, whose technology along with genomic selection, speed breeding, and high-throughput phenotyping make up the most recent frontiers for future wheat improvement. FINAL CONSIDERATION Agriculture and plant breeding are constantly evolving, wheat has played a major role in these processes and will continue through decades to come.
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Affiliation(s)
- Eduardo Venske
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Federal University of Pelotas, Capão do Leão Campus, Capão do Leão, Rio Grande do Sul 96010-610 Brazil
| | - Railson Schreinert dos Santos
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Federal University of Pelotas, Capão do Leão Campus, Capão do Leão, Rio Grande do Sul 96010-610 Brazil
| | - Carlos Busanello
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Federal University of Pelotas, Capão do Leão Campus, Capão do Leão, Rio Grande do Sul 96010-610 Brazil
| | - Perry Gustafson
- Plant Sciences Division, 1–32 Agriculture, University of Missouri, Columbia, MO 65211 USA
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Federal University of Pelotas, Capão do Leão Campus, Capão do Leão, Rio Grande do Sul 96010-610 Brazil
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Jamil M, Ali A, Gul A, Ghafoor A, Napar AA, Ibrahim AMH, Naveed NH, Yasin NA, Mujeeb-Kazi A. Genome-wide association studies of seven agronomic traits under two sowing conditions in bread wheat. BMC PLANT BIOLOGY 2019; 19:149. [PMID: 31003597 PMCID: PMC6475106 DOI: 10.1186/s12870-019-1754-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 04/02/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Wheat is a cool seasoned crop requiring low temperature during grain filling duration and therefore increased temperature causes significant yield reduction. A set of 125 spring wheat genotypes from International Maize and Wheat Improvement Centre (CIMMYT-Mexico) was evaluated for phenological and yield related traits at three locations in Pakistan under normal sowing time and late sowing time for expose to prolonged high temperature. With the help of genome-wide association study using genotyping-by-sequencing, marker trait associations (MTAs) were observed separately for the traits under normal and late sown conditions. RESULTS Significant reduction ranging from 9 to 74% was observed in all traits under high temperature. Especially 30, 25, 41 and 66% reduction was observed for days to heading (DH), plant height (PH), spikes per plant (SPP) and yield respectively. We identified 55,954 single nucleotide polymorphisms (SNPs) using genotyping by sequencing of these 125 hexaploid spring wheat genotypes and conducted genome-wide association studies (GWAS) for days to heading (DH), grain filled duration (GFD), plant height (PH), spikes per plant (SPP), grain number per spike (GNS), thousand kernel weight (TKW) and grain yield per plot (GY). Genomic regions identified through GWAS explained up to 13% of the phenotypic variance, on average. A total of 139 marker-trait associations (MTAs) across three wheat genomes (56 on genome A, 55 on B and 28 on D) were identified for all the seven traits studied. For days to heading, 20; grain filled duration, 21; plant height, 23; spikes per plant, 13; grain numbers per spike, 8; thousand kernel weight, 21 and for grain yield, 33 MTAs were detected under normal and late sown conditions. CONCLUSIONS This study identifies the essential resource of genetics research and underpins the chromosomal regions of seven agronomic traits under normal and high temperature. Significant relationship was observed between the number of favored alleles and trait observations. Fourteen protein coding genes with their respective annotations have been searched with the sequence of seven MTAs which were identified in this study. These findings will be helpful in the development of a breeder friendly platform for the selection of high yielding wheat lines at high temperature areas.
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Affiliation(s)
- Muhammad Jamil
- Department of Botany, University of Sargodha, Sargodha, Punjab Pakistan
| | - Aamir Ali
- Department of Botany, University of Sargodha, Sargodha, Punjab Pakistan
| | - Alvina Gul
- Atta-ur-Rehman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Abdul Ghafoor
- Plant Genetic Resources Institute (PGRI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Abdul Aziz Napar
- Institute of Plant Sciences, University of Sind Jamshoro, Sind, Pakistan
| | - Amir M. H. Ibrahim
- Soil and Crop Sciences Department, Texas A&M University, College Station, USA
| | - Naima Huma Naveed
- Department of Botany, University of Sargodha, Sargodha, Punjab Pakistan
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Brinton J, Uauy C. A reductionist approach to dissecting grain weight and yield in wheat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:337-358. [PMID: 30421518 PMCID: PMC6492019 DOI: 10.1111/jipb.12741] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/07/2018] [Indexed: 05/20/2023]
Abstract
Grain yield is a highly polygenic trait that is influenced by the environment and integrates events throughout the life cycle of a plant. In wheat, the major grain yield components often present compensatory effects among them, which alongside the polyploid nature of wheat, makes their genetic and physiological study challenging. We propose a reductionist and systematic approach as an initial step to understand the gene networks regulating each individual yield component. Here, we focus on grain weight and discuss the importance of examining individual sub-components, not only to help in their genetic dissection, but also to inform our mechanistic understanding of how they interrelate. This knowledge should allow the development of novel combinations, across homoeologs and between complementary modes of action, thereby advancing towards a more integrated strategy for yield improvement. We argue that this will break barriers in terms of phenotypic variation, enhance our understanding of the physiology of yield, and potentially deliver improved on-farm yield.
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Affiliation(s)
- Jemima Brinton
- John Innes CentreNorwich Research ParkNorwich NR4 7UHUnited Kingdom
| | - Cristobal Uauy
- John Innes CentreNorwich Research ParkNorwich NR4 7UHUnited Kingdom
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Koppolu R, Schnurbusch T. Developmental pathways for shaping spike inflorescence architecture in barley and wheat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:278-295. [PMID: 30609316 DOI: 10.1111/jipb.12771] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/18/2018] [Indexed: 05/19/2023]
Abstract
Grass species display a wide array of inflorescences ranging from highly branched compound/panicle inflorescences to unbranched spike inflorescences. The unbranched spike is a characteristic feature of the species of tribe Triticeae, including economically important crops, such as wheat and barley. In this review, we describe two important developmental genetic mechanisms regulating spike inflorescence architecture in barley and wheat. These include genetic regulation of (i) row-type pathway specific to Hordeum species and (ii) unbranched spike development in barley and wheat. For a comparative understanding, we describe the branched inflorescence phenotypes of rice and maize along with unbranched Triticeae inflorescences. In the end, we propose a simplified model describing a probable mechanism leading to unbranched spike formation in Triticeae species.
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Affiliation(s)
- Ravi Koppolu
- Independant HEISENBERG-Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - Thorsten Schnurbusch
- Independant HEISENBERG-Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
- Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin-Luther-University, Halle-Wittenberg, 06120 Halle, Germany
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60
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Gauley A, Boden SA. Genetic pathways controlling inflorescence architecture and development in wheat and barley. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:296-309. [PMID: 30325110 PMCID: PMC6900778 DOI: 10.1111/jipb.12732] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/15/2018] [Indexed: 05/18/2023]
Abstract
Modifications of inflorescence architecture have been crucial for the successful domestication of wheat and barley, which are central members of the Triticeae tribe that provide essential grains for the human diet. Investigation of the genes and alleles that underpin domestication-related traits has provided valuable insights into the molecular regulation of inflorescence development of the Triticeae, and further investigation of modified forms of architecture are proving to be equally fruitful. The identified genes are involved in diverse biological processes, including transcriptional regulation, hormone biosynthesis and metabolism, post-transcriptional and post-translational regulation, which alter inflorescence architecture by modifying the development and fertility of lateral organs, called spikelets and florets. Recent advances in sequencing capabilities and the generation of mutant populations are accelerating the identification of genes that influence inflorescence development, which is important given that genetic variation for this trait promises to be a valuable resource for optimizing grain production. This review assesses recent advances in our understanding of the genes controlling inflorescence development in wheat and barley, with the aim of highlighting the importance of improvements in developmental biology for optimizing the agronomic performance of staple crop plants.
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Affiliation(s)
- Adam Gauley
- Department of Crop GeneticsJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUnited Kingdom
| | - Scott A. Boden
- Department of Crop GeneticsJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUnited Kingdom
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61
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Yan X, Zhao L, Ren Y, Dong Z, Cui D, Chen F. Genome-wide association study revealed that the TaGW8 gene was associated with kernel size in Chinese bread wheat. Sci Rep 2019; 9:2702. [PMID: 30804359 PMCID: PMC6389898 DOI: 10.1038/s41598-019-38570-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/17/2018] [Indexed: 11/09/2022] Open
Abstract
Using Wheat 90 K SNP assay, kernel-related traits of Chinese bread wheat were used to perform association mapping in 14 environments by GWAS. Results indicated that 996 and 953 of 4417 and 3172 significant SNPs for kernel length and thousand-kernel weight were located on the chromosome 7B. Haplotype analysis of these SNPs on 7B generated the block containing the predicted TaGW8-B1 gene. TaGW8-B1 gene was further cloned by sequencing in bread wheat and a 276-bp InDel was found in the first intron. TaGW8-B1 without and with the 276-bp InDel were designated as TaGW8-B1a and TaGW8-B1b, respectively. Analysis of agronomic traits indicated that cultivars with TaGW8-B1a possessed significantly wider kernel width, significantly more kernel number per spike, longer kernel length, higher thousand-kernel weight and more spikelet number per spike than cultivars with TaGW8-B1b. Furthermore, cultivars with TaGW8-B1a possessed significantly higher yield than cultivars with TaGW8-B1b. Therefore, TaGW8-B1a was considered as a potentially superior allele. Meanwhile, TaGW8-B1a possessed a significantly higher expression level than TaGW8-B1b in mature seeds by qRT-PCR. It possibly suggested that the high expression of TaGW8-B1 was positively associated with kernel size in bread wheat. Distribution of TaGW8-B1 allele indicated that TaGW8-B1a has been positively selected in Chinese wheat.
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Affiliation(s)
- Xuefang Yan
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Lei Zhao
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yan Ren
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhongdong Dong
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Dangqun Cui
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Feng Chen
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China.
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Abstract
Floret fertility is a key determinant of the number of grains per inflorescence in cereals. During the evolution of wheat (Triticum sp.), floret fertility has increased, such that current bread wheat (Triticum aestivum) cultivars set three to five grains per spikelet. However, little is known regarding the genetic basis of floret fertility. The locus Grain Number Increase 1 (GNI1) is shown here to be an important contributor to floret fertility. GNI1 evolved in the Triticeae through gene duplication. The gene, which encodes a homeodomain leucine zipper class I (HD-Zip I) transcription factor, was expressed most abundantly in the most apical floret primordia and in parts of the rachilla, suggesting that it acts to inhibit rachilla growth and development. The level of GNI1 expression has decreased over the course of wheat evolution under domestication, leading to the production of spikes bearing more fertile florets and setting more grains per spikelet. Genetic analysis has revealed that the reduced-function allele GNI-A1 contributes to the increased number of fertile florets per spikelet. The RNAi-based knockdown of GNI1 led to an increase in the number of both fertile florets and grains in hexaploid wheat. Mutants carrying an impaired GNI-A1 allele out-yielded WT allele carriers under field conditions. The data show that gene duplication generated evolutionary novelty affecting floret fertility while mutations favoring increased grain production have been under selection during wheat evolution under domestication.
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Genetic modification of spikelet arrangement in wheat increases grain number without significantly affecting grain weight. Mol Genet Genomics 2018; 294:457-468. [PMID: 30591960 DOI: 10.1007/s00438-018-1523-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/17/2018] [Indexed: 10/27/2022]
Abstract
Crop yield is determined by the acquisition and allocation of photoassimilates in sink organs. Therefore, genetic modification of sink size is essential for understanding the complex signaling network regulating sink strength and source activities. Sink size in wheat depends on the number of spikelets per spike, floret/grain number per spikelet as well as the grain weight or dry matter accumulation. Hence, increasing spikelet number and improving sink size are targets for wheat breeding. The main objective of the present work was to genetically modify the wheat spike architecture, i.e., the sink size by introgressing the 'Miracle wheat' or the bht-A1 allele into an elite durum wheat cv. Floradur. After four generations of backcrossing to the recurrent parent, Floradur (FL), we have successfully developed Near Isogenic Lines (NILs) with a modified spikelet arrangement thereby increasing spikelet and grain number per spike. Genotyping of bht-A1 NILs using the Genotyping-By-Sequencing approach revealed that the size of the introgressed donor segments carrying bht-A1 ranged from 2.3 to 38 cM. The size of the shortest donor segment introgressed into bht-A1 NILs was estimated to be 9.8 mega base pairs (Mbp). Phenotypic analysis showed that FL-bht-A1-NILs (BC3F2 and BC3F3) carry up to seven additional spikelets per spike, leading to up to 29% increase in spike dry weight at harvest (SDWh). The increased SDWh was accompanied by up to 23% more grains per spike. More interestingly, thousand kernel weight (TKW) did not show significant differences between FL-bht-A1-NILs and Floradur, suggesting that besides increasing spikelet number, bht-A1 could also be targeted for increasing grain yield in wheat. Our study suggests that the genetic modification of spikelet number in wheat can be an entry point for improving grain yield, most interestingly and also unexpectedly without the trade-off effects on TKW. Hence, FL-bht-A1-NILs are not only essential for increasing grain number, but also for understanding the molecular and genetic mechanism of the source-sink interaction for a clearer picture of the complex signaling network regulating sink strength and source activities.
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Guo Z, Liu G, Röder MS, Reif JC, Ganal MW, Schnurbusch T. Genome-wide association analyses of plant growth traits during the stem elongation phase in wheat. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:2042-2052. [PMID: 29723916 PMCID: PMC6230955 DOI: 10.1111/pbi.12937] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 02/17/2018] [Accepted: 03/31/2018] [Indexed: 05/18/2023]
Abstract
One of the primary objectives of wheat breeding was to increase grain yield. Floral abortion during the stem elongation phase (SEP) leads to a loss of more than 50% of the grain number potential. In this study, we quantified 75 plant growth-associated traits at seven stages during the SEP and mapped 15 696 single nucleotide polymorphism (SNP) markers in 210 accessions of wheat (Triticum aestivum). Our genomewide association study identified trait-associated SNPs that are shared among various stages of the SEP, as well as SNPs that are shared between plant growth traits and grain yield in the field. The genomic selection analysis shows variation among the prediction abilities of various traits and stages. Furthermore, we found that the allelic variants of Ppd-D1 (chromosome 2D) and Rht-D1 (chromosome 4D) loci affect some plant growth traits (e.g. leaf area and spike length). These results have identified a narrow time window within the SEP in which plant growth traits can be manipulated to alter grain yield. This suggests that there may be multiple ways to regulate plant growth during the SEP, to ultimately influence grain number in wheat.
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Affiliation(s)
- Zifeng Guo
- Independent HEISENBERG Research Group Plant ArchitectureLeibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
| | - Guozheng Liu
- Research Group Quantitative GeneticsDepartment of Breeding ResearchLeibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
| | - Marion S. Röder
- Research Group Gene and Genome MappingDepartment of Breeding ResearchLeibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
| | - Jochen C. Reif
- Research Group Quantitative GeneticsDepartment of Breeding ResearchLeibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
| | | | - Thorsten Schnurbusch
- Independent HEISENBERG Research Group Plant ArchitectureLeibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
- Faculty of Natural Sciences IIIInstitute of Agricultural and Nutritional SciencesMartin Luther University Halle‐WittenbergHalleGermany
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Würschum T, Leiser WL, Langer SM, Tucker MR, Longin CFH. Phenotypic and genetic analysis of spike and kernel characteristics in wheat reveals long-term genetic trends of grain yield components. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2071-2084. [PMID: 29959471 DOI: 10.1007/s00122-018-3133-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/21/2018] [Indexed: 05/24/2023]
Abstract
Phenotypic and genetic analysis of six spike and kernel characteristics in wheat revealed geographic patterns as well as long-term trends arising from breeding progress, particularly in regard to spikelet fertility, i.e. the number of kernels per spikelet, a grain yield component that appears to underlie the increase in the number of kernels per spike. Wheat is a staple crop of global relevance that faces continuous demands for improved grain yield. In this study, we evaluated a panel of 407 winter wheat cultivars for six characteristics of spike and kernel development. All traits showed a large genotypic variation and had high heritabilities. We observed geographic patterns for some traits in addition to long-term trends showing a continuous increase in the number of kernels per spike. This breeding progress is likely due to the increase in spikelet fertility, i.e. the number of kernels per spikelet. While the number of kernels per spike and spikelet fertility were significantly positively correlated, both traits showed a significant negative correlation with thousand-kernel weight. Genome-wide association mapping identified only small- and moderate-effect QTL and an effect of the phenology loci Rht-D1 and Ppd-D1 on some of the traits. The allele frequencies of some QTL matched the observed geographic patterns. The quantitative inheritance of all traits with contributions of additional small-effect QTL was substantiated by genomic prediction. Taken together, our results suggest that some of the examined traits were already the basis of grain yield progress in wheat in the past decades. A more targeted exploitation of the available variation, potentially coupled with genomic approaches, may assist wheat breeding in continuing to increase yield levels globally.
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Affiliation(s)
- Tobias Würschum
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany.
| | - Willmar L Leiser
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany
| | - Simon M Langer
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany
- Bayer AG, European Wheat Breeding Center, Am Schwabeplan 8, 06466, Gatersleben, Germany
| | - Matthew R Tucker
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
| | - C Friedrich H Longin
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany
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66
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Guo Z, Zhao Y, Röder MS, Reif JC, Ganal MW, Chen D, Schnurbusch T. Manipulation and prediction of spike morphology traits for the improvement of grain yield in wheat. Sci Rep 2018; 8:14435. [PMID: 30258057 PMCID: PMC6158183 DOI: 10.1038/s41598-018-31977-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 08/22/2018] [Indexed: 12/11/2022] Open
Abstract
In wheat (Triticum spp.), modifying inflorescence (spike) morphology can increase grain number and size and thus improve yield. Here, we demonstrated the potential for manipulating and predicting spike morphology, based on 44 traits. In 12 wheat cultivars, we observed that detillering (removal of branches), which alters photosynthate distribution, changed spike morphology. Our genome-wide association study detected close associations between carbon partitioning (e.g. tiller number, main shoot dry weight) and spike morphology (e.g. spike length, spikelet density) traits in 210 cultivars. Most carbon-partitioning traits (e.g. tiller dry weight, harvest index) demonstrated high prediction abilities (>0.5). For spike morphology, some traits (e.g. total and fertile spikelet number, spike length) displayed high prediction abilities (0.3-0.5), but others (e.g. spikelet fertility, spikelet density) exhibited low prediction abilities (<0.2). Grain size traits were closely correlated in field and greenhouse experiments. Stepwise regression analysis suggests that significantly associated traits in the greenhouse explain 35.35% of the variation in grain yield and 67.63% of the variation in thousand-kernel weight in the field. Therefore, the traits identified in this study affect spike morphology; these traits can be used to predict and improve plant architecture and thus increase yield.
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Affiliation(s)
- Zifeng Guo
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Gatersleben, Germany
| | - Yusheng Zhao
- Research Group Quantitative Genetics, Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Gatersleben, Germany
| | - Marion S Röder
- Research Group Gene and Genome Mapping, Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Gatersleben, Germany
| | - Jochen C Reif
- Research Group Quantitative Genetics, Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Gatersleben, Germany
| | | | - Dijun Chen
- Research Group Image Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Gatersleben, Germany
| | - Thorsten Schnurbusch
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Gatersleben, Germany.
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67
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Peng Y, Liu H, Chen J, Shi T, Zhang C, Sun D, He Z, Hao Y, Chen W. Genome-Wide Association Studies of Free Amino Acid Levels by Six Multi-Locus Models in Bread Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1196. [PMID: 30154817 PMCID: PMC6103272 DOI: 10.3389/fpls.2018.01196] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 07/26/2018] [Indexed: 05/02/2023]
Abstract
Genome-wide association studies (GWAS) have been widely used to dissect the complex biosynthetic processes of plant metabolome. Most studies have used single-locus GWAS approaches, such as mixed linear model (MLM), and little is known about more efficient algorithms to implement multi-locus GWAS. Here, we report a comprehensive GWAS of 20 free amino acid (FAA) levels in kernels of bread wheat (Triticumaestivum L.) based on 14,646 SNPs by six multi-locus models (FASTmrEMMA, FASTmrMLM, ISISEM-BLASSO, mrMLM, pKWmEB, and pLARmEB). Our results showed that 328 significant quantitative trait nucleotides (QTNs) were identified in total (38, 8, 92, 45, 117, and 28, respectively, for the above six models). Among them, 66 were repeatedly detected by more than two models, and 155 QTNs appeared only in one model, indicating the reliability and complementarity of these models. We also found that the number of significant QTNs for different FAAs varied from 8 to 41, which revealed the complexity of the genetic regulation of metabolism, and further demonstrated the necessity of the multi-locus GWAS. Around these significant QTNs, 15 candidate genes were found to be involved in FAA biosynthesis, and one candidate gene (TraesCS1D01G052500, annotated as tryptophan decarboxylase) was functionally identified to influence the content of tryptamine in vitro. Our study demonstrated the power and efficiency of multi-locus GWAS models in crop metabolome research and provided new insights into understanding FAA biosynthesis in wheat.
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Affiliation(s)
- Yanchun Peng
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Jie Chen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Taotao Shi
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chi Zhang
- School of Chemical Science and Engineering, Royal Institute of Technology, Stockholm, Sweden
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanfeng Hao
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Chen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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Kadam NN, Struik PC, Rebolledo MC, Yin X, Jagadish SVK. Genome-wide association reveals novel genomic loci controlling rice grain yield and its component traits under water-deficit stress during the reproductive stage. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4017-4032. [PMID: 29767744 PMCID: PMC6054195 DOI: 10.1093/jxb/ery186] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/11/2018] [Indexed: 05/04/2023]
Abstract
A diversity panel comprising of 296 indica rice genotypes was phenotyped under non-stress and water-deficit stress conditions during the reproductive stage in the 2013 and 2014 dry seasons (DSs) at IRRI, Philippines. We investigated the genotypic variability for grain yield, yield components, and related traits, and conducted genome-wide association studies (GWAS) using high-density 45K single nucleotide polymorphisms. We detected 38 loci in 2013 and 64 loci in 2014 for non-stress conditions and 69 loci in 2013 and 55 loci in 2014 for water-deficit stress. Desynchronized flowering time confounded grain yield and its components under water-deficit stress in the 2013 experiment. Statistically corrected grain yield and yield component values using days to flowering helped to detect 31 additional genetic loci for grain yield, its components, and the harvest index in 2013. There were few overlaps in the detected loci between years and treatments, and when compared with previous studies using the same panel, indicating the complexity of yield formation under stress. Nevertheless, our analyses provided important insights into the potential links between grain yield with seed set and assimilate partitioning. Our findings demonstrate the complex genetic architecture of yield formation and we propose exploring the genetic basis of less complex component traits as an alternative route for further yield enhancement.
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Affiliation(s)
- Niteen N Kadam
- International Rice Research Institute, DAPO, Metro Manila, Philippines
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & Research, AK Wageningen, The Netherlands
| | - Paul C Struik
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & Research, AK Wageningen, The Netherlands
| | - Maria C Rebolledo
- CIRAD, UMR AGAP, Montpellier, France. AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIAT, Agrobiodiversity, AA, Cali, Colombia
| | - Xinyou Yin
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & Research, AK Wageningen, The Netherlands
| | - S V Krishna Jagadish
- International Rice Research Institute, DAPO, Metro Manila, Philippines
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
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69
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Guo Z, Chen D, Röder MS, Ganal MW, Schnurbusch T. Genetic dissection of pre-anthesis sub-phase durations during the reproductive spike development of wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:909-918. [PMID: 29906301 DOI: 10.1111/tpj.13998] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/09/2018] [Accepted: 04/17/2018] [Indexed: 05/18/2023]
Abstract
Flowering time is an important factor affecting grain yield in wheat. In this study, we divided reproductive spike development into eight sub-phases. These sub-phases have the potential to be delicately manipulated to increase grain yield. We measured 36 traits with regard to sub-phase durations, determined three grain yield-related traits in eight field environments and mapped 15 696 single nucleotide polymorphism (SNP, based on 90k Infinium chip and 35k Affymetrix chip) markers in 210 wheat genotypes. Phenotypic and genetic associations between grain yield traits and sub-phase durations showed significant consistency (Mantel test; r = 0.5377, P < 0.001). The shared quantitative trait loci (QTLs) revealed by the genome-wide association study suggested a close association between grain yield and sub-phase duration, which may be attributed to effects on spikelet initiation/spikelet number (double ridge to terminal spikelet stage, DR-TS) and assimilate accumulation (green anther to anthesis stage, GA-AN). Moreover, we observed that the photoperiod-sensitivity allele at the Ppd-D1 locus on chromosome 2D markedly extended all sub-phase durations, which may contribute to its positive effects on grain yield traits. The dwarfing allele at the Rht-D1 (chromosome 4D) locus altered the sub-phase duration and displayed positive effects on grain yield traits. Data for 30 selected genotypes (from among the original 210 genotypes) in the field displayed a close association with that from the greenhouse. Most importantly, this study demonstrated specific connections to grain yield in narrower time windows (i.e. the eight sub-phases), rather than the entire stem elongation phase as a whole.
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Affiliation(s)
- Zifeng Guo
- Independent Heisenberg Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Dijun Chen
- Department of Breeding Research, Research Group Image Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Marion S Röder
- Research Group Gene and Genome Mapping, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Martin W Ganal
- TraitGenetics GmbH, Stadt Seeland, Gatersleben, 06466, OT, Germany
| | - Thorsten Schnurbusch
- Independent Heisenberg Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
- Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin-Luther-University, Halle-Wittenberg, Halle, 06099, Germany
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Prieto P, Ochagavía H, Savin R, Griffiths S, Slafer GA. Dynamics of floret initiation/death determining spike fertility in wheat as affected by Ppd genes under field conditions. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2633-2645. [PMID: 29562264 PMCID: PMC5920323 DOI: 10.1093/jxb/ery105] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 03/10/2018] [Indexed: 05/28/2023]
Abstract
As wheat yield is linearly related to grain number, understanding the physiological determinants of the number of fertile florets based on floret development dynamics due to the role of the particular genes is relevant. The effects of photoperiod genes on dynamics of floret development are largely ignored. Field experiments were carried out to (i) characterize the dynamics of floret primordia initiation and degeneration and (ii) to determine which are the most critical traits of such dynamics in establishing genotypic differences in the number of fertile florets at anthesis in near isogenic lines (NILs) carrying photoperiod-insensitive alleles. Results varied in magnitude between the two growing seasons, but in general introgression of Ppd-1a alleles reduced the number of fertile florets. The actual effect was affected not only by the genome and the doses but also by the source of the alleles. Differences in the number of fertile florets were mainly explained by differences in the floret generation/degeneration dynamics, and in most cases associated with floret survival. Manipulating photoperiod insensitivity, unquestionably useful for changing flowering time, may reduce spike fertility but much less than proportionally to the change in duration of development, as the insensitivity alleles did increase the rate of floret development.
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Affiliation(s)
- Paula Prieto
- Department of Crop and Forest Sciences and AGROTECNIO (Center for Research in Agrotechnology), University of Lleida, Lleida, Spain
| | - Helga Ochagavía
- Department of Crop and Forest Sciences and AGROTECNIO (Center for Research in Agrotechnology), University of Lleida, Lleida, Spain
| | - Roxana Savin
- Department of Crop and Forest Sciences and AGROTECNIO (Center for Research in Agrotechnology), University of Lleida, Lleida, Spain
| | - Simon Griffiths
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | - Gustavo A Slafer
- Department of Crop and Forest Sciences and AGROTECNIO (Center for Research in Agrotechnology), University of Lleida, Lleida, Spain
- ICREA, Catalonian Institution for Research and Advanced Studies, Spain
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Guo J, Shi W, Zhang Z, Cheng J, Sun D, Yu J, Li X, Guo P, Hao C. Association of yield-related traits in founder genotypes and derivatives of common wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2018; 18:38. [PMID: 29458339 PMCID: PMC5819277 DOI: 10.1186/s12870-018-1234-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 01/14/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Yield improvement is an ever-important objective of wheat breeding. Studying and understanding the phenotypes and genotypes of yield-related traits has potential for genetic improvement of crops. RESULTS The genotypes of 215 wheat cultivars including 11 founder parents and 106 derivatives were analyzed by the 9 K wheat SNP iSelect assay. A total of 4138 polymorphic single nucleotide polymorphism (SNP) loci were detected on 21 chromosomes, of which 3792 were mapped to single chromosome locations. All genotypes were phenotyped for six yield-related traits including plant height (PH), spike length (SL), spikelet number per spike (SNPS), kernel number per spike (KNPS), kernel weight per spike (KWPS), and thousand kernel weight (TKW) in six irrigated environments. Genome-wide association analysis detected 117 significant associations of 76 SNPs on 15 chromosomes with phenotypic explanation rates (R 2 ) ranging from 2.03 to 12.76%. In comparing allelic variation between founder parents and their derivatives (106) and other cultivars (98) using the 76 associated SNPs, we found that the region 116.0-133.2 cM on chromosome 5A in founder parents and derivatives carried alleles positively influencing kernel weight per spike (KWPS), rarely found in other cultivars. CONCLUSION The identified favorable alleles could mark important chromosome regions in derivatives that were inherited from founder parents. Our results unravel the genetic of yield in founder genotypes, and provide tools for marker-assisted selection for yield improvement.
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Affiliation(s)
- Jie Guo
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Weiping Shi
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Zheng Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Jingye Cheng
- College of Agronomy, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Daizhen Sun
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Jin Yu
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Xinlei Li
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Pingyi Guo
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Giunta F, De Vita P, Mastrangelo AM, Sanna G, Motzo R. Environmental and Genetic Variation for Yield-Related Traits of Durum Wheat as Affected by Development. FRONTIERS IN PLANT SCIENCE 2018; 9:8. [PMID: 29403518 PMCID: PMC5778143 DOI: 10.3389/fpls.2018.00008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/03/2018] [Indexed: 05/27/2023]
Abstract
Phenology has a profound effect on adaptation and productivity of crops. The impact of phenology on tillering and fertility traits of durum wheat (Triticum turgidum L. subsp. durum Desf.) was evaluated with the aim of specifying which group of flowering genes (Vrn, Ppd, or eps) was involved in their control. A recombinant inbred line population was grown under four contrasting conditions of vernalization and daylength. Phenotyping was carried out according to robust phenological models dissecting both phenological and yield related traits. Whole-genome profiling was performed using the DArT-Seq technology. The genetic variability for tillering was mainly related to the genetic variability for vernalization sensitivity, as shown by the many quantitative trait loci (QTLs) identified in non-vernalized plants associated to both tillering and phenological traits. No effects of photoperiod sensitivity on spikelet number were detected in short-day-grown plants, apparently because of limited genetic variability in photoperiod sensitivity of the population. Earliness per se was involved in control of spikelet number via final leaf number, with these traits genetically correlated and sharing some QTLs. Chaff weight and number of kernels per g chaff were negatively associated and related to anthesis date under most conditions. QTL mapping uncovered novel loci involved in phenological control of tillering and fertility traits, and confirmed the presence of several well-established loci. Phenotyping of both phenology and kernel number according to a robust physiological model amplified the possibility of identifying genetic factors underlying their variations. Also, isolating known flowering gene cues by manipulation of environmental conditions provided the opportunity for each group of genes to be expressed without confounding effects of the others. This information helps to predict the consequences of either genetic manipulation of flowering genes and changes in environmental conditions on the potential yield of durum wheat.
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Affiliation(s)
- Francesco Giunta
- Sez. Agronomia, Coltivazioni erbacee e Genetica, Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - Pasquale De Vita
- Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), Foggia, Italy
| | - Anna M. Mastrangelo
- Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), Foggia, Italy
- Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), Bergamo, Italy
| | - Gavino Sanna
- Sez. Agronomia, Coltivazioni erbacee e Genetica, Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - Rosella Motzo
- Sez. Agronomia, Coltivazioni erbacee e Genetica, Dipartimento di Agraria, University of Sassari, Sassari, Italy
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Mangini G, Gadaleta A, Colasuonno P, Marcotuli I, Signorile AM, Simeone R, De Vita P, Mastrangelo AM, Laidò G, Pecchioni N, Blanco A. Genetic dissection of the relationships between grain yield components by genome-wide association mapping in a collection of tetraploid wheats. PLoS One 2018; 13:e0190162. [PMID: 29324803 PMCID: PMC5764242 DOI: 10.1371/journal.pone.0190162] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/09/2017] [Indexed: 11/29/2022] Open
Abstract
Increasing grain yield potential in wheat has been a major target of most breeding programs. Genetic advance has been frequently hindered by negative correlations among yield components that have been often observed in segregant populations and germplasm collections. A tetraploid wheat collection was evaluated in seven environments and genotyped with a 90K SNP assay to identify major and stable quantitative trait loci (QTL) for grain yield per spike (GYS), kernel number per spike (KNS) and thousand-kernel weight (TKW), and to analyse the genetic relationships between the yield components at QTL level. The genome-wide association analysis detected eight, eleven and ten QTL for KNS, TKW and GYS, respectively, significant in at least three environments or two environments and the mean across environments. Most of the QTL for TKW and KNS were found located in different marker intervals, indicating that they are genetically controlled independently by each other. Out of eight KNS QTL, three were associated to significant increases of GYS, while the increased grain number of five additional QTL was completely or partially compensated by decreases in grain weight, thus producing no or reduced effects on GYS. Similarly, four consistent and five suggestive TKW QTL resulted in visible increase of GYS, while seven additional QTL were associated to reduced effects in grain number and no effects on GYS. Our results showed that QTL analysis for detecting TKW or KNS alleles useful for improving grain yield potential should consider the pleiotropic effects of the QTL or the association to other QTLs.
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Affiliation(s)
- Giacomo Mangini
- Department of Soil, Plant & Food Sciences, Genetics and Plant Breeding Section, University Aldo Moro, Bari, Italy
| | - Agata Gadaleta
- Department of Agricultural & Environmental Science, Research Unit of “Genetics and Plant Biotechnology”, University Aldo Moro, Bari, Italy
- * E-mail:
| | - Pasqualina Colasuonno
- Department of Agricultural & Environmental Science, Research Unit of “Genetics and Plant Biotechnology”, University Aldo Moro, Bari, Italy
| | - Ilaria Marcotuli
- Department of Agricultural & Environmental Science, Research Unit of “Genetics and Plant Biotechnology”, University Aldo Moro, Bari, Italy
| | - Antonio M. Signorile
- Department of Soil, Plant & Food Sciences, Genetics and Plant Breeding Section, University Aldo Moro, Bari, Italy
| | - Rosanna Simeone
- Department of Soil, Plant & Food Sciences, Genetics and Plant Breeding Section, University Aldo Moro, Bari, Italy
| | - Pasquale De Vita
- Council for Agricultural Research and Economics—Cereal Research Centre, Foggia, Italy
| | - Anna M. Mastrangelo
- Council for Agricultural Research and Economics—Cereal Research Centre, Foggia, Italy
| | - Giovanni Laidò
- Council for Agricultural Research and Economics—Cereal Research Centre, Foggia, Italy
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics—Cereal Research Centre, Foggia, Italy
| | - Antonio Blanco
- Department of Soil, Plant & Food Sciences, Genetics and Plant Breeding Section, University Aldo Moro, Bari, Italy
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74
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Liu J, Xu Z, Fan X, Zhou Q, Cao J, Wang F, Ji G, Yang L, Feng B, Wang T. A Genome-Wide Association Study of Wheat Spike Related Traits in China. FRONTIERS IN PLANT SCIENCE 2018; 9:1584. [PMID: 30429867 PMCID: PMC6220075 DOI: 10.3389/fpls.2018.01584] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/11/2018] [Indexed: 05/22/2023]
Abstract
Rapid detection of allelic variation and identification of advantage haplotypes responsible for spike related traits play a crucial role in wheat yield improvement. The released genome sequence of hexaploid wheat (Chinese Spring) provides an extraordinary opportunity for rapid detection of natural variation and promotes breeding application. Here, selection signals detection and genome-wide association study (GWAS) were conducted for spike related traits. Based on the genotyping results by 90K SNP chip, 192 common wheat samples from southwest China were analyzed. One hundred and forty-six selective windows and one hundred and eighty-four significant SNPs (51 for spike length, 28 for kernels per spike, 39 for spikelet number, 30 for thousand kernel weight, and 36 for spike number per plant) were detected. Furthermore, tightly linkage and environmental stability window clusters and SNP clusters were also obtained. As a result, four SNP clusters associated with spike length were detected on chromosome 2A, 2B, 2D, and 6A. Two SNP clusters correlated to kernels per spike were detected on 2A and 2B. One pleiotropy SNP cluster correlated to spikelet number and kernels per spike was detected on 7B. According to the genome sequence, these SNP clusters and their overlapped/flanking QTLs which have been reported previously were integrated to a physical map. The candidate genes responsible for spike length, kernels per spike and spikelet number were predicted. Based on the genotypes of cultivars in south China, two advantage haplotypes associated with spike length and one advantage haplotype associated with kernels per spike/spikelet number were detected which have not been effectively transited into cultivars. According to these haplotypes, KASP markers were developed and diagnosed across landraces and cultivars which were selected from south and north China. Consequently, KASP assay, consistent with the GWAS results, provides reliable haplotypes for MAS in wheat yield improvement.
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Turuspekov Y, Baibulatova A, Yermekbayev K, Tokhetova L, Chudinov V, Sereda G, Ganal M, Griffiths S, Abugalieva S. GWAS for plant growth stages and yield components in spring wheat (Triticum aestivum L.) harvested in three regions of Kazakhstan. BMC PLANT BIOLOGY 2017; 17:190. [PMID: 29143598 PMCID: PMC5688510 DOI: 10.1186/s12870-017-1131-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
BACKGROUND Spring wheat is the largest agricultural crop grown in Kazakhstan with an annual sowing area of 12 million hectares in 2016. Annually, the country harvests around 15 million tons of high quality grain. Despite environmental stress factors it is predicted that the use of new technologies may lead to increases in productivity from current levels of 1.5 to up to 3 tons per hectare. One way of improving wheat productivity is by the application of new genomic oriented approaches in plant breeding projects. Genome wide association studies (GWAS) are emerging as powerful tools for the understanding of the inheritance of complex traits via utilization of high throughput genotyping technologies and phenotypic assessments of plant collections. In this study, phenotyping and genotyping data on 194 spring wheat accessions from Kazakhstan, Russia, Europe, and CIMMYT were assessed for the identification of marker-trait associations (MTA) of agronomic traits by using GWAS. RESULTS Field trials in Northern, Central and Southern regions of Kazakhstan using 194 spring wheat accessions revealed strong correlations of yield with booting date, plant height, biomass, number of spikes per plant, and number of kernels per spike. The accessions from Europe and CIMMYT showed high breeding potential for Southern and Central regions of the country in comparison with the performance of the local varieties. The GGE biplot method, using average yield per plant, suggested a clear separation of accessions into their three breeding origins in relationship to the three environments in which they were evaluated. The genetic variation in the three groups of accessions was further studied using 3245 polymorphic SNP (single nucleotide polymorphism) markers. The application of Principal Coordinate analysis clearly grouped the 194 accessions into three clades according to their breeding origins. GWAS on data from nine field trials allowed the identification of 114 MTAs for 12 different agronomic traits. CONCLUSIONS Field evaluation of foreign germplasm revealed its poor yield performance in Northern Kazakhstan, which is the main wheat growing region in the country. However, it was found that EU and CIMMYT germplasm has high breeding potential to improve yield performance in Central and Southern regions. The use of Principal Coordinate analysis clearly separated the panel into three distinct groups according to their breeding origin. GWAS based on use of the TASSEL 5.0 package allowed the identification of 114 MTAs for twelve agronomic traits. The study identifies a network of key genes for improvement of yield productivity in wheat growing regions of Kazakhstan.
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Affiliation(s)
- Yerlan Turuspekov
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan 050040
| | - Aida Baibulatova
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan 050040
| | - Kanat Yermekbayev
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan 050040
| | - Laura Tokhetova
- Kazakh Rice Research Institute, Kyzylorda, Kazakhstan 120016
| | | | - Grigoriy Sereda
- Karaganda Research Institute of Agriculture, Karaganda region, Kazakhstan 100435
| | | | - Simon Griffiths
- John Innes Centre, Norwich Research Park, Norwich, NR47UH UK
| | - Saule Abugalieva
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan 050040
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76
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Wang M, Wang S, Liang Z, Shi W, Gao C, Xia G. From Genetic Stock to Genome Editing: Gene Exploitation in Wheat. Trends Biotechnol 2017; 36:160-172. [PMID: 29102241 DOI: 10.1016/j.tibtech.2017.10.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 10/01/2017] [Accepted: 10/02/2017] [Indexed: 10/18/2022]
Abstract
Bread wheat (Triticum aestivum) ranks as one of our most important staple crops. However, its hexaploid nature has complicated our understanding of the genetic bases underlying many of its traits. Historically, functional genetic studies in wheat have focused on identifying natural variations and have contributed to assembling and enriching its genetic stock. Recently, mold-breaking advances in whole genome sequencing, exome-capture based mutant libraries, and genome editing have revolutionized strategies for genetic research in wheat. We review new trends in wheat functional genetic studies along with germplasm conservation and innovation, including the relevance of genetic stocks, and the application of sequencing-based mutagenesis and genome editing. We also highlight the potential of multiplex genome editing toolkits in addressing species-specific challenges in wheat.
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Affiliation(s)
- Meng Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, China; State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; These authors contributed equally to this work
| | - Shubin Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, China; These authors contributed equally to this work
| | - Zhen Liang
- State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Guangmin Xia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, China.
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Dwivedi SL, Scheben A, Edwards D, Spillane C, Ortiz R. Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes. FRONTIERS IN PLANT SCIENCE 2017; 8:1461. [PMID: 28900432 PMCID: PMC5581882 DOI: 10.3389/fpls.2017.01461] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/07/2017] [Indexed: 05/03/2023]
Abstract
There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses.
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Affiliation(s)
| | - Armin Scheben
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, PerthWA, Australia
| | - David Edwards
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, PerthWA, Australia
| | - Charles Spillane
- Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland GalwayGalway, Ireland
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural SciencesAlnarp, Sweden
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78
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Sun C, Zhang F, Yan X, Zhang X, Dong Z, Cui D, Chen F. Genome-wide association study for 13 agronomic traits reveals distribution of superior alleles in bread wheat from the Yellow and Huai Valley of China. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:953-969. [PMID: 28055148 PMCID: PMC5506658 DOI: 10.1111/pbi.12690] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/23/2016] [Accepted: 12/29/2016] [Indexed: 05/18/2023]
Abstract
Bread wheat is a leading cereal crop worldwide. Limited amount of superior allele loci restricted the progress of molecular improvement in wheat breeding. Here, we revealed new allelic variation distribution for 13 yield-related traits in series of genome-wide association studies (GWAS) using the wheat 90K genotyping assay, characterized in 163 bread wheat cultivars. Agronomic traits were investigated in 14 environments at three locations over 3 years. After filtering SNP data sets, GWAS using 20 689 high-quality SNPs associated 1769 significant loci that explained, on average, ~20% of the phenotypic variation, both detected already reported loci and new promising genomic regions. Of these, repetitive and pleiotropic SNPs on chromosomes 6AS, 6AL, 6BS, 5BL and 7AS were significantly linked to thousand kernel weight, for example BS00021705_51 on 6BS and wsnp_Ex_c32624_41252144 on 6AS, with phenotypic variation explained (PVE) of ~24%, consistently identified in 12 and 13 of the 14 environments, respectively. Kernel length-related SNPs were mainly identified on chromosomes 7BS, 6AS, 5AL and 5BL. Plant height-related SNPs on chromosomes 4DS, 6DL, 2DS and 1BL were, respectively, identified in more than 11 environments, with averaged PVE of ~55%. Four SNPs were confirmed to be important genetic loci in two RIL populations. Based on repetivity and PVE, a total of 41 SNP loci possibly played the key role in modulating yield-related traits of the cultivars surveyed. Distribution of superior alleles at the 41 SNP loci indicated that superior alleles were getting popular with time and modern cultivars had integrated many superior alleles, especially for peduncle length- and plant height-related superior alleles. However, there were still 19 SNP loci showing less than percentages of 50% in modern cultivars, suggesting they should be paid more attention to improve yield-related traits of cultivars in the Yellow and Huai wheat region. This study could provide useful information for dissection of yield-related traits and valuable genetic loci for marker-assisted selection in Chinese wheat breeding programme.
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Affiliation(s)
- Congwei Sun
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Fuyan Zhang
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Henan Key Laboratory of Nuclear Agricultural Sciences/Isotope Institute Co., LtdHenan Academy of SciencesZhengzhouChina
| | - Xuefang Yan
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Xiangfen Zhang
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Zhongdong Dong
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Dangqun Cui
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Feng Chen
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
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