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Koua AP, Oyiga BC, Baig MM, Léon J, Ballvora A. Breeding Driven Enrichment of Genetic Variation for Key Yield Components and Grain Starch Content Under Drought Stress in Winter Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:684205. [PMID: 34484257 PMCID: PMC8415485 DOI: 10.3389/fpls.2021.684205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/20/2021] [Indexed: 05/12/2023]
Abstract
Drought is one of the major abiotic stress factors limiting wheat production worldwide, thus threatening food security. The dissection of the genetic footprint of drought stress response offers strong opportunities toward understanding and improving drought tolerance (DT) in wheat. In this study, we investigated the genotypic variability for drought response among 200 diverse wheat cultivars (genotypes) using agronomic, developmental, and grain quality traits (GQT), and conducted genome-wide association studies (GWAS) to uncover the genetic architectures of these important traits. Results indicated significant effects of genotype, water regime and their interactions for all agronomic traits. Grain yield (GY) was the most drought-responsive trait and was highly correlated with kernels number per meter square (KN). Genome-wide association studies revealed 17 and 20 QTL regions under rainfed and drought conditions, respectively, and identified one LD block on chromosome 3A and two others on 5D associated with breeding progress (BP). The major haplotypes of these LD blocks have been positively selected through breeding and are associated with higher starch accumulation and GY under drought conditions. Upon validation, the identified QTL regions caring favorable alleles for high starch and yield will shed light on mechanisms of tolerance to drought and can be used to develop drought resistant cultivars.
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Affiliation(s)
- Ahossi Patrice Koua
- Department of Plant Breeding, Institut für Nutzpflanzenwissenschaften und Ressourcenschutz (INRES), Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Benedict Chijioke Oyiga
- Department of Plant Breeding, Institut für Nutzpflanzenwissenschaften und Ressourcenschutz (INRES), Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Mirza Majid Baig
- Department of Plant Breeding, Institut für Nutzpflanzenwissenschaften und Ressourcenschutz (INRES), Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Jens Léon
- Department of Plant Breeding, Institut für Nutzpflanzenwissenschaften und Ressourcenschutz (INRES), Rheinische Friedrich-Wilhelms-University, Bonn, Germany
- Field Lab Campus Klein-Altendorf, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Agim Ballvora
- Department of Plant Breeding, Institut für Nutzpflanzenwissenschaften und Ressourcenschutz (INRES), Rheinische Friedrich-Wilhelms-University, Bonn, Germany
- *Correspondence: Agim Ballvora
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Li D, Zhou Z, Lu X, Jiang Y, Li G, Li J, Wang H, Chen S, Li X, Würschum T, Reif JC, Xu S, Li M, Liu W. Genetic Dissection of Hybrid Performance and Heterosis for Yield-Related Traits in Maize. FRONTIERS IN PLANT SCIENCE 2021; 12:774478. [PMID: 34917109 PMCID: PMC8670227 DOI: 10.3389/fpls.2021.774478] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/01/2021] [Indexed: 05/14/2023]
Abstract
Heterosis contributes a big proportion to hybrid performance in maize, especially for grain yield. It is attractive to explore the underlying genetic architecture of hybrid performance and heterosis. Considering its complexity, different from former mapping method, we developed a series of linear mixed models incorporating multiple polygenic covariance structures to quantify the contribution of each genetic component (additive, dominance, additive-by-additive, additive-by-dominance, and dominance-by-dominance) to hybrid performance and midparent heterosis variation and to identify significant additive and non-additive (dominance and epistatic) quantitative trait loci (QTL). Here, we developed a North Carolina II population by crossing 339 recombinant inbred lines with two elite lines (Chang7-2 and Mo17), resulting in two populations of hybrids signed as Chang7-2 × recombinant inbred lines and Mo17 × recombinant inbred lines, respectively. The results of a path analysis showed that kernel number per row and hundred grain weight contributed the most to the variation of grain yield. The heritability of midparent heterosis for 10 investigated traits ranged from 0.27 to 0.81. For the 10 traits, 21 main (additive and dominance) QTL for hybrid performance and 17 dominance QTL for midparent heterosis were identified in the pooled hybrid populations with two overlapping QTL. Several of the identified QTL showed pleiotropic effects. Significant epistatic QTL were also identified and were shown to play an important role in ear height variation. Genomic selection was used to assess the influence of QTL on prediction accuracy and to explore the strategy of heterosis utilization in maize breeding. Results showed that treating significant single nucleotide polymorphisms as fixed effects in the linear mixed model could improve the prediction accuracy under prediction schemes 2 and 3. In conclusion, the different analyses all substantiated the different genetic architecture of hybrid performance and midparent heterosis in maize. Dominance contributes the highest proportion to heterosis, especially for grain yield, however, epistasis contributes the highest proportion to hybrid performance of grain yield.
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Affiliation(s)
- Dongdong Li
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohuan Lu
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Germany
| | - Guoliang Li
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Junhui Li
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Haoying Wang
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Shaojiang Chen
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tobias Würschum
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Germany
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
- *Correspondence: Wenxin Liu,
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Mingshun Li,
| | - Wenxin Liu
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Shizhong Xu,
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Liu H, Zhang X, Xu Y, Ma F, Zhang J, Cao Y, Li L, An D. Identification and validation of quantitative trait loci for kernel traits in common wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2020; 20:529. [PMID: 33225903 PMCID: PMC7682089 DOI: 10.1186/s12870-020-02661-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 09/23/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Kernel weight and morphology are important traits affecting cereal yields and quality. Dissecting the genetic basis of thousand kernel weight (TKW) and its related traits is an effective method to improve wheat yield. RESULTS In this study, we performed quantitative trait loci (QTL) analysis using recombinant inbred lines derived from the cross 'PuBing3228 × Gao8901' (PG-RIL) to dissect the genetic basis of kernel traits. A total of 17 stable QTLs related to kernel traits were identified, notably, two stable QTLs QTkw.cas-1A.2 and QTkw.cas-4A explained the largest portion of the phenotypic variance for TKW and kernel length (KL), and the other two stable QTLs QTkw.cas-6A.1 and QTkw.cas-7D.2 contributed more effects on kernel width (KW). Conditional QTL analysis revealed that the stable QTLs for TKW were mainly affected by KW. The QTLs QTkw.cas-7D.2 and QKw.cas-7D.1 associated with TKW and KW were delimited to the physical interval of approximately 3.82 Mb harboring 47 candidate genes. Among them, the candidate gene TaFT-D1 had a 1 bp insertions/deletion (InDel) within the third exon, which might be the reason for diversity in TKW and KW between the two parents. A Kompetitive Allele-Specific PCR (KASP) marker of TaFT-D1 allele was developed and verified by PG-RIL and a natural population consisted of 141 cultivar/lines. It was found that the favorable TaFT-D1 (G)-allele has been positively selected during Chinese wheat breeding. Thus, these results can be used for further positional cloning and marker-assisted selection in wheat breeding programs. CONCLUSIONS Seventeen stable QTLs related to kernel traits were identified. The stable QTLs for thousand kernel weight were mainly affected by kernel width. TaFT-D1 could be the candidate gene for QTLs QTkw.cas-7D.2 and QKw.cas-7D.1.
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Affiliation(s)
- Hong Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Xiaotao Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunfeng Xu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Feifei Ma
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinpeng Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanwei Cao
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lihui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Diaoguo An
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China.
- The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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Arriagada O, Marcotuli I, Gadaleta A, Schwember AR. Molecular Mapping and Genomics of Grain Yield in Durum Wheat: A Review. Int J Mol Sci 2020; 21:ijms21197021. [PMID: 32987666 PMCID: PMC7582296 DOI: 10.3390/ijms21197021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
Durum wheat is the most relevant cereal for the whole of Mediterranean agriculture, due to its intrinsic adaptation to dryland and semi-arid environments and to its strong historical cultivation tradition. It is not only relevant for the primary production sector, but also for the food industry chains associated with it. In Mediterranean environments, wheat is mostly grown under rainfed conditions and the crop is frequently exposed to environmental stresses, with high temperatures and water scarcity especially during the grain filling period. For these reasons, and due to recurrent disease epidemics, Mediterranean wheat productivity often remains under potential levels. Many studies, using both linkage analysis (LA) and a genome-wide association study (GWAS), have identified the genomic regions controlling the grain yield and the associated markers that can be used for marker-assisted selection (MAS) programs. Here, we have summarized all the current studies identifying quantitative trait loci (QTLs) and/or candidate genes involved in the main traits linked to grain yield: kernel weight, number of kernels per spike and number of spikes per unit area.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, 306-22 Santiago, Chile;
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, 70121 Bari, Italy; (I.M.); (A.G.)
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, 70121 Bari, Italy; (I.M.); (A.G.)
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, 306-22 Santiago, Chile;
- Correspondence: ; Tel.: +56-223544123
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Pang Y, Liu C, Wang D, St Amand P, Bernardo A, Li W, He F, Li L, Wang L, Yuan X, Dong L, Su Y, Zhang H, Zhao M, Liang Y, Jia H, Shen X, Lu Y, Jiang H, Wu Y, Li A, Wang H, Kong L, Bai G, Liu S. High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat. MOLECULAR PLANT 2020; 13:1311-1327. [PMID: 32702458 DOI: 10.1016/j.molp.2020.07.008] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/08/2020] [Accepted: 07/17/2020] [Indexed: 05/18/2023]
Abstract
Wheat (Triticum aestivum) is a major staple food crop worldwide. Genetic dissection of important agronomic traits is essential for continuous improvement of wheat yield to meet the demand of the world's growing population. We conducted a large-scale genome-wide association study (GWAS) using a panel of 768 wheat cultivars that were genotyped with 327 609 single-nucleotide polymorphisms generated by genotyping-by-sequencing and detected 395 quantitative trait loci (QTLs) for 12 traits under 7 environments. Among them, 273 QTLs were delimited to ≤1.0-Mb intervals and 7 of them are either known genes (Rht-D, Vrn-B1, and Vrn-D1) that have been cloned or known QTLs (TaGA2ox8, APO1, TaSus1-7B, and Rht12) that were previously mapped. Eight putative candidate genes were identified for three QTLs that enhance spike seed setting and grain size using gene expression data and were validated in three bi-parental populations. Protein sequence analysis identified 33 putative wheat orthologs that have high identity with rice genes in QTLs affecting similar traits. Large r2 values for additive effects observed among the QTLs for most traits indicated that the phenotypes of these identified QTLs were highly predictable. Results from this study demonstrated that significantly increasing GWAS population size and marker density greatly improves detection and identification of candidate genes underlying a QTL, solidifying the foundation for large-scale QTL fine mapping, candidate gene validation, and developing functional markers for genomics-based breeding in wheat.
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Affiliation(s)
- Yunlong Pang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Chunxia Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Danfeng Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Paul St Amand
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA
| | - Amy Bernardo
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA; Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Wenhui Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Fang He
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China; College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Linzhi Li
- Yantai Academy of Agricultural Sciences, Yantai 265500, China
| | - Liming Wang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Xiufang Yuan
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Lei Dong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yu Su
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Huirui Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Meng Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yunlong Liang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Hongze Jia
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Xitong Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yue Lu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Hongming Jiang
- Yantai Academy of Agricultural Sciences, Yantai 265500, China
| | - Yuye Wu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Anfei Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Honggang Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA.
| | - Shubing Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.
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Liu N, Cheng F. Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome. BMC PLANT BIOLOGY 2020; 20:245. [PMID: 32487017 PMCID: PMC7265254 DOI: 10.1186/s12870-020-02449-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 05/18/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Allelic variation underlying the quantitative traits in plants is caused by the extremely complex regulation process. Tree peony originated in China is a peculiar ornamental, medicinal and oil woody plant. Paeonia rockii, one of tree peony species, is a precious emerging woody oil crop. However, in this valuable plant, the study of functional loci associated with yield traits has rarely been identified. Therefore, to explore the genetic architecture of 24 yield quantitative traits, the association mapping was first reported in 420 unrelated cultivated P. rockii individuals based on the next-generation sequencing (NGS) and single-molecule long-read sequencing (SMLRS). RESULTS The developed 58 pairs of polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers from 959 candidate transcription factors (TFs) associated with yield were used for genotyping the 420 P. rockii accessions. We observed a high level of genetic diversity (polymorphic information content, PIC = 0.514) and low linkage disequilibrium (LD) between EST-SSRs. Moreover, four subpopulations in the association population were revealed by STRUCTURE analyses. Further, single-marker association analysis identified 141 significant associations, involving 17 quantitative traits and 41 EST-SSRs. These loci were mainly from AP2, TCP, MYB, HSF, bHLH, GATA, and B3 gene families and showed a small proportion of the phenotypic variance (3.79 to 37.45%). CONCLUSIONS Our results summarize a valuable collection of functional loci associated with yield traits in P. rockii, and provide a precious resource that reveals allelic variation underlying quantitative traits in Paeonia and other woody oil crops.
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Affiliation(s)
- Na Liu
- Peony International Institute, Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Fangyun Cheng
- Peony International Institute, Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
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Cao S, Xu D, Hanif M, Xia X, He Z. Genetic architecture underpinning yield component traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1811-1823. [PMID: 32062676 DOI: 10.1007/s00122-020-03562-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 02/06/2020] [Indexed: 05/19/2023]
Abstract
Genetic atlas, reliable QTL and candidate genes of yield component traits in wheat were figured out, laying concrete foundations for map-based gene cloning and dissection of regulatory mechanisms underlying yield. Mining genetic loci for yield is challenging due to the polygenic nature, large influence of environment and complex relationship among yield component traits (YCT). Many genetic loci related to wheat yield have been identified, but its genetic architecture and key genetic loci for selection are largely unknown. Wheat yield potential can be determined by three YCT, thousand kernel weight, kernel number per spike and spike number. Here, we summarized the genetic loci underpinning YCT from QTL mapping, association analysis and homology-based gene cloning. The major loci determining yield-associated agronomic traits, such as flowering time and plant height, were also included in comparative analyses with those for YCT. We integrated yield-related genetic loci onto chromosomes based on their physical locations. To identify the major stable loci for YCT, 58 QTL-rich clusters (QRC) were defined based on their distribution on chromosomes. Candidate genes in each QRC were predicted according to gene annotation of the wheat reference genome and previous information on validation of those genes in other species. Finally, a technological route was proposed to take full advantage of the resultant resources for gene cloning, molecular marker-assisted breeding and dissection of molecular regulatory mechanisms underlying wheat yield.
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Affiliation(s)
- Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
| | - Dengan Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Mamoona Hanif
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
- International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China.
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Reduced response diversity does not negatively impact wheat climate resilience. Proc Natl Acad Sci U S A 2020; 116:10623-10624. [PMID: 31138710 DOI: 10.1073/pnas.1901882116] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Sakuma S, Schnurbusch T. Of floral fortune: tinkering with the grain yield potential of cereal crops. THE NEW PHYTOLOGIST 2020; 225:1873-1882. [PMID: 31509613 DOI: 10.1111/nph.16189] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/28/2019] [Indexed: 05/19/2023]
Abstract
Enhancing the yield potential and stability of small-grain cereals, such as wheat (Triticum sp.), rice (Oryza sativa), and barley (Hordeum vulgare), is a priority for global food security. Over the last several decades, plant breeders have increased grain yield mainly by increasing the number of grains produced in each inflorescence. This trait is determined by the number of spikelets per spike and the number of fertile florets per spikelet. Recent genetic and genomic advances in cereal grass species have identified the molecular determinants of grain number and facilitated the exchange of information across genera. In this review, we focus on the genetic basis of inflorescence architecture in Triticeae crops, highlighting recent insights that have helped to improve grain yield by, for example, reducing the preprogrammed abortion of floral organs. The accumulating information on inflorescence development can be harnessed to enhance grain yield by comparative trait reconstruction and rational design to boost the yield potential of grain crops.
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Affiliation(s)
- Shun Sakuma
- Faculty of Agriculture, Tottori University, Tottori, 680-8553, Japan
| | - Thorsten Schnurbusch
- 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, Germany
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Würschum T, Langer SM, Longin CFH, Tucker MR, Leiser WL. Refining the genetic architecture of flag leaf glaucousness in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:981-991. [PMID: 31953547 PMCID: PMC7021748 DOI: 10.1007/s00122-019-03522-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/20/2019] [Indexed: 05/27/2023]
Abstract
The cuticle is the plant's barrier against abiotic and biotic stresses, and the deposition of epicuticular wax crystals results in the scattering of light, an effect termed glaucousness. Here, we dissect the genetic architecture of flag leaf glaucousness in wheat toward a future targeted design of the cuticle. The cuticle serves as a barrier that protects plants against abiotic and biotic stresses. Differences in cuticle composition can be detected by the scattering of light on epicuticular wax crystals, which causes a phenotype termed glaucousness. In this study, we dissected the genetic architecture of flag leaf glaucousness in a panel of 1106 wheat cultivars of global origin. We observed a large genotypic variation, but the geographic pattern suggests that other wax layer characteristics besides glaucousness may be important in conferring tolerance to abiotic stresses such as heat and drought. Genome-wide association mapping identified two major quantitative trait loci (QTL) on chromosomes 3A and 2B. The latter corresponds to the W1 locus, but further characterization revealed that it is likely to contain additional QTL. The same holds true for the major QTL on 3A, which was also found to show an epistatic interaction with another locus located a few centiMorgan distal to it. Genome-wide prediction and the identification of a few additional putative QTL revealed that small-effect QTL also contribute to the trait. Collectively, our results illustrate the complexity of the genetic control of flag leaf glaucousness, with additive effects and epistasis, and lay the foundation for the cloning of the underlying genes toward a more targeted design of the cuticle by plant breeding.
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Affiliation(s)
- Tobias Würschum
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany.
| | - Simon M Langer
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany
- BASF Agricultural Solutions GmbH, Gatersleben, Germany
| | - C Friedrich H Longin
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany
| | - Matthew R Tucker
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
| | - Willmar L Leiser
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany
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61
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Identification of quantitative trait loci associated with nitrogen use efficiency in winter wheat. PLoS One 2020; 15:e0228775. [PMID: 32092066 PMCID: PMC7039505 DOI: 10.1371/journal.pone.0228775] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/22/2020] [Indexed: 11/26/2022] Open
Abstract
Maintaining winter wheat (Triticum aestivum L.) productivity with more efficient nitrogen (N) management will enable growers to increase profitability and reduce the negative environmental impacts associated with nitrogen loss. Wheat breeders would therefore benefit greatly from the identification and application of genetic markers associated with nitrogen use efficiency (NUE). To investigate the genetics underlying N response, two bi-parental mapping populations were developed and grown in four site-seasons under low and high N rates. The populations were derived from a cross between previously identified high NUE parents (VA05W-151 and VA09W-52) and a shared common low NUE parent, ‘Yorktown.’ The Yorktown × VA05W-151 population was comprised of 136 recombinant inbred lines while the Yorktown × VA09W-52 population was comprised of 138 doubled haploids. Phenotypic data was collected on parental lines and their progeny for 11 N-related traits and genotypes were sequenced using a genotyping-by-sequencing platform to detect more than 3,100 high quality single nucleotide polymorphisms in each population. A total of 130 quantitative trait loci (QTL) were detected on 20 chromosomes, six of which were associated with NUE and N-related traits in multiple testing environments. Two of the six QTL for NUE were associated with known photoperiod (Ppd-D1 on chromosome 2D) and disease resistance (FHB-4A) genes, two were reported in previous investigations, and one QTL, QNue.151-1D, was novel. The NUE QTL on 1D, 6A, 7A, and 7D had LOD scores ranging from 2.63 to 8.33 and explained up to 18.1% of the phenotypic variation. The QTL identified in this study have potential for marker-assisted breeding for NUE traits in soft red winter wheat.
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Lichthardt C, Chen TW, Stahl A, Stützel H. Co-Evolution of Sink and Source in the Recent Breeding History of Winter Wheat in Germany. FRONTIERS IN PLANT SCIENCE 2020; 10:1771. [PMID: 32117340 PMCID: PMC7019858 DOI: 10.3389/fpls.2019.01771] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/18/2019] [Indexed: 05/24/2023]
Abstract
Optimizing the interplay between sinks and sources is of crucial importance for breeding progress in winter wheat. However, the physiological limitations of yield from source (e.g. green canopy duration, GCD) and sink (e.g. grain number) are still unclear. Furthermore, there is little information on how the source traits have been modified during the breeding history of winter wheat. This study analyzed the breeding progress of sink and source components and their relationships to yield components. Field trials were conducted over three years with 220 cultivars representing the German breeding history of the past five decades. In addition, genetic associations of QTL for the traits were assessed with genome-wide association studies. Breeding progress mainly resulted from an increase in grain numbers per spike, a sink component, whose variations were largely explained by the photosynthetic activity around anthesis, a source component. Surprisingly, despite significant breeding progress in GCD and other source components, they showed no direct influence on thousand grain weights, indicating that grain filling was not limited by the source strength. Our results suggest that, 1) the potential longevity of the green canopy is predetermined at the time point that the number of grains is fixed; 2) a co-evolution of source and sink strength during the breeding history contribute to the yield formation of the modern cultivars. For future breeding we suggest to choose parental lines with high grain numbers per spike on the sink side, and high photosynthetic activity around anthesis and canopy duration on the source side, and to place emphasis on these traits throughout selection.
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Affiliation(s)
- Carolin Lichthardt
- Vegetable Systems Modelling Section, Institute of Horticultural Production Systems, University of Hannover, Hannover, Germany
| | - Tsu-Wei Chen
- Vegetable Systems Modelling Section, Institute of Horticultural Production Systems, University of Hannover, Hannover, Germany
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Hartmut Stützel
- Vegetable Systems Modelling Section, Institute of Horticultural Production Systems, University of Hannover, Hannover, Germany
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63
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Genome-wide and SNP network analyses reveal genetic control of spikelet sterility and yield-related traits in wheat. Sci Rep 2020; 10:2098. [PMID: 32034248 PMCID: PMC7005900 DOI: 10.1038/s41598-020-59004-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 01/21/2020] [Indexed: 02/03/2023] Open
Abstract
Revealing the genetic factors underlying yield and agronomic traits in wheat are an imperative need for covering the global food demand. Yield boosting requires a deep understanding of the genetic basis of grain yield-related traits (e.g., spikelet fertility and sterility). Here, we have detected much natural variation among ancient hexaploid wheat accessions in twenty-two agronomic traits collected over eight years of field experiments. A genome-wide association study (GWAS) using 15 K single nucleotide polymorphisms (SNPs) was applied to detect the genetic basis of studied traits. Subsequently, the GWAS output was reinforced via other statistical and bioinformatics analyses to detect putative candidate genes. Applying the genome-wide SNP-phenotype network defined the most decisive SNPs underlying the traits. Six pivotal SNPs, co-located physically within the genes encoding enzymes, hormone response, metal ion transport, and response to oxidative stress have been identified. Of these, metal ion transport and Gibberellin 2-oxidases (GA2oxs) genes showed strong involvement in controlling the spikelet sterility, which had not been reported previously in wheat. SNP-gene haplotype analysis confirmed that these SNPs influence spikelet sterility, especially the SNP co-located on the exon of the GA2ox gene. Interestingly, these genes were highly expressed in the grain and spike, demonstrating their pivotal role in controlling the trait. The integrative analysis strategy applied in this study, including GWAS, SNP-phenotype network, SNP-gene haplotype, expression analysis, and genome-wide prediction (GP), empower the identification of functional SNPs and causal genes. GP outputs obtained in this study are encouraging for the implementation of the traits to accelerate yield improvement by making an early prediction of complex yield-related traits in wheat. Our findings demonstrate the usefulness of the ancient wheat material as a valuable resource for yield-boosting. This is the first comprehensive genome-wide analysis for spikelet sterility in wheat, and the results provide insights into yield improvement.
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64
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Chen Z, Cheng X, Chai L, Wang Z, Bian R, Li J, Zhao A, Xin M, Guo W, Hu Z, Peng H, Yao Y, Sun Q, Ni Z. Dissection of genetic factors underlying grain size and fine mapping of QTgw.cau-7D in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:149-162. [PMID: 31570967 DOI: 10.1007/s00122-019-03447-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/21/2019] [Indexed: 05/26/2023]
Abstract
Thirty environmentally stable QTL controlling grain size and/or plant height were identified, among which QTgw.cau-7D was delimited into the physical interval of approximately 4.4 Mb. Grain size and plant height (PHT) are important agronomic traits in wheat breeding. To dissect the genetic basis of these traits, we conducted a quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs). In total, 30 environmentally stable QTL for thousand grain weight (TGW), grain length (GL), grain width (GW) and PHT were detected. Notably, one major pleiotropic QTL on chromosome arm 3DS explained the highest phenotypic variance for TGW, GL and PHT, and two stable QTL (QGw.cau-4B and QGw.cau-7D) on chromosome arms 4BS and 7DS contributed greater effects for GW. Furthermore, the stable QTL controlling grain size (QTgw.cau-7D and QGw.cau-7D) were delimited into the physical interval of approximately 4.4 Mb harboring 56 annotated genes. The elite NILs of QTgw.cau-7D increased TGW by 12.79-21.75% and GW by 4.10-8.47% across all three environments. Collectively, these results provide further insight into the genetic basis of TGW, GL, GW and PHT, and the fine-mapped QTgw.cau-7D will be an attractive target for positional cloning and marker-assisted selection in wheat breeding programs.
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Affiliation(s)
- Zhaoyan Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Xuejiao Cheng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Lingling Chai
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhihui Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Ruolin Bian
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Jiang Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Aiju Zhao
- Hebei Crop Genetic Breeding Laboratory, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
- National Plant Gene Research Centre, Beijing, 100193, China.
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65
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Lozada DN, Godoy JV, Ward BP, Carter AH. Genomic Prediction and Indirect Selection for Grain Yield in US Pacific Northwest Winter Wheat Using Spectral Reflectance Indices from High-Throughput Phenotyping. Int J Mol Sci 2019; 21:E165. [PMID: 31881728 PMCID: PMC6981971 DOI: 10.3390/ijms21010165] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/21/2019] [Accepted: 12/22/2019] [Indexed: 12/23/2022] Open
Abstract
Secondary traits from high-throughput phenotyping could be used to select for complex target traits to accelerate plant breeding and increase genetic gains. This study aimed to evaluate the potential of using spectral reflectance indices (SRI) for indirect selection of winter-wheat lines with high yield potential and to assess the effects of including secondary traits on the prediction accuracy for yield. A total of five SRIs were measured in a diversity panel, and F5 and doubled haploid wheat breeding populations planted between 2015 and 2018 in Lind and Pullman, WA. The winter-wheat panels were genotyped with 11,089 genotyping-by-sequencing derived markers. Spectral traits showed moderate to high phenotypic and genetic correlations, indicating their potential for indirect selection of lines with high yield potential. Inclusion of correlated spectral traits in genomic prediction models resulted in significant (p < 0.001) improvement in prediction accuracy for yield. Relatedness between training and test populations and heritability were among the principal factors affecting accuracy. Our results demonstrate the potential of using spectral indices as proxy measurements for selecting lines with increased yield potential and for improving prediction accuracy to increase genetic gains for complex traits in US Pacific Northwest winter wheat.
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Affiliation(s)
- Dennis N. Lozada
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA; (D.N.L.); (J.V.G.)
| | - Jayfred V. Godoy
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA; (D.N.L.); (J.V.G.)
| | - Brian P. Ward
- USDA-ARS Plant Science Research Unit, Raleigh, NC 27695, USA;
| | - Arron H. Carter
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA; (D.N.L.); (J.V.G.)
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66
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Chernook AG, Kroupin PY, Bespalova LA, Panchenko VV, Kovtunenko VY, Bazhenov MS, Nazarova LA, Karlov GI, Kroupina AY, Divashuk MG. Phenotypic effects of the dwarfing gene Rht-17 in spring durum wheat under two climatic conditions. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Alleles of the genes, conferring a dwarfing phenotype, play a crucial role in wheat breeding, as they not only reduce plant height, ensuring their resistance to lodging, but also have a number of positive and negative pleiotropic effects on plant productivity. Durum wheat carries only two subgenomes (A and B), which limits the use of the D-subgenome genes and requires the expansion of the arsenal of dwarfing alleles and the study of their effects on height and agronomically important traits. We studied the effect of the gibberellin-insensitive allele Rht-B1p in the B2F2:3 families, developed by crossing Chris Mutant /#517//LD222 in a field experiment in Moscow and Krasnodar. In our experiments, plants homozygous for Rht-B1p were shorter than those homozygous for the wild-type allele Rht-B1a by 36.3 cm (40 %) in Moscow and 49.5 cm (48 %) in Krasnodar. In the field experiment in Krasnodar, each plant with Rht-B1p had one less internode than any plant with Rht-B1a, which additionally contributed to the decrease in plant height. Grain weight per main spike was lower in plants with Rht-B1p than in plants with Rht-B1a by 12 % in Moscow and by 23 % in Krasnodar due to a decrease in 1000 grain weight in both regions of the field experiment. The number of grains per main spike in plants with Rht-B1p was higher in comparison to that with Rht-B1a by 6.5 % in Moscow due to an increase in spikelet number per main spike and by 11 % in Krasnodar due to an increase in grain number per spikelet. The onset of heading in plants with Rht-B1p in comparison with the plants with the wild-type allele Rht-B1a was 7 days later in Krasnodar. The possibility and prospects for the use of Rht-B1p in the breeding of durum wheat are discussed.
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Affiliation(s)
- A. G. Chernook
- All-Russian Research Institute of Agricultural Biotechnology, Laboratory of Applied Genomics and Crop Breeding; Russian State Agrarian University – Moscow Timiryazev Agricultural Academy, Centre for Molecular Biotechnology
| | - P. Yu. Kroupin
- All-Russian Research Institute of Agricultural Biotechnology, Laboratory of Applied Genomics and Crop Breeding; Russian State Agrarian University – Moscow Timiryazev Agricultural Academy, Centre for Molecular Biotechnology
| | | | | | | | - M. S. Bazhenov
- All-Russian Research Institute of Agricultural Biotechnology, Laboratory of Applied Genomics and Crop Breeding; Russian State Agrarian University – Moscow Timiryazev Agricultural Academy, Centre for Molecular Biotechnology
| | - L. A. Nazarova
- All-Russian Research Institute of Agricultural Biotechnology, Laboratory of Applied Genomics and Crop Breeding
| | - G. I. Karlov
- All-Russian Research Institute of Agricultural Biotechnology, Laboratory of Applied Genomics and Crop Breeding; Russian State Agrarian University – Moscow Timiryazev Agricultural Academy, Centre for Molecular Biotechnology
| | - A. Yu. Kroupina
- All-Russian Research Institute of Agricultural Biotechnology, Laboratory of Applied Genomics and Crop Breeding
| | - M. G. Divashuk
- All-Russian Research Institute of Agricultural Biotechnology, Laboratory of Applied Genomics and Crop Breeding; Russian State Agrarian University – Moscow Timiryazev Agricultural Academy, Centre for Molecular Biotechnology
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67
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Tshikunde NM, Mashilo J, Shimelis H, Odindo A. Agronomic and Physiological Traits, and Associated Quantitative Trait Loci (QTL) Affecting Yield Response in Wheat ( Triticum aestivum L.): A Review. FRONTIERS IN PLANT SCIENCE 2019; 10:1428. [PMID: 31749826 PMCID: PMC6848381 DOI: 10.3389/fpls.2019.01428] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/15/2019] [Indexed: 05/21/2023]
Abstract
Enhanced grain yield has been achieved in bread wheat (Triticum aestivum L.) through development and cultivation of superior genotypes incorporating yield-related agronomic and physiological traits derived from genetically diverse and complementary genetic pool. Despite significant breeding progress, yield levels in wheat have remained relatively low and stagnant under marginal growing environments. There is a need for genetic improvement of wheat using yield-promoting morpho-physiological attributes and desired genotypes under the target production environments to meet the demand for food and feed. This review presents breeding progress in wheat for yield gains using agronomic and physiological traits. Further, the paper discusses globally available wheat genetic resources to identify and select promising genotypes possessing useful agronomic and physiological traits to enhance water, nutrient-, and radiation-use efficiency to improve grain yield potential and tolerance to abiotic stresses (i.e. elevated CO2, high temperature, and drought stresses). Finally, the paper highlights quantitative trait loci (QTL) linked to agronomic and physiological traits to aid breeding of high-performing wheat genotypes.
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Affiliation(s)
- Nkhathutsheleni Maureen Tshikunde
- African Centre for Crop Improvement (ACCI), University of KwaZulu-Natal, Pietermaritzburg, South Africa
- School of Agricultural, Earth and Environmental Sciences, Discipline of Crop Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Jacob Mashilo
- African Centre for Crop Improvement (ACCI), University of KwaZulu-Natal, Pietermaritzburg, South Africa
- School of Agricultural, Earth and Environmental Sciences, Discipline of Crop Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Limpopo Department of Agriculture and Rural Development, Research Services, Towoomba Research Station, Bela-Bela, South Africa
| | - Hussein Shimelis
- African Centre for Crop Improvement (ACCI), University of KwaZulu-Natal, Pietermaritzburg, South Africa
- School of Agricultural, Earth and Environmental Sciences, Discipline of Crop Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Alfred Odindo
- School of Agricultural, Earth and Environmental Sciences, Discipline of Crop Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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68
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Michel S, Löschenberger F, Ametz C, Pachler B, Sparry E, Bürstmayr H. Combining grain yield, protein content and protein quality by multi-trait genomic selection in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2767-2780. [PMID: 31263910 PMCID: PMC6763414 DOI: 10.1007/s00122-019-03386-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/24/2019] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE Simultaneous genomic selection for grain yield, protein content and dough rheological traits enables the development of resource-use efficient varieties that combine superior yield potential with comparably high end-use quality. Selecting simultaneously for grain yield and baking quality is a major challenge in wheat breeding, and several concepts like grain protein deviations have been developed for shifting the undesirable negative correlation between both traits. The protein quality is, however, not considered in these concepts, although it is an important aspect and might facilitate the selection of genotypes that use available resources more efficiently with respect to the quantity and quality of the final end products. A population of 480 lines from an applied wheat breeding programme that was phenotyped for grain yield, protein content, protein yield and dough rheological traits was thus used to assess the potential of using integrated genomic selection indices to ease selection decisions with regard to the plethora of quality traits. Additionally, the feasibility of achieving a simultaneous genetic improvement in grain yield, protein content and protein quality was investigated to develop more resource-use efficient varieties. Dough rheological traits related to either gluten strength or viscosity were combined in two separate indices, both of which showed a substantially smaller negative trade-off with grain yield than the protein content. Genomic selection indices based on regression deviations for the two latter traits were subsequently extended by the gluten strength or viscosity indices. They revealed a large merit for identifying resource-use efficient genotypes that combine both superior yield potential with comparably high end-use quality. Hence, genomic selection opens up the opportunity for multi-trait selection in early generations, which will most likely increase the efficiency when developing new and improved varieties.
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Affiliation(s)
- Sebastian Michel
- Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria.
| | | | - Christian Ametz
- Saatzucht Donau GesmbH & CoKG, Saatzuchtstrasse 11, 2301, Probstdorf, Austria
| | - Bernadette Pachler
- Saatzucht Donau GesmbH & CoKG, Saatzuchtstrasse 11, 2301, Probstdorf, Austria
| | - Ellen Sparry
- C&M Seeds, 6180 5th Line, Palmerston, ON, N0G 2P0, Canada
| | - Hermann Bürstmayr
- Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
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69
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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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70
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Kuzay S, Xu Y, Zhang J, Katz A, Pearce S, Su Z, Fraser M, Anderson JA, Brown-Guedira G, DeWitt N, Peters Haugrud A, Faris JD, Akhunov E, Bai G, Dubcovsky J. Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2689-2705. [PMID: 31254024 PMCID: PMC6708044 DOI: 10.1007/s00122-019-03382-5] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/12/2019] [Accepted: 06/16/2019] [Indexed: 05/21/2023]
Abstract
A high-resolution genetic map combined with haplotype analyses identified a wheat ortholog of rice gene APO1 as the best candidate gene for a 7AL locus affecting spikelet number per spike. A better understanding of the genes controlling differences in wheat grain yield components can accelerate the improvements required to satisfy future food demands. In this study, we identified a promising candidate gene underlying a quantitative trait locus (QTL) on wheat chromosome arm 7AL regulating spikelet number per spike (SNS). We used large heterogeneous inbred families ( > 10,000 plants) from two crosses to map the 7AL QTL to an 87-kb region (674,019,191-674,106,327 bp, RefSeq v1.0) containing two complete and two partial genes. In this region, we found three major haplotypes that were designated as H1, H2 and H3. The H2 haplotype contributed the high-SNS allele in both H1 × H2 and H2 × H3 segregating populations. The ancestral H3 haplotype is frequent in wild emmer (48%) but rare (~ 1%) in cultivated wheats. By contrast, the H1 and H2 haplotypes became predominant in modern cultivated durum and common wheat, respectively. Among the four candidate genes, only TraesCS7A02G481600 showed a non-synonymous polymorphism that differentiated H2 from the other two haplotypes. This gene, designated here as WHEAT ORTHOLOG OF APO1 (WAPO1), is an ortholog of the rice gene ABERRANT PANICLE ORGANIZATION 1 (APO1), which affects spikelet number. Taken together, the high-resolution genetic map, the association between polymorphisms in the different mapping populations with differences in SNS, and the known role of orthologous genes in other grass species suggest that WAPO-A1 is the most likely candidate gene for the 7AL SNS QTL among the four genes identified in the candidate gene region.
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Affiliation(s)
- Saarah Kuzay
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yunfeng Xu
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Junli Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Andrew Katz
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Zhenqi Su
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Max Fraser
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Noah DeWitt
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | | | - Justin D Faris
- USDA-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA.
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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71
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Voss-Fels KP, Keeble-Gagnère G, Hickey LT, Tibbits J, Nagornyy S, Hayden MJ, Pasam RK, Kant S, Friedt W, Snowdon RJ, Appels R, Wittkop B. High-resolution mapping of rachis nodes per rachis, a critical determinant of grain yield components in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2707-2719. [PMID: 31254025 DOI: 10.1007/s00122-019-03383-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/16/2019] [Indexed: 05/23/2023]
Abstract
Exploring large genomic data sets based on the latest reference genome assembly identifies the rice ortholog APO1 as a key candidate gene for number of rachis nodes per spike in wheat. Increasing grain yield in wheat is a key breeding objective worldwide. Several component traits contribute to grain yield with spike attributes being among the most important. In this study, we performed a genome-wide association analysis for 12 grain yield and component traits measured in field trials with contrasting agrochemical input levels in a panel of 220 hexaploid winter wheats. A highly significant, environmentally consistent QTL was detected for number of rachis nodes per rachis (NRN) on chromosome 7AL. The five most significant SNPs formed a strong linkage disequilibrium (LD) block and tagged a 2.23 Mb region. Using pairwise LD for exome SNPs located across this interval in a large worldwide hexaploid wheat collection, we reduced the genomic region for NRN to a 258 Kb interval containing four of the original SNP and six high-confidence genes. The ortholog of one (TraesCS7A01G481600) of these genes in rice was ABBERANT PANICLE ORGANIZATION1 (APO1), which is known to have significant effects on panicle attributes. The APO1 ortholog was the best candidate for NRN and was associated with a 115 bp promoter deletion and two amino acid (C47F and D384 N) changes. Using a large worldwide collection of tetraploid and hexaploid wheat, we found 12 haplotypes for the NRN QTL and evidence for positive enrichment of two haplotypes in modern germplasm. Comparison of five QTL haplotypes in Australian yield trials revealed their relative, context-dependent contribution to grain yield. Our study provides diagnostic SNPs and value propositions to support deployment of the NRN trait in wheat breeding.
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Affiliation(s)
- Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Gabriel Keeble-Gagnère
- Agriculture Victoria Research, Department of Job, Precincts and Regions (DJPR), AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Josquin Tibbits
- Agriculture Victoria Research, Department of Job, Precincts and Regions (DJPR), AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Sergej Nagornyy
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Matthew J Hayden
- Agriculture Victoria Research, Department of Job, Precincts and Regions (DJPR), AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Raj K Pasam
- Agriculture Victoria Research, Department of Job, Precincts and Regions (DJPR), AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Surya Kant
- Agriculture Victoria Research, Department of Job, Precincts and Regions (DJPR), AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Wolfgang Friedt
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Rudi Appels
- Agriculture Victoria Research, Department of Job, Precincts and Regions (DJPR), AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
| | - Benjamin Wittkop
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
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72
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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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73
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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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74
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Rapp M, Sieber A, Kazman E, Leiser WL, Würschum T, Longin CFH. Evaluation of the genetic architecture and the potential of genomics-assisted breeding of quality traits in two large panels of durum wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1873-1886. [PMID: 30887094 DOI: 10.1007/s00122-019-03323-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
New QTL for important quality traits in durum were identified, but for most QTL their effect varies depending on the investigated germplasm. Most of the global durum wheat (Triticum turgidum ssp. durum) production is used for human consumption via pasta and to a lower extent couscous and bulgur. Therefore, durum wheat varieties have to fulfill high demands regarding quality traits. In this study, we evaluated the quality traits protein content, sedimentation volume, falling number, vitreousity and thousand kernel weight in a Central European (CP) and a Southern and Western European panel (SP) with 183 and 159 durum lines, respectively, and investigated their genetic architecture by genome-wide association mapping. Except for protein content, we identified QTL explaining a large proportion of the genotypic variance for different traits. However, most of them were identified only in one panel. Nevertheless, for sedimentation volume a genomic region on chromosome 1B appeared important in both durum panels and a BLAST search against the emmer and bread wheat reference genomes points toward the candidate gene Glu-B3. This was further supported by the protein subunit banding pattern via SDS-PAGE gel electrophoresis. For vitreousity, genomic regions on chromosome 7A explained a larger proportion of the genotypic variance in both panels, whereas one QTL, possibly related to the Pinb-2 locus, also slightly influenced the protein content. Within each panel, high prediction abilities for genomic selection were obtained, which, however, dropped considerably when predicting across both panels. Nevertheless, the across-panel prediction ability was still larger than 0.4 for protein content and sedimentation volume, underlining the potential for genomics-aided durum breeding, if laboratory and logistical facilities are available.
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Affiliation(s)
- M Rapp
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany
| | - A Sieber
- Wheat Initiative, 14195, Berlin, Germany
| | | | - Willmar L Leiser
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany
| | - T Würschum
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany
| | - C F H Longin
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany.
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75
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Desiderio F, Zarei L, Licciardello S, Cheghamirza K, Farshadfar E, Virzi N, Sciacca F, Bagnaresi P, Battaglia R, Guerra D, Palumbo M, Cattivelli L, Mazzucotelli E. Genomic Regions From an Iranian Landrace Increase Kernel Size in Durum Wheat. FRONTIERS IN PLANT SCIENCE 2019; 10:448. [PMID: 31057571 PMCID: PMC6482228 DOI: 10.3389/fpls.2019.00448] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/25/2019] [Indexed: 05/27/2023]
Abstract
Kernel size and shape are important parameters determining the wheat profitability, being main determinants of yield and its technological quality. In this study, a segregating population of 118 recombinant inbred lines, derived from a cross between the Iranian durum landrace accession "Iran_249" and the Iranian durum cultivar "Zardak", was used to investigate durum wheat kernel morphology factors and their relationships with kernel weight, and to map the corresponding QTLs. A high density genetic map, based on wheat 90k iSelect Infinium SNP assay, comprising 6,195 markers, was developed and used to perform the QTL analysis for kernel length and width, traits related to kernel shape and weight, and heading date, using phenotypic data from three environments. Overall, a total of 31 different QTLs and 9 QTL interactions for kernel size, and 21 different QTLs and 5 QTL interactions for kernel shape were identified. The landrace Iran_249 contributed the allele with positive effect for most of the QTLs related to kernel length and kernel weight suggesting that the landrace might have considerable potential toward enhancing the existing gene pool for grain shape and size traits and for further yield improvement in wheat. The correlation among traits and co-localization of corresponding QTLs permitted to define 11 clusters suggesting causal relationships between simplest kernel size trait, like kernel length and width, and more complex secondary trait, like kernel shape and weight related traits. Lastly, the recent release of the T. durum reference genome sequence allowed to define the physical interval of our QTL/clusters and to hypothesize novel candidate genes inspecting the gene content of the genomic regions associated to target traits.
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Affiliation(s)
- Francesca Desiderio
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Leila Zarei
- Department of Agronomy and Plant Breeding, Razi University, Kermanshah, Iran
| | - Stefania Licciardello
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | | | | | - Nino Virzi
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | - Fabiola Sciacca
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Raffaella Battaglia
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Davide Guerra
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Massimo Palumbo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
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76
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Shirley NJ, Aubert MK, Wilkinson LG, Bird DC, Lora J, Yang X, Tucker MR. Translating auxin responses into ovules, seeds and yield: Insight from Arabidopsis and the cereals. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:310-336. [PMID: 30474296 DOI: 10.1111/jipb.12747] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/16/2018] [Indexed: 05/27/2023]
Abstract
Grain production in cereal crops depends on the stable formation of male and female gametes in the flower. In most angiosperms, the female gamete is produced from a germline located deep within the ovary, protected by several layers of maternal tissue, including the ovary wall, ovule integuments and nucellus. In the field, germline formation and floret fertility are major determinants of yield potential, contributing to traits such as seed number, weight and size. As such, stimuli affecting the timing and duration of reproductive phases, as well as the viability, size and number of cells within reproductive organs can significantly impact yield. One key stimulant is the phytohormone auxin, which influences growth and morphogenesis of female tissues during gynoecium development, gametophyte formation, and endosperm cellularization. In this review we consider the role of the auxin signaling pathway during ovule and seed development, first in the context of Arabidopsis and then in the cereals. We summarize the gene families involved and highlight distinct expression patterns that suggest a range of roles in reproductive cell specification and fate. This is discussed in terms of seed production and how targeted modification of different tissues might facilitate improvements.
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Affiliation(s)
- Neil J Shirley
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Matthew K Aubert
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Laura G Wilkinson
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Dayton C Bird
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Jorge Lora
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Xiujuan Yang
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Matthew R Tucker
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
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77
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Lichthardt C, Chen TW, Stahl A, Stützel H. Co-Evolution of Sink and Source in the Recent Breeding History of Winter Wheat in Germany. FRONTIERS IN PLANT SCIENCE 2019. [PMID: 32117340 DOI: 10.3389/fpls.2019.0177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Optimizing the interplay between sinks and sources is of crucial importance for breeding progress in winter wheat. However, the physiological limitations of yield from source (e.g. green canopy duration, GCD) and sink (e.g. grain number) are still unclear. Furthermore, there is little information on how the source traits have been modified during the breeding history of winter wheat. This study analyzed the breeding progress of sink and source components and their relationships to yield components. Field trials were conducted over three years with 220 cultivars representing the German breeding history of the past five decades. In addition, genetic associations of QTL for the traits were assessed with genome-wide association studies. Breeding progress mainly resulted from an increase in grain numbers per spike, a sink component, whose variations were largely explained by the photosynthetic activity around anthesis, a source component. Surprisingly, despite significant breeding progress in GCD and other source components, they showed no direct influence on thousand grain weights, indicating that grain filling was not limited by the source strength. Our results suggest that, 1) the potential longevity of the green canopy is predetermined at the time point that the number of grains is fixed; 2) a co-evolution of source and sink strength during the breeding history contribute to the yield formation of the modern cultivars. For future breeding we suggest to choose parental lines with high grain numbers per spike on the sink side, and high photosynthetic activity around anthesis and canopy duration on the source side, and to place emphasis on these traits throughout selection.
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Affiliation(s)
- Carolin Lichthardt
- Vegetable Systems Modelling Section, Institute of Horticultural Production Systems, University of Hannover, Hannover, Germany
| | - Tsu-Wei Chen
- Vegetable Systems Modelling Section, Institute of Horticultural Production Systems, University of Hannover, Hannover, Germany
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Hartmut Stützel
- Vegetable Systems Modelling Section, Institute of Horticultural Production Systems, University of Hannover, Hannover, Germany
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78
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Michel S, Löschenberger F, Hellinger J, Strasser V, Ametz C, Pachler B, Sparry E, Bürstmayr H. Improving and Maintaining Winter Hardiness and Frost Tolerance in Bread Wheat by Genomic Selection. FRONTIERS IN PLANT SCIENCE 2019; 10:1195. [PMID: 31632427 PMCID: PMC6781858 DOI: 10.3389/fpls.2019.01195] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/30/2019] [Indexed: 05/18/2023]
Abstract
Winter hardiness is a major constraint for autumn sown crops in temperate regions, and thus an important breeding goal in the development of new winter wheat varieties. Winter hardiness is though influenced by many environmental factors rendering phenotypic selection under field conditions a difficult task due to irregular occurrence or absence of winter damage in field trials. Controlled frost tolerance tests in growth chamber experiments are, on the other hand, even with few genotypes, often costly and laborious, which makes a genomic breeding strategy for early generation selection an attractive alternative. The aims of this study were thus to compare the merit of marker-assisted selection using the major frost tolerance QTL Fr-A2 with genomic prediction for winter hardiness and frost tolerance, and to assess the potential of combining both measures with a genomic selection index using a high density marker map or a reduced set of pre-selected markers. Cross-validation within two training populations phenotyped for frost tolerance and winter hardiness underpinned the importance of Fr-A2 for frost tolerance especially when upweighting its effect in genomic prediction models, while a combined genomic selection index increased the prediction accuracy for an independent validation population in comparison to training with winter hardiness data alone. The prediction accuracy could moreover be maintained with pre-selected marker sets, which is highly relevant when employing cost reducing fingerprinting techniques such as targeted genotyping-by-sequencing. Genomic selection showed thus large potential to improve or maintain the performance of winter wheat for these difficult, costly, and laborious to phenotype traits.
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Affiliation(s)
- Sebastian Michel
- Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Tulln, Austria
- *Correspondence: Sebastian Michel,
| | | | - Jakob Hellinger
- Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Tulln, Austria
| | - Verena Strasser
- Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Tulln, Austria
| | | | | | | | - Hermann Bürstmayr
- Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Tulln, Austria
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