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Calderón-González Á, Pérez-Vich B, Pouilly N, Boniface MC, Louarn J, Velasco L, Muños S. Association mapping for broomrape resistance in sunflower. FRONTIERS IN PLANT SCIENCE 2023; 13:1056231. [PMID: 36714707 PMCID: PMC9875907 DOI: 10.3389/fpls.2022.1056231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Sunflower breeding for resistance to the parasitic plant sunflower broomrape (Orobanche cumana Wallr.) requires the identification of novel resistance genes. In this research, we conducted a genome-wide association study (GWAS) to identify QTLs associated with broomrape resistance. METHODS The marker-trait associations were examined across a germplasm set composed of 104 sunflower accessions. They were genotyped with a 600k AXIOM® genome-wide array and evaluated for resistance to three populations of the parasite with varying levels of virulence (races EFR, FGV, and GTK) in two environments. RESULTS AND DISCUSSION The analysis of the genetic structure of the germplasm set revealed the presence of two main groups. The application of optimized treatments based on the general linear model (GLM) and the mixed linear model (MLM) allowed the detection of 14 SNP markers significantly associated with broomrape resistance. The highest number of marker-trait associations were identified on chromosome 3, clustered in two different genomic regions of this chromosome. Other associations were identified on chromosomes 5, 10, 13, and 16. Candidate genes for the main genomic regions associated with broomrape resistance were studied and discussed. Particularly, two significant SNPs on chromosome 3 associated with races EFR and FGV were found at two tightly linked SWEET sugar transporter genes. The results of this study have confirmed the role of some QTL on resistance to sunflower broomrape and have revealed new ones that may play an important role in the development of durable resistance to this parasitic weed in sunflower.
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Affiliation(s)
- Álvaro Calderón-González
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
| | - Begoña Pérez-Vich
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
| | - Nicolas Pouilly
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
| | - Marie-Claude Boniface
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
| | - Johann Louarn
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
| | - Leonardo Velasco
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
| | - Stéphane Muños
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
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Bercovich N, Genze N, Todesco M, Owens GL, Légaré JS, Huang K, Rieseberg LH, Grimm DG. HeliantHOME, a public and centralized database of phenotypic sunflower data. Sci Data 2022; 9:735. [PMID: 36450875 PMCID: PMC9712528 DOI: 10.1038/s41597-022-01842-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 11/11/2022] [Indexed: 12/02/2022] Open
Abstract
Genomic studies often attempt to link natural genetic variation with important phenotypic variation. To succeed, robust and reliable phenotypic data, as well as curated genomic assemblies, are required. Wild sunflowers, originally from North America, are adapted to diverse and often extreme environments and have historically been a widely used model plant system for the study of population genomics, adaptation, and speciation. Moreover, cultivated sunflower, domesticated from a wild relative (Helianthus annuus) is a global oil crop, ranking fourth in production of vegetable oils worldwide. Public availability of data resources both for the plant research community and for the associated agricultural sector, are extremely valuable. We have created HeliantHOME ( http://www.helianthome.org ), a curated, public, and interactive database of phenotypes including developmental, structural and environmental ones, obtained from a large collection of both wild and cultivated sunflower individuals. Additionally, the database is enriched with external genomic data and results of genome-wide association studies. Finally, being a community open-source platform, HeliantHOME is expected to expand as new knowledge and resources become available.
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Affiliation(s)
- Natalia Bercovich
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Nikita Genze
- grid.6936.a0000000123222966Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany ,grid.4819.40000 0001 0704 7467Weihenstephan-Triesdorf University of Applied Sciences, Straubing, Germany
| | - Marco Todesco
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Gregory L. Owens
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada ,grid.143640.40000 0004 1936 9465Department of Biology, University of Victoria, Victoria, BC Canada
| | - Jean-Sébastien Légaré
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada ,grid.17091.3e0000 0001 2288 9830Department of Computer Science, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Data Science Institute, University of British Columbia, Vancouver, British Columbia Canada
| | - Kaichi Huang
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Loren H. Rieseberg
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Dominik G. Grimm
- grid.6936.a0000000123222966Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany ,grid.4819.40000 0001 0704 7467Weihenstephan-Triesdorf University of Applied Sciences, Straubing, Germany ,grid.6936.a0000000123222966Technical University of Munich, Department of Informatics, Garching, Germany
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Lee JS, Jahani M, Huang K, Mandel JR, Marek LF, Burke JM, Langlade NB, Owens GL, Rieseberg LH. Expression complementation of gene presence/absence polymorphisms in hybrids contributes importantly to heterosis in sunflower. J Adv Res 2022; 42:83-98. [PMID: 36513422 PMCID: PMC9788961 DOI: 10.1016/j.jare.2022.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/01/2022] [Accepted: 04/16/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Numerous crops have transitioned to hybrid seed production to increase yields and yield stability through heterosis. However, the molecular mechanisms underlying heterosis and its stability across environments are not yet fully understood. OBJECTIVES This study aimed to (1) elucidate the genetic and molecular mechanisms underlying heterosis in sunflower, and (2) determine how heterosis is maintained under different environments. METHODS Genome-wide association (GWA) analyses were employed to assess the effects of presence/absence variants (PAVs) and stop codons on 16 traits phenotyped in the sunflower association mapping population at three locations. To link the GWA results to transcriptomic variation, we sequenced the transcriptomes of two sunflower cultivars and their F1 hybrid (INEDI) under both control and drought conditions and analyzed patterns of gene expression and alternative splicing. RESULTS Thousands of PAVs were found to affect phenotypic variation using a relaxed significance threshold, and at most such loci the "absence" allele reduced values of heterotic traits, but not those of non-heterotic traits. This pattern was strengthened for PAVs that showed expression complementation in INEDI. Stop codons were much rarer than PAVs and less likely to reduce heterotic trait values. Hybrid expression patterns were enriched for the GO category, sensitivity to stimulus, but all genotypes responded to drought similarily - by up-regulating water stress response pathways and down-regulating metabolic pathways. Changes in alternative splicing were strongly negatively correlated with expression variation, implying that alternative splicing in this system largely acts to reinforce expression responses. CONCLUSION Our results imply that complementation of expression of PAVs in hybrids is a major contributor to heterosis in sunflower, consistent with the dominance model of heterosis. This mechanism can account for yield stability across different environments. Moreover, given the much larger numbers of PAVs in plant vs. animal genomes, it also offers an explanation for the stronger heterotic responses seen in the former.
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Affiliation(s)
- Joon Seon Lee
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Mojtaba Jahani
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jennifer R. Mandel
- Department of Biological Sciences and Center for Biodiversity, University of Memphis, Memphis, TN 38152, USA
| | - Laura F. Marek
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - John M. Burke
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens 30602, Georgia
| | | | - Gregory L. Owens
- Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada,Corresponding author.
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Stahlhut KN, Dowell JA, Temme AA, Burke JM, Goolsby EW, Mason CM. Genetic control of arbuscular mycorrhizal colonization by Rhizophagus intraradices in Helianthus annuus (L.). MYCORRHIZA 2021; 31:723-734. [PMID: 34480215 DOI: 10.1007/s00572-021-01050-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Plant symbiosis with arbuscular mycorrhizal (AM) fungi provides many benefits, including increased nutrient uptake, drought tolerance, and belowground pathogen resistance. To develop a better understanding of the genetic architecture of mycorrhizal symbiosis, we conducted a genome-wide association study (GWAS) of this plant-fungal interaction in cultivated sunflower. A diversity panel of cultivated sunflower (Helianthus annuus L.) was phenotyped for root colonization under inoculation with the AM fungus Rhizophagus intraradices. Using a mixed linear model approach with a high-density genetic map, we identified genomic regions that are likely associated with R. intraradices colonization in sunflower. Additionally, we used a set of twelve diverse lines to assess the effect that inoculation with R. intraradices has on dried shoot biomass and macronutrient uptake. Colonization among lines in the mapping panel ranged from 0-70% and was not correlated with mycorrhizal growth response, shoot phosphorus response, or shoot potassium response among the Core 12 lines. Association mapping yielded three single-nucleotide polymorphisms (SNPs) that were significantly associated with R. intraradices colonization. This is the first study to use GWAS to identify genomic regions associated with AM colonization in an Asterid eudicot species. Three genes of interest identified from the regions containing these SNPs are likely related to plant defense.
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Affiliation(s)
| | - Jordan A Dowell
- Department of Biology, University of Central Florida, Orlando, FL, 32816, USA
| | - Andries A Temme
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - John M Burke
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Eric W Goolsby
- Department of Biology, University of Central Florida, Orlando, FL, 32816, USA
| | - Chase M Mason
- Department of Biology, University of Central Florida, Orlando, FL, 32816, USA.
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5
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Chernova AI, Gubaev RF, Singh A, Sherbina K, Goryunova SV, Martynova EU, Goryunov DV, Boldyrev SV, Vanyushkina AA, Anikanov NA, Stekolshchikova EA, Yushina EA, Demurin YN, Mukhina ZM, Gavrilova VA, Anisimova IN, Karabitsina YI, Alpatieva NV, Chang PL, Khaitovich P, Mazin PV, Nuzhdin SV. Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content. BMC Genomics 2021; 22:505. [PMID: 34225652 PMCID: PMC8256595 DOI: 10.1186/s12864-021-07768-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 06/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sunflower is an important oilseed crop domesticated in North America approximately 4000 years ago. During the last century, oil content in sunflower was under strong selection. Further improvement of oil properties achieved by modulating its fatty acid composition is one of the main directions in modern oilseed crop breeding. RESULTS We searched for the genetic basis of fatty acid content variation by genotyping 601 inbred sunflower lines and assessing their lipid and fatty acid composition. Our genome-wide association analysis based on the genotypes for 15,483 SNPs and the concentrations of 23 fatty acids, including minor fatty acids, revealed significant genetic associations for eleven of them. Identified genomic regions included the loci involved in rare fatty acids variation on chromosomes 3 and 14, explaining up to 34.5% of the total variation of docosanoic acid (22:0) in sunflower oil. CONCLUSIONS This is the first large scale implementation of high-throughput lipidomic profiling to sunflower germplasm characterization. This study contributes to the genetic characterization of Russian sunflower collections, which made a substantial contribution to the development of sunflower as the oilseed crop worldwide, and provides new insights into the genetic control of oil composition that can be implemented in future studies.
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Affiliation(s)
- Alina I Chernova
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia. .,LLC "OIL GENE", Skolkovo Innovation Center, Moscow, Russia.
| | - Rim F Gubaev
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,LLC "OIL GENE", Skolkovo Innovation Center, Moscow, Russia
| | - Anupam Singh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Katrina Sherbina
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Svetlana V Goryunova
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin st. 3, Moscow, 119991, Russia.,FSBSI Lorch Potato Research Institute, Lorkha Str. 23, Kraskovo, 140051, Russia
| | - Elena U Martynova
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Denis V Goryunov
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,MSU A.N. Belozersky Institute of Physico-Chemical Biology, Leninsky Gori 1, Building 40, Moscow, 119992, Russia
| | - Stepan V Boldyrev
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,LLC "OIL GENE", Skolkovo Innovation Center, Moscow, Russia
| | - Anna A Vanyushkina
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Nikolay A Anikanov
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Elena A Stekolshchikova
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Ekaterina A Yushina
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,FSBSI N P Bochkov Research Center of Medical Genetics, Moskvorechye St.1, Moscow, 115522, Russia
| | - Yakov N Demurin
- Pustovoit All-Russia Research Institute of Oilseed Crops, Filatova St. 17, Krasnodar, 350038, Russia
| | | | - Vera A Gavrilova
- N. I. Vavilov Research Institute of Plant Genetic Resources (VIR), 42 B. Morskaja, St. Petersburg, 190000, Russia
| | - Irina N Anisimova
- N. I. Vavilov Research Institute of Plant Genetic Resources (VIR), 42 B. Morskaja, St. Petersburg, 190000, Russia
| | - Yulia I Karabitsina
- N. I. Vavilov Research Institute of Plant Genetic Resources (VIR), 42 B. Morskaja, St. Petersburg, 190000, Russia
| | - Natalia V Alpatieva
- N. I. Vavilov Research Institute of Plant Genetic Resources (VIR), 42 B. Morskaja, St. Petersburg, 190000, Russia
| | - Peter L Chang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Pavel V Mazin
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
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Xu P, Guo Q, Meng S, Zhang X, Xu Z, Guo W, Shen X. Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum. BMC Genomics 2021; 22:26. [PMID: 33407102 PMCID: PMC7789578 DOI: 10.1186/s12864-020-07321-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 12/10/2020] [Indexed: 12/12/2022] Open
Abstract
Background Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect its growth and development significantly. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance. Results In this study, a genome-wide association study (GWAS) of salt tolerance related traits at seedling stage was performed based on 2 years of phenotype identification for 217 representative upland cotton cultivars by genotyping-by-sequencing (GBS) platform. A total of 51,060 single nucleotide polymorphisms (SNPs) unevenly distributed among 26 chromosomes were screened across the cotton cultivars, and 25 associations with 27 SNPs scattered over 12 chromosomes were detected significantly (−log10p > 4) associated with three salt tolerance related traits in 2016 and 2017. Among these, the associations on chromosome A13 and D08 for relative plant height (RPH), A07 for relative shoot fresh matter weight (RSFW), A08 and A13 for relative shoot dry matter weight (RSDW) were expressed in both environments, indicating that they were likely to be stable quantitative trait loci (QTLs). A total of 12 salt-induced candidate genes were identified differentially expressed by the combination of GWAS and transcriptome analysis. Three promising genes were selected for preliminary function verification of salt tolerance. The increase of GH_A13G0171-silenced plants in salt related traits under salt stress indicated its negative function in regulating the salt stress response. Conclusions These results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton.
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Affiliation(s)
- Peng Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.,Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China
| | - Qi Guo
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China
| | - Shan Meng
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China
| | - Xianggui Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China
| | - Zhenzhen Xu
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Xinlian Shen
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China.
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7
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Xu P, Guo Q, Meng S, Zhang X, Xu Z, Guo W, Shen X. Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum. BMC Genomics 2021; 22:26. [PMID: 33407102 DOI: 10.21203/rs.3.rs-66236/v4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 12/10/2020] [Indexed: 05/29/2023] Open
Abstract
BACKGROUND Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect its growth and development significantly. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance. RESULTS In this study, a genome-wide association study (GWAS) of salt tolerance related traits at seedling stage was performed based on 2 years of phenotype identification for 217 representative upland cotton cultivars by genotyping-by-sequencing (GBS) platform. A total of 51,060 single nucleotide polymorphisms (SNPs) unevenly distributed among 26 chromosomes were screened across the cotton cultivars, and 25 associations with 27 SNPs scattered over 12 chromosomes were detected significantly (-log10p > 4) associated with three salt tolerance related traits in 2016 and 2017. Among these, the associations on chromosome A13 and D08 for relative plant height (RPH), A07 for relative shoot fresh matter weight (RSFW), A08 and A13 for relative shoot dry matter weight (RSDW) were expressed in both environments, indicating that they were likely to be stable quantitative trait loci (QTLs). A total of 12 salt-induced candidate genes were identified differentially expressed by the combination of GWAS and transcriptome analysis. Three promising genes were selected for preliminary function verification of salt tolerance. The increase of GH_A13G0171-silenced plants in salt related traits under salt stress indicated its negative function in regulating the salt stress response. CONCLUSIONS These results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton.
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Affiliation(s)
- Peng Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China
| | - Qi Guo
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China
| | - Shan Meng
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China
| | - Xianggui Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China
| | - Zhenzhen Xu
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Xinlian Shen
- Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China.
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8
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Wang Y, Donovan LA, Temme AA. Plasticity and the role of mass-scaling in allocation, morphology, and anatomical trait responses to above- and belowground resource limitation in cultivated sunflower ( Helianthus annuus L.). PLANT DIRECT 2020; 4:e00274. [PMID: 33103045 PMCID: PMC7576876 DOI: 10.1002/pld3.274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 06/03/2020] [Accepted: 09/12/2020] [Indexed: 06/11/2023]
Abstract
In the face of resource limitations, plants show plasticity in multiple trait categories, including biomass allocation, morphology, and anatomy, yet inevitably also grow less. The extent to which passive mass-scaling plays a role in trait responses that contribute to increased potential for resource acquisition is poorly understood. Here, we assessed the role of mass-scaling on the direction, magnitude, and coordination of trait plasticity to light and/or nutrient limitation in cultivated sunflower (Helianthus annuus). We grew seedlings of 10 sunflower genotypes for 3 weeks in a factorial of light (50% shade) and nutrient (10% supply) limitation in the greenhouse and measured a suite of allocational, morphological, and anatomical traits for leaves, stems, fine roots, and tap roots. Under resource limitation, plants were smaller and more biomass was allocated to the organ capturing the most limiting resource, as expected. Traits varied in the magnitude of plasticity and the extent to which the observed response was passive (scaled with plant mass) and/or had an additional active component. None of the allocational responses were primarily passive. Plastic changes to specific leaf area and specific root length were primarily active, and adjusted toward more acquisitive trait values under light and nutrient limitation, respectively. For many traits, the observed response was a mixture of active and passive components, and for some traits, the active adjustment was antagonistic to the direction of passive adjustment, for example, stem height, and tap root and stem theoretical hydraulic conductance. Passive scaling with size played a major role in the coordinated response to light, but correcting for mass clarified that the active responses to both limitations were more similar in magnitude, although still resource and organ specific. Our results demonstrate that both passive plasticity and active plasticity can contribute to increased uptake capacity for limiting resources in a manner that is resource, organ, and trait specific. Indeed, passive adjustments (scaling with mass) of traits due to resource stress extend well beyond just mass allocation traits. For a full understanding of plants' response to environmental stress, both passive and active plasticity need to be taken into account.
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Affiliation(s)
- Yan Wang
- College of ForestryShandong Agriculture UniversityTaianShandongChina
- Department of Plant BiologyFranklin College of Arts and SciencesThe University of GeorgiaAthensGAUSA
| | - Lisa A. Donovan
- Department of Plant BiologyFranklin College of Arts and SciencesThe University of GeorgiaAthensGAUSA
| | - Andries A. Temme
- Department of Plant BiologyFranklin College of Arts and SciencesThe University of GeorgiaAthensGAUSA
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Filippi CV, Zubrzycki JE, Di Rienzo JA, Quiroz FJ, Puebla AF, Alvarez D, Maringolo CA, Escande AR, Hopp HE, Heinz RA, Paniego NB, Lia VV. Unveiling the genetic basis of Sclerotinia head rot resistance in sunflower. BMC PLANT BIOLOGY 2020; 20:322. [PMID: 32641108 PMCID: PMC7346337 DOI: 10.1186/s12870-020-02529-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 06/26/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Sclerotinia sclerotiorum is a necrotrophic fungus that causes Sclerotinia head rot (SHR) in sunflower, with epidemics leading to severe yield losses. In this work, we present an association mapping (AM) approach to investigate the genetic basis of natural resistance to SHR in cultivated sunflower, the fourth most widely grown oilseed crop in the world. RESULTS Our association mapping population (AMP), which comprises 135 inbred breeding lines (ILs), was genotyped using 27 candidate genes, a panel of 9 Simple Sequence Repeat (SSR) markers previously associated with SHR resistance via bi-parental mapping, and a set of 384 SNPs located in genes with molecular functions related to stress responses. Moreover, given the complexity of the trait, we evaluated four disease descriptors (i.e, disease incidence, disease severity, area under the disease progress curve for disease incidence, and incubation period). As a result, this work constitutes the most exhaustive AM study of disease resistance in sunflower performed to date. Mixed linear models accounting for population structure and kinship relatedness were used for the statistical analysis of phenotype-genotype associations, allowing the identification of 13 markers associated with disease reduction. The number of favourable alleles was negatively correlated to disease incidence, disease severity and area under the disease progress curve for disease incidence, whereas it was positevily correlated to the incubation period. CONCLUSIONS Four of the markers identified here as associated with SHR resistance (HA1848, HaCOI_1, G33 and G34) validate previous research, while other four novel markers (SNP117, SNP136, SNP44, SNP128) were consistently associated with SHR resistance, emerging as promising candidates for marker-assisted breeding. From the germplasm point of view, the five ILs carrying the largest combination of resistance alleles provide a valuable resource for sunflower breeding programs worldwide.
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Affiliation(s)
- C V Filippi
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - J E Zubrzycki
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- Present address: Biocódices, San Martín, Buenos Aires, Argentina
| | - J A Di Rienzo
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Ing Agr. Felix Aldo Marrone 746 (5000), Córdoba, Argentina
| | - F J Quiroz
- Estación Experimental Agropecuaria INTA Balcarce, Ruta 226 Km 73.5 (7620), Balcarce, Buenos Aires, Argentina
| | - A F Puebla
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
| | - D Alvarez
- Estación Experimental Agropecuaria INTA Manfredi, Ruta 9 Km 636 (5988), Manfredi, Córdoba, Argentina
| | - C A Maringolo
- Estación Experimental Agropecuaria INTA Balcarce, Ruta 226 Km 73.5 (7620), Balcarce, Buenos Aires, Argentina
| | - A R Escande
- Estación Experimental Agropecuaria INTA Balcarce, Ruta 226 Km 73.5 (7620), Balcarce, Buenos Aires, Argentina
| | - H E Hopp
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires, Intendente Güiraldes 2160, (1428), Ciudad Autónoma de Buenos Aires, Argentina
| | - R A Heinz
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires, Intendente Güiraldes 2160, (1428), Ciudad Autónoma de Buenos Aires, Argentina
| | - N B Paniego
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - V V Lia
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Ciudad Autónoma de Buenos Aires, Argentina.
- Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires, Intendente Güiraldes 2160, (1428), Ciudad Autónoma de Buenos Aires, Argentina.
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10
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Asselin SR, Brûlé-Babel AL, Van Tassel DL, Cattani DJ. Genetic Analysis of Domestication Parallels in Annual and Perennial Sunflowers ( Helianthus spp.): Routes to Crop Development. FRONTIERS IN PLANT SCIENCE 2020; 11:834. [PMID: 32595690 PMCID: PMC7304338 DOI: 10.3389/fpls.2020.00834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
Parallels exist between the domestication of new species and the improvement of various crops through selection on traits which favor the sowing, harvest and retention of yield potential and the directed efforts to improve their agronomics, disease resistance and quality characteristics. Common selection pressures may result in the parallel selection of orthologs underlying these traits and homologies between crop species can be exploited by plant breeders to improve germplasm. Perennial grains and oilseeds are a class of proposed crops for improving the diversity and sustainability of agricultural systems. Maximilian sunflower (Helianthus maximiliani Schrad.) is a perennial crop wild relative of sunflower (Helianthus annuus L.) and a candidate perennial oilseed species. Understanding parallels between cultivated H. annuus and H. maximiliani may provide new tools for the development of Maximilian sunflower and other wild relatives of sunflower as crops to enhance functional diversity in cropping systems. F2 populations of Maximilian sunflower segregating for traits associated with the domestication ideotype of cultivated sunflower including branching architecture, capitulum morphology and flowering time were developed to investigate parallels between H. maximiliani and H. annuus. Genotype-by-sequencing (GBS) was employed to genotype novel Maximilian sunflower populations and perform quantitative-trait-loci (QTL) analysis. A total of 11 QTL in five regions were identified across 21 linkage groups using 4142 GBS derived single nucleotide polymorphism markers called using the sunflower reference genome as a guide. A major QTL on linkage group 17b, associated with aspects of floral development and apical dominance, was discovered and corresponds with a known domestication QTL hotspot in H. annuus and candidate genes were identified. This suggests the potential to exploit orthologs for neo-domestication of H. maximiliani for traits such as branching architecture, timing of anthesis, and capitulum size and morphology for the development of a perennial oilseed crop from wild relatives of cultivated sunflower.
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Affiliation(s)
- Sean R. Asselin
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | | | | | - Douglas J. Cattani
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
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11
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Inheritance and molecular mapping of powdery mildew ( Golovinomyces orontii) resistance gene(s) in sunflower ( Helianthus annuus L.). 3 Biotech 2020; 10:234. [PMID: 32399384 DOI: 10.1007/s13205-020-02224-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/24/2020] [Indexed: 10/24/2022] Open
Abstract
Sources of resistance to powdery mildew incited by Golovinomyces orontii have been identified in wild sunflowers and few exotic lines. The present investigation has been undertaken to study the inheritance of powdery mildew resistance and to map the quantitative trait loci (QTLs) governing resistance to powdery mildew in a multiple disease resistance line, TX16R (PI 642072). The inheritance was observed as a continuous distribution in a set of 264 F2 population and 93 recombinant inbred lines (RILs) of a cross between a highly susceptible accession PS 2023 and TX16R. Screening of the two population sets was done with 484 sunflower-specific SSR primers of which 175 primers showed polymorphism between the parents. Based on the phenotyping and genotyping data, the linkage map was constructed with 93 RILs. The map spanned 1200 cM and included 64 markers distributed along the 17 sunflower chromosomes in the haploid set. Quantitative trait loci (QTL) analysis identified three genomic regions for resistance to powdery mildew, two of which mapped on chromosome 10 and one on chromosome 5. This is the first report on mapping of powdery mildew resistance in sunflower and paves the way in fine mapping and introgression of resistance for powdery mildew in sunflower through marker-assisted breeding.
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12
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Filippi CV, Merino GA, Montecchia JF, Aguirre NC, Rivarola M, Naamati G, Fass MI, Álvarez D, Di Rienzo J, Heinz RA, Contreras Moreira B, Lia VV, Paniego NB. Genetic Diversity, Population Structure and Linkage Disequilibrium Assessment among International Sunflower Breeding Collections. Genes (Basel) 2020; 11:E283. [PMID: 32155892 PMCID: PMC7140877 DOI: 10.3390/genes11030283] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/01/2020] [Accepted: 03/03/2020] [Indexed: 12/20/2022] Open
Abstract
Sunflower germplasm collections are valuable resources for broadening the genetic base of commercial hybrids and ameliorate the risk of climate events. Nowadays, the most studied worldwide sunflower pre-breeding collections belong to INTA (Argentina), INRA (France), and USDA-UBC (United States of America-Canada). In this work, we assess the amount and distribution of genetic diversity (GD) available within and between these collections to estimate the distribution pattern of global diversity. A mixed genotyping strategy was implemented, by combining proprietary genotyping-by-sequencing data with public whole-genome-sequencing data, to generate an integrative 11,834-common single nucleotide polymorphism matrix including the three breeding collections. In general, the GD estimates obtained were moderate. An analysis of molecular variance provided evidence of population structure between breeding collections. However, the optimal number of subpopulations, studied via discriminant analysis of principal components (K = 12), the bayesian STRUCTURE algorithm (K = 6) and distance-based methods (K = 9) remains unclear, since no single unifying characteristic is apparent for any of the inferred groups. Different overall patterns of linkage disequilibrium (LD) were observed across chromosomes, with Chr10, Chr17, Chr5, and Chr2 showing the highest LD. This work represents the largest and most comprehensive inter-breeding collection analysis of genomic diversity for cultivated sunflower conducted to date.
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Affiliation(s)
- Carla V. Filippi
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
- Programa Académico para la Investigación e Innovación en Biotecnología, Universidad Nacional de Moreno–UNM, Moreno 1744, Argentina
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gabriela A. Merino
- Instituto de Investigación y Desarrollo en Bioingeniería y Bioinformática–IBB, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Entre Ríos, Oro Verde 3100, Argentina
- Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional-sinc(i), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Juan F. Montecchia
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Natalia C. Aguirre
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Máximo Rivarola
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mónica I. Fass
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Daniel Álvarez
- Estación Experimental Agropecuaria INTA Manfredi, Manfredi 5988, Argentina
| | - Julio Di Rienzo
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Ruth A. Heinz
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Bruno Contreras Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Verónica V. Lia
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Norma B. Paniego
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
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13
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Reinert S, Gao Q, Ferguson B, Portlas ZM, Prasifka JR, Hulke BS. Seed and floret size parameters of sunflower are determined by partially overlapping sets of quantitative trait loci with epistatic interactions. Mol Genet Genomics 2019; 295:143-154. [PMID: 31559504 DOI: 10.1007/s00438-019-01610-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 09/10/2019] [Indexed: 11/26/2022]
Abstract
KEY MESSAGE Floret and seed traits are moderately correlated phenotypically in modern sunflower cultivars, but the underlying genetics are mostly independent. Seed traits in particular are governed in part by epistatic effects among quantitative trait loci. Seed size is an important quality component in marketing commercial sunflower (Helianthus annuus L.), particularly for the in-shell confectionery market, where long and broad seed types are preferred as a directly consumed snack food globally. Floret size is also important because corolla tube length was previously shown to be inversely correlated with pollinator visitation, impacting bee foraging potential and pollinator services to the plant. Commercial sunflower production benefits from pollinator visits, despite being self-compatible, and bees are required in hybrid seed production, where "female" and "male" inbred lines are crossed at field scale. Issues with pollination of long-seed confectionery sunflower suggest that there may be an unfavorable correlation between seed and floret traits; thus, our objective was to determine the strength of the correlation between seed and floret traits, and confirm any co-localization of seed and floret trait loci using genome-wide association analysis in the SAM diversity panel of sunflower. Our results indicate that phenotypic correlations between seed and floret traits are generally low to moderate, regardless of market class, a component of population substructure. Association mapping results mirror the correlations: while a few loci overlap, many loci for the two traits are not overlapping or even adjacent. The genetics of these traits, while modestly quantitative and influenced by epistatic effects, are not a barrier to simultaneous improvement of seed length and pollinator-friendly floret traits. We conclude that breeding for large seed size, which is required for the confectionery seed market, is possible without producing florets too long for efficient use by pollinators, which promotes bee foraging and associated pollination services.
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Affiliation(s)
- Stephan Reinert
- Ecology and Evolutionary Biology Department, University of Colorado, 1900 Pleasant Street, 334 UCB, Boulder, CO, 80309-0334, USA
| | - Qingming Gao
- USDA-ARS Edward T Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND, 58102-2765, USA
- Cibus, 6455 Nancy Ridge Drive, San Diego, CA, 92024, USA
| | - Beth Ferguson
- USDA-ARS Edward T Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND, 58102-2765, USA
| | - Zoe M Portlas
- USDA-ARS Edward T Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND, 58102-2765, USA
- Department of Plant Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Jarrad R Prasifka
- USDA-ARS Edward T Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND, 58102-2765, USA
| | - Brent S Hulke
- USDA-ARS Edward T Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND, 58102-2765, USA.
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14
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Presotto A, Hernández F, Mercer KL. Phenotypic selection under two contrasting environments in wild sunflower and its crop-wild hybrid. Evol Appl 2019; 12:1703-1717. [PMID: 31462924 PMCID: PMC6708420 DOI: 10.1111/eva.12828] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/16/2019] [Accepted: 05/23/2019] [Indexed: 01/20/2023] Open
Abstract
Hybridization is a common phenomenon in plants and can lead to the introgression of alleles from one population into another, generate new hybrid lineages, or cause species extinction. The environmental conditions and the genetic background of the participating populations may influence these outcomes since they can affect the fitness of hybrids, thereby increasing or decreasing the chances of introgression. Thus, it is important to understand the context-dependent prospects for introgression of alleles into diverse populations and under multiple ecological environments. Crop-wild hybridization presents an opportunity to explore these dynamics in agroecosystems. To this end, we used diverse wild and hybrid sunflowers from across the northern United States as a basis for evaluating variation in morphological traits and assessing context-dependent selection. These crop-wild hybrids and their wild counterparts were grown under agricultural conditions in the field with and without wheat competition. Interactions between origin and cross type affected expression of early functional traits, while interactions between competition and cross type acted on reproductive traits. A smattering of early and reproductive traits was affected by interactions between cross type and competition that varied by origin (i.e., 3-way interactions). Seven functional traits, especially number of branches and tertiary head diameter, underwent net and direct directional selection, while six out of these seven traits appear to also be experiencing nonlinear selection dynamics. In general, wild-like traits were favored under both sets of conditions, while, under wheat competition, some crop-like traits related to fast growth and primary head diameter became important. These data reaffirm the hypothesis that stressful conditions establish a scenario more suitable for crop introgression and clarify that nonlinear selection dynamics may play a role in this process.
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Affiliation(s)
- Alejandro Presotto
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Departamento de AgronomíaUniversidad Nacional del Sur (UNS)‐ CONICETBahía BlancaBuenos AiresArgentina
| | - Fernando Hernández
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Departamento de AgronomíaUniversidad Nacional del Sur (UNS)‐ CONICETBahía BlancaBuenos AiresArgentina
| | - Kristin L. Mercer
- Department of Horticulture and Crop ScienceOhio State UniversityColumbusOH
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15
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Horn R, Radanovic A, Fuhrmann L, Sprycha Y, Hamrit S, Jockovic M, Miladinovic D, Jansen C. Development and Validation of Markers for the Fertility Restorer Gene Rf1 in Sunflower. Int J Mol Sci 2019; 20:ijms20061260. [PMID: 30871146 PMCID: PMC6471545 DOI: 10.3390/ijms20061260] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/05/2019] [Accepted: 03/10/2019] [Indexed: 01/14/2023] Open
Abstract
Hybrid breeding in sunflowers based on CMS PET1 requires development of restorer lines carrying, in most cases, the restorer gene Rf1. Markers for marker-assisted selection have been developed, but there is still need for closer, more versatile, and co-dominant markers linked to Rf1. Homology searches against the reference sunflower genome using sequences of cloned markers, as well as Bacterial Artificial Chromosome (BAC)-end sequences of clones hybridizing to them, allowed the identification of two genomic regions of 30 and 3.9 Mb, respectively, as possible physical locations of the restorer gene Rf1 on linkage group 13. Nine potential candidate genes, encoding six pentatricopeptide repeat proteins, one tetratricopeptide-like helical domain, a probable aldehyde dehydrogenase 22A1, and a probable poly(A) polymerase 3 (PAPS3), were identified in these two genomic regions. Amplicon targeted next generation sequencing of these nine candidate genes for Rf1 was performed in an association panel consisting of 27 maintainer and 32 restorer lines and revealed the presence of 210 Single Nucleotide Polymorphisms (SNPs) and 67 Insertions/Deletions (INDELs). Association studies showed significant associations of 10 SNPs with fertility restoration (p-value < 10−4), narrowing Rf1 down to three candidate genes. Three new markers, one co-dominant marker 67N04_P and two dominant markers, PPR621.5R for restorer, and PPR621.5M for maintainer lines were developed and verified in the association panel of 59 sunflower lines. The versatility of the three newly developed markers, as well as of three existing markers for the restorer gene Rf1 (HRG01 and HRG02, Cleaved Amplified Polymorphic Sequence (CAPS)-marker H13), was analyzed in a large association panel consisting of 557 accessions.
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Affiliation(s)
- Renate Horn
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Aleksandra Radanovic
- Industrial Crops Department, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia.
| | - Lena Fuhrmann
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Yves Sprycha
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Sonia Hamrit
- Strube Research GmbH & Co. KG, Hauptstr. 1, D-38387 Söllingen, Germany.
| | - Milan Jockovic
- Industrial Crops Department, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia.
| | - Dragana Miladinovic
- Industrial Crops Department, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia.
| | - Constantin Jansen
- Strube Research GmbH & Co. KG, Hauptstr. 1, D-38387 Söllingen, Germany.
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16
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Masalia RR, Temme AA, Torralba NDL, Burke JM. Multiple genomic regions influence root morphology and seedling growth in cultivated sunflower (Helianthus annuus L.) under well-watered and water-limited conditions. PLoS One 2018; 13:e0204279. [PMID: 30235309 PMCID: PMC6147562 DOI: 10.1371/journal.pone.0204279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/05/2018] [Indexed: 11/18/2022] Open
Abstract
With climate change and an ever-increasing human population threatening food security, developing a better understanding of the genetic basis of crop performance under stressful conditions has become increasingly important. Here, we used genome-wide association studies to genetically dissect variation in seedling growth traits in cultivated sunflower (Helianthus annuus L.) under well-watered and water-limited (i.e., osmotic stress) conditions, with a particular focus on root morphology. Water limitation reduced seedling size and produced a shift toward deeper rooting. These effects varied across genotypes, and we identified 13 genomic regions that were associated with traits of interest across the two environments. These regions varied in size from a single marker to 186.2 Mbp and harbored numerous genes, some of which are known to be involved in the plant growth/development as well as the response to osmotic stress. In many cases, these associations corresponded to growth traits where the common allele outperformed the rare variant, suggesting that selection for increased vigor during the evolution of cultivated sunflower might be responsible for the relatively high frequency of these alleles. We also found evidence of pleiotropy across multiple traits, as well as numerous environmentally independent genetic effects. Overall, our results indicate the existence of genetic variation in root morphology and allocation and further suggest that the majority of alleles associated with these traits have consistent effects across environments.
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Affiliation(s)
- Rishi R. Masalia
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Andries A. Temme
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Nicole de leon Torralba
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - John M. Burke
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
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Bonnafous F, Fievet G, Blanchet N, Boniface MC, Carrère S, Gouzy J, Legrand L, Marage G, Bret-Mestries E, Munos S, Pouilly N, Vincourt P, Langlade N, Mangin B. Comparison of GWAS models to identify non-additive genetic control of flowering time in sunflower hybrids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018. [PMID: 29098310 DOI: 10.1101/188235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
This study compares five models of GWAS, to show the added value of non-additive modeling of allelic effects to identify genomic regions controlling flowering time of sunflower hybrids. Genome-wide association studies are a powerful and widely used tool to decipher the genetic control of complex traits. One of the main challenges for hybrid crops, such as maize or sunflower, is to model the hybrid vigor in the linear mixed models, considering the relatedness between individuals. Here, we compared two additive and three non-additive association models for their ability to identify genomic regions associated with flowering time in sunflower hybrids. A panel of 452 sunflower hybrids, corresponding to incomplete crossing between 36 male lines and 36 female lines, was phenotyped in five environments and genotyped for 2,204,423 SNPs. Intra-locus effects were estimated in multi-locus models to detect genomic regions associated with flowering time using the different models. Thirteen quantitative trait loci were identified in total, two with both model categories and one with only non-additive models. A quantitative trait loci on LG09, detected by both the additive and non-additive models, is located near a GAI homolog and is presented in detail. Overall, this study shows the added value of non-additive modeling of allelic effects for identifying genomic regions that control traits of interest and that could participate in the heterosis observed in hybrids.
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Affiliation(s)
- Fanny Bonnafous
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France.
| | - Ghislain Fievet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Nicolas Blanchet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | | | - Jérôme Gouzy
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Ludovic Legrand
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Gwenola Marage
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | - Stéphane Munos
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Nicolas Pouilly
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Patrick Vincourt
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Nicolas Langlade
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Brigitte Mangin
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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18
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Bonnafous F, Fievet G, Blanchet N, Boniface MC, Carrère S, Gouzy J, Legrand L, Marage G, Bret-Mestries E, Munos S, Pouilly N, Vincourt P, Langlade N, Mangin B. Comparison of GWAS models to identify non-additive genetic control of flowering time in sunflower hybrids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:319-332. [PMID: 29098310 PMCID: PMC5787229 DOI: 10.1007/s00122-017-3003-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 10/07/2017] [Indexed: 05/08/2023]
Abstract
This study compares five models of GWAS, to show the added value of non-additive modeling of allelic effects to identify genomic regions controlling flowering time of sunflower hybrids. Genome-wide association studies are a powerful and widely used tool to decipher the genetic control of complex traits. One of the main challenges for hybrid crops, such as maize or sunflower, is to model the hybrid vigor in the linear mixed models, considering the relatedness between individuals. Here, we compared two additive and three non-additive association models for their ability to identify genomic regions associated with flowering time in sunflower hybrids. A panel of 452 sunflower hybrids, corresponding to incomplete crossing between 36 male lines and 36 female lines, was phenotyped in five environments and genotyped for 2,204,423 SNPs. Intra-locus effects were estimated in multi-locus models to detect genomic regions associated with flowering time using the different models. Thirteen quantitative trait loci were identified in total, two with both model categories and one with only non-additive models. A quantitative trait loci on LG09, detected by both the additive and non-additive models, is located near a GAI homolog and is presented in detail. Overall, this study shows the added value of non-additive modeling of allelic effects for identifying genomic regions that control traits of interest and that could participate in the heterosis observed in hybrids.
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Affiliation(s)
- Fanny Bonnafous
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France.
| | - Ghislain Fievet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Nicolas Blanchet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | | | - Jérôme Gouzy
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Ludovic Legrand
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Gwenola Marage
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | - Stéphane Munos
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Nicolas Pouilly
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Patrick Vincourt
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Nicolas Langlade
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Brigitte Mangin
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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19
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Dimitrijevic A, Horn R. Sunflower Hybrid Breeding: From Markers to Genomic Selection. FRONTIERS IN PLANT SCIENCE 2018; 8:2238. [PMID: 29387071 PMCID: PMC5776114 DOI: 10.3389/fpls.2017.02238] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 12/20/2017] [Indexed: 05/03/2023]
Abstract
In sunflower, molecular markers for simple traits as, e.g., fertility restoration, high oleic acid content, herbicide tolerance or resistances to Plasmopara halstedii, Puccinia helianthi, or Orobanche cumana have been successfully used in marker-assisted breeding programs for years. However, agronomically important complex quantitative traits like yield, heterosis, drought tolerance, oil content or selection for disease resistance, e.g., against Sclerotinia sclerotiorum have been challenging and will require genome-wide approaches. Plant genetic resources for sunflower are being collected and conserved worldwide that represent valuable resources to study complex traits. Sunflower association panels provide the basis for genome-wide association studies, overcoming disadvantages of biparental populations. Advances in technologies and the availability of the sunflower genome sequence made novel approaches on the whole genome level possible. Genotype-by-sequencing, and whole genome sequencing based on next generation sequencing technologies facilitated the production of large amounts of SNP markers for high density maps as well as SNP arrays and allowed genome-wide association studies and genomic selection in sunflower. Genome wide or candidate gene based association studies have been performed for traits like branching, flowering time, resistance to Sclerotinia head and stalk rot. First steps in genomic selection with regard to hybrid performance and hybrid oil content have shown that genomic selection can successfully address complex quantitative traits in sunflower and will help to speed up sunflower breeding programs in the future. To make sunflower more competitive toward other oil crops higher levels of resistance against pathogens and better yield performance are required. In addition, optimizing plant architecture toward a more complex growth type for higher plant densities has the potential to considerably increase yields per hectare. Integrative approaches combining omic technologies (genomics, transcriptomics, proteomics, metabolomics and phenomics) using bioinformatic tools will facilitate the identification of target genes and markers for complex traits and will give a better insight into the mechanisms behind the traits.
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Affiliation(s)
| | - Renate Horn
- Institut für Biowissenschaften, Abteilung Pflanzengenetik, Universität Rostock, Rostock, Germany
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20
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He Y, Wu D, Wei D, Fu Y, Cui Y, Dong H, Tan C, Qian W. GWAS, QTL mapping and gene expression analyses in Brassica napus reveal genetic control of branching morphogenesis. Sci Rep 2017; 7:15971. [PMID: 29162897 PMCID: PMC5698412 DOI: 10.1038/s41598-017-15976-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 11/03/2017] [Indexed: 01/04/2023] Open
Abstract
Branch number is an important trait in plant architecture that can influence crop yield and quality in Brassica napus. Here, we detected the QTLs responsible for branch number in a DH population and its reconstructed F2 population over two years. Further, a GWAS research on branch number was performed using a panel of 327 accessions with 33186 genomic SNPs from the 60 K Brassica Illumina® Infinium SNP array. Through combining linkage analysis and association mapping, a new QTL was fine mapped onto C03. Subsequently, we tested the correlations between the SNP polymorphisms and mRNA expression levels of genes in the target interval to identify potential loci or genes that control branch number through expression. The results show that 4 SNP loci are associated with the corresponding gene expression levels, and one locus (BnaC03g63480D) exhibited a significant correlation between the phenotype variation and gene expression levels. Our results provide insights into the genetic basis for branching morphogenesis and may be valuable for optimizing architecture in rapeseed breeding.
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Affiliation(s)
- Yajun He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Daoming Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Dayong Wei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Ying Fu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Hongli Dong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Chuandong Tan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
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21
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Plekhanova E, Vishnyakova MA, Bulyntsev S, Chang PL, Carrasquilla-Garcia N, Negash K, Wettberg EV, Noujdina N, Cook DR, Samsonova MG, Nuzhdin SV. Genomic and phenotypic analysis of Vavilov's historic landraces reveals the impact of environment and genomic islands of agronomic traits. Sci Rep 2017; 7:4816. [PMID: 28684880 PMCID: PMC5500531 DOI: 10.1038/s41598-017-05087-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 05/24/2017] [Indexed: 12/30/2022] Open
Abstract
The Vavilov Institute of Plant Genetic Resources (VIR), in St. Petersburg, Russia, houses a unique genebank, with historical collections of landraces. When they were collected, the geographical distribution and genetic diversity of most crops closely reflected their historical patterns of cultivation established over the preceding millennia. We employed a combination of genomics, computational biology and phenotyping to characterize VIR's 147 chickpea accessions from Turkey and Ethiopia, representing chickpea's center of origin and a major location of secondary diversity. Genotyping by sequencing identified 14,059 segregating polymorphisms and genome-wide association studies revealed 28 GWAS hits in potential candidate genes likely to affect traits of agricultural importance. The proportion of polymorphisms shared among accessions is a strong predictor of phenotypic resemblance, and of environmental similarity between historical sampling sites. We found that 20 out of 28 polymorphisms, associated with multiple traits, including days to maturity, plant phenology, and yield-related traits such as pod number, localized to chromosome 4. We hypothesize that selection and introgression via inadvertent hybridization between more and less advanced morphotypes might have resulted in agricultural improvement genes being aggregated to genomic 'agro islands', and in genotype-to-phenotype relationships resembling widespread pleiotropy.
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Affiliation(s)
- Elena Plekhanova
- Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
| | - Margarita A Vishnyakova
- Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - Sergey Bulyntsev
- Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - Peter L Chang
- Department of Plant Pathology, University of California, Davis, CA, USA.,Program Molecular and Computation Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Kassaye Negash
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Eric von Wettberg
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, USA
| | - Nina Noujdina
- School of Architecture, University of Southern California, Los Angeles, CA, USA
| | - Douglas R Cook
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Maria G Samsonova
- Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
| | - Sergey V Nuzhdin
- Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia. .,Program Molecular and Computation Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, USA.
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Genetic Mapping of Millions of SNPs in Safflower (Carthamus tinctorius L.) via Whole-Genome Resequencing. G3-GENES GENOMES GENETICS 2016; 6:2203-11. [PMID: 27226165 PMCID: PMC4938673 DOI: 10.1534/g3.115.026690] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Accurate assembly of complete genomes is facilitated by very high density genetic maps. We performed low-coverage, whole-genome shotgun sequencing on 96 F6 recombinant inbred lines (RILs) of a cross between safflower (Carthamus tinctorius L.) and its wild progenitor (C. palaestinus Eig). We also produced a draft genome assembly of C. tinctorius covering 866 million bp (∼two-thirds) of the expected 1.35 Gbp genome after sequencing a single, short insert library to ∼21 × depth. Sequence reads from the RILs were mapped to this genome assembly to facilitate SNP identification, and the resulting polymorphisms were used to construct a genetic map. The resulting map included 2,008,196 genetically located SNPs in 1178 unique positions. A total of 57,270 scaffolds, each containing five or more mapped SNPs, were anchored to the map. This resulted in the assignment of sequence covering 14% of the expected genome length to a genetic position. Comparison of this safflower map to genetic maps of sunflower and lettuce revealed numerous chromosomal rearrangements, and the resulting patterns were consistent with a whole-genome duplication event in the lineage leading to sunflower. This sequence-based genetic map provides a powerful tool for the assembly of a low-cost draft genome of safflower, and the same general approach is expected to work for other species.
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