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Thakur NR, Gorthy S, Vemula A, Odeny DA, Ruperao P, Sargar PR, Mehtre SP, Kalpande HV, Habyarimana E. Genome-wide association study and expression of candidate genes for Fe and Zn concentration in sorghum grains. Sci Rep 2024; 14:12729. [PMID: 38830906 PMCID: PMC11148041 DOI: 10.1038/s41598-024-63308-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/27/2024] [Indexed: 06/05/2024] Open
Abstract
Sorghum germplasm showed grain Fe and Zn genetic variability, but a few varieties were biofortified with these minerals. This work contributes to narrowing this gap. Fe and Zn concentrations along with 55,068 high-quality GBS SNP data from 140 sorghum accessions were used in this study. Both micronutrients exhibited good variability with respective ranges of 22.09-52.55 ppm and 17.92-43.16 ppm. Significant marker-trait associations were identified on chromosomes 1, 3, and 5. Two major effect SNPs (S01_72265728 and S05_58213541) explained 35% and 32% of Fe and Zn phenotypic variance, respectively. The SNP S01_72265728 was identified in the cytochrome P450 gene and showed a positive effect on Fe accumulation in the kernel, while S05_58213541 was intergenic near Sobic.005G134800 (zinc-binding ribosomal protein) and showed negative effect on Zn. Tissue-specific in silico expression analysis resulted in higher levels of Sobic.003G350800 gene product in several tissues such as leaf, root, flower, panicle, and stem. Sobic.005G188300 and Sobic.001G463800 were expressed moderately at grain maturity and anthesis in leaf, root, panicle, and seed tissues. The candidate genes expressed in leaves, stems, and grains will be targeted to improve grain and stover quality. The haplotypes identified will be useful in forward genetics breeding.
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Affiliation(s)
- Niranjan Ravindra Thakur
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
- Vasantrao Naik Marathwada Agriculture University, Parbhani, Maharashtra, India
| | - Sunita Gorthy
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - AnilKumar Vemula
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Pradeep Ruperao
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Pramod Ramchandra Sargar
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
- Vasantrao Naik Marathwada Agriculture University, Parbhani, Maharashtra, India
| | | | - Hirakant V Kalpande
- Vasantrao Naik Marathwada Agriculture University, Parbhani, Maharashtra, India
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India.
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Zhu L, Li G, Guo D, Li X, Xue M, Jiang H, Yan Q, Xie F, Ning X, Xie L. Genome-wide association study and genomic selection of flax powdery mildew in Xinjiang Province. FRONTIERS IN PLANT SCIENCE 2024; 15:1403276. [PMID: 38863531 PMCID: PMC11165360 DOI: 10.3389/fpls.2024.1403276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/10/2024] [Indexed: 06/13/2024]
Abstract
Flax powdery mildew (PM), caused by Oidium lini, is a globally distributed fungal disease of flax, and seriously impairs its yield and quality. To data, only three resistance genes and a few putative quantitative trait loci (QTL) have been reported for flax PM resistance. To dissect the resistance mechanism against PM and identify resistant genetic regions, based on four years of phenotypic datasets (2017, 2019 to 2021), a genome-wide association study (GWAS) was performed on 200 flax core accessions using 674,074 SNPs and 7 models. A total of 434 unique quantitative trait nucleotides (QTNs) associated with 331 QTL were detected. Sixty-four loci shared in at least two datasets were found to be significant in haplotype analyses, and 20 of these sites were shared by multiple models. Simultaneously, a large-effect locus (qDI 11.2) was detected repeatedly, which was present in the mapping study of flax pasmo resistance loci. Oil flax had more QTL with positive-effect or favorable alleles (PQTL) and showed higher PM resistance than fiber flax, indicating that effects of these QTL were mainly additive. Furthermore, an excellent resistant variety C120 was identified and can be used to promote planting. Based on 331 QTLs identified through GWAS and the statistical model GBLUP, a genomic selection (GS) model related to flax PM resistance was constructed, and the prediction accuracy rate was 0.96. Our results provide valuable insights into the genetic basis of resistance and contribute to the advancement of breeding programs.
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Affiliation(s)
- Leilei Zhu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Gongze Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Zhengzhou, China
| | - Dongliang Guo
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Xiao Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
- Department of Basic Medicine, Xinjiang Second Medical College, Karamay, China
| | - Min Xue
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Haixia Jiang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
- Key Laboratory of Plant Stress Biology in Arid Land, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Qingcheng Yan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Fang Xie
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Xuefei Ning
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Liqiong Xie
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
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Hoque A, Anderson JV, Rahman M. Genomic prediction for agronomic traits in a diverse Flax (Linum usitatissimum L.) germplasm collection. Sci Rep 2024; 14:3196. [PMID: 38326469 PMCID: PMC10850546 DOI: 10.1038/s41598-024-53462-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/31/2024] [Indexed: 02/09/2024] Open
Abstract
Breeding programs require exhaustive phenotyping of germplasms, which is time-demanding and expensive. Genomic prediction helps breeders harness the diversity of any collection to bypass phenotyping. Here, we examined the genomic prediction's potential for seed yield and nine agronomic traits using 26,171 single nucleotide polymorphism (SNP) markers in a set of 337 flax (Linum usitatissimum L.) germplasm, phenotyped in five environments. We evaluated 14 prediction models and several factors affecting predictive ability based on cross-validation schemes. Models yielded significant variation among predictive ability values across traits for the whole marker set. The ridge regression (RR) model covering additive gene action yielded better predictive ability for most of the traits, whereas it was higher for low heritable traits by models capturing epistatic gene action. Marker subsets based on linkage disequilibrium decay distance gave significantly higher predictive abilities to the whole marker set, but for randomly selected markers, it reached a plateau above 3000 markers. Markers having significant association with traits improved predictive abilities compared to the whole marker set when marker selection was made on the whole population instead of the training set indicating a clear overfitting. The correction for population structure did not increase predictive abilities compared to the whole collection. However, stratified sampling by picking representative genotypes from each cluster improved predictive abilities. The indirect predictive ability for a trait was proportionate to its correlation with other traits. These results will help breeders to select the best models, optimum marker set, and suitable genotype set to perform an indirect selection for quantitative traits in this diverse flax germplasm collection.
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Affiliation(s)
- Ahasanul Hoque
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - James V Anderson
- USDA-ARS, Edward T. Schafer Agricultural Research Center, Fargo, ND, USA
| | - Mukhlesur Rahman
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA.
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Zhang Y, Zhang M, Ye J, Xu Q, Feng Y, Xu S, Hu D, Wei X, Hu P, Yang Y. Integrating genome-wide association study into genomic selection for the prediction of agronomic traits in rice ( Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:81. [PMID: 37965378 PMCID: PMC10641074 DOI: 10.1007/s11032-023-01423-y] [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: 07/11/2023] [Accepted: 10/09/2023] [Indexed: 11/16/2023]
Abstract
Accurately identifying varieties with targeted agronomic traits was thought to contribute to genetic selection and accelerate rice breeding progress. Genomic selection (GS) is a promising technique that uses markers covering the whole genome to predict the genomic-estimated breeding values (GEBV), with the ability to select before phenotypes are measured. To choose the appropriate GS models for breeding work, we analyzed the predictability of nine agronomic traits measured from a population of 459 diverse rice varieties. By the comparison of eight representative GS models, we found that the prediction accuracies ranged from 0.407 to 0.896, with reproducing kernel Hilbert space (RKHS) having the highest predictive ability in most traits. Further results demonstrated the predictivity of GS is altered by several factors. Moreover, we assessed the method of integrating genome-wide association study (GWAS) into various GS models. The predictabilities of GS combined peak-associated markers generated from six different GWAS models were significantly different; a recommendation of Mixed Linear Model (MLM)-RKHS was given for the GWAS-GS-integrated prediction. Finally, based on the above result, we experimented with applying the P-values obtained from optimal GWAS models into ridge regression best linear unbiased prediction (rrBLUP), which benefited the low predictive traits in rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01423-y.
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Affiliation(s)
- Yuanyuan Zhang
- Zhejiang Lab, Hangzhou, 311121 China
- CNRRI-Zhejiang Lab Computational Breeding Joint Laboratory, China National Rice Research Institute, Hangzhou, China
| | - Mengchen Zhang
- Zhejiang Lab, Hangzhou, 311121 China
- CNRRI-Zhejiang Lab Computational Breeding Joint Laboratory, China National Rice Research Institute, Hangzhou, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024 China
| | - Junhua Ye
- CNRRI-Zhejiang Lab Computational Breeding Joint Laboratory, China National Rice Research Institute, Hangzhou, China
| | - Qun Xu
- CNRRI-Zhejiang Lab Computational Breeding Joint Laboratory, China National Rice Research Institute, Hangzhou, China
| | - Yue Feng
- CNRRI-Zhejiang Lab Computational Breeding Joint Laboratory, China National Rice Research Institute, Hangzhou, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024 China
| | - Siliang Xu
- CNRRI-Zhejiang Lab Computational Breeding Joint Laboratory, China National Rice Research Institute, Hangzhou, China
| | - Dongxiu Hu
- CNRRI-Zhejiang Lab Computational Breeding Joint Laboratory, China National Rice Research Institute, Hangzhou, China
| | - Xinghua Wei
- Zhejiang Lab, Hangzhou, 311121 China
- CNRRI-Zhejiang Lab Computational Breeding Joint Laboratory, China National Rice Research Institute, Hangzhou, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024 China
| | - Peisong Hu
- Zhejiang Lab, Hangzhou, 311121 China
- CNRRI-Zhejiang Lab Computational Breeding Joint Laboratory, China National Rice Research Institute, Hangzhou, China
| | - Yaolong Yang
- Zhejiang Lab, Hangzhou, 311121 China
- CNRRI-Zhejiang Lab Computational Breeding Joint Laboratory, China National Rice Research Institute, Hangzhou, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024 China
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He L, Sui Y, Che Y, Wang H, Rashid KY, Cloutier S, You FM. Genome-wide association studies using multi-models and multi-SNP datasets provide new insights into pasmo resistance in flax. FRONTIERS IN PLANT SCIENCE 2023; 14:1229457. [PMID: 37954993 PMCID: PMC10634603 DOI: 10.3389/fpls.2023.1229457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/24/2023] [Indexed: 11/14/2023]
Abstract
Introduction Flax (Linum usitatissimum L.) is an economically important crop due to its oil and fiber. However, it is prone to various diseases, including pasmo caused by the fungus Septoria linicola. Methods In this study, we conducted field evaluations of 445 flax accessions over a five-year period (2012-2016) to assess their resistance to pasmo A total of 246,035 single nucleotide polymorphisms (SNPs) were used for genetic analysis. Four statistical models, including the single-locus model GEMMA and the multi-locus models FarmCPU, mrMLM, and 3VmrMLM, were assessed to identify quantitative trait nucleotides (QTNs) associated with pasmo resistance. Results We identified 372 significant QTNs or 132 tag QTNs associated with pasmo resistance from five pasmo resistance datasets (PAS2012-PAS2016 and the 5-year average, namely PASmean) and three genotypic datasets (the all SNPs/ALL, the gene-based SNPs/GB and the RGA-based SNPs/RGAB). The tag QTNs had R2 values of 0.66-16.98% from the ALL SNP dataset, 0.68-20.54%from the GB SNP dataset, and 0.52-22.42% from the RGAB SNP dataset. Of these tag QTNs, 93 were novel. Additionally, 37 resistance gene analogs (RGAs)co-localizing with 39 tag QTNs were considered as potential candidates for controlling pasmo resistance in flax and 50 QTN-by-environment interactions(QEIs) were identified to account for genes by environmental interactions. Nine RGAs were predicted as candidate genes for ten QEIs. Discussion Our results suggest that pasmo resistance in flax is polygenic and potentially influenced by environmental factors. The identified QTNs provide potential targets for improving pasmo resistance in flax breeding programs. This study sheds light on the genetic basis of pasmo resistance and highlights the importance of considering both genetic and environmental factors in breeding programs for flax.
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Affiliation(s)
- Liqiang He
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Yao Sui
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Yanru Che
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Huixian Wang
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Khalid Y. Rashid
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
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Sui Y, Che Y, Zhong Y, He L. Genome-Wide Association Studies Using 3VmrMLM Model Provide New Insights into Branched-Chain Amino Acid Contents in Rice Grains. PLANTS (BASEL, SWITZERLAND) 2023; 12:2970. [PMID: 37631180 PMCID: PMC10459631 DOI: 10.3390/plants12162970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
Rice (Oryza sativa L.) is a globally important food source providing carbohydrates, amino acids, and dietary fiber for humans and livestock. The branched-chain amino acid (BCAA) level is a complex trait related to the nutrient quality of rice. However, the genetic mechanism underlying the BCAA (valine, leucine, and isoleucine) accumulation in rice grains remains largely unclear. In this study, the grain BCAA contents and 239,055 SNPs of a diverse panel containing 422 rice accessions were adopted to perform a genome-wide association study (GWAS) using a recently proposed 3VmrMLM model. A total of 357 BCAA-content-associated main-effect quantitative trait nucleotides (QTNs) were identified from 15 datasets (12 BCAA content datasets and 3 BLUP datasets of BCAA). Furthermore, the allelic variation of two novel candidate genes, LOC_Os01g52530 and LOC_Os06g15420, responsible for the isoleucine (Ile) content alteration were identified. To reveal the genetic basis of the potential interactions between the gene and environmental factor, 53 QTN-by-environment interactions (QEIs) were detected using the 3VmrMLM model. The LOC_Os03g24460, LOC_Os01g55590, and LOC_Os12g31820 were considered as the candidate genes potentially contributing to the valine (Val), leucine (Leu), and isoleucine (Ile) accumulations, respectively. Additionally, 10 QTN-by-QTN interactions (QQIs) were detected using the 3VmrMLM model, which were putative gene-by-gene interactions related to the Leu and Ile contents. Taken together, these findings suggest that the implementation of the 3VmrMLM model in a GWAS may provide new insights into the deeper understanding of BCAA accumulation in rice grains. The identified QTNs/QEIs/QQIs serve as potential targets for the genetic improvement of rice with high BCAA levels.
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Affiliation(s)
| | | | | | - Liqiang He
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou 570228, China
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Moyse J, Lecomte S, Marcou S, Mongelard G, Gutierrez L, Höfte M. Overview and Management of the Most Common Eukaryotic Diseases of Flax ( Linum usitatissimum). PLANTS (BASEL, SWITZERLAND) 2023; 12:2811. [PMID: 37570965 PMCID: PMC10420651 DOI: 10.3390/plants12152811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023]
Abstract
Flax is an important crop cultivated for its seeds and fibers. It is widely grown in temperate regions, with an increase in cultivation areas for seed production (linseed) in the past 50 years and for fiber production (fiber flax) in the last decade. Among fiber-producing crops, fiber flax is the most valuable species. Linseed is the highest omega-3 oleaginous crop, and its consumption provides several benefits for animal and human health. However, flax production is impacted by various abiotic and biotic factors that affect yield and quality. Among biotic factors, eukaryotic diseases pose a significant threat to both seed production and fiber quality, which highlights the economic importance of controlling these diseases. This review focuses on the major eukaryotic diseases that affect flax in the field, describing the pathogens, their transmission modes and the associated plant symptoms. Moreover, this article aims to identify the challenges in disease management and provide future perspectives to overcome these biotic stresses in flax cultivation. By emphasizing the key diseases and their management, this review can aid in promoting sustainable and profitable flax production.
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Affiliation(s)
- Julie Moyse
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure Links 653, 9000 Ghent, Belgium; (J.M.); (S.M.)
- Centre de Ressources Régionales en Biologie Moléculaire, University of Picardie Jules Verne, UFR Sciences, 33 Rue St-Leu, 80039 Amiens, France;
| | - Sylvain Lecomte
- LINEA–Semences, 20 Avenue Saget, 60210 Grandvilliers, France;
| | - Shirley Marcou
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure Links 653, 9000 Ghent, Belgium; (J.M.); (S.M.)
| | - Gaëlle Mongelard
- Centre de Ressources Régionales en Biologie Moléculaire, University of Picardie Jules Verne, UFR Sciences, 33 Rue St-Leu, 80039 Amiens, France;
| | - Laurent Gutierrez
- Centre de Ressources Régionales en Biologie Moléculaire, University of Picardie Jules Verne, UFR Sciences, 33 Rue St-Leu, 80039 Amiens, France;
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure Links 653, 9000 Ghent, Belgium; (J.M.); (S.M.)
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Anilkumar C, Muhammed Azharudheen TP, Sah RP, Sunitha NC, Devanna BN, Marndi BC, Patra BC. Gene based markers improve precision of genome-wide association studies and accuracy of genomic predictions in rice breeding. Heredity (Edinb) 2023; 130:335-345. [PMID: 36792661 PMCID: PMC10163052 DOI: 10.1038/s41437-023-00599-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
It is hypothesized that the genome-wide genic markers may increase the prediction accuracy of genomic selection for quantitative traits. To test this hypothesis, a set of candidate gene-based markers for yield and grain traits-related genes cloned across the rice genome were custom-designed. A multi-model, multi-locus genome-wide association study (GWAS) was performed using new genic markers developed to test their effectiveness for gene discovery. Two multi-locus models, FarmCPU and mrMLM, along with a single-locus mixed linear model (MLM), identified 28 significant marker-trait associations. These associations revealed novel causative alleles for grain weight and pleiotropic associations with other traits. For instance, the marker YD91 derived from the gene OsAAP3 on chromosome 1 was consistently associated with grain weight, while the gene has a significant effect on grain yield. Furthermore, nine genomic selection methods, including regression-based and machine learning-based models, were used to predict grain weight using a leave-one-out five-fold cross-validation approach to optimize the genomic selection model with genic markers. Among nine prediction models, Kernel Hilbert Space Regression (RKHS) is the best among regression-based models, and Random Forest Regression (RFR) is the best among machine learning-based models. Genomic prediction accuracies with and without GWAS significant markers were compared to assess the effectiveness of markers. The rapid decreases in prediction accuracy upon dropping GWAS significant markers indicate the effectiveness of new genic markers in genomic selection. Apart from that, the candidate gene-based markers were found to be more effective in genomic selection programs for better accuracy.
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Jiang GL, Rajcan I, Zhang YM, Han T, Mian R. Editorial: Soybean molecular breeding and genetics. FRONTIERS IN PLANT SCIENCE 2023; 14:1157632. [PMID: 36925748 PMCID: PMC10013459 DOI: 10.3389/fpls.2023.1157632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Guo-Liang Jiang
- Agricultural Research Station, Virginia State University, VA, Petersburg, United States
| | - Istvan Rajcan
- Department of Plant Agriculture, Ontario Agriculture College, University of Guelph, Guelph, ON, Canada
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tianfu Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rouf Mian
- Soybean and Nitrogen Fixation Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Raleigh, NC, United States
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Anilkumar C, Sunitha NC, Devate NB, Ramesh S. Advances in integrated genomic selection for rapid genetic gain in crop improvement: a review. PLANTA 2022; 256:87. [PMID: 36149531 DOI: 10.1007/s00425-022-03996-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 09/11/2022] [Indexed: 06/16/2023]
Abstract
Genomic selection and its importance in crop breeding. Integration of GS with new breeding tools and developing SOP for GS to achieve maximum genetic gain with low cost and time. The success of conventional breeding approaches is not sufficient to meet the demand of a growing population for nutritious food and other plant-based products. Whereas, marker assisted selection (MAS) is not efficient in capturing all the favorable alleles responsible for economic traits in the process of crop improvement. Genomic selection (GS) developed in livestock breeding and then adapted to plant breeding promised to overcome the drawbacks of MAS and significantly improve complicated traits controlled by gene/QTL with small effects. Large-scale deployment of GS in important crops, as well as simulation studies in a variety of contexts, addressed G × E interaction effects and non-additive effects, as well as lowering breeding costs and time. The current study provides a complete overview of genomic selection, its process, and importance in modern plant breeding, along with insights into its application. GS has been implemented in the improvement of complex traits including tolerance to biotic and abiotic stresses. Furthermore, this review hypothesises that using GS in conjunction with other crop improvement platforms accelerates the breeding process to increase genetic gain. The objective of this review is to highlight the development of an appropriate GS model, the global open source network for GS, and trans-disciplinary approaches for effective accelerated crop improvement. The current study focused on the application of data science, including machine learning and deep learning tools, to enhance the accuracy of prediction models. Present study emphasizes on developing plant breeding strategies centered on GS combined with routine conventional breeding principles by developing GS-SOP to achieve enhanced genetic gain.
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Affiliation(s)
- C Anilkumar
- ICAR-National Rice Research Institute, Cuttack, India
| | - N C Sunitha
- University of Agricultural Sciences, Bangalore, India
| | | | - S Ramesh
- University of Agricultural Sciences, Bangalore, India.
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Yadav B, Kaur V, Narayan OP, Yadav SK, Kumar A, Wankhede DP. Integrated omics approaches for flax improvement under abiotic and biotic stress: Current status and future prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:931275. [PMID: 35958216 PMCID: PMC9358615 DOI: 10.3389/fpls.2022.931275] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 05/03/2023]
Abstract
Flax (Linum usitatissimum L.) or linseed is one of the important industrial crops grown all over the world for seed oil and fiber. Besides oil and fiber, flax offers a wide range of nutritional and therapeutic applications as a feed and food source owing to high amount of α-linolenic acid (omega-3 fatty acid), lignans, protein, minerals, and vitamins. Periodic losses caused by unpredictable environmental stresses such as drought, heat, salinity-alkalinity, and diseases pose a threat to meet the rising market demand. Furthermore, these abiotic and biotic stressors have a negative impact on biological diversity and quality of oil/fiber. Therefore, understanding the interaction of genetic and environmental factors in stress tolerance mechanism and identification of underlying genes for economically important traits is critical for flax improvement and sustainability. In recent technological era, numerous omics techniques such as genomics, transcriptomics, metabolomics, proteomics, phenomics, and ionomics have evolved. The advancements in sequencing technologies accelerated development of genomic resources which facilitated finer genetic mapping, quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection in major cereal and oilseed crops including flax. Extensive studies in the area of genomics and transcriptomics have been conducted post flax genome sequencing. Interestingly, research has been focused more for abiotic stresses tolerance compared to disease resistance in flax through transcriptomics, while the other areas of omics such as metabolomics, proteomics, ionomics, and phenomics are in the initial stages in flax and several key questions remain unanswered. Little has been explored in the integration of omic-scale data to explain complex genetic, physiological and biochemical basis of stress tolerance in flax. In this review, the current status of various omics approaches for elucidation of molecular pathways underlying abiotic and biotic stress tolerance in flax have been presented and the importance of integrated omics technologies in future research and breeding have been emphasized to ensure sustainable yield in challenging environments.
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Affiliation(s)
- Bindu Yadav
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Vikender Kaur
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Om Prakash Narayan
- College of Arts and Sciences, University of Florida, Gainesville, FL, United States
| | - Shashank Kumar Yadav
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ashok Kumar
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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Jia B, Conner RL, Penner WC, Zheng C, Cloutier S, Hou A, Xia X, You FM. Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (Phaseolus vulgaris L.). Int J Mol Sci 2022; 23:ijms23147639. [PMID: 35886986 PMCID: PMC9324509 DOI: 10.3390/ijms23147639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023] Open
Abstract
Common bean (Phaseolus vulgaris L.) is a food crop that is an important source of dietary proteins and carbohydrates. Marsh spot is a physiological disorder that diminishes seed quality in beans. Prior research suggested that this disease is likely caused by manganese (Mn) deficiency during seed development and that marsh spot resistance is controlled by at least four genes. In this study, genetic mapping was performed to identify quantitative trait loci (QTL) and the potential candidate genes associated with marsh spot resistance. All 138 recombinant inbred lines (RILs) from a bi-parental population were evaluated for marsh spot resistance during five years from 2015 to 2019 in sandy and heavy clay soils in Morden, Manitoba, Canada. The RILs were sequenced using a genotyping by sequencing approach. A total of 52,676 single nucleotide polymorphisms (SNPs) were identified and filtered to generate a high-quality set of 2066 SNPs for QTL mapping. A genetic map based on 1273 SNP markers distributed on 11 chromosomes and covering 1599 cm was constructed. A total of 12 stable and 4 environment-specific QTL were identified using additive effect models, and an additional two epistatic QTL interacting with two of the 16 QTL were identified using an epistasis model. Genome-wide scans of the candidate genes identified 13 metal transport-related candidate genes co-locating within six QTL regions. In particular, two QTL (QTL.3.1 and QTL.3.2) with the highest R2 values (21.8% and 24.5%, respectively) harbored several metal transport genes Phvul.003G086300, Phvul.003G092500, Phvul.003G104900, Phvul.003G099700, and Phvul.003G108900 in a large genomic region of 16.8–27.5 Mb on chromosome 3. These results advance the current understanding of the genetic mechanisms of marsh spot resistance in cranberry common bean and provide new genomic resources for use in genomics-assisted breeding and for candidate gene isolation and functional characterization.
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Affiliation(s)
- Bosen Jia
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (B.J.); (C.Z.); (S.C.)
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada;
| | - Robert L. Conner
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (R.L.C.); (W.C.P.)
| | - Waldo C. Penner
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (R.L.C.); (W.C.P.)
| | - Chunfang Zheng
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (B.J.); (C.Z.); (S.C.)
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (B.J.); (C.Z.); (S.C.)
| | - Anfu Hou
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (R.L.C.); (W.C.P.)
- Correspondence: (A.H.); (F.M.Y.); Tel.: +1-204-822-7528 (A.H.); +1-613-759-1539 (F.M.Y.)
| | - Xuhua Xia
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada;
| | - Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (B.J.); (C.Z.); (S.C.)
- Correspondence: (A.H.); (F.M.Y.); Tel.: +1-204-822-7528 (A.H.); +1-613-759-1539 (F.M.Y.)
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13
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Saroha A, Pal D, Gomashe SS, Akash, Kaur V, Ujjainwal S, Rajkumar S, Aravind J, Radhamani J, Kumar R, Chand D, Sengupta A, Wankhede DP. Identification of QTNs Associated With Flowering Time, Maturity, and Plant Height Traits in Linum usitatissimum L. Using Genome-Wide Association Study. Front Genet 2022; 13:811924. [PMID: 35774513 PMCID: PMC9237403 DOI: 10.3389/fgene.2022.811924] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/02/2022] [Indexed: 12/21/2022] Open
Abstract
Early flowering, maturity, and plant height are important traits for linseed to fit in rice fallows, for rainfed agriculture, and for economically viable cultivation. Here, Multi-Locus Genome-Wide Association Study (ML-GWAS) was undertaken in an association mapping panel of 131 accessions, genotyped using 68,925 SNPs identified by genotyping by sequencing approach. Phenotypic evaluation data of five environments comprising 3 years and two locations were used. GWAS was performed for three flowering time traits including days to 5%, 50%, and 95% flowering, days to maturity, and plant height by employing five ML-GWAS methods: FASTmrEMMA, FASTmrMLM, ISIS EM-BLASSO, mrMLM, and pLARmEB. A total of 335 unique QTNs have been identified for five traits across five environments. 109 QTNs were stable as observed in ≥2 methods and/or environments, explaining up to 36.6% phenotypic variance. For three flowering time traits, days to maturity, and plant height, 53, 30, and 27 stable QTNs, respectively, were identified. Candidate genes having roles in flower, pollen, embryo, seed and fruit development, and xylem/phloem histogenesis have been identified. Gene expression of candidate genes for flowering and plant height were studied using transcriptome of an early maturing variety Sharda (IC0523807). The present study unravels QTNs/candidate genes underlying complex flowering, days to maturity, and plant height traits in linseed.
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You FM, Rashid KY, Zheng C, Khan N, Li P, Xiao J, He L, Yao Z, Cloutier S. Insights into the Genetic Architecture and Genomic Prediction of Powdery Mildew Resistance in Flax ( Linum usitatissimum L.). Int J Mol Sci 2022; 23:ijms23094960. [PMID: 35563347 PMCID: PMC9104541 DOI: 10.3390/ijms23094960] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 12/29/2022] Open
Abstract
Powdery mildew (PM), caused by the fungus Oidium lini in flax, can cause defoliation and reduce seed yield and quality. To date, one major dominant gene (Pm1) and three quantitative trait loci (QTL) on chromosomes 1, 7 and 9 have been reported for PM resistance. To fully dissect the genetic architecture of PM resistance and identify QTL, a diverse flax core collection of 372 accessions augmented with an additional 75 breeding lines were sequenced, and PM resistance was evaluated in the field for eight years (2010–2017) in Morden, Manitoba, Canada. Genome-wide association studies (GWAS) were performed using two single-locus and seven multi-locus statistical models with 247,160 single nucleotide polymorphisms (SNPs) and the phenotypes of the 447 individuals for each year separately as well as the means over years. A total of 349 quantitative trait nucleotides (QTNs) were identified, of which 44 large-effect QTNs (R2 = 10–30%) were highly stable over years. The total number of favourable alleles per accession was significantly correlated with PM resistance (r = 0.74), and genomic selection (GS) models using all identified QTNs generated significantly higher predictive ability (r = 0.93) than those constructed using the 247,160 genome-wide random SNP (r = 0.69), validating the overall reliability of the QTNs and showing the additivity of PM resistance in flax. The QTNs were clustered on the distal ends of all 15 chromosomes, especially on chromosome 5 (0.4–5.6 Mb and 9.4–16.9 Mb) and 13 (4.7–5.2 Mb). To identify candidate genes, a dataset of 3230 SNPs located in resistance gene analogues (RGAs) was used as input for GWAS, from which an additional 39 RGA-specific QTNs were identified. Overall, 269 QTN loci harboured 445 RGAs within the 200 Kb regions spanning the QTNs, including 45 QTNs located within the RGAs. These RGAs supported by significant QTN/SNP allele effects were mostly nucleotide binding site and leucine-rich repeat receptors (NLRs) belonging to either coiled-coil (CC) NLR (CNL) or toll interleukin-1 (TIR) NLR (TNL), receptor-like kinase (RLK), receptor-like protein kinase (RLP), transmembrane-coiled-coil (TM-CC), WRKY, and mildew locus O (MLO) genes. These results constitute an important genomic tool for resistance breeding and gene cloning for PM in flax.
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Affiliation(s)
- Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Correspondence: (F.M.Y.); (S.C.); Tel.: +1-613-759-1539 (F.M.Y.); +1-613-759-1744 (S.C.)
| | - Khalid Y. Rashid
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (K.Y.R.); (Z.Y.)
| | - Chunfang Zheng
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
| | - Nadeem Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Pingchuan Li
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
| | - Jin Xiao
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China;
| | - Liqiang He
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China;
| | - Zhen Yao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (K.Y.R.); (Z.Y.)
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Correspondence: (F.M.Y.); (S.C.); Tel.: +1-613-759-1539 (F.M.Y.); +1-613-759-1744 (S.C.)
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Li M, Zhang YW, Zhang ZC, Xiang Y, Liu MH, Zhou YH, Zuo JF, Zhang HQ, Chen Y, Zhang YM. A compressed variance component mixed model for detecting QTNs and QTN-by-environment and QTN-by-QTN interactions in genome-wide association studies. MOLECULAR PLANT 2022; 15:630-650. [PMID: 35202864 DOI: 10.1016/j.molp.2022.02.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 01/26/2022] [Accepted: 02/19/2022] [Indexed: 05/25/2023]
Abstract
Although genome-wide association studies are widely used to mine genes for quantitative traits, the effects to be estimated are confounded, and the methodologies for detecting interactions are imperfect. To address these issues, the mixed model proposed here first estimates the genotypic effects for AA, Aa, and aa, and the genotypic polygenic background replaces additive and dominance polygenic backgrounds. Then, the estimated genotypic effects are partitioned into additive and dominance effects using a one-way analysis of variance model. This strategy was further expanded to cover QTN-by-environment interactions (QEIs) and QTN-by-QTN interactions (QQIs) using the same mixed-model framework. Thus, a three-variance-component mixed model was integrated with our multi-locus random-SNP-effect mixed linear model (mrMLM) method to establish a new methodological framework, 3VmrMLM, that detects all types of loci and estimates their effects. In Monte Carlo studies, 3VmrMLM correctly detected all types of loci and almost unbiasedly estimated their effects, with high powers and accuracies and a low false positive rate. In re-analyses of 10 traits in 1439 rice hybrids, detection of 269 known genes, 45 known gene-by-environment interactions, and 20 known gene-by-gene interactions strongly validated 3VmrMLM. Further analyses of known genes showed more small (67.49%), minor-allele-frequency (35.52%), and pleiotropic (30.54%) genes, with higher repeatability across datasets (54.36%) and more dominance loci. In addition, a heteroscedasticity mixed model in multiple environments and dimension reduction methods in quite a number of environments were developed to detect QEIs, and variable selection under a polygenic background was proposed for QQI detection. This study provides a new approach for revealing the genetic architecture of quantitative traits.
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Affiliation(s)
- Mei Li
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ya-Wen Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; State Key Laboratory of Cotton Biology, Anyang 455000, China
| | - Ze-Chang Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu Xiang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming-Hui Liu
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ya-Hui Zhou
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian-Fang Zuo
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Han-Qing Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Chen
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Delfini J, Moda-Cirino V, dos Santos Neto J, Zeffa DM, Nogueira AF, Ribeiro LAB, Ruas PM, Gepts P, Gonçalves LSA. Genome-Wide Association Study Identifies Genomic Regions for Important Morpho-Agronomic Traits in Mesoamerican Common Bean. FRONTIERS IN PLANT SCIENCE 2021; 12:748829. [PMID: 34691125 PMCID: PMC8528967 DOI: 10.3389/fpls.2021.748829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/15/2021] [Indexed: 05/25/2023]
Abstract
The population growth trend in recent decades has resulted in continuing efforts to guarantee food security in which leguminous plants, such as the common bean (Phaseolus vulgaris L.), play a particularly important role as they are relatively cheap and have high nutritional value. To meet this demand for food, the main target for genetic improvement programs is to increase productivity, which is a complex quantitative trait influenced by many component traits. This research aims to identify Quantitative Trait Nucleotides (QTNs) associated with productivity and its components using multi-locus genome-wide association studies. Ten morpho-agronomic traits [plant height (PH), first pod insertion height (FPIH), number of nodules (NN), pod length (PL), total number of pods per plant (NPP), number of locules per pod (LP), number of seeds per pod (SP), total seed weight per plant (TSW), 100-seed weight (W100), and grain yield (YLD)] were evaluated in four environments for 178 Mesoamerican common bean domesticated accessions belonging to the Brazilian Diversity Panel. In order to identify stable QTNs, only those identified by multiple methods (mrMLM, FASTmrMLM, pLARmEB, and ISIS EM-BLASSO) or in multiple environments were selected. Among the identified QTNs, 64 were detected at least thrice by different methods or in different environments, and 39 showed significant phenotypic differences between their corresponding alleles. The alleles that positively increased the corresponding traits, except PH (for which lower values are desired), were considered favorable alleles. The most influenced trait by the accumulation of favorable alleles was PH, showing a 51.7% reduction, while NN, TSW, YLD, FPIH, and NPP increased between 18 and 34%. Identifying QTNs in several environments (four environments and overall adjusted mean) and by multiple methods reinforces the reliability of the associations obtained and the importance of conducting these studies in multiple environments. Using these QTNs through molecular techniques for genetic improvement, such as marker-assisted selection or genomic selection, can be a strategy to increase common bean production.
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Affiliation(s)
- Jessica Delfini
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Vânia Moda-Cirino
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
| | - José dos Santos Neto
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Douglas Mariani Zeffa
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Brazil
| | - Alison Fernando Nogueira
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Luriam Aparecida Brandão Ribeiro
- Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Paulo Maurício Ruas
- Departamento de Biologia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Paul Gepts
- Section of Crop and Ecosystem Sciences, Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Leandro Simões Azeredo Gonçalves
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Brazil
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Yan W, Karikari B, Chang F, Zhao F, Zhang Y, Li D, Zhao T, Jiang H. Genome-Wide Association Study to Map Genomic Regions Related to the Initiation Time of Four Growth Stage Traits in Soybean. Front Genet 2021; 12:715529. [PMID: 34594361 PMCID: PMC8476948 DOI: 10.3389/fgene.2021.715529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/09/2021] [Indexed: 12/13/2022] Open
Abstract
The time to flowering (DF), pod beginning (DPB), seed formation (DSF), and maturity initiation (DMI) in soybean (Glycine max [L.] Merr) are important characteristics of growth stage traits (GSTs) in Chinese summer-sowing soybean, and are influenced by genetic as well as environmental factors. To better understand the molecular mechanism underlying the initiation times of GSTs, we investigated four GSTs of 309 diverse soybean accessions in six different environments and Best Linear Unbiased Prediction values. Furthermore, the genome-wide association study was conducted by a Fixed and random model Circulating Probability Unification method using over 60,000 single nucleotide polymorphism (SNP) markers to identify the significant quantitative trait nucleotide (QTN) regions with phenotypic data. As a result, 212 SNPs within 102 QTN regions were associated with four GSTs. Of which, eight stable regions were repeatedly detected in least three datasets for one GST. Interestingly, half of the QTN regions overlapped with previously reported quantitative trait loci or well-known soybean growth period genes. The hotspots associated with all GSTs were concentrated on chromosome 10. E2 (Glyma10g36600), a gene with a known function in regulating flowering and maturity in soybean, is also found on this chromosome. Thus, this genomic region may account for the strong correlation among the four GSTs. All the significant SNPs in the remaining 7 QTN regions could cause the significant phenotypic variation with both the major and minor alleles. Two hundred and seventy-five genes in soybean and their homologs in Arabidopsis were screened within ± 500 kb of 7 peak SNPs in the corresponding QTN regions. Most of the genes are involved in flowering, response to auxin stimulus, or regulation of seed germination, among others. The findings reported here provide an insight for genetic improvement which will aid in breeding of soybean cultivars that can be adapted to the various summer sowing areas in China and beyond.
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Affiliation(s)
- Wenliang Yan
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China.,College of Artificial Intelligence, Nanjing Agricultural University, Nanjing, China
| | - Benjamin Karikari
- Department of Crop Science, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Fangguo Chang
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China
| | - Fangzhou Zhao
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China
| | - Yinghu Zhang
- Institute of Agricultural Sciences in Jiangsu Coastal Region, Yancheng, China
| | - Dongmei Li
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China.,College of Artificial Intelligence, Nanjing Agricultural University, Nanjing, China
| | - Tuanjie Zhao
- Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China
| | - Haiyan Jiang
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing, China
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Amas J, Anderson R, Edwards D, Cowling W, Batley J. Status and advances in mining for blackleg (Leptosphaeria maculans) quantitative resistance (QR) in oilseed rape (Brassica napus). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3123-3145. [PMID: 34104999 PMCID: PMC8440254 DOI: 10.1007/s00122-021-03877-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/29/2021] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE Quantitative resistance (QR) loci discovered through genetic and genomic analyses are abundant in the Brassica napus genome, providing an opportunity for their utilization in enhancing blackleg resistance. Quantitative resistance (QR) has long been utilized to manage blackleg in Brassica napus (canola, oilseed rape), even before major resistance genes (R-genes) were extensively explored in breeding programmes. In contrast to R-gene-mediated qualitative resistance, QR reduces blackleg symptoms rather than completely eliminating the disease. As a polygenic trait, QR is controlled by numerous genes with modest effects, which exerts less pressure on the pathogen to evolve; hence, its effectiveness is more durable compared to R-gene-mediated resistance. Furthermore, combining QR with major R-genes has been shown to enhance resistance against diseases in important crops, including oilseed rape. For these reasons, there has been a renewed interest among breeders in utilizing QR in crop improvement. However, the mechanisms governing QR are largely unknown, limiting its deployment. Advances in genomics are facilitating the dissection of the genetic and molecular underpinnings of QR, resulting in the discovery of several loci and genes that can be potentially deployed to enhance blackleg resistance. Here, we summarize the efforts undertaken to identify blackleg QR loci in oilseed rape using linkage and association analysis. We update the knowledge on the possible mechanisms governing QR and the advances in searching for the underlying genes. Lastly, we lay out strategies to accelerate the genetic improvement of blackleg QR in oilseed rape using improved phenotyping approaches and genomic prediction tools.
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Affiliation(s)
- Junrey Amas
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001 Australia
| | - Robyn Anderson
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001 Australia
| | - David Edwards
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001 Australia
| | - Wallace Cowling
- School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
| | - Jacqueline Batley
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001 Australia
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Delfini J, Moda-Cirino V, Dos Santos Neto J, Zeffa DM, Nogueira AF, Ribeiro LAB, Ruas PM, Gepts P, Gonçalves LSA. Genome-wide association study for grain mineral content in a Brazilian common bean diversity panel. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2795-2811. [PMID: 34027567 DOI: 10.1007/s00122-021-03859-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
QTNs significantly associated to nine mineral content in grains of common bean were identified. The accumulation of favorable alleles was associated with a gradually increasing nutrient content in the grain. Biofortification is one of the strategies developed to address malnutrition in developing countries, the aim of which is to improve the nutritional content of crops. The common bean (Phaseolus vulgaris L.), a staple food in several African and Latin American countries, has excellent nutritional attributes and is considered a strong candidate for biofortification. The objective of this study was to identify genomic regions associated with nutritional content in common bean grains using 178 Mesoamerican accessions belonging to a Brazilian Diversity Panel (BDP) and 25,011 good-quality single nucleotide polymorphisms. The BDP was phenotyped in three environments for nine nutrients (phosphorus, potassium, calcium, magnesium, copper, manganese, sulfur, zinc, and iron) using four genome-wide association multi-locus methods. To obtain more accurate results, only quantitative trait nucleotides (QTNs) that showed repeatability (i.e., those detected at least twice using different methods or environments) were considered. Forty-eight QTNs detected for the nine minerals showed repeatability and were considered reliable. Pleiotropic QTNs and overlapping genomic regions surrounding the QTNs were identified, demonstrating the possible association between the deposition mechanisms of different nutrients in grains. The accumulation of favorable alleles in the same accession was associated with a gradually increasing nutrient content in the grain. The BDP proved to be a valuable source for association studies. The investigation of different methods and environments showed the reliability of markers associated with minerals. The loci identified in this study will potentially contribute to the improvement of Mesoamerican common beans, particularly carioca and black beans, the main groups consumed in Brazil.
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Affiliation(s)
- Jessica Delfini
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
- Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil
| | - Vânia Moda-Cirino
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
| | - José Dos Santos Neto
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
- Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil
| | - Douglas Mariani Zeffa
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
- Agronomy Department, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Alison Fernando Nogueira
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
- Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil
| | - Luriam Aparecida Brandão Ribeiro
- Plant Breeding, Instituto de Desenvolvimento Rural do Paraná-IDR-Paraná-Emater (IDR-Paraná), Londrina, Brazil
- Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil
| | - Paulo Maurício Ruas
- Biology Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil
| | - Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA, USA
| | - Leandro Simões Azeredo Gonçalves
- Agronomy Department, Universidade Estadual de Londrina (UEL), Londrina, Brazil.
- Agronomy Department, Universidade Estadual de Maringá, Maringá, Paraná, Brazil.
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Sertse D, You FM, Ravichandran S, Soto-Cerda BJ, Duguid S, Cloutier S. Loci harboring genes with important role in drought and related abiotic stress responses in flax revealed by multiple GWAS models. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:191-212. [PMID: 33047220 DOI: 10.1007/s00122-020-03691-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 09/18/2020] [Indexed: 05/19/2023]
Abstract
QTNs associated with drought tolerance traits and indices were identified in a flax mini-core collection through multiple GWAS models and phenotyping at multiple locations under irrigated and non-irrigated field conditions. Drought is a critical phenomenon challenging today's agricultural sector. Crop varieties adapted to moisture deficit are becoming vital. Flax can be greatly affected by limiting moisture conditions, especially during the early development and reproductive stages. Here, a mini-core collection comprising genotypes from more than 20 major growing countries was evaluated for 11 drought-related traits in irrigated and non-irrigated fields for 3 years. Heritability of the traits ranged from 44.7 to 86%. Six of the 11 traits showed significant phenotypic difference between irrigated and non-irrigated conditions. A genome-wide association study (GWAS) was performed for these six traits and their corresponding stress indices based on 106 genotypes and 12,316 single nucleotide polymorphisms (SNPs) using six multi-locus and one single-locus models. The SNPs were then assigned to 8050 linkage disequilibrium (LD) blocks to which a restricted two-stage multi-locus multi-allele GWAS was applied. A total of 144 quantitative trait nucleotides (QTNs) and 13 LD blocks were associated with at least one trait or stress index. Of these, 16 explained more than 15% of the genetic variance. Most large-effect QTN loci harbored gene(s) previously predicted to play role(s) in the associated traits. Genes mediating responses to abiotic stresses resided at loci associated with stress indices. Flax genes Lus10009480 and Lus10030150 that are predicted to encode WAX INDUCER1 and STRESS-ASSOCIATED PROTEIN (SAP), respectively, are among the important candidates detected. Accessions with multiple favorable alleles outperformed others for grain yield, thousand seed weight and fiber/biomass in non-irrigated conditions, suggesting their potential usefulness in breeding and genomic selection.
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Affiliation(s)
- Demissew Sertse
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada
| | - Sridhar Ravichandran
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada
| | - Braulio J Soto-Cerda
- Agriaquaculture Nutritional Genomic Centre (CGNA), Las Heras 350, 4781158, Temuco, Chile
| | - Scott Duguid
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, Canada
| | - Sylvie Cloutier
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada.
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada.
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21
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Galinousky D, Mokshina N, Padvitski T, Ageeva M, Bogdan V, Kilchevsky A, Gorshkova T. The Toolbox for Fiber Flax Breeding: A Pipeline From Gene Expression to Fiber Quality. Front Genet 2020; 11:589881. [PMID: 33281880 PMCID: PMC7690631 DOI: 10.3389/fgene.2020.589881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/22/2020] [Indexed: 01/22/2023] Open
Abstract
The goal of any plant breeding program is to improve quality of a target crop. Crop quality is a comprehensive feature largely determined by biological background. To improve the quality parameters of crops grown for the production of fiber, a functional approach was used to search for genes suitable for the effective manipulation of technical fiber quality. A key step was to identify genes with tissue and stage-specific pattern of expression in the developing fibers. In the current study, we investigated the relationship between gene expression evaluated in bast fibers of developing flax plants and the quality parameters of technical fibers measured after plant harvesting. Based on previously published transcriptomic data, two sets of genes that are upregulated in fibers during intrusive growth and tertiary cell wall deposition were selected. The expression level of the selected genes and fiber quality parameters were measured in fiber flax, linseed (oil flax) cultivars, and wild species that differ in type of yield and fiber quality parameters. Based on gene expression data, linear regression models for technical stem length, fiber tensile strength, and fiber flexibility were constructed, resulting in the identification of genes that have high potential for manipulating fiber quality. Chromosomal localization and single nucleotide polymorphism distribution in the selected genes were characterized for the efficacy of their use in conventional breeding and genome editing programs. Transcriptome-based selection is a highly targeted functional approach that could be used during the development of new cultivars of various crops.
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Affiliation(s)
- Dmitry Galinousky
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
- Laboratory of Ecological Genetics and Biotechnology, Institute of Genetics and Cytology, The National Academy of Sciences of Belarus, Minsk, Belarus
| | - Natalia Mokshina
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Tsimafei Padvitski
- Cellular Network and Systems Biology Group, University of Cologne, CECAD, Cologne, Germany
| | - Marina Ageeva
- Laboratory of Microscopy, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Victor Bogdan
- Laboratory of Fiber Flax Breeding, Institute of Flax, Ustie, Belarus
| | - Alexander Kilchevsky
- Laboratory of Ecological Genetics and Biotechnology, Institute of Genetics and Cytology, The National Academy of Sciences of Belarus, Minsk, Belarus
| | - Tatyana Gorshkova
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
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Wang S, Xu Y, Qu H, Cui Y, Li R, Chater JM, Yu L, Zhou R, Ma R, Huang Y, Qiao Y, Hu X, Xie W, Jia Z. Boosting predictabilities of agronomic traits in rice using bivariate genomic selection. Brief Bioinform 2020; 22:5867560. [PMID: 34020535 DOI: 10.1093/bib/bbaa103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/27/2020] [Accepted: 05/04/2020] [Indexed: 12/24/2022] Open
Abstract
The multivariate genomic selection (GS) models have not been adequately studied and their potential remains unclear. In this study, we developed a highly efficient bivariate (2D) GS method and demonstrated its significant advantages over the univariate (1D) rival methods using a rice dataset, where four traditional traits (i.e. yield, 1000-grain weight, grain number and tiller number) as well as 1000 metabolomic traits were analyzed. The novelty of the method is the incorporation of the HAT methodology in the 2D BLUP GS model such that the computational efficiency has been dramatically increased by avoiding the conventional cross-validation. The results indicated that (1) the 2D BLUP-HAT GS analysis generally produces higher predictabilities for two traits than those achieved by the analysis of individual traits using 1D GS model, and (2) selected metabolites may be utilized as ancillary traits in the new 2D BLUP-HAT GS method to further boost the predictability of traditional traits, especially for agronomically important traits with low 1D predictabilities.
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Affiliation(s)
| | | | - Han Qu
- University of California, Riverside, USA
| | - Yanru Cui
- Hebei Agricultural University, China
| | - Ruidong Li
- University of California, Riverside, USA
| | | | - Lei Yu
- University of California, Riverside, USA
| | - Rui Zhou
- South China University of Technology, Chinaa
| | | | | | - Yiru Qiao
- University of California, Riverside, USA
| | - Xuehai Hu
- Huazhong Agricultural University, China
| | - Weibo Xie
- Huazhong Agricultural University, China
| | - Zhenyu Jia
- University of California, Riverside, USA
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Akhmetshina AO, Strygina KV, Khlestkina EK, Porokhovinova EA, Brutch NB. High-throughput sequencing techniques to flax genetics and breeding. ECOLOGICAL GENETICS 2020. [PMID: 0 DOI: 10.17816/ecogen16126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Flax (Linum usitatissimum L.) is an important oil and fiber crop. Using modern methods for flax breeding allows accelerating the introduction of some desired genes into the genotypes of future varieties. Today, an important condition for their creation is the development of research, that is based on next-generation sequencing (NGS). This review summarizes the results obtained using NGS in flax research. To date, a linkage map with a high marker density has been obtained for L. usitatissimum, which is already being used for a more efficient search for quantitative traits loci. Comparative studies of transcriptomes and miRNomes of flax under stress and in control conditions elucidated molecular-genetic mechanisms of abiotic and biotic stress responses. The very accurate model for genomic selection of flax resistant to pasmo was constructed. Based on NGS-sequencing also some details of the genus Linum evolution were clarified. The knowledge systematized in the review can be useful for researchers working in flax breeding and whereas fundamental interest for understanding the phylogenetic relationships within the genus Linum, the ontogenesis, and the mechanisms of the response of flax plants to various stress factors.
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Lan S, Zheng C, Hauck K, McCausland M, Duguid SD, Booker HM, Cloutier S, You FM. Genomic Prediction Accuracy of Seven Breeding Selection Traits Improved by QTL Identification in Flax. Int J Mol Sci 2020; 21:ijms21051577. [PMID: 32106624 PMCID: PMC7084455 DOI: 10.3390/ijms21051577] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/23/2020] [Accepted: 02/23/2020] [Indexed: 01/21/2023] Open
Abstract
Molecular markers are one of the major factors affecting genomic prediction accuracy and the cost of genomic selection (GS). Previous studies have indicated that the use of quantitative trait loci (QTL) as markers in GS significantly increases prediction accuracy compared with genome-wide random single nucleotide polymorphism (SNP) markers. To optimize the selection of QTL markers in GS, a set of 260 lines from bi-parental populations with 17,277 genome-wide SNPs were used to evaluate the prediction accuracy for seed yield (YLD), days to maturity (DTM), iodine value (IOD), protein (PRO), oil (OIL), linoleic acid (LIO), and linolenic acid (LIN) contents. These seven traits were phenotyped over four years at two locations. Identification of quantitative trait nucleotides (QTNs) for the seven traits was performed using three types of statistical models for genome-wide association study: two SNP-based single-locus (SS), seven SNP-based multi-locus (SM), and one haplotype-block-based multi-locus (BM) models. The identified QTNs were then grouped into QTL based on haplotype blocks. For all seven traits, 133, 355, and 1208 unique QTL were identified by SS, SM, and BM, respectively. A total of 1420 unique QTL were obtained by SS+SM+BM, ranging from 254 (OIL, LIO) to 361 (YLD) for individual traits, whereas a total of 427 unique QTL were achieved by SS+SM, ranging from 56 (YLD) to 128 (LIO). SS models alone did not identify sufficient QTL for GS. The highest prediction accuracies were obtained using single-trait QTL identified by SS+SM+BM for OIL (0.929 ± 0.016), PRO (0.893 ± 0.023), YLD (0.892 ± 0.030), and DTM (0.730 ± 0.062), and by SS+SM for LIN (0.837 ± 0.053), LIO (0.835 ± 0.049), and IOD (0.835 ± 0.041). In terms of the number of QTL markers and prediction accuracy, SS+SM outperformed other models or combinations thereof. The use of all SNPs or QTL of all seven traits significantly reduced the prediction accuracy of traits. The results further validated that QTL outperformed high-density genome-wide random markers, and demonstrated that the combined use of single and multi-locus models can effectively identify a comprehensive set of QTL that improve prediction accuracy, but further studies on detection and removal of redundant or false-positive QTL to maximize prediction accuracy and minimize the number of QTL markers in GS are warranted.
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Affiliation(s)
- Samuel Lan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (S.L.); (C.Z.); (K.H.); (M.M.)
- Department of Mathematics and Statistics, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Chunfang Zheng
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (S.L.); (C.Z.); (K.H.); (M.M.)
| | - Kyle Hauck
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (S.L.); (C.Z.); (K.H.); (M.M.)
- Department of Mathematics and Statistics, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Madison McCausland
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (S.L.); (C.Z.); (K.H.); (M.M.)
- Department of Plant Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Scott D. Duguid
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada;
| | - Helen M. Booker
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada;
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (S.L.); (C.Z.); (K.H.); (M.M.)
- Correspondence: (F.M.Y.); (S.C); Tel.: +1-613-759-1539 (F.M.Y.); +1-613-759-1744 (S.C.)
| | - Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (S.L.); (C.Z.); (K.H.); (M.M.)
- Correspondence: (F.M.Y.); (S.C); Tel.: +1-613-759-1539 (F.M.Y.); +1-613-759-1744 (S.C.)
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Zhang YM, Jia Z, Dunwell JM. Editorial: The Applications of New Multi-Locus GWAS Methodologies in the Genetic Dissection of Complex Traits. FRONTIERS IN PLANT SCIENCE 2019; 10:100. [PMID: 30804969 DOI: 10.3389/978-2-88945-834-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 01/22/2019] [Indexed: 05/22/2023]
Affiliation(s)
- Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Jim M Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
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Zhang YM, Jia Z, Dunwell JM. Editorial: The Applications of New Multi-Locus GWAS Methodologies in the Genetic Dissection of Complex Traits. FRONTIERS IN PLANT SCIENCE 2019; 10:100. [PMID: 30804969 PMCID: PMC6378272 DOI: 10.3389/fpls.2019.00100] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 01/22/2019] [Indexed: 05/04/2023]
Affiliation(s)
- Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Yuan-Ming Zhang
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Jim M. Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
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