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Li K, Yu Y, Zhang N, Xie L, Huang W, Qi X, Li W, Li C, Wen T, Zhu W, Yan S, Li G, Guo X, Hu J. Unlocking the genetic basis of vitamin E content in sweet corn kernels: Expanding breeding targets through genome-wide association studies. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 348:112233. [PMID: 39173886 DOI: 10.1016/j.plantsci.2024.112233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/23/2024] [Accepted: 08/15/2024] [Indexed: 08/24/2024]
Abstract
Tocochromanols, collectively known as Vitamin E, serve as natural lipid-soluble antioxidants that are exclusively obtained through dietary intake in humans. Synthesized by all plants, tocochromanols play an important role in protecting polyunsaturated fatty acids in plant seeds from lipid peroxidation. While the genes involved in tocochromanol biosynthesis have been fully elucidated in Arabidopsis thaliana, Oryza sativa and Zea mays, the genetic basis of tocochromanol accumulation in sweet corn remains poorly understood. This gap is a consequence of limited natural genetic diversity and harvest at immature growth stages. In this study, we conducted comprehensive genome-wide association studies (GWAS) on a sweet corn panel of 295 individuals with a high-density molecular marker set. In total, thirteen quantitative trait loci (QTLs) for individual and derived tocochromanol traits were identified. Our analysis identified novel roles for three genes, ZmCS2, Zmshki1 and ZmB4FMV1, in the regulation of α-tocopherol accumulation in sweet corn kernels. We genetically validated the role of Zmshki1 through the generation of a knock-out line using CRISPR-Cas9 technology. Further gene-based GWAS revealed the function of the canonical tyrosine metabolic enzymes ZmCS2 and Zmhppd1 in the regulation of total tocochromanol content. This comprehensive assessment of the genetic basis for variation in vitamin E content establishes a solid foundation for enhancing vitamin E content not only in sweet corn, but also in other cereal crops.
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Affiliation(s)
- Kun Li
- Crop Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Yongtao Yu
- Crop Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Nan Zhang
- Crop Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Lihua Xie
- Crop Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, China; School of Food Science and Engineering, South China University of Technology, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, Guangzhou, China
| | - Wenjie Huang
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xitao Qi
- Crop Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Wu Li
- Crop Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Chunyan Li
- Crop Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Tianxiang Wen
- Crop Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Wenguang Zhu
- Crop Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Gaoke Li
- Crop Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, China.
| | - Xinbo Guo
- School of Food Science and Engineering, South China University of Technology, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, Guangzhou, China.
| | - Jianguang Hu
- Crop Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Crop Genetic Improvement, Guangzhou, China.
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Chen J, Zhang Y, Wei J, Hu X, Yin H, Liu W, Li D, Tian W, Hao Y, He Z, Fernie AR, Chen W. Beyond pathways: Accelerated flavonoids candidate identification and novel exploration of enzymatic properties using combined mapping populations of wheat. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2033-2050. [PMID: 38408119 PMCID: PMC11182594 DOI: 10.1111/pbi.14323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
Although forward-genetics-metabolomics methods such as mGWAS and mQTL have proven effective in providing myriad loci affecting metabolite contents, they are somehow constrained by their respective constitutional flaws such as the hidden population structure for GWAS and insufficient recombinant rate for QTL. Here, the combination of mGWAS and mQTL was performed, conveying an improved statistical power to investigate the flavonoid pathways in common wheat. A total of 941 and 289 loci were, respectively, generated from mGWAS and mQTL, within which 13 of them were co-mapped using both approaches. Subsequently, the mGWAS or mQTL outputs alone and their combination were, respectively, utilized to delineate the metabolic routes. Using this approach, we identified two MYB transcription factor encoding genes and five structural genes, and the flavonoid pathway in wheat was accordingly updated. Moreover, we have discovered some rare-activity-exhibiting flavonoid glycosyl- and methyl-transferases, which may possess unique biological significance, and harnessing these novel catalytic capabilities provides potentially new breeding directions. Collectively, we propose our survey illustrates that the forward-genetics-metabolomics approaches including multiple populations with high density markers could be more frequently applied for delineating metabolic pathways in common wheat, which will ultimately contribute to metabolomics-assisted wheat crop improvement.
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Affiliation(s)
- Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
- Yazhouwan National LaboratorySanyaChina
| | - Yueqi Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Jiaqi Wei
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
- Wuhan Academy of Agricultural SciencesWuhanChina
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Huanran Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Wei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| | - Wenfei Tian
- National Wheat Improvement Center, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yuanfeng Hao
- National Wheat Improvement Center, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | | | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
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Chen B, Wang M, Guo Y, Zhang Z, Zhou W, Cao L, Zhang T, Ali S, Xie L, Li Y, Zinta G, Sun S, Zhang Q. Climate-related naturally occurring epimutation and their roles in plant adaptation in A. thaliana. Mol Ecol 2024:e17356. [PMID: 38634782 DOI: 10.1111/mec.17356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/27/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
DNA methylation has been proposed to be an important mechanism that allows plants to respond to their environments sometimes entirely uncoupled from genetic variation. To understand the genetic basis, biological functions and climatic relationships of DNA methylation at a population scale in Arabidopsis thaliana, we performed a genome-wide association analysis with high-quality single nucleotide polymorphisms (SNPs), and found that ~56% on average, especially in the CHH sequence context (71%), of the differentially methylated regions (DMRs) are not tagged by SNPs. Among them, a total of 3235 DMRs are significantly associated with gene expressions and potentially heritable. 655 of the 3235 DMRs are associated with climatic variables, and we experimentally verified one of them, HEI10 (HUMAN ENHANCER OF CELL INVASION NO.10). Such epigenetic loci could be subjected to natural selection thereby affecting plant adaptation, and would be expected to be an indicator of accessions at risk. We therefore incorporated these climate-related DMRs into a gradient forest model, and found that the natural A. thaliana accessions in Southern Europe that may be most at risk under future climate change. Our findings highlight the importance of integrating DNA methylation that is independent of genetic variations, and climatic data to predict plants' vulnerability to future climate change.
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Affiliation(s)
- Bowei Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
- College of Biology Resources and Environmental Sciences, Jishou University, Jishou, China
| | - Min Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Yile Guo
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zihui Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Wei Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Lesheng Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Shahid Ali
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Linan Xie
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Yuhua Li
- College of Life Science, Northeast Forestry University, Harbin, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Gaurav Zinta
- Integrative Plant AdaptOmics Lab (iPAL), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (CSIR-IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shanwen Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
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Kassem MA, Knizia D, Meksem K. A Summary of Two Decades of QTL and Candidate Genes That Control Seed Tocopherol Contents in Maize ( Zea mays L.). Genes (Basel) 2024; 15:472. [PMID: 38674406 PMCID: PMC11049817 DOI: 10.3390/genes15040472] [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: 12/28/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Tocopherols are secondary metabolites synthesized through the shikimate biosynthetic pathway in the plastids of most plants. It is well known that α-Tocopherol (vitamin E) has many health benefits for humans and animals; therefore, it is highly used in human and animal diets. Tocopherols vary considerably in most crop (and plant) species and within cultivars of the same species depending on environmental and growth conditions; tocopherol content is a polygenic, complex traits, and its inheritance is poorly understood. The objective of this review paper was to summarize all identified quantitative trait loci (QTL) that control seed tocopherols and related contents identified in maize (Zea mays) during the past two decades (2002-2022). Candidate genes identified within these QTL regions are also discussed. The QTL described here, and candidate genes identified within these genomic regions could be used in breeding programs to develop maize cultivars with high, beneficial levels of seed tocopherol contents.
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Affiliation(s)
- My Abdelmajid Kassem
- Plant Genomics and Biotechnology Laboratory, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA
| | - Dounya Knizia
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (K.M.)
| | - Khalid Meksem
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (K.M.)
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Gao J, Li J, Zhang J, Sun Y, Ju X, Li W, Duan H, Xue Z, Sun L, Hussain Sahito J, Fu Z, Zhang X, Tang J. Identification of Novel QTL for Mercury Accumulation in Maize Using an Enlarged SNP Panel. Genes (Basel) 2024; 15:257. [PMID: 38397246 PMCID: PMC10888321 DOI: 10.3390/genes15020257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/14/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
Mercury (Hg) pollution not only poses a threat to the environment but also adversely affects the growth and development of plants, with potential repercussions for animals and humans through bioaccumulation in the food chain. Maize, a crucial source of food, industrial materials, and livestock feed, requires special attention in understanding the genetic factors influencing mercury accumulation. Developing maize varieties with low mercury accumulation is vital for both maize production and human health. In this study, a comprehensive genome-wide association study (GWAS) was conducted using an enlarged SNP panel comprising 1.25 million single nucleotide polymorphisms (SNPs) in 230 maize inbred lines across three environments. The analysis identified 111 significant SNPs within 78 quantitative trait loci (QTL), involving 169 candidate genes under the Q model. Compared to the previous study, the increased marker density and optimized statistical model led to the discovery of 74 additional QTL, demonstrating improved statistical power. Gene ontology (GO) enrichment analysis revealed that most genes participate in arsenate reduction and stress responses. Notably, GRMZM2G440968, which has been reported in previous studies, is associated with the significant SNP chr6.S_155668107 in axis tissue. It encodes a cysteine proteinase inhibitor, implying its potential role in mitigating mercury toxicity by inhibiting cysteine. Haplotype analyses provided further insights, indicating that lines carrying hap3 exhibited the lowest mercury content compared to other haplotypes. In summary, our study significantly enhances the statistical power of GWAS, identifying additional genes related to mercury accumulation and metabolism. These findings offer valuable insights into unraveling the genetic basis of mercury content in maize and contribute to the development of maize varieties with low mercury accumulation.
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Affiliation(s)
- Jionghao Gao
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Jianxin Li
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Jihong Zhang
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Yan Sun
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Xiaolong Ju
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Wenlong Li
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Haiyang Duan
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Zhengjie Xue
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Li Sun
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Javed Hussain Sahito
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Zhiyuan Fu
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Xuehai Zhang
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Jihua Tang
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
- The Shennong Laboratory, Zhengzhou 450002, China
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Sahito JH, Zhang H, Gishkori ZGN, Ma C, Wang Z, Ding D, Zhang X, Tang J. Advancements and Prospects of Genome-Wide Association Studies (GWAS) in Maize. Int J Mol Sci 2024; 25:1918. [PMID: 38339196 PMCID: PMC10855973 DOI: 10.3390/ijms25031918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Genome-wide association studies (GWAS) have emerged as a powerful tool for unraveling intricate genotype-phenotype association across various species. Maize (Zea mays L.), renowned for its extensive genetic diversity and rapid linkage disequilibrium (LD), stands as an exemplary candidate for GWAS. In maize, GWAS has made significant advancements by pinpointing numerous genetic loci and potential genes associated with complex traits, including responses to both abiotic and biotic stress. These discoveries hold the promise of enhancing adaptability and yield through effective breeding strategies. Nevertheless, the impact of environmental stress on crop growth and yield is evident in various agronomic traits. Therefore, understanding the complex genetic basis of these traits becomes paramount. This review delves into current and future prospectives aimed at yield, quality, and environmental stress resilience in maize and also addresses the challenges encountered during genomic selection and molecular breeding, all facilitated by the utilization of GWAS. Furthermore, the integration of omics, including genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics has enriched our understanding of intricate traits in maize, thereby enhancing environmental stress tolerance and boosting maize production. Collectively, these insights not only advance our understanding of the genetic mechanism regulating complex traits but also propel the utilization of marker-assisted selection in maize molecular breeding programs, where GWAS plays a pivotal role. Therefore, GWAS provides robust support for delving into the genetic mechanism underlying complex traits in maize and enhancing breeding strategies.
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Affiliation(s)
- Javed Hussain Sahito
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Hao Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zeeshan Ghulam Nabi Gishkori
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chenhui Ma
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhihao Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
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7
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Tanaka R, Wu D, Li X, Tibbs-Cortes LE, Wood JC, Magallanes-Lundback M, Bornowski N, Hamilton JP, Vaillancourt B, Li X, Deason NT, Schoenbaum GR, Buell CR, DellaPenna D, Yu J, Gore MA. Leveraging prior biological knowledge improves prediction of tocochromanols in maize grain. THE PLANT GENOME 2023; 16:e20276. [PMID: 36321716 DOI: 10.1002/tpg2.20276] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
With an essential role in human health, tocochromanols are mostly obtained by consuming seed oils; however, the vitamin E content of the most abundant tocochromanols in maize (Zea mays L.) grain is low. Several large-effect genes with cis-acting variants affecting messenger RNA (mRNA) expression are mostly responsible for tocochromanol variation in maize grain, with other relevant associated quantitative trait loci (QTL) yet to be fully resolved. Leveraging existing genomic and transcriptomic information for maize inbreds could improve prediction when selecting for higher vitamin E content. Here, we first evaluated a multikernel genomic best linear unbiased prediction (MK-GBLUP) approach for modeling known QTL in the prediction of nine tocochromanol grain phenotypes (12-21 QTL per trait) within and between two panels of 1,462 and 242 maize inbred lines. On average, MK-GBLUP models improved predictive abilities by 7.0-13.6% when compared with GBLUP. In a second approach with a subset of 545 lines from the larger panel, the highest average improvement in predictive ability relative to GBLUP was achieved with a multi-trait GBLUP model (15.4%) that had a tocochromanol phenotype and transcript abundances in developing grain for a few large-effect candidate causal genes (1-3 genes per trait) as multiple response variables. Taken together, our study illustrates the enhancement of prediction models when informed by existing biological knowledge pertaining to QTL and candidate causal genes.
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Affiliation(s)
- Ryokei Tanaka
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
| | - Di Wu
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
| | - Xiaowei Li
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
| | | | - Joshua C Wood
- Institute for Plant Breeding, Genetics & Genomics, Center for Applied Genetic Technologies, Dep. of Crop & Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | | | - Nolan Bornowski
- Dep. of Plant Biology, Michigan State Univ., East Lansing, MI, 48824, USA
| | - John P Hamilton
- Institute for Plant Breeding, Genetics & Genomics, Center for Applied Genetic Technologies, Dep. of Crop & Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | - Brieanne Vaillancourt
- Institute for Plant Breeding, Genetics & Genomics, Center for Applied Genetic Technologies, Dep. of Crop & Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | - Xianran Li
- USDA ARS, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA, 99164, USA
| | - Nicholas T Deason
- Dep. of Biochemistry and Molecular Biology, Michigan State Univ., East Lansing, MI, 48824, USA
| | | | - C Robin Buell
- Institute for Plant Breeding, Genetics & Genomics, Center for Applied Genetic Technologies, Dep. of Crop & Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | - Dean DellaPenna
- Dep. of Biochemistry and Molecular Biology, Michigan State Univ., East Lansing, MI, 48824, USA
| | - Jianming Yu
- Dep. of Agronomy, Iowa State Univ., Ames, IA, 50011, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
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8
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Kumar R, Brar MS, Kunduru B, Ackerman AJ, Yang Y, Luo F, Saski CA, Bridges WC, de Leon N, McMahan C, Kaeppler SM, Sekhon RS. Genetic architecture of source-sink-regulated senescence in maize. PLANT PHYSIOLOGY 2023; 193:2459-2479. [PMID: 37595026 DOI: 10.1093/plphys/kiad460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/12/2023] [Accepted: 07/21/2023] [Indexed: 08/20/2023]
Abstract
Source and sink interactions play a critical but mechanistically poorly understood role in the regulation of senescence. To disentangle the genetic and molecular mechanisms underlying source-sink-regulated senescence (SSRS), we performed a phenotypic, transcriptomic, and systems genetics analysis of senescence induced by the lack of a strong sink in maize (Zea mays). Comparative analysis of genotypes with contrasting SSRS phenotypes revealed that feedback inhibition of photosynthesis, a surge in reactive oxygen species, and the resulting endoplasmic reticulum (ER) stress were the earliest outcomes of weakened sink demand. Multienvironmental evaluation of a biparental population and a diversity panel identified 12 quantitative trait loci and 24 candidate genes, respectively, underlying SSRS. Combining the natural diversity and coexpression networks analyses identified 7 high-confidence candidate genes involved in proteolysis, photosynthesis, stress response, and protein folding. The role of a cathepsin B like protease 4 (ccp4), a candidate gene supported by systems genetic analysis, was validated by analysis of natural alleles in maize and heterologous analyses in Arabidopsis (Arabidopsis thaliana). Analysis of natural alleles suggested that a 700-bp polymorphic promoter region harboring multiple ABA-responsive elements is responsible for differential transcriptional regulation of ccp4 by ABA and the resulting variation in SSRS phenotype. We propose a model for SSRS wherein feedback inhibition of photosynthesis, ABA signaling, and oxidative stress converge to induce ER stress manifested as programed cell death and senescence. These findings provide a deeper understanding of signals emerging from loss of sink strength and offer opportunities to modify these signals to alter senescence program and enhance crop productivity.
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Affiliation(s)
- Rohit Kumar
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Manwinder S Brar
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Bharath Kunduru
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Arlyn J Ackerman
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Yuan Yang
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC 29634, USA
| | - Feng Luo
- School of Computing, Clemson University, Clemson, SC 29634, USA
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA
| | - William C Bridges
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC 29634, USA
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA
| | - Christopher McMahan
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC 29634, USA
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA
| | - Rajandeep S Sekhon
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
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9
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Tang J, Liu H, Quan Y, Yao Y, Li K, Tang G, Du D. Fine mapping and causal gene identification of a novel QTL for early flowering by QTL-seq, Target-seq and RNA-seq in spring oilseed rape. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:80. [PMID: 36952057 DOI: 10.1007/s00122-023-04310-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
A novel quantitative trait locus for early flowering in spring oilseed rape, BnaC08cqDTF, was mapped to an 86-kb region on chromosome C08, and its causal gene, CRY2, was uncovered. Days to flowering is a very important agronomic and adaptive trait of Brassica napus oilseed rape (AACC, 2n = 38). We previously identified BnaC08cqDTF as a novel candidate quantitative trait locus (QTL) for early flowering in spring oilseed rape. Here, we present fine mapping of the locus and a study of its causal gene. Initial mapping was performed by QTL sequencing of DNA pools of BC3F2 plants with extreme flowering times derived from crosses between the spring-type cv. No. 4512 (early flowering) and cv. No. 5246 (late flowering), along with fine mapping by target sequencing of the BC3F2 and BC4F2 populations. Fine mapping narrowed down BnaC08cqDTF to an 86-kb region on chromosome C08. The region harbored fifteen genes. After comparative analyses of the DNA sequences for mutation between A and C syntenic regions and detected by RNA-seq and qRT-PCR between the two parents, we found that BnaC08G0010400ZS harbors an A/G nonsynonymous mutation in exon 3. This single nucleotide polymorphism (SNP) haplotype was also correlated with early flowering in a 256 accession panel. BnaC08G0010400ZS is a homolog of the AT1G04400 gene (CRY2) in Arabidopsis. The analyses of transgenic Arabidopsis verified that BnaC08G0010400ZS is responsible for early flowering. Our results contribute to a better understanding of the genetic control mechanism of early flowering in spring Brassica napus and will promote the breeding for early mature varieties.
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Affiliation(s)
- Jie Tang
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai Spring Rape Engineering Research Center, Qinghai Research Branch of the National Oil Crop Genetic Improvement Center, Spring Rape Scientific Observation Experimental Station of Ministry of Agriculture and Rural Areas, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
- Crop Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, Jiangxi, China
| | - Haidong Liu
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai Spring Rape Engineering Research Center, Qinghai Research Branch of the National Oil Crop Genetic Improvement Center, Spring Rape Scientific Observation Experimental Station of Ministry of Agriculture and Rural Areas, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
| | - Youjuan Quan
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai Spring Rape Engineering Research Center, Qinghai Research Branch of the National Oil Crop Genetic Improvement Center, Spring Rape Scientific Observation Experimental Station of Ministry of Agriculture and Rural Areas, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
| | - Yanmei Yao
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai Spring Rape Engineering Research Center, Qinghai Research Branch of the National Oil Crop Genetic Improvement Center, Spring Rape Scientific Observation Experimental Station of Ministry of Agriculture and Rural Areas, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
| | - Kaixiang Li
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai Spring Rape Engineering Research Center, Qinghai Research Branch of the National Oil Crop Genetic Improvement Center, Spring Rape Scientific Observation Experimental Station of Ministry of Agriculture and Rural Areas, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
| | - Guoyong Tang
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai Spring Rape Engineering Research Center, Qinghai Research Branch of the National Oil Crop Genetic Improvement Center, Spring Rape Scientific Observation Experimental Station of Ministry of Agriculture and Rural Areas, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China.
| | - Dezhi Du
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai Spring Rape Engineering Research Center, Qinghai Research Branch of the National Oil Crop Genetic Improvement Center, Spring Rape Scientific Observation Experimental Station of Ministry of Agriculture and Rural Areas, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China.
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10
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Wan W, Wu Y, Hu D, Ye F, Wu X, Qi X, Liang H, Zhou H, Xue J, Xu S, Zhang X. Genome-wide association analysis of kernel nutritional quality in two natural maize populations. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:18. [PMID: 37313300 PMCID: PMC10248675 DOI: 10.1007/s11032-023-01360-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/05/2023] [Indexed: 06/15/2023]
Abstract
As one of the three staple crops, nutritional traits in maize are important for human and animal nutrition. Grain quality-related traits are closely related to grain commercial value. Understanding the genetic basis of quality-related traits in maize would be helpful for breeding high-quality maize varieties. In this study, two association panels (AM122 and AM180) were subjected to genome-wide association analysis of grain quality-related traits, including protein content, oil content, starch content, and fiber content. In total, 98 SNPs (P < 1 × 10-4) were identified to be significantly associated with these four grain quality-related traits. By integrating two sets of public transcriptome data, 31 genes located in 200 kb regions flanking the associated SNP showed high expression during kernel development and were differentially expressed in two maize inbred lines, KA225 and KB035, with significantly different quality. These genes might regulate maize grain quality by participating in plant hormone processes, autophagy processes, and others. All these results could provide important reference information for breeding high‑quality maize varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01360-w.
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Affiliation(s)
- Wenting Wan
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Ying Wu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Die Hu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Fan Ye
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Xiaopeng Wu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Xingyue Qi
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Hangyu Liang
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Haiyang Zhou
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jiquan Xue
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Shutu Xu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Xinghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
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11
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Chen G, Xiao Y, Dai S, Dai Z, Wang X, Li B, Jaqueth JS, Li W, Lai Z, Ding J, Yan J. Genetic basis of resistance to southern corn leaf blight in the maize multi-parent population and diversity panel. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:506-520. [PMID: 36383026 PMCID: PMC9946143 DOI: 10.1111/pbi.13967] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Southern corn leaf blight (SLB), caused by the necrotrophic pathogen Cochliobolus heterostrophus, is one of the maize foliar diseases and poses a great threat to corn production around the world. Identification of genetic variations underlying resistance to SLB is of paramount importance to maize yield and quality. Here, we used a random-open-parent association mapping population containing eight recombinant inbred line populations and one association mapping panel consisting of 513 diversity maize inbred lines with high-density genetic markers to dissect the genetic basis of SLB resistance. Overall, 109 quantitative trait loci (QTLs) with predominantly small or moderate additive effects, and little epistatic effects were identified. We found 35 (32.1%) novel loci in comparison with the reported QTLs. We revealed that resistant alleles were significantly enriched in tropical accessions and the frequency of about half of resistant alleles decreased during the adaptation process owing to the selection of agronomic traits. A large number of annotated genes located in the SLB-resistant QTLs were shown to be involved in plant defence pathways. Integrating genome-wide association study, transcriptomic profiling, resequencing and gene editing, we identified ZmFUT1 and MYBR92 as the putative genes responsible for the major QTLs for resistance to C. heterostrophus. Our results present a comprehensive insight into the genetic basis of SLB resistance and provide resistant loci or genes as direct targets for crop genetic improvement.
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Affiliation(s)
- Gengshen Chen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Sha Dai
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zhikang Dai
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xiaoming Wang
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | | | | | - Wenqiang Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zhibing Lai
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Junqiang Ding
- College of AgronomyHenan Agricultural UniversityZhengzhouChina
- The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
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12
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Yuan W, Huang J, Li H, Ma Y, Gui C, Huang F, Feng X, Yu D, Wang H, Kan G. Genetic dissection reveals the complex architecture of amino acid composition in soybean seeds. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:17. [PMID: 36670242 DOI: 10.1007/s00122-023-04280-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Five loci related to soybean protein and amino acid contents were colocated by performing linkage mapping and GWAS. The haplotype analysis showed that Glyma.08G109100 may be useful to improve the soybean seed composition. Soybean (Glycine max (L.) Merr.) seeds are good protein sources. Although genetic variation is abundant, natural variation in seed amino acids and their derived traits is lacking across soybean accessions. Here, we determined the contents of protein and 17 amino acids, obtained 36 derived traits based on the protein and total amino acid contents, and derived 34 traits based on seven amino acid family groups. Furthermore, we performed a linkage analysis of the contents of 17 amino acids and 73 amino acid-derived traits based on the recombinant inbred line (RIL)-derived Kefeng No. 1 × Nannong 1138-2. Six hundred thirty-nine quantitative trait loci (QTLs) were identified, explaining 6.07-39.00% of the phenotypic variation. Among these loci, five were detected in diverse soybean accessions using a genome-wide association study. A network analysis revealed that some loci that were significantly associated with multiple amino acids were tightly linked on chromosome 8 based on linkage disequilibrium values, which also further confirmed the results of the correlation analysis among amino acid traits. Through a combination of a genome-wide association study, linkage analysis, qRT-PCR, and genomic polymorphism comparison, Glyma.08G109100 on chromosome 8, which may affect amino acid contents, was selected. The haplotype analysis showed that Hap-T of Glyma.08G109100 may be useful to improve the contents of protein and 16 amino acids in soybean. This study provides new insights into the genetic basis of the amino acid composition in soybean seeds and may facilitate marker-based breeding of soybean with improved nutritional value.
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Affiliation(s)
- Wenjie Yuan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Jie Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Haiyang Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yujie Ma
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Chunju Gui
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Fang Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Deyue Yu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Hui Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China.
| | - Guizhen Kan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China.
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13
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Devgan M, Gill GK, Praba UP, Singh G, Garg T, Karnatam KS, Kaur A, Vikal Y. Biochemical and molecular characterization of sub-tropical maize germplasm for tocopherols. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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Shahidi F, Danielski R, Rhein SO, Meisel LA, Fuentes J, Speisky H, Schwember AR, de Camargo AC. Wheat and Rice beyond Phenolic Acids: Genetics, Identification Database, Antioxidant Properties, and Potential Health Effects. PLANTS (BASEL, SWITZERLAND) 2022; 11:3283. [PMID: 36501323 PMCID: PMC9739071 DOI: 10.3390/plants11233283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Wheat and rice play a vital role in human nutrition and food security. A better understanding of the potential health benefits associated with consuming these cereals, combined with studies by plant scientists and food chemists to view the entire food value chain from the field, pre and post-harvest processing, and subsequent "fork" consumption, may provide the necessary tools to optimize wheat and rice production towards the goal of better human health improvement and food security, providing tools to better adapt to the challenges associated with climate change. Since the available literature usually focuses on only one food chain segment, this narrative review was designed to address the identities and concentration of phenolics of these cereal crops from a farm-to-fork perspective. Wheat and rice genetics, phenolic databases, antioxidant properties, and potential health effects are summarized. These cereals contain much more than phenolic acids, having significant concentrations of flavonoids (including anthocyanins) and proanthocyanidins in a cultivar-dependent manner. Their potential health benefits in vitro have been extensively studied. According to a number of in vivo studies, consumption of whole wheat, wheat bran, whole rice, and rice bran may be strategies to improve health. Likewise, anthocyanin-rich cultivars have shown to be very promising as functional foods.
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Affiliation(s)
- Fereidoon Shahidi
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Renan Danielski
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Samantha Ottani Rhein
- Nutrition and Food Technology Institute, University of Chile, Santiago 7830490, Chile
| | - Lee A. Meisel
- Nutrition and Food Technology Institute, University of Chile, Santiago 7830490, Chile
| | - Jocelyn Fuentes
- Nutrition and Food Technology Institute, University of Chile, Santiago 7830490, Chile
| | - Hernan Speisky
- Nutrition and Food Technology Institute, University of Chile, Santiago 7830490, Chile
| | - Andrés R. Schwember
- Departament of Plant Sciences, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
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15
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Niu Y, Zhang Q, Wang J, Li Y, Wang X, Bao Y. Vitamin E synthesis and response in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:994058. [PMID: 36186013 PMCID: PMC9515888 DOI: 10.3389/fpls.2022.994058] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Vitamin E, also known as tocochromanol, is a lipid-soluble antioxidant that can only be produced by photosynthetic organisms in nature. Vitamin E is not only essential in human diets, but also required for plant environment adaptions. To synthesize vitamin E, specific prenyl groups needs to be incorporated with homogentisate as the first step of reaction. After decades of studies, an almost complete roadmap has been revealed for tocochromanol biosynthesis pathway. However, chlorophyll-derived prenyl precursors for synthesizing tocochromanols are still a mystery. In recent years, by employing forward genetic screening and genome-wide-association approaches, significant achievements were acquired in studying vitamin E. In this review, by summarizing the recent progresses in vitamin E, we provide to date the most updated whole view of vitamin E biosynthesis pathway. Also, we discussed about the role of vitamin E in plants stress response and its potential as signaling molecules.
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Affiliation(s)
- Yue Niu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Zhang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaojiao Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjie Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinhua Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Bao
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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16
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Mural RV, Sun G, Grzybowski M, Tross MC, Jin H, Smith C, Newton L, Andorf CM, Woodhouse MR, Thompson AM, Sigmon B, Schnable JC. Association mapping across a multitude of traits collected in diverse environments in maize. Gigascience 2022; 11:giac080. [PMID: 35997208 PMCID: PMC9396454 DOI: 10.1093/gigascience/giac080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/25/2022] [Indexed: 11/14/2022] Open
Abstract
Classical genetic studies have identified many cases of pleiotropy where mutations in individual genes alter many different phenotypes. Quantitative genetic studies of natural genetic variants frequently examine one or a few traits, limiting their potential to identify pleiotropic effects of natural genetic variants. Widely adopted community association panels have been employed by plant genetics communities to study the genetic basis of naturally occurring phenotypic variation in a wide range of traits. High-density genetic marker data-18M markers-from 2 partially overlapping maize association panels comprising 1,014 unique genotypes grown in field trials across at least 7 US states and scored for 162 distinct trait data sets enabled the identification of of 2,154 suggestive marker-trait associations and 697 confident associations in the maize genome using a resampling-based genome-wide association strategy. The precision of individual marker-trait associations was estimated to be 3 genes based on a reference set of genes with known phenotypes. Examples were observed of both genetic loci associated with variation in diverse traits (e.g., above-ground and below-ground traits), as well as individual loci associated with the same or similar traits across diverse environments. Many significant signals are located near genes whose functions were previously entirely unknown or estimated purely via functional data on homologs. This study demonstrates the potential of mining community association panel data using new higher-density genetic marker sets combined with resampling-based genome-wide association tests to develop testable hypotheses about gene functions, identify potential pleiotropic effects of natural genetic variants, and study genotype-by-environment interaction.
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Affiliation(s)
- Ravi V Mural
- Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, NE 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE 68588, USA
| | - Guangchao Sun
- Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, NE 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE 68588, USA
| | - Marcin Grzybowski
- Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, NE 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE 68588, USA
| | - Michael C Tross
- Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, NE 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE 68588, USA
| | - Hongyu Jin
- Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, NE 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE 68588, USA
| | - Christine Smith
- Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, NE 68588, USA
| | - Linsey Newton
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Carson M Andorf
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50010, USA
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | | | - Addie M Thompson
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Brandi Sigmon
- Department of Plant Pathology, University of Nebraska–Lincoln, Lincoln, NE 68588, USA
| | - James C Schnable
- Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, NE 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE 68588, USA
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17
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Role of Tocochromanols in Tolerance of Cereals to Biotic Stresses: Specific Focus on Pathogenic and Toxigenic Fungal Species. Int J Mol Sci 2022; 23:ijms23169303. [PMID: 36012567 PMCID: PMC9408828 DOI: 10.3390/ijms23169303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Fungal pathogens capable of producing mycotoxins are one of the main threats to the cultivation of cereals and the safety of the harvested kernels. Improving the resistance of crops to fungal disease and accumulation of mycotoxins is therefore a crucial issue. Achieving this goal requires a deep understanding of plant defense mechanisms, most of them involving specialized metabolites. However, while numerous studies have addressed the contribution of phenylpropanoids and carotenoids to plant chemical defense, very few have dealt with tocochromanols. Tocochromanols, which encompass tocopherols and tocotrienols and constitute the vitamin E family, are widely distributed in cereal kernels; their biosynthetic pathway has been extensively studied with the aim to enrich plant oils and combat vitamin E deficiency in humans. Here we provide strong assumptions arguing in favor of an involvement of tocochromanols in plant–fungal pathogen interactions. These assumptions are based on both direct effects resulting from their capacity to scavenge reactive oxygen species, including lipid peroxyl radicals, on their potential to inhibit fungal growth and mycotoxin yield, and on more indirect effects mainly based on their role in plant protection against abiotic stresses.
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18
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Wu D, Li X, Tanaka R, Wood JC, Tibbs-Cortes LE, Magallanes-Lundback M, Bornowski N, Hamilton JP, Vaillancourt B, Diepenbrock CH, Li X, Deason NT, Schoenbaum GR, Yu J, Buell CR, DellaPenna D, Gore MA. Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain. Genetics 2022; 221:6603118. [PMID: 35666198 PMCID: PMC9339294 DOI: 10.1093/genetics/iyac091] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/01/2022] [Indexed: 11/20/2022] Open
Abstract
Tocochromanols (tocopherols and tocotrienols, collectively vitamin E) are lipid-soluble antioxidants important for both plant fitness and human health. The main dietary sources of vitamin E are seed oils that often accumulate high levels of tocopherol isoforms with lower vitamin E activity. The tocochromanol biosynthetic pathway is conserved across plant species but an integrated view of the genes and mechanisms underlying natural variation of tocochromanol levels in seed of most cereal crops remains limited. To address this issue, we utilized the high mapping resolution of the maize Ames panel of ∼1,500 inbred lines scored with 12.2 million single-nucleotide polymorphisms to generate metabolomic (mature grain tocochromanols) and transcriptomic (developing grain) data sets for genetic mapping. By combining results from genome- and transcriptome-wide association studies, we identified a total of 13 candidate causal gene loci, including 5 that had not been previously associated with maize grain tocochromanols: 4 biosynthetic genes (arodeH2 paralog, dxs1, vte5, and vte7) and a plastid S-adenosyl methionine transporter (samt1). Expression quantitative trait locus (eQTL) mapping of these 13 gene loci revealed that they are predominantly regulated by cis-eQTL. Through a joint statistical analysis, we implicated cis-acting variants as responsible for colocalized eQTL and GWAS association signals. Our multiomics approach provided increased statistical power and mapping resolution to enable a detailed characterization of the genetic and regulatory architecture underlying tocochromanol accumulation in maize grain and provided insights for ongoing biofortification efforts to breed and/or engineer vitamin E and antioxidant levels in maize and other cereals.
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Affiliation(s)
| | | | | | - Joshua C Wood
- Department of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, GA 30602, USA
| | | | - Maria Magallanes-Lundback
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Nolan Bornowski
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - John P Hamilton
- Department of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, GA 30602, USA
| | - Brieanne Vaillancourt
- Department of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, GA 30602, USA
| | | | - Xianran Li
- United States Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164, USA
| | - Nicholas T Deason
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - C Robin Buell
- Department of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, GA 30602, USA
| | - Dean DellaPenna
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Michael A Gore
- Corresponding author: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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19
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Medina-Lozano I, Díaz A. Applications of Genomic Tools in Plant Breeding: Crop Biofortification. Int J Mol Sci 2022; 23:3086. [PMID: 35328507 PMCID: PMC8950180 DOI: 10.3390/ijms23063086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 12/02/2022] Open
Abstract
Crop breeding has mainly been focused on increasing productivity, either directly or by decreasing the losses caused by biotic and abiotic stresses (that is, incorporating resistance to diseases and enhancing tolerance to adverse conditions, respectively). Quite the opposite, little attention has been paid to improve the nutritional value of crops. It has not been until recently that crop biofortification has become an objective within breeding programs, through either conventional methods or genetic engineering. There are many steps along this long path, from the initial evaluation of germplasm for the content of nutrients and health-promoting compounds to the development of biofortified varieties, with the available and future genomic tools assisting scientists and breeders in reaching their objectives as well as speeding up the process. This review offers a compendium of the genomic technologies used to explore and create biodiversity, to associate the traits of interest to the genome, and to transfer the genomic regions responsible for the desirable characteristics into potential new varieties. Finally, a glimpse of future perspectives and challenges in this emerging area is offered by taking the present scenario and the slow progress of the regulatory framework as the starting point.
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Affiliation(s)
- Inés Medina-Lozano
- Departamento de Ciencia Vegetal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Universidad de Zaragoza, Avda. Montañana 930, 50059 Zaragoza, Spain;
- Instituto Agroalimentario de Aragón—IA2, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Aurora Díaz
- Departamento de Ciencia Vegetal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Universidad de Zaragoza, Avda. Montañana 930, 50059 Zaragoza, Spain;
- Instituto Agroalimentario de Aragón—IA2, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Universidad de Zaragoza, 50013 Zaragoza, Spain
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20
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Boursiac Y, Protto V, Rishmawi L, Maurel C. Experimental and conceptual approaches to root water transport. PLANT AND SOIL 2022; 478:349-370. [PMID: 36277078 PMCID: PMC9579117 DOI: 10.1007/s11104-022-05427-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/03/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Root water transport, which critically contributes to the plant water status and thereby plant productivity, has been the object of extensive experimental and theoretical studies. However, root systems represent an intricate assembly of cells in complex architectures, including many tissues at distinct developmental stages. Our comprehension of where and how molecular actors integrate their function in order to provide the root with its hydraulic properties is therefore still limited. SCOPE Based on current literature and prospective discussions, this review addresses how root water transport can be experimentally measured, what is known about the underlying molecular actors, and how elementary water transport processes are scaled up in numerical/mathematical models. CONCLUSIONS The theoretical framework and experimental procedures on root water transport that are in use today have been established a few decades ago. However, recent years have seen the appearance of new techniques and models with enhanced resolution, down to a portion of root or to the tissue level. These advances pave the way for a better comprehension of the dynamics of water uptake by roots in the soil.
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Affiliation(s)
- Yann Boursiac
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Virginia Protto
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Louai Rishmawi
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Christophe Maurel
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
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21
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Kumar R, Gyawali A, Morrison GD, Saski CA, Robertson DJ, Cook DD, Tharayil N, Schaefer RJ, Beissinger TM, Sekhon RS. Genetic Architecture of Maize Rind Strength Revealed by the Analysis of Divergently Selected Populations. PLANT & CELL PHYSIOLOGY 2021; 62:1199-1214. [PMID: 34015110 DOI: 10.1093/pcp/pcab059] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 05/04/2021] [Accepted: 05/19/2021] [Indexed: 06/12/2023]
Abstract
The strength of the stalk rind, measured as rind penetrometer resistance (RPR), is an important contributor to stalk lodging resistance. To enhance the genetic architecture of RPR, we combined selection mapping on populations developed by 15 cycles of divergent selection for high and low RPR with time-course transcriptomic and metabolic analyses of the stalks. Divergent selection significantly altered allele frequencies of 3,656 and 3,412 single- nucleotide polymorphisms (SNPs) in the high and low RPR populations, respectively. Surprisingly, only 110 (1.56%) SNPs under selection were common in both populations, while the majority (98.4%) were unique to each population. This result indicated that high and low RPR phenotypes are produced by biologically distinct mechanisms. Remarkably, regions harboring lignin and polysaccharide genes were preferentially selected in high and low RPR populations, respectively. The preferential selection was manifested as higher lignification and increased saccharification of the high and low RPR stalks, respectively. The evolution of distinct gene classes according to the direction of selection was unexpected in the context of parallel evolution and demonstrated that selection for a trait, albeit in different directions, does not necessarily act on the same genes. Tricin, a grass-specific monolignol that initiates the incorporation of lignin in the cell walls, emerged as a key determinant of RPR. Integration of selection mapping and transcriptomic analyses with published genetic studies of RPR identified several candidate genes including ZmMYB31, ZmNAC25, ZmMADS1, ZmEXPA2, ZmIAA41 and hk5. These findings provide a foundation for an enhanced understanding of RPR and the improvement of stalk lodging resistance.
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Affiliation(s)
- Rohit Kumar
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Abiskar Gyawali
- Division of Biological Sciences, University of Missouri, 105 Tucker Hall, Columbia, MO 65211, USA
| | - Ginnie D Morrison
- Division of Biological Sciences, University of Missouri, 105 Tucker Hall, Columbia, MO 65211, USA
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA
| | - Daniel J Robertson
- Department of Mechanical Engineering, University of Idaho, Moscow, ID, USA
| | - Douglas D Cook
- Department of Mechanical Engineering, Brigham Young University, Provo, UT, USA
| | - Nishanth Tharayil
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA
| | | | - Timothy M Beissinger
- Department of Plant Breeding Methodology, University of Göttingen, Göttingen 37075, Germany
- Center for Integrated Breeding Research, University of Göttingen, Göttingen 37075, Germany
| | - Rajandeep S Sekhon
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
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22
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Chen J, Xue M, Liu H, Fernie AR, Chen W. Exploring the genic resources underlying metabolites through mGWAS and mQTL in wheat: From large-scale gene identification and pathway elucidation to crop improvement. PLANT COMMUNICATIONS 2021; 2:100216. [PMID: 34327326 PMCID: PMC8299079 DOI: 10.1016/j.xplc.2021.100216] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/04/2021] [Accepted: 06/28/2021] [Indexed: 05/23/2023]
Abstract
Common wheat (Triticum aestivum L.) is a leading cereal crop, but has lagged behind with respect to the interpretation of the molecular mechanisms of phenotypes compared with other major cereal crops such as rice and maize. The recently available genome sequence of wheat affords the pre-requisite information for efficiently exploiting the potential molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets. Meanwhile, the successful application of metabolomics as an emergent large-scale profiling methodology in several species has demonstrated this approach to be accessible for reaching the above goals. One such productive avenue is combining metabolomics approaches with genetic designs. However, this trial is not as widespread as that for sequencing technologies, especially when the acquisition, understanding, and application of metabolic approaches in wheat populations remain more difficult and even arguably underutilized. In this review, we briefly introduce the techniques used in the acquisition of metabolomics data and their utility in large-scale identification of functional candidate genes. Considerable progress has been made in delivering improved varieties, suggesting that the inclusion of information concerning these metabolites and genes and metabolic pathways enables a more explicit understanding of phenotypic traits and, as such, this procedure could serve as an -omics-informed roadmap for executing similar improvement strategies in wheat and other species.
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Affiliation(s)
- Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingyun Xue
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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23
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Medeiros DB, Brotman Y, Fernie AR. The utility of metabolomics as a tool to inform maize biology. PLANT COMMUNICATIONS 2021; 2:100187. [PMID: 34327322 PMCID: PMC8299083 DOI: 10.1016/j.xplc.2021.100187] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/26/2021] [Accepted: 04/19/2021] [Indexed: 05/04/2023]
Abstract
With the rise of high-throughput omics tools and the importance of maize and its products as food and bioethanol, maize metabolism has been extensively explored. Modern maize is still rich in genetic and phenotypic variation, yielding a wide range of structurally and functionally diverse metabolites. The maize metabolome is also incredibly dynamic in terms of topology and subcellular compartmentalization. In this review, we examine a broad range of studies that cover recent developments in maize metabolism. Particular attention is given to current methodologies and to the use of metabolomics as a tool to define biosynthetic pathways and address biological questions. We also touch upon the use of metabolomics to understand maize natural variation and evolution, with a special focus on research that has used metabolite-based genome-wide association studies (mGWASs).
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Affiliation(s)
- David B. Medeiros
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
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24
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Shikha K, Shahi JP, Vinayan MT, Zaidi PH, Singh AK, Sinha B. Genome-wide association mapping in maize: status and prospects. 3 Biotech 2021; 11:244. [PMID: 33968587 PMCID: PMC8085158 DOI: 10.1007/s13205-021-02799-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/19/2021] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association study (GWAS) provides a robust and potent tool to retrieve complex phenotypic traits back to their underlying genetics. Maize is an excellent crop for performing GWAS due to diverse genetic variability, rapid decay of linkage disequilibrium, availability of distinct sub-populations and abundant SNP information. The application of GWAS in maize has resulted in successful identification of thousands of genomic regions associated with many abiotic and biotic stresses. Many agronomic and quality traits of maize are severely affected by such stresses and, significantly affecting its growth and productivity. To improve productivity of maize crop in countries like India which contribute only 2% to the world's total production in 2019-2020, it is essential to understand genetic complexity of underlying traits. Various DNA markers and trait associations have been revealed using conventional linkage mapping methods. However, it has achieved limited success in improving polygenic complex traits due to lower resolution of trait mapping. The present review explores the prospects of GWAS in improving yield, quality and stress tolerance in maize besides, strengths and challenges of using GWAS for molecular breeding and genomic selection. The information gathered will facilitate elucidation of genetic mechanisms of complex traits and improve efficiency of marker-assisted selection in maize breeding. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02799-4.
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Affiliation(s)
- Kumari Shikha
- Department of Genetics and Plant Breeding, Institute of Agriculltural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh India
| | - J. P. Shahi
- Department of Genetics and Plant Breeding, Institute of Agriculltural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh India
| | - M. T. Vinayan
- International Maize and Wheat Improvement Centre (CIMMYT)-Asia, ICRISAT Campus, Patancheru, Hyderabad, Telangana India
| | - P. H. Zaidi
- International Maize and Wheat Improvement Centre (CIMMYT)-Asia, ICRISAT Campus, Patancheru, Hyderabad, Telangana India
| | - A. K. Singh
- Department of Genetics and Plant Breeding, Institute of Agriculltural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh India
| | - B. Sinha
- Department of Genetics and Plant Breeding, Institute of Agriculltural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh India
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25
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Zhang H, Lu Y, Ma Y, Fu J, Wang G. Genetic and molecular control of grain yield in maize. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:18. [PMID: 37309425 PMCID: PMC10236077 DOI: 10.1007/s11032-021-01214-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/07/2021] [Indexed: 06/14/2023]
Abstract
Understanding the genetic and molecular basis of grain yield is important for maize improvement. Here, we identified 49 consensus quantitative trait loci (cQTL) controlling maize yield-related traits using QTL meta-analysis. Then, we collected yield-related traits associated SNPs detected by association mapping and identified 17 consensus significant loci. Comparing the physical positions of cQTL with those of significant SNPs revealed that 47 significant SNPs were located within 20 cQTL regions. Furthermore, intensive reviews of 31 genes regulating maize yield-related traits found that the functions of many genes were conservative in maize and other plant species. The functional conservation indicated that some of the 575 maize genes (orthologous to 247 genes controlling yield or seed traits in other plant species) might be functionally related to maize yield-related traits, especially the 49 maize orthologous genes in cQTL regions, and 41 orthologous genes close to the physical positions of significant SNPs. In the end, we prospected on the integration of the public sources for exploring the genetic and molecular mechanisms of maize yield-related traits, and on the utilization of genetic and molecular mechanisms for maize improvement. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01214-3.
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Affiliation(s)
- Hongwei Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 The People’s Republic of China
| | - Yantian Lu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 The People’s Republic of China
| | - Yuting Ma
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 The People’s Republic of China
| | - Junjie Fu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 The People’s Republic of China
| | - Guoying Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 The People’s Republic of China
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26
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Burgos E, Belen De Luca M, Diouf I, de Haro LA, Albert E, Sauvage C, Tao ZJ, Bermudez L, Asís R, Nesi AN, Matringe M, Bréhélin C, Guiraud T, Ferrand C, Atienza I, Jorly J, Mauxion JP, Baldet P, Fernie AR, Quadrana L, Rothan C, Causse M, Carrari F. Validated MAGIC and GWAS population mapping reveals the link between vitamin E content and natural variation in chorismate metabolism in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:907-923. [PMID: 33179365 DOI: 10.1111/tpj.15077] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/27/2020] [Indexed: 05/21/2023]
Abstract
Tocochromanols constitute the different forms of vitamin E (VTE), essential components of the human diet, and display a high membrane protectant activity. By combining interval mapping and genome-wide association studies (GWAS), we unveiled the genetic determinants of tocochromanol accumulation in tomato (Solanum lycopersicum) fruits. To enhance the nutritional value of this highly consumed vegetable, we dissected the natural intraspecific variability of tocochromanols in tomato fruits and genetically engineered their biosynthetic pathway. These analyses allowed the identification of a total of 25 quantitative trait loci interspersed across the genome pinpointing the chorismate-tyrosine pathway as a regulatory hub controlling the supply of the aromatic head group for tocochromanol biosynthesis. To validate the link between the chorismate-tyrosine pathway and VTE, we engineered tomato plants to bypass the pathway at the arogenate branch point. Transgenic tomatoes showed moderate increments in tocopherols (up to approximately 20%) and a massive accumulation of tocotrienols (up to approximately 3400%). Gene expression analyses of these plants reveal a trade-off between VTE and natural variation in chorismate metabolism explained by transcriptional reprogramming of specific structural genes of the pathway. By restoring the accumulation of alpha-tocotrienols (α-t3) in fruits, the plants produced here are of high pharmacological and nutritional interest.
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Affiliation(s)
- Estanislao Burgos
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, C1428EHA, Argentina
| | - Maria Belen De Luca
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, C1428EHA, Argentina
| | - Isidore Diouf
- INRAE, Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, 67 Allée des Chênes, Domaine Saint Maurice CS60094, Montfavet, 84143, France
| | - Luis A de Haro
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, C1428EHA, Argentina
| | - Elise Albert
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | | | - Zhao J Tao
- INRAE, Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, 67 Allée des Chênes, Domaine Saint Maurice CS60094, Montfavet, 84143, France
| | - Luisa Bermudez
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria, and Consejo Nacional de Investigaciones Científicas y Técnicas, PO Box 25, Castelar, B1712WAA, Argentina
- Facultad de Agronomía, Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ramon Asís
- CIBICI, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, CC, 5000, Argentina
| | - Adriano N Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Michel Matringe
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168 CNRS-CEA-INRAE, Université Joseph Fourier, CEA Grenoble, PCV, Grenoble Cedex 9, Grenoble, 38054, France
| | - Claire Bréhélin
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168 CNRS-CEA-INRAE, Université Joseph Fourier, CEA Grenoble, PCV, Grenoble Cedex 9, Grenoble, 38054, France
| | - Thomas Guiraud
- Univ. Bordeaux, Biologie du Fruit et Pathologie, INRAE, Villenave d'OrnoF-33140, Villenave d'Ornon Cedex, UMR 1332, France
| | - Carine Ferrand
- Univ. Bordeaux, Biologie du Fruit et Pathologie, INRAE, Villenave d'OrnoF-33140, Villenave d'Ornon Cedex, UMR 1332, France
| | - Isabelle Atienza
- Univ. Bordeaux, Biologie du Fruit et Pathologie, INRAE, Villenave d'OrnoF-33140, Villenave d'Ornon Cedex, UMR 1332, France
| | - Joana Jorly
- Univ. Bordeaux, Biologie du Fruit et Pathologie, INRAE, Villenave d'OrnoF-33140, Villenave d'Ornon Cedex, UMR 1332, France
| | - Jean P Mauxion
- Univ. Bordeaux, Biologie du Fruit et Pathologie, INRAE, Villenave d'OrnoF-33140, Villenave d'Ornon Cedex, UMR 1332, France
| | - Pierre Baldet
- Univ. Bordeaux, Biologie du Fruit et Pathologie, INRAE, Villenave d'OrnoF-33140, Villenave d'Ornon Cedex, UMR 1332, France
| | - Alisdair R Fernie
- Institute of Molecular Plant Physiology, Max-Planck, Am Muehlenberg 1, Potsdam-Golm, 14476, Germany
| | - Leandro Quadrana
- Centre National de la Recherche Scientifique (CNRS), Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, F-75005, France
| | - Christophe Rothan
- Univ. Bordeaux, Biologie du Fruit et Pathologie, INRAE, Villenave d'OrnoF-33140, Villenave d'Ornon Cedex, UMR 1332, France
| | - Mathilde Causse
- INRAE, Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, 67 Allée des Chênes, Domaine Saint Maurice CS60094, Montfavet, 84143, France
| | - Fernando Carrari
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, C1428EHA, Argentina
- Facultad de Agronomía, Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
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Dai D, Ma Z, Song R. Maize kernel development. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:2. [PMID: 37309525 PMCID: PMC10231577 DOI: 10.1007/s11032-020-01195-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/03/2020] [Indexed: 06/14/2023]
Abstract
Maize (Zea mays) is a leading cereal crop in the world. The maize kernel is the storage organ and the harvest portion of this crop and is closely related to its yield and quality. The development of maize kernel is initiated by the double fertilization event, leading to the formation of a diploid embryo and a triploid endosperm. The embryo and endosperm are then undergone independent developmental programs, resulting in a mature maize kernel which is comprised of a persistent endosperm, a large embryo, and a maternal pericarp. Due to the well-characterized morphogenesis and powerful genetics, maize kernel has long been an excellent model for the study of cereal kernel development. In recent years, with the release of the maize reference genome and the development of new genomic technologies, there has been an explosive expansion of new knowledge for maize kernel development. In this review, we overviewed recent progress in the study of maize kernel development, with an emphasis on genetic mapping of kernel traits, transcriptome analysis during kernel development, functional gene cloning of kernel mutants, and genetic engineering of kernel traits.
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Affiliation(s)
- Dawei Dai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444 China
| | - Zeyang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
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Cao J, Shang Y, Xu D, Xu K, Cheng X, Pan X, Liu X, Liu M, Gao C, Yan S, Yao H, Gao W, Lu J, Zhang H, Chang C, Xia X, Xiao S, Ma C. Identification and Validation of New Stable QTLs for Grain Weight and Size by Multiple Mapping Models in Common Wheat. Front Genet 2020; 11:584859. [PMID: 33262789 PMCID: PMC7686802 DOI: 10.3389/fgene.2020.584859] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/21/2020] [Indexed: 11/13/2022] Open
Abstract
Improvement of grain weight and size is an important objective for high-yield wheat breeding. In this study, 174 recombinant inbred lines (RILs) derived from the cross between Jing 411 and Hongmangchun 21 were used to construct a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq). Three mapping methods, including inclusive composite interval mapping (ICIM), genome-wide composite interval mapping (GCIM), and a mixed linear model performed with forward-backward stepwise (NWIM), were used to identify QTLs for thousand grain weight (TGW), grain width (GW), and grain length (GL). In total, we identified 30, 15, and 18 putative QTLs for TGW, GW, and GL that explain 1.1-33.9%, 3.1%-34.2%, and 1.7%-22.8% of the phenotypic variances, respectively. Among these, 19 (63.3%) QTLs for TGW, 10 (66.7%) for GW, and 7 (38.9%) for GL were consistent with those identified by genome-wide association analysis in 192 wheat varieties. Five new stable QTLs, including 3 for TGW (Qtgw.ahau-1B.1, Qtgw.ahau-4B.1, and Qtgw.ahau-4B.2) and 2 for GL (Qgl.ahau-2A.1 and Qgl.ahau-7A.2), were detected by the three aforementioned mapping methods across environments. Subsequently, five cleaved amplified polymorphic sequence (CAPS) markers corresponding to these QTLs were developed and validated in 180 Chinese mini-core wheat accessions. In addition, 19 potential candidate genes for Qtgw.ahau-4B.2 in a 0.31-Mb physical interval were further annotated, of which TraesCS4B02G376400 and TraesCS4B02G376800 encode a plasma membrane H+-ATPase and a serine/threonine-protein kinase, respectively. These new QTLs and CAPS markers will be useful for further marker-assisted selection and map-based cloning of target genes.
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Affiliation(s)
- Jiajia Cao
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Yaoyao Shang
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Dongmei Xu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Kangle Xu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xinran Cheng
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xu Pan
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xue Liu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Mingli Liu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Chang Gao
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Shengnan Yan
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Hui Yao
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Wei Gao
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Jie Lu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Haiping Zhang
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Cheng Chang
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shihe Xiao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chuanxi Ma
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
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Zeng Z, Han N, Liu C, Buerte B, Zhou C, Chen J, Wang M, Zhang Y, Tang Y, Zhu M, Wang J, Yang Y, Bian H. Functional dissection of HGGT and HPT in barley vitamin E biosynthesis via CRISPR/Cas9-enabled genome editing. ANNALS OF BOTANY 2020; 126:929-942. [PMID: 32575125 PMCID: PMC7539355 DOI: 10.1093/aob/mcaa115] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/18/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS Vitamin E (tocochromanol) is a lipid-soluble antioxidant and an essential nutrient for human health. Among cereal crops, barley (Hordeum vulgare) contains a high level of vitamin E, which includes both tocopherols and tocotrienols. Although the vitamin E biosynthetic pathway has been characterized in dicots, such as Arabidopsis, which only accumulate tocopherols, knowledge regarding vitamin E biosynthesis in monocots is limited because of the lack of functional mutants. This study aimed to obtain gene knockout mutants to elucidate the genetic control of vitamin E composition in barley. METHODS Targeted knockout mutations of HvHPT and HvHGGT in barley were created with CRISPR/Cas9-enabled genome editing. High-performance liquid chromatography (HPLC) was performed to analyse the content of tocochromanol isomers in transgene-free homozygous Hvhpt and Hvhggt mutants. KEY RESULTS Mutagenesis efficiency among T0 regenerated plantlets was 50-65 % as a result of two simultaneously expressed guide RNAs targeting each gene; most of the mutations were stably inherited by the next generation. The transgene-free homozygous mutants of Hvhpt and Hvhggt exhibited decreased grain size and weight, and the HvHGGT mutation led to a shrunken phenotype and significantly lower total starch content in grains. HPLC analysis revealed that targeted mutation of HvHPT significantly reduced the content of both tocopherols and tocotrienols, whereas mutations in HvHGGT completely blocked tocotrienol biosynthesis in barley grains. Transient overexpression of an HvHPT homologue in tobacco leaves significantly increased the production of γ- and δ-tocopherols, which may partly explain why targeted mutation of HvHPT in barley grains did not eliminate tocopherol production. CONCLUSIONS Our results functionally validated that HvHGGT is the only committed gene for the production of tocotrienols, whereas HvHPT is partly responsible for tocopherol biosynthesis in barley.
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Affiliation(s)
- Zhanghui Zeng
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ning Han
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Cuicui Liu
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - B Buerte
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chenlu Zhou
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jianshu Chen
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Mengyao Wang
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yuhong Zhang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Yawei Tang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Muyuan Zhu
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Junhui Wang
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yinong Yang
- Department of Plant Pathology and Environment Microbiology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Hongwu Bian
- Institute of Genetics and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, China
- For correspondence. E-mail
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Zhang X, Guan Z, Li Z, Liu P, Ma L, Zhang Y, Pan L, He S, Zhang Y, Li P, Ge F, Zou C, He Y, Gao S, Pan G, Shen Y. A combination of linkage mapping and GWAS brings new elements on the genetic basis of yield-related traits in maize across multiple environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2881-2895. [PMID: 32594266 DOI: 10.1007/s00122-020-03639-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 06/18/2020] [Indexed: 05/05/2023]
Abstract
Using GWAS and QTL mapping identified 100 QTL and 138 SNPs, which control yield-related traits in maize. The candidate gene GRMZM2G098557 was further validated to regulate ear row number by using a segregation population. Understanding the genetic basis of yield-related traits contributes to the improvement of grain yield in maize. This study used an inter-mated B73 × Mo17 (IBM) Syn10 doubled-haploid (DH) population and an association panel to identify the genetic loci responsible for nine yield-related traits in maize. Using quantitative trait loci (QTL) mapping, 100 QTL influencing these traits were detected across different environments in the IBM Syn10 DH population, with 25 co-detected in multiple environments. Using a genome-wide association study (GWAS), 138 single-nucleotide polymorphisms (SNPs) were identified as correlated with these traits (P < 2.04E-06) in the association panel. Twenty-one pleiotropic QTL/SNPs were identified to control different traits in both populations. A combination of QTL mapping and GWAS uncovered eight significant SNPs (PZE-101097575, PZE-103169263, ZM011204-0763, PZE-104044017, PZE-104123110, SYN8062, PZE-108060911, and PZE-102043341) that were co-located within seven QTL confidence intervals. According to the eight co-localized SNPs by the two populations, 52 candidate genes were identified, among which the ear row number (ERN)-associated SNP SYN8062 was closely linked to SBP-transcription factor 7 (GRMZM2G098557). Several SBP-transcription factors were previously demonstrated to modulate maize ERN. We then validated the phenotypic effects of SYN8062 in the IBM Syn10 DH population, indicating that the ERN of the lines with the A-allele in SYN8062 was significantly (P < 0.05) larger than that of the lines with the G-allele in SYN8062 in each environment. These findings provide valuable information for understanding the genetic mechanisms of maize grain yield formation and for improving molecular marker-assisted selection for the high-yield breeding of maize.
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Affiliation(s)
- Xiaoxiang Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhongrong Guan
- Chongqing Yudongnan Academy of Agricultural Sciences, Chongqing, 408000, China
| | - Zhaoling Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Peng Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Langlang Ma
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yinchao Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shijiang He
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yanling Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Peng Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fei Ge
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoying Zou
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yongcong He
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shibin Gao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China.
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Guo J, Jin M, Chen Y, Liu J. An embedded gene selection method using knockoffs optimizing neural network. BMC Bioinformatics 2020; 21:414. [PMID: 32962627 PMCID: PMC7510330 DOI: 10.1186/s12859-020-03717-w] [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: 04/03/2020] [Accepted: 08/19/2020] [Indexed: 11/30/2022] Open
Abstract
Background Gene selection refers to find a small subset of discriminant genes from the gene expression profiles. How to select genes that affect specific phenotypic traits effectively is an important research work in the field of biology. The neural network has better fitting ability when dealing with nonlinear data, and it can capture features automatically and flexibly. In this work, we propose an embedded gene selection method using neural network. The important genes can be obtained by calculating the weight coefficient after the training is completed. In order to solve the problem of black box of neural network and further make the training results interpretable in neural network, we use the idea of knockoffs to construct the knockoff feature genes of the original feature genes. This method not only make each feature gene to compete with each other, but also make each feature gene compete with its knockoff feature gene. This approach can help to select the key genes that affect the decision-making of neural networks. Results We use maize carotenoids, tocopherol methyltransferase, raffinose family oligosaccharides and human breast cancer dataset to do verification and analysis. Conclusions The experiment results demonstrate that the knockoffs optimizing neural network method has better detection effect than the other existing algorithms, and specially for processing the nonlinear gene expression and phenotype data.
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Affiliation(s)
- Juncheng Guo
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.,Institute of Information Engineering, Chinese Academy of Sciences, Beijing, 10049, China.,School of Cyber Security, University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Min Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuanyuan Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianxiao Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China. .,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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Correa SM, Fernie AR, Nikoloski Z, Brotman Y. Towards model-driven characterization and manipulation of plant lipid metabolism. Prog Lipid Res 2020; 80:101051. [PMID: 32640289 DOI: 10.1016/j.plipres.2020.101051] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/20/2020] [Accepted: 06/21/2020] [Indexed: 01/09/2023]
Abstract
Plant lipids have versatile applications and provide essential fatty acids in human diet. Therefore, there has been a growing interest to better characterize the genetic basis, regulatory networks, and metabolic pathways that shape lipid quantity and composition. Addressing these issues is challenging due to context-specificity of lipid metabolism integrating environmental, developmental, and tissue-specific cues. Here we systematically review the known metabolic pathways and regulatory interactions that modulate the levels of storage lipids in oilseeds. We argue that the current understanding of lipid metabolism provides the basis for its study in the context of genome-wide plant metabolic networks with the help of approaches from constraint-based modeling and metabolic flux analysis. The focus is on providing a comprehensive summary of the state-of-the-art of modeling plant lipid metabolic pathways, which we then contrast with the existing modeling efforts in yeast and microalgae. We then point out the gaps in knowledge of lipid metabolism, and enumerate the recent advances of using genome-wide association and quantitative trait loci mapping studies to unravel the genetic regulations of lipid metabolism. Finally, we offer a perspective on how advances in the constraint-based modeling framework can propel further characterization of plant lipid metabolism and its rational manipulation.
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Affiliation(s)
- Sandra M Correa
- Genetics of Metabolic Traits Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel; Departamento de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín 050010, Colombia.
| | - Alisdair R Fernie
- Central Metabolism Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Zoran Nikoloski
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; Systems Biology and Mathematical Modelling Group, Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm 14476, Germany.
| | - Yariv Brotman
- Genetics of Metabolic Traits Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
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Genetic variability for kernel tocopherols and haplotype analysis of γ-tocopherol methyl transferase (vte4) gene among exotic- and indigenous- maize inbreds. J Food Compost Anal 2020. [DOI: 10.1016/j.jfca.2020.103446] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Wang H, Yan M, Xiong M, Wang P, Liu Y, Xin Q, Wan L, Yang G, Hong D. Genetic dissection of thousand-seed weight and fine mapping of cqSW.A03-2 via linkage and association analysis in rapeseed (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1321-1335. [PMID: 32002584 DOI: 10.1007/s00122-020-03553-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE: cqSW.A03-2, one of the six identified quantitative trait loci associated with thousand-seed weight in rapeseed, is mapped to a 61.6-kb region on chromosome A03 and corresponds to the candidate gene BnaA03G37960D. Seed weight is an important factor that determines the seed yield of oilseed rape (Brassica napus L.). To elucidate the genetic mechanism of thousand-seed weight (TSW), quantitative trait locus (QTL) mapping was conducted using a double haploid population derived from the cross between an elite line ZY50 and a pol cytoplasmic male sterility restorer line 7-5. The genetic basis of TSW was dissected into six major QTLs. One major QTL denoted as cqSW.A03-2, which explained 8.46-13.70% of the phenotypic variation, was detected across multiple environments. To uncover the genetic basis of cqSW.A03-2, a set of near-isogenic lines were developed. Based on the test of self-pollinated progenies, cqSW.A03-2 was identified as a single Mendelian factor and the ZY50 allele at cqSW.A03-2 showed a positive effect on TSW. Fine mapping delimited the cqSW.A03-2 locus into a 61.6-kb region, and 18 genes within this region were predicted. Candidate gene association analysis and expression analysis indicated that a histidine kinase gene (BnaA03G37960D) is likely to be the candidate gene for the cqSW.A03-2 locus. Our results may contribute to a better understanding of the molecular mechanism of seed weight regulation and promote the breeding program for yield improvement in rapeseed.
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Affiliation(s)
- Hao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Min Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Mei Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ying Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, China
| | - Qiang Xin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Lili Wan
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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Liao N, Hu Z, Li Y, Hao J, Chen S, Xue Q, Ma Y, Zhang K, Mahmoud A, Ali A, Malangisha GK, Lyu X, Yang J, Zhang M. Ethylene-responsive factor 4 is associated with the desirable rind hardness trait conferring cracking resistance in fresh fruits of watermelon. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1066-1077. [PMID: 31610078 PMCID: PMC7061880 DOI: 10.1111/pbi.13276] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/26/2019] [Accepted: 10/06/2019] [Indexed: 05/11/2023]
Abstract
Fruit rind plays a pivotal role in alleviating water loss and disease and particularly in cracking resistance as well as the transportability, storability and shelf-life quality of the fruit. High susceptibility to cracking due to low rind hardness is largely responsible for severe annual yield losses of fresh fruits such as watermelon in the field and during the postharvest process. However, the candidate gene controlling the rind hardness phenotype remains unclear to date. Herein, we report, for the first time, an ethylene-responsive transcription factor 4 (ClERF4) associated with variation in rind hardness via a combinatory genetic map with bulk segregant analysis (BSA). Strikingly, our fine-mapping approach revealed an InDel of 11 bp and a neighbouring SNP in the ClERF4 gene on chromosome 10, conferring cracking resistance in F2 populations with variable rind hardness. Furthermore, the concomitant kompetitive/competitive allele-specific PCR (KASP) genotyping data sets of 104 germplasm accessions strongly supported candidate ClERF4 as a causative gene associated with fruit rind hardness variability. In conclusion, our results provide new insight into the underlying mechanism controlling rind hardness, a desirable trait in fresh fruit. Moreover, the findings will further enable the molecular improvement of fruit cracking resistance in watermelon via precisely targeting the causative gene relevant to rind hardness, ClERF4.
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Affiliation(s)
- Nanqiao Liao
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
- Key laboratory of Horticultural Plant growthDevelopment and Quality ImprovementMinistry of AgricultureHangzhouChina
| | - Yingying Li
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Junfang Hao
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Shuna Chen
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Qin Xue
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Yuyuan Ma
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Kejia Zhang
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Ahmed Mahmoud
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Abid Ali
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Guy Kateta Malangisha
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
- Key laboratory of Horticultural Plant growthDevelopment and Quality ImprovementMinistry of AgricultureHangzhouChina
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
- Key laboratory of Horticultural Plant growthDevelopment and Quality ImprovementMinistry of AgricultureHangzhouChina
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Li P, Zhou H, Yang H, Xia D, Liu R, Sun P, Wang Q, Gao G, Zhang Q, Wang G, He Y. Genome-Wide Association Studies Reveal the Genetic Basis of Fertility Restoration of CMS-WA and CMS-HL in xian/indica and aus Accessions of Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2020; 13:11. [PMID: 32040640 PMCID: PMC7010892 DOI: 10.1186/s12284-020-0372-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/28/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Wild-abortive cytoplasmic male sterility (CMS-WA) and Honglian CMS (CMS-HL) are the two main CMS types utilized in production of three-line hybrid rice in xian/indica (XI) rice. Dissection of the genetic basis of fertility restoration of CMS-WA and CMS-HL in the core germplasm population would provide valuable gene and material resources for development of three-line hybrid combinations. RESULTS In this study, two F1 populations with CMS-WA and CMS-HL background respectively were developed using 337 XI and aus accessions being paternal parents. Genome-wide association studies on three fertility-related traits of the two populations for two consecutive years revealed that both fertility restoration of CMS-WA and CMS-HL were controlled by a major locus and several minor loci respectively. The major locus for fertility restoration of CMS-WA was co-located with Rf4, and that for fertility restoration of CMS-HL was co-located with Rf5, which are cloned major restorer of fertility (Rf) genes. Furthermore, haplotype analysis of Rf4, Rf5 and Rf6, the three cloned major Rf genes, were conducted using the 337 paternal accessions. Four main haplotypes were identified for Rf4, and displayed different subgroup preferences. Two main haplotypes were identified for Rf5, and the functional type was carried by the majority of paternal accessions. In addition, eight haplotypes were identified for Rf6. CONCLUSIONS Haplotype analysis of three Rf genes, Rf4, Rf5 and Rf6, could provide valuable sequence variations that can be utilized in marker-aided selection of corresponding genes in rice breeding. Meanwhile, fertility evaluation of 337 accessions under the background of CMS could provide material resources for development of maintainer lines and restorers.
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Affiliation(s)
- Pingbo Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hanyuan Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Duo Xia
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rongjia Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ping Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Quanxiu Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China.
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Yang W, Feng H, Zhang X, Zhang J, Doonan JH, Batchelor WD, Xiong L, Yan J. Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives. MOLECULAR PLANT 2020; 13:187-214. [PMID: 31981735 DOI: 10.1016/j.molp.2020.01.008] [Citation(s) in RCA: 239] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 05/18/2023]
Abstract
Since whole-genome sequencing of many crops has been achieved, crop functional genomics studies have stepped into the big-data and high-throughput era. However, acquisition of large-scale phenotypic data has become one of the major bottlenecks hindering crop breeding and functional genomics studies. Nevertheless, recent technological advances provide us potential solutions to relieve this bottleneck and to explore advanced methods for large-scale phenotyping data acquisition and processing in the coming years. In this article, we review the major progress on high-throughput phenotyping in controlled environments and field conditions as well as its use for post-harvest yield and quality assessment in the past decades. We then discuss the latest multi-omics research combining high-throughput phenotyping with genetic studies. Finally, we propose some conceptual challenges and provide our perspectives on how to bridge the phenotype-genotype gap. It is no doubt that accurate high-throughput phenotyping will accelerate plant genetic improvements and promote the next green revolution in crop breeding.
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Affiliation(s)
- Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China.
| | - Hui Feng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crops Science/College of Agronomy, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Jian Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - John H Doonan
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | | | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
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Liu J, Fernie AR, Yan J. The Past, Present, and Future of Maize Improvement: Domestication, Genomics, and Functional Genomic Routes toward Crop Enhancement. PLANT COMMUNICATIONS 2020; 1:100010. [PMID: 33404535 PMCID: PMC7747985 DOI: 10.1016/j.xplc.2019.100010] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/07/2019] [Accepted: 11/22/2019] [Indexed: 05/14/2023]
Abstract
After being domesticated from teosinte, cultivated maize (Zea mays ssp. mays) spread worldwide and now is one of the most important staple crops. Due to its tremendous phenotypic and genotypic diversity, maize also becomes to be one of the most widely used model plant species for fundamental research, with many important discoveries reported by maize researchers. Here, we provide an overview of the history of maize domestication and key genes controlling major domestication-related traits, review the currently available resources for functional genomics studies in maize, and discuss the functions of most of the maize genes that have been positionally cloned and can be used for crop improvement. Finally, we provide some perspectives on future directions regarding functional genomics research and the breeding of maize and other crops.
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Affiliation(s)
- Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author
| | - Alisdair R. Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author
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Zhang T, Wu T, Wang L, Jiang B, Zhen C, Yuan S, Hou W, Wu C, Han T, Sun S. A Combined Linkage and GWAS Analysis Identifies QTLs Linked to Soybean Seed Protein and Oil Content. Int J Mol Sci 2019; 20:E5915. [PMID: 31775326 PMCID: PMC6928826 DOI: 10.3390/ijms20235915] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 12/30/2022] Open
Abstract
Soybean is an excellent source of vegetable protein and edible oil. Understanding the genetic basis of protein and oil content will improve the breeding programs for soybean. Linkage analysis and genome-wide association study (GWAS) tools were combined to detect quantitative trait loci (QTL) that are associated with protein and oil content in soybean. Three hundred and eight recombinant inbred lines (RILs) containing 3454 single nucleotide polymorphism (SNP) markers and 200 soybean accessions, including 94,462 SNPs and indels, were applied to identify QTL intervals and significant SNP loci. Intervals on chromosomes 1, 15, and 20 were correlated with both traits, and QTL qPro15-1, qPro20-1, and qOil5-1 reproducibly correlated with large phenotypic variations. SNP loci on chromosome 20 that overlapped with qPro20-1 were reproducibly connected to both traits by GWAS (p < 10-4). Twenty-five candidate genes with putative roles in protein and/or oil metabolisms within two regions (qPro15-1, qPro20-1) were identified, and eight of these genes showed differential expressions in parent lines during late reproductive growth stages, consistent with a role in controlling protein and oil content. The new well-defined QTL should significantly improve molecular breeding programs, and the identified candidate genes may help elucidate the mechanisms of protein and oil biosynthesis.
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Affiliation(s)
- Tengfei Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (L.W.); (C.Z.); (S.Y.); (W.H.); (C.W.); (T.H.)
| | - Tingting Wu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (L.W.); (C.Z.); (S.Y.); (W.H.); (C.W.); (T.H.)
| | - Liwei Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (L.W.); (C.Z.); (S.Y.); (W.H.); (C.W.); (T.H.)
| | - Bingjun Jiang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (L.W.); (C.Z.); (S.Y.); (W.H.); (C.W.); (T.H.)
| | - Caixin Zhen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (L.W.); (C.Z.); (S.Y.); (W.H.); (C.W.); (T.H.)
| | - Shan Yuan
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (L.W.); (C.Z.); (S.Y.); (W.H.); (C.W.); (T.H.)
| | - Wensheng Hou
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (L.W.); (C.Z.); (S.Y.); (W.H.); (C.W.); (T.H.)
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cunxiang Wu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (L.W.); (C.Z.); (S.Y.); (W.H.); (C.W.); (T.H.)
| | - Tianfu Han
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (L.W.); (C.Z.); (S.Y.); (W.H.); (C.W.); (T.H.)
| | - Shi Sun
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (L.W.); (C.Z.); (S.Y.); (W.H.); (C.W.); (T.H.)
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Park C, Dwiyanti MS, Nagano AJ, Liu B, Yamada T, Abe J. Identification of quantitative trait loci for increased α-tocopherol biosynthesis in wild soybean using a high-density genetic map. BMC PLANT BIOLOGY 2019; 19:510. [PMID: 31752696 PMCID: PMC6873731 DOI: 10.1186/s12870-019-2117-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/04/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Soybean is one of the most important crop sources of tocopherols (Toc). However, the content of α-Toc, an isoform with the highest vitamin E activity in humans, is low in most cultivars. With the aim of broadening genetic variability, we performed quantitative trait locus (QTL) analysis for a high seed α-Toc trait detected in a wild soybean and characterized the sequence polymorphisms and expression profiles of γ-tocopherol methyltransferase (γ-TMT) genes as potential candidates. RESULTS A recombinant inbred line population was developed from a cross between the low α-Toc breeding line TK780 and the high α-Toc wild accession B04009. The α-Toc content in seeds correlated strongly with the ratio of α-Toc to γ-Toc contents. QTL analysis using a high-density map constructed with 7710 single nucleotide polymorphisms (SNPs) generated by restriction site-associated DNA sequencing detected six QTLs involved in α-Toc biosynthesis. Of these, three in chromosomes (Chr) 9, 11, and 12 produced consistent effects during a 2-year trial. B04009 allele at QTLs in Chr9 and Chr12 and TK780 allele at the QTL in Chr11 each promoted the conversion of γ-Toc to α-Toc, which elevated the seed α-Toc content. SNPs and indels were detected between the parents in three γ-TMT genes (γ-TMT1, γ-TMT2, and γ-TMT3) co-located in the QTLs in Chr9 and Chr12, of which some existed in the cis-regulatory elements associated with seed development and functions. In immature cotyledons, γ-TMT3 was expressed at higher levels in B04009 than TK780, irrespective of two thermal conditions tested, whereas the expression of γ-TMT2 was markedly upregulated under higher temperatures, particularly in B04009. CONCLUSIONS We identified QTLs consistently controlling α-Toc biosynthesis in wild soybean seeds in 2-year trials. The QTL on Chr9 had been previously identified in soybean, whereas the QTLs on Chr11 and Chr12 were novel. Further molecular dissections and characterization of the QTLs may facilitate the use of high α-Toc alleles from wild soybean in soybean breeding and an understanding of the molecular mechanisms underlying α-Toc biosynthesis in soybean seeds.
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Affiliation(s)
- Cheolwoo Park
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | | | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, 520-2194, Japan
| | - Baohui Liu
- School of Life Science, Guangzhou University, Guangzhou, 510000, China
| | - Tetsuya Yamada
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
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Xu J, Chen G, Hermanson PJ, Xu Q, Sun C, Chen W, Kan Q, Li M, Crisp PA, Yan J, Li L, Springer NM, Li Q. Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize. Genome Biol 2019; 20:243. [PMID: 31744513 PMCID: PMC6862797 DOI: 10.1186/s13059-019-1859-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 10/10/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND DNA methylation can provide a source of heritable information that is sometimes entirely uncoupled from genetic variation. However, the extent of this uncoupling and the roles of DNA methylation in shaping diversity of both gene expression and phenotypes are hotly debated. Here, we investigate the genetic basis and biological functions of DNA methylation at a population scale in maize. RESULTS We perform targeted DNA methylation profiling for a diverse panel of 263 maize inbred genotypes. All genotypes show similar levels of DNA methylation globally, highlighting the importance of DNA methylation in maize development. Nevertheless, we identify more than 16,000 differentially methylated regions (DMRs) that are distributed across the 10 maize chromosomes. Genome-wide association analysis with high-density genetic markers reveals that over 60% of the DMRs are not tagged by SNPs, suggesting the presence of unique information in DMRs. Strong associations between DMRs and the expression of many genes are identified in both the leaf and kernel tissues, pointing to the biological significance of methylation variation. Association analysis with 986 metabolic traits suggests that DNA methylation is associated with phenotypic variation of 156 traits. There are some traits that only show significant associations with DMRs and not with SNPs. CONCLUSIONS These results suggest that DNA methylation can provide unique information to explain phenotypic variation in maize.
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Affiliation(s)
- Jing Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Guo Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091 China
| | - Peter J. Hermanson
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108 USA
| | - Qiang Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Changshuo Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wenqing Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Qiuxin Kan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Minqi Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Peter A. Crisp
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108 USA
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Nathan M. Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108 USA
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
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Zhang L, Luo Y, Liu B, Zhang L, Zhang W, Chen R, Wang L. Overexpression of the maize γ-tocopherol methyltransferase gene (ZmTMT) increases α-tocopherol content in transgenic Arabidopsis and maize seeds. Transgenic Res 2019; 29:95-104. [PMID: 31673914 DOI: 10.1007/s11248-019-00180-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/22/2019] [Indexed: 11/25/2022]
Abstract
The vitamin E family includes tocopherols and tocotrienols, which are essential lipid-soluble antioxidants necessary for human and livestock health. The seeds of many plant species, including maize, have high gamma (γ)-tocopherol but low alpha (α)-tocopherol contents; however, α-tocopherol is the most effective antioxidant. Therefore, it is necessary to optimize the tocopherol composition in plants. α-Tocopherol is synthesized from γ-tocopherol by γ-tocopherol methyltransferase (γ-TMT, VTE4) in the final step of the tocopherol biosynthetic pathway. In the present study, the full-length coding sequence (CDS) of γ-TMT was isolated from Zea mays, named ZmTMT. The ZmTMT CDS was 1059 bp in size, encoding 352 amino acids. Recombinant ZmTMT was expressed in Escherichia coli and the purified protein effectively converted γ-tocopherol into α-tocopherol in vitro. A comparison of enzyme activities showed that the activity of ZmTMT was higher than that of GmTMT2a (Glycine max) and AtTMT (Arabidopsis thaliana). Overexpression of ZmTMT increased the α-tocopherol content 4-5-fold in transgenic Arabidopsis and around 6.5-fold in transgenic maize kernels, and increased the α-/γ-tocopherol ratio to approximately 15 and 17, respectively. These results show that it is feasible to overexpress ZmTMT to optimize the tocopherol composition in maize; such a corn product might be useful in the feed industry in the near future.
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Affiliation(s)
- Lan Zhang
- National Key Facility of Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanzhong Luo
- National Key Facility of Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Bin Liu
- National Key Facility of Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Liang Zhang
- National Key Facility of Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Zhang
- National Key Facility of Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Rumei Chen
- National Key Facility of Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lei Wang
- National Key Facility of Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Zhan W, Liu J, Pan Q, Wang H, Yan S, Li K, Deng M, Li W, Liu N, Kong Q, Fernie AR, Yan J. An allele of ZmPORB2 encoding a protochlorophyllide oxidoreductase promotes tocopherol accumulation in both leaves and kernels of maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:114-127. [PMID: 31169939 DOI: 10.1111/tpj.14432] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 05/27/2023]
Abstract
Phytol is one of the key precursors for tocopherol synthesis in plants, however, the underlying mechanisms concerning the accumulation of tocopherol remain poorly understood. In this study, qVE5, a major QTL affecting tocopherol accumulation in maize kernels was identified via a positional cloning approach. qVE5 encodes a protochlorophyllide oxidoreductase (ZmPORB2), which localizes to the chloroplast. Overexpression of ZmPORB2 increased tocopherol content in both leaves and kernels. Candidate gene association analysis identified a 5/8-bp insertion/deletion (InDel058) in the 5' untranslated region (UTR) as the causal polymorphism in affecting ZmPORB2 expression and being highly associated with tocopherol content. We showed that higher expression of ZmPORB2 correlated with more chlorophyll metabolites in the leaf following pollination. RNA-sequencing and metabolic analysis in near isogenic lines (NILs) support that ZmPORB2 participates in chlorophyll metabolism enabling the production of phytol, an important precursor of tocopherol. We also found that the tocopherol content in the kernel is mainly determined by the maternal genotype, a fact that was further confirmed by in vitro culture experiments. Finally, a PCR-based marker based on Indel058 was developed in order to facilitate the high tocopherol (vitamin E) maize breeding.
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Affiliation(s)
- Wei Zhan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Crop Germplasm Resources of Northern China (Ministry of Education), Hebei Sub-center of National Maize Improvement Center of China, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Shijuan Yan
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Kun Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Min Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nannan Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qian Kong
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Schuy C, Groth J, Ammon A, Eydam J, Baier S, Schweizer G, Hanemann A, Herz M, Voll LM, Sonnewald U. Deciphering the genetic basis for vitamin E accumulation in leaves and grains of different barley accessions. Sci Rep 2019; 9:9470. [PMID: 31263124 PMCID: PMC6602966 DOI: 10.1038/s41598-019-45572-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 06/04/2019] [Indexed: 01/22/2023] Open
Abstract
Tocopherols and tocotrienols, commonly referred to as vitamin E, are essential compounds in food and feed. Due to their lipophilic nature they protect biomembranes by preventing the propagation of lipid-peroxidation especially during oxidative stress. Since their synthesis is restricted to photosynthetic organisms, plant-derived products are the major source of natural vitamin E. In the present study the genetic basis for high vitamin E accumulation in leaves and grains of different barley (Hordeum vulgare L.) accessions was uncovered. A genome wide association study (GWAS) allowed the identification of two genes located on chromosome 7H, homogentisate phytyltransferase (HPT-7H) and homogentisate geranylgeranyltransferase (HGGT) that code for key enzymes controlling the accumulation of tocopherols in leaves and tocotrienols in grains, respectively. Transcript profiling showed a correlation between HPT-7H expression and vitamin E content in leaves. Allele sequencing allowed to decipher the allelic variation of HPT-7H and HGGT genes corresponding to high and low vitamin E contents in the respective tissues. Using the obtained sequence information molecular markers have been developed which can be used to assist smart breeding of high vitamin E barley varieties. This will facilitate the selection of genotypes more tolerant to oxidative stress and producing high-quality grains.
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Affiliation(s)
- Christian Schuy
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058, Erlangen, Germany.
| | - Jennifer Groth
- Institut für Pflanzenbau und Pflanzenzüchtung, Bavarian State Research Center for Agriculture, Am Gereuth 8, D-85354, Freising, Germany
| | - Alexandra Ammon
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058, Erlangen, Germany
| | - Julia Eydam
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058, Erlangen, Germany
| | - Steffen Baier
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058, Erlangen, Germany
- Saatzucht Josef Breun GmbH & Co. KG, Amselweg 1, D-91074, Herzogenaurach, Germany
| | - Günther Schweizer
- Institut für Pflanzenbau und Pflanzenzüchtung, Bavarian State Research Center for Agriculture, Am Gereuth 8, D-85354, Freising, Germany
| | - Anja Hanemann
- Saatzucht Josef Breun GmbH & Co. KG, Amselweg 1, D-91074, Herzogenaurach, Germany
| | - Markus Herz
- Institut für Pflanzenbau und Pflanzenzüchtung, Bavarian State Research Center for Agriculture, Am Gereuth 8, D-85354, Freising, Germany
| | - Lars M Voll
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058, Erlangen, Germany
- Division of Plant Physiology, Department Biology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043, Marburg, Germany
| | - Uwe Sonnewald
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058, Erlangen, Germany
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Baseggio M, Murray M, Magallanes-Lundback M, Kaczmar N, Chamness J, Buckler ES, Smith ME, DellaPenna D, Tracy WF, Gore MA. Genome-Wide Association and Genomic Prediction Models of Tocochromanols in Fresh Sweet Corn Kernels. THE PLANT GENOME 2019; 12:180038. [PMID: 30951088 DOI: 10.3835/plantgenome2018.06.0038] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Sweet corn ( L.), a highly consumed fresh vegetable in the United States, varies for tocochromanol (tocopherol and tocotrienol) levels but makes only a limited contribution to daily intake of vitamin E and antioxidants. We performed a genome-wide association study of six tocochromanol compounds and 14 derivative traits across a sweet corn inbred line association panel to identify genes associated with natural variation for tocochromanols and vitamin E in fresh kernels. Concordant with prior studies in mature maize kernels, an association was detected between γ-tocopherol methyltransferase (vte4) and α-tocopherol content, along with () and () for tocotrienol variation. Additionally, two kernel starch synthesis genes, () and (), were associated with tocotrienols, with the strongest evidence for in combination with fixed, strong and alleles, accounting for the greater amount of tocotrienols in and lines. In prediction models with genome-wide markers, predictive abilities were higher for tocotrienols than tocopherols, and these models were superior to those that used marker sets targeting a priori genes involved in the biosynthesis and/or genetic control of tocochromanols. Through this quantitative genetic analysis, we have established a key step for increasing tocochromanols in fresh kernels of sweet corn for human health and nutrition.
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Strobbe S, De Lepeleire J, Van Der Straeten D. From in planta Function to Vitamin-Rich Food Crops: The ACE of Biofortification. FRONTIERS IN PLANT SCIENCE 2018; 9:1862. [PMID: 30619424 PMCID: PMC6305313 DOI: 10.3389/fpls.2018.01862] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/03/2018] [Indexed: 05/11/2023]
Abstract
Humans are highly dependent on plants to reach their dietary requirements, as plant products contribute both to energy and essential nutrients. For many decades, plant breeders have been able to gradually increase yields of several staple crops, thereby alleviating nutritional needs with varying degrees of success. However, many staple crops such as rice, wheat and corn, although delivering sufficient calories, fail to satisfy micronutrient demands, causing the so called 'hidden hunger.' Biofortification, the process of augmenting nutritional quality of food through the use of agricultural methodologies, is a pivotal asset in the fight against micronutrient malnutrition, mainly due to vitamin and mineral deficiencies. Several technical advances have led to recent breakthroughs. Nutritional genomics has come to fruition based on marker-assisted breeding enabling rapid identification of micronutrient related quantitative trait loci (QTL) in the germplasm of interest. As a complement to these breeding techniques, metabolic engineering approaches, relying on a continuously growing fundamental knowledge of plant metabolism, are able to overcome some of the inevitable pitfalls of breeding. Alteration of micronutrient levels does also require fundamental knowledge about their role and influence on plant growth and development. This review focuses on our knowledge about provitamin A (beta-carotene), vitamin C (ascorbate) and the vitamin E group (tocochromanols). We begin by providing an overview of the functions of these vitamins in planta, followed by highlighting some of the achievements in the nutritional enhancement of food crops via conventional breeding and genetic modification, concluding with an evaluation of the need for such biofortification interventions. The review further elaborates on the vast potential of creating nutritionally enhanced crops through multi-pathway engineering and the synergistic potential of conventional breeding in combination with genetic engineering, including the impact of novel genome editing technologies.
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Alseekh S, Bermudez L, de Haro LA, Fernie AR, Carrari F. Crop metabolomics: from diagnostics to assisted breeding. Metabolomics 2018; 14:148. [PMID: 30830402 DOI: 10.1007/s11306-018-1446-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/26/2018] [Indexed: 01/02/2023]
Abstract
BACKGROUND Until recently, plant metabolomics have provided a deep understanding on the metabolic regulation in individual plants as experimental units. The application of these techniques to agricultural systems subjected to more complex interactions is a step towards the implementation of translational metabolomics in crop breeding. AIM OF REVIEW We present here a review paper discussing advances in the knowledge reached in the last years derived from the application of metabolomic techniques that evolved from biomarker discovery to improve crop yield and quality. KEY SCIENTIFIC CONCEPTS OF REVIEW Translational metabolomics applied to crop breeding programs.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Luisa Bermudez
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Luis Alejandro de Haro
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Fernando Carrari
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina.
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, 05508-090, Brazil.
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina.
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