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Yang B, Chen M, Zhan C, Liu K, Cheng Y, Xie T, Zhu P, He Y, Zeng P, Tang H, Tsugama D, Chen S, Zhang H, Cheng J. Identification of OsPK5 involved in rice glycolytic metabolism and GA/ABA balance for improving seed germination via genome-wide association study. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3446-3461. [PMID: 35191960 PMCID: PMC9162179 DOI: 10.1093/jxb/erac071] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 02/19/2022] [Indexed: 06/12/2023]
Abstract
Seed germination plays a pivotal role in the plant life cycle, and its precise regulatory mechanisms are not clear. In this study, 19 quantitative trait loci (QTLs) associated with rice seed germination were identified through genome-wide association studies (GWAS) of the following traits in 2016 and 2017: germination rate (GR) at 3, 5, and 7 days after imbibition (DAI) and germination index (GI). Two major stable QTLs, qSG4 and qSG11.1, were found to be associated with GR and GI over 2 continuous years. Furthermore, OsPK5, encoding a pyruvate kinase, was shown to be a crucial regulator of seed germination in rice, and might be a causal gene of the key QTL qSG11.1, on chromosome 11. Natural variation in OsPK5 function altered the activity of pyruvate kinase. The disruption of OsPK5 function resulted in slow germination and seedling growth during seed germination, blocked glycolytic metabolism, caused glucose accumulation, decreased energy levels, and affected the GA/ABA balance. Taken together, our results provide novel insights into the roles of OsPK5 in seed germination, and facilitate its application in rice breeding to improve seed vigour.
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Affiliation(s)
| | | | | | - Kexin Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanhao Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Xie
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Peiwen Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Zeng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Haijuan Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Daisuke Tsugama
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo-shi, Tokyo 188-0002, Japan
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
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102
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Bai X, Wang X, Wang Y, Wei Y, Fu Y, Rao J, Ma Y, Zeng Z, Li F, Wang M, Zhu S. Genome-Wide Association Study of Six Forage Traits in Ramie ( Boehmeria nivea L. Gaud). PLANTS (BASEL, SWITZERLAND) 2022; 11:1443. [PMID: 35684216 PMCID: PMC9182863 DOI: 10.3390/plants11111443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Genome-wide association study (GWAS) of six forage traits using whole-genome sequencing data generated from 301 ramie accessions found that traits were continuously distributed; the maximum variant coefficient was fresh weight per clump (FWPC) (2019) and individual plant height (IPH) (2019) minimum. Correlation analysis demonstrated that 2019 and 2020 results were similar; all traits were correlated. GWAS analysis demonstrated that six traits exhibited consistent and precise association signals. Of the latter, 104 were significant and detected in 43 genomic regions. By screening forage trait-associated single nucleotide polymorphisms and combining Manhattan map with genome annotation, signals were categorized according to functional annotations. One loci associated with fresh weight per plant (FWP) (chromosome 5; Bnt05G007759), two associated with FWPC (chromosome 13; Bnt13G018582, and Bnt13G018583), and two associated with leaf dry weight per plant (LDWP) and dry weight per plant (DWP) (chromosome 4; Bnt04G005779 and Bnt04G005780), were identified. We describe forage trait candidate genes that are highly correlated with FWP and FWPC; Bnt05G007759 may be involved in nitrogen metabolism, while Bnt13G018582 and Bnt13G018583 may encode TEOSINTE branch 1/CYCLOIDEA/proliferating cytokine 1 (TCP) domains. Bnt04G005779 and Bnt04G005780, which may regulate growth and development, are highly related to LDWP and DWP. These genomic resources will provide a basis for breeding varieties.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Siyuan Zhu
- Correspondence: ; Tel.: +86-138-7580-0740
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103
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Songsomboon K, Crawford R, Crawford J, Hansen J, Cummings J, Mattson N, Bergstrom GC, Viands DR. Genome-Wide Associations with Resistance to Bipolaris Leaf Spot (Bipolaris oryzae (Breda de Haan) Shoemaker) in a Northern Switchgrass Population (Panicum virgatum L.). PLANTS 2022; 11:plants11101362. [PMID: 35631787 PMCID: PMC9144872 DOI: 10.3390/plants11101362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022]
Abstract
Switchgrass (Panicum virgatum L.), a northern native perennial grass, suffers from yield reduction from Bipolaris leaf spot caused by Bipolaris oryzae (Breda de Haan) Shoemaker. This study aimed to determine the resistant populations via multiple phenotyping approaches and identify potential resistance genes from genome-wide association studies (GWAS) in the switchgrass northern association panel. The disease resistance was evaluated from both natural (field evaluations in Ithaca, New York and Phillipsburg, Philadelphia) and artificial inoculations (detached leaf and leaf disk assays). The most resistant populations based on a combination of three phenotyping approaches—detached leaf, leaf disk, and mean from two locations—were ‘SW788’, ‘SW806’, ‘SW802’, ‘SW793’, ‘SW781’, ‘SW797’, ‘SW798’, ‘SW803’, ‘SW795’, ‘SW805’. The GWAS from the association panel showed 27 significant SNPs on 12 chromosomes: 1K, 2K, 2N, 3K, 3N, 4N, 5K, 5N, 6N, 7K, 7N, and 9N. These markers accumulatively explained the phenotypic variance of the resistance ranging from 3.28 to 26.52%. Within linkage disequilibrium of 20 kb, these SNP markers linked with the potential resistance genes included the genes encoding for NBS-LRR, PPR, cell-wall related proteins, homeostatic proteins, anti-apoptotic proteins, and ABC transporter.
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Affiliation(s)
- Kittikun Songsomboon
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; (R.C.); (J.C.); (J.H.); (D.R.V.)
- Correspondence:
| | - Ryan Crawford
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; (R.C.); (J.C.); (J.H.); (D.R.V.)
| | - Jamie Crawford
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; (R.C.); (J.C.); (J.H.); (D.R.V.)
| | - Julie Hansen
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; (R.C.); (J.C.); (J.H.); (D.R.V.)
| | | | - Neil Mattson
- Section of Horticulture, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA;
| | - Gary C. Bergstrom
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA;
| | - Donald R. Viands
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; (R.C.); (J.C.); (J.H.); (D.R.V.)
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104
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Yu Y, Ma L, Wang X, Zhao Z, Wang W, Fan Y, Liu K, Jiang T, Xiong Z, Song Q, Li C, Wang P, Ma W, Xu H, Wang X, Zhao Z, Wang J, Zhang H, Bao Y. Genome-Wide Association Study Identifies a Rice Panicle Blast Resistance Gene, Pb2, Encoding NLR Protein. Int J Mol Sci 2022; 23:ijms23105668. [PMID: 35628477 PMCID: PMC9145240 DOI: 10.3390/ijms23105668] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/15/2022] [Accepted: 05/15/2022] [Indexed: 12/24/2022] Open
Abstract
Rice blast is one of the main diseases in rice and can occur in different rice growth stages. Due to the complicated procedure of panicle blast identification and instability of panicle blast infection influenced by the environment, most cloned rice resistance genes are associated with leaf blast. In this study, a rice panicle blast resistance gene, Pb2, was identified by genome-wide association mapping based on the panicle blast resistance phenotypes of 230 Rice Diversity Panel 1 (RDP1) accessions with 700,000 single-nucleotide polymorphism (SNP) markers. A genome-wide association study identified 18 panicle blast resistance loci (PBRL) within two years, including 9 reported loci and 2 repeated loci (PBRL2 and PBRL13, PBRL10 and PBRL18). Among them, the repeated locus (PBRL10 and PBRL18) was located in chromosome 11. By haplotype and expression analysis, one of the Nucleotide-binding domain and Leucine-rich Repeat (NLR) Pb2 genes was highly conserved in multiple resistant rice cultivars, and its expression was significantly upregulated after rice blast infection. Pb2 encodes a typical NBS-LRR protein with NB-ARC domain and LRR domain. Compared with wild type plants, the transgenic rice of Pb2 showed enhanced resistance to panicle and leaf blast with reduced lesion number. Subcellular localization of Pb2 showed that it is located on plasma membrane, and GUS tissue-staining observation found that Pb2 is highly expressed in grains, leaf tips and stem nodes. The Pb2 transgenic plants showed no difference in agronomic traits with wild type plants. It indicated that Pb2 could be useful for breeding of rice blast resistance.
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Affiliation(s)
- Yao Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Lu Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Xinying Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Zhi Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Wei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Yunxin Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Kunquan Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Tingting Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Ziwei Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Qisheng Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Changqing Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Panting Wang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Wenjing Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Huanan Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Xinyu Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Zijing Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Jianfei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Yongmei Bao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
- Correspondence:
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105
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Ćalić I, Groen SC, Choi JY, Joly‐Lopez Z, Hamann E, Natividad MA, Dorph K, Cabral CLU, Torres RO, Vergara GV, Henry A, Purugganan MD, Franks SJ. The influence of genetic architecture on responses to selection under drought in rice. Evol Appl 2022; 15:1670-1690. [PMID: 36330294 PMCID: PMC9624088 DOI: 10.1111/eva.13419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 11/29/2022] Open
Abstract
Accurately predicting responses to selection is a major goal in biology and important for successful crop breeding in changing environments. However, evolutionary responses to selection can be constrained by such factors as genetic and cross‐environment correlations, linkage, and pleiotropy, and our understanding of the extent and impact of such constraints is still developing. Here, we conducted a field experiment to investigate potential constraints to selection for drought resistance in rice (Oryza sativa) using phenotypic selection analysis and quantitative genetics. We found that traits related to drought response were heritable, and some were under selection, including selection for earlier flowering, which could allow drought escape. However, patterns of selection generally were not opposite under wet and dry conditions, and we did not find individual or closely linked genes that influenced multiple traits, indicating a lack of evidence that antagonistic pleiotropy, linkage, or cross‐environment correlations would constrain selection for drought resistance. In most cases, genetic correlations had little influence on responses to selection, with direct and indirect selection largely congruent. The exception to this was seed mass under drought, which was predicted to evolve in the opposite direction of direct selection due to correlations. Because of this indirect effect on selection on seed mass, selection for drought resistance was not accompanied by a decrease in seed mass, and yield increased with fecundity. Furthermore, breeding lines with high fitness and yield under drought also had high fitness and yield under wet conditions, indicating that there was no evidence for a yield penalty on drought resistance. We found multiple genes in which expression influenced both water use efficiency (WUE) and days to first flowering, supporting a genetic basis for the trade‐off between drought escape and avoidance strategies. Together, these results can provide helpful guidance for understanding and managing evolutionary constraints and breeding stress‐resistant crops.
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Affiliation(s)
- Irina Ćalić
- Department of Biological Sciences Fordham University Bronx NY USA
- Institute of Botany University of Cologne Cologne Germany
| | - Simon C. Groen
- Department of Nematology University of California at Riverside Riverside CA USA
- Center for Genomics and Systems Biology, Department of Biology New York University New York NY USA
| | - Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology New York University New York NY USA
| | - Zoé Joly‐Lopez
- Center for Genomics and Systems Biology, Department of Biology New York University New York NY USA
- Département de Chimie Université du Québec à Montréal Montréal Québec Canada
| | - Elena Hamann
- Department of Biological Sciences Fordham University Bronx NY USA
- Department of Genetics and Odum School of Ecology University of Georgia Athens GA USA
| | | | - Katherine Dorph
- Center for Genomics and Systems Biology, Department of Biology New York University New York NY USA
| | | | | | - Georgina V. Vergara
- International Rice Research Institute Los Baños Laguna Philippines
- Institute of Crop Science, University of the Philippines Los Baños, 4031 College Laguna Philippines
| | - Amelia Henry
- International Rice Research Institute Los Baños Laguna Philippines
| | - Michael D. Purugganan
- Center for Genomics and Systems Biology, Department of Biology New York University New York NY USA
- Center for Genomics and Systems Biology NYU Abu Dhabi Research Institute New York University Abu Dhabi, Saadiyat Island Abu Dhabi United Arab Emirates
| | - Steven J. Franks
- Department of Biological Sciences Fordham University Bronx NY USA
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106
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Ma Y, Li D, Xu Z, Gu R, Wang P, Fu J, Wang J, Du W, Zhang H. Dissection of the Genetic Basis of Yield Traits in Line per se and Testcross Populations and Identification of Candidate Genes for Hybrid Performance in Maize. Int J Mol Sci 2022; 23:5074. [PMID: 35563470 PMCID: PMC9102962 DOI: 10.3390/ijms23095074] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 12/31/2022] Open
Abstract
Dissecting the genetic basis of yield traits in hybrid populations and identifying the candidate genes are important for molecular crop breeding. In this study, a BC1F3:4 population, the line per se (LPS) population, was constructed by using elite inbred lines Zheng58 and PH4CV as the parental lines. The population was genotyped with 55,000 SNPs and testcrossed to Chang7-2 and PH6WC (two testers) to construct two testcross (TC) populations. The three populations were evaluated for hundred kernel weight (HKW) and yield per plant (YPP) in multiple environments. Marker-trait association analysis (MTA) identified 24 to 151 significant SNPs in the three populations. Comparison of the significant SNPs identified common and specific quantitative trait locus/loci (QTL) in the LPS and TC populations. Genetic feature analysis of these significant SNPs proved that these SNPs were associated with the tested traits and could be used to predict trait performance of both LPS and TC populations. RNA-seq analysis was performed using maize hybrid varieties and their parental lines, and differentially expressed genes (DEGs) between hybrid varieties and parental lines were identified. Comparison of the chromosome positions of DEGs with those of significant SNPs detected in the TC population identified potential candidate genes that might be related to hybrid performance. Combining RNA-seq analysis and MTA results identified candidate genes for hybrid performance, providing information that could be useful for maize hybrid breeding.
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Affiliation(s)
- Yuting Ma
- Agronomy College, Shenyang Agricultural University, Shenyang 110866, China;
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.L.); (P.W.); (J.F.)
| | - Dongdong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.L.); (P.W.); (J.F.)
| | - Zhenxiang Xu
- Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Z.X.); (R.G.); (J.W.)
| | - Riliang Gu
- Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Z.X.); (R.G.); (J.W.)
| | - Pingxi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.L.); (P.W.); (J.F.)
| | - Junjie Fu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.L.); (P.W.); (J.F.)
| | - Jianhua Wang
- Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Z.X.); (R.G.); (J.W.)
| | - Wanli Du
- Agronomy College, Shenyang Agricultural University, Shenyang 110866, China;
| | - Hongwei Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.L.); (P.W.); (J.F.)
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107
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Tan J, Zeng D, Zhao Y, Wang Y, Liu T, Li S, Xue Y, Luo Y, Xie X, Chen L, Liu Y, Zhu Q. PhieABEs: a PAM-less/free high-efficiency adenine base editor toolbox with wide target scope in plants. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:934-943. [PMID: 34984801 PMCID: PMC9055815 DOI: 10.1111/pbi.13774] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/14/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Adenine base editors (ABEs), which are generally engineered adenosine deaminases and Cas variants, introduce site-specific A-to-G mutations for agronomic trait improvement. However, notably varying editing efficiencies, restrictive requirements for protospacer-adjacent motifs (PAMs) and a narrow editing window greatly limit their application. Here, we developed a robust high-efficiency ABE (PhieABE) toolbox for plants by fusing an evolved, highly active form of the adenosine deaminase TadA8e and a single-stranded DNA-binding domain (DBD), based on PAM-less/free Streptococcus pyogenes Cas9 (SpCas9) nickase variants that recognize the PAM NGN (for SpCas9n-NG and SpGn) or NNN (for SpRYn). By targeting 29 representative targets in rice and assessing the results, we demonstrate that PhieABEs have significantly improved base-editing activity, expanded target range and broader editing windows compared to the ABE7.10 and general ABE8e systems. Among these PhieABEs, hyper ABE8e-DBD-SpRYn (hyABE8e-SpRY) showed nearly 100% editing efficiency at some tested sites, with a high proportion of homozygous base substitutions in the editing windows and no single guide RNA (sgRNA)-dependent off-target changes. The original sgRNA was more compatible with PhieABEs than the evolved sgRNA. In conclusion, the DBD fusion effectively promotes base-editing efficiency, and this novel PhieABE toolbox should have wide applications in plant functional genomics and crop improvement.
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Affiliation(s)
- Jiantao Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Dongchang Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yanchang Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yaxi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Taoli Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Shuangchun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yang Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yuyu Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yao‐Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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108
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Mathew B, Hauptmann A, Léon J, Sillanpää MJ. NeuralLasso: Neural Networks Meet Lasso in Genomic Prediction. FRONTIERS IN PLANT SCIENCE 2022; 13:800161. [PMID: 35574107 PMCID: PMC9100816 DOI: 10.3389/fpls.2022.800161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/18/2022] [Indexed: 06/15/2023]
Abstract
Prediction of complex traits based on genome-wide marker information is of central importance for both animal and plant breeding. Numerous models have been proposed for the prediction of complex traits and still considerable effort has been given to improve the prediction accuracy of these models, because various genetics factors like additive, dominance and epistasis effects can influence of the prediction accuracy of such models. Recently machine learning (ML) methods have been widely applied for prediction in both animal and plant breeding programs. In this study, we propose a new algorithm for genomic prediction which is based on neural networks, but incorporates classical elements of LASSO. Our new method is able to account for the local epistasis (higher order interaction between the neighboring markers) in the prediction. We compare the prediction accuracy of our new method with the most commonly used prediction methods, such as BayesA, BayesB, Bayesian Lasso (BL), genomic BLUP and Elastic Net (EN) using the heterogenous stock mouse and rice field data sets.
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Affiliation(s)
- Boby Mathew
- Bayer CropScience, Monheim am Rhein, Germany
- Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Andreas Hauptmann
- Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland
- Department of Computer Science, University College London, London, United Kingdom
| | - Jens Léon
- Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Mikko J. Sillanpää
- Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland
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109
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Lee C, Cheon KS, Shin Y, Oh H, Jeong YM, Jang H, Park YC, Kim KY, Cho HC, Won YJ, Baek J, Cha YS, Kim SL, Kim KH, Ji H. Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice. Genes (Basel) 2022; 13:genes13050794. [PMID: 35627177 PMCID: PMC9141132 DOI: 10.3390/genes13050794] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/25/2022] Open
Abstract
The development of efficient, robust, and high-throughput SNP genotyping platforms is pivotal for crop genetics and breeding. Recently, SNP genotyping platforms based on target capture sequencing, which is very flexible in terms of the number of SNP markers, have been developed for maize, cassava, and fava bean. We aimed to develop a target capture sequencing SNP genotyping platform for rice. A target capture sequencing panel containing 2565 SNPs, including 1225 SNPs informative for japonica and 1339 SNPs informative for indica, was developed. This platform was used in diversity analysis of 50 rice varieties. Of the 2565 SNP markers, 2341 (91.3%) produced useful polymorphic genotype data, enabling the production of a phylogenetic tree of the 50 varieties. The mean number of markers polymorphic between any two varieties was 854. The platform was used for QTL mapping of preharvest sprouting (PHS) resistance in an F8 recombinant inbred line population derived from the cross Odae × Joun. A genetic map comprising 475 markers was constructed, and two QTLs for PHS resistance were identified on chromosomes 4 and 11. This system is a powerful tool for rice genetics and breeding and will facilitate QTL studies and gene mapping, germplasm diversity analysis, and marker-assisted selection.
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Affiliation(s)
- Chaewon Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
- Department of Crop Science and Biotechnology, Chonbuk National University, Jeonju 54896, Korea
| | - Kyeong-Seong Cheon
- Division of Forest Tree Improvement and Biotechnology, Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Korea;
| | - Yunji Shin
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
- Genecell Biotech Inc., Wanju, 55322, Korea
| | - Hyoja Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Young-Min Jeong
- Seed Industry Promotion Center, Korea Agriculture Technology Promotion Agency (KOAT), Gimje 54324, Korea;
| | - Hoon Jang
- CELEMICS, Seoul 08506, Korea; (H.J.); (Y.-C.P.)
| | | | - Kyung-Yun Kim
- INSILICOGEN, Yongin 16954, Korea; (K.-Y.K.); (H.-C.C.)
| | - Hang-Chul Cho
- INSILICOGEN, Yongin 16954, Korea; (K.-Y.K.); (H.-C.C.)
| | - Yong-Jae Won
- Cheorwon Branch, National Institute of Crop Science, Rural Development Administration (RDA), Cheorwon 24010, Korea;
| | - Jeongho Baek
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Young-Soon Cha
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Song-Lim Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Kyung-Hwan Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Hyeonso Ji
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
- Correspondence: ; Tel.: +82-63-238-4657
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110
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Vikas VK, Pradhan AK, Budhlakoti N, Mishra DC, Chandra T, Bhardwaj SC, Kumar S, Sivasamy M, Jayaprakash P, Nisha R, Shajitha P, Peter J, Geetha M, Mir RR, Singh K, Kumar S. Multi-locus genome-wide association studies (ML-GWAS) reveal novel genomic regions associated with seedling and adult plant stage leaf rust resistance in bread wheat (Triticum aestivum L.). Heredity (Edinb) 2022; 128:434-449. [PMID: 35418669 DOI: 10.1038/s41437-022-00525-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 01/02/2023] Open
Abstract
Leaf rust is one of the important diseases limiting global wheat production and productivity. To identify quantitative trait nucleotides (QTNs) or genomic regions associated with seedling and adult plant leaf rust resistance, multilocus genome-wide association studies (ML-GWAS) were performed on a panel of 400 diverse wheat genotypes using 35 K single-nucleotide polymorphism (SNP) genotyping assays and trait data of leaf rust resistance. Association analyses using six multi-locus GWAS models revealed a set of 201 significantly associated QTNs for seedling and 65 QTNs for adult plant resistance (APR), explaining 1.98-31.72% of the phenotypic variation for leaf rust. Among these QTNs, 51 reliable QTNs for seedling and 15 QTNs for APR were consistently detected in at least two GWAS models and were considered reliable QTNs. Three genomic regions were pleiotropic, each controlling two to three pathotype-specific seedling resistances to leaf rust. We also identified candidate genes, such as leucine-rich repeat receptor-like (LRR) protein kinases, P-loop containing nucleoside triphosphate hydrolase and serine-threonine/tyrosine-protein kinases (STPK), which have a role in pathogen recognition and disease resistance linked to the significantly associated genomic regions. The QTNs identified in this study can prove useful in wheat molecular breeding programs aimed at enhancing resistance to leaf rust and developing next-generation leaf rust-resistant varieties.
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Affiliation(s)
- V K Vikas
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, 643 231, India
| | | | - Neeraj Budhlakoti
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.
| | | | - Tilak Chandra
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - S C Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal Pradesh, 171002, India
| | - Subodh Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal Pradesh, 171002, India
| | - M Sivasamy
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, 643 231, India
| | - P Jayaprakash
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, 643 231, India
| | - R Nisha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, 643 231, India
| | - P Shajitha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, 643 231, India
| | - John Peter
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, 643 231, India
| | - M Geetha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, 643 231, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, India
| | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India.,Genetic Resource Division, ICRISAT, Patancheru, Hyderabad, India
| | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India.
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111
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Li S, Li S, Su S, Zhang H, Shen J, Wen Y. Gene Region Association Analysis of Longitudinal Quantitative Traits Based on a Function-On-Function Regression Model. Front Genet 2022; 13:781740. [PMID: 35265102 PMCID: PMC8899465 DOI: 10.3389/fgene.2022.781740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
In the process of growth and development in life, gene expressions that control quantitative traits will turn on or off with time. Studies of longitudinal traits are of great significance in revealing the genetic mechanism of biological development. With the development of ultra-high-density sequencing technology, the associated analysis has tremendous challenges to statistical methods. In this paper, a longitudinal functional data association test (LFDAT) method is proposed based on the function-on-function regression model. LFDAT can simultaneously treat phenotypic traits and marker information as continuum variables and analyze the association of longitudinal quantitative traits and gene regions. Simulation studies showed that: 1) LFDAT performs well for both linkage equilibrium simulation and linkage disequilibrium simulation, 2) LFDAT has better performance for gene regions (include common variants, low-frequency variants, rare variants and mixture), and 3) LFDAT can accurately identify gene switching in the growth and development stage. The longitudinal data of the Oryza sativa projected shoot area is analyzed by LFDAT. It showed that there is the advantage of quick calculations. Further, an association analysis was conducted between longitudinal traits and gene regions by integrating the micro effects of multiple related variants and using the information of the entire gene region. LFDAT provides a feasible method for studying the formation and expression of longitudinal traits.
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Affiliation(s)
- Shijing Li
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou, China.,> Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shiqin Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shaoqiang Su
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hui Zhang
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou, China.,> Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiayu Shen
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou, China.,> Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongxian Wen
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou, China.,> Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou, China
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112
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Sharma P, Lew TTS. Principles of Nanoparticle Design for Genome Editing in Plants. Front Genome Ed 2022; 4:846624. [PMID: 35330692 PMCID: PMC8940305 DOI: 10.3389/fgeed.2022.846624] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/15/2022] [Indexed: 12/04/2022] Open
Abstract
Precise plant genome editing technologies have provided new opportunities to accelerate crop improvement and develop more sustainable agricultural systems. In particular, the prokaryote-derived CRISPR platforms allow precise manipulation of the crop genome, enabling the generation of high-yielding and stress-tolerant crop varieties. Nanotechnology has the potential to catalyze the development of a novel molecular toolbox even further by introducing the possibility of a rapid, universal delivery method to edit the plant genome in a species-independent manner. In this Perspective, we highlight how nanoparticles can help unlock the full potential of CRISPR/Cas technology in targeted manipulation of the plant genome to improve agricultural output. We discuss current challenges hampering progress in nanoparticle-enabled plant gene-editing research and application in the field, and highlight how rational nanoparticle design can overcome them. Finally, we examine the implications of the regulatory frameworks and social acceptance for the future of nano-enabled precision breeding in the developing world.
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Affiliation(s)
- Pushkal Sharma
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Tedrick Thomas Salim Lew
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- *Correspondence: Tedrick Thomas Salim Lew, , orcid.org/0000-0002-4815-9921
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113
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Panahabadi R, Ahmadikhah A, McKee LS, Ingvarsson PK, Farrokhi N. Genome-wide association study for lignocellulosic compounds and fermentable sugar in rice straw. THE PLANT GENOME 2022; 15:e20174. [PMID: 34806838 DOI: 10.1002/tpg2.20174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Cellulose and lignin are the two main components of secondary plant cell walls with substantial impact on stalk in the field and on straw during industrial processing. The amount of fermentable sugar that can be accessed is another important parameter affecting various industrial applications. In the present study, genetic variability of rice (Oryza sativa L.) genotypes for cellulose, lignin, and fermentable sugars contents was analyzed in rice straw. A genome-wide association study of 33,484 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) >0.05 was performed. The genome-wide association study identified seven, three, and three genomic regions to be significantly associated with cellulose, lignin, and fermentable sugar contents, respectively. Candidate genes in the associated genomic regions were enzymes mainly involved in cell wall metabolism. Novel SNP markers associated with cellulose were tagged to GH16, peroxidase, GT6, GT8, and CSLD2. For lignin content, Villin protein, OsWAK1/50/52/53, and GH16 were identified. For fermentable sugar content, UTP-glucose-1-phosphate uridylyltransferase, BRASSINOSTEROID INSENSITIVE 1, and receptor-like protein kinase 5 were found. The results of this study should improve our understanding of the genetic basis of the factors that might be involved in biosynthesis, turnover, and modification of major cell wall components and saccharides in rice straw.
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Affiliation(s)
- Rahele Panahabadi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, 106 91, Sweden
| | | | - Lauren S McKee
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, 106 91, Sweden
- Wallenberg Wood Science Centre, Teknikringen 56-58, Stockholm, 100 44, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Dep. of Plant Biology, Swedish Univ. of Agricultural Sciences, Uppsala, Sweden
| | - Naser Farrokhi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
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114
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Sandhu N, Singh J, Singh G, Sethi M, Singh MP, Pruthi G, Raigar OP, Kaur R, Kaur R, Sarao PS, Lore JS, Singh UM, Dixit S, Sagare DB, Singh S, Satturu V, Singh VK, Kumar A. Development and validation of a novel core set of KASP markers for the traits improving grain yield and adaptability of rice under direct-seeded cultivation conditions. Genomics 2022; 114:110269. [DOI: 10.1016/j.ygeno.2022.110269] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/12/2021] [Accepted: 01/16/2022] [Indexed: 11/28/2022]
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115
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Peng L, Sun S, Yang B, Zhao J, Li W, Huang Z, Li Z, He Y, Wang Z. Genome-wide association study reveals that the cupin domain protein OsCDP3.10 regulates seed vigour in rice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:485-498. [PMID: 34665915 PMCID: PMC8882794 DOI: 10.1111/pbi.13731] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 05/06/2023]
Abstract
Seed vigour is an imperative trait for the direct seeding of rice. In this study, we examined the genetic regulation of seedling percentage at the early germination using a genome-wide association study in rice. One major quantitative trait loci qSP3 for seedling percentage was identified, and the candidate gene was validated as qSP3, encoding a cupin domain protein OsCDP3.10 for the synthesis of 52 kDa globulin. Disruption of this gene in Oscdp3.10 mutants reduced the seed vigour, including the germination potential and seedling percentage, at the early germination in rice. The lacking accumulation of 52 kDa globulin was observed in the mature grains of the Oscdp3.10 mutants. The significantly lower amino acid contents were observed in the mature grains and the early germinating seeds of the Oscdp3.10 mutants compared with those of wild-type. Rice OsCDP3.10 regulated seed vigour mainly via modulating the amino acids e.g. Met, Glu, His, and Tyr that contribute to hydrogen peroxide (H2 O2 ) accumulation in the germinating seeds. These results provide important insights into the application of seed priming with the amino acids and the selection of OsCDP3.10 to improve seed vigour in rice.
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Affiliation(s)
- Liling Peng
- The Laboratory of Seed Science and TechnologyGuangdong Key Laboratory of Plant Molecular BreedingGuangdong Laboratory of Lingnan Modern AgricultureState Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Shan Sun
- The Laboratory of Seed Science and TechnologyGuangdong Key Laboratory of Plant Molecular BreedingGuangdong Laboratory of Lingnan Modern AgricultureState Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Bin Yang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm ResourcesZhongkai University of Agriculture and EngineeringGuangzhouChina
| | - Jia Zhao
- The Laboratory of Seed Science and TechnologyGuangdong Key Laboratory of Plant Molecular BreedingGuangdong Laboratory of Lingnan Modern AgricultureState Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Wenjun Li
- The Laboratory of Seed Science and TechnologyGuangdong Key Laboratory of Plant Molecular BreedingGuangdong Laboratory of Lingnan Modern AgricultureState Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Zhibo Huang
- The Laboratory of Seed Science and TechnologyGuangdong Key Laboratory of Plant Molecular BreedingGuangdong Laboratory of Lingnan Modern AgricultureState Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Ziyin Li
- The Laboratory of Seed Science and TechnologyGuangdong Key Laboratory of Plant Molecular BreedingGuangdong Laboratory of Lingnan Modern AgricultureState Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Yongqi He
- The Laboratory of Seed Science and TechnologyGuangdong Key Laboratory of Plant Molecular BreedingGuangdong Laboratory of Lingnan Modern AgricultureState Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Zhoufei Wang
- The Laboratory of Seed Science and TechnologyGuangdong Key Laboratory of Plant Molecular BreedingGuangdong Laboratory of Lingnan Modern AgricultureState Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
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116
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Kaler AS, Purcell LC, Beissinger T, Gillman JD. Genomic prediction models for traits differing in heritability for soybean, rice, and maize. BMC PLANT BIOLOGY 2022; 22:87. [PMID: 35219296 PMCID: PMC8881851 DOI: 10.1186/s12870-022-03479-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Genomic selection is a powerful tool in plant breeding. By building a prediction model using a training set with markers and phenotypes, genomic estimated breeding values (GEBVs) can be used as predictions of breeding values in a target set with only genotype data. There is, however, limited information on how prediction accuracy of genomic prediction can be optimized. The objective of this study was to evaluate the performance of 11 genomic prediction models across species in terms of prediction accuracy for two traits with different heritabilities using several subsets of markers and training population proportions. Species studied were maize (Zea mays, L.), soybean (Glycine max, L.), and rice (Oryza sativa, L.), which vary in linkage disequilibrium (LD) decay rates and have contrasting genetic architectures. RESULTS Correlations between observed and predicted GEBVs were determined via cross validation for three training-to-testing proportions (90:10, 70:30, and 50:50). Maize, which has the shortest extent of LD, showed the highest prediction accuracy. Amongst all the models tested, Bayes B performed better than or equal to all other models for each trait in all the three crops. Traits with higher broad-sense and narrow-sense heritabilities were associated with higher prediction accuracy. When subsets of markers were selected based on LD, the accuracy was similar to that observed from the complete set of markers. However, prediction accuracies were significantly improved when using a subset of total markers that were significant at P ≤ 0.05 or P ≤ 0.10. As expected, exclusion of QTL-associated markers in the model reduced prediction accuracy. Prediction accuracy varied among different training population proportions. CONCLUSIONS We conclude that prediction accuracy for genomic selection can be improved by using the Bayes B model with a subset of significant markers and by selecting the training population based on narrow sense heritability.
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Affiliation(s)
- Avjinder S Kaler
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72704, USA
| | - Larry C Purcell
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72704, USA
| | - Timothy Beissinger
- Department of Crop Science & Center for Integrated Breeding Research, University of Goettingen, 37075, Goettingen, Germany
| | - Jason D Gillman
- Plant Genetics Research Unit, USDA-ARS, 205 Curtis Hall, University of Missouri, Columbia, MO, 65211, USA.
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Chen G, Hu K, Zhao J, Guo F, Shan W, Jiang Q, Zhang J, Guo Z, Feng Z, Chen Z, Wu X, Zhang S, Zuo S. Genome-Wide Association Analysis for Salt-Induced Phenotypic and Physiologic Responses in Rice at Seedling and Reproductive Stages. FRONTIERS IN PLANT SCIENCE 2022; 13:822618. [PMID: 35222481 PMCID: PMC8863738 DOI: 10.3389/fpls.2022.822618] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Salinity is one of the main adverse environmental factors severely inhibiting rice growth and decreasing grain productivity. Developing rice varieties with salt tolerance (ST) is one of the most economical approaches to cope with salinity stress. In this study, the salt tolerance of 220 rice accessions from rice diversity panel l (RDP1), representing five subpopulations, were evaluated based on 16 ST indices at both seedling and reproductive stages under salt stress. An apparent inconsistency was found for ST between the two stages. Through a gene-based/tightly linked genome-wide association study with 201,332 single nucleotide polymorphisms (SNPs) located within genes and their flanking regions were used, a total of 214 SNPs related to 251 genes, significantly associated with 16 ST-related indices, were detected at both stages. Eighty-two SNPs with low frequency favorable (LFF) alleles in the population were proposed to hold high breeding potential in improving rice ST. Fifty-four rice accessions collectively containing all these LFF alleles were identified as donors of these alleles. Through the integration of meta-quantitative trait locus (QTL) for ST and the response patterns of differential expression genes to salt stress, thirty-eight candidate genes were suggested to be involved in the regulation of rice ST. In total, the present study provides valuable information for further characterizing ST-related genes and for breeding ST varieties across whole developmental stages through marker-assisted selection (MAS).
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Affiliation(s)
- Gang Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Co-innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Keming Hu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Co-innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Jianhua Zhao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Feifei Guo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Wenfeng Shan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Qiuqing Jiang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Jinqiao Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Zilong Guo
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiming Feng
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Co-innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Zongxiang Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Co-innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Xiaoxia Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Co-innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Shengwei Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Shimin Zuo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Co-innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Institutes of Agricultural Science and Technology Development, Yangzhou University, The Ministry of Education of China, Yangzhou, China
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A transcriptome-based association study of growth, wood quality, and oleoresin traits in a slash pine breeding population. PLoS Genet 2022; 18:e1010017. [PMID: 35108269 PMCID: PMC8843129 DOI: 10.1371/journal.pgen.1010017] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 02/14/2022] [Accepted: 01/04/2022] [Indexed: 12/04/2022] Open
Abstract
Slash pine (Pinus elliottii Engelm.) is an important timber and resin species in the United States, China, Brazil and other countries. Understanding the genetic basis of these traits will accelerate its breeding progress. We carried out a genome-wide association study (GWAS), transcriptome-wide association study (TWAS) and weighted gene co-expression network analysis (WGCNA) for growth, wood quality, and oleoresin traits using 240 unrelated individuals from a Chinese slash pine breeding population. We developed high quality 53,229 single nucleotide polymorphisms (SNPs). Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 SNPs significantly were associated with growth and oleoresin traits, accounting for the phenotypic variance ranging from 12.3% to 21.8% and from 10.6% to 16.7%, respectively; and (3) six genes encoding PeTLP, PeAP2/ERF, PePUP9, PeSLP, PeHSP, and PeOCT1 proteins were identified and validated by quantitative real time polymerase chain reaction for their association with growth and oleoresin traits. These results could be useful for tree breeding and functional studies in advanced slash pine breeding program. Slash pine is an important source of original timber and resin production on commercial forest plantations. It is necessary to implement precise breeding strategies to improve timber quality and resin yield. However, little is known about the species’ molecular genetic basis. Using a transcriptome dataset with sequencing from 240 individuals in the slash pine population, we combined multiple approaches (based on gene variation, expression variation and co-expression network) to dissect the genetic structure for slash pine major breeding traits. We found that the research population could be divided into three genetic groups with a mean heterozygosity of 0.2246. We also found that six genes with important functions in slash pine resin synthesis and timber formation through association studies. Four new SNPs associatation with the average ring width were also discovered. Our results provide new insights into the molecular genetic basis of important traits in slash pine and provide a comprehensive method for association analyses of conifer tree species with large genome.
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119
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Hussain I, Ali S, Liu W, Awais M, Li J, Liao Y, Zhu M, Fu C, Liu D, Wang F. Identification of Heterotic Groups and Patterns Based on Genotypic and Phenotypic Characteristics Among Rice Accessions of Diverse Origins. Front Genet 2022; 13:811124. [PMID: 35154278 PMCID: PMC8832281 DOI: 10.3389/fgene.2022.811124] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
Identification of the right parental combinations to maximize heterosis is the major goal of hybrid breeding, which could be achieved through identification of heterotic groups. The main objective of this study was to identify promising heterotic groups for future rice breeding programs. A collection of 359 rice genotypes of diverse origins of China and abroad, composed of inbreds, maintainers, restorers, and temperature-sensitive genic male sterile (TGMS) lines were genotyped using 10K SNP chips. The SNP data set was subjected to genomic analyses for estimation of genetic divergence and diversity. Significant variations were observed in the germplasm with the identification of six different genetic groups. These lines were assigned to the genetic groups independent of their origin. Taking an account of commercially used heterotic groups present in each cluster, three cytoplasmic male sterile (CMS) lines and 14 inbred and restorer lines with moderate to high genetic distances selected from five heterotic patterns were crossed and obtained 42 F1 hybrids. A total of 14 hybrids were found with significant maximum mid- and better-parent heterosis, namely, TaifengA × Guang122, TaifengA × Wushansimiao, and TaifengA × Minghui63 for earliness; Guang8A × Huazhan for dwarf stature; and Guang8A × Huanghuzhan-1, TaifengA × Yuexiangzhan, Guang8A × Minhui3301, TianfengA × Guang122, Guang8A × Yahui2115, TianfengA × Huanghuazhan, TianfengA × Minghui63, TianfengA × Minhui3301, TaifengA × Gui99, and Guang8A × Yuenongsimiao for yield and yield-related traits. Mid-parent and better-parent heterotic F1 hybrids were in positive correlation with the genetic distances as that manifested by commercially used heterotic groups, encouraging the use of genotypic data for identification of heterotic groups. Our study provides an informative strategy for the development of early maturing, lodging resistant and high-yielding commercial hybrids and cultivars in future heterosis breeding programs.
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Affiliation(s)
- Izhar Hussain
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Sajid Ali
- Department of Agriculture, Hazara University Mansehra, Mansehra, Pakistan
| | - Wuge Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Muhammad Awais
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jinhua Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Yilong Liao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Manshan Zhu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Chongyun Fu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Dilin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- *Correspondence: Dilin Liu, ; Feng Wang,
| | - Feng Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- *Correspondence: Dilin Liu, ; Feng Wang,
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120
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Wang L, Liu Y, Gao L, Yang X, Zhang X, Xie S, Chen M, Wang YH, Li J, Shen Y. Identification of Candidate Forage Yield Genes in Sorghum ( Sorghum bicolor L.) Using Integrated Genome-Wide Association Studies and RNA-Seq. FRONTIERS IN PLANT SCIENCE 2022; 12:788433. [PMID: 35087554 PMCID: PMC8787639 DOI: 10.3389/fpls.2021.788433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/06/2021] [Indexed: 05/26/2023]
Abstract
Genetic dissection of forage yield traits is critical to the development of sorghum as a forage crop. In the present study, association mapping was performed with 85,585 SNP markers on four forage yield traits, namely plant height (PH), tiller number (TN), stem diameter (SD), and fresh weight per plant (FW) among 245 sorghum accessions evaluated in four environments. A total of 338 SNPs or quantitative trait nucleotides (QTNs) were associated with the four traits, and 21 of these QTNs were detected in at least two environments, including four QTNs for PH, ten for TN, six for SD, and one for FW. To identify candidate genes, dynamic transcriptome expression profiling was performed at four stages of sorghum development. One hundred and six differentially expressed genes (DEGs) that were enriched in hormone signal transduction pathways were found in all stages. Weighted gene correlation network analysis for PH and SD indicated that eight modules were significantly correlated with PH and that three modules were significantly correlated with SD. The blue module had the highest positive correlation with PH and SD, and the turquoise module had the highest negative correlation with PH and SD. Eight candidate genes were identified through the integration of genome-wide association studies (GWAS) and RNA sequencing. Sobic.004G143900, an indole-3-glycerol phosphate synthase gene that is involved in indoleacetic acid biosynthesis, was down-regulated as sorghum plants grew in height and was identified in the blue module, and Sobic.003G375100, an SD candidate gene, encoded a DNA repair RAD52-like protein 1 that plays a critical role in DNA repair-linked cell cycle progression. These findings demonstrate that the integrative analysis of omics data is a promising approach to identify candidate genes for complex traits.
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Affiliation(s)
- Lihua Wang
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Yanlong Liu
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Li Gao
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Xiaocui Yang
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Xu Zhang
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Shaoping Xie
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Meng Chen
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Yi-Hong Wang
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, United States
| | - Jieqin Li
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Yixin Shen
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
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121
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Zhou E, Song N, Xiao Q, Farooq Z, Jia Z, Wen J, Dai C, Ma C, Tu J, Shen J, Fu T, Yi B. Construction of transgenic detection system of Brassica napus L. based on single nucleotide polymorphism chip. 3 Biotech 2022; 12:11. [PMID: 34966634 PMCID: PMC8655060 DOI: 10.1007/s13205-021-03062-6] [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: 04/10/2021] [Accepted: 11/09/2021] [Indexed: 01/03/2023] Open
Abstract
Brassica napus L. is a vital oil crop in China. As auxiliary tools for rapeseed breeding, transgenic technologies play a considerable role in heterosis, variety improvement, and pest resistance. Research on transgenic detection technologies is of great significance for the introduction, supervision, and development of transgenic rapeseed in China. However, the transgenic detection methods currently in use are complex and time-consuming, with low output. A single nucleotide polymorphism (SNP) chip can effectively overcome such limitations. In the present study, we collected 40 transgenic elements and designed 291 probes. The probe sequences were submitted to Illumina Company, and the Infinium chip technology was used to prepare SNP chips. In the present Brassica napus transgenic detection experiment, 84 high-quality probes of 17 transgenic elements were preliminarily screened, and genotyping effect was optimised for the probe signal value. Ultimately, a transgenic detection system for B. napus was developed. The developed system has the advantages of simple operation, minimal technical errors, and stable detection outcomes. A transgenic detection sensitivity test revealed that the probe designed could accurately detect 1% of transgenic samples and had high detection sensitivity. In addition, in repeatability tests, the CaMV35S promoter coefficient of variation was approximately 3.58%. Therefore, the SNP chip had suitable repeatability in transgene detection. The SNP chip developed could be used to construct transgenic detection systems for B. napus. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03062-6.
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Affiliation(s)
- Enqiang Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Nuan Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Qing Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Zunaira Farooq
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Zhibo Jia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
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Bartholomé J, Prakash PT, Cobb JN. Genomic Prediction: Progress and Perspectives for Rice Improvement. Methods Mol Biol 2022; 2467:569-617. [PMID: 35451791 DOI: 10.1007/978-1-0716-2205-6_21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Genomic prediction can be a powerful tool to achieve greater rates of genetic gain for quantitative traits if thoroughly integrated into a breeding strategy. In rice as in other crops, the interest in genomic prediction is very strong with a number of studies addressing multiple aspects of its use, ranging from the more conceptual to the more practical. In this chapter, we review the literature on rice (Oryza sativa) and summarize important considerations for the integration of genomic prediction in breeding programs. The irrigated breeding program at the International Rice Research Institute is used as a concrete example on which we provide data and R scripts to reproduce the analysis but also to highlight practical challenges regarding the use of predictions. The adage "To someone with a hammer, everything looks like a nail" describes a common psychological pitfall that sometimes plagues the integration and application of new technologies to a discipline. We have designed this chapter to help rice breeders avoid that pitfall and appreciate the benefits and limitations of applying genomic prediction, as it is not always the best approach nor the first step to increasing the rate of genetic gain in every context.
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Affiliation(s)
- Jérôme Bartholomé
- CIRAD, UMR AGAP Institut, Montpellier, France.
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France.
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines.
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Hamazaki K, Iwata H. Bayesian optimization of multivariate genomic prediction models based on secondary traits for improved accuracy gains and phenotyping costs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:35-50. [PMID: 34609531 DOI: 10.1007/s00122-021-03949-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
We propose a novel approach to the Bayesian optimization of multivariate genomic prediction models based on secondary traits to improve accuracy gains and phenotyping costs via efficient Pareto frontier estimation. Multivariate genomic prediction based on secondary traits, such as data from various omics technologies including high-throughput phenotyping (e.g., unmanned aerial vehicle-based remote sensing), has attracted much attention because it offers improved accuracy gains compared with genomic prediction based only on marker genotypes. Although there is a trade-off between accuracy gains and phenotyping costs of secondary traits, no attempt has been made to optimize these trade-offs. In this study, we propose a novel approach to optimize multivariate genomic prediction models for secondary traits measurable at early growth stages for improved accuracy gains and phenotyping costs. The proposed approach employs Bayesian optimization for efficient Pareto frontier estimation, representing the maximum accuracy at a given cost. The proposed approach successfully estimated the optimal secondary trait combinations across a range of costs while providing genomic predictions for only about [Formula: see text] of all possible combinations. The simulation results reflecting the characteristics of each scenario of the simulated target traits showed that the obtained optimal combinations were reasonable. Analysis of real-time target trait data showed that the proposed multivariate genomic prediction model had significantly superior accuracy compared to the univariate genomic prediction model.
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Affiliation(s)
- Kosuke Hamazaki
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- JSPS Research Fellow, Tokyo, Japan
| | - Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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124
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Si A, Sun Z, Li Z, Chen B, Gu Q, Zhang Y, Wu L, Zhang G, Wang X, Ma Z. A Genome Wide Association Study Revealed Key Single Nucleotide Polymorphisms/Genes Associated With Seed Germination in Gossypium hirsutum L. FRONTIERS IN PLANT SCIENCE 2022; 13:844946. [PMID: 35371175 PMCID: PMC8967292 DOI: 10.3389/fpls.2022.844946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/21/2022] [Indexed: 05/17/2023]
Abstract
Fast and uniform seed germination is essential to stabilize crop yields in agricultural production. It is important to understand the genetic basis of seed germination for improving the vigor of crop seeds. However, little is known about the genetic basis of seed vigor in cotton. In this study, we evaluated four seed germination-related traits of a core collection consisting of 419 cotton accessions, and performed a genome-wide association study (GWAS) to explore important loci associated with seed vigor using 3.66 million high-quality single nucleotide polymorphisms (SNPs). The results showed that four traits, including germination potential, germination rate, germination index, and vigor index, exhibited broad variations and high correlations. A total of 92 significantly associated SNPs located within or near 723 genes were identified for these traits, of which 13 SNPs could be detected in multiple traits. Among these candidate genes, 294 genes were expressed at seed germination stage. Further function validation of the two genes of higher expression showed that Gh_A11G0176 encoding Hsp70-Hsp90 organizing protein negatively regulated Arabidopsis seed germination, while Gh_A09G1509 encoding glutathione transferase played a positive role in regulating tobacco seed germination and seedling growth. Furthermore, Gh_A09G1509 might promote seed germination and seedling establishment through regulating glutathione metabolism in the imbibitional seeds. Our findings provide unprecedented information for deciphering the genetic basis of seed germination and performing molecular breeding to improve field emergence through genomic selection in cotton.
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Affiliation(s)
- Aijun Si
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture, Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Zhengwen Sun
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Zhikun Li
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Bin Chen
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Qishen Gu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Liqiang Wu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Guiyin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
- Xingfen Wang,
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
- *Correspondence: Zhiying Ma,
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Shen Y, Zhang H, Yao S, Su F, Wang H, Yin J, Fang Y, Tan L, Zhang K, Fan X, Zhong M, Zhou Q, He J, Zhang Z. Methionine oxidation of CLK4 promotes the metabolic switch and redox homeostasis in esophageal carcinoma via inhibiting MITF selective autophagy. Clin Transl Med 2022; 12:e719. [PMID: 35092699 PMCID: PMC8800482 DOI: 10.1002/ctm2.719] [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: 09/05/2021] [Revised: 01/08/2022] [Accepted: 01/14/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Metabolic reprogramming and redox homeostasis contribute to esophageal squamous cell carcinoma (ESCC). CDC-like kinase 4 (CLK4) is a dual-specificity kinase that can phosphorylate substrates' tyrosine or serine/threonine residue. However, the role and mechanism of CLK4 in ESCC remain unknown. METHODS CLK4 expression was analysed using publicly available datasets and confirmed in ESCC tissues and cell lines. The biological roles of CLK4 were studied with gain and loss-of-function experiments. Mass spectrometry was employed to examine the effects of CLK4 on metabolic profiling. In vitro kinase assay, co-immunoprecipitation, glutathione S-transferase pulldown, chromatin immunoprecipitation and luciferase reporter were used to elucidate the relationship among CLK4, microphthalmia-associated transcription factor (MITF), COP1 and ZRANB1. RESULTS CLK4 down-regulation was observed in ESCC cell lines and clinical samples and associated with the methylation of its promoter. Low levels of CLK4 promoted ESCC development by affecting the purine synthesis pathway and nicotinamide adenine dinucleotide phosphate (NADPH)/nicotinamide adenine dinucleotide phosphate (NADP+ ) ratio. Interestingly, CLK4 inhibited ESCC development by blocking MITF-enhanced de novo purine synthesis and redox balance. Mechanistically, wild type CLK4 (WT-CLK4) but not kinase-dead CLK4-K189R mutant phosphorylated MITF at Y360. This modification promoted its interaction with E3 ligase COP1 and its K63-linked ubiquitination at K308/K372, leading to sequestosome 1 recognition and autophagic degradation. However, the deubiquitinase ZRANB1 rescued MITF ubiquitination and degradation. In turn, MITF bound to E- rather than M-boxes in CLK4 promoter and transcriptionally down-regulated its expression in ESCC. Clinically, the negative correlations were observed between CLK4, MITF, and purine metabolic markers, which predicts a poor clinical outcome of ESCC patients. Notably, CLK4 itself was a redox-sensitive kinase, and its methionine oxidation at M307 impaired kinase activity, enhanced mitochondria length and inhibited lipid peroxidation, contributing to ESCC. CONCLUSIONS Our data highlight the potential role of CLK4 in modulating redox status and nucleotide metabolism, suggesting potential therapeutic targets in ESCC treatment.
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Affiliation(s)
- Yaxing Shen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Heng Zhang
- Department of Histology and Embryology, Xiang Ya School of Medicine, Central South University, Changsha, China
| | - Shihua Yao
- Department of Thoracic Surgery, Navy Military Medical University Affiliated Changhai Hospital, Shanghai, China
| | - Feng Su
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hao Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jun Yin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yong Fang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lijie Tan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Kaiguang Zhang
- Department of Digestive Disease, The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Hefei, China
| | - Xiangshan Fan
- Department of Pathology, The affiliated Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Ming Zhong
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qingxin Zhou
- Department of Gastrointestinal Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhiyong Zhang
- National Center for International Research of Biological Targeting Diagnosis and Therapy (Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research), Guangxi Medical University, Nanning, China
- Department of Surgery, Robert-Wood-Johnson Medical School University Hospital, Rutgers University, State University of New Jersey, New Brunswick, New Jersey, USA
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Fujino K, Kawahara Y, Shirasawa K. Artificial selection in the expansion of rice cultivation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:291-299. [PMID: 34731272 DOI: 10.1007/s00122-021-03966-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Gene distributions and population genomics suggest artificial selection of ghd7 osprr37, for extremely early heading date of rice, in the Tohoku region of Japan. The ranges of cultivated crops expanded into various environmental conditions around the world after their domestication. Hokkaido, Japan, lies at the northern limit of cultivation of rice, which originated in the tropics. Novel genotypes for extremely early heading date in Hokkaido are controlled by loss-of-function of both Grain number, plant height and heading date 7 (Ghd7) and Oryza sativa Pseudo-Response Regulator 37 (OsPRR37). We traced genotypes for extremely early heading date and analyzed the phylogeny of rice varieties grown historically in Japan. The mutations in Ghd7 and OsPRR37 had distinct local distributions. Population genomics revealed that varieties collected from the Tohoku region of northern Japan formed three clusters. Mutant alleles of Ghd7 and OsPRR37 appear to have allowed rice cultivation to spread into Hokkaido. Our results show that the mutations of two genes might be occurred in the process of artificial selection during early rice cultivation in the Tohoku region.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization (NARO), Sapporo, 062-8555, Japan.
- Institute of Crop Science, National Agricultural Research Organization, Tsukuba, 305-8518, Japan.
| | - Yoshihiro Kawahara
- Institute of Crop Science, NARO, Tsukuba, 305-8518, Japan
- Advanced Analysis Center, NARO, Tsukuba, 305-8602, Japan
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127
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Chakraborty D. Use of Allele-Specific Amplification for Rapid Identification of Aromatic and Non-aromatic Rice Germplasms. Methods Mol Biol 2022; 2512:269-279. [PMID: 35818011 DOI: 10.1007/978-1-0716-2429-6_16] [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] [Indexed: 06/15/2023]
Abstract
In the current context of global climate change trends, threat to food and nutrition security, collection, conservation and management, and characterization and evaluation of crop germplasms especially traditional landraces are gaining momentum more than ever before. Aromatic rice is an elite category of cultivated rice having huge sociocultural heritage value, fetching premium prices globally. Hence, its identification, in situ conservation, and appropriate characterization are likely to augment reliability of this distinctive category of rice, and rice commodity chain actors. badh2.1 is recognised as the major allele responsible for rice 2-acetyl-1-pyrroline aroma production in a vast number of aromatic rice globally. However, most of the previous works on the genetics and biochemical pathways of aroma expression in rice have encompassed mainly Basmati, Sadri, Della, Jasmine, and a few modern hybrids. But apart from these spotlighted varieties, a myriad of indigenous, aromatic rice germplasms exists. Allele-specific amplification, a low-cost, accurate method invented by Bradbury et al. 2005, can be utilized successfully for discriminating the rarely explored aromatic and nonaromatic rice as described.
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Affiliation(s)
- Debarati Chakraborty
- Department of Molecular Biology and Biotechnology, University of Kalyani, Kalyani, India.
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128
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Chen R, Deng Y, Ding Y, Guo J, Qiu J, Wang B, Wang C, Xie Y, Zhang Z, Chen J, Chen L, Chu C, He G, He Z, Huang X, Xing Y, Yang S, Xie D, Liu Y, Li J. Rice functional genomics: decades' efforts and roads ahead. SCIENCE CHINA. LIFE SCIENCES 2022. [PMID: 34881420 DOI: 10.1007/s11427-021-2024-2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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Affiliation(s)
- Rongzhi Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yiwen Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yanglin Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Bing Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Changsheng Wang
- National Center for Gene Research, Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Yongyao Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zhihua Zhang
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Jiaxin Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Daoxin Xie
- MOE Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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129
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Rice functional genomics: decades' efforts and roads ahead. SCIENCE CHINA. LIFE SCIENCES 2021; 65:33-92. [PMID: 34881420 DOI: 10.1007/s11427-021-2024-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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130
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Xu W, Liu X, Liao M, Xiao S, Zheng M, Yao T, Chen Z, Huang L, Zhang Z. FMixFN: A Fast Big Data-Oriented Genomic Selection Model Based on an Iterative Conditional Expectation algorithm. Front Genet 2021; 12:721600. [PMID: 34868200 PMCID: PMC8637923 DOI: 10.3389/fgene.2021.721600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
Genomic selection is an approach to select elite breeding stock based on the use of dense genetic markers and that has led to the development of various models to derive a predictive equation. However, the current genomic selection software faces several issues such as low prediction accuracy, low computational efficiency, or an inability to handle large-scale sample data. We report the development of a genomic prediction model named FMixFN with four zero-mean normal distributions as the prior distributions to optimize the predictive ability and computing efficiency. The variance of the prior distributions in our model is precisely determined based on an F2 population, and genomic estimated breeding values (GEBV) can be obtained accurately and quickly in combination with an iterative conditional expectation algorithm. We demonstrated that FMixFN improves computational efficiency and predictive ability compared to other methods, such as GBLUP, SSgblup, MIX, BayesR, BayesA, and BayesB. Most importantly, FMixFN may handle large-scale sample data, and thus should be able to meet the needs of large breeding companies or combined breeding schedules. Our study developed a Bayes genomic selection model called FMixFN, which combines stable predictive ability and high computational efficiency, and is a big data-oriented genomic selection model that has potential in the future. The FMixFN method can be freely accessed at https://zenodo.org/record/5560913 (DOI: 10.5281/zenodo.5560913).
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Affiliation(s)
- Wenwu Xu
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xiaodong Liu
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Mingfu Liao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Shijun Xiao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Min Zheng
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Tianxiong Yao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Zuoquan Chen
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Zhiyan Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
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131
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Chen YC, Hu CC, Chang FY, Chen CY, Chen WL, Tung CW, Shen WC, Wu CW, Cheng AH, Liao DJ, Liao CY, Liu LYD, Chung CL. Marker-Assisted Development and Evaluation of Monogenic Lines of Rice cv. Kaohsiung 145 Carrying Blast Resistance Genes. PLANT DISEASE 2021; 105:3858-3868. [PMID: 34181437 DOI: 10.1094/pdis-01-21-0142-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Rice blast is a serious threat to global rice production. Large-scale and long-term cultivation of rice varieties with a single blast resistance gene usually leads to breakdown of resistance. To effectively control rice blast in Taiwan, marker-assisted backcrossing was conducted to develop monogenic lines carrying different blast resistance genes in the genetic background of an elite japonica rice cultivar, Kaohsiung 145 (KH145). Eleven International Rice Research Institute (IRRI)-bred blast-resistant lines (IRBLs) showing broad-spectrum resistance to local Pyricularia oryzae isolates were used as resistance donors. Sequencing analysis revealed that the recurrent parent, KH145, does not carry known resistance alleles at the target Pi2/9, Pik, Pita, and Ptr loci. For each IRBL × KH145 cross, we screened 21 to 370 (average of 108) plants per generation from the BC1F1 to BC3F1/BC4F1 generation. A total of 1,499 BC3F2/BC4F2 lines carrying homozygous resistance alleles were selected and self-crossed for four to six successive generations. The derived lines were also evaluated for background genotype using genotyping by sequencing, for blast resistance under artificial inoculation and natural infection conditions, and for agronomic performance in multiple field trials. In Chiayi and Taitung blast nurseries in 2018 to 2020, Pi2, Pi9, and Ptr conferred high resistance, Pi20 and Pik-h moderate resistance, and Pi1, Pi7, Pik-p, and Pik susceptibility to leaf blast; only Pi2, Pi9, and Ptr conferred effective resistance against panicle blast. The monogenic lines showed agronomic traits, yield, and grain quality similar to those of KH145, suggesting the potential of growing a mixture of lines to achieve durable resistance in the field.
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Affiliation(s)
- Yi-Chia Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Chih-Chieh Hu
- Kaohsiung District Agricultural Research and Extension Station, Council of Agriculture, No. 26, Dehe Rd., Pingtung County 90846, Taiwan
| | - Fang-Yu Chang
- Kaohsiung District Agricultural Research and Extension Station, Council of Agriculture, No. 26, Dehe Rd., Pingtung County 90846, Taiwan
| | - Chieh-Yi Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Wei-Lun Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Chih-Wei Tung
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Wei-Chiang Shen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Chih-Wen Wu
- Kaohsiung District Agricultural Research and Extension Station, Council of Agriculture, No. 26, Dehe Rd., Pingtung County 90846, Taiwan
| | - An-Hsiu Cheng
- Tainan District Agricultural Research and Extension Station, No. 70, Muchang Rd., Hsinhua District, Council of Agriculture, Tainan 71246, Taiwan
| | - Dah-Jing Liao
- Department of Agronomy, Chiayi Agricultural Experiment Branch, Taiwan Agricultural Research Institute, Council of Agriculture, No. 2, Minquan Rd., Chiayi City 600015, Taiwan
| | - Ching-Ying Liao
- Taitung District Agricultural Research and Extension Station, Council of Agriculture, No. 675, Chunghua Rd., Sec. 1, Taitung City 95055, Taiwan
| | - Li-Yu D Liu
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Chia-Lin Chung
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
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Ding C, Lin X, Zuo Y, Yu Z, Baerson SR, Pan Z, Zeng R, Song Y. Transcription factor OsbZIP49 controls tiller angle and plant architecture through the induction of indole-3-acetic acid-amido synthetases in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1346-1364. [PMID: 34582078 DOI: 10.1111/tpj.15515] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Tiller angle is an important determinant of plant architecture in rice (Oryza sativa L.). Auxins play a critical role in determining plant architecture; however, the underlying metabolic and signaling mechanisms are still largely unknown. In this study, we have identified a member of the bZIP family of TGA class transcription factors, OsbZIP49, that participates in the regulation of plant architecture and is specifically expressed in gravity-sensing tissues, including the shoot base, nodes and lamina joints. Transgenic rice plants overexpressing OsbZIP49 displayed a tiller-spreading phenotype with reduced plant height and internode lengths. In contrast, CRISPR/Cas9-mediated knockout of OsbZIP49 resulted in a compact architecture. Follow-up studies indicated that the effects of OsbZIP49 on tiller angles are mediated through changes in shoot gravitropic responses. Additionally, we provide evidence that OsbZIP49 activates the expression of indole-3-acetic acid-amido synthetases OsGH3-2 and OsGH3-13 by directly binding to TGACG motifs located within the promoters of both genes. Increased GH3-catalyzed conjugation of indole-3-acetic acid (IAA) in rice transformants overexpressing OsbZIP49 resulted in the increased accumulation of IAA-Asp and IAA-Glu, and a reduction in local free auxin, tryptamine and IAA-Glc levels. Exogenous IAA or naphthylacetic acid (NAA) partially restored shoot gravitropic responses in OsbZIP49-overexpressing plants. Knockout of OsbZIP49 led to reduced expression of both OsGH3-2 and OsGH3-13 within the shoot base, and increased accumulation of IAA and increased OsIAA20 expression levels were observed in transformants following gravistimulation. Taken together, the present results reveal the role transcription factor OsbZIP49 plays in determining plant architecture, primarily due to its influence on local auxin homeostasis.
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Affiliation(s)
- Chaohui Ding
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xianhui Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ying Zuo
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhilin Yu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Scott R Baerson
- United States Department of Agriculture-Agricultural Research Service, Natural Products Utilization Research Unit, University, Mississippi, 38677, USA
| | - Zhiqiang Pan
- United States Department of Agriculture-Agricultural Research Service, Natural Products Utilization Research Unit, University, Mississippi, 38677, USA
| | - Rensen Zeng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuanyuan Song
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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133
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Huang Z, Ying J, Peng L, Sun S, Huang C, Li C, Wang Z, He Y. A genome-wide association study reveals that the cytochrome b5 involved in seed reserve mobilization during seed germination in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:4067-4076. [PMID: 34546380 DOI: 10.1007/s00122-021-03948-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
A candidate gene cytochrome b5 for the major QTL qSRMP9 for rice seed reserve mobilization was validated during seed germination using a genome-wide association study approach. Seed reserve mobilization plays important roles in the early seedling growth in rice. However, the genetic basis underlying this process is poorly understood. In this study, the genetic architecture of variation in seed reserve mobilization during seed germination was studied using a genome-wide association study approach in rice. Three quantitative trait loci (QTL) including qSRMP6, qSRMP9, and qSRMP12 for seed reserve mobilization percentage were identified. In which, the candidate gene cytochrome b5 (OsCyb5) for the major QTL qSRMP9 was validated. Disruption of this gene in Oscyb5 mutants reduced the seed reserve mobilization and seedling growth compared with wild-type (WT) in rice. There were no significant differences of grain size, starch, protein and total soluble sugar content in the mature grains between Oscyb5 mutants and WT. However, the α-amylase activity in the germinating seeds of Oscyb5 mutants was significantly decreased compared to that of WT, and then, the starch and sugar mobilization and the glucose accumulation during seed germination were significantly decreased in Oscyb5 mutants. Two elite haplotypes of OsCyb5 associated with the higher seed reserve mobilization percentage and its elite single nucleotide polymorphism variations were mainly existed in the INDICA and AUS accessions. The natural variation of OsCyb5 contributing to seed reserve mobilization might be useful for the future rice breeding.
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Affiliation(s)
- Zhibo Huang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Jifeng Ying
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Liling Peng
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shan Sun
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Chengwei Huang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Can Li
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
| | - Yongqi He
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
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Khan N, Essemine J, Hamdani S, Qu M, Lyu MJA, Perveen S, Stirbet A, Govindjee G, Zhu XG. Natural variation in the fast phase of chlorophyll a fluorescence induction curve (OJIP) in a global rice minicore panel. PHOTOSYNTHESIS RESEARCH 2021; 150:137-158. [PMID: 33159615 DOI: 10.1007/s11120-020-00794-z] [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: 05/11/2020] [Accepted: 10/26/2020] [Indexed: 06/11/2023]
Abstract
Photosynthesis can be probed through Chlorophyll a fluorescence induction (FI), which provides detailed insight into the electron transfer process in Photosystem II, and beyond. Here, we have systematically studied the natural variation of the fast phase of the FI, i.e. the OJIP phase, in rice. The OJIP phase of the Chl a fluorescence induction curve is referred to as "fast transient" lasting for less than a second; it is obtained after a dark-adapted sample is exposed to saturating light. In the OJIP curve, "O" stands for "origin" (minimal fluorescence), "P" for "peak" (maximum fluorescence), and J and I for inflection points between the O and P levels. Further, Fo is the fluorescence intensity at the "O" level, whereas Fm is the intensity at the P level, and Fv (= Fm - Fo) is the variable fluorescence. We surveyed a set of quantitative parameters derived from the FI curves of 199 rice accessions, grown under both field condition (FC) and growth room condition (GC). Our results show a significant variation between Japonica (JAP) and Indica (IND) subgroups, under both the growth conditions, in almost all the parameters derived from the OJIP curves. The ratio of the variable to the maximum (Fv/Fm) and of the variable to the minimum (Fv/Fo) fluorescence, the performance index (PIabs), as well as the amplitude of the I-P phase (AI-P) show higher values in JAP compared to that in the IND subpopulation. In contrast, the amplitude of the O-J phase (AO-J) and the normalized area above the OJIP curve (Sm) show an opposite trend. The performed genetic analysis shows that plants grown under GC appear much more affected by environmental factors than those grown in the field. We further conducted a genome-wide association study (GWAS) using 11 parameters derived from plants grown in the field. In total, 596 non-unique significant loci based on these parameters were identified by GWAS. Several photosynthesis-related proteins were identified to be associated with different OJIP parameters. We found that traits with high correlation are usually associated with similar genomic regions. Specifically, the thermal phase of FI, which includes the amplitudes of the J-I and I-P subphases (AJ-I and AI-P) of the OJIP curve, is, in turn, associated with certain common genomic regions. Our study is the first one dealing with the natural variations in rice, with the aim to characterize potential candidate genes controlling the magnitude and half-time of each of the phases in the OJIP FI curve.
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Affiliation(s)
- Naveed Khan
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Institute of Nutrition and Health, University of Chinese Academy of Science, Chinese Academy of Sciences, Shanghai, 200031, China
- State Key Laboratory for Plant Molecular Genetics and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jemaa Essemine
- State Key Laboratory for Plant Molecular Genetics and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Saber Hamdani
- State Key Laboratory for Plant Molecular Genetics and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Mingnan Qu
- State Key Laboratory for Plant Molecular Genetics and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ming-Ju Amy Lyu
- State Key Laboratory for Plant Molecular Genetics and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shahnaz Perveen
- State Key Laboratory for Plant Molecular Genetics and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | | | - Govindjee Govindjee
- Department of Plant Biology, Department of Biochemistry, and Center of Biophysics & Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Xin-Guang Zhu
- State Key Laboratory for Plant Molecular Genetics and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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135
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Recent advances in CRISPR/Cas9 and applications for wheat functional genomics and breeding. ABIOTECH 2021; 2:375-385. [PMID: 36304421 PMCID: PMC9590522 DOI: 10.1007/s42994-021-00042-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/17/2021] [Indexed: 12/21/2022]
Abstract
Common wheat (Triticum aestivum L.) is one of the three major food crops in the world; thus, wheat breeding programs are important for world food security. Characterizing the genes that control important agronomic traits and finding new ways to alter them are necessary to improve wheat breeding. Functional genomics and breeding in polyploid wheat has been greatly accelerated by the advent of several powerful tools, especially CRISPR/Cas9 genome editing technology, which allows multiplex genome engineering. Here, we describe the development of CRISPR/Cas9, which has revolutionized the field of genome editing. In addition, we emphasize technological breakthroughs (e.g., base editing and prime editing) based on CRISPR/Cas9. We also summarize recent applications and advances in the functional annotation and breeding of wheat, and we introduce the production of CRISPR-edited DNA-free wheat. Combined with other achievements, CRISPR and CRISPR-based genome editing will speed progress in wheat biology and promote sustainable agriculture.
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Siddiqui MN, Teferi TJ, Ambaw AM, Gabi MT, Koua P, Léon J, Ballvora A. New drought-adaptive loci underlying candidate genes on wheat chromosome 4B with improved photosynthesis and yield responses. PHYSIOLOGIA PLANTARUM 2021; 173:2166-2180. [PMID: 34549429 DOI: 10.1111/ppl.13566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Flag leaf serves as an essential source of assimilates during grain filling, thereby contributing to grain yield up to 48%. Thus, high-throughput phenotyping of flag leaves is crucial to determine their physiological and genetic basis of yield formation and drought adaptation. Here, we utilized 200 wheat cultivars to identify drought-adaptive loci underlying candidate genes associated with flag leaf biomass and photosynthesis-related traits using a genome-wide association study (GWAS). GWAS revealed 21 significant marker-trait associations for key photosynthetic traits in response to drought stress. Analysis of linkage disequilibrium (LD) in these SNPs intervals discovered 103 significant SNPs that established distinct LD blocks containing a total of 382 candidate genes putatively involved in physiological processes, including photosynthesis and water responses. Further, in silico transcript analysis identified two candidate genes in locus AX-580365925 on chromosome 4B, those were found to be highly expressed under drought and associated with proton-transporting ATP synthase activity and stress response pathways. Accordingly, we identified significant allelic haplotype differences on this same locus. The tolerant haplotype (higher chlorophyll content under drought) representing major allele was more abundant and stably increased photosynthetic efficiency and yield under drought scenarios. Collectively, this study offers new adaptive loci and beneficial alleles to reshape the flag leaf physiological and associated photosynthetic components for better yield and sustainability to water-deficit stress.
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Affiliation(s)
- Md Nurealam Siddiqui
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Tesfaye J Teferi
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Abebaw M Ambaw
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Melesech T Gabi
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Patrice Koua
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
- Field Lab Campus Klein-Altendorf, University of Bonn, Rheinbach, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
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137
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Quero G, Bonnecarrère V, Simondi S, Santos J, Fernández S, Gutierrez L, Garaycochea S, Borsani O. Genetic architecture of photosynthesis energy partitioning as revealed by a genome-wide association approach. PHOTOSYNTHESIS RESEARCH 2021; 150:97-115. [PMID: 32072456 DOI: 10.1007/s11120-020-00721-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
The photosynthesis process is determined by the intensity level and spectral quality of the light; therefore, leaves need to adapt to a changing environment. The incident energy absorbed can exceed the sink capability of the photosystems, and, in this context, photoinhibition may occur in both photosystem II (PSII) and photosystem I (PSI). Quantum yield parameters analyses reveal how the energy is managed. These parameters are genotype-dependent, and this genotypic variability is a good opportunity to apply mapping association strategies to identify genomic regions associated with photosynthesis energy partitioning. An experimental and mathematical approach is proposed for the determination of an index which estimates the energy per photon flux for each spectral bandwidth (Δλ) of the light incident (QI index). Based on the QI, the spectral quality of the plant growth, environmental lighting, and the actinic light of PAM were quantitatively very similar which allowed an accurate phenotyping strategy of a rice population. A total of 143 genomic single regions associated with at least one trait of chlorophyll fluorescence were identified. Moreover, chromosome 5 gathers most of these regions indicating the importance of this chromosome in the genetic regulation of the photochemistry process. Through a GWAS strategy, 32 genes of rice genome associated with the main parameters of the photochemistry process of photosynthesis in rice were identified. Association between light-harvesting complexes and the potential quantum yield of PSII, as well as the relationship between coding regions for PSI-linked proteins in energy distribution during the photochemical process of photosynthesis is analyzed.
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Affiliation(s)
- Gastón Quero
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Garzón 809, Montevideo, Uruguay.
| | - Victoria Bonnecarrère
- Unidad de Biotecnología, Estación Experimental Wilson Ferreira Aldunate, Instituto Nacional de Investigación Agropecuaria (INIA), Ruta 48, Km 10, Rincón del Colorado, 90200, Canelones, Uruguay
| | - Sebastián Simondi
- Área de Matemática, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (FCEN-UNCuyo), Padre Contreras 1300, Mendoza, Argentina
| | - Jorge Santos
- Área de Física, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (FCEN-UNCuyo), Padre Contreras 1300, Mendoza, Argentina
| | - Sebastián Fernández
- Facultad de Ingeniería, Instituto de Ingeniería Eléctrica, Universidad de La República, Julio Herrera y Reissig 565, Montevideo, Uruguay
| | - Lucía Gutierrez
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Dr., Madison, WI, 53706, USA
- Departamento de Biometría, Estadística y Cómputos, Facultad de Agronomía, Universidad de la República, Garzón 780, Montevideo, Uruguay
| | - Silvia Garaycochea
- Unidad de Biotecnología, Estación Experimental Wilson Ferreira Aldunate, Instituto Nacional de Investigación Agropecuaria (INIA), Ruta 48, Km 10, Rincón del Colorado, 90200, Canelones, Uruguay
| | - Omar Borsani
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Garzón 809, Montevideo, Uruguay
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138
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Wang D, Liu Z, Xiao Y, Liu X, Chen Y, Zhang Z, Kang H, Wang X, Jiang S, Peng S, Tan X, Zhang D, Liu Y, Wang GL, Li C. Association Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage. RICE (NEW YORK, N.Y.) 2021; 14:98. [PMID: 34825994 PMCID: PMC8626552 DOI: 10.1186/s12284-021-00538-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Cold tolerance at the bud burst stage (CTB) is a key trait for direct-seeded rice. Although quantitative trait loci (QTL) affecting CTB in rice have been mapped using traditional linkage mapping and genome-wide association study (GWAS) methods, the underlying genes remain unknown. In this study, we evaluated the CTB phenotype of 339 cultivars in the Rice Diversity Panel II (RDP II) collection. GWAS identified four QTLs associated with CTB (qCTBs), distributed on chromosomes 1-3. Among them, qCTB-1-1 overlaps with Osa-miR319b, a known cold tolerance micro RNA gene. The other three qCTBs have not been reported. In addition, we characterised the candidate gene OsRab11C1 for qCTB-1-2 that encodes a Rab protein belonging to the small GTP-binding protein family. Overexpression of OsRab11C1 significantly reduced CTB, while gene knockout elevated CTB as well as cold tolerance at the seedling stage, suggesting that OsRab11C1 negatively regulates rice cold tolerance. Molecular analysis revealed that OsRab11C1 modulates cold tolerance by suppressing the abscisic acid signalling pathway and proline biosynthesis. Using RDP II and GWAS, we identified four qCTBs that are involved in CTB and determined the function of the candidate gene OsRab11C1 in cold tolerance. Our results demonstrate that OsRab11C1 is a negative regulator of cold tolerance and knocking out of the gene by genome-editing may provide enhanced cold tolerance in rice.
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Affiliation(s)
- Dan Wang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China.
| | - Zhuo Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yinghui Xiao
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xionglun Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yue Chen
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Zhuo Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xuli Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Su Jiang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Shasha Peng
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xinqiu Tan
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Deyong Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Yong Liu
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, 43210, USA.
| | - Chenggang Li
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
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139
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Sabag I, Morota G, Peleg Z. Genome-wide association analysis uncovers the genetic architecture of tradeoff between flowering date and yield components in sesame. BMC PLANT BIOLOGY 2021; 21:549. [PMID: 34809568 PMCID: PMC8607594 DOI: 10.1186/s12870-021-03328-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/08/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Unrevealing the genetic makeup of crop morpho-agronomic traits is essential for improving yield quality and sustainability. Sesame (Sesamum indicum L.) is one of the oldest oil-crops in the world. Despite its economic and agricultural importance, it is an 'orphan crop-plant' that has undergone limited modern selection, and, as a consequence preserved wide genetic diversity. Here we established a new sesame panel (SCHUJI) that contains 184 genotypes representing wide phenotypic variation and is geographically distributed. We harnessed the natural variation of this panel to perform genome-wide association studies for morpho-agronomic traits under the Mediterranean climate conditions. RESULTS Field-based phenotyping of the SCHUJI panel across two seasons exposed wide phenotypic variation for all traits. Using 20,294 single-nucleotide polymorphism markers, we detected 50 genomic signals associated with these traits. Major genomic region on LG2 was associated with flowering date and yield-related traits, exemplified the key role of the flowering date on productivity. CONCLUSIONS Our results shed light on the genetic architecture of flowering date and its interaction with yield components in sesame and may serve as a basis for future sesame breeding programs in the Mediterranean basin.
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Affiliation(s)
- Idan Sabag
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, 7610001, Rehovot, Israel
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, 24061, USA
| | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, 24061, USA.
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, 7610001, Rehovot, Israel.
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140
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Singh M, Nara U, Kumar A, Choudhary A, Singh H, Thapa S. Salinity tolerance mechanisms and their breeding implications. J Genet Eng Biotechnol 2021; 19:173. [PMID: 34751850 PMCID: PMC8578521 DOI: 10.1186/s43141-021-00274-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/26/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND The era of first green revolution brought about by the application of chemical fertilizers surely led to the explosion of food grains, but left behind the notable problem of salinity. Continuous application of these fertilizers coupled with fertilizer-responsive crops make the country self-reliant, but continuous deposition of these led to altered the water potential and thus negatively affecting the proper plant functioning from germination to seed setting. MAIN BODY Increased concentration of anion and cations and their accumulation and distribution cause cellular toxicity and ionic imbalance. Plants respond to salinity stress by any one of two mechanisms, viz., escape or tolerate, by either limiting their entry via root system or controlling their distribution and storage. However, the understanding of tolerance mechanism at the physiological, biochemical, and molecular levels will provide an insight for the identification of related genes and their introgression to make the crop more resilient against salinity stress. SHORT CONCLUSION Novel emerging approaches of plant breeding and biotechnologies such as genome-wide association studies, mutational breeding, marker-assisted breeding, double haploid production, hyperspectral imaging, and CRISPR/Cas serve as engineering tools for dissecting the in-depth physiological mechanisms. These techniques have well-established implications to understand plants' adaptions to develop more tolerant varieties and lower the energy expenditure in response to stress and, constitutively fulfill the void that would have led to growth resistance and yield penalty.
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Affiliation(s)
- Mandeep Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | - Usha Nara
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Antul Kumar
- Department of Botany, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Anuj Choudhary
- Department of Botany, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Hardeep Singh
- Department of Agronomy, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Sittal Thapa
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
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141
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Roy J, Shaikh TM, Del Río Mendoza L, Hosain S, Chapara V, Rahman M. Genome-wide association mapping and genomic prediction for adult stage sclerotinia stem rot resistance in Brassica napus (L) under field environments. Sci Rep 2021; 11:21773. [PMID: 34741104 PMCID: PMC8571315 DOI: 10.1038/s41598-021-01272-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/22/2021] [Indexed: 12/11/2022] Open
Abstract
Sclerotinia stem rot (SSR) is a fungal disease of rapeseed/canola that causes significant seed yield losses and reduces its oil content and quality. In the present study, the reaction of 187 diverse canola genotypes to SSR was characterized at full flowering stage using the agar plug to stem inoculation method in four environments. Genome-wide association study (GWAS) using three different algorithms identified 133 significant SNPs corresponding with 123 loci for disease traits like stem lesion length (LL), lesion width (LW), and plant mortality at 14 (PM_14D) and 21 (PM_21D) days. The explained phenotypic variation of these SNPs ranged from 3.6 to 12.1%. Nineteen significant SNPs were detected in two or more environments, disease traits with at least two GWAS algorithms. The strong correlations observed between LL and other three disease traits evaluated, suggest they could be used as proxies for SSR resistance phenotyping. Sixty-nine candidate genes associated with disease resistance mechanisms were identified. Genomic prediction (GP) analysis with all the four traits employing genome-wide markers resulted in 0.41-0.64 predictive ability depending on the model specifications. The highest predictive ability for PM_21D with three models was about 0.64. From our study, the identified resistant genotypes and stable significant SNP markers will serve as a valuable resource for future SSR resistance breeding. Our study also suggests that genomic selection holds promise for accelerating canola breeding progress by enabling breeders to select SSR resistance genotypes at the early stage by reducing the need to phenotype large numbers of genotypes.
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Affiliation(s)
- Jayanta Roy
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - T M Shaikh
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Luis Del Río Mendoza
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Shakil Hosain
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Venkat Chapara
- Langdon Extension Research Extension Center, North Dakota State University, Langdon, ND, 58249, USA
| | - Mukhlesur Rahman
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.
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142
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Dzievit MJ, Guo T, Li X, Yu J. Comprehensive analytical and empirical evaluation of genomic prediction across diverse accessions in maize. THE PLANT GENOME 2021; 14:e20160. [PMID: 34661990 DOI: 10.1002/tpg2.20160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Efficiently exploiting natural genetic diversity captured by accessions stored in genebanks is crucial to genetic improvement of major crops. Selecting accessions of interest from genebanks has traditionally required information from extensive and expensive evaluation; however, low-cost genotyping combined with genomic prediction have enabled us to generate predicted genetic merits for the entire set with targeted phenotypic evaluation of representative subsets. To explore this general approach, analytical assessment and empirical validation of the maize (Zea mays L.) association population (MAP) as a training population were conducted in the present study. Cross-validation within the MAP revealed mostly modest to strong predictive ability for 36 traits, generally in parallel with the square root of heritability. The MAP was then used to train the prediction models to generate genomic estimated breeding values (GEBVs) for the Ames Diversity Panel. Empirical validation conducted for nine traits across two validation populations confirmed the accuracy level indicated by the cross-validation of the training population. An upper bound for reliability (U value) was calculated for the accessions in the prediction population using genotypic data. The group of accessions with high U values generally had high predictive ability, even though the range of observed trait values was similar to the group of accessions with low U values. Our comprehensive analysis validated the general approach of turbocharging genebanks with genomics and genomic prediction. In addition, breeders and researchers can consider both GEBVs and U values to balance the needs of improving specific traits and broadening genetic diversity when selecting accessions from genebanks.
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Affiliation(s)
| | - Tingting Guo
- Dep. of Agronomy, Iowa State Univ., Ames, IA, 50011, USA
| | - Xianran Li
- Dep. of Agronomy, Iowa State Univ., Ames, IA, 50011, USA
| | - Jianming Yu
- Dep. of Agronomy, Iowa State Univ., Ames, IA, 50011, USA
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143
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Puig ML, Rodríguez AA, Vidal AA, Bezus R, Maiale SJ. Patterns of physiological parameters and nitrogen partitioning in flag leaf explain differential grain protein content in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 168:457-464. [PMID: 34717177 DOI: 10.1016/j.plaphy.2021.10.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/18/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
The grain protein content (GPC) in rice is low, and more efforts with agronomic and molecular approaches were performed to increase them. However, the rice research focusing on the plant physiological behaviour that modulates the phenomenon of grain protein filling is very scarce. This work contains physiological parameters related to photosynthetic activity in the flag leaf in the grain filling period and N partitioning assays of high (Nutriar) and traditional (Camba) GPC cultivars. Results indicated a higher photosynthetic capacity, a better capacity to provide CO2 to the chloroplast and a healthier PSII structure in Camba relative to Nutriar. Chlorophyll fluorescence parameters decreased more steeply over time in the high protein variety, and a strong negative correlation was observed between GPC and PSII structure parameters. N content in the flag leaf at anthesis showed lower values and higher remobilisation during the grain filling period in Nutriar compared to Camba. The results of this work suggested that the inactivation of some PSII structures in higher GPC cultivars is associated with N remobilisation and would contribute to an increase in the free N available to be translocated to the grain.
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Affiliation(s)
- María Lucrecia Puig
- Instituto Tecnológico de Chascomús (INTECH) Consejo Nacional de Investigaciones Científicas y Técnicas, Int. Marino Km 8, Chascomús, CP:7130, Buenos Aires, Argentina
| | - Andrés Alberto Rodríguez
- Instituto Tecnológico de Chascomús (INTECH) Consejo Nacional de Investigaciones Científicas y Técnicas, Int. Marino Km 8, Chascomús, CP:7130, Buenos Aires, Argentina
| | - Alfonso Andrés Vidal
- Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de la Plata, 60 y 119, La Plata, CP:1900, Buenos Aires, Argentina
| | - Rodolfo Bezus
- Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de la Plata, 60 y 119, La Plata, CP:1900, Buenos Aires, Argentina
| | - Santiago Javier Maiale
- Instituto Tecnológico de Chascomús (INTECH) Consejo Nacional de Investigaciones Científicas y Técnicas, Int. Marino Km 8, Chascomús, CP:7130, Buenos Aires, Argentina.
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144
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Wang Z, Cheng H. Single-Trait and Multiple-Trait Genomic Prediction From Multi-Class Bayesian Alphabet Models Using Biological Information. Front Genet 2021; 12:717457. [PMID: 34707638 PMCID: PMC8542848 DOI: 10.3389/fgene.2021.717457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
Genomic prediction has been widely used in multiple areas and various genomic prediction methods have been developed. The majority of these methods, however, focus on statistical properties and ignore the abundant useful biological information like genome annotation or previously discovered causal variants. Therefore, to improve prediction performance, several methods have been developed to incorporate biological information into genomic prediction, mostly in single-trait analysis. A commonly used method to incorporate biological information is allocating molecular markers into different classes based on the biological information and assigning separate priors to molecular markers in different classes. It has been shown that such methods can achieve higher prediction accuracy than conventional methods in some circumstances. However, these methods mainly focus on single-trait analysis, and available priors of these methods are limited. Thus, in both single-trait and multiple-trait analysis, we propose the multi-class Bayesian Alphabet methods, in which multiple Bayesian Alphabet priors, including RR-BLUP, BayesA, BayesB, BayesCΠ, and Bayesian LASSO, can be used for markers allocated to different classes. The superior performance of the multi-class Bayesian Alphabet in genomic prediction is demonstrated using both real and simulated data. The software tool JWAS offers open-source routines to perform these analyses.
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Affiliation(s)
- Zigui Wang
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Hao Cheng
- Department of Animal Science, University of California, Davis, Davis, CA, United States
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145
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Sharmin RA, Karikari B, Chang F, Al Amin GM, Bhuiyan MR, Hina A, Lv W, Chunting Z, Begum N, Zhao T. Genome-wide association study uncovers major genetic loci associated with seed flooding tolerance in soybean. BMC PLANT BIOLOGY 2021; 21:497. [PMID: 34715792 PMCID: PMC8555181 DOI: 10.1186/s12870-021-03268-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/29/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Seed flooding stress is one of the threatening environmental stressors that adversely limits soybean at the germination stage across the globe. The knowledge on the genetic basis underlying seed-flooding tolerance is limited. Therefore, we performed a genome-wide association study (GWAS) using 34,718 single nucleotide polymorphism (SNPs) in a panel of 243 worldwide soybean collections to identify genetic loci linked to soybean seed flooding tolerance at the germination stage. RESULTS In the present study, GWAS was performed with two contrasting models, Mixed Linear Model (MLM) and Multi-Locus Random-SNP-Effect Mixed Linear Model (mrMLM) to identify significant SNPs associated with electrical conductivity (EC), germination rate (GR), shoot length (ShL), and root length (RL) traits at germination stage in soybean. With MLM, a total of 20, 40, 4, and 9 SNPs associated with EC, GR, ShL and RL, respectively, whereas in the same order mrMLM detected 27, 17, 13, and 18 SNPs. Among these SNPs, two major SNPs, Gm_08_11971416, and Gm_08_46239716 were found to be consistently connected with seed-flooding tolerance related traits, namely EC and GR across two environments. We also detected two SNPs, Gm_05_1000479 and Gm_01_53535790 linked to ShL and RL, respectively. Based on Gene Ontology enrichment analysis, gene functional annotations, and protein-protein interaction network analysis, we predicted eight candidate genes and three hub genes within the regions of the four SNPs with Cis-elements in promoter regions which may be involved in seed-flooding tolerance in soybeans and these warrant further screening and functional validation. CONCLUSIONS Our findings demonstrate that GWAS based on high-density SNP markers is an efficient approach to dissect the genetic basis of complex traits and identify candidate genes in soybean. The trait associated SNPs could be used for genetic improvement in soybean breeding programs. The candidate genes could help researchers better understand the molecular mechanisms underlying seed-flooding stress tolerance in soybean.
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Affiliation(s)
- Ripa Akter Sharmin
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Jagannath University, Dhaka, 1100, Bangladesh
| | - Benjamin Karikari
- Department of Crop Science, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Fangguo Chang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - G M Al Amin
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mashiur Rahman Bhuiyan
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Aiman Hina
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenhuan Lv
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhang Chunting
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Naheeda Begum
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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146
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Vejchasarn P, Shearman JR, Chaiprom U, Phansenee Y, Suthanthangjai A, Jairin J, Chamarerk V, Tulyananda T, Amornbunchornvej C. Population Structure of Nation-Wide Rice in Thailand. RICE (NEW YORK, N.Y.) 2021; 14:88. [PMID: 34693480 PMCID: PMC8542525 DOI: 10.1186/s12284-021-00528-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Thailand is a country with large diversity in rice varieties due to its rich and diverse ecology. In this paper, 300 rice accessions from all across Thailand were sequenced to identify SNP variants allowing for the population structure to be explored. RESULTS The result of inferred population structure from admixture and clustering analysis illustrated strong evidence of substructure in each geographical region. The results of phylogenetic tree, PCA analysis, and machine learning on population identifying SNPs also supported the inferred population structure. CONCLUSION The population structure inferred in this study contains five subpopulations that tend to group individuals based on location. So, each subpopulation has unique genetic patterns, agronomic traits, as well as different environmental conditions. This study can serve as a reference point of the nation-wide population structure for supporting breeders and researchers who are interested in Thai rice.
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Affiliation(s)
| | - Jeremy R. Shearman
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, 12120 Pathum Thani, Thailand
| | - Usawadee Chaiprom
- National Biobank of Thailand (NBT), 144 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120 Pathum Thani, Thailand
| | | | | | - Jirapong Jairin
- Ubonratchathani Rice Research Center, 34000 Ubonratchathani, Thailand
| | | | - Tatpong Tulyananda
- School of Bioinnovation and Bio-Based Product Intelligence, Faculty of Science, Mahidol University, 10400 Bangkok, Thailand
| | - Chainarong Amornbunchornvej
- National Electronics and Computer Technology Center (NECTEC), 112 Phahonyothin Road, Khlong Nueng, Khlong Luang District, 12120 Pathum Thani, Thailand
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147
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Beena R, Kirubakaran S, Nithya N, Manickavelu A, Sah RP, Abida PS, Sreekumar J, Jaslam PM, Rejeth R, Jayalekshmy VG, Roy S, Manju RV, Viji MM, Siddique KHM. Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces. BMC PLANT BIOLOGY 2021; 21:484. [PMID: 34686134 PMCID: PMC8539776 DOI: 10.1186/s12870-021-03272-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/29/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND Asian cultivars were predominantly represented in global rice panel selected for sequencing and to identify novel alleles for drought tolerance. Diverse genetic resources adapted to Indian subcontinent were not represented much in spite harboring useful alleles that could improve agronomic traits, stress resilience and productivity. These rice accessions are valuable genetic resource in developing rice varieties suited to different rice ecosystem that experiences varying drought stress level, and at different crop stages. A core collection of rice germplasm adapted to Southwestern Indian peninsular genotyped using SSR markers and characterized by contrasting water regimes to associate genomic regions for physiological, root traits and yield related traits. Genotyping-By-Sequencing of selected accessions within the diverse panel revealed haplotype variation in genic content within genomic regions mapped for physiological, morphological and root traits. RESULTS Diverse rice panel (99 accessions) were evaluated in field and measurements on plant physiological, root traits and yield related traits were made over five different seasons experiencing varying drought stress intensity at different crop stages. Traits like chlorophyll stability index, leaf rolling, days to 50% flowering, chlorophyll content, root volume and root biomass were identified as best predictors of grain yield under stress. Association mapping revealed genetic variation among accessions and revealed 14 genomic targets associated with different physiological, root and plant production traits. Certain accessions were found to have beneficial allele to improve traits, plant height, root length and spikelet fertility, that contribute to the grain yield under stress. Genomic characterization of eleven accessions revealed haplotype variation within key genomic targets on chromosomes 1, 4, 6 and 11 for potential use as molecular markers to combine drought avoidance and tolerance traits. Genes mined within the genomic QTL intervals identified were prioritized based on tissue specific expression level in publicly available rice transcriptome data. CONCLUSION The genetic and genomic resources identified will enable combining traits with agronomic value to optimize yield under stress and hasten trait introgression into elite cultivars. Alleles associated with plant height, specific leaf area, root length from PTB8 and spikelet fertility and grain weight from PTB26 can be harnessed in future rice breeding program.
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Affiliation(s)
- Radha Beena
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | | | - Narayanan Nithya
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Alagu Manickavelu
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala India
| | - Rameshwar Prasad Sah
- Indian Council of Agricultural Research (ICAR)-Central Rice Research Institute, currently named National Rice Research Institute (NRRI), Cuttack, Odisha India
| | - Puthenpeedikal Salim Abida
- Regional Agricultural Research Station, Pattambi, Kerala Agricultural University, Palakkad, Kerala India
| | - Janardanan Sreekumar
- Indian Council of Agricultural Research (ICAR)-Central Tuber Crops Research Institute, Sreekaryam, Thiruvananthapuram, Kerala India
| | | | - Rajendrakumar Rejeth
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Vijayalayam Gengamma Jayalekshmy
- Department of Plant Breeding and Genetics, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Stephen Roy
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Ramakrishnan Vimala Manju
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Mariasoosai Mary Viji
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
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148
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Shi L, Li Y, Liu Q, Zhang L, Wang L, Liu X, Gao H, Hou X, Zhao F, Yan H, Wang L. Identification of SNPs and Candidate Genes for Milk Production Ability in Yorkshire Pigs. Front Genet 2021; 12:724533. [PMID: 34675963 PMCID: PMC8523896 DOI: 10.3389/fgene.2021.724533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 09/22/2021] [Indexed: 12/01/2022] Open
Abstract
Sow milk production ability is an important limiting factor impacting suboptimal growth and the survival of piglets. Through pig genetic improvement, litter sizes have been increased. Larger litters need more suckling mammary glands, which results in increased milk from the lactating sow. Hence, there is much significance to exploring sow lactation performance. For milk production ability, it is not practical to directly measure the milk yield, we used litter weight gain (LWG) throughout sow lactation as an indicator. In this study, we estimated the heritability of LWG, namely, 0.18 ± 0.07. We then performed a GWAS, and detected seven significant SNPs, namely, Sus scrofa Chromosome (SSC) 2: ASGA0010040 (p = 7.73E-11); SSC2:MARC0029355 (p = 1.30E-08), SSC6: WU_10.2_6_65751151 (p = 1.32E-10), SSC7: MARC0058875 (p = 4.99E-09), SSC10: WU_10.2_10_49571394 (p = 6.79E-08), SSC11: M1GA0014659 (p = 1.19E-07), and SSC15: MARC0042106 (p = 1.16E-07). We performed the distribution of phenotypes corresponding to the genotypes of seven significant SNPs and showed that ASGA0010040, MARC0029355, MARC0058875, WU_10.2_10_49571394, M1GA0014659, and MARC0042106 had extreme phenotypic values that corresponded to the homozygous genotypes, while the intermediate values corresponded to the heterozygous genotypes. We screened for flanking regions ± 200 kb nearby the seven significant SNPs, and identified 38 genes in total. Among them, 28 of the candidates were involved in lactose metabolism, colostrum immunity, milk protein, and milk fat by functional enrichment analysis. Through the combined analysis between 28 candidate genes and transcriptome data of the sow mammary gland, we found nine commons (ANO3, MUC15, DISP3, FBXO6, CLCN6, HLA-DRA, SLA-DRB1, SLA-DQB1, and SLA-DQA1). Furthermore, by comparing the chromosome positions of the candidate genes with the quantitative trait locus (QTLs) as previously reported, a total of 17 genes were found to be within 0.86–94.02 Mb of the reported QTLs for sow milk production ability, in which, NAV2 was found to be located with 0.86 Mb of the QTL region ssc2: 40936355. In conclusion, we identified seven significant SNPs located on SSC2, 6, 7, 10, 11, and 15, and propose 28 candidate genes for the ability to produce milk in Yorkshire pigs, 10 of which were key candidates.
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Affiliation(s)
- Lijun Shi
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qian Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Longchao Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ligang Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongmei Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinhua Hou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fuping Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hua Yan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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149
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Xiao J, Zhou Y, He S, Ren WL. An Efficient Score Test Integrated with Empirical Bayes for Genome-Wide Association Studies. Front Genet 2021; 12:742752. [PMID: 34659362 PMCID: PMC8517403 DOI: 10.3389/fgene.2021.742752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/13/2021] [Indexed: 11/30/2022] Open
Abstract
Many methods used in multi-locus genome-wide association studies (GWAS) have been developed to improve statistical power. However, most existing multi-locus methods are not quicker than single-locus methods. To address this concern, we proposed a fast score test integrated with Empirical Bayes (ScoreEB) for multi-locus GWAS. Firstly, a score test was conducted for each single nucleotide polymorphism (SNP) under a linear mixed model (LMM) framework, taking into account the genetic relatedness and population structure. Then, all of the potentially associated SNPs were selected with a less stringent criterion. Finally, Empirical Bayes in a multi-locus model was performed for all of the selected SNPs to identify the true quantitative trait nucleotide (QTN). Our new method ScoreEB adopts the similar strategy of multi-locus random-SNP-effect mixed linear model (mrMLM) and fast multi-locus random-SNP-effect EMMA (FASTmrEMMA), and the only difference is that we use the score test to select all the potentially associated markers. Monte Carlo simulation studies demonstrate that ScoreEB significantly improved the computational efficiency compared with the popular methods mrMLM, FASTmrEMMA, iterative modified-sure independence screening EM-Bayesian lasso (ISIS EM-BLASSO), hybrid of restricted and penalized maximum likelihood (HRePML) and genome-wide efficient mixed model association (GEMMA). In addition, ScoreEB remained accurate in QTN effect estimation and effectively controlled false positive rate. Subsequently, ScoreEB was applied to re-analyze quantitative traits in plants and animals. The results show that ScoreEB not only can detect previously reported genes, but also can mine new genes.
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Affiliation(s)
- Jing Xiao
- Department of Epidemiology and Medical Statistics, School of Public Health, Nantong University, Nantong, China
| | - Yang Zhou
- Department of Epidemiology and Medical Statistics, School of Public Health, Nantong University, Nantong, China
| | - Shu He
- Department of Epidemiology and Medical Statistics, School of Public Health, Nantong University, Nantong, China
| | - Wen-Long Ren
- Department of Epidemiology and Medical Statistics, School of Public Health, Nantong University, Nantong, China
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150
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Feng L, Ma A, Song B, Yu S, Qi X. Mapping causal genes and genetic interactions for agronomic traits using a large F2 population in rice. G3 (BETHESDA, MD.) 2021; 11:6369515. [PMID: 34515770 PMCID: PMC8527483 DOI: 10.1093/g3journal/jkab318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022]
Abstract
Dissecting the genetic mechanisms underlying agronomic traits is of great importance for crop breeding. Agronomic traits are usually controlled by multiple quantitative trait loci (QTLs) and genetic interactions, and mapping the underlying causal genes is still labor-intensive and time-consuming. Here, we present a genetic tool for directly targeting the specific causal genes by using a single-gene resolution linkage map that was constructed from 3756 F2 rice plants via targeted sequencing technology and Tukey-Kramer multiple comparisons test. Three large- and moderate-effect QTLs, qHD6-2, qGL3-1, and qGW5-2, were successfully mapped to their specific causal genes, Hd1, GS3, and GW5, respectively. A complex genetic interaction network containing 30 QTL-QTL interactions was constructed, revealing that the alternative allele of hub QTL, qHD6-2, can hide or release the genetic contributions of the alleles at interacting loci. Moreover, arranging genetic interactions in the models lead to more accurate phenotypic predictions. These results provide a community resource and new feasible strategy for deciphering the genetic mechanisms of complex agronomic traits and accelerating crop breeding.
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Affiliation(s)
- Laibao Feng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100049, China
| | - Aimin Ma
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100049, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100049, China
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