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Kumar M, Kumar S, Sandhu KS, Kumar N, Saripalli G, Prakash R, Nambardar A, Sharma H, Gautam T, Balyan HS, Gupta PK. GWAS and genomic prediction for pre-harvest sprouting tolerance involving sprouting score and two other related traits in spring wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:14. [PMID: 37313293 PMCID: PMC10248620 DOI: 10.1007/s11032-023-01357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 01/26/2023] [Indexed: 06/15/2023]
Abstract
In wheat, a genome-wide association study (GWAS) and genomic prediction (GP) analysis were conducted for pre-harvest sprouting (PHS) tolerance and two of its related traits. For this purpose, an association panel of 190 accessions was phenotyped for PHS (using sprouting score), falling number, and grain color over two years and genotyped with 9904 DArTseq based SNP markers. GWAS for main-effect quantitative trait nucleotides (M-QTNs) using three different models (CMLM, SUPER, and FarmCPU) and epistatic QTNs (E-QTNs) using PLINK were performed. A total of 171 M-QTNs (CMLM, 47; SUPER, 70; FarmCPU, 54) for all three traits, and 15 E-QTNs involved in 20 first-order epistatic interactions were identified. Some of the above QTNs overlapped the previously reported QTLs, MTAs, and cloned genes, allowing delineating 26 PHS-responsive genomic regions that spread over 16 wheat chromosomes. As many as 20 definitive and stable QTNs were considered important for use in marker-assisted recurrent selection (MARS). The gene, TaPHS1, for PHS tolerance (PHST) associated with one of the QTNs was also validated using the KASP assay. Some of the M-QTNs were shown to have a key role in the abscisic acid pathway involved in PHST. Genomic prediction accuracies (based on the cross-validation approach) using three different models ranged from 0.41 to 0.55, which are comparable to the results of previous studies. In summary, the results of the present study improved our understanding of the genetic architecture of PHST and its related traits in wheat and provided novel genomic resources for wheat breeding based on MARS and GP. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01357-5.
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Affiliation(s)
- Manoj Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Sachin Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | | | - Neeraj Kumar
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC USA
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD USA
| | - Ram Prakash
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Akash Nambardar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Hemant Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Tinku Gautam
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP India
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Li Z, Chen Y, Ou X, Wang M, Wang N, Li W, Deng Y, Diao Y, Sun Z, Luo Q, Li X, Zhao L, Yan T, Peng W, Jiang Q, Fang Y, Ren Z, Tan F, Luo P, Ren T. Identification of a stable major-effect quantitative trait locus for pre-harvest sprouting in common wheat (Triticum aestivum L.) via high-density SNP-based genotyping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4183-4195. [PMID: 36068440 DOI: 10.1007/s00122-022-04211-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
A major and stable QTL cQSGR.sau.3D, which can explain 33.25% of the phenotypic variation in SGR, was mapped and validated, and cQSGR.sau.3D was found to be independent of GI. In this study, a recombinant inbred line (RIL) population containing 304 lines derived from the cross of Chuan-nong17 (CN17) and Chuan-nong11 (CN11) was genotyped using the Wheat55K single-nucleotide polymorphism array. A high-density genetic map consisting of 8329 markers spanning 4131.54 cM and distributed across 21 wheat chromosomes was constructed. QTLs for whole spike germination rate (SGR) were identified in multiple years. Six and fourteen QTLs were identified using the Inclusive Composite Interval Mapping-Biparental Populations and Multi-Environment Trial methods, respectively. A total of 106 digenic epistatic QTLs were also detected in this study. One of the additive QTLs, cQSGR.sau.3D, which was mapped in the region from 3.5 to 4.5 cM from linkage group 3D-2 on chromosome 3D, can explain 33.25% of the phenotypic variation in SGR and be considered a major and stable QTL for SGR. This QTL was independent of the seeds' germination traits, such as germination index. One Kompetitive Allele-Specific PCR (KASP) marker, KASP-AX-110772653, which is tightly linked to cQSGR.sau.3D, was developed. The genetic effect of cQSGR.sau.3D on SGR in the RIL and natural populations was successfully confirmed. Furthermore, within the interval in which cQSGR.sau.3D is located in Chinese Spring reference genomes, thirty-seven genes were found. cQSGR.sau.3D may provide new resources for pre-harvest sprouting resistance breeding of wheat in the future.
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Affiliation(s)
- Zhi Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yongyan Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Xia Ou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Mengning Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Nanxin Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Wei Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yawen Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yixin Diao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Zixin Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Qinyi Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Xinli Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Liqi Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Tong Yan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Wanhua Peng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Qing Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yi Fang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Zhenglong Ren
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Feiquan Tan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Peigao Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Tianheng Ren
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
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Rehal PK, Tuan PA, Nguyen TN, Cattani DJ, Humphreys DG, Ayele BT. Genetic variation of seed dormancy in wheat (Triticum aestivum L.) is mediated by transcriptional regulation of abscisic acid metabolism and signaling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111432. [PMID: 36029895 DOI: 10.1016/j.plantsci.2022.111432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/09/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Abscisic acid (ABA) regulates seed dormancy and therefore preharvest sprouting (PHS) in wheat. This study investigated the contribution of transcriptional regulation of ABA metabolism and signaling genes to genetic variation in dormancy of wheat seeds. Our results showed that genetic variation in seed dormancy is highly correlated with ABA content (r > 0.86), which, in turn, was closely associated with the expression levels of ABA biosynthesis genes, TaNCED1 (r = 0.78) and TaNCED2 (r = 0.67). A relatively lower correlation was observed between ABA content and the expression levels of ABA catabolism genes, TaCYP707A1 (r = 0.51) and TaCYP707A2 (r = 0.57). The expression level of TaABI5 exhibited strong associations with the levels of ABA (r = 0.8) and seed dormancy (r > 0.9), indicating the importance of seed ABA sensitivity in mediating genetic variation in dormancy. Furthermore, high positive correlations were prevalent between the expression patterns of TaABI5 and TaNCED1 (r = 0.91) or TaNCED2 (r = 0.82). Overall, our results implicated the significance of TaNCEDs and TaABI5 in regulating genetic variation in ABA level and sensitivity and thereby seed dormancy, highlighting the potential use of these genes to develop molecular markers for incorporating PHS resistance in wheat.
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Affiliation(s)
- Pawanpuneet K Rehal
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, Manitoba R3T 2N2, Canada
| | - Pham Anh Tuan
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, Manitoba R3T 2N2, Canada
| | - Tran-Nguyen Nguyen
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, Manitoba R3T 2N2, Canada
| | - Douglas J Cattani
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, Manitoba R3T 2N2, Canada
| | - D Gavin Humphreys
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, KW Neatby Building, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Belay T Ayele
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, Manitoba R3T 2N2, Canada.
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Utsugi S, Ashikawa I, Nakamura S, Shibasaka M. TaABI5, a wheat homolog of Arabidopsis thaliana ABA insensitive 5, controls seed germination. JOURNAL OF PLANT RESEARCH 2020; 133:245-256. [PMID: 32048094 DOI: 10.1007/s10265-020-01166-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 01/20/2020] [Indexed: 05/25/2023]
Abstract
Abscisic acid (ABA) response element (ABRE)-binding factors (ABFs) are basic region/leucine zipper motif (bZIP) transcription factors that regulate the expression of ABA-induced genes containing ABRE in their promoters. The amino acid sequence of the wheat bZIP protein, TaABI5, showed high homology to that of Arabidopsis ABA insensitive 5 (ABI5). TaABI5 was classified into the clade of ABI5s in Arabidopsis and rice, unlike TRAB1 of rice, Wabi5 of wheat, and HvABI5 of barley in the bZIP Group A family, by a phylogenetic analysis. TaABI5 was strongly expressed in seeds during the late ripening and maturing stages; however, its expression level markedly decreased after germination. An in situ hybridization analysis showed that TaABI5 mRNA accumulated in seed embryos, particularly the scutellum. In a transient assay using wheat aleurone cells, TaABI5 activated the promoter of Em containing ABRE, which is an embryogenesis abundant protein gene, indicating that TaABI5 acts as a transcription factor in wheat seeds. Furthermore, the seeds of transgenic Arabidopsis lines introduced with 35S:TaABI5 exhibited high sensitivity to ABA and the inhibition of germination. The seed dormancy of the transgenic Arabidopsis lines was stronger than that of Col. These results support TaABI5 playing an important role in mature seeds, particularly before seed germination, and acting as a functional ortholog to Arabidopsis ABI5.
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Affiliation(s)
- Shigeko Utsugi
- Institute of Plant Science and Resources (IPSR), Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
| | - Ikuo Ashikawa
- Institute of Crop Science, NARO, 2-1-2 Kannonndai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Shingo Nakamura
- Institute of Crop Science, NARO, 2-1-2 Kannonndai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Mineo Shibasaka
- Institute of Plant Science and Resources (IPSR), Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
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