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Zhang C, Sha Y, Wang Q, Liu J, Zhang P, Cheng S, Qin P. Integrative metabolome and transcriptome profiling provide insights into elucidation of the synthetic mechanisms of phenolic compounds in Yunnan hulled wheat (Triticum aestivum ssp. yunnanense King). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:4109-4127. [PMID: 38308467 DOI: 10.1002/jsfa.13293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/11/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
BACKGROUND Yunnan hulled wheat grains (YHWs) have abundant phenolic compounds (PCs). However, a systematic elucidation of the phenolic characteristics and molecular basis in YHWs is currently lacking. The aim of the study, for the first time, was to conduct metabolomic and transcriptomic analyses of YHWs at different developmental stages. RESULTS A total of five phenolic metabolite classes (phenolic acids, flavonoids, quinones, lignans and coumarins, and tannins) and 361 PCs were identified, with flavonoids and phenolic acids being the most abundant components. The relative abundance of the identified PCs showed a dynamic decreasing pattern with grain development, and the most significant differences in accumulation were between the enlargement and mature stage, which is consistent with the gene regulation patterns of the corresponding phenolic biosynthesis pathway. Through co-expression and co-network analysis, PAL, HCT, CCR, F3H, CHS, CHI and bZIP were identified and predicted as candidate key enzymes and transcription factors. CONCLUSION The results broaden our understanding of PC accumulation in wheat whole grains, especially the differential transfer between immature and mature grains. The identified PCs and potential regulatory factors provide important information for future in-depth research on the biosynthesis of PCs and the improvement of wheat nutritional quality. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Chuanli Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
- College of Tropical Crops, Yunnan Agricultural University, Kunming, China
| | - Yun Sha
- Agricultural Technology Extension Station of Lincang, Lincang, China
| | - Qianchao Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Junna Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Ping Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Shunhe Cheng
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
- Jiangshu Lixiahe Institue of Agriculture Science, Yangzhou, China
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
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Atsbeha G, Mekonnen T, Kebede M, Haileselassie T, Goodwin SB, Tesfaye K. Genetic architecture of adult-plant resistance to stripe rust in bread wheat ( Triticum aestivum L.) association panel. FRONTIERS IN PLANT SCIENCE 2023; 14:1256770. [PMID: 38130484 PMCID: PMC10733515 DOI: 10.3389/fpls.2023.1256770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a severe disease in wheat worldwide, including Ethiopia, causing up to 100% wheat yield loss in the worst season. The use of resistant cultivars is considered to be the most effective and durable management technique for controlling the disease. Therefore, the present study targeted the genetic architecture of adult plant resistance to yellow rust in 178 wheat association panels. The panel was phenotyped for yellow rust adult-plant resistance at three locations. Phonological, yield, yield-related, and agro-morphological traits were recorded. The association panel was fingerprinted using the genotyping-by-sequencing (GBS) platform, and a total of 6,788 polymorphic single nucleotide polymorphisms (SNPs) were used for genome-wide association analysis to identify effective yellow rust resistance genes. The marker-trait association analysis was conducted using the Genome Association and Prediction Integrated Tool (GAPIT). The broad-sense heritability for the considered traits ranged from 74.52% to 88.64%, implying the presence of promising yellow rust resistance alleles in the association panel that could be deployed to improve wheat resistance to the disease. The overall linkage disequilibrium (LD) declined within an average physical distance of 31.44 Mbp at r2 = 0.2. Marker-trait association (MTA) analysis identified 148 loci significantly (p = 0.001) associated with yellow rust adult-plant resistance. Most of the detected resistance quantitative trait loci (QTLs) were located on the same chromosomes as previously reported QTLs for yellow rust resistance and mapped on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6A, 6B, 7A, and 7D. However, 12 of the discovered MTAs were not previously documented in the wheat literature, suggesting that they could represent novel loci for stripe rust resistance. Zooming into the QTL regions in IWGSC RefSeq Annotation v1 identified crucial disease resistance-associated genes that are key in plants' defense mechanisms against pathogen infections. The detected QTLs will be helpful for marker-assisted breeding of wheat to increase resistance to stripe rust. Generally, the present study identified putative QTLs for field resistance to yellow rust and some important agronomic traits. Most of the discovered QTLs have been reported previously, indicating the potential to improve wheat resistance to yellow rust by deploying the QTLs discovered by marker-assisted selection.
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Affiliation(s)
- Genet Atsbeha
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Tilahun Mekonnen
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mulugeta Kebede
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Stephen B. Goodwin
- USDA-Agricultural Research Service, Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Bio and Emerging Technology Institute. Affiliated with the Institute of Biotechnology, Addis Ababa, University, Addis Ababa, Ethiopia
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Zhang C, Zhang P, Zhang X, Wang Q, Liu J, Li L, Cheng S, Qin P. Integrated Metabolome and Transcriptome Analyses Reveal Amino Acid Biosynthesis Mechanisms during the Physiological Maturity of Grains in Yunnan Hulled Wheat ( Triticum aestivum ssp. yunnanense King). Int J Mol Sci 2023; 24:13475. [PMID: 37686281 PMCID: PMC10487551 DOI: 10.3390/ijms241713475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Yunnan hulled wheat (YHW) possesses excellent nutritional characteristics; however, the precise amino acid (AA) composition, contents, and molecular mechanisms underlying AA biosynthesis in YHW grains remain unclear. In this study, we aimed to perform metabolomic and transcriptomic profiling to identify the composition and genetic factors regulating AA biosynthesis during the physiological maturation of grains of two YHW genotypes, Yunmai and Dikemail, with high and low grain protein contents, respectively. A total of 40 and 14 differentially accumulated amino acids (AAs) or AA derivatives were identified between the waxy grain (WG) and mature grain (MG) phenological stages of Yunmai and Dikemail, respectively. The AA composition differed between WG and MG, and the abundance of AAs-especially that of essential AAs-was significantly higher in WG than in MG (only 38.74-58.26% of WG). Transcriptome analysis revealed differential regulation of structural genes associated with the relatively higher accumulation of AAs in WG. Weighted gene co-expression network analysis and correlation analyses of WG and MG indicated differences in the expression of clusters of genes encoding both upstream elements of AA biosynthesis and enzymes that are directly involved in AA synthesis. The expression of these genes directly impacted the synthesis of various AAs. Together, these results contribute to our understanding of the mechanism of AA biosynthesis during the different developmental stages of grains and provide a foundation for further research to improve the nutritional value of wheat products.
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Affiliation(s)
- Chuanli Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (C.Z.); (P.Z.); (X.Z.); (Q.W.); (J.L.); (L.L.)
- College of Tropical Crops, Yunnan Agricultural University, Kunming 650201, China
| | - Ping Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (C.Z.); (P.Z.); (X.Z.); (Q.W.); (J.L.); (L.L.)
| | - Xuesong Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (C.Z.); (P.Z.); (X.Z.); (Q.W.); (J.L.); (L.L.)
| | - Qianchao Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (C.Z.); (P.Z.); (X.Z.); (Q.W.); (J.L.); (L.L.)
| | - Junna Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (C.Z.); (P.Z.); (X.Z.); (Q.W.); (J.L.); (L.L.)
| | - Li Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (C.Z.); (P.Z.); (X.Z.); (Q.W.); (J.L.); (L.L.)
| | - Shunhe Cheng
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (C.Z.); (P.Z.); (X.Z.); (Q.W.); (J.L.); (L.L.)
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (C.Z.); (P.Z.); (X.Z.); (Q.W.); (J.L.); (L.L.)
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Zhang G, Liu W, Wang L, Cheng X, Tian X, Du Z, Kang Z, Zhao J. Evaluation of the Potential Risk of the Emerging Yr5-Virulent Races of Puccinia striiformis f. sp. tritici to 165 Chinese Wheat Cultivars. PLANT DISEASE 2022; 106:1867-1874. [PMID: 35021876 DOI: 10.1094/pdis-11-21-2622-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In 2017, a new race (TSA-6) of the wheat stripe rust pathogen, Puccinia striiformis f. sp. tritici, virulent to resistance gene Yr5, was detected in China. However, whether Chinese wheat cultivars are resistant to the new race was unknown. In this study, two isolates (TSA-6 and TSA-9) with virulence to Yr5 were tested on other wheat Yr gene lines for their avirulence and virulence patterns and used, together with prevalent races CYR32 and CYR34 without the Yr5 virulence, to evaluate 165 major Chinese wheat cultivars for their reactions. Isolates TSA-6 and TSA-9 had similar but different virulence spectra and therefore should be considered two different races. Their avirulence and virulence patterns were remarkably different from that of CYR34 but quite similar to that of CYR32. Of the 165 wheat cultivars, 21 had all-stage resistance to TSA-6, 34 to TSA-9, and 20 to both races. Adult plant resistance (APR) was detected in 35 cultivars to TSA-6 and 27 to TSA-9, but only three cultivars showed APR to both new races. Slow rusting resistance was observed in 24 cultivars to TSA-6 and 33 to TSA-9. Analysis of variance of disease index indicated a significant difference between cultivars but not between the four races. Based on the molecular marker data, a low percentage of wheat cultivars carried Yr5, Yr7, Yr10, Yr15, Yr26, or YrSP. Because TSA-6 and TSA-9 can be a serious threat to wheat production in China, continual monitoring of TSA-6, TSA-9, and other races is needed.
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Affiliation(s)
- Gensheng Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wei Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiangrui Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiaxia Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhimin Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
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Zhang X, Huang T, Wang Q, Guo Y, Zhang P, Xie H, Liu J, Li L, Zhang C, Qin P. Mechanisms of Resistance to Spot Blotch in Yunnan Iron Shell Wheat Based on Metabolome and Transcriptomics. Int J Mol Sci 2022; 23:5184. [PMID: 35563578 PMCID: PMC9104156 DOI: 10.3390/ijms23095184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 11/17/2022] Open
Abstract
Spot blotch (SB) is a fungal disease that threatens wheat yield and quality. Presently, the molecular mechanism against SB is unclear. In this study, the resistant variety Zhenkang iron shell wheat (Yunmai 0030) and susceptible variety Lincang iron shell wheat (Yunmai 0608) were selected by identifying SB of Yunnan iron shell wheat. The metabolome and transcriptome of leaves of two varieties at different positions were detected using the systemic acquired resistance theory to investigate the molecular and physiological changes in Yunnan iron shell wheat under SB stress. We found that the genes and metabolites related to benzoxazinoid biosynthesis and arginine and proline metabolism were highly enriched after infection with leaf blight. The enriched differential metabolites mainly included phenolic acids, alkaloids, and flavonoids. We further observed that DIBOA- and DIMBOA-glucoside positively affected iron shell wheat resistance to leaf blight and proline and its derivatives were important for plant self-defense. Furthermore, we confirmed that the related metabolites in benzoxazinoid biosynthesis and arginine and proline metabolism positively affected Triticum aestivum ssp. resistance to SB. This study provides new insights into the dynamic physiological changes of wheat in response to SB, helps us better understand the mechanism of resistance to SB, and contributes to the breeding and utilization of resistant varieties.
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Affiliation(s)
- Xuesong Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (T.H.); (Q.W.); (Y.G.); (P.Z.); (H.X.); (J.L.); (L.L.)
| | - Tingzhi Huang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (T.H.); (Q.W.); (Y.G.); (P.Z.); (H.X.); (J.L.); (L.L.)
| | - Qianchao Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (T.H.); (Q.W.); (Y.G.); (P.Z.); (H.X.); (J.L.); (L.L.)
| | - Yirui Guo
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (T.H.); (Q.W.); (Y.G.); (P.Z.); (H.X.); (J.L.); (L.L.)
| | - Ping Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (T.H.); (Q.W.); (Y.G.); (P.Z.); (H.X.); (J.L.); (L.L.)
| | - Heng Xie
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (T.H.); (Q.W.); (Y.G.); (P.Z.); (H.X.); (J.L.); (L.L.)
| | - Junna Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (T.H.); (Q.W.); (Y.G.); (P.Z.); (H.X.); (J.L.); (L.L.)
| | - Li Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (T.H.); (Q.W.); (Y.G.); (P.Z.); (H.X.); (J.L.); (L.L.)
| | - Chuanli Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (T.H.); (Q.W.); (Y.G.); (P.Z.); (H.X.); (J.L.); (L.L.)
- College of Tropical Crops, Yunnan Agricultural University, Pu’er 665000, China
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (X.Z.); (T.H.); (Q.W.); (Y.G.); (P.Z.); (H.X.); (J.L.); (L.L.)
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Saini DK, Chopra Y, Singh J, Sandhu KS, Kumar A, Bazzer S, Srivastava P. Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:1. [PMID: 37309486 PMCID: PMC10248672 DOI: 10.1007/s11032-021-01272-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Genome-wide association studies (GWAS) are effectively applied to detect the marker trait associations (MTAs) using whole genome-wide variants for complex quantitative traits in different crop species. GWAS has been applied in wheat for different quality, biotic and abiotic stresses, and agronomic and yield-related traits. Predictions for marker-trait associations are controlled with the development of better statistical models taking population structure and familial relatedness into account. In this review, we have provided a detailed overview of the importance of association mapping, population design, high-throughput genotyping and phenotyping platforms, advancements in statistical models and multiple threshold comparisons, and recent GWA studies conducted in wheat. The information about MTAs utilized for gene characterization and adopted in breeding programs is also provided. In the literature that we surveyed, as many as 86,122 wheat lines have been studied under various GWA studies reporting 46,940 loci. However, further utilization of these is largely limited. The future breakthroughs in area of genomic selection, multi-omics-based approaches, machine, and deep learning models in wheat breeding after exploring the complex genetic structure with the GWAS are also discussed. This is a most comprehensive study of a large number of reports on wheat GWAS and gives a comparison and timeline of technological developments in this area. This will be useful to new researchers or groups who wish to invest in GWAS.
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Affiliation(s)
- Dinesh K. Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Yuvraj Chopra
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004 India
| | - Jagmohan Singh
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163 USA
| | - Anand Kumar
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur, 202002 India
| | - Sumandeep Bazzer
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
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