1
|
Thapa S, Gill HS, Halder J, Rana A, Ali S, Maimaitijiang M, Gill U, Bernardo A, St Amand P, Bai G, Sehgal SK. Integrating genomics, phenomics, and deep learning improves the predictive ability for Fusarium head blight-related traits in winter wheat. THE PLANT GENOME 2024:e20470. [PMID: 38853339 DOI: 10.1002/tpg2.20470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/07/2024] [Accepted: 04/14/2024] [Indexed: 06/11/2024]
Abstract
Fusarium head blight (FHB) remains one of the most destructive diseases of wheat (Triticum aestivum L.), causing considerable losses in yield and end-use quality. Phenotyping of FHB resistance traits, Fusarium-damaged kernels (FDK), and deoxynivalenol (DON), is either prone to human biases or resource expensive, hindering the progress in breeding for FHB-resistant cultivars. Though genomic selection (GS) can be an effective way to select these traits, inaccurate phenotyping remains a hurdle in exploiting this approach. Here, we used an artificial intelligence (AI)-based precise FDK estimation that exhibits high heritability and correlation with DON. Further, GS using AI-based FDK (FDK_QVIS/FDK_QNIR) showed a two-fold increase in predictive ability (PA) compared to GS for traditionally estimated FDK (FDK_V). Next, the AI-based FDK was evaluated along with other traits in multi-trait (MT) GS models to predict DON. The inclusion of FDK_QNIR and FDK_QVIS with days to heading as covariates improved the PA for DON by 58% over the baseline single-trait GS model. We next used hyperspectral imaging of FHB-infected wheat kernels as a novel avenue to improve the MT GS for DON. The PA for DON using selected wavebands derived from hyperspectral imaging in MT GS models surpassed the single-trait GS model by around 40%. Finally, we evaluated phenomic prediction for DON by integrating hyperspectral imaging with deep learning to directly predict DON in FHB-infected wheat kernels and observed an accuracy (R2 = 0.45) comparable to best-performing MT GS models. This study demonstrates the potential application of AI and vision-based platforms to improve PA for FHB-related traits using genomic and phenomic selection.
Collapse
Affiliation(s)
- Subash Thapa
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, South Dakota, USA
| | - Harsimardeep S Gill
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, South Dakota, USA
| | - Jyotirmoy Halder
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, South Dakota, USA
| | - Anshul Rana
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, South Dakota, USA
| | - Shaukat Ali
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, South Dakota, USA
| | - Maitiniyazi Maimaitijiang
- Department of Geography & Geospatial Sciences, Geospatial Sciences Center of Excellence, South Dakota State University, Brookings, South Dakota, USA
| | - Upinder Gill
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| | - Amy Bernardo
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, USA
| | - Paul St Amand
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, USA
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, USA
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, South Dakota, USA
| |
Collapse
|
2
|
Kaushal S, Gill HS, Billah MM, Khan SN, Halder J, Bernardo A, Amand PS, Bai G, Glover K, Maimaitijiang M, Sehgal SK. Enhancing the potential of phenomic and genomic prediction in winter wheat breeding using high-throughput phenotyping and deep learning. FRONTIERS IN PLANT SCIENCE 2024; 15:1410249. [PMID: 38872880 PMCID: PMC11169824 DOI: 10.3389/fpls.2024.1410249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 05/06/2024] [Indexed: 06/15/2024]
Abstract
Integrating high-throughput phenotyping (HTP) based traits into phenomic and genomic selection (GS) can accelerate the breeding of high-yielding and climate-resilient wheat cultivars. In this study, we explored the applicability of Unmanned Aerial Vehicles (UAV)-assisted HTP combined with deep learning (DL) for the phenomic or multi-trait (MT) genomic prediction of grain yield (GY), test weight (TW), and grain protein content (GPC) in winter wheat. Significant correlations were observed between agronomic traits and HTP-based traits across different growth stages of winter wheat. Using a deep neural network (DNN) model, HTP-based phenomic predictions showed robust prediction accuracies for GY, TW, and GPC for a single location with R2 of 0.71, 0.62, and 0.49, respectively. Further prediction accuracies increased (R2 of 0.76, 0.64, and 0.75) for GY, TW, and GPC, respectively when advanced breeding lines from multi-locations were used in the DNN model. Prediction accuracies for GY varied across growth stages, with the highest accuracy at the Feekes 11 (Milky ripe) stage. Furthermore, forward prediction of GY in preliminary breeding lines using DNN trained on multi-location data from advanced breeding lines improved the prediction accuracy by 32% compared to single-location data. Next, we evaluated the potential of incorporating HTP-based traits in multi-trait genomic selection (MT-GS) models in the prediction of GY, TW, and GPC. MT-GS, models including UAV data-based anthocyanin reflectance index (ARI), green chlorophyll index (GCI), and ratio vegetation index 2 (RVI_2) as covariates demonstrated higher predictive ability (0.40, 0.40, and 0.37, respectively) as compared to single-trait model (0.23) for GY. Overall, this study demonstrates the potential of integrating HTP traits into DL-based phenomic or MT-GS models for enhancing breeding efficiency.
Collapse
Affiliation(s)
- Swas Kaushal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Harsimardeep S. Gill
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Mohammad Maruf Billah
- Department of Geography and Geospatial Sciences, Geospatial Sciences Center of Excellence, South Dakota State University, Brookings, SD, United States
| | - Shahid Nawaz Khan
- Department of Geography and Geospatial Sciences, Geospatial Sciences Center of Excellence, South Dakota State University, Brookings, SD, United States
| | - Jyotirmoy Halder
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Amy Bernardo
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, United States
| | - Paul St. Amand
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, United States
| | - Guihua Bai
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, United States
| | - Karl Glover
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Maitiniyazi Maimaitijiang
- Department of Geography and Geospatial Sciences, Geospatial Sciences Center of Excellence, South Dakota State University, Brookings, SD, United States
| | - Sunish K. Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| |
Collapse
|
3
|
Walker PL, Belmonte MF, McCallum BD, McCartney CA, Randhawa HS, Henriquez MA. Dual RNA-sequencing of Fusarium head blight resistance in winter wheat. FRONTIERS IN PLANT SCIENCE 2024; 14:1299461. [PMID: 38239218 PMCID: PMC10794533 DOI: 10.3389/fpls.2023.1299461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/29/2023] [Indexed: 01/22/2024]
Abstract
Fusarium head blight (FHB) is a devastating fungal disease responsible for significant yield losses in wheat and other cereal crops across the globe. FHB infection of wheat spikes results in grain contamination with mycotoxins, reducing both grain quality and yield. Breeding strategies have resulted in the production of FHB-resistant cultivars, however, the underlying molecular mechanisms of resistance in the majority of these cultivars are still poorly understood. To improve our understanding of FHB-resistance, we performed a transcriptomic analysis of FHB-resistant AC Emerson, FHB-moderately resistant AC Morley, and FHB-susceptible CDC Falcon in response to Fusarium graminearum. Wheat spikelets located directly below the point of inoculation were collected at 7-days post inoculation (dpi), where dual RNA-sequencing was performed to explore differential expression patterns between wheat cultivars in addition to the challenging pathogen. Differential expression analysis revealed distinct defense responses within FHB-resistant cultivars including the enrichment of physical defense through the lignin biosynthesis pathway, and DON detoxification through the activity of UDP-glycosyltransferases. Nucleotide sequence variants were also identified broadly between these cultivars with several variants being identified within differentially expressed putative defense genes. Further, F. graminearum demonstrated differential expression of mycotoxin biosynthesis pathways during infection, leading to the identification of putative pathogenicity factors.
Collapse
Affiliation(s)
- Philip L. Walker
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Mark F. Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Brent D. McCallum
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Curt A. McCartney
- Department of Plant Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Harpinder S. Randhawa
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Maria A. Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
- Department of Plant Sciences, University of Manitoba, Winnipeg, MB, Canada
| |
Collapse
|
4
|
Reddy SS, Saini DK, Singh GM, Sharma S, Mishra VK, Joshi AK. Genome-wide association mapping of genomic regions associated with drought stress tolerance at seedling and reproductive stages in bread wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1166439. [PMID: 37251775 PMCID: PMC10213333 DOI: 10.3389/fpls.2023.1166439] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/14/2023] [Indexed: 05/31/2023]
Abstract
Understanding the genetic architecture of drought stress tolerance in bread wheat at seedling and reproductive stages is crucial for developing drought-tolerant varieties. In the present study, 192 diverse wheat genotypes, a subset from the Wheat Associated Mapping Initiative (WAMI) panel, were evaluated at the seedling stage in a hydroponics system for chlorophyll content (CL), shoot length (SLT), shoot weight (SWT), root length (RLT), and root weight (RWT) under both drought and optimum conditions. Following that, a genome-wide association study (GWAS) was carried out using the phenotypic data recorded during the hydroponics experiment as well as data available from previously conducted multi-location field trials under optimal and drought stress conditions. The panel had previously been genotyped using the Infinium iSelect 90K SNP array with 26,814 polymorphic markers. Using single as well as multi-locus models, GWAS identified 94 significant marker-trait associations (MTAs) or SNPs associated with traits recorded at the seedling stage and 451 for traits recorded at the reproductive stage. The significant SNPs included several novel, significant, and promising MTAs for different traits. The average LD decay distance for the whole genome was approximately 0.48 Mbp, ranging from 0.07 Mbp (chromosome 6D) to 4.14 Mbp (chromosome 2A). Furthermore, several promising SNPs revealed significant differences among haplotypes for traits such as RLT, RWT, SLT, SWT, and GY under drought stress. Functional annotation and in silico expression analysis revealed important putative candidate genes underlying the identified stable genomic regions such as protein kinases, O-methyltransferases, GroES-like superfamily proteins, NAD-dependent dehydratases, etc. The findings of the present study may be useful for improving yield potential, and stability under drought stress conditions.
Collapse
Affiliation(s)
- S Srinatha Reddy
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - G Mahendra Singh
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Sandeep Sharma
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Vinod Kumar Mishra
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Arun Kumar Joshi
- Borlaug Institute of South Asia (BISA), NASC Complex, DPS Marg, New Delhi, India
- CIMMYT, NASC Complex, DPS Marg, New Delhi, India
| |
Collapse
|
5
|
Halder J, Gill HS, Zhang J, Altameemi R, Olson E, Turnipseed B, Sehgal SK. Genome-wide association analysis of spike and kernel traits in the U.S. hard winter wheat. THE PLANT GENOME 2023; 16:e20300. [PMID: 36636831 DOI: 10.1002/tpg2.20300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/20/2022] [Indexed: 05/10/2023]
Abstract
A better understanding of the genetic control of spike and kernel traits that have higher heritability can help in the development of high-yielding wheat varieties. Here, we identified the marker-trait associations (MTAs) for various spike- and kernel-related traits in winter wheat (Triticum aestivum L.) through genome-wide association studies (GWAS). An association mapping panel comprising 297 hard winter wheat accessions from the U.S. Great Plains was evaluated for eight spike- and kernel-related traits in three different environments. A GWAS using 15,590 single-nucleotide polymorphisms (SNPs) identified a total of 53 MTAs for seven spike- and kernel-related traits, where the highest number of MTAs were identified for spike length (16) followed by the number of spikelets per spike (15) and spikelet density (11). Out of 53 MTAs, 14 were considered to represent stable quantitative trait loci (QTL) as they were identified in multiple environments. Five multi-trait MTAs were identified for various traits including the number of spikelets per spike (NSPS), spikelet density (SD), kernel width (KW), and kernel area (KA) that could facilitate the pyramiding of yield-contributing traits. Further, a significant additive effect of accumulated favorable alleles on the phenotype of four spike-related traits suggested that breeding lines and cultivars with a higher number of favorable alleles could be a valuable resource for breeders to improve yield-related traits. This study improves the understanding of the genetic basis of yield-related traits in hard winter wheat and provides reliable molecular markers that will facilitate marker-assisted selection (MAS) in wheat breeding programs.
Collapse
Affiliation(s)
- Jyotirmoy Halder
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
| | - Harsimardeep S Gill
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
| | - Jinfeng Zhang
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
| | - Rami Altameemi
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
| | - Eric Olson
- Dep. of Plant, Soil and Microbial Sciences, Michigan State Univ., East Lansing, MI, 48824, USA
| | - Brent Turnipseed
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
| | - Sunish K Sehgal
- Dep. of Agronomy, Horticulture & Plant Science, South Dakota State Univ., Brookings, SD, 57007, USA
| |
Collapse
|
6
|
Delfan S, Bihamta MR, Dadrezaei ST, Abbasi A, Alipoor H. Exploring genomic regions involved in bread wheat resistance to leaf rust at seedling/adult stages by using GWAS analysis. BMC Genomics 2023; 24:83. [PMID: 36810004 PMCID: PMC9945389 DOI: 10.1186/s12864-022-09096-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/22/2022] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Global wheat productivity is seriously challenged by a range of rust pathogens, especially leaf rust derived from Puccinia triticina. Since the most efficient approach to control leaf rust is genetic resistance, many efforts have been made to uncover resistance genes; however, it demands an ongoing exploration for effective resistance sources because of the advent of novel virulent races. Thus, the current study was focused on detecting leaf rust resistance-related genomic loci against the P. triticina prevalent races by GWAS in a set of Iranian cultivars and landraces. RESULTS Evaluation of 320 Iranian bread wheat cultivars and landraces against four prevalent rust pathotypes of P. triticina (LR-99-2, LR-98-12, LR-98-22, and LR-97-12) indicated the diversity in wheat accessions responses to P. triticina. From GWAS results, 80 leaf rust resistance QTLs were located in the surrounding known QTLs/genes on almost chromosomes, except for 1D, 3D, 4D, and 7D. Of these, six MTAs (rs20781/rs20782 associated with resistance to LR-97-12; rs49543/rs52026 for LR-98-22; rs44885/rs44886 for LR-98-22/LR-98-1/LR-99-2) were found on genomic regions where no resistance genes previously reported, suggesting new loci conferring resistance to leaf rust. The GBLUP genomic prediction model appeared better than RR-BLUP and BRR, reflecting that GBLUP is a potent model for genomic selection in wheat accessions. CONCLUSIONS Overall, the newly identified MTAs as well as the highly resistant accessions in the recent work provide an opportunity towards improving leaf rust resistance.
Collapse
Affiliation(s)
- Saba Delfan
- grid.46072.370000 0004 0612 7950Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Mohammad Reza Bihamta
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran.
| | - Seyed Taha Dadrezaei
- grid.473705.20000 0001 0681 7351Department of Cereal Research, Seed and Plant Improvement Institute, Agricultural Research and Education Organization (AREEO), Karaj, Iran
| | - Alireza Abbasi
- grid.46072.370000 0004 0612 7950Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Hadi Alipoor
- grid.412763.50000 0004 0442 8645Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| |
Collapse
|