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Gaire R, de Arruda MP, Mohammadi M, Brown-Guedira G, Kolb FL, Rutkoski J. Multi-trait genomic selection can increase selection accuracy for deoxynivalenol accumulation resulting from fusarium head blight in wheat. Plant Genome 2022; 15:e20188. [PMID: 35043582 DOI: 10.1002/tpg2.20188] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/18/2021] [Indexed: 06/14/2023]
Abstract
Multi-trait genomic prediction (MTGP) can improve selection accuracy for economically valuable 'primary' traits by incorporating data on correlated secondary traits. Resistance to Fusarium head blight (FHB), a fungal disease of wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), is evaluated using four genetically correlated traits: incidence (INC), severity (SEV), Fusarium damaged kernels (FDK), and deoxynivalenol content (DON). Both FDK and DON are primary traits; DON evaluation is expensive and usually requires several months for wheat breeders to get results from service laboratories performing the evaluations. We evaluated MTGP for DON using three soft red winter wheat breeding datasets: two diversity panels from the University of Illinois (IL) and Purdue University (PU) and a dataset consisting of 2019-2020 University of Illinois breeding cohorts. For DON, relative to single-trait (ST) genomic prediction, MTGP including phenotypic data for secondary traits on both validation and training sets, resulted in 23.4 and 10.6% higher predictive abilities in IL and PU panels, respectively. The MTGP models were advantageous only when secondary traits were included in both training and validation sets. In addition, MTGP models were more accurate than ST models only when FDK was included, and once FDK was included in the model, adding additional traits hardly improved accuracy. Evaluation of MTGP models across testing cohorts indicated that MTGP could increase accuracy by more than twofold in the early stages. Overall, we show that MTGP can increase selection accuracy for resistance to DON accumulation in wheat provided FDK is evaluated on the selection candidates.
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Affiliation(s)
- Rupesh Gaire
- Crop Sciences, Univ. of Illinois at Urbana-Champaign, 1102 S. Goodwin Avenue, Urbana, IL, 61801, USA
| | | | - Mohsen Mohammadi
- Agronomy Dep., Purdue Univ., 915 W State St, West Lafayette, IN, 47907, USA
| | - Gina Brown-Guedira
- USDA-ARS Plant Science Research & Crop and Soil Sciences, North Carolina State University, Williams Hall 4114A, Raleigh, NC, 27695, USA
| | - Frederic L Kolb
- Crop Sciences, Univ. of Illinois at Urbana-Champaign, 1102 S. Goodwin Avenue, Urbana, IL, 61801, USA
| | - Jessica Rutkoski
- Crop Sciences, Univ. of Illinois at Urbana-Champaign, 1102 S. Goodwin Avenue, Urbana, IL, 61801, USA
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Gaire R, Sneller C, Brown-Guedira G, Van Sanford D, Mohammadi M, Kolb FL, Olson E, Sorrells M, Rutkoski J. Genetic Trends in Fusarium Head Blight Resistance from 20 Years of Winter Wheat Breeding and Cooperative Testing in the Northern U.S.A. Plant Dis 2022; 106:364-372. [PMID: 34282926 DOI: 10.1094/pdis-04-21-0891-sr] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fusarium head blight (FHB) is a devastating disease of wheat and barley. In the U.S.A., a significant long-term investment in breeding FHB-resistant cultivars began after the 1990s. However, to this date, no study has been performed to understand and monitor the rate of genetic progress in FHB resistance as a result of this investment. Using 20 years of data (1998 to 2018) from the Northern Uniform and Preliminarily Northern Uniform winter wheat scab nurseries that consisted of 1,068 genotypes originating from nine different institutions, we studied the genetic trends in FHB resistance within the northern soft red winter wheat growing region using mixed model analyses. For the FHB resistance traits incidence, severity, Fusarium-damaged kernels, and deoxynivalenol content, the rate of genetic gain in disease resistance was estimated to be 0.30 ± 0.1, 0.60 ± 0.09, and 0.37 ± 0.11 points per year, and 0.11 ± 0.05 parts per million per year, respectively. Among the five FHB-resistance quantitative trait loci assayed for test entries from 2012 to 2018, the frequencies of favorable alleles from Fhb 2DL Wuhan1 W14, Fhb Ernie 3Bc, and Fhb 5A Ning7840 were close to zero across the years. The frequency of the favorable at Fhb1 and Fhb 5A Ernie ranged from 0.08 to 0.33 and 0.06 to 0.20, respectively, across years, and there was no trend in changes in allele frequencies over years. Overall, this study showed that substantial genetic progress has been made toward improving resistance to FHB. It is apparent that today's investment in public wheat breeding for FHB resistance is achieving results and will continue to play a vital role in reducing FHB levels in growers' fields.
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Affiliation(s)
- Rupesh Gaire
- University of Illinois at Urbana-Champaign, Crop Sciences Department, Urbana, IL 61801
| | - Clay Sneller
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH 43210
| | - Gina Brown-Guedira
- U.S. Department of Agriculture's Agricultural Research Service, Plant Science Research, Raleigh, NC 27695
| | - David Van Sanford
- Wheat Breeding and Genetics, Department of Plant and Soil Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546-0312
| | - Mohsen Mohammadi
- Department of Agronomy, Purdue University, West Lafayette, IN 47907
| | - Frederic L Kolb
- University of Illinois at Urbana-Champaign, Crop Sciences Department, Urbana, IL 61801
| | - Eric Olson
- Michigan State Wheat Breeding and Genetics, Department of Plant, Soil and Microbial Sciences, College of Agriculture & Natural Resources, Michigan State University, East Lansing, MI 48824
| | - Mark Sorrells
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Jessica Rutkoski
- University of Illinois at Urbana-Champaign, Crop Sciences Department, Urbana, IL 61801
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Gaire R, Brown-Guedira G, Dong Y, Ohm H, Mohammadi M. Genome-Wide Association Studies for Fusarium Head Blight Resistance and Its Trade-Off With Grain Yield in Soft Red Winter Wheat. Plant Dis 2021; 105:2435-2444. [PMID: 33560886 DOI: 10.1094/pdis-06-20-1361-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Identification of quantitative trait loci for Fusarium head blight (FHB) resistance from different sources and pyramiding them into cultivars could provide effective protection against FHB. The objective of this study was to characterize a soft red winter wheat (SRWW) breeding population that has been subjected to intense germplasm introduction and alien introgression for FHB resistance in the past. The population was evaluated under misted FHB nurseries inoculated with Fusarium graminearum-infested corn spawn for two years. Phenotypic data included disease incidence (INC), disease severity (SEV), Fusarium damaged kernels (FDK), FHB index (FHBdx), and deoxynivalenol concentration (DON). Genome-wide association studies using 13,784 SNP markers identified 25 genomic regions at -logP ≥ 4.0 that were associated with five FHB-related traits. Of these 25, the marker trait associations that explained more than 5% phenotypic variation were localized on chromosomes 1A, 2B, 3B, 5A, 7A, 7B, and 7D, and from diverse sources including adapted SRWW lines such as Truman and Bess, and unadapted common wheat lines such as Ning7840 and Fundulea 201R. Furthermore, individuals with favorable alleles at the four loci Fhb1, Qfhb.nc-2B.1 (Q2B.1), Q7D.1, and Q7D.2 showed better FDK and DON scores (but not INC, SEV, and FHBdx) compared with other allelic combinations. Our data also showed while pyramiding multiple loci provides protection against FHB disease, it has a significant trade-off with grain yield.
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Affiliation(s)
- Rupesh Gaire
- Agronomy Department, Purdue University, West Lafayette, IN 47907
| | - Gina Brown-Guedira
- USDA-ARS Plant Science Research, Department of Crop Science, North Carolina State University, Raleigh, NC 27695
| | - Yanhong Dong
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Herbert Ohm
- Agronomy Department, Purdue University, West Lafayette, IN 47907
| | - Mohsen Mohammadi
- Agronomy Department, Purdue University, West Lafayette, IN 47907
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Gaire R, Ohm H, Brown-Guedira G, Mohammadi M. Identification of regions under selection and loci controlling agronomic traits in a soft red winter wheat population. Plant Genome 2020; 13:e20031. [PMID: 33016613 DOI: 10.1002/tpg2.20031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/11/2020] [Accepted: 04/12/2020] [Indexed: 05/28/2023]
Abstract
Comprehensive information of a breeding population is a necessity to design promising crosses. This study was conducted to characterize a soft red winter wheat breeding population that was subject of intensive germplasm introductions and introgression from exotic germplasm. We used genome-wide markers and phenotypic assessment to identify signatures of selection and loci controlling agronomic traits in a soft red winter wheat population. The study of linkage disequilibrium (LD) revealed that the extent of LD and its decay varied among chromosomes with chromosomes 2B and 7D showing the most extended islands of high-LD with slow rates of decay. Four sub-populations, two with North American origin and two with Australian and Chinese origins, were identified. Genome-wide scans for selection signatures using FST and hapFLK identified 13 genomic regions under selection, of which five loci (LT, Fr-A2, Vrn-A1, Vrn-B1, Vrn3) were associated with environmental adaptation and two loci were associated with disease resistance genes (Sr36 and Fhb1). Genome-wide association studies identified major loci controlling yield and yield related traits. For days to heading and plant height, major loci with effects sizes of 2.2 days and 5 cm were identified on chromosomes 7B and 6A respectively. For test weight, number of spikes per square meter, and number of kernels per square meter, large effect loci were identified on chromosomes 1A, 4B, and 5A, respectively. However, for yield alone, no major loci were detected. A combination of selection for large effect loci for yield components and genomic selection could be a promising approach for yield improvement.
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Affiliation(s)
- Rupesh Gaire
- Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
| | - Herbert Ohm
- Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
| | - Gina Brown-Guedira
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
- US Department of Agriculture, Agricultural Research Services, Southeast Area, Plant Science Research, Raleigh, NC, 27695, USA
| | - Mohsen Mohammadi
- Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
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Gaire R, Dahal KR, Amgain LP. Effect of different mulching materials on weed dynamics and yield of direct seeded rice in Chitwan, Nepal. ACTA ACUST UNITED AC 2013. [DOI: 10.3126/ajn.v3i0.9008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
An experiment was carried out at farmers' field to compare the effects of live mulches and herbicide on weed growth and dynamics, yield, and economic performance of direct seeded rice under humid sub-tropical condition at Phulbari, Chitwan in 2009. The experiment was conducted in Randomized Complete Block Design with eight treatments and three replications. The treatments consisted of i) control, ii) three hand weeding, iii) herbicide application (bispyribac sodium @ 80 ml/ha) + one hand weeding, iv) wheat straw mulch @ 5t/ha + one hand weeding, v) Eupatorium mulch @ 5t/ha + one hand weeding, vi) brown manuring with Sesbania aculeata @ 30 kg/ha, vii) brown manuring with Sesamum indicum @ 2kg/ha, and viii) brown manuring with Crotolaria juncea @ 30 kg/ha. Weed dry matter accumulation was significantly lower with herbicide application (1.15 g/m2) than wheat straw mulch (6.75 g/m2). The treatments with brown manuring and Eupatorium mulch were found to be equally effective in suppressing the weed growth by reducing both dry matter content and weed density. Application of Eupatorium mulch one day after sowing produced significantly higher grain yield (3.5 t/ha) than control (1.77 t/ha), Sesamum brown manuring (2.97 t/ha) and wheat straw mulch (2.83 t/ha). Yield attributes like effective tillers/m2, panicle length and panicle weight were positively correlated with grain yield (r = 0.540, 0.705, 0.531 and 0.613 respectively). The net profit (Rs. 63.17 x 1000/ha) obtained from the treatment with Eupatorium mulch was higher than other tested treatments. Eupatorium mulch and herbicide application recorded equal benefit cost ratio of 2.4. Cultivation of direct seeded rice with the application of Eupatorium mulch or brown manuring (BM) of Sesamum was found effective for increasing yield and net returns in humid subtropical condition of Chitwan. Live mulching could be an eco-friendly weed control options in DSR. The BM option also provides crop residue for the addition of organic matter. This result suggests that BM is a potential alternative of herbicide application. Either mulching with Eupatorium and wheat straw or growing of Sesbania and Crotolaria as BM with rice up to 30 DAS are advisable to increase productivity with reduced cost of production at Chitwan and similar condition. Agronomy Journal of Nepal (Agron JN) Vol. 3. 2013, Page 73-81 DOI: http://dx.doi.org/10.3126/ajn.v3i0.9008
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