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Asea G, Kwemoi DB, Sneller C, Kasozi CL, Das B, Musundire L, Makumbi D, Beyene Y, Prasanna BM. Genetic trends for yield and key agronomic traits in pre-commercial and commercial maize varieties between 2008 and 2020 in Uganda. Front Plant Sci 2023; 14:1020667. [PMID: 36968404 PMCID: PMC10036907 DOI: 10.3389/fpls.2023.1020667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Estimating genetic gains is vital to optimize breeding programs for increased efficiency. Genetic gains should translate into productivity gains if returns to investments in breeding and impact are to be realized. The objective of this study was to estimate genetic gain for grain yield and key agronomic traits in pre-commercial and commercial maize varieties from public and private breeding programs tested in (i) national performance trials (NPT), (ii) era trial and, (iii) compare the trends with the national average. The study used (i) historical NPT data on 419 improved maize varieties evaluated in 23 trials at 6-8 locations each between 2008 and 2020, and (ii) data from an era trial of 54 maize hybrids released between 1999 and 2020. The NPT data was first analyzed using a mixed model and resulting estimate for each entry was regressed onto its first year of testing. Analysis was done over all entries, only entries from National Agricultural Research Organization (NARO), International Maize and Wheat Improvement Center (CIMMYT), or private seed companies. Estimated genetic gain was 2.25% or 81 kg ha-1 year-1 from the NPT analysis. A comparison of genetic trends by source indicated that CIMMYT entries had a gain of 1.98% year-1 or 106 kg ha-1 year-1. In contrast, NARO and private sector maize entries recorded genetic gains of 1.30% year-1 (59 kg ha-1 year-1) and 1.71% year-1 (79 kg ha-1 year-1), respectively. Varieties from NARO and private sector showed comparable mean yields of 4.56 t ha-1 and 4.62 t ha-1, respectively, while hybrids from CIMMYT had a mean of 5.37 t ha-1. Era analysis indicated significant genetic gain of 1.69% year-1 or 55 kg ha-1 year-1, while a significant national productivity gain of 1.48% year-1 (37 kg ha-1 year-1) was obtained. The study, thus, demonstrated the importance of public-private partnerships in development and delivery of new genetics to farmers in Uganda.
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Affiliation(s)
- Godfrey Asea
- National Crops Resources Research Institute, National Agricultural Research Organization, Kampala, Uganda
| | - Daniel Bomet Kwemoi
- National Crops Resources Research Institute, National Agricultural Research Organization, Kampala, Uganda
| | - Clay Sneller
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, United States
| | - Charles L. Kasozi
- National Crops Resources Research Institute, National Agricultural Research Organization, Kampala, Uganda
| | - Biswanath Das
- Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Lennin Musundire
- Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Dan Makumbi
- Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Yoseph Beyene
- Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Boddupalli M. Prasanna
- Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
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Malik P, Huang M, Neelam K, Bhatia D, Kaur R, Yadav B, Singh J, Sneller C, Singh K. Genotyping-by-Sequencing Based Investigation of Population Structure and Genome Wide Association Studies for Seven Agronomically Important Traits in a Set of 346 Oryza rufipogon Accessions. Rice (N Y) 2022; 15:37. [PMID: 35819660 PMCID: PMC9276952 DOI: 10.1186/s12284-022-00582-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Being one of the most important staple dietary constituents globally, genetic enhancement of cultivated rice for yield, agronomically important traits is of substantial importance. Even though the climatic factors and crop management practices impact complex traits like yield immensely, the contribution of variation by underlying genetic factors surpasses them all. Previous studies have highlighted the importance of utilizing exotic germplasm, landraces in enhancing the diversity of gene pool, leading to better selections and thus superior cultivars. Thus, to fully exploit the potential of progenitor of Asian cultivated rice for productivity related traits, genome wide association study (GWAS) for seven agronomically important traits was conducted on a panel of 346 O. rufipogon accessions using a set of 15,083 high-quality single nucleotide polymorphic markers. The phenotypic data analysis indicated large continuous variation for all the traits under study, with a significant negative correlation observed between grain parameters and agronomic parameters like plant height, culm thickness. The presence of 74.28% admixtures in the panel as revealed by investigating population structure indicated the panel to be very poorly genetically differentiated, with rapid LD decay. The genome-wide association analyses revealed a total of 47 strong MTAs with 19 SNPs located in/close to previously reported QTL/genic regions providing a positive analytic proof for our studies. The allelic differences of significant MTAs were found to be statistically significant at 34 genomic regions. A total of 51 O. rufipogon accessions harboured combination of superior alleles and thus serve as potential candidates for accelerating rice breeding programs. The present study identified 27 novel SNPs to be significantly associated with different traits. Allelic differences between cultivated and wild rice at significant MTAs determined superior alleles to be absent at 12 positions implying substantial scope of improvement by their targeted introgression into cultivars. Introgression of novel significant genomic regions into breeder's pool would broaden the genetic base of cultivated rice, thus making the crop more resilient.
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Affiliation(s)
- Palvi Malik
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- Department of Horticulture and Crop Science, OARDC, The Ohio State University, Wooster, USA
| | - Mao Huang
- Department of Horticulture and Crop Science, OARDC, The Ohio State University, Wooster, USA
| | - Kumari Neelam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Ramanjeet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Bharat Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- Crop Pathology and Genetics Lab, University of British Columbia, Vancouver, Canada
| | - Jasdeep Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Clay Sneller
- Department of Horticulture and Crop Science, OARDC, The Ohio State University, Wooster, USA
| | - Kuldeep Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
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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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Stanley AE, Menkir A, Ifie B, Paterne AA, Unachukwu NN, Meseka S, Mengesha WA, Bossey B, Kwadwo O, Tongoona PB, Oladejo O, Sneller C, Gedil M. Association analysis for resistance to Striga hermonthica in diverse tropical maize inbred lines. Sci Rep 2021; 11:24193. [PMID: 34921181 PMCID: PMC8683441 DOI: 10.1038/s41598-021-03566-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/18/2021] [Indexed: 11/25/2022] Open
Abstract
Striga hermonthica is a widespread, destructive parasitic plant that causes substantial yield loss to maize productivity in sub-Saharan Africa. Under severe Striga infestation, yield losses can range from 60 to 100% resulting in abandonment of farmers’ lands. Diverse methods have been proposed for Striga management; however, host plant resistance is considered the most effective and affordable to small-scale famers. Thus, conducting a genome-wide association study to identify quantitative trait nucleotides controlling S. hermonthica resistance and mining of relevant candidate genes will expedite the improvement of Striga resistance breeding through marker-assisted breeding. For this study, 150 diverse maize inbred lines were evaluated under Striga infested and non-infested conditions for two years and genotyped using the genotyping-by-sequencing platform. Heritability estimates of Striga damage ratings, emerged Striga plants and grain yield, hereafter referred to as Striga resistance-related traits, were high under Striga infested condition. The mixed linear model (MLM) identified thirty SNPs associated with the three Striga resistance-related traits based on the multi-locus approaches (mrMLM, FASTmrMLM, FASTmrEMMA and pLARmEB). These SNPs explained up to 14% of the total phenotypic variation. Under non-infested condition, four SNPs were associated with grain yield, and these SNPs explained up to 17% of the total phenotypic variation. Gene annotation of significant SNPs identified candidate genes (Leucine-rich repeats, putative disease resistance protein and VQ proteins) with functions related to plant growth, development, and defense mechanisms. The marker-effect prediction was able to identify alleles responsible for predicting high yield and low Striga damage rating in the breeding panel. This study provides valuable insight for marker validation and deployment for Striga resistance breeding in maize.
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Affiliation(s)
- A E Stanley
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana.,International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - A Menkir
- International Institute of Tropical Agriculture, Ibadan, Nigeria.
| | - B Ifie
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - A A Paterne
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - N N Unachukwu
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - S Meseka
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - W A Mengesha
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - B Bossey
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - O Kwadwo
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - P B Tongoona
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - O Oladejo
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - C Sneller
- Ohio Agriculture Research and Development Center, Ohio State University, Wooster, OH, USA
| | - M Gedil
- International Institute of Tropical Agriculture, Ibadan, Nigeria
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Borrenpohl D, Huang M, Olson E, Sneller C. The value of early-stage phenotyping for wheat breeding in the age of genomic selection. Theor Appl Genet 2020; 133:2499-2520. [PMID: 32488300 DOI: 10.1007/s00122-020-03613-0] [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: 10/08/2019] [Accepted: 05/15/2020] [Indexed: 06/11/2023]
Abstract
Genomic selection using data from an on-going breeding program can improve gain from selection, relative to phenotypic selection, by significantly increasing the number of lines that can be evaluated. The early stages of phenotyping involve few observations and can be quite inaccurate. Genomic selection (GS) could improve selection accuracy and alter resource allocation. Our objectives were (1) to compare the prediction accuracy of GS and phenotyping in stage-1 and stage-2 field evaluations and (2) to assess the value of stage-1 phenotyping for advancing lines to stage-2 testing. We built training populations from 1769 wheat breeding lines that were genotyped and phenotyped for yield, test weight, Fusarium head blight resistance, heading date, and height. The lines were in cohorts, and analyses were done by cohort. Phenotypes or GS estimated breeding values were used to determine the trait value of stage-1 lines, and these values were correlated with their phenotypes from stage-2 trials. This was repeated for stage-2 to stage-3 trials. The prediction accuracy of GS and phenotypes was similar to each other regardless of the amount (0, 50, 100%) of stage-1 data incorporated in the GS model. Ranking of stage-1 lines by GS predictions that used no stage-1 phenotypic data had marginally lower correspondence to stage-2 phenotypic rankings than rankings of stage-1 lines based on phenotypes. Stage-1 lines ranked high by GS had slightly inferior phenotypes in stage-2 trials than lines ranked high by phenotypes. Cost analysis indicated that replacing stage-1 phenotyping with GS would allow nearly three times more stage-1 candidates to be assessed and provide 0.84-2.23 times greater gain from selection. We conclude that GS can complement or replace phenotyping in early stages of phenotyping.
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Affiliation(s)
- Daniel Borrenpohl
- Department of Horticulture and Crop Science, Ohio Agriculture Research and Development Center, The Ohio State University, 1680 Madison Av, Wooster, OH, 44691, USA
| | - Mao Huang
- Department of Horticulture and Crop Science, Ohio Agriculture Research and Development Center, The Ohio State University, 1680 Madison Av, Wooster, OH, 44691, USA
| | - Eric Olson
- Department of Plant, Soil, and Microbial Science, Michigan State University, 1066 Bogue St, East Lansing, MI, 48824, USA
| | - Clay Sneller
- Department of Horticulture and Crop Science, Ohio Agriculture Research and Development Center, The Ohio State University, 1680 Madison Av, Wooster, OH, 44691, USA.
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Akohoue F, Achigan-Dako EG, Sneller C, Van Deynze A, Sibiya J. Genetic diversity, SNP-trait associations and genomic selection accuracy in a west African collection of Kersting's groundnut [Macrotyloma geocarpum(Harms) Maréchal & Baudet]. PLoS One 2020; 15:e0234769. [PMID: 32603370 PMCID: PMC7326195 DOI: 10.1371/journal.pone.0234769] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/02/2020] [Indexed: 11/19/2022] Open
Abstract
Understanding the mechanisms governing complex traits variation is a requirement for efficient crop improvement. In this study, the molecular characterization, marker-trait associations and the possibility for genomic selection in a collection of 281 Kersting's groundnut accessions were carried out. The diversity panel was phenotyped using an Alpha lattice design with two replicates in two contrasting environments. Accessions were genotyped using genotyping by sequencing technology. Genome-wide association analyses were performed between single nucleotide polymorphism markers and yield-related traits across tested environments. SNP markers were used to calculate the observed (Ho) and expected heterozygosity (He), and the total gene diversity (Ht). Genetic differentiation among accessions across ecological regions of origin was analysed. Our results revealed 493 quality SNPs of which 113 had a minor allele frequency>0.05, a total gene diversity of 0.43 and average Ho and He values of 0.04 and 0.22, respectively. Four clusters, highly differentiated by seed coat colour (Fst = 0.79), were identified. The population structure analysis showed two subpopulations with high differentiation across ecological regions (Fst = 0.37). The GWAS revealed 10 significant marker-trait associations, of which six SNPs were consistent across environments. The genomic selection through cross-validation showed moderate to high prediction accuracies for leaflet length, seed dimension traits, 100 seed weight, days to 50% flowering and days to maturity. This demonstrates the existence of genetic variability within Kersting's groundnut and shows the potential for the improvement of the species. The findings also provide a first insight into the phenotype-to-genotype relationships in Kersting's groundnut, using SNP markers.
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Affiliation(s)
- Félicien Akohoue
- Laboratory of Genetics, Horticulture and Seed Science, Faculty of Agronomic Sciences, University of Abomey-Calavi, Cotonou, Republic of Benin
- School of Agriculture, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, Republic of South Africa
| | - Enoch Gbenato Achigan-Dako
- Laboratory of Genetics, Horticulture and Seed Science, Faculty of Agronomic Sciences, University of Abomey-Calavi, Cotonou, Republic of Benin
| | - Clay Sneller
- Biosciences Eastern and Central Africa (BecA) Hub, International Livestock Research Institute, Nairobi, Kenya
| | - Allen Van Deynze
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Julia Sibiya
- School of Agriculture, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, Republic of South Africa
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Garcia-Santamaria G, Hua D, Sneller C. Quantitative trait loci associated with soft wheat quality in a cross of good by moderate quality parents. PeerJ 2018; 6:e4498. [PMID: 29593939 PMCID: PMC5868479 DOI: 10.7717/peerj.4498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/21/2018] [Indexed: 11/20/2022] Open
Abstract
Information on the genetic control of the quality traits of soft wheat (Triticum aestivum) is essential for breeding. Our objective was to identify QTL associated with end-use quality. We developed 150 F4-derived lines from a cross of Pioneer 26R46 × SS550 and tested them in four environments. We measured flour yield (FY), softness equivalent (SE), test weight (TW), flour protein content (FP), alkaline water retention capacity (AWRC), and solvent retention capacity (SRC) of water (WA), lactic acid (LA), sucrose (SU), sodium carbonate (SO). Parents differed for nine traits, transgressive segregants were noted, and heritability was high (0.67 to 0.90) for all traits. We detected QTL distributed on eight genomic regions. The QTL with the greatest effects were located on chromosome 1A, 1B, and 6B with each affecting at least five of ten quality traits. Pioneer 26R46 is one of the best quality soft wheats. The large-effect QTL on 1A novel and accounted for much of the variation for AWRC (r2 = 0.26), SO (0.26) and SE (0.25), and FY (0.15) and may explain why Pioneer 26R46 has such superior quality. All alleles that increased a trait came from the parent with the highest trait value. This suggests that in any population that marker-assisted selection for these quality traits could be conducted by simply selecting for the alleles at key loci from the parent with the best phenotype without prior mapping.
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Affiliation(s)
| | - Duc Hua
- Department of Horticulture and Crop Sciences, Ohio State University-Wooster, Wooster, OH, United States of America
| | - Clay Sneller
- Department of Horticulture and Crop Sciences, Ohio State University-Wooster, Wooster, OH, United States of America
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Mgonja EM, Park CH, Kang H, Balimponya EG, Opiyo S, Bellizzi M, Mutiga SK, Rotich F, Ganeshan VD, Mabagala R, Sneller C, Correll J, Zhou B, Talbot NJ, Mitchell TK, Wang GL. Genotyping-by-Sequencing-Based Genetic Analysis of African Rice Cultivars and Association Mapping of Blast Resistance Genes Against Magnaporthe oryzae Populations in Africa. Phytopathology 2017; 107:1039-1046. [PMID: 28719243 DOI: 10.1094/phyto-12-16-0421-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding the genetic diversity of rice germplasm is important for the sustainable use of genetic materials in rice breeding and production. Africa is rich in rice genetic resources that can be utilized to boost rice productivity on the continent. A major constraint to rice production in Africa is rice blast, caused by the hemibiotrophic fungal pathogen Magnaporthe oryzae. In this report, we present the results of a genotyping-by-sequencing (GBS)-based diversity analysis of 190 African rice cultivars and an association mapping of blast resistance (R) genes and quantitative trait loci (QTLs). The 190 African cultivars were clustered into three groups based on the 184K single nucleotide polymorphisms generated by GBS. We inoculated the rice cultivars with six African M. oryzae isolates. Association mapping identified 25 genomic regions associated with blast resistance (RABRs) in the rice genome. Moreover, PCR analysis indicated that RABR_23 is associated with the Pi-ta gene on chromosome 12. Our study demonstrates that the combination of GBS-based genetic diversity population analysis and association mapping is effective in identifying rice blast R genes/QTLs that contribute to resistance against African populations of M. oryzae. The identified markers linked to the RABRs and 14 highly resistant cultivars in this study will be useful for rice breeding in Africa.
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Affiliation(s)
- Emmanuel M Mgonja
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Chan Ho Park
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Houxiang Kang
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Elias G Balimponya
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Stephen Opiyo
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Maria Bellizzi
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Samuel K Mutiga
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Felix Rotich
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Veena Devi Ganeshan
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Robert Mabagala
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Clay Sneller
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Jim Correll
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Bo Zhou
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Nicholas J Talbot
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Thomas K Mitchell
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Guo-Liang Wang
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
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9
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Mgonja EM, Balimponya EG, Kang H, Bellizzi M, Park CH, Li Y, Mabagala R, Sneller C, Correll J, Opiyo S, Talbot NJ, Mitchell T, Wang GL. Genome-Wide Association Mapping of Rice Resistance Genes Against Magnaporthe oryzae Isolates from Four African Countries. Phytopathology 2016; 106:1359-1365. [PMID: 27454702 DOI: 10.1094/phyto-01-16-0028-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Rice blast disease is emerging as a major constraint to rice production in Africa. Although a traditional gene-tagging strategy using biparental crosses can effectively identify resistance (R) genes or quantitative trait loci (QTL) against Magnaporthe oryzae, the mapping procedure required is time consuming and requires many populations to investigate the genetics of resistance. In this report, we conducted a genome-wide association study (GWAS) to rapidly map rice genes conferring resistance against eight M. oryzae isolates from four African countries. We inoculated 162 rice cultivars, which were part of the rice diversity panel 1 (RDP1) and were previously genotyped with the 44,000 single-nucleotide polymorphism (SNP) chip, with the eight isolates. The GWAS identified 31 genomic regions associated with blast resistance (RABR) in the rice genome. In addition, we used polymerase chain reaction analysis to confirm the association between the Pish gene and a major RABR on chromosome 1 that was associated with resistance to four M. oryzae isolates. Our study has demonstrated the power of GWAS for the rapid identification of rice blast R or QTL genes that are effective against African populations of M. oryzae. The identified SNP markers associated with RABR can be used in breeding for resistance against rice blast in Africa.
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Affiliation(s)
- Emmanuel M Mgonja
- First, fourth, fifth, sixth, tenth, twelfth, and thirteenth authors: Department of Plant Pathology, and second and eighth authors: Department of Horticulture and Crop Science, The Ohio State University, Columbus; third and thirteenth authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing; seventh author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and eleventh author: School of Biosciences, University of Exeter, UK
| | - Elias G Balimponya
- First, fourth, fifth, sixth, tenth, twelfth, and thirteenth authors: Department of Plant Pathology, and second and eighth authors: Department of Horticulture and Crop Science, The Ohio State University, Columbus; third and thirteenth authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing; seventh author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and eleventh author: School of Biosciences, University of Exeter, UK
| | - Houxiang Kang
- First, fourth, fifth, sixth, tenth, twelfth, and thirteenth authors: Department of Plant Pathology, and second and eighth authors: Department of Horticulture and Crop Science, The Ohio State University, Columbus; third and thirteenth authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing; seventh author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and eleventh author: School of Biosciences, University of Exeter, UK
| | - Maria Bellizzi
- First, fourth, fifth, sixth, tenth, twelfth, and thirteenth authors: Department of Plant Pathology, and second and eighth authors: Department of Horticulture and Crop Science, The Ohio State University, Columbus; third and thirteenth authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing; seventh author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and eleventh author: School of Biosciences, University of Exeter, UK
| | - Chan Ho Park
- First, fourth, fifth, sixth, tenth, twelfth, and thirteenth authors: Department of Plant Pathology, and second and eighth authors: Department of Horticulture and Crop Science, The Ohio State University, Columbus; third and thirteenth authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing; seventh author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and eleventh author: School of Biosciences, University of Exeter, UK
| | - Ya Li
- First, fourth, fifth, sixth, tenth, twelfth, and thirteenth authors: Department of Plant Pathology, and second and eighth authors: Department of Horticulture and Crop Science, The Ohio State University, Columbus; third and thirteenth authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing; seventh author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and eleventh author: School of Biosciences, University of Exeter, UK
| | - Robert Mabagala
- First, fourth, fifth, sixth, tenth, twelfth, and thirteenth authors: Department of Plant Pathology, and second and eighth authors: Department of Horticulture and Crop Science, The Ohio State University, Columbus; third and thirteenth authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing; seventh author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and eleventh author: School of Biosciences, University of Exeter, UK
| | - Clay Sneller
- First, fourth, fifth, sixth, tenth, twelfth, and thirteenth authors: Department of Plant Pathology, and second and eighth authors: Department of Horticulture and Crop Science, The Ohio State University, Columbus; third and thirteenth authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing; seventh author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and eleventh author: School of Biosciences, University of Exeter, UK
| | - Jim Correll
- First, fourth, fifth, sixth, tenth, twelfth, and thirteenth authors: Department of Plant Pathology, and second and eighth authors: Department of Horticulture and Crop Science, The Ohio State University, Columbus; third and thirteenth authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing; seventh author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and eleventh author: School of Biosciences, University of Exeter, UK
| | - Stephen Opiyo
- First, fourth, fifth, sixth, tenth, twelfth, and thirteenth authors: Department of Plant Pathology, and second and eighth authors: Department of Horticulture and Crop Science, The Ohio State University, Columbus; third and thirteenth authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing; seventh author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and eleventh author: School of Biosciences, University of Exeter, UK
| | - Nicholas J Talbot
- First, fourth, fifth, sixth, tenth, twelfth, and thirteenth authors: Department of Plant Pathology, and second and eighth authors: Department of Horticulture and Crop Science, The Ohio State University, Columbus; third and thirteenth authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing; seventh author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and eleventh author: School of Biosciences, University of Exeter, UK
| | - Thomas Mitchell
- First, fourth, fifth, sixth, tenth, twelfth, and thirteenth authors: Department of Plant Pathology, and second and eighth authors: Department of Horticulture and Crop Science, The Ohio State University, Columbus; third and thirteenth authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing; seventh author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and eleventh author: School of Biosciences, University of Exeter, UK
| | - Guo-Liang Wang
- First, fourth, fifth, sixth, tenth, twelfth, and thirteenth authors: Department of Plant Pathology, and second and eighth authors: Department of Horticulture and Crop Science, The Ohio State University, Columbus; third and thirteenth authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing; seventh author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and eleventh author: School of Biosciences, University of Exeter, UK
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10
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Huang M, Cabrera A, Hoffstetter A, Griffey C, Van Sanford D, Costa J, McKendry A, Chao S, Sneller C. Genomic selection for wheat traits and trait stability. Theor Appl Genet 2016; 129:1697-710. [PMID: 27262436 DOI: 10.1007/s00122-016-2733-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/21/2016] [Indexed: 05/02/2023]
Abstract
Based on the estimates of accuracy, genomic selection would be useful for selecting for improved trait values and trait stability for agronomic and quality traits in wheat. Trait values and trait stability estimated by two methods were generally independent indicating a breeder could select for both simultaneously. Genomic selection (GS) is a new marker-assisted selection tool for breeders to achieve higher genetic gain faster and cheaper. Breeders face challenges posed by genotype by environment interaction (GEI) pattern and selecting for trait stability. Obtaining trait stability is costly, as it requires data from multiple environments. There are few studies that evaluate the efficacy of GS for predicting trait stability. A soft winter wheat population of 273 lines was genotyped with 90 K single nucleotide polymorphism markers and phenotyped for four agronomic and seven quality traits. Additive main effect and multiplicative interaction (AMMI) model and Eberhart and Russell regression (ERR) were used to estimate trait stability. Significant GEI variation was observed and stable lines were identified for all traits in this study. The accuracy of GS ranged from 0.33 to 0.67 for most traits and trait stability. Accuracy of trait stability was greater than trait itself for yield (0.44 using AMMI versus 0.33) and heading date (0.65 using ERR versus 0.56). The opposite trend was observed for the other traits. GS did not predict the stability of the quality traits except for flour protein, lactic acid and softness equivalent. Significant GS accuracy for some trait stability indicated that stability was under genetic control for these traits. The magnitude of GS accuracies for all the traits and most of the trait stability index suggests the possibility of rapid selection for these trait and trait stability in wheat breeding.
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Affiliation(s)
- Mao Huang
- Ohio Agriculture Research and Development Center, The Ohio State University, 1680 Madison Ave., Wooster, OH, 44691, USA
| | - Antonio Cabrera
- Ohio Agriculture Research and Development Center, The Ohio State University, 1680 Madison Ave., Wooster, OH, 44691, USA
| | - Amber Hoffstetter
- Ohio Agriculture Research and Development Center, The Ohio State University, 1680 Madison Ave., Wooster, OH, 44691, USA
| | - Carl Griffey
- University of Virginia Tech, 185 Ag Quad Lane, Blacksburg, VA, 24061, USA
| | - David Van Sanford
- University of Kentucky, 1405 Veterans Drive, Lexington, KY, 40546, USA
| | | | | | - Shiaoman Chao
- Cereal Crops Research Unit, USDA-ARS, Fargo, ND, 58102, USA
| | - Clay Sneller
- Ohio Agriculture Research and Development Center, The Ohio State University, 1680 Madison Ave., Wooster, OH, 44691, USA.
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11
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Crossa J, Jarquín D, Franco J, Pérez-Rodríguez P, Burgueño J, Saint-Pierre C, Vikram P, Sansaloni C, Petroli C, Akdemir D, Sneller C, Reynolds M, Tattaris M, Payne T, Guzman C, Peña RJ, Wenzl P, Singh S. Genomic Prediction of Gene Bank Wheat Landraces. G3 (Bethesda) 2016; 6:1819-34. [PMID: 27172218 PMCID: PMC4938637 DOI: 10.1534/g3.116.029637] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/15/2016] [Indexed: 12/30/2022]
Abstract
This study examines genomic prediction within 8416 Mexican landrace accessions and 2403 Iranian landrace accessions stored in gene banks. The Mexican and Iranian collections were evaluated in separate field trials, including an optimum environment for several traits, and in two separate environments (drought, D and heat, H) for the highly heritable traits, days to heading (DTH), and days to maturity (DTM). Analyses accounting and not accounting for population structure were performed. Genomic prediction models include genotype × environment interaction (G × E). Two alternative prediction strategies were studied: (1) random cross-validation of the data in 20% training (TRN) and 80% testing (TST) (TRN20-TST80) sets, and (2) two types of core sets, "diversity" and "prediction", including 10% and 20%, respectively, of the total collections. Accounting for population structure decreased prediction accuracy by 15-20% as compared to prediction accuracy obtained when not accounting for population structure. Accounting for population structure gave prediction accuracies for traits evaluated in one environment for TRN20-TST80 that ranged from 0.407 to 0.677 for Mexican landraces, and from 0.166 to 0.662 for Iranian landraces. Prediction accuracy of the 20% diversity core set was similar to accuracies obtained for TRN20-TST80, ranging from 0.412 to 0.654 for Mexican landraces, and from 0.182 to 0.647 for Iranian landraces. The predictive core set gave similar prediction accuracy as the diversity core set for Mexican collections, but slightly lower for Iranian collections. Prediction accuracy when incorporating G × E for DTH and DTM for Mexican landraces for TRN20-TST80 was around 0.60, which is greater than without the G × E term. For Iranian landraces, accuracies were 0.55 for the G × E model with TRN20-TST80. Results show promising prediction accuracies for potential use in germplasm enhancement and rapid introgression of exotic germplasm into elite materials.
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Affiliation(s)
- José Crossa
- Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico
| | - Diego Jarquín
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 321 Keim Hall, Lincoln, Nebraska 68583-0915
| | - Jorge Franco
- Departamento de Biometría, Estadística y Computación, Facultad de Agronomía, Universidad de la República (Udelar), Paysandú, Uruguay
| | | | - Juan Burgueño
- Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico
| | - Carolina Saint-Pierre
- Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico
| | - Prashant Vikram
- Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico
| | - Carolina Sansaloni
- Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico
| | - Cesar Petroli
- Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico
| | - Deniz Akdemir
- Department of Plant Breeding & Genetics, Cornell University, Ithaca, New York 14853
| | - Clay Sneller
- Department of Horticulture and Crop Science, Ohio State University, Wooster, Ohio 44691
| | - Matthew Reynolds
- Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico
| | - Maria Tattaris
- Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico
| | - Thomas Payne
- Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico
| | - Carlos Guzman
- Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico
| | - Roberto J Peña
- Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico
| | - Peter Wenzl
- Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico
| | - Sukhwinder Singh
- Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico
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12
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Vikram P, Franco J, Burgueño-Ferreira J, Li H, Sehgal D, Pierre CS, Ortiz C, Sneller C, Tattaris M, Guzman C, Sansaloni CP, Ellis M, Fuentes-Davila G, Reynolds M, Sonder K, Singh P, Payne T, Wenzl P, Sharma A, Bains NS, Singh GP, Crossa J, Singh S. Corrigendum: Unlocking the genetic diversity of Creole wheats. Sci Rep 2016; 6:26216. [PMID: 27198041 PMCID: PMC4873783 DOI: 10.1038/srep26216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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13
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Cabrera A, Guttieri M, Smith N, Souza E, Sturbaum A, Hua D, Griffey C, Barnett M, Murphy P, Ohm H, Uphaus J, Sorrells M, Heffner E, Brown-Guedira G, Van Sanford D, Sneller C. Identification of milling and baking quality QTL in multiple soft wheat mapping populations. Theor Appl Genet 2015; 128:2227-2242. [PMID: 26188588 DOI: 10.1007/s00122-015-2580-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/07/2015] [Indexed: 06/04/2023]
Abstract
Two mapping approaches were use to identify and validate milling and baking quality QTL in soft wheat. Two LG were consistently found important for multiple traits and we recommend the use marker-assisted selection on specific markers reported here. Wheat-derived food products require a range of characteristics. Identification and understanding of the genetic components controlling end-use quality of wheat is important for crop improvement. We assessed the underlying genetics controlling specific milling and baking quality parameters of soft wheat including flour yield, softness equivalent, flour protein, sucrose, sodium carbonate, water absorption and lactic acid, solvent retention capacities in a diversity panel and five bi-parental mapping populations. The populations were genotyped with SSR and DArT markers, with markers specific for the 1BL.1RS translocation and sucrose synthase gene. Association analysis and composite interval mapping were performed to identify quantitative trait loci (QTL). High heritability was observed for each of the traits evaluated, trait correlations were consistent over populations, and transgressive segregants were common in all bi-parental populations. A total of 26 regions were identified as potential QTL in the diversity panel and 74 QTL were identified across all five bi-parental mapping populations. Collinearity of QTL from chromosomes 1B and 2B was observed across mapping populations and was consistent with results from the association analysis in the diversity panel. Multiple regression analysis showed the importance of the two 1B and 2B regions and marker-assisted selection for the favorable alleles at these regions should improve quality.
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Affiliation(s)
- Antonio Cabrera
- Department of Horticulture and Crop Science, The Ohio State University and the Ohio Agriculture Research and Development Center, 1680 Madison Ave, Wooster, OH, 44691, USA.
| | - Mary Guttieri
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Kein Hall, Lincoln, NE, 68583-0915, USA
| | - Nathan Smith
- BHN Research, P. O. Box 3267, Immokalee, FL, 34143, USA
| | - Edward Souza
- Bayer Crop Science LP, 202 Keim Hall, Lincoln, NE, USA
| | - Anne Sturbaum
- Soft Wheat Quality Laboratory, USDA Agricultural Research Service, Wooster, OH, 44691, USA
| | - Duc Hua
- Department of Horticulture and Crop Science, The Ohio State University and the Ohio Agriculture Research and Development Center, 1680 Madison Ave, Wooster, OH, 44691, USA
| | - Carl Griffey
- Department of Crop and Soil Environmental Sciences, Virginia Polytechnic Institute, State University, Blacksburg, VA, 24061, USA
| | - Marla Barnett
- Limagrain Cereal Seeds LLC, 6414 N Sheridian, Wichita, KS, 67204, USA
| | - Paul Murphy
- Department of Crop Science, North Carolina State University, Campus Box 7620, Raleigh, NC, 27695-7620, USA
| | - Herb Ohm
- Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
| | - Jim Uphaus
- Pioneer HiBreed International, INC., Windfall, IN, USA
| | - Mark Sorrells
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Elliot Heffner
- DuPont Pioneer Hi Bred International Inc, Des Moines, IA, 50316, USA
| | | | - David Van Sanford
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
| | - Clay Sneller
- Department of Horticulture and Crop Science, The Ohio State University and the Ohio Agriculture Research and Development Center, 1680 Madison Ave, Wooster, OH, 44691, USA.
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Sneller C, Guttieri M, Paul P, Costa J, Jackwood R. Variation for resistance to kernel infection and toxin accumulation in winter wheat infected with Fusarium graminearum. Phytopathology 2012; 102:306-314. [PMID: 21848396 DOI: 10.1094/phyto-05-11-0143] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Host resistance is the main way to control Fusarium head blight (FHB) in wheat. Despite improved levels of resistance to infection and spread in vegetative tissue, the toxin deoxynivalenol (DON) can still accumulate to unacceptable concentration levels. In this study, our objectives were to assess the genetic variation for resistance to kernel infection (RKI) and resistance to toxin accumulation (RTA) and their role in controlling DON. We collected spikes with different levels of visual symptoms from each of 32 wheat genotypes and at four environments and determined DON and fungal biomass (FB) from each sample. We assessed RKI by regressing FB on the level of visual symptoms and RTA by regressing DON on FB for each genotype. Significant genetic effects were found for RKI and RTA. Some genotypes consistently had low FB in their grain despite increasing visual symptoms suggesting RKI. Additionally, some genotypes consistently had low DON in their grain despite increasing FB levels suggesting a higher RTA in these genotypes. The variation for RKI and RTA explained a significant fraction of the variation for DON among genotypes with moderate visual symptoms using independent grain samples. Although RKI and RTA were significantly correlated (r = 0.58, P = 0.05), RTA was more predictive of DON accumulation because it modeled 32 to 44% of the genotype sum of squares for DON, while only 9 to 10% were predicted using RKI. Thus, variation for RTA was important in explaining variation for DON among genotypes with acceptable levels of resistance to fungal infection and spread. This work indicates that there is a need to develop a better understanding of RTA and rapid screening methods for this trait.
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Affiliation(s)
- Clay Sneller
- Department of Horticulture and Crop Science, The Ohio State University and the Ohio Agriculture Research and Development Center, Wooster, Ohio 44691, USA.
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Affiliation(s)
- Edward J. Souza
- United States Department of Agriculture, Agricultural Research Service, Soft Wheat Quality Laboratory, Wooster, OH 44691
- Corresponding author. E-mail:
| | - Mary J. Guttieri
- Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
| | - Clay Sneller
- Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
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Affiliation(s)
- Edward J. Souza
- United States Department of Agriculture, Agricultural Research Service, Soft Wheat Quality Laboratory, Wooster, OH 44691
- Corresponding author. E-mail:
| | - Mary Guttieri
- Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
| | - Clay Sneller
- Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
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Affiliation(s)
- Mary J. Guttieri
- The Ohio State University, Ohio Agricultural Research and Development Center
| | - Edward J. Souza
- United States Department of Agriculture, Agricultural Research Service, Soft Wheat Quality Laboratory, Wooster, OH 44691
- Corresponding author. E-mail:
| | - Clay Sneller
- The Ohio State University, Ohio Agricultural Research and Development Center
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Abstract
Nonstarch polysaccharides in wheat flour have significant capacity to affect the processing quality of wheat flour dough and the finished quality of wheat flour products. Most research has focused on the effects of arabinoxylans (AX) in bread making. This study found that water-extractable AX and arabinogalactan peptides can predict variation in pastry wheat quality as captured by the wire-cut cookie model system. The sum of water-extractable AX plus arabinogalactan was highly predictive of cookie spread factor. The combination of cookie spread factor and the ratio of water-extractable arabinose to xylose predicted peak force of the three-point bend test of cookie texture.
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Affiliation(s)
- Mary J Guttieri
- US Department of Agriculture, Agricultural Research Service, Soft Wheat Quality Laboratory, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio 44691, USA
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Browne RA, Murphy JP, Cooke BM, Devaney D, Walsh EJ, Griffey CA, Hancock JA, Harrison SA, Hart P, Kolb FL, McKendry AL, Milus EA, Sneller C, Van Sanford DA. Evaluation of Components of Fusarium Head Blight Resistance in Soft Red Winter Wheat Germ Plasm Using a Detached Leaf Assay. Plant Dis 2005; 89:404-411. [PMID: 30795457 DOI: 10.1094/pd-89-0404] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A large environmental influence on phenotypic estimates of disease resistance and the complex polygenic nature of Fusarium head blight (FHB) resistance in wheat (Triticum aestivum) are impediments to developing resistant cultivars. The objective of this research was to investigate the utility of a detached leaf assay, inoculated using inoculum from isolates of Microdochium nivale var. majus, to identify components of FHB resistance among 30 entries of U.S. soft red winter wheat in the 2002 Uniform Southern FHB Nursery (USFHBN). Whole plant FHB resistance of the USFHBN entries was evaluated in replicated, mist-irrigated field trials at 10 locations in eight states during the 2001-2002 season. Incubation period (days from inoculation to the first appearance of a dull gray-green water-soaked lesion) was the only detached leaf variable significantly correlated across all FHB resistance parameters accounting for 45% of the variation in FHB incidence, 27% of FHB severity, 30% of Fusarium damaged kernels, and 26% of the variation in grain deoxynivalenol (DON) concentration. The results for incubation period contrasted with previous studies of moderately resistant European cultivars, in that longer incubation period was correlated with greater FHB susceptibility, but agreed with previous findings for the Chinese cultivar Sumai 3 and CIMMYT germ plasm containing diverse sources of FHB resistance. The results support the view that the detached leaf assay method has potential for use to distinguish between specific sources of FHB resistance when combined with data on FHB reaction and pedigree information. For example, entry 28, a di-haploid line from the cross between the moderately resistant U.S. cultivar Roane and the resistant Chinese line W14, exhibited detached leaf parameters that suggested a combination of both sources of FHB resistance. The USFHBN represents the combination of adapted and exotic germ plasm, but four moderately resistant U.S. commercial cultivars (Roane, McCormick, NC-Neuse, and Pat) had long incubation and latent periods and short lesion lengths in the detached leaf assay as observed in moderately FHB resistant European cultivars. The dichotomy in the relationship between incubation period and FHB resistance indicates that this may need to be considered to effectively combine exotic and existing/adapted sources of FHB resistance.
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Affiliation(s)
- R A Browne
- Department of Environmental Resource Management, University College Dublin, Belfield, Dublin 4, Ireland
| | - J P Murphy
- Department of Crop Science, North Carolina State University, Raleigh 27695
| | - B M Cooke
- Department of Environmental Resource Management, University College Dublin, Belfield, Dublin 4, Ireland
| | - D Devaney
- Department of Environmental Resource Management, University College Dublin, Belfield, Dublin 4, Ireland
| | - E J Walsh
- Department of Crop Science, Horticulture and Forestry, University College Dublin, Belfield, Dublin 4, Ireland
| | - C A Griffey
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA 24061
| | | | - S A Harrison
- Department of Agronomy, Louisiana State University, Baton Rouge 70803
| | - P Hart
- Dept. of Plant Pathology, Michigan State University, East Lansing 48824
| | - F L Kolb
- Department of Crop Sciences, University of Illinois, Urbana 61801
| | - A L McKendry
- Department of Agronomy, University of Missouri, Colombia 65211
| | - E A Milus
- Department of Plant Pathology, University of Arkansas, Fayetteville 72701
| | - C Sneller
- Department of Crop Science and Horticulture, Ohio State University, Wooster 44691
| | - D A Van Sanford
- Department of Agronomy, University of Kentucky, Lexington 40546
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Pandjaitan N, Hettiarachchy N, Crandall ZJUP, Sneller C, Dombek D. Enrichment of Genistein in Soy Protein Concentrate with Hydrocolloids and β-glucosidase. J Food Sci 2000. [DOI: 10.1111/j.1365-2621.2000.tb16055.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pandjaitan N, Hettiarachchy N, Ju Z, Crandall P, Sneller C, Dombek D. Evaluation of Genistin and Genistein Contents in Soybean Varieties and Soy Protein Concentrate Prepared with 3 Basic Methods. J Food Sci 2000. [DOI: 10.1111/j.1365-2621.2000.tb16015.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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