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Wang Z, Dhakal S, Cerit M, Wang S, Rauf Y, Yu S, Maulana F, Huang W, Anderson JD, Ma XF, Rudd JC, Ibrahim AMH, Xue Q, Hays DB, Bernardo A, St. Amand P, Bai G, Baker J, Baker S, Liu S. QTL mapping of yield components and kernel traits in wheat cultivars TAM 112 and Duster. Front Plant Sci 2022; 13:1057701. [PMID: 36570880 PMCID: PMC9768232 DOI: 10.3389/fpls.2022.1057701] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
In the Southern Great Plains, wheat cultivars have been selected for a combination of outstanding yield and drought tolerance as a long-term breeding goal. To understand the underlying genetic mechanisms, this study aimed to dissect the quantitative trait loci (QTL) associated with yield components and kernel traits in two wheat cultivars `TAM 112' and `Duster' under both irrigated and dryland environments. A set of 182 recombined inbred lines (RIL) derived from the cross of TAM 112/Duster were planted in 13 diverse environments for evaluation of 18 yield and kernel related traits. High-density genetic linkage map was constructed using 5,081 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). QTL mapping analysis detected 134 QTL regions on all 21 wheat chromosomes, including 30 pleiotropic QTL regions and 21 consistent QTL regions, with 10 QTL regions in common. Three major pleiotropic QTL on the short arms of chromosomes 2B (57.5 - 61.6 Mbps), 2D (37.1 - 38.7 Mbps), and 7D (66.0 - 69.2 Mbps) colocalized with genes Ppd-B1, Ppd-D1, and FT-D1, respectively. And four consistent QTL associated with kernel length (KLEN), thousand kernel weight (TKW), plot grain yield (YLD), and kernel spike-1 (KPS) (Qklen.tamu.1A.325, Qtkw.tamu.2B.137, Qyld.tamu.2D.3, and Qkps.tamu.6A.113) explained more than 5% of the phenotypic variation. QTL Qklen.tamu.1A.325 is a novel QTL with consistent effects under all tested environments. Marker haplotype analysis indicated the QTL combinations significantly increased yield and kernel traits. QTL and the linked markers identified in this study will facilitate future marker-assisted selection (MAS) for pyramiding the favorable alleles and QTL map-based cloning.
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Affiliation(s)
- Zhen Wang
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Smit Dhakal
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Mustafa Cerit
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Shichen Wang
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX, United States
| | - Yahya Rauf
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Shuhao Yu
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Frank Maulana
- Noble Research Institute, Ardmore, OK, United States
| | - Wangqi Huang
- Noble Research Institute, Ardmore, OK, United States
| | | | - Xue-Feng Ma
- Noble Research Institute, Ardmore, OK, United States
| | - Jackie C. Rudd
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Amir M. H. Ibrahim
- Department of Soil and Crop Science, Texas A&M University, College Station, TX, United States
| | - Qingwu Xue
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Dirk B. Hays
- Department of Soil and Crop Science, Texas A&M University, College Station, TX, United States
| | - Amy Bernardo
- Central Small Grain Genotyping Lab and Hard Winter Wheat Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Manhattan, KS, United States
| | - Paul St. Amand
- Central Small Grain Genotyping Lab and Hard Winter Wheat Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Manhattan, KS, United States
| | - Guihua Bai
- Central Small Grain Genotyping Lab and Hard Winter Wheat Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Manhattan, KS, United States
| | - Jason Baker
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Shannon Baker
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Shuyu Liu
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
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2
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Chu C, Wang S, Rudd JC, Ibrahim AMH, Xue Q, Devkota RN, Baker JA, Baker S, Simoneaux B, Opena G, Dong H, Liu X, Jessup KE, Chen MS, Hui K, Metz R, Johnson CD, Zhang ZS, Liu S. A new strategy for using historical imbalanced yield data to conduct genome-wide association studies and develop genomic prediction models for wheat breeding. Mol Breed 2022; 42:18. [PMID: 37309459 PMCID: PMC10248704 DOI: 10.1007/s11032-022-01287-8] [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] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Using imbalanced historical yield data to predict performance and select new lines is an arduous breeding task. Genome-wide association studies (GWAS) and high throughput genotyping based on sequencing techniques can increase prediction accuracy. An association mapping panel of 227 Texas elite (TXE) wheat breeding lines was used for GWAS and a training population to develop prediction models for grain yield selection. An imbalanced set of yield data collected from 102 environments (year-by-location) over 10 years, through testing yield in 40-66 lines each year at 6-14 locations with 38-41 lines repeated in the test in any two consecutive years, was used. Based on correlations among data from different environments within two adjacent years and heritability estimated in each environment, yield data from 87 environments were selected and assigned to two correlation-based groups. The yield best linear unbiased estimation (BLUE) from each group, along with reaction to greenbug and Hessian fly in each line, was used for GWAS to reveal genomic regions associated with yield and insect resistance. A total of 74 genomic regions were associated with grain yield and two of them were commonly detected in both correlation-based groups. Greenbug resistance in TXE lines was mainly controlled by Gb3 on chromosome 7DL in addition to two novel regions on 3DL and 6DS, and Hessian fly resistance was conferred by the region on 1AS. Genomic prediction models developed in two correlation-based groups were validated using a set of 105 new advanced breeding lines and the model from correlation-based group G2 was more reliable for prediction. This research not only identified genomic regions associated with yield and insect resistance but also established the method of using historical imbalanced breeding data to develop a genomic prediction model for crop improvement. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01287-8.
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Affiliation(s)
- Chenggen Chu
- Texas A&M AgriLife Research Center, Amarillo, TX 79106 USA
- Sugarbeet & Potato Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND 58102 USA
| | - Shichen Wang
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX 77843 USA
| | - Jackie C. Rudd
- Texas A&M AgriLife Research Center, Amarillo, TX 79106 USA
| | - Amir M. H. Ibrahim
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX 77843 USA
| | - Qingwu Xue
- Texas A&M AgriLife Research Center, Amarillo, TX 79106 USA
| | | | - Jason A. Baker
- Texas A&M AgriLife Research Center, Amarillo, TX 79106 USA
| | - Shannon Baker
- Texas A&M AgriLife Research Center, Amarillo, TX 79106 USA
| | - Bryan Simoneaux
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX 77843 USA
| | - Geraldine Opena
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX 77843 USA
| | - Haixiao Dong
- Soil and Crop Sciences Department, Washington State University, Pullman, WA 99164 USA
| | - Xiaoxiao Liu
- Texas A&M AgriLife Research Center, Amarillo, TX 79106 USA
| | - Kirk E. Jessup
- Texas A&M AgriLife Research Center, Amarillo, TX 79106 USA
| | - Ming-Shun Chen
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS 66506 USA
| | - Kele Hui
- Texas A&M AgriLife Research Center, Amarillo, TX 79106 USA
| | - Richard Metz
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX 77843 USA
| | - Charles D. Johnson
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX 77843 USA
| | - Zhiwu S. Zhang
- Soil and Crop Sciences Department, Washington State University, Pullman, WA 99164 USA
| | - Shuyu Liu
- Texas A&M AgriLife Research Center, Amarillo, TX 79106 USA
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3
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Dhakal S, Liu X, Chu C, Yang Y, Rudd JC, Ibrahim AMH, Xue Q, Devkota RN, Baker JA, Baker SA, Simoneaux BE, Opena GB, Sutton R, Jessup KE, Hui K, Wang S, Johnson CD, Metz RP, Liu S. Genome-wide QTL mapping of yield and agronomic traits in two widely adapted winter wheat cultivars from multiple mega-environments. PeerJ 2021; 9:e12350. [PMID: 34900409 PMCID: PMC8627123 DOI: 10.7717/peerj.12350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 06/15/2021] [Accepted: 09/29/2021] [Indexed: 12/01/2022] Open
Abstract
Quantitative trait loci (QTL) analysis could help to identify suitable molecular markers for marker-assisted breeding (MAB). A mapping population of 124 F5:7recombinant inbred lines derived from the cross ‘TAM 112’/‘TAM 111’ was grown under 28 diverse environments and evaluated for grain yield, test weight, heading date, and plant height. The objective of this study was to detect QTL conferring grain yield and agronomic traits from multiple mega-environments. Through a linkage map with 5,948 single nucleotide polymorphisms (SNPs), 51 QTL were consistently identified in two or more environments or analyses. Ten QTL linked to two or more traits were also identified on chromosomes 1A, 1D, 4B, 4D, 6A, 7B, and 7D. Those QTL explained up to 13.3% of additive phenotypic variations with the additive logarithm of odds (LOD(A)) scores up to 11.2. The additive effect increased yield up to 8.16 and 6.57 g m−2 and increased test weight by 2.14 and 3.47 kg m−3 with favorable alleles from TAM 111 and TAM 112, respectively. Seven major QTL for yield and six for TW with one in common were of our interest on MAB as they explained 5% or more phenotypic variations through additive effects. This study confirmed previously identified loci and identified new QTL and the favorable alleles for improving grain yield and agronomic traits.
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Affiliation(s)
- Smit Dhakal
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Xiaoxiao Liu
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Chenggen Chu
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America.,Edward T. Schafer Agricultural Research Center, Sugarbeet & Potato Research Unit, USDA-ARS, Fargo, ND, United States of America
| | - Yan Yang
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Jackie C Rudd
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Amir M H Ibrahim
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States of America
| | - Qingwu Xue
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Ravindra N Devkota
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Jason A Baker
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Shannon A Baker
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Bryan E Simoneaux
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States of America
| | - Geraldine B Opena
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States of America
| | - Russell Sutton
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States of America
| | - Kirk E Jessup
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Kele Hui
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
| | - Shichen Wang
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX, United States of America
| | - Charles D Johnson
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX, United States of America
| | - Richard P Metz
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX, United States of America
| | - Shuyu Liu
- Texas A&M AgriLife Research and Extension Center, Texas A&M AgriLife Research, Amarillo, TX, United States of America
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4
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Jordan KW, Bradbury PJ, Miller ZR, Nyine M, He F, Fraser M, Anderson J, Mason E, Katz A, Pearce S, Carter AH, Prather S, Pumphrey M, Chen J, Cook J, Liu S, Rudd JC, Wang Z, Chu C, Ibrahim AMH, Turkus J, Olson E, Nagarajan R, Carver B, Yan L, Taagen E, Sorrells M, Ward B, Ren J, Akhunova A, Bai G, Bowden R, Fiedler J, Faris J, Dubcovsky J, Guttieri M, Brown-Guedira G, Buckler E, Jannink JL, Akhunov ED. Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation. G3 (Bethesda) 2021; 12:6423995. [PMID: 34751373 PMCID: PMC9210282 DOI: 10.1093/g3journal/jkab390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/21/2021] [Indexed: 12/04/2022]
Abstract
To improve the efficiency of high-density genotype data storage and imputation in bread wheat (Triticum aestivum L.), we applied the Practical Haplotype Graph (PHG) tool. The Wheat PHG database was built using whole-exome capture sequencing data from a diverse set of 65 wheat accessions. Population haplotypes were inferred for the reference genome intervals defined by the boundaries of the high-quality gene models. Missing genotypes in the inference panels, composed of wheat cultivars or recombinant inbred lines genotyped by exome capture, genotyping-by-sequencing (GBS), or whole-genome skim-seq sequencing approaches, were imputed using the Wheat PHG database. Though imputation accuracy varied depending on the method of sequencing and coverage depth, we found 92% imputation accuracy with 0.01× sequence coverage, which was slightly lower than the accuracy obtained using the 0.5× sequence coverage (96.6%). Compared to Beagle, on average, PHG imputation was ∼3.5% (P-value < 2 × 10−14) more accurate, and showed 27% higher accuracy at imputing a rare haplotype introgressed from a wild relative into wheat. We found reduced accuracy of imputation with independent 2× GBS data (88.6%), which increases to 89.2% with the inclusion of parental haplotypes in the database. The accuracy reduction with GBS is likely associated with the small overlap between GBS markers and the exome capture dataset, which was used for constructing PHG. The highest imputation accuracy was obtained with exome capture for the wheat D genome, which also showed the highest levels of linkage disequilibrium and proportion of identity-by-descent regions among accessions in the PHG database. We demonstrate that genetic mapping based on genotypes imputed using PHG identifies SNPs with a broader range of effect sizes that together explain a higher proportion of genetic variance for heading date and meiotic crossover rate compared to previous studies.
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Affiliation(s)
- Katherine W Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.,USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66502, USA
| | - Peter J Bradbury
- USDA-ARS, Plant Soil and Nutrition Research Unit, Ithaca, NY, 14853, USA
| | - Zachary R Miller
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Moses Nyine
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Max Fraser
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jim Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Esten Mason
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80521, USA
| | - Andrew Katz
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80521, USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80521, USA
| | - Arron H Carter
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Samuel Prather
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Jianli Chen
- Department of Plant Sciences, University of Idaho, Aberdeen, ID, 83210, USA
| | - Jason Cook
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Shuyu Liu
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Jackie C Rudd
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Zhen Wang
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Chenggen Chu
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Amir M H Ibrahim
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Jonathan Turkus
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Eric Olson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Ragupathi Nagarajan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74075, USA
| | - Brett Carver
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74075, USA
| | - Liuling Yan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74075, USA
| | - Ellie Taagen
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Mark Sorrells
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Brian Ward
- USDA-ARS, Plant Science Research Unit, Raleigh, NC, 27695, USA
| | - Jie Ren
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.,Integrative Genomics Facility, Kansas State University, Manhattan, KS, 66506 USA
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.,Integrative Genomics Facility, Kansas State University, Manhattan, KS, 66506 USA
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66502, USA
| | - Robert Bowden
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66502, USA
| | - Jason Fiedler
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND, 58102, USA
| | - Justin Faris
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND, 58102, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California-Davis, Davis, CA, 95616, USA
| | - Mary Guttieri
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66502, USA
| | | | - Ed Buckler
- USDA-ARS, Plant Soil and Nutrition Research Unit, Ithaca, NY, 14853, USA
| | - Jean-Luc Jannink
- USDA-ARS, Plant Soil and Nutrition Research Unit, Ithaca, NY, 14853, USA
| | - Eduard D Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
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5
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Chu C, Wang S, Paetzold L, Wang Z, Hui K, Rudd JC, Xue Q, Ibrahim AMH, Metz R, Johnson CD, Rush CM, Liu S. RNA-seq analysis reveals different drought tolerance mechanisms in two broadly adapted wheat cultivars 'TAM 111' and 'TAM 112'. Sci Rep 2021; 11:4301. [PMID: 33619336 PMCID: PMC7900135 DOI: 10.1038/s41598-021-83372-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/27/2021] [Indexed: 01/31/2023] Open
Abstract
Wheat cultivars 'TAM 111' and 'TAM 112' have been dominantly grown in the Southern U.S. Great Plains for many years due to their high yield and drought tolerance. To identify the molecular basis and genetic control of drought tolerance in these two landmark cultivars, RNA-seq analysis was conducted to compare gene expression difference in flag leaves under fully irrigated (wet) and water deficient (dry) conditions. A total of 2254 genes showed significantly altered expression patterns under dry and wet conditions in the two cultivars. TAM 111 had 593 and 1532 dry-wet differentially expressed genes (DEGs), and TAM 112 had 777 and 1670 at heading and grain-filling stages, respectively. The two cultivars have 1214 (53.9%) dry-wet DEGs in common, which agreed with their excellent adaption to drought, but 438 and 602 dry-wet DEGs were respectively shown only in TAM 111 and TAM 112 suggested that each has a specific mechanism to cope with drought. Annotations of all 2254 genes showed 1855 have functions related to biosynthesis, stress responses, defense responses, transcription factors and cellular components related to ion or protein transportation and signal transduction. Comparing hierarchical structure of biological processes, molecule functions and cellular components revealed the significant regulation differences between TAM 111 and TAM 112, particularly for genes of phosphorylation and adenyl ribonucleotide binding, and proteins located in nucleus and plasma membrane. TAM 112 showed more active than TAM 111 in response to drought and carried more specific genes with most of them were up-regulated in responses to stresses of water deprivation, heat and oxidative, ABA-induced signal pathway and transcription regulation. In addition, 258 genes encoding predicted uncharacterized proteins and 141 unannotated genes with no similar sequences identified in the databases may represent novel genes related to drought response in TAM 111 or TAM 112. This research thus revealed different drought-tolerance mechanisms in TAM 111 and TAM 112 and identified useful drought tolerance genes for wheat adaption. Data of gene sequence and expression regulation from this study also provided useful information of annotating novel genes associated with drought tolerance in the wheat genome.
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Affiliation(s)
- Chenggen Chu
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX, 79106, USA.
- Sugarbeet and Potato Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, 1616 Albrecht Blvd. N, Fargo, ND, 58102, USA.
| | - Shichen Wang
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX, 77843, USA
| | - Li Paetzold
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX, 79106, USA
| | - Zhen Wang
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX, 79106, USA
| | - Kele Hui
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX, 79106, USA
| | - Jackie C Rudd
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX, 79106, USA
| | - Qingwu Xue
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX, 79106, USA
| | - Amir M H Ibrahim
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX, 77843, USA
| | - Richard Metz
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX, 77843, USA
| | - Charles D Johnson
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX, 77843, USA
| | - Charles M Rush
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX, 79106, USA
| | - Shuyu Liu
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX, 79106, USA.
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6
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Adhikari A, Basnet BR, Crossa J, Dreisigacker S, Camarillo F, Bhati PK, Jarquin D, Manes Y, Ibrahim AMH. Genome-Wide Association Mapping and Genomic Prediction of Anther Extrusion in CIMMYT Hybrid Wheat Breeding Program via Modeling Pedigree, Genomic Relationship, and Interaction With the Environment. Front Genet 2020; 11:586687. [PMID: 33363570 PMCID: PMC7755068 DOI: 10.3389/fgene.2020.586687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 07/23/2020] [Accepted: 10/13/2020] [Indexed: 11/13/2022] Open
Abstract
Anther extrusion (AE) is the most important male floral trait for hybrid wheat seed production. AE is a complex quantitative trait that is difficult to phenotype reliably in field experiments not only due to high genotype-by-environment effects but also due to the short expression window in the field condition. In this study, we conducted a genome-wide association scan (GWAS) and explored the possibility of applying genomic prediction (GP) for AE in the CIMMYT hybrid wheat breeding program. An elite set of male lines (n = 603) were phenotype for anther count (AC) and anther visual score (VS) across three field experiments in 2017–2019 and genotyped with the 20K Infinitum is elect SNP array. GWAS produced five marker trait associations with small effects. For GP, the main effects of lines (L), environment (E), genomic (G) and pedigree relationships (A), and their interaction effects with environments were used to develop seven statistical models of incremental complexity. The base model used only L and E, whereas the most complex model included L, E, G, A, and G × E and A × E. These models were evaluated in three cross-validation scenarios (CV0, CV1, and CV2). In cross-validation CV0, data from two environments were used to predict an untested environment; in random cross-validation CV1, the test set was never evaluated in any environment; and in CV2, the genotypes in the test set were evaluated in only a subset of environments. The prediction accuracies ranged from −0.03 to 0.74 for AC and −0.01 to 0.54 for VS across different models and CV schemes. For both traits, the highest prediction accuracies with low variance were observed in CV2, and inclusion of the interaction effects increased prediction accuracy for AC only. In CV0, the prediction accuracy was 0.73 and 0.45 for AC and VS, respectively, indicating the high reliability of across environment prediction. Genomic prediction appears to be a very reliable tool for AE in hybrid wheat breeding. Moreover, high prediction accuracy in CV0 demonstrates the possibility of implementing genomic selection across breeding cycles in related germplasm, aiding the rapid breeding cycle.
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Affiliation(s)
- Anil Adhikari
- Texas A&M University, College Station, TX, United States.,Department of Horticulture, University of Wisconsin, Madison, WI, United States
| | - Bhoja Raj Basnet
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Fatima Camarillo
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Diego Jarquin
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
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Guo J, Khan J, Pradhan S, Shahi D, Khan N, Avci M, Mcbreen J, Harrison S, Brown-Guedira G, Murphy JP, Johnson J, Mergoum M, Esten Mason R, Ibrahim AMH, Sutton R, Griffey C, Babar MA. Multi-Trait Genomic Prediction of Yield-Related Traits in US Soft Wheat under Variable Water Regimes. Genes (Basel) 2020; 11:genes11111270. [PMID: 33126620 PMCID: PMC7716228 DOI: 10.3390/genes11111270] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 11/16/2022] Open
Abstract
The performance of genomic prediction (GP) on genetically correlated traits can be improved through an interdependence multi-trait model under a multi-environment context. In this study, a panel of 237 soft facultative wheat (Triticum aestivum L.) lines was evaluated to compare single- and multi-trait models for predicting grain yield (GY), harvest index (HI), spike fertility (SF), and thousand grain weight (TGW). The panel was phenotyped in two locations and two years in Florida under drought and moderately drought stress conditions, while the genotyping was performed using 27,957 genotyping-by-sequencing (GBS) single nucleotide polymorphism (SNP) makers. Five predictive models including Multi-environment Genomic Best Linear Unbiased Predictor (MGBLUP), Bayesian Multi-trait Multi-environment (BMTME), Bayesian Multi-output Regressor Stacking (BMORS), Single-trait Multi-environment Deep Learning (SMDL), and Multi-trait Multi-environment Deep Learning (MMDL) were compared. Across environments, the multi-trait statistical model (BMTME) was superior to the multi-trait DL model for prediction accuracy in most scenarios, but the DL models were comparable to the statistical models for response to selection. The multi-trait model also showed 5 to 22% more genetic gain compared to the single-trait model across environment reflected by the response to selection. Overall, these results suggest that multi-trait genomic prediction can be an efficient strategy for economically important yield component related traits in soft wheat.
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Affiliation(s)
- Jia Guo
- Department of Agronomy, University of Florida, Gainesville, FL 32611, USA; (J.G.); (J.K.); (S.P.); (D.S.); (N.K.); (M.A.); (J.M.)
| | - Jahangir Khan
- Department of Agronomy, University of Florida, Gainesville, FL 32611, USA; (J.G.); (J.K.); (S.P.); (D.S.); (N.K.); (M.A.); (J.M.)
| | - Sumit Pradhan
- Department of Agronomy, University of Florida, Gainesville, FL 32611, USA; (J.G.); (J.K.); (S.P.); (D.S.); (N.K.); (M.A.); (J.M.)
| | - Dipendra Shahi
- Department of Agronomy, University of Florida, Gainesville, FL 32611, USA; (J.G.); (J.K.); (S.P.); (D.S.); (N.K.); (M.A.); (J.M.)
| | - Naeem Khan
- Department of Agronomy, University of Florida, Gainesville, FL 32611, USA; (J.G.); (J.K.); (S.P.); (D.S.); (N.K.); (M.A.); (J.M.)
| | - Muhsin Avci
- Department of Agronomy, University of Florida, Gainesville, FL 32611, USA; (J.G.); (J.K.); (S.P.); (D.S.); (N.K.); (M.A.); (J.M.)
| | - Jordan Mcbreen
- Department of Agronomy, University of Florida, Gainesville, FL 32611, USA; (J.G.); (J.K.); (S.P.); (D.S.); (N.K.); (M.A.); (J.M.)
| | - Stephen Harrison
- School of Plant Environment and Soil Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
| | | | - Joseph Paul Murphy
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27607, USA;
| | - Jerry Johnson
- Department of Crop and Soil Sciences, University of Georgia, Griffin, GA 32223, USA; (J.J.); (M.M.)
| | - Mohamed Mergoum
- Department of Crop and Soil Sciences, University of Georgia, Griffin, GA 32223, USA; (J.J.); (M.M.)
| | - Richanrd Esten Mason
- Department of Crop Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Amir M. H. Ibrahim
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (A.M.H.I.); (R.S.)
| | - Russel Sutton
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (A.M.H.I.); (R.S.)
| | - Carl Griffey
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA;
| | - Md Ali Babar
- Department of Agronomy, University of Florida, Gainesville, FL 32611, USA; (J.G.); (J.K.); (S.P.); (D.S.); (N.K.); (M.A.); (J.M.)
- Correspondence:
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Adhikari A, Basnet BR, Crossa J, Dreisigacker S, Camarillo F, Bhati PK, Jarquin D, Manes Y, Ibrahim AMH. Genome-Wide Association Mapping and Genomic Prediction of Anther Extrusion in CIMMYT Hybrid Wheat Breeding Program via Modeling Pedigree, Genomic Relationship, and Interaction With the Environment. Front Genet 2020. [PMID: 33363570 DOI: 10.3389/fgene.2020.586687.\] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
Anther extrusion (AE) is the most important male floral trait for hybrid wheat seed production. AE is a complex quantitative trait that is difficult to phenotype reliably in field experiments not only due to high genotype-by-environment effects but also due to the short expression window in the field condition. In this study, we conducted a genome-wide association scan (GWAS) and explored the possibility of applying genomic prediction (GP) for AE in the CIMMYT hybrid wheat breeding program. An elite set of male lines (n = 603) were phenotype for anther count (AC) and anther visual score (VS) across three field experiments in 2017-2019 and genotyped with the 20K Infinitum is elect SNP array. GWAS produced five marker trait associations with small effects. For GP, the main effects of lines (L), environment (E), genomic (G) and pedigree relationships (A), and their interaction effects with environments were used to develop seven statistical models of incremental complexity. The base model used only L and E, whereas the most complex model included L, E, G, A, and G × E and A × E. These models were evaluated in three cross-validation scenarios (CV0, CV1, and CV2). In cross-validation CV0, data from two environments were used to predict an untested environment; in random cross-validation CV1, the test set was never evaluated in any environment; and in CV2, the genotypes in the test set were evaluated in only a subset of environments. The prediction accuracies ranged from -0.03 to 0.74 for AC and -0.01 to 0.54 for VS across different models and CV schemes. For both traits, the highest prediction accuracies with low variance were observed in CV2, and inclusion of the interaction effects increased prediction accuracy for AC only. In CV0, the prediction accuracy was 0.73 and 0.45 for AC and VS, respectively, indicating the high reliability of across environment prediction. Genomic prediction appears to be a very reliable tool for AE in hybrid wheat breeding. Moreover, high prediction accuracy in CV0 demonstrates the possibility of implementing genomic selection across breeding cycles in related germplasm, aiding the rapid breeding cycle.
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Affiliation(s)
- Anil Adhikari
- Texas A&M University, College Station, TX, United States
- Department of Horticulture, University of Wisconsin, Madison, WI, United States
| | - Bhoja Raj Basnet
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Fatima Camarillo
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Diego Jarquin
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
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Easterly AC, Stroup WW, Garst N, Belamkar V, Sarazin JB, Moittié T, Ibrahim AMH, Rudd JC, Souza E, Baenziger PS. Determining the Efficacy of a Hybridizing Agent in Wheat (Triticum aestivum L.). Sci Rep 2019; 9:20173. [PMID: 31882883 PMCID: PMC6934762 DOI: 10.1038/s41598-019-56664-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 07/26/2019] [Accepted: 12/16/2019] [Indexed: 11/24/2022] Open
Abstract
Hybrid wheat (Triticum spp.) has the potential to boost yields and enhance production under changing climates to feed the growing global population. Production of hybrid wheat seed relies on male sterility, the blocking of pollen production, to prevent self-pollination. One method of preventing self-pollination in the female plants is to apply a chemical hybridizing agent (CHA). However, some combinations of CHA and genotypes have lower levels of sterility, resulting in decreased hybrid purity. Differences in CHA efficacy are a challenge in producing hybrid wheat lines for commercial and experimental use. Our primary research questions were to estimate the levels of sterility for wheat genotypes treated with a CHA and determine the best way to analyze differences. We applied the CHA sintofen (1-(4-chlorphyl)-1,4-dihydro-5-(2-methoxyethoxy)-4-oxocinnoline-3-carboxylic acid; Croisor 100) to 27 genotypes in replicate. After spraying, we counted seed in bagged female heads to evaluate CHA efficacy and CHA-by-genotype interaction. Using logit and probit models with a threshold of 7 seeds, we found differences among genotypes in 2015. Sterility was higher in 2016 and fewer genotypic differences were found. When CHA-induced sterilization is less uniform as in 2015, zero-inflated and hurdle count models were superior to standard mixed models. These models calculate mean seed number and fit data with limit-bounded scales collected by agronomists and plant breeders to compare genotypic differences. These analyses can assist in selecting parents and identifying where additional optimization of CHA application needs to occur. There is little work in the literature examining the relationship between CHAs and genotypes, making this work fundamental to the future of hybrid wheat breeding.
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Affiliation(s)
- Amanda C Easterly
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583-0915, United States.
| | - Walter W Stroup
- Department of Statistics, University of Nebraska, Lincoln, NE, 68583-0963, United States
| | - Nicholas Garst
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583-0915, United States
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583-0915, United States
| | | | | | - Amir M H Ibrahim
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, United States
| | - Jackie C Rudd
- Texas AgriLife Research and Extension Center at Amarillo, Amarillo, TX, 79106, United States
| | | | - P Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583-0915, United States
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Jamil M, Ali A, Gul A, Ghafoor A, Napar AA, Ibrahim AMH, Naveed NH, Yasin NA, Mujeeb-Kazi A. Genome-wide association studies of seven agronomic traits under two sowing conditions in bread wheat. BMC Plant Biol 2019; 19:149. [PMID: 31003597 PMCID: PMC6475106 DOI: 10.1186/s12870-019-1754-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 04/02/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Wheat is a cool seasoned crop requiring low temperature during grain filling duration and therefore increased temperature causes significant yield reduction. A set of 125 spring wheat genotypes from International Maize and Wheat Improvement Centre (CIMMYT-Mexico) was evaluated for phenological and yield related traits at three locations in Pakistan under normal sowing time and late sowing time for expose to prolonged high temperature. With the help of genome-wide association study using genotyping-by-sequencing, marker trait associations (MTAs) were observed separately for the traits under normal and late sown conditions. RESULTS Significant reduction ranging from 9 to 74% was observed in all traits under high temperature. Especially 30, 25, 41 and 66% reduction was observed for days to heading (DH), plant height (PH), spikes per plant (SPP) and yield respectively. We identified 55,954 single nucleotide polymorphisms (SNPs) using genotyping by sequencing of these 125 hexaploid spring wheat genotypes and conducted genome-wide association studies (GWAS) for days to heading (DH), grain filled duration (GFD), plant height (PH), spikes per plant (SPP), grain number per spike (GNS), thousand kernel weight (TKW) and grain yield per plot (GY). Genomic regions identified through GWAS explained up to 13% of the phenotypic variance, on average. A total of 139 marker-trait associations (MTAs) across three wheat genomes (56 on genome A, 55 on B and 28 on D) were identified for all the seven traits studied. For days to heading, 20; grain filled duration, 21; plant height, 23; spikes per plant, 13; grain numbers per spike, 8; thousand kernel weight, 21 and for grain yield, 33 MTAs were detected under normal and late sown conditions. CONCLUSIONS This study identifies the essential resource of genetics research and underpins the chromosomal regions of seven agronomic traits under normal and high temperature. Significant relationship was observed between the number of favored alleles and trait observations. Fourteen protein coding genes with their respective annotations have been searched with the sequence of seven MTAs which were identified in this study. These findings will be helpful in the development of a breeder friendly platform for the selection of high yielding wheat lines at high temperature areas.
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Affiliation(s)
- Muhammad Jamil
- Department of Botany, University of Sargodha, Sargodha, Punjab Pakistan
| | - Aamir Ali
- Department of Botany, University of Sargodha, Sargodha, Punjab Pakistan
| | - Alvina Gul
- Atta-ur-Rehman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Abdul Ghafoor
- Plant Genetic Resources Institute (PGRI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Abdul Aziz Napar
- Institute of Plant Sciences, University of Sind Jamshoro, Sind, Pakistan
| | - Amir M. H. Ibrahim
- Soil and Crop Sciences Department, Texas A&M University, College Station, USA
| | - Naima Huma Naveed
- Department of Botany, University of Sargodha, Sargodha, Punjab Pakistan
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Jamil M, Ali A, Gul A, Ghafoor A, Ibrahim AMH, Mujeeb-Kazi A. Genome-Wide Association Studies for Spot Blotch (Cochliobolus sativus) Resistance in Bread Wheat Using Genotyping-by-Sequencing. Phytopathology 2018; 108:1307-1314. [PMID: 30277843 DOI: 10.1094/phyto-02-18-0047-r] [Citation(s) in RCA: 6] [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: 05/13/2023]
Abstract
Spot blotch is a severe biotic menace of wheat caused by Cochliobolus sativus (syn. Bipolaris sorokiniana). Spot blotch is liable to major yield losses in warm humid regions. A genome-wide association study using genotyping-by-sequencing (GBS) markers was conducted to identify genomic regions associated with spot blotch resistance in a diversity panel of 159 spring wheat genotypes. In total, 87,096 GBS markers covering the whole genome, with an average polymorphism information content value of 0.276, were applied. Linkage disequilibrium (LD) analysis indicated that the LD decay extent was approximately 100 Mbp. The panel was evaluated for disease severity (DS) and area under disease progress curve (AUDPC) for 2 years. In total, 24 marker-trait associations (MTA) were identified for DS and AUDPC of spot blotch, with 11 on chromosome 5B, 3 on 3A, 2 on 6B, and 1 each on 1A, 2A, 1D, 2D, 4B, 5A, 7A, and 7B. A marker on chromosome 7B significantly explained 14% of the phenotypic variation of spot blotch severity as well as 11% of AUDPC. Five markers-three on chromosome 5B, one on 3A, and one on 7B-were associated with both DS and AUDPC with R2 ranging from 8 to 12%. Significant MTA can be utilized to develop wheat germplasm with resistance to spot blotch.
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Affiliation(s)
- Muhammad Jamil
- First and second authors: Department of Botany, University of Sargohda, Sargodha. Pakistan; third author: Atta-ur-Rehman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan and United States Department of Agriculture-Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA; fourth author: Plant Genetic Resources Institute, National Agriculture Research Center, Islamabad, Pakistan; fifth author: Soil and Crop Sciences Department, Texas A&M University, TX 77843-2474; and sixth author: Texas A&M University, Amarillo, TX 79106
| | - Aamir Ali
- First and second authors: Department of Botany, University of Sargohda, Sargodha. Pakistan; third author: Atta-ur-Rehman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan and United States Department of Agriculture-Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA; fourth author: Plant Genetic Resources Institute, National Agriculture Research Center, Islamabad, Pakistan; fifth author: Soil and Crop Sciences Department, Texas A&M University, TX 77843-2474; and sixth author: Texas A&M University, Amarillo, TX 79106
| | - Alvina Gul
- First and second authors: Department of Botany, University of Sargohda, Sargodha. Pakistan; third author: Atta-ur-Rehman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan and United States Department of Agriculture-Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA; fourth author: Plant Genetic Resources Institute, National Agriculture Research Center, Islamabad, Pakistan; fifth author: Soil and Crop Sciences Department, Texas A&M University, TX 77843-2474; and sixth author: Texas A&M University, Amarillo, TX 79106
| | - Abdul Ghafoor
- First and second authors: Department of Botany, University of Sargohda, Sargodha. Pakistan; third author: Atta-ur-Rehman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan and United States Department of Agriculture-Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA; fourth author: Plant Genetic Resources Institute, National Agriculture Research Center, Islamabad, Pakistan; fifth author: Soil and Crop Sciences Department, Texas A&M University, TX 77843-2474; and sixth author: Texas A&M University, Amarillo, TX 79106
| | - Amir M H Ibrahim
- First and second authors: Department of Botany, University of Sargohda, Sargodha. Pakistan; third author: Atta-ur-Rehman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan and United States Department of Agriculture-Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA; fourth author: Plant Genetic Resources Institute, National Agriculture Research Center, Islamabad, Pakistan; fifth author: Soil and Crop Sciences Department, Texas A&M University, TX 77843-2474; and sixth author: Texas A&M University, Amarillo, TX 79106
| | - Abdul Mujeeb-Kazi
- First and second authors: Department of Botany, University of Sargohda, Sargodha. Pakistan; third author: Atta-ur-Rehman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan and United States Department of Agriculture-Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA; fourth author: Plant Genetic Resources Institute, National Agriculture Research Center, Islamabad, Pakistan; fifth author: Soil and Crop Sciences Department, Texas A&M University, TX 77843-2474; and sixth author: Texas A&M University, Amarillo, TX 79106
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Assanga SO, Fuentealba M, Zhang G, Tan C, Dhakal S, Rudd JC, Ibrahim AMH, Xue Q, Haley S, Chen J, Chao S, Baker J, Jessup K, Liu S. Mapping of quantitative trait loci for grain yield and its components in a US popular winter wheat TAM 111 using 90K SNPs. PLoS One 2017; 12:e0189669. [PMID: 29267314 PMCID: PMC5739412 DOI: 10.1371/journal.pone.0189669] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 06/02/2017] [Accepted: 11/29/2017] [Indexed: 11/18/2022] Open
Abstract
Stable quantitative trait loci (QTL) are important for deployment in marker assisted selection in wheat (Triticum aestivum L.) and other crops. We reported QTL discovery in wheat using a population of 217 recombinant inbred lines and multiple statistical approach including multi-environment, multi-trait and epistatic interactions analysis. We detected nine consistent QTL linked to different traits on chromosomes 1A, 2A, 2B, 5A, 5B, 6A, 6B and 7A. Grain yield QTL were detected on chromosomes 2B.1 and 5B across three or four models of GenStat, MapQTL, and QTLNetwork while the QTL on chromosomes 5A.1, 6A.2, and 7A.1 were only significant with yield from one or two models. The phenotypic variation explained (PVE) by the QTL on 2B.1 ranged from 3.3–25.1% based on single and multi-environment models in GenStat and was pleiotropic or co-located with maturity (days to heading) and yield related traits (test weight, thousand kernel weight, harvest index). The QTL on 5B at 211 cM had PVE range of 1.8–9.3% and had no significant pleiotropic effects. Other consistent QTL detected in this study were linked to yield related traits and agronomic traits. The QTL on 1A was consistent for the number of spikes m-2 across environments and all the four analysis models with a PVE range of 5.8–8.6%. QTL for kernels spike-1 were found in chromosomes 1A, 2A.1, 2B.1, 6A.2, and 7A.1 with PVE ranged from 5.6–12.8% while QTL for thousand kernel weight were located on chromosomes 1A, 2B.1, 5A.1, 6A.2, 6B.1 and 7A.1 with PVEranged from 2.7–19.5%. Among the consistent QTL, five QTL had significant epistatic interactions (additive × additive) at least for one trait and none revealed significant additive × additive × environment interactions. Comparative analysis revealed that the region within the confidence interval of the QTL on 5B from 211.4–244.2 cM is also linked to genes for aspartate-semialdehyde dehydrogenase, splicing regulatory glutamine/lysine-rich protein 1 isoform X1, and UDP-glucose 6-dehydrogenase 1-like isoform X1. The stable QTL could be important for further validation, high throughput SNP development, and marker-assisted selection (MAS) in wheat.
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Affiliation(s)
- Silvano O Assanga
- Texas A&M AgriLife Research, Amarillo, Texas, United States of America.,Department of Soil and Crop Science, Texas A&M University, College Station, Texas, United States of America
| | - Maria Fuentealba
- Texas A&M AgriLife Research, Amarillo, Texas, United States of America
| | - Guorong Zhang
- Agricultural Research Center-Hays, Kansas State University, Hays, Kansas, United States of America
| | - ChorTee Tan
- Texas A&M AgriLife Research, Amarillo, Texas, United States of America
| | - Smit Dhakal
- Texas A&M AgriLife Research, Amarillo, Texas, United States of America.,Department of Soil and Crop Science, Texas A&M University, College Station, Texas, United States of America
| | - Jackie C Rudd
- Texas A&M AgriLife Research, Amarillo, Texas, United States of America
| | - Amir M H Ibrahim
- Department of Soil and Crop Science, Texas A&M University, College Station, Texas, United States of America
| | - Qingwu Xue
- Texas A&M AgriLife Research, Amarillo, Texas, United States of America
| | - Scott Haley
- Soil and Crop Sciences Department, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jianli Chen
- Department of Plant, Soil and Entomological Sciences, University of Idaho Aberdeen Research and Extension Center, Aberdeen, Idaho, United States of America
| | - Shiaoman Chao
- USDAARS Bioscience Research Laboratory, Fargo, North Dakota, United States of America
| | - Jason Baker
- Texas A&M AgriLife Research, Amarillo, Texas, United States of America
| | - Kirk Jessup
- Texas A&M AgriLife Research, Amarillo, Texas, United States of America
| | - Shuyu Liu
- Texas A&M AgriLife Research, Amarillo, Texas, United States of America
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13
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Tan CT, Yu H, Yang Y, Xu X, Chen M, Rudd JC, Xue Q, Ibrahim AMH, Garza L, Wang S, Sorrells ME, Liu S. Development and validation of KASP markers for the greenbug resistance gene Gb7 and the Hessian fly resistance gene H32 in wheat. Theor Appl Genet 2017; 130:1867-1884. [PMID: 28624908 DOI: 10.1007/s00122-017-2930-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/30/2017] [Indexed: 05/19/2023]
Abstract
Greenbug and Hessian fly are important pests that decrease wheat production worldwide. We developed and validated breeder-friendly KASP markers for marker-assisted breeding to increase selection efficiency. Greenbug (Schizaphis graminum Rondani) and Hessian fly [Mayetiola destructor (Say)] are two major destructive insect pests of wheat (Triticum aestivum L.) throughout wheat production regions in the USA and worldwide. Greenbug and Hessian fly infestation can significantly reduce grain yield and quality. Breeding for resistance to these two pests using marker-assisted selection (MAS) is the most economical strategy to minimize losses. In this study, doubled haploid lines from the Synthetic W7984 × Opata M85 wheat reference population were used to construct linkage maps for the greenbug resistance gene Gb7 and the Hessian fly resistance gene H32 with genotyping-by-sequencing (GBS) and 90K array-based single nucleotide polymorphism (SNP) marker data. Flanking markers were closely linked to Gb7 and H32 and were located on chromosome 7DL and 3DL, respectively. Gb7-linked markers (synopGBS773 and synopGBS1141) and H32-linked markers (synopGBS901 and IWB65911) were converted into Kompetitive Allele Specific PCR (KASP) assays for MAS in wheat breeding. In addition, comparative mapping identified syntenic regions in Brachypodium distachyon, rice (Oryza sativa), and sorghum (Sorghum bicolor) for Gb7 and H32 that can be used for fine mapping and map-based cloning of the genes. The KASP markers developed in this study are the first set of SNPs tightly linked to Gb7 and H32 and will be very useful for MAS in wheat breeding programs and future genetic studies of greenbug and Hessian fly resistance.
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Affiliation(s)
- Chor-Tee Tan
- Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Hangjin Yu
- Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Yan Yang
- Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
- Department of Soil and Crop Science, Texas A&M University, College Station, TX, 77843, USA
| | - Xiangyang Xu
- USDA-ARS Wheat, Peanut and Other Field Crop Research Unit, Stillwater, OK, 74075, USA
| | - Mingshun Chen
- USDA-ARS and Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jackie C Rudd
- Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Qingwu Xue
- Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Amir M H Ibrahim
- Department of Soil and Crop Science, Texas A&M University, College Station, TX, 77843, USA
| | - Lisa Garza
- Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Shichen Wang
- Genomic and Bioinformatics Services, Texas A&M AgriLife Research, College Station, TX, 77845, USA
| | - Mark E Sorrells
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Shuyu Liu
- Texas A&M AgriLife Research, Amarillo, TX, 79106, USA.
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Klos KE, Yimer BA, Babiker EM, Beattie AD, Bonman JM, Carson ML, Chong J, Harrison SA, Ibrahim AMH, Kolb FL, McCartney CA, McMullen M, Fetch JM, Mohammadi M, Murphy JP, Tinker NA. Genome-Wide Association Mapping of Crown Rust Resistance in Oat Elite Germplasm. Plant Genome 2017; 10. [PMID: 28724060 DOI: 10.3835/plantgenome2016.10.0107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Oat crown rust, caused by f. sp. , is a major constraint to oat ( L.) production in many parts of the world. In this first comprehensive multienvironment genome-wide association map of oat crown rust, we used 2972 single-nucleotide polymorphisms (SNPs) genotyped on 631 oat lines for association mapping of quantitative trait loci (QTL). Seedling reaction to crown rust in these lines was assessed as infection type (IT) with each of 10 crown rust isolates. Adult plant reaction was assessed in the field in a total of 10 location-years as percentage severity (SV) and as infection reaction (IR) in a 0-to-1 scale. Overall, 29 SNPs on 12 linkage groups were predictive of crown rust reaction in at least one experiment at a genome-wide level of statistical significance. The QTL identified here include those in regions previously shown to be linked with seedling resistance genes , , , , , and and also with adult-plant resistance and adaptation-related QTL. In addition, QTL on linkage groups Mrg03, Mrg08, and Mrg23 were identified in regions not previously associated with crown rust resistance. Evaluation of marker genotypes in a set of crown rust differential lines supported as the identity of . The SNPs with rare alleles associated with lower disease scores may be suitable for use in marker-assisted selection of oat lines for crown rust resistance.
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Chen Y, Cothren JT, Chen D, Ibrahim AMH, Lombardini L. Effect of 1-MCP on Cotton Plants under Abiotic Stress Caused by Ethephon. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ajps.2014.520317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Basnet BR, Singh RP, Herrera-Foessel SA, Ibrahim AMH, Huerta-Espino J, Calvo-Salazar V, Rudd JC. Genetic Analysis of Adult Plant Resistance to Yellow Rust and Leaf Rust in Common Spring Wheat Quaiu 3. Plant Dis 2013; 97:728-736. [PMID: 30722591 DOI: 10.1094/pdis-02-12-0141-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Identifying and utilizing rust resistance genes in wheat has been hampered by the continuous and rapid emergence of new pathogen races. A major focus of many wheat breeding programs is achieving durable adult plant resistance (APR) to yellow (stripe) rust (YR) and leaf (brown) rust (LR), caused by Puccinia striiformis and P. triticina, respectively. This study aimed to determine the genetic basis of resistance to YR and LR in the common spring wheat 'Quaiu 3'. To that end, we evaluated 198 F5 recombinant inbred lines (RILs), derived from a cross of susceptible 'Avocet-YrA' with Quaiu 3, for APR to LR and YR in artificially inoculated field trials conducted in Mexico during the 2009 and 2010 growing seasons. High narrow-sense heritability (h2) estimates, ranging between 0.91 and 0.95, were obtained for both LR and YR disease severities for both years. The quantitative and qualitative approaches used to estimate gene numbers showed that, in addition to known resistance genes, there are at least two to three APR genes associated with LR and YR resistance in the RIL population. The moderately effective race-specific resistance gene Lr42 and the pleiotropic slow-rusting APR gene Lr46/Yr29 were found to interact with additional unidentified APR genes. The unidentified APR genes should be of particular interest for further characterization through molecular mapping, and for utilization by wheat breeding programs.
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Affiliation(s)
- B R Basnet
- International Maize and Wheat Improvement Center (CIMMYT) Apdo. Postal 6-641, C.P. 06600, D.F., Mexico and Department of Soil and Crop Sciences, Texas A&M University, College Station 77843
| | | | | | - A M H Ibrahim
- Department of Soil and Crop Sciences, Texas A&M University
| | - J Huerta-Espino
- Campo Experimental Valle de Mexico INIFAP, Apdo. Postal 10, 56230 Chapingo, Edo. de Mexico, Mexico
| | | | - J C Rudd
- Department of Soil and Crop Sciences, Texas A&M University
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