1
|
Fu C, Zhou Y, Liu A, Chen R, Yin L, Li C, Mao H. Genome-wide association study for seedling heat tolerance under two temperature conditions in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2024; 24:430. [PMID: 38773371 PMCID: PMC11107014 DOI: 10.1186/s12870-024-05116-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND As the greenhouse effect intensifies, global temperatures are steadily increasing, posing a challenge to bread wheat (Triticum aestivum L.) production. It is imperative to comprehend the mechanism of high temperature tolerance in wheat and implement breeding programs to identify and develop heat-tolerant wheat germplasm and cultivars. RESULTS To identify quantitative trait loci (QTL) related to heat stress tolerance (HST) at seedling stage in wheat, a panel of 253 wheat accessions which were re-sequenced used to conduct genome-wide association studies (GWAS) using the factored spectrally transformed linear mixed models (FaST-LMM). For most accessions, the growth of seedlings was found to be inhibited under heat stress. Analysis of the phenotypic data revealed that under heat stress conditions, the main root length, total root length, and shoot length of seedlings decreased by 47.46%, 49.29%, and 15.19%, respectively, compared to those in normal conditions. However, 17 varieties were identified as heat stress tolerant germplasm. Through GWAS analysis, a total of 115 QTLs were detected under both heat stress and normal conditions. Furthermore, 15 stable QTL-clusters associated with heat response were identified. By combining gene expression, haplotype analysis, and gene annotation information within the physical intervals of the 15 QTL-clusters, two novel candidate genes, TraesCS4B03G0152700/TaWRKY74-B and TraesCS4B03G0501400/TaSnRK3.15-B, were responsive to temperature and identified as potential regulators of HST in wheat at the seedling stage. CONCLUSIONS This study conducted a detailed genetic analysis and successfully identified two genes potentially associated with HST in wheat at the seedling stage, laying a foundation to further dissect the regulatory mechanism underlying HST in wheat under high temperature conditions. Our finding could serve as genomic landmarks for wheat breeding aimed at improving adaptation to heat stress in the face of climate change.
Collapse
Affiliation(s)
- Chao Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ying Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ankui Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rui Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Yin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cong Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
2
|
Gao J, Hu X, Gao C, Chen G, Feng H, Jia Z, Zhao P, Yu H, Li H, Geng Z, Fu J, Zhang J, Cheng Y, Yang B, Pang Z, Xiang D, Jia J, Su H, Mao H, Lan C, Chen W, Yan W, Gao L, Yang W, Li Q. Deciphering genetic basis of developmental and agronomic traits by integrating high-throughput optical phenotyping and genome-wide association studies in wheat. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1966-1977. [PMID: 37392004 PMCID: PMC10502759 DOI: 10.1111/pbi.14104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/11/2023] [Accepted: 06/07/2023] [Indexed: 07/02/2023]
Abstract
Dissecting the genetic basis of complex traits such as dynamic growth and yield potential is a major challenge in crops. Monitoring the growth throughout growing season in a large wheat population to uncover the temporal genetic controls for plant growth and yield-related traits has so far not been explored. In this study, a diverse wheat panel composed of 288 lines was monitored by a non-invasive and high-throughput phenotyping platform to collect growth traits from seedling to grain filling stage and their relationship with yield-related traits was further explored. Whole genome re-sequencing of the panel provided 12.64 million markers for a high-resolution genome-wide association analysis using 190 image-based traits and 17 agronomic traits. A total of 8327 marker-trait associations were detected and clustered into 1605 quantitative trait loci (QTLs) including a number of known genes or QTLs. We identified 277 pleiotropic QTLs controlling multiple traits at different growth stages which revealed temporal dynamics of QTLs action on plant development and yield production in wheat. A candidate gene related to plant growth that was detected by image traits was further validated. Particularly, our study demonstrated that the yield-related traits are largely predictable using models developed based on i-traits and provide possibility for high-throughput early selection, thus to accelerate breeding process. Our study explored the genetic architecture of growth and yield-related traits by combining high-throughput phenotyping and genotyping, which further unravelled the complex and stage-specific contributions of genetic loci to optimize growth and yield in wheat.
Collapse
Affiliation(s)
- Jie Gao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xin Hu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Chunyan Gao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Guang Chen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Hui Feng
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zhen Jia
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Peimin Zhao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Haiyang Yu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Huaiwen Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zedong Geng
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Jingbo Fu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Jun Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Yikeng Cheng
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Bo Yang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zhanghan Pang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Daoquan Xiang
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSaskatchewanCanada
| | - Jizeng Jia
- Institute of Crop SciencesChinese Academy of Crop Sciences (CAAS)BeijingChina
| | - Handong Su
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Caixia Lan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Wei Chen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Lifeng Gao
- Institute of Crop SciencesChinese Academy of Crop Sciences (CAAS)BeijingChina
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Qiang Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- The Center of Crop NanobiotechnologyHuazhong Agricultural UniversityWuhanChina
| |
Collapse
|
3
|
Ramappa S, Joshi MA, Krishna H, Dunna V, Jain N, Sreevathsa R, Devate NB. Unravelling the Genetic Basis of Moisture Deficit Stress Tolerance in Wheat for Seedling Vigour-Related Traits and Root Traits Using Genome-Wide Association Study. Genes (Basel) 2023; 14:1902. [PMID: 37895250 PMCID: PMC10606372 DOI: 10.3390/genes14101902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
A key abiotic stress that negatively affects seed germination, plant development, and crop yield is moisture deficit stress. Achieving higher vigour and uniform germination under stress conditions is essential for crop establishment and productivity and to enhance the yield. Hence, revealing wheat's capacity to withstand moisture deficit stress during seed germination and early growth stages is fundamental in improving its overall performance. However, the genetic regulation of moisture deficit stress tolerance during the seed germination phase remains largely unexplored. In this study, a total of 193 wheat genotypes were subjected to simulated moisture deficit stress using PEG-6000 (-0.4 MPa) during the seed germination stage. The induced moisture deficit stress significantly reduced various seedling-vigour-related traits. The genetic regions linked to these traits were found using a genome-wide association study (GWAS). The analysis identified 235 MTAs with a significance -log10(p) value of >4. After applying the Bonferroni correction, the study identified 47 unique single nucleotide polymorphisms (SNPs) that are linked to candidate genes important for the trait of interest. The current study emphasises the effectiveness of genome-wide association studies (GWAS) in identifying promising candidate genes, improving wheat seedling vigour and root traits, and offering essential information for the development of wheat cultivars tolerant to moisture deficit stress.
Collapse
Affiliation(s)
- S Ramappa
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Monika A. Joshi
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Vijay Dunna
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rohini Sreevathsa
- Division of Molecular Biology and Biotechnology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Narayana Bhat Devate
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| |
Collapse
|
4
|
Hou M, Cao Y, Zhang X, Zhang S, Jia T, Yang J, Han S, Wang L, Li J, Wang H, Zhang L, Wu X, Duan C, Li H. Genome-wide association study of maize resistance to Pythium aristosporum stalk rot. FRONTIERS IN PLANT SCIENCE 2023; 14:1239635. [PMID: 37662167 PMCID: PMC10470045 DOI: 10.3389/fpls.2023.1239635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/28/2023] [Indexed: 09/05/2023]
Abstract
Stalk rot, a severe and widespread soil-borne disease in maize, globally reduces yield and quality. Recent documentation reveals that Pythium aristosporum has emerged as one of the dominant causal agents of maize stalk rot. However, a previous study of maize stalk rot disease resistance mechanisms and breeding had mainly focused on other pathogens, neglecting P. aristosporum. To mitigate crop loss, resistance breeding is the most economical and effective strategy against this disease. This study involved characterizing resistance in 295 inbred lines using the drilling inoculation method and genotyping them via sequencing. By combining with population structure, disease resistance phenotype, and genome-wide association study (GWAS), we identified 39 significant single-nucleotide polymorphisms (SNPs) associated with P. aristosporum stalk rot resistance by utilizing six statistical methods. Bioinformatics analysis of these SNPs revealed 69 potential resistance genes, among which Zm00001d051313 was finally evaluated for its roles in host defense response to P. aristosporum infection. Through virus-induced gene silencing (VIGS) verification and physiological index determination, we found that transient silencing of Zm00001d051313 promoted P. aristosporum infection, indicating a positive regulatory role of this gene in maize's antifungal defense mechanism. Therefore, these findings will help advance our current understanding of the underlying mechanisms of maize defense to Pythium stalk rot.
Collapse
Affiliation(s)
- Mengwei Hou
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yanyong Cao
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xingrui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shulin Zhang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Tengjiao Jia
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jiwei Yang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Shengbo Han
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Lifeng Wang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jingjing Li
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hao Wang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Lili Zhang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaolin Wu
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Canxing Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiyong Li
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| |
Collapse
|
5
|
Mroz T, Dieseth JA, Lillemo M. Grain yield and adaptation of spring wheat to Norwegian growing conditions is driven by allele frequency changes at key adaptive loci discovered by genome-wide association mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:191. [PMID: 37589760 PMCID: PMC10435424 DOI: 10.1007/s00122-023-04424-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/24/2023] [Indexed: 08/18/2023]
Abstract
KEY MESSAGE Adaptation to the Norwegian environment is associated with polymorphisms in the Vrn-A1 locus. Historical selection for grain yield in Nordic wheat is associated with TaGS5-3A and TaCol-5 loci. Grain yields in Norwegian spring wheat increased by 18 kg ha-1 per year between 1972 and 2019 due to introduction of new varieties. These gains were associated with increments in the number of grains per spike and extended length of the vegetative period. However, little is known about the genetic background of this progress. To fill this gap, we conducted genome-wide association study on a panel consisting of both adapted (historical and current varieties and lines in the Nordics) and important not adapted accessions used as parents in the Norwegian wheat breeding program. The study concerned grain yield, plant height, and heading and maturity dates, and detected 12 associated loci, later validated using independent sets of recent breeding lines. Adaptation to the Norwegian cropping conditions was found to be associated with the Vrn-A1 locus, and a previously undescribed locus on chromosome 1B associated with heading date. Two loci associated with grain yield, corresponding to the TaGS5-3A and TaCol-5 loci, indicated historical selection pressure for high grain yield. A locus on chromosome 2A explained the tallness of the oldest accessions. We investigated the origins of the beneficial alleles associated with the wheat breeding progress in the Norwegian material, tracing them back to crosses with Swedish, German, or CIMMYT lines. This study contributes to the understanding of wheat adaptation to the Norwegian growing conditions, sheds light on the genetic basis of historical wheat improvement and aids future breeding efforts by discovering loci associated with important agronomic traits in wheat.
Collapse
Affiliation(s)
- Tomasz Mroz
- Department of Plant Sciences, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Jon Arne Dieseth
- Graminor, AS, Bjørke Gård, Hommelstadvegen 60, 2322, Ridabu, Norway
| | - Morten Lillemo
- Department of Plant Sciences, Norwegian University of Life Sciences, 1432, Ås, Norway.
| |
Collapse
|
6
|
Abdi H, Alipour H, Bernousi I, Jafarzadeh J, Rodrigues PC. Identification of novel putative alleles related to important agronomic traits of wheat using robust strategies in GWAS. Sci Rep 2023; 13:9927. [PMID: 37336905 DOI: 10.1038/s41598-023-36134-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/30/2023] [Indexed: 06/21/2023] Open
Abstract
Principal component analysis (PCA) is widely used in various genetics studies. In this study, the role of classical PCA (cPCA) and robust PCA (rPCA) was evaluated explicitly in genome-wide association studies (GWAS). We evaluated 294 wheat genotypes under well-watered and rain-fed, focusing on spike traits. First, we showed that some phenotypic and genotypic observations could be outliers based on cPCA and different rPCA algorithms (Proj, Grid, Hubert, and Locantore). Hubert's method provided a better approach to identifying outliers, which helped to understand the nature of these samples. These outliers led to the deviation of the heritability of traits from the actual value. Then, we performed GWAS with 36,000 single nucleotide polymorphisms (SNPs) based on the traditional approach and two robust strategies. In the conventional approach and using the first three components of cPCA as population structure, 184 and 139 marker-trait associations (MTAs) were identified for five traits in well-watered and rain-fed environments, respectively. In the first robust strategy and when rPCA was used as population structure in GWAS, we observed that the Hubert and Grid methods identified new MTAs, especially for yield and spike weight on chromosomes 7A and 6B. In the second strategy, we followed the classical and robust principal component-based GWAS, where the first two PCs obtained from phenotypic variables were used instead of traits. In the recent strategy, despite the similarity between the methods, some new MTAs were identified that can be considered pleiotropic. Hubert's method provided a better linear combination of traits because it had the most MTAs in common with the traditional approach. Newly identified SNPs, including rs19833 (5B) and rs48316 (2B), were annotated with important genes with vital biological processes and molecular functions. The approaches presented in this study can reduce the misleading GWAS results caused by the adverse effect of outlier observations.
Collapse
Affiliation(s)
- Hossein Abdi
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Hadi Alipour
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Iraj Bernousi
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran.
| | - Jafar Jafarzadeh
- Dryland Agricultural Research Institute (DARI), Agriculture Research, Education and Extension Organization (AREEO), Maragheh, Iran
| | | |
Collapse
|
7
|
Wang X, Zhang J, Mao W, Guan P, Wang Y, Chen Y, Liu W, Guo W, Yao Y, Hu Z, Xin M, Ni Z, Sun Q, Peng H. Association mapping identifies loci and candidate genes for grain-related traits in spring wheat in response to heat stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 331:111676. [PMID: 36933836 DOI: 10.1016/j.plantsci.2023.111676] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/05/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
Heat stress is a limiting factor in wheat production along with global warming. Development of heat-tolerant wheat varieties and generation of suitable pre-breeding materials are the major goals in current wheat breeding programs. Our understanding on the genetic basis of thermotolerance remains sparse. In this study, we genotyped a collection of 211 core spring wheat accessions and conducted field trials to evaluate the grain-related traits under heat stress and non-stress conditions in two different locations for three consecutive years. Based on SNP datasets and grain-related traits, we performed genome-wide association study (GWAS) to detect stable loci related to thermotolerance. Thirty-three quantitative trait loci (QTL) were identified, nine of them are the same loci as previous studies, and 24 are potentially novel loci. Functional candidate genes at these QTL are predicted and proved to be relevant to heat stress and grain-related traits such as TaELF3-A1 (1A) for earliness per se (Eps), TaHSFA1-B1 (5B) influencing heat tolerance and TaVIN2-A1 (6A) for grain size. Functional markers of TaELF3-A1 were detected and converted to KASP markers, with their function and genetic diversity being analyzed in the natural populations. In addition, our results unveiled favor alleles controlling agronomic traits and/or heat stress tolerance. In summary, we provide insights into heritable correlation between yield and heat stress tolerance, which will accelerate the development of new cultivars with high and stable yield of wheat in the future.
Collapse
Affiliation(s)
- Xiaobo Wang
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jinbo Zhang
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China; Institute of Crop Germplasm Resource, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Weiwei Mao
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Panfeng Guan
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yongfa Wang
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Wangqing Liu
- Crop Research Institute of Ningxia Academy of Agriculture and Forestry Sciences, Ningxia, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.
| |
Collapse
|
8
|
Singh VK, Chaturvedi D, Pundir S, Kumar D, Sharma R, Kumar S, Sharma S, Sharma S. GWAS scans of cereal cyst nematode (Heterodera avenae) resistance in Indian wheat germplasm. Mol Genet Genomics 2023; 298:579-601. [PMID: 36884084 DOI: 10.1007/s00438-023-01996-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 02/04/2023] [Indexed: 03/09/2023]
Abstract
Significant yield losses in major cereal-growing regions around the world have been linked to cereal cyst nematodes (Heterodera spp.). Identifying and deploying natural sources of resistance is of utmost importance due to increasing concerns associated with chemical methods over the years. We screened 141 diverse wheat genotypes collected from pan-Indian wheat cultivation states for nematode resistance over two years, alongside two resistant (Raj MR1, W7984 (M6)) and two susceptible (WH147, Opata M85) checks. We performed genome-wide association analysis using four single-locus models (GLM, MLM, CMLM, and ECMLM) and three multi-locus models (Blink, FarmCPU, and MLMM). Single locus models identified nine significant MTAs (-log10 (P) > 3.0) on chromosomes 2A, 3B, and 4B whereas, multi-locus models identified 11 significant MTAs on chromosomes 1B, 2A, 3B, 3D and 4B. Single and multi-locus models identified nine common significant MTAs. Candidate gene analysis identified 33 genes like F-box-like domain superfamily, Cytochrome P450 superfamily, Leucine-rich repeat, cysteine-containing subtype Zinc finger RING/FYVE/PHD-type, etc., having a putative role in disease resistance. Such genetic resources can help to reduce the impact of this disease on wheat production. Additionally, these results can be used to design new strategies for controlling the spread of H. avenae, such as the development of resistant varieties or the use of resistant cultivars. Finally, the obtained results can also be used to identify new sources of resistance to this pathogen and develop novel control methods.
Collapse
Affiliation(s)
- Vikas Kumar Singh
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, 250 004, Uttar Pradesh, India
| | - Deepti Chaturvedi
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, 250 004, Uttar Pradesh, India
| | - Saksham Pundir
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, 250 004, Uttar Pradesh, India.,Department of Botany, Chaudhary Charan Singh University (CCSU), Meerut, 250 004, Uttar Pradesh, India
| | - Deepak Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, 250 004, Uttar Pradesh, India.,Department of Botany, Chaudhary Charan Singh University (CCSU), Meerut, 250 004, Uttar Pradesh, India
| | - Rajiv Sharma
- Scotland's Rural College (SRUC), Peter Wilson Building, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Sundeep Kumar
- Division of Genomic Resources, National Bureau of Plant Genetic Resources (NBPGR), Pusa Campus, New Delhi, 110 012, India
| | - Shiveta Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, 250 004, Uttar Pradesh, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, 250 004, Uttar Pradesh, India.
| |
Collapse
|
9
|
Ahmed S, Iqbal M, Ahmad Z, Iqbal MA, Artyszak A, Sabagh AEL, Alharby HF, Hossain A. Foliar application of silicon-based nanoparticles improve the adaptability of maize (Zea mays L.) in cadmium contaminated soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:41002-41013. [PMID: 36626058 DOI: 10.1007/s11356-023-25189-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Heavy metals (HMs) especially cadmium (Cd) absorbed by the roots of crop plants like maize have emerged as one of the most serious threats by causing stunted plant growth along with disturbing the photosynthetic machinery and nutrient homeostasis process. A trial was conducted for inducing Cd stress tolerance in maize by exogenous application of silicon nanoparticles (SiNPs) using five doses of SiNPs (0, 100, 200, 300, and 400 ppm) and three levels of Cd (0, 15, and 30 ppm) for maize hybrid (SF-9515). The response variables included morphological traits and biochemical parameters of maize. The results indicated that Cd level of 30 ppm remained the most drastic for maize plants by recording the minimum traits such as shoot length (39.35 cm), shoot fresh weight (9.52 g) and shoot dry weight (3.20 g), leaf pigments such as chlorophyll a (0.55 mg/g FW), chlorophyll b (0.27 mg/g FW), total contents (0.84 mg/g FW), and carotenoid contents (0.19 µg/g FW). Additionally, the same Cd level disrupted biochemical traits such as TSP (4.85 mg/g FW), TP (252.94 nmol/g FW), TSAA (18.92 µmol g-1 FW), TSS (0.85 mg/g FW), and antioxidant activities such as POD (99.39 min-1 g-1 FW), CAT (81.58 min-1 g-1 FW), APX (2.04 min-1 g-1 FW), and SOD (172.79 min-1 g-1 FW). However, a higher level of Cd resulted in greater root length (87.63 cm), root fresh weight (16.43 g), and root dry weight (6.14 g) along with higher Cd concentration in the root (2.52 µg/g-1) and shoot (0.48 µg/g-1). The silicon nanoparticles (Si NPs) treatment significantly increased all measured attributes of maize. The highest value was noted of all the parameters such as chlorophyll a (0.91 mg/g FW), chlorophyll b (0.57 mg/g FW), total chlorophyll contents (1.48 mg/g FW), total carotenoid contents (0.40 µg/g FW), TSP (6.12 mg/g FW), TP (384.56 nmol/g FW), TSAA (24.64 µmol g-1 FW), TSS (1.87 mg/g FW), POD (166.10 min-1 g-1 FW), CAT (149.54 min-1 g-1 FW), APX (3.49 min-1 g-1 FW), and SOD (225.57 min-1 g-1 FW). Based on recorded findings, it might be inferred that higher levels of Cd tend to drastically reduce morpho-physiological traits of maize and foliage-applied silver nanoparticles hold the potential to ameliorate the adverse effect of Cd stress on maize.
Collapse
Affiliation(s)
- Sarfraz Ahmed
- Department of Botany, University of Okara, Okara, 56300, Punjab, Pakistan
| | - Muhammad Iqbal
- Department of Botany, University of Okara, Okara, 56300, Punjab, Pakistan
| | - Zahoor Ahmad
- Department of Botany, University of Central Punjab, Constituent College, Bahawalpur, 63100, Pakistan.
| | - Muhammad Aamir Iqbal
- Department of Agronomy, University of Poonch Rawalakot, Azad Kashmir, Poonch Rawalakot, Pakistan
| | - Arkadiusz Artyszak
- Department of Agronomy, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | - Ayman E L Sabagh
- Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Shaikh, Egypt
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt, Turkey
| | - Hesham F Alharby
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Plant Biology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Akbar Hossain
- Soil Science Division, Bangladesh Wheat and Maize Research Institute, Dinajpur, 5200, Bangladesh
| |
Collapse
|
10
|
Mulugeta B, Tesfaye K, Ortiz R, Johansson E, Hailesilassie T, Hammenhag C, Hailu F, Geleta M. Marker-trait association analyses revealed major novel QTLs for grain yield and related traits in durum wheat. FRONTIERS IN PLANT SCIENCE 2023; 13:1009244. [PMID: 36777537 PMCID: PMC9909559 DOI: 10.3389/fpls.2022.1009244] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
The growing global demand for wheat for food is rising due to the influence of population growth and climate change. The dissection of complex traits by employing a genome-wide association study (GWAS) allows the identification of DNA markers associated with complex traits to improve the productivity of crops. We used GWAS with 10,045 single nucleotide polymorphism (SNP) markers to search for genomic regions associated with grain yield and related traits based on diverse panels of Ethiopian durum wheat. In Ethiopia, multi-environment trials of the genotypes were carried out at five locations. The genotyping was conducted using the 25k Illumina Wheat SNP array to explore population structure, linkage disequilibrium (LD), and marker-trait associations (MTAs). For GWAS, the multi-locus Fixed and Random Model Circulating Probability Unification (FarmCPU) model was applied. Broad-sense heritability estimates were high, ranging from 0.63 (for grain yield) to 0.97 (for thousand-kernel weight). The population structure based on principal component analysis, and model-based cluster analysis revealed two genetically distinct clusters with limited admixtures. The LD among SNPs declined within the range of 2.02-10.04 Mbp with an average of 4.28 Mbp. The GWAS scan based on the mean performance of the genotypes across the environments identified 44 significant MTAs across the chromosomes. Twenty-six of these MTAs are novel, whereas the remaining 18 were previously reported and confirmed in this study. We also identified candidate genes for the novel loci potentially regulating the traits. Hence, this study highlights the significance of the Ethiopian durum wheat gene pool for improving durum wheat globally. Furthermore, a breeding strategy focusing on accumulating favorable alleles at these loci could improve durum wheat production in the East African highlands and elsewhere.
Collapse
Affiliation(s)
- Behailu Mulugeta
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
- Sinana Agricultural Research Center, Oromia Agricultural Research Institute, Bale-Robe, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Director General, Bio and Emerging Technology Institute (BETin), Addis Ababa, Ethiopia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Faris Hailu
- Department of Biology and Biotechnology, Wollo University, Dessie, Ethiopia
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| |
Collapse
|
11
|
Singh S, Gaurav SS, Vasistha NK, Kumar U, Joshi AK, Mishra VK, Chand R, Gupta PK. Genetics of spot blotch resistance in bread wheat ( Triticum aestivum L.) using five models for GWAS. FRONTIERS IN PLANT SCIENCE 2023; 13:1036064. [PMID: 36743576 PMCID: PMC9891466 DOI: 10.3389/fpls.2022.1036064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Genetic architecture of resistance to spot blotch in wheat was examined using a Genome-Wide Association Study (GWAS) involving an association panel comprising 303 diverse genotypes. The association panel was evaluated at two different locations in India including Banaras Hindu University (BHU), Varanasi (Uttar Pradesh), and Borlaug Institute for South Asia (BISA), Pusa, Samastipur (Bihar) for two consecutive years (2017-2018 and 2018-2019), thus making four environments (E1, BHU 2017-18; E2, BHU 2018-19; E3, PUSA, 2017-18; E4, PUSA, 2018-19). The panel was genotyped for 12,196 SNPs based on DArT-seq (outsourced to DArT Ltd by CIMMYT); these SNPs included 5,400 SNPs, which could not be assigned to individual chromosomes and were therefore, described as unassigned by the vendor. Phenotypic data was recorded on the following three disease-related traits: (i) Area Under Disease Progress Curve (AUDPC), (ii) Incubation Period (IP), and (iii) Lesion Number (LN). GWAS was conducted using each of five different models, which included two single-locus models (CMLM and SUPER) and three multi-locus models (MLMM, FarmCPU, and BLINK). This exercise gave 306 MTAs, but only 89 MTAs (33 for AUDPC, 30 for IP and 26 for LN) including a solitary MTA detected using all the five models and 88 identified using four of the five models (barring SUPER) were considered to be important. These were used for further analysis, which included identification of candidate genes (CGs) and their annotation. A majority of these MTAs were novel. Only 70 of the 89 MTAs were assigned to individual chromosomes; the remaining 19 MTAs belonged to unassigned SNPs, for which chromosomes were not known. Seven MTAs were selected on the basis of minimum P value, number of models, number of environments and location on chromosomes with respect to QTLs reported earlier. These 7 MTAs, which included five main effect MTAs and two for epistatic interactions, were considered to be important for marker-assisted selection (MAS). The present study thus improved our understanding of the genetics of resistance against spot blotch in wheat and provided seven MTAs, which may be used for MAS after due validation.
Collapse
Affiliation(s)
- Sahadev Singh
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Shailendra Singh Gaurav
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Neeraj Kumar Vasistha
- Department of Genetics-Plant Breeding and Biotechnology, Dr Khem Singh Gill, Akal College of Agriculture, Eternal University, Sirmaur, India
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Arun Kumar Joshi
- The International Maize and Wheat Improvement Center (CIMMYT), Borlaug Institute for South Asia (BISA), G-2, B-Block, NASC Complex, DPS Marg, New Delhi, India
| | - Vinod Kumar Mishra
- Department of Genetics and Plant Breeding, Indian Institute of Agricultural Science, Banaras Hindu University, Varanasi, India
| | - Ramesh Chand
- Department of Mycology and Plant Pathology, Indian Institute of Agricultural Science Banaras Hindu University, Varanasi, India
| | - Pushpendra Kumar Gupta
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Borlaug Institute for South Asia (BISA), Ludhiana, India
- Murdoch’s Centre for Crop & Food Innovation, Murdoch University, Murdoch, WA, Australia
| |
Collapse
|
12
|
Devate NB, Krishna H, Mishra CN, Manjunath KK, Sunilkumar VP, Chauhan D, Singh S, Sinha N, Jain N, Singh GP, Singh PK. Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and drought stress conditions in wheat. FRONTIERS IN PLANT SCIENCE 2023; 13:1082513. [PMID: 36726675 PMCID: PMC9885108 DOI: 10.3389/fpls.2022.1082513] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/15/2022] [Indexed: 06/18/2023]
Abstract
Introduction Wheat is grown and consumed worldwide, making it an important staple food crop for both its calorific and nutritional content. In places where wheat is used as a staple food, suboptimal micronutrient content levels, especially of grain iron (Fe) and zinc (Zn), can lead to malnutrition. Grain nutrient content is influenced by abiotic stresses, such as drought and heat stress. The best method for addressing micronutrient deficiencies is the biofortification of food crops. The prerequisites for marker-assisted varietal development are the identification of the genomic region responsible for high grain iron and zinc contents and an understanding of their genetics. Methods A total of 193 diverse wheat genotypes were evaluated under drought and heat stress conditions across the years at the Indian Agricultural Research Institute (IARI), New Delhi, under timely sown irrigated (IR), restricted irrigated (RI) and late sown (LS) conditions. Grain iron content (GFeC) and grain zinc content (GZnC) were estimated from both the control and treatment groups. Genotyping of all the lines under study was carried out with the single nucleotide polymorphisms (SNPs) from Breeder's 35K Axiom Array. Result and Discussion Three subgroups were observed in the association panel based on both principal component analysis (PCA) and dendrogram analysis. A large whole-genome linkage disequilibrium (LD) block size of 3.49 Mb was observed. A genome-wide association study identified 16 unique stringent marker trait associations for GFeC, GZnC, and 1000-grain weight (TGW). In silico analysis demonstrated the presence of 28 potential candidate genes in the flanking region of 16 linked SNPs, such as synaptotagmin-like mitochondrial-lipid-binding domain, HAUS augmin-like complex, di-copper center-containing domain, protein kinase, chaperonin Cpn60, zinc finger, NUDIX hydrolase, etc. Expression levels of these genes in vegetative tissues and grain were also found. Utilization of identified markers in marker-assisted breeding may lead to the rapid development of biofortified wheat genotypes to combat malnutrition.
Collapse
Affiliation(s)
- Narayana Bhat Devate
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | | | | | - V. P. Sunilkumar
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | - Divya Chauhan
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | - Shweta Singh
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | - Nivedita Sinha
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| | | | - Pradeep Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, India
| |
Collapse
|
13
|
Lisker A, Maurer A, Schmutzer T, Kazman E, Cöster H, Holzapfel J, Ebmeyer E, Alqudah AM, Sannemann W, Pillen K. A Haplotype-Based GWAS Identified Trait-Improving QTL Alleles Controlling Agronomic Traits under Contrasting Nitrogen Fertilization Treatments in the MAGIC Wheat Population WM-800. PLANTS (BASEL, SWITZERLAND) 2022; 11:3508. [PMID: 36559621 PMCID: PMC9784842 DOI: 10.3390/plants11243508] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/27/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The multi-parent-advanced-generation-intercross (MAGIC) population WM-800 was developed by intercrossing eight modern winter wheat cultivars to enhance the genetic diversity present in breeding populations. We cultivated WM-800 during two seasons in seven environments under two contrasting nitrogen fertilization treatments. WM-800 lines exhibited highly significant differences between treatments, as well as high heritabilities among the seven agronomic traits studied. The highest-yielding WM-line achieved an average yield increase of 4.40 dt/ha (5.2%) compared to the best founder cultivar Tobak. The subsequent genome-wide-association-study (GWAS), which was based on haplotypes, located QTL for seven agronomic traits including grain yield. In total, 40, 51, and 46 QTL were detected under low, high, and across nitrogen treatments, respectively. For example, the effect of QYLD_3A could be associated with the haplotype allele of cultivar Julius increasing yield by an average of 4.47 dt/ha (5.2%). A novel QTL on chromosome 2B exhibited pleiotropic effects, acting simultaneously on three-grain yield components (ears-per-square-meter, grains-per-ear, and thousand-grain-weight) and plant-height. These effects may be explained by a member of the nitrate-transporter-1 (NRT1)/peptide-family, TaNPF5.34, located 1.05 Mb apart. The WM-800 lines and favorable QTL haplotypes, associated with yield improvements, are currently implemented in wheat breeding programs to develop advanced nitrogen-use efficient wheat cultivars.
Collapse
Affiliation(s)
- Antonia Lisker
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Thomas Schmutzer
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Ebrahim Kazman
- Syngenta Seeds GmbH, Kroppenstedter Str. 4, 39387 Oschersleben, Germany
| | | | - Josef Holzapfel
- Secobra Saatzucht GmbH, Feldkirchen 3, 85368 Moosburg an der Isar, Germany
| | - Erhard Ebmeyer
- KWS Lochow GMBH, Ferdinand-Lochow-Str. 5, 29303 Bergen, Germany
| | - Ahmad M. Alqudah
- Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, Doha P.O. Box 2713, Qatar
| | - Wiebke Sannemann
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| |
Collapse
|
14
|
Genome-Wide Association Analysis for Hybrid Breeding in Wheat. Int J Mol Sci 2022; 23:ijms232315321. [PMID: 36499647 PMCID: PMC9740285 DOI: 10.3390/ijms232315321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/24/2022] [Accepted: 11/27/2022] [Indexed: 12/12/2022] Open
Abstract
Disclosure of markers that are significantly associated with plant traits can help develop new varieties with desirable properties. This study determined the genome-wide associations based on DArTseq markers for six agronomic traits assessed in eight environments for wheat. Moreover, the association study for heterosis and analysis of the effects of markers grouped by linkage disequilibrium were performed based on mean values over all experiments. All results were validated using data from post-registration trials. GWAS revealed 1273 single nucleotide polymorphisms with biologically significant effects. Most polymorphisms were predicted to be modifiers of protein translation, with only two having a more pronounced effect. Markers significantly associated with the considered set of features were clustered within chromosomes based on linkage disequilibrium in 327 LD blocks. A GWAS for heterosis revealed 1261 markers with significant effects.
Collapse
|
15
|
Shi H, Chen M, Gao L, Wang Y, Bai Y, Yan H, Xu C, Zhou Y, Xu Z, Chen J, Tang W, Wang S, Shi Y, Wu Y, Sun D, Jia J, Ma Y. Genome-wide association study of agronomic traits related to nitrogen use efficiency in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4289-4302. [PMID: 36136127 DOI: 10.1007/s00122-022-04218-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
GWAS identified 347 QTLs associated with eight traits related to nitrogen use efficiency in a 389-count wheat panel. Four novel candidate transcription factor genes were verified using qRT-PCR. Nitrogen is an essential nutrient for plants that determines crop yield. Improving nitrogen use efficiency (NUE) should considerably increase wheat yield and reduce the use of nitrogen fertilisers. However, knowledge on the genetic basis of NUE during wheat maturity is limited. In this study, a diversity panel incorporating 389 wheat accessions was phenotyped for eight NUE-related agronomic traits across five different environments. A total of 347 quantitative trait loci (QTLs) for low nitrogen tolerance indices (ratio of agronomic characters under low and high nitrogen conditions) were identified through a genome-wide association study utilising 397,384 single nucleotide polymorphisms (SNPs) within the MLM (Q + K) model, including 11 stable QTLs. Furthermore, 69 candidate genes were predicted for low nitrogen tolerance indices of best linear unbiased predictions values of the eight studied agronomic traits, and four novel candidate transcription factors (TraesCS5A02G237500 for qFsnR5A.2, TraesCS5B02G384500 and TraesCS5B02G384600 for qSLR5B.1, and TraesCS3B02G068800 for qTKWR3B.1) showed differing expression patterns in contrasting low-nitrogen-tolerant wheat genotypes. Moreover, the number of favourable marker alleles calculated using NUE that were significantly related to SNP in accessions decreased over the decades, indicating a decline in the NUE of the 389 wheat varieties. These findings denote promising NUE markers that could be useful in breeding high-NUE wheat varieties, and the candidate genes could further detail the NUE-related regulation network in wheat.
Collapse
Affiliation(s)
- Huawei Shi
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Ming Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Lifeng Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Yanxia Wang
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Research Center of Wheat Engineering Technology of Hebei, Shijiazhuang, 050041, Hebei, China
| | - Yanming Bai
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Huishu Yan
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Chengjie Xu
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Yongbin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Zhaoshi Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Jun Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Wensi Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Shuguang Wang
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yugang Shi
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yuxiang Wu
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Daizhen Sun
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Jizeng Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
| | - Youzhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
| |
Collapse
|
16
|
Rahim MS, Kumar V, Roy J. Genetic dissection of quantitative traits loci identifies new genes for gelatinization parameters of starch and amylose-lipid complex (Resistant starch 5) in bread wheat. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111452. [PMID: 36087884 DOI: 10.1016/j.plantsci.2022.111452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/08/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Starch is a major component of cereal grains such as wheat. Physicochemical and functional properties of starch affect end-use food quality and nutrients. To improve cultivars that preserve superior starch quality, the genetic foundation of the wheat starch and amylose-lipid complex (ALc, Resistant starch type 5) gelatinization are needed. This genome-wide association (GWA) mapping used 192 wheat genotypes (previously reported) to generate SNPs using an enhanced version of sequencing termed ddRAD on the Illumina Hi-seq X platform and 3696 high-quality influential SNPs were filtered out. The heterozygosity and Fst ranges in five subpopulations were 0.31-0.40 and 0.18-0.30 respectively. Nucleotide diversity and PIC ranged from 0.21 (6A) to 0.32 (2A) and 0.29 (6A) to 0.39 (4D) respectively. The Shannon waiver index was 1.7 and the whole-genome LD decay was 22 Mb at r2 = 0.38. Following FDR, 23 and 8 SNPs showed association with starch properties in the year 2017 and 2018, respectively while 93 and 20 SNPs were associated with ALc gelatinization in the year 2017 and 2018 respectively. The identified potential new genes (GSK3-alpha, RING-type domain-containing protein, Tetratricopeptide repeat, Hexosyltransferase, GLP, SNF1, and WRKY transcription factor) within LD range (∼16 Kb to ∼15 Mb), BLUP value, and cis and trans-position of SNPs network provide valuable information for the future wheat breeding strategy for the improvement of the starch quality trait.
Collapse
Affiliation(s)
- Mohammed Saba Rahim
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali-140 306, Punjab, India; Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda.
| | - Vinay Kumar
- Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda.
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali-140 306, Punjab, India.
| |
Collapse
|
17
|
Genome-Wide Association Study in Bread Wheat Identifies Genomic Regions Associated with Grain Yield and Quality under Contrasting Water Availability. Int J Mol Sci 2022; 23:ijms231810575. [PMID: 36142488 PMCID: PMC9505613 DOI: 10.3390/ijms231810575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
The objectives of this study were to identify genetic loci in the bread wheat genome that would influence yield stability and quality under water stress, and to identify accessions that can be recommended for cultivation in dry and hot regions. We performed a genome-wide association study (GWAS) using a panel of 232 wheat accessions spanning diverse ecogeographic regions. Plants were evaluated in the Israeli Northern Negev, under two environments: water-limited (D; 250 mm) and well-watered (W; 450 mm) conditions; they were genotyped with ~71,500 SNPs derived from exome capture sequencing. Of the 14 phenotypic traits evaluated, 12 had significantly lower values under D compared to W conditions, while the values for two traits were higher under D. High heritability (H2 = 0.5–0.9) was observed for grain yield, spike weight, number of grains per spike, peduncle length, and plant height. Days to heading and grain yield could be partitioned based on accession origins. GWAS identified 154 marker-trait associations (MTAs) for yield and quality-related traits, 82 under D and 72 under W, and identified potential candidate genes. We identified 24 accessions showing high and/or stable yields under D conditions that can be recommended for cultivation in regions under the threat of global climate change.
Collapse
|
18
|
Khan H, Krishnappa G, Kumar S, Mishra CN, Krishna H, Devate NB, Rathan ND, Parkash O, Yadav SS, Srivastava P, Biradar S, Kumar M, Singh GP. Genome-wide association study for grain yield and component traits in bread wheat (Triticum aestivum L.). Front Genet 2022; 13:982589. [PMID: 36092913 PMCID: PMC9458894 DOI: 10.3389/fgene.2022.982589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022] Open
Abstract
Genomic regions governing days to heading (DH), grain filling duration (GFD), grain number per spike (GNPS), grain weight per spike (GWPS), plant height (PH), and grain yield (GY) were investigated in a set of 280 diverse bread wheat genotypes. The genome-wide association studies (GWAS) panel was genotyped using a 35K Axiom Array and phenotyped in five environments. The GWAS analysis showed a total of 27 Bonferroni-corrected marker-trait associations (MTAs) on 15 chromosomes representing all three wheat subgenomes. The GFD showed the highest MTAs (8), followed by GWPS (7), GY (4), GNPS (3), PH (3), and DH (2). Furthermore, 20 MTAs were identified with more than 10% phenotypic variation. A total of five stable MTAs (AX-95024590, AX-94425015, AX-95210025 AX-94539354, and AX-94978133) were identified in more than one environment and associated with the expression of DH, GFD, GNPS, and GY. Similarly, two novel pleiotropic genomic regions with associated MTAs i.e. AX-94978133 (4D) and AX-94539354 (6A) harboring co-localized QTLs governing two or more traits were also identified. In silico analysis revealed that the SNPs were located on important putative candidate genes such as F-box-like domain superfamily, Lateral organ boundaries, LOB, Thioredoxin-like superfamily Glutathione S-transferase, RNA-binding domain superfamily, UDP-glycosyltransferase family, Serine/threonine-protein kinase, Expansin, Patatin, Exocyst complex component Exo70, DUF1618 domain, Protein kinase domain involved in the regulation of grain size, grain number, growth and development, grain filling duration, and abiotic stress tolerance. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection (MAS).
Collapse
Affiliation(s)
- Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Gopalareddy Krishnappa
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
- *Correspondence: Gopalareddy Krishnappa, ; Gyanendra Pratap Singh,
| | - Satish Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Hari Krishna
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Om Parkash
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sonu Singh Yadav
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Suma Biradar
- University of Agricultural Sciences, Dharwad, India
| | - Monu Kumar
- ICAR-Indian Agricultural Research Institute, Jharkhand, India
| | - Gyanendra Pratap Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
- *Correspondence: Gopalareddy Krishnappa, ; Gyanendra Pratap Singh,
| |
Collapse
|
19
|
Devate NB, Krishna H, Parmeshwarappa SKV, Manjunath KK, Chauhan D, Singh S, Singh JB, Kumar M, Patil R, Khan H, Jain N, Singh GP, Singh PK. Genome-wide association mapping for component traits of drought and heat tolerance in wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:943033. [PMID: 36061792 PMCID: PMC9429996 DOI: 10.3389/fpls.2022.943033] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/25/2022] [Indexed: 06/01/2023]
Abstract
Identification of marker trait association is a prerequisite for marker-assisted breeding. To find markers linked with traits under heat and drought stress in bread wheat (Triticum aestivum L.), we performed a genome-wide association study (GWAS). GWAS mapping panel used in this study consists of advanced breeding lines from the IARI stress breeding programme produced by pairwise and complex crosses. Phenotyping was done at multi locations namely New Delhi, Karnal, Indore, Jharkhand and Pune with augmented-RCBD design under different moisture and heat stress regimes, namely timely sown irrigated (IR), timely sown restricted irrigated (RI) and late sown (LS) conditions. Yield and its component traits, viz., Days to Heading (DH), Days to Maturity (DM), Normalized Difference Vegetation Index (NDVI), Chlorophyll Content (SPAD), Canopy temperature (CT), Plant Height (PH), Thousand grain weight (TGW), Grain weight per spike (GWPS), Plot Yield (PLTY) and Biomass (BMS) were phenotyped. Analysis of variance and descriptive statistics revealed significant differences among the studied traits. Genotyping was done using the 35k SNP Wheat Breeder's Genotyping Array. Population structure and diversity analysis using filtered 10,546 markers revealed two subpopulations with sufficient diversity. A large whole genome LD block size of 7.15 MB was obtained at half LD decay value. Genome-wide association search identified 57 unique markers associated with various traits across the locations. Twenty-three markers were identified to be stable, among them nine pleiotropic markers were also identified. In silico search of the identified markers against the IWGSC ref genome revealed the presence of a majority of the SNPs at or near the gene coding region. These SNPs can be used for marker-assisted transfer of genes/QTLs after validation to develop climate-resilient cultivars.
Collapse
Affiliation(s)
- Narayana Bhat Devate
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Divya Chauhan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shweta Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jang Bahadur Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Monu Kumar
- Division of Genetics and Plant Breeding, ICAR-Indian Agricultural Research Institute, Gauria Karma, India
| | - Ravindra Patil
- Genetics and Plant Breeding Group, Agharkar Research Institute, Pune, India
| | - Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Pradeep Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| |
Collapse
|
20
|
Hussain S, Habib M, Ahmed Z, Sadia B, Bernardo A, Amand PS, Bai G, Ghori N, Khan AI, Awan FS, Maqbool R. Genotyping-by-Sequencing Based Molecular Genetic Diversity of Pakistani Bread Wheat ( Triticum aestivum L.) Accessions. Front Genet 2022; 13:772517. [PMID: 35464861 PMCID: PMC9019749 DOI: 10.3389/fgene.2022.772517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/07/2022] [Indexed: 11/29/2022] Open
Abstract
Spring wheat (Triticum aestivum L.) is one of the most imperative staple food crops, with an annual production of 765 million tons globally to feed ∼40% world population. Genetic diversity in available germplasm is crucial for sustainable wheat improvement to ensure global food security. A diversity panel of 184 Pakistani wheat accessions was genotyped using 123,596 high-quality single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing with 42% of the SNPs mapped on B, 36% on A, and 22% on D sub-genomes of wheat. Chromosome 2B contains the most SNPs (9,126), whereas 4D has the least (2,660) markers. The mean polymorphic information content, genetic diversity, and major allele frequency of the population were 0.157, 0.1844, and 0.87, respectively. Analysis of molecular variance revealed a higher genetic diversity (80%) within the sub-population than among the sub-populations (20%). The genome-wide linkage disequilibrium was 0.34 Mbp for the whole wheat genome. Among the three subgenomes, A has the highest LD decay value (0.29 Mbp), followed by B (0.2 Mbp) and D (0.07 Mbp) genomes, respectively. The results of population structure, principal coordinate analysis, phylogenetic tree, and kinship analysis also divided the whole population into three clusters comprising 31, 33, and 120 accessions in group 1, group 2, and group 3, respectively. All groups were dominated by the local wheat accessions. Estimation of genetic diversity will be a baseline for the selection of breeding parents for mutations and the genome-wide association and marker-assisted selection studies.
Collapse
Affiliation(s)
- Shabbir Hussain
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Madiha Habib
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Zaheer Ahmed
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Bushra Sadia
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Amy Bernardo
- USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Paul St Amand
- USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Guihua Bai
- USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Nida Ghori
- USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Azeem I Khan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Faisal S Awan
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Rizwana Maqbool
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| |
Collapse
|
21
|
Tian Y, Sang W, Liu P, Liu J, Xiang J, Cui F, Xu H, Han X, Nie Y, Kong D, Li W, Mu P. Genome-wide Association Study for Starch Pasting Properties in Chinese Spring Wheat. Front Genet 2022; 13:830644. [PMID: 35401682 PMCID: PMC8990798 DOI: 10.3389/fgene.2022.830644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
In order to understand the genetic basis of starch pasting viscosity characteristics of Chinese spring wheat, we assessed the genetic variation of RVA parameters determined by the Rapid Visco Analyser in a panel of 192 Chinese spring wheat accessions grown in Er’shi, Shihezi and Zhaosu during 2012 and 2013 cropping seasons. A genome-wide association study with 47,362 single nucleotide polymorphism (SNP) markers was conducted to detect marker-trait associations using mixed linear model. Phenotypic variations of RVA parameters ranged from 1.6 to 30.7% and broad-sense heritabilities ranged from 0.62 to 0.91. Forty-one SNP markers at 25 loci were significantly associated with seven RVA traits in at least two environments; among these, 20 SNPs were located in coding sequences (CDS) of 18 annotation genes, which can lead to discovering novel genes underpinning starch gelatinization in spring wheat. Haplotype analysis revealed one block for breakdown (BD) on chromosome 3B and two blocks for pasting temperature (T) on chromosome 7B. Cultivars with superior haplotypes at these loci showed better starch pasting viscosity than the average of all cultivars surveyed. The identified loci and associated markers provide valuable sources for future functional characterization and genetic improvement of starch quality in wheat.
Collapse
Affiliation(s)
- Yousheng Tian
- The Key Laboratory of the Oasis Ecological Agriculture, College of Agriculture, Shihezi University, Shihezi, China
- Department of Administrative Management, Xinjiang Academy of Agri-reclamation Sciences, Shihezi, China
| | - Wei Sang
- Institute of Crop Science, Xinjiang Academy of Agri-reclamation Sciences/Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, China
| | - Pengpeng Liu
- Institute of Crop Science, Xinjiang Academy of Agri-reclamation Sciences/Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, China
| | - Jindong Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jishan Xiang
- Institute of Crop Science, Xinjiang Academy of Agri-reclamation Sciences/Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, China
| | - Fengjuan Cui
- Institute of Crop Science, Xinjiang Academy of Agri-reclamation Sciences/Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, China
| | - Hongjun Xu
- Institute of Crop Science, Xinjiang Academy of Agri-reclamation Sciences/Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, China
| | - Xinnian Han
- Institute of Crop Science, Xinjiang Academy of Agri-reclamation Sciences/Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, China
| | - Yingbin Nie
- Institute of Crop Science, Xinjiang Academy of Agri-reclamation Sciences/Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, China
| | - Dezhen Kong
- Institute of Crop Science, Xinjiang Academy of Agri-reclamation Sciences/Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, China
| | - Weihua Li
- The Key Laboratory of the Oasis Ecological Agriculture, College of Agriculture, Shihezi University, Shihezi, China
- *Correspondence: Weihua Li, ; Peiyuan Mu,
| | - Peiyuan Mu
- Institute of Crop Science, Xinjiang Academy of Agri-reclamation Sciences/Key Lab of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Shihezi, China
- *Correspondence: Weihua Li, ; Peiyuan Mu,
| |
Collapse
|
22
|
Omics: a tool for resilient rice genetic improvement strategies. Mol Biol Rep 2022; 49:5075-5088. [PMID: 35298758 DOI: 10.1007/s11033-022-07189-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 01/24/2022] [Indexed: 10/18/2022]
Abstract
Rice is pivotal pyramid of about half of the world population. Bearing small genome size and worldwide utmost food crop rice has been known as ideal cereal crop for genome research. Currently, decreasing water table and soil fatigue are big challenges and intense consequences in changing climate. Whole sequenced genome of rice sized 389 Mb of which 95% is covered with excellent mapping order. Sequenced rice genome helps in molecular biology and transcriptomics of cereals as it provides whole genome sequence of indica and japonica sub species. Through rice genome sequencing and functional genomics, QTLs or genes, genetic variability and halophyte blocks for agronomic characters were identified which have proved much more useful in molecular breeding and direct selection. There are different numbers of genes or QTLs identified for yield related traits i.e., 6 QTLs/genes for plant architecture, 6 for panicle characteristics, 4 for grain number, 1 gene/QTL for tiller, HGW, grain filling and shattering. QTLS/genes for grain quality, biotic stresses and for abiotic stresses are 7, 23 and 13 respectively. Low yield, inferior quality and susceptibility to biotic and abiotic stresses of a crop is due to narrow genetic background of new evolving rice verities. Wild rice provides genetic resources for improvement of these characters, molecular and genomics tool at different stages can overcome these stresses and improve yield and quality of rice crop.
Collapse
|
23
|
Malik P, Kumar J, Sharma S, Meher PK, Balyan HS, Gupta PK, Sharma S. GWAS for main effects and epistatic interactions for grain morphology traits in wheat. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:651-668. [PMID: 35465203 PMCID: PMC8986918 DOI: 10.1007/s12298-022-01164-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 06/05/2023]
Abstract
In the present study in wheat, GWAS was conducted for identification of marker trait associations (MTAs) for the following six grain morphology traits: (1) grain cross-sectional area (GCSA), (2) grain perimeter (GP), (3) grain length (GL), (4) grain width (GWid), (5) grain length-width ratio (GLWR) and (6) grain form-density (GFD). The data were recorded on a subset of spring wheat reference set (SWRS) comprising 225 diverse genotypes, which were genotyped using 10,904 SNPs and phenotyped for two consecutive years (2017-2018, 2018-2019). GWAS was conducted using five different models including two single-locus models (CMLM, SUPER), one multi-locus model (FarmCPU), one multi-trait model (mvLMM) and a model for Q x Q epistatic interactions. False discovery rate (FDR) [P value -log10(p) ≥ 5] and Bonferroni correction [P value -log10(p) ≥ 6] (corrected p value < 0.05) were applied to eliminate false positives due to multiple testing. This exercise gave 88 main effect and 29 epistatic MTAs after FDR and 13 main effect and 6 epistatic MTAs after Bonferroni corrections. MTAs obtained after Bonferroni corrections were further utilized for identification of 55 candidate genes (CGs). In silico expression analysis of CGs in different tissues at different parts of the seed at different developmental stages was also carried out. MTAs and CGs identified during the present study are useful addition to available resources for MAS to supplement wheat breeding programmes after due validation and also for future strategic basic research. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01164-w.
Collapse
Affiliation(s)
- Parveen Malik
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
| | - Jitendra Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
- Department of Biotechnology, National Agri-Food Biotechnology Institute (NABI), Govt. of India, Sector 81 (Knowledge City), S.A.S. Nagar, Mohali, Punjab 140306 India
| | - Shiveta Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
| | - Prabina Kumar Meher
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
| |
Collapse
|
24
|
Lal MK, Tiwari RK, Gahlaut V, Mangal V, Kumar A, Singh MP, Paul V, Kumar S, Singh B, Zinta G. Physiological and molecular insights on wheat responses to heat stress. PLANT CELL REPORTS 2022; 41:501-518. [PMID: 34542670 DOI: 10.1007/s00299-021-02784-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/07/2021] [Indexed: 05/25/2023]
Abstract
Increasing temperature is a key component of global climate change, affecting crop growth and productivity worldwide. Wheat is a major cereal crop grown in various parts of the globe, which is affected severely by heat stress. The morphological parameters affected include germination, seedling establishment, source-sink activity, leaf area, shoot and root growth. The physiological parameters such as photosynthesis, respiration, leaf senescence, water and nutrient relation are also affected by heat. At the cellular level, heat stress leads to the generation of reactive oxygen species that disrupt the membrane system of thylakoid, chloroplast and plasma membrane. The deactivation of the photosystem, reduction in photosynthesis and inactivation of rubisco affect the production of photoassimilates and their allocation. This ultimately affects anthesis, grain filling, size, number and maturity of wheat grains, which hamper crop productivity. The interplay of various systems comprising antioxidants and hormones plays a crucial role in imparting heat stress tolerance in wheat. Thus, implementation of various omics technologies could foster in-depth insights on heat stress effects, eventually devising heat stress mitigation strategies by conventional and modern breeding to develop heat-tolerant wheat varieties. This review provides an integrative view of heat stress responses in wheat and also discusses approaches to develop heat-tolerant wheat varieties.
Collapse
Affiliation(s)
- Milan Kumar Lal
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rahul Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Vijay Gahlaut
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Vikas Mangal
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Awadhesh Kumar
- ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Madan Pal Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Vijay Paul
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sudhir Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Brajesh Singh
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
| | - Gaurav Zinta
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
| |
Collapse
|
25
|
Liu H, Mullan D, Zhao S, Zhang Y, Ye J, Wang Y, Zhang A, Zhao X, Liu G, Zhang C, Chan K, Lu Z, Yan G. Genomic regions controlling yield-related traits in spring wheat: A mini review and a case study for rainfed environments in Australia and China. Genomics 2022; 114:110268. [PMID: 35065191 DOI: 10.1016/j.ygeno.2022.110268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/11/2022] [Accepted: 01/15/2022] [Indexed: 01/17/2023]
|
26
|
Shariatipour N, Heidari B, Tahmasebi A, Richards C. Comparative Genomic Analysis of Quantitative Trait Loci Associated With Micronutrient Contents, Grain Quality, and Agronomic Traits in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:709817. [PMID: 34712248 PMCID: PMC8546302 DOI: 10.3389/fpls.2021.709817] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/06/2021] [Indexed: 05/02/2023]
Abstract
Comparative genomics and meta-quantitative trait loci (MQTLs) analysis are important tools for the identification of reliable and stable QTLs and functional genes controlling quantitative traits. We conducted a meta-analysis to identify the most stable QTLs for grain yield (GY), grain quality traits, and micronutrient contents in wheat. A total of 735 QTLs retrieved from 27 independent mapping populations reported in the last 13 years were used for the meta-analysis. The results showed that 449 QTLs were successfully projected onto the genetic consensus map which condensed to 100 MQTLs distributed on wheat chromosomes. This consolidation of MQTLs resulted in a three-fold reduction in the confidence interval (CI) compared with the CI for the initial QTLs. Projection of QTLs revealed that the majority of QTLs and MQTLs were in the non-telomeric regions of chromosomes. The majority of micronutrient MQTLs were located on the A and D genomes. The QTLs of thousand kernel weight (TKW) were frequently associated with QTLs for GY and grain protein content (GPC) with co-localization occurring at 55 and 63%, respectively. The co- localization of QTLs for GY and grain Fe was found to be 52% and for QTLs of grain Fe and Zn, it was found to be 66%. The genomic collinearity within Poaceae allowed us to identify 16 orthologous MQTLs (OrMQTLs) in wheat, rice, and maize. Annotation of promising candidate genes (CGs) located in the genomic intervals of the stable MQTLs indicated that several CGs (e.g., TraesCS2A02G141400, TraesCS3B02G040900, TraesCS4D02G323700, TraesCS3B02G077100, and TraesCS4D02G290900) had effects on micronutrients contents, yield, and yield-related traits. The mapping refinements leading to the identification of these CGs provide an opportunity to understand the genetic mechanisms driving quantitative variation for these traits and apply this information for crop improvement programs.
Collapse
Affiliation(s)
- Nikwan Shariatipour
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Bahram Heidari
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Ahmad Tahmasebi
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Christopher Richards
- USDA ARS National Laboratory for Genetic Resources Preservation, Fort Collins, CO, United States
| |
Collapse
|
27
|
Kaur P, Sachan S, Sharma A. Weed competitive ability in wheat: a peek through in its functional significance, present status and future prospects. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2165-2179. [PMID: 34744359 PMCID: PMC8526637 DOI: 10.1007/s12298-021-01079-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/02/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Weed competitive ability of a crop is one of the most widely explored aspects in the current scenario of aftermaths of synthetic herbicides such as herbicide resistant weeds emergence, residue accumulation in trophic levels; increased demands of organic produce, global climatic shifts, and other environmental issues. Further weed infestations are known to cause much more economic losses relative to crop attacks by pests. To understand the basic characteristics and underlying processes governing the competitive ability of a crop is therefore prudent, particularly in staples such as wheat. We discuss here an overview of the existing attributes of wheat-weed environment, the significance of crop competitiveness and various associated above-ground and below-ground traits (pertaining to early seed vigor and early seedling germination) discerned through biological, classical genetics and high throughput omics toolbox to provide numerous resources in terms of genome and transcriptome sequences, potential QTLs, genetic variation, molecular markers, association mapping studies, and others. Competitiveness is a cumulative response manifested as morphological, physiological, biochemical or allelochemical response ultimately driven through genetic architecture of a crop and its interaction with environment. Development of wheat competitive cultivar thus requires interdisciplinary approaches and germplasm screening to identify potential donors for competitiveness is an attractive and feasible alternative. For which utilization of landraces and other wild species, already proven to house sufficient genetic heterogeneity, thus poses a competitive advantage. Further, the availability of novel breeding techniques such as rapid generation advance could speed up the development of competitive wheat ideotype.
Collapse
Affiliation(s)
- Parampreet Kaur
- School of Organic Farming, Punjab Agricultural University, Ludhiana, Punjab India
| | - Shephali Sachan
- School of Organic Farming, Punjab Agricultural University, Ludhiana, Punjab India
| | - Achla Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab India
| |
Collapse
|
28
|
Mekonnen T, Sneller CH, Haileselassie T, Ziyomo C, Abeyo BG, Goodwin SB, Lule D, Tesfaye K. Genome-Wide Association Study Reveals Novel Genetic Loci for Quantitative Resistance to Septoria Tritici Blotch in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:671323. [PMID: 34630445 PMCID: PMC8500178 DOI: 10.3389/fpls.2021.671323] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Septoria tritici blotch, caused by the fungus Zymoseptoria titici, poses serious and persistent challenges to wheat cultivation in Ethiopia and worldwide. Deploying resistant cultivars is a major component of controlling septoria tritici blotch (STB). Thus, the objective of this study was to elucidate the genomic architecture of STB resistance in an association panel of 178 bread wheat genotypes. The association panel was phenotyped for STB resistance, phenology, yield, and yield-related traits in three locations for 2 years. The panel was also genotyped for single nucleotide polymorphism (SNP) markers using the genotyping-by-sequencing (GBS) method, and a total of 7,776 polymorphic SNPs were used in the subsequent analyses. Marker-trait associations were also computed using a genome association and prediction integrated tool (GAPIT). The study then found that the broad-sense heritability for STB resistance ranged from 0.58 to 0.97 and 0.72 to 0.81 at the individual and across-environment levels, respectively, indicating the presence of STB resistance alleles in the association panel. Population structure and principal component analyses detected two sub-groups with greater degrees of admixture. A linkage disequilibrium (LD) analysis in 338,125 marker pairs also detected the existence of significant (p ≤ 0.01) linkage in 27.6% of the marker pairs. Specifically, in all chromosomes, the LD between SNPs declined within 2.26-105.62 Mbp, with an overall mean of 31.44 Mbp. Furthermore, the association analysis identified 53 loci that were significantly (false discovery rate, FDR, <0.05) associated with STB resistance, further pointing to 33 putative quantitative trait loci (QTLs). Most of these shared similar chromosomes with already published Septoria resistance genes, which were distributed across chromosomes 1B, 1D, 2A, 2B, 2D, 3A,3 B, 3D, 4A, 5A, 5B, 6A, 7A, 7B, and 7D. However, five of the putative QTLs identified on chromosomes 1A, 5D, and 6B appeared to be novel. Dissecting the detected loci on IWGSC RefSeq Annotation v2.1 revealed the existence of disease resistance-associated genes in the identified QTL regions that are involved in plant defense responses. These putative QTLs explained 2.7-13.2% of the total phenotypic variation. Seven of the QTLs (R 2 = 2.7-10.8%) for STB resistance also co-localized with marker-trait associations (MTAs) for agronomic traits. Overall, this analysis reported on putative QTLs for adult plant resistance to STB and some important agronomic traits. The reported and novel QTLs have been identified previously, indicating the potential to improve STB resistance by pyramiding QTLs by marker-assisted selection.
Collapse
Affiliation(s)
- Tilahun Mekonnen
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Clay H. Sneller
- Biosciences Eastern and Central Africa (BecA), Nairobi, Kenya
| | | | - Cathrine Ziyomo
- Biosciences Eastern and Central Africa (BecA), Nairobi, Kenya
| | - Bekele G. Abeyo
- International Maize and Wheat Improvement Center- CIMMYT (Ethiopia), Addis Ababa, Ethiopia
| | - Stephen B. Goodwin
- United States Department of Agriculture (USDA)-Agricultural Research Service, West Lafayette, IN, United States
| | - Dagnachew Lule
- Oromia Agricultural Research Institute (OARI), Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute (EBTi), Addis Ababa, Ethiopia
| |
Collapse
|
29
|
Li Z, Zheng B, He Y. Understanding the Effects of Growing Seasons, Genotypes, and Their Interactions on the Anthesis Date of Wheat Sown in North China. BIOLOGY 2021; 10:biology10100955. [PMID: 34681054 PMCID: PMC8533131 DOI: 10.3390/biology10100955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/12/2021] [Accepted: 09/17/2021] [Indexed: 11/30/2022]
Abstract
Simple Summary Wheat anthesis date is an important turning point for wheat from vegetative growth stage to reproductive growth stage, which is crucial for wheat to adapt to environment and increase grain yield. In this study, a panel of adaptive wheat varieties including historical varieties from the 1940s and current varieties was used to understand the contribution of growing season, genotypes and their interaction effects to anthesis date. Based on our results, we can conclude that growing seasons contributed tremendously to the anthesis date of wheat. In future wheat breeding, more consideration should be given to growing seasons, and the gene combination with the strongest adaptability to the growing seasons should be selected. Abstract Quantitative studies on the effects of growing season, genotype (including photoperiod genes and vernalization genes), and their interaction (GGI) on the anthesis date of winter wheat (Triticum aestivum L.) are helpful to provide a scientific reference for selecting or developing adaptive varieties in target environments. In this study, we collected 100 winter wheat varieties with ecological adaptability in North China and identified the anthesis date under field conditions for three consecutive years from 2016 to 2019 with mapped photoperiod and vernalization alleles. Our results showed that the number of the photoperiod-insensitive Ppd-D1a allele increased with variety replacement, while the haplotype Ppd-A1b + Ppd-D1b + vrn-D1 (A4B2) decreased from the 1940s to 2000s. The anthesis date of A4B2 was significantly delayed due to the photoperiod-insensitive alleles Ppd-A1b and Ppd-D1b. The additive main effect and multiplicative interaction (AMMI) model and GGI biplot analysis were used for data analysis. A large portion of the total variation was explained by growing seasons (66.3%), while genotypes and GGIs explained 21.9% and 10.1% of the anthesis dates, respectively. The varieties from the 1940s and before had a great influence on the anthesis date, suggesting these germplasms tend to avoid premature anthesis and could facilitate the development of phenological resilient varieties.
Collapse
Affiliation(s)
- Ziwei Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Bangyou Zheng
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, QLD 4067, Australia;
| | - Yong He
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
- Correspondence:
| |
Collapse
|
30
|
Jung WJ, Lee YJ, Kang CS, Seo YW. Identification of genetic loci associated with major agronomic traits of wheat (Triticum aestivum L.) based on genome-wide association analysis. BMC PLANT BIOLOGY 2021; 21:418. [PMID: 34517837 PMCID: PMC8436466 DOI: 10.1186/s12870-021-03180-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/11/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Bread wheat (Triticum aestivum L.) is one of the most widely consumed cereal crops, but its complex genome makes it difficult to investigate the genetic effect on important agronomic traits. Genome-wide association (GWA) analysis is a useful method to identify genetic loci controlling complex phenotypic traits. With the RNA-sequencing based gene expression analysis, putative candidate genes governing important agronomic trait can be suggested and also molecular markers can be developed. RESULTS We observed major quantitative agronomic traits of wheat; the winter survival rate (WSR), days to heading (DTH), days to maturity (DTM), stem length (SL), spike length (SPL), awn length (AL), liter weight (LW), thousand kernel weight (TKW), and the number of seeds per spike (SPS), of 287 wheat accessions from diverse country origins. A significant correlation was observed between the observed traits, and the wheat genotypes were divided into three subpopulations according to the population structure analysis. The best linear unbiased prediction (BLUP) values of the genotypic effect for each trait under different environments were predicted, and these were used for GWA analysis based on a mixed linear model (MLM). A total of 254 highly significant marker-trait associations (MTAs) were identified, and 28 candidate genes closely located to the significant markers were predicted by searching the wheat reference genome and RNAseq data. Further, it was shown that the phenotypic traits were significantly affected by the accumulation of favorable or unfavorable alleles. CONCLUSIONS From this study, newly identified MTA and putative agronomically useful genes will help to study molecular mechanism of each phenotypic trait. Further, the agronomically favorable alleles found in this study can be used to develop wheats with superior agronomic traits.
Collapse
Affiliation(s)
- Woo Joo Jung
- Department of Plant Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Yong Jin Lee
- Department of Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Chon-Sik Kang
- National Institute of Crop Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Yong Weon Seo
- Department of Plant Biotechnology, Korea University, Seoul, 02841, South Korea.
- Department of Biotechnology, Korea University, Seoul, 02841, South Korea.
| |
Collapse
|
31
|
Joukhadar R, Thistlethwaite R, Trethowan R, Keeble-Gagnère G, Hayden MJ, Ullah S, Daetwyler HD. Meta-analysis of genome-wide association studies reveal common loci controlling agronomic and quality traits in a wide range of normal and heat stressed environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2113-2127. [PMID: 33768282 DOI: 10.1007/s00122-021-03809-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Several stable QTL were detected using metaGWAS analysis for different agronomic and quality traits under 26 normal and heat stressed environments. Heat stress, exacerbated by global warming, has a negative influence on wheat production worldwide and climate resilient cultivars can help mitigate these impacts. Selection decisions should therefore depend on multi-environment experiments representing a range of temperatures at critical stages of development. Here, we applied a meta-genome wide association analysis (metaGWAS) approach to detect stable QTL with significant effects across multiple environments. The metaGWAS was applied to 11 traits scored in 26 trials that were sown at optimal or late times of sowing (TOS1 and TOS2, respectively) at five locations. A total of 2571 unique wheat genotypes (13,959 genotypes across all environments) were included and the analysis conducted on TOS1, TOS2 and both times of sowing combined (TOS1&2). The germplasm was genotyped using a 90 k Infinium chip and imputed to exome sequence level, resulting in 341,195 single nucleotide polymorphisms (SNPs). The average accuracy across all imputed SNPs was high (92.4%). The three metaGWAS analyses revealed 107 QTL for the 11 traits, of which 16 were detected in all three analyses and 23 were detected in TOS1&2 only. The remaining QTL were detected in either TOS1 or TOS2 with or without TOS1&2, reflecting the complex interactions between the environments and the detected QTL. Eight QTL were associated with grain yield and seven with multiple traits. The identified QTL provide an important resource for gene enrichment and fine mapping to further understand the mechanisms of gene × environment interaction under both heat stressed and unstressed conditions.
Collapse
Affiliation(s)
- Reem Joukhadar
- Agriculture Victoria, Centre for AgriBioscience, AgriBio, Bundoora, VIC, Australia.
| | - Rebecca Thistlethwaite
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, Australia
| | - Richard Trethowan
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, Australia
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Cobbitty, NSW, Australia
| | | | - Matthew J Hayden
- Agriculture Victoria, Centre for AgriBioscience, AgriBio, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Smi Ullah
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, Australia
| | - Hans D Daetwyler
- Agriculture Victoria, Centre for AgriBioscience, AgriBio, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| |
Collapse
|
32
|
Malik P, Kumar J, Singh S, Sharma S, Meher PK, Sharma MK, Roy JK, Sharma PK, Balyan HS, Gupta PK, Sharma S. Single-trait, multi-locus and multi-trait GWAS using four different models for yield traits in bread wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:46. [PMID: 37309385 PMCID: PMC10236106 DOI: 10.1007/s11032-021-01240-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/30/2021] [Indexed: 06/14/2023]
Abstract
A genome-wide association study (GWAS) for 10 yield and yield component traits was conducted using an association panel comprising 225 diverse spring wheat genotypes. The panel was genotyped using 10,904 SNPs and evaluated for three years (2016-2019), which constituted three environments (E1, E2 and E3). Heritability for different traits ranged from 29.21 to 97.69%. Marker-trait associations (MTAs) were identified for each trait using data from each environment separately and also using BLUP values. Four different models were used, which included three single trait models (CMLM, FarmCPU, SUPER) and one multi-trait model (mvLMM). Hundreds of MTAs were obtained using each model, but after Bonferroni correction, only 6 MTAs for 3 traits were available using CMLM, and 21 MTAs for 4 traits were available using FarmCPU; none of the 525 MTAs obtained using SUPER could qualify after Bonferroni correction. Using BLUP, 20 MTAs were available, five of which also figured among MTAs identified for individual environments. Using mvLMM model, after Bonferroni correction, 38 multi-trait MTAs, for 15 different trait combinations were available. Epistatic interactions involving 28 pairs of MTAs were also available for seven of the 10 traits; no epistatic interactions were available for GNPS, PH, and BYPP. As many as 164 putative candidate genes (CGs) were identified using all the 50 MTAs (CMLM, 3; FarmCPU, 9; mvLMM, 6, epistasis, 21 and BLUP, 11 MTAs), which ranged from 20 (CMLM) to 66 (epistasis) CGs. In-silico expression analysis of CGs was also conducted in different tissues at different developmental stages. The information generated through the present study proved useful for developing a better understanding of the genetics of each of the 10 traits; the study also provided novel markers for marker-assisted selection (MAS) to be utilized for the development of wheat cultivars with improved agronomic traits. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01240-1.
Collapse
Affiliation(s)
- Parveen Malik
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Jitendra Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
- National Agri-Food Biotechnology Institute (NABI), Sector 81, Sahibzada Ajit Singh Nagar, 140306 Punjab India
| | - Sahadev Singh
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Shiveta Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Prabina Kumar Meher
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Mukesh Kumar Sharma
- Department of Mathematics, Chaudhary Charan Singh University, Meerut 250004, India
| | - Joy Kumar Roy
- National Agri-Food Biotechnology Institute (NABI), Sector 81, Sahibzada Ajit Singh Nagar, 140306 Punjab India
| | - Pradeep Kumar Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| |
Collapse
|
33
|
Islam M, Abdullah, Zubaida B, Amin N, Khan RI, Shafqat N, Masood R, Waseem S, Tahir J, Ahmed I, Naeem M, Ahmad H. Agro-Morphological, Yield, and Genotyping-by-Sequencing Data of Selected Wheat ( Triticum aestivum) Germplasm From Pakistan. Front Genet 2021; 12:617772. [PMID: 34163518 PMCID: PMC8216712 DOI: 10.3389/fgene.2021.617772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/19/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Madiha Islam
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Abdullah
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Bibi Zubaida
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Nageena Amin
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Rashid Iqbal Khan
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Noshin Shafqat
- Department of Agriculture, Hazara University, Mansehra, Pakistan
| | - Rabia Masood
- Department of Botany, Hazara University, Mansehra, Pakistan
| | | | - Jibran Tahir
- Terrestrial Bioscience New Zealand Limited, Auckland, New Zealand
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Muhammad Naeem
- Federal Seed Certification and Registration Department, Islamabad, Pakistan
| | - Habib Ahmad
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| |
Collapse
|
34
|
Vikram P, Sehgal D, Sharma A, Bhavani S, Gupta P, Randhawa M, Pardo N, Basandra D, Srivastava P, Singh S, Sood T, Sansaloni CP, Rahman H, Singh S. Genome-wide association analysis of Mexican bread wheat landraces for resistance to yellow and stem rust. PLoS One 2021; 16:e0246015. [PMID: 33513167 PMCID: PMC7846011 DOI: 10.1371/journal.pone.0246015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/12/2021] [Indexed: 11/18/2022] Open
Abstract
Deploying under-utilized landraces in wheat breeding has been advocated to accelerate genetic gains in current era of genomics assisted breeding. Mexican bread wheat landraces (Creole wheats) represent an important resource for the discovery of novel alleles including disease resistance. A core set of 1,098 Mexican landraces was subjected to multi-location testing for rust diseases in India, Mexico and Kenya. The landrace core set showed a continuous variation for yellow (YR) and stem rust (SR) disease severity. Principal component analysis differentiated Mexican landraces into three groups based on their respective collection sites. Linkage disequilibrium (LD) decay varied from 10 to 32 Mb across chromosomes with an averge of 23Mb across whole genome. Genome-wide association analysis revealed marker-trait associations for YR resistance in India and Mexico as well as for SR resistance in Kenya. In addition, significant additive-additive interaction effects were observed for both YR and SR resistance including genomic regions on chromosomes 1BL and 3BS, which co-locate with pleiotropic genes Yr29/Lr46/Sr58/Pm39/Ltn2 and Sr2/Yr30/Lr27, respectively. Study reports novel genomic associations for YR (chromosomes 1AL, 2BS, and 3BL) and SR (chromosomes 2AL, 4DS, and 5DS). The novel findings in Creole wheat landraces can be efficiently utilized for the wheat genetic improvement.
Collapse
Affiliation(s)
- Prashant Vikram
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Mexico
- International Center for Biosaline Agriculture, Academic Ciy, Dubai, UAE
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Mexico
| | - Achala Sharma
- Department Plant Breeding & Genetics, Punjab Agriculture University, Ludhiana, India
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Mexico
| | - Priyanka Gupta
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Instituts, Rabat, Morocco
| | - Mandeep Randhawa
- CIMMYT—World Agroforestry Centre (ICRAF), Gigiri, Nairobi, Kenya
| | - Neftali Pardo
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Mexico
| | - Daisy Basandra
- Department Plant Breeding & Genetics, CSK HPKV Palampur, H.P. India
| | - Puja Srivastava
- Department Plant Breeding & Genetics, Punjab Agriculture University, Ludhiana, India
| | - Sanjay Singh
- ICAR-National Institute of Plant Biotechnology, Pusa, New Delhi, India
| | - Tanvi Sood
- Department Plant Breeding & Genetics, CSK HPKV Palampur, H.P. India
| | | | - Hifzur Rahman
- International Center for Biosaline Agriculture, Academic Ciy, Dubai, UAE
| | - Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Mexico
| |
Collapse
|
35
|
Genome-Wide Association Study of Morpho-Physiological Traits in Aegilops tauschii to Broaden Wheat Genetic Diversity. PLANTS 2021; 10:plants10020211. [PMID: 33499189 PMCID: PMC7911611 DOI: 10.3390/plants10020211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 11/16/2022]
Abstract
Aegilops tauschii, the D-genome donor of bread wheat, is a storehouse of genetic diversity that can be used for wheat improvement. This species consists of two main lineages (TauL1 and TauL2) and one minor lineage (TauL3). Its morpho-physiological diversity is large, with adaptations to a wide ecological range. Identification of allelic diversity in Ae. tauschii is of utmost importance for efficient breeding and widening of the genetic base of wheat. This study aimed at identifying markers or genes associated with morpho-physiological traits in Ae. tauschii, and at understanding the difference in genetic diversity between the two main lineages. We performed genome-wide association studies of 11 morpho-physiological traits of 343 Ae. tauschii accessions representing the entire range of habitats using 34,829 DArTseq markers. We observed a wide range of morpho-physiological variation among all accessions. We identified 23 marker-trait associations (MTAs) in all accessions, 15 specific to TauL1 and eight specific to TauL2, suggesting independent evolution in each lineage. Some of the MTAs could be novel and have not been reported in bread wheat. The markers or genes identified in this study will help reveal the genes controlling the morpho-physiological traits in Ae. tauschii, and thus in bread wheat even if the plant morphology is different.
Collapse
|
36
|
Kokhmetova A, Sehgal D, Ali S, Atishova M, Kumarbayeva M, Leonova I, Dreisigacker S. Genome-Wide Association Study of Tan Spot Resistance in a Hexaploid Wheat Collection From Kazakhstan. Front Genet 2021; 11:581214. [PMID: 33505423 PMCID: PMC7831376 DOI: 10.3389/fgene.2020.581214] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/09/2020] [Indexed: 11/13/2022] Open
Abstract
Tan spot, caused by Pyrenophora tritici-repentis, is a serious foliar disease of wheat in Kazakhstan with reported yield losses as high as 50% during epidemic years. Here, we report the evaluation of a collection of 191 hexaploid spring and winter wheat lines for tan spot resistance and its underlying genetic architecture using genome-wide association study (GWAS). Our wheat collection comprised candidate varieties from Kazakhstan, Russia, and CIMMYT. It was genotyped using the DArTseq technology and phenotyped for resistance to tan spot at seedling and adult plant stages in Kazakhstan. DArTseq SNPs revealed high genetic diversity (average polymorphic information content = 0.33) in the panel and genome-wide linkage disequilibrium decay at 22 Mb (threshold r2 = 0.1). Principal component analysis revealed a clear separation of Eurasian germplasm from CIMMYT and IWWIP lines. GWAS identified 34 marker-trait associations (MTA) for resistance to tan spot and the amount of phenotypic variation explained by these MTA ranged from 4% to 13.7%. Our results suggest the existence of novel valuable resistant alleles on chromosomes 3BS, and 5DL and 6AL for resistance to Race 1 and Race 5, respectively, in addition to known genes tsn1 and tsc2. On chromosome 6AL, a genomic region spanning 3 Mb was identified conferring resistance to both Race 1 and Race 5. Epistatic interaction of associated loci was revealed on chromosomes 1B, 5B, 7B, 5A, and 6A contributing to additional variation of 3.2–11.7%. Twenty-five lines with the best allele combinations of SNPs associated with resistance to both races have been identified as candidates for future variety release and breeding. The results of the present study will be further validated in other independent genetic backgrounds to be able to use markers in breeding.
Collapse
Affiliation(s)
- Alma Kokhmetova
- Laboratory of Breeding and Genetics, Institute of Plant Biology and Biotechnology (IPBB), Almaty, Kazakhstan.,Faculty of Agronomy, Kazakh National Agrarian University, Almaty, Kazakhstan
| | - Deepmala Sehgal
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Shaukat Ali
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
| | - Makpal Atishova
- Laboratory of Breeding and Genetics, Institute of Plant Biology and Biotechnology (IPBB), Almaty, Kazakhstan
| | - Madina Kumarbayeva
- Laboratory of Breeding and Genetics, Institute of Plant Biology and Biotechnology (IPBB), Almaty, Kazakhstan.,Faculty of Agronomy, Kazakh National Agrarian University, Almaty, Kazakhstan
| | - Irina Leonova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Susanne Dreisigacker
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| |
Collapse
|
37
|
Lou H, Zhang R, Liu Y, Guo D, Zhai S, Chen A, Zhang Y, Xie C, You M, Peng H, Liang R, Ni Z, Sun Q, Li B. Genome-wide association study of six quality-related traits in common wheat (Triticum aestivum L.) under two sowing conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:399-418. [PMID: 33155062 DOI: 10.1007/s00122-020-03704-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/08/2020] [Indexed: 05/20/2023]
Abstract
We identified genomic regions associated with six quality-related traits in wheat under two sowing conditions and analyzed the effects of multienvironment-significant SNPs on the stability of these traits. Grain quality affects the nutritional and commercial value of wheat (Triticum aestivum L.) and is a critical factor influencing consumer preferences for specific wheat varieties. Climate change is predicted to increase environmental stress and thereby reduce wheat quality. Here, we performed a genotyping assay involving the use of the wheat 90 K array in a genome-wide association study of six quality-related traits in 486 wheat accessions under two sowing conditions (normal and late sowing) over 4 years. We identified 64 stable quantitative trait loci (QTL), including 10 for grain protein content, 9 for wet gluten content, 4 for grain starch content, 14 for water absorption, 15 for dough stability time and 12 for grain hardness in wheat under two sowing conditions. These QTL harbored 175 single nucleotide polymorphisms (SNPs), explaining approximately 3-13% of the phenotypic variation in multiple environments. Some QTL on chromosomes 6A and 5D were associated with multiple traits simultaneously, and two (QNGPC.cau-6A, QNGH.cau-5D) harbored known genes, such as NAM-A1 for grain protein content and Pinb for grain hardness, whereas other QTL could facilitate gene discovery. Forty-three SNPs that were detected under late or both normal and late sowing conditions appear to be related to phenotypic stability. The effects of these SNP alleles were confirmed in the association population. The results of this study will be useful for further dissecting the genetic basis of quality-related traits in wheat and developing new wheat cultivars with desirable alleles to improve the stability of grain quality.
Collapse
Affiliation(s)
- Hongyao Lou
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
| | - Runqi Zhang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
| | - Yitong Liu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Dandan Guo
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
| | - Shanshan Zhai
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
| | - Aiyan Chen
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
| | - Yufeng Zhang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
| | - Chaojie Xie
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
| | - Mingshan You
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
| | - Rongqi Liang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Baoyun Li
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
38
|
Wang X, Guan P, Xin M, Wang Y, Chen X, Zhao A, Liu M, Li H, Zhang M, Lu L, Zhang J, Ni Z, Yao Y, Hu Z, Peng H, Sun Q. Genome-wide association study identifies QTL for thousand grain weight in winter wheat under normal- and late-sown stressed environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:143-157. [PMID: 33030571 DOI: 10.1007/s00122-020-03687-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 09/16/2020] [Indexed: 05/27/2023]
Abstract
GWAS identified stable loci for TGW and stress tolerance in winter wheat based on two sowing conditions, which will provide opportunities for developing new cultivars with high yield and yield stability. Wheat is an important food crop widely cultivated in the world. Breeding new varieties with high yields and superior adaptability is the main goal of modern wheat breeding program. In order to determine the marker-trait associations (MATs), a set of 688 diverse winter wheat accessions were subjected to genome-wide association study (GWAS) using the wheat 90K array. Field trials under normal-sown (NS) and late-sown (LS) conditions were conducted for thousand grain weight (TGW) and stress susceptibility index (SSI) at three different sites across two consecutive years. A total of 179 (NS) and 158 (LS) MATs corresponded with TGW; of these, 16 and 6 stable MATs for TGWNS and TGWLS were identified on chromosomes 1B, 2B, 3A, 3B, 5A, 5B, 5D, 6B, and 7D across at least three environments. Notably, a QTL hot spot controlling TGW under NS and LS conditions was found on chromosome 5A (140-142 cM). Moreover, 8 of 228 stable MATs on chromosomes 4B, 5A, and 5D for SSI were detected. A haplotype block associated with TGW and SSI was located on chromosome 5A at 91 cM, nearby the vernalization gene VRN-A1. Additionally, analysis of wheat varieties from the different eras revealed that the grain weight and stress tolerance are not improved concurrently. Overall, our results provide promising alleles controlling grain weight and stress tolerance (particularly for thermotolerance) for wheat breeders, which can be used in marker-assisted selection for improving grain yield and yield stability in wheat.
Collapse
Affiliation(s)
- Xiaobo Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Panfeng Guan
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongfa Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiyong Chen
- Hebei Crop Genetic Breeding Laboratory, Institute of Cereal and Oil Crops of Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Aiju Zhao
- Hebei Crop Genetic Breeding Laboratory, Institute of Cereal and Oil Crops of Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Manshuang Liu
- Agronomy College, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hongxia Li
- Agronomy College, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mingyi Zhang
- Institute of Wheat, Shanxi Academy of Agricultural Sciences, Linfen, 041000, China
| | - Lahu Lu
- Institute of Wheat, Shanxi Academy of Agricultural Sciences, Linfen, 041000, China
| | - Jinbo Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
39
|
Akram S, Arif MAR, Hameed A. A GBS-based GWAS analysis of adaptability and yield traits in bread wheat (Triticum aestivum L.). J Appl Genet 2020; 62:27-41. [PMID: 33128382 DOI: 10.1007/s13353-020-00593-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/20/2020] [Accepted: 10/28/2020] [Indexed: 01/20/2023]
Abstract
Wheat is a foremost food grain of Pakistan and occupies a vital position in agricultural policies of the country. Wheat demand will be increased by 60% by 2050 which is a serious concern to meet this demand. Conventional breeding approaches are not enough to meet the demand of growing human population. It is paramount to integrate underutilized genetic diversity into wheat gene pool through efficient and accurate breeding tools and technology. In this study, we present the genetic analysis of a 312 diverse pre-breeding lines using DArT-seq SNPs seeking to elucidate the genetic components of emergence percentage, heading time, plant height, lodging, thousand kernel weight, and yield (Yd) which resulted in detection of 201 significant (p value < 10-3) and 61 highly significant associations (p value < 1.45 × 10-4). More importantly, chromosomes 1B and 2A carried loci linked to Yd in two different seasons, and an increase of up to 8.20% is possible in Yd by positive allele mining. We identified seven lines with > 4 positive alleles for Yd whose pedigree carried Aegilops squarrosa as one of the parents providing evidence that Aegilops species, apart from imparting resistance against biotic stresses, may also provide alleles for yield enhancement.
Collapse
Affiliation(s)
- Saba Akram
- Nuclear Institute for Agriculture and Biology College. Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Jhang Road, Faisalabad, Pakistan
| | - Mian Abdur Rehman Arif
- Nuclear Institute for Agriculture and Biology College. Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Jhang Road, Faisalabad, Pakistan.
| | - Amjad Hameed
- Nuclear Institute for Agriculture and Biology College. Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Jhang Road, Faisalabad, Pakistan
| |
Collapse
|
40
|
Pang Y, Liu C, Wang D, St Amand P, Bernardo A, Li W, He F, Li L, Wang L, Yuan X, Dong L, Su Y, Zhang H, Zhao M, Liang Y, Jia H, Shen X, Lu Y, Jiang H, Wu Y, Li A, Wang H, Kong L, Bai G, Liu S. High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat. MOLECULAR PLANT 2020; 13:1311-1327. [PMID: 32702458 DOI: 10.1016/j.molp.2020.07.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/08/2020] [Accepted: 07/17/2020] [Indexed: 05/18/2023]
Abstract
Wheat (Triticum aestivum) is a major staple food crop worldwide. Genetic dissection of important agronomic traits is essential for continuous improvement of wheat yield to meet the demand of the world's growing population. We conducted a large-scale genome-wide association study (GWAS) using a panel of 768 wheat cultivars that were genotyped with 327 609 single-nucleotide polymorphisms generated by genotyping-by-sequencing and detected 395 quantitative trait loci (QTLs) for 12 traits under 7 environments. Among them, 273 QTLs were delimited to ≤1.0-Mb intervals and 7 of them are either known genes (Rht-D, Vrn-B1, and Vrn-D1) that have been cloned or known QTLs (TaGA2ox8, APO1, TaSus1-7B, and Rht12) that were previously mapped. Eight putative candidate genes were identified for three QTLs that enhance spike seed setting and grain size using gene expression data and were validated in three bi-parental populations. Protein sequence analysis identified 33 putative wheat orthologs that have high identity with rice genes in QTLs affecting similar traits. Large r2 values for additive effects observed among the QTLs for most traits indicated that the phenotypes of these identified QTLs were highly predictable. Results from this study demonstrated that significantly increasing GWAS population size and marker density greatly improves detection and identification of candidate genes underlying a QTL, solidifying the foundation for large-scale QTL fine mapping, candidate gene validation, and developing functional markers for genomics-based breeding in wheat.
Collapse
Affiliation(s)
- Yunlong Pang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Chunxia Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Danfeng Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Paul St Amand
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA
| | - Amy Bernardo
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA; Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Wenhui Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Fang He
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China; College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Linzhi Li
- Yantai Academy of Agricultural Sciences, Yantai 265500, China
| | - Liming Wang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Xiufang Yuan
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Lei Dong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yu Su
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Huirui Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Meng Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yunlong Liang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Hongze Jia
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Xitong Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yue Lu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Hongming Jiang
- Yantai Academy of Agricultural Sciences, Yantai 265500, China
| | - Yuye Wu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Anfei Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Honggang Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA.
| | - Shubing Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.
| |
Collapse
|
41
|
Chaurasia S, Singh AK, Songachan LS, Sharma AD, Bhardwaj R, Singh K. Multi-locus genome-wide association studies reveal novel genomic regions associated with vegetative stage salt tolerance in bread wheat (Triticum aestivum L.). Genomics 2020; 112:4608-4621. [PMID: 32771624 DOI: 10.1016/j.ygeno.2020.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/27/2020] [Accepted: 08/04/2020] [Indexed: 10/23/2022]
Abstract
Soil salinity is one of the typical abiotic stresses affecting sustainability of wheat production worldwide. In the present study, we performed a 35 K SNP genotyping assay on association panel of 135 diverse wheat genotypes evaluated for vegetative stage tolerance in hydroponics. Association analyses using five multi-locus GWAS models revealed 42 reliable QTNs for 10 salt tolerance associated traits. Among these 42 reliable QTNs, 9, 17 and 16 QTNs were associated with physiological, biomass and shoot ionic traits respectively. Novel major QTNs were identified for chlorophyll content, shoot fresh weight, seedling total biomass, Na+ and K+ concentration and Na+/K+ ratio in shoots. Further, 10 major QTNs showed significant effect on the corresponding salt tolerance traits. Gene ontology analysis of the associated genomic regions identified 58 candidate genes. The information generated in this study will be of potential value for improvement of salt tolerance of wheat cultivars using marker assisted selection.
Collapse
Affiliation(s)
- Shiksha Chaurasia
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India; Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Amit Kumar Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India.
| | - L S Songachan
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Axma Dutt Sharma
- Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Rakesh Bhardwaj
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| |
Collapse
|
42
|
Muhammad A, Hu W, Li Z, Li J, Xie G, Wang J, Wang L. Appraising the Genetic Architecture of Kernel Traits in Hexaploid Wheat Using GWAS. Int J Mol Sci 2020; 21:ijms21165649. [PMID: 32781752 PMCID: PMC7460857 DOI: 10.3390/ijms21165649] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/02/2020] [Accepted: 08/05/2020] [Indexed: 12/14/2022] Open
Abstract
Kernel morphology is one of the major yield traits of wheat, the genetic architecture of which is always important in crop breeding. In this study, we performed a genome-wide association study (GWAS) to appraise the genetic architecture of the kernel traits of 319 wheat accessions using 22,905 single nucleotide polymorphism (SNP) markers from a wheat 90K SNP array. As a result, 111 and 104 significant SNPs for Kernel traits were detected using four multi-locus GWAS models (mrMLM, FASTmrMLM, FASTmrEMMA, and pLARmEB) and three single-locus models (FarmCPU, MLM, and MLMM), respectively. Among the 111 SNPs detected by the multi-locus models, 24 SNPs were simultaneously detected across multiple models, including seven for kernel length, six for kernel width, six for kernels per spike, and five for thousand kernel weight. Interestingly, the five most stable SNPs (RAC875_29540_391, Kukri_07961_503, tplb0034e07_1581, BS00074341_51, and BobWhite_049_3064) were simultaneously detected by at least three multi-locus models. Integrating these newly developed multi-locus GWAS models to unravel the genetic architecture of kernel traits, the mrMLM approach detected the maximum number of SNPs. Furthermore, a total of 41 putative candidate genes were predicted to likely be involved in the genetic architecture underlining kernel traits. These findings can facilitate a better understanding of the complex genetic mechanisms of kernel traits and may lead to the genetic improvement of grain yield in wheat.
Collapse
Affiliation(s)
- Ali Muhammad
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
| | - Weicheng Hu
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
| | - Zhaoyang Li
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
| | - Jianguo Li
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning 530004, China
| | - Guosheng Xie
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
| | - Jibin Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning 530004, China
- Correspondence: (J.W.); (L.W.)
| | - Lingqiang Wang
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning 530004, China
- Correspondence: (J.W.); (L.W.)
| |
Collapse
|
43
|
Navrotskyi S, Belamkar V, Baenziger PS, Rose DJ. Insights into the Genetic Architecture of Bran Friability and Water Retention Capacity, Two Important Traits for Whole Grain End-Use Quality in Winter Wheat. Genes (Basel) 2020; 11:E838. [PMID: 32717821 PMCID: PMC7466047 DOI: 10.3390/genes11080838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 11/16/2022] Open
Abstract
Bran friability (particle size distribution after milling) and water retention capacity (WRC) impact wheat bran functionality in whole grain milling and baking applications. The goal of this study was to identify genomic regions and underlying genes that may be responsible for these traits. The Hard Winter Wheat Association Mapping Panel, which comprised 299 lines from breeding programs in the Great Plains region of the US, was used in a genome-wide association study. Bran friability ranged from 34.5% to 65.9% (median, 51.1%) and WRC ranged from 159% to 458% (median, 331%). Two single-nucleotide polymorphisms (SNPs) on chromosome 5D were significantly associated with bran friability, accounting for 11-12% of the phenotypic variation. One of these SNPs was located within the Puroindoline-b gene, which is known for influencing endosperm texture. Two SNPs on chromosome 4A were tentatively associated with WRC, accounting for 4.6% and 4.4% of phenotypic variation. The favorable alleles at the SNP sites were present in only 15% (friability) and 34% (WRC) of lines, indicating a need to develop new germplasm for these whole-grain end-use quality traits. Validation of these findings in independent populations will be useful for breeding winter wheat cultivars with improved functionality for whole grain food applications.
Collapse
Affiliation(s)
- Sviatoslav Navrotskyi
- Department of Food Science & Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Vikas Belamkar
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA;
| | - P. Stephen Baenziger
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA;
| | - Devin J. Rose
- Department of Food Science & Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA;
| |
Collapse
|
44
|
Peng H, Wang K, Chen Z, Cao Y, Gao Q, Li Y, Li X, Lu H, Du H, Lu M, Yang X, Liang C. MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice. Nucleic Acids Res 2020; 48:D1085-D1092. [PMID: 31624841 PMCID: PMC7145604 DOI: 10.1093/nar/gkz921] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 11/25/2022] Open
Abstract
To date, large amounts of genomic and phenotypic data have been accumulated in the fields of crop genetics and genomic research, and the data are increasing very quickly. However, the bottleneck to using big data in breeding is integrating the data and developing tools for revealing the relationship between genotypes and phenotypes. Here, we report a rice sub-database of an integrated omics knowledgebase (MBKbase-rice, www.mbkbase.org/rice), which integrates rice germplasm information, multiple reference genomes with a united set of gene loci, population sequencing data, phenotypic data, known alleles and gene expression data. In addition to basic data search functions, MBKbase provides advanced web tools for genotype searches at the population level and for visually displaying the relationship between genotypes and phenotypes. Furthermore, the database also provides online tools for comparing two samples by their genotypes and finding target germplasms by genotype or phenotype information, as well as for analyzing the user submitted SNP or sequence data to find important alleles in the germplasm. A soybean sub-database is planned for release in 3 months and wheat and maize will be added in 1–2 years. The data and tools integrated in MBKbase will facilitate research in crop functional genomics and molecular breeding.
Collapse
Affiliation(s)
- Hua Peng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhuo Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yinghao Cao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiuxiu Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongwei Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Yang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
45
|
Calleja-Cabrera J, Boter M, Oñate-Sánchez L, Pernas M. Root Growth Adaptation to Climate Change in Crops. FRONTIERS IN PLANT SCIENCE 2020; 11:544. [PMID: 32457782 PMCID: PMC7227386 DOI: 10.3389/fpls.2020.00544] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/09/2020] [Indexed: 05/05/2023]
Abstract
Climate change is threatening crop productivity worldwide and new solutions to adapt crops to these environmental changes are urgently needed. Elevated temperatures driven by climate change affect developmental and physiological plant processes that, ultimately, impact on crop yield and quality. Plant roots are responsible for water and nutrients uptake, but changes in soil temperatures alters this process limiting crop growth. With the predicted variable climatic forecast, the development of an efficient root system better adapted to changing soil and environmental conditions is crucial for enhancing crop productivity. Root traits associated with improved adaptation to rising temperatures are increasingly being analyzed to obtain more suitable crop varieties. In this review, we will summarize the current knowledge about the effect of increasing temperatures on root growth and their impact on crop yield. First, we will describe the main alterations in root architecture that different crops undergo in response to warmer soils. Then, we will outline the main coordinated physiological and metabolic changes taking place in roots and aerial parts that modulate the global response of the plant to increased temperatures. We will discuss on some of the main regulatory mechanisms controlling root adaptation to warmer soils, including the activation of heat and oxidative pathways to prevent damage of root cells and disruption of root growth; the interplay between hormonal regulatory pathways and the global changes on gene expression and protein homeostasis. We will also consider that in the field, increasing temperatures are usually associated with other abiotic and biotic stresses such as drought, salinity, nutrient deficiencies, and pathogen infections. We will present recent advances on how the root system is able to integrate and respond to complex and different stimuli in order to adapt to an increasingly changing environment. Finally, we will discuss the new prospects and challenges in this field as well as the more promising pathways for future research.
Collapse
Affiliation(s)
| | | | | | - M. Pernas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| |
Collapse
|
46
|
Gupta PK, Balyan HS, Sharma S, Kumar R. Genetics of yield, abiotic stress tolerance and biofortification in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1569-1602. [PMID: 32253477 DOI: 10.1007/s00122-020-03583-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/13/2020] [Indexed: 05/18/2023]
Abstract
A review of the available literature on genetics of yield and its component traits, tolerance to abiotic stresses and biofortification should prove useful for future research in wheat in the genomics era. The work reviewed in this article mainly covers the available information on genetics of some important quantitative traits including yield and its components, tolerance to abiotic stresses (heat, drought, salinity and pre-harvest sprouting = PHS) and biofortification (Fe/Zn and phytate contents with HarvestPlus Program) in wheat. Major emphasis is laid on the recent literature on QTL interval mapping and genome-wide association studies, giving lists of known QTL and marker-trait associations. Candidate genes for different traits and the cloned and characterized genes for yield traits along with the molecular mechanism are also described. For each trait, an account of the present status of marker-assisted selection has also been included. The details of available results have largely been presented in the form of tables; some of these tables are included as supplementary files.
Collapse
Affiliation(s)
- Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India.
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Rahul Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| |
Collapse
|
47
|
Lozada DN, Ward BP, Carter AH. Gains through selection for grain yield in a winter wheat breeding program. PLoS One 2020; 15:e0221603. [PMID: 32343696 PMCID: PMC7188280 DOI: 10.1371/journal.pone.0221603] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 03/26/2020] [Indexed: 11/19/2022] Open
Abstract
Increased genetic gain for complex traits in plant breeding programs can be achieved through different selection strategies. The objective of this study was to compare potential gains for grain yield in a winter wheat breeding program through estimating response to selection R values across several selection approaches including phenotypic (PS), marker-based (MS), genomic (GS), and a combination of PS and GS (PS+GS). Ten populations of Washington State University (WSU) winter wheat breeding lines including a diversity panel and F5 and double haploid lines evaluated from 2015 to 2019 growing seasons for grain yield in Lind and Pullman, WA, USA were used in the study. Selection was conducted by selecting the top 20% of lines based on observed yield (PS strategy), genomic estimated breeding values (GS), presence of yield "enhancing" alleles of the most significant single nucleotide polymorphism (SNP) markers identified from genome-wide association mapping (MS), and high observed yield and estimated breeding values (PS+GS). Overall, PS compared to other individual selection strategies (MS and GS) showed the highest mean response (R = 0.61) within the same environment. When combined with GS, a 23% improvement in R for yield was observed, indicating that gains could be improved by complementing traditional PS with GS within the same environment. Validating selection strategies in different environments resulted in low to negative R values indicating the effects of genotype-by-environment interactions for grain yield. MS was not successful in terms of R relative to the other selection approaches; using this strategy resulted in a significant (P < 0.05) decrease in response to selection compared with the other approaches. An integrated PS+GS approach could result in optimal genetic gain within the same environment, whereas a PS strategy might be a viable option for grain yield validated in different environments. Altogether, we demonstrated that gains through increased response to selection for yield could be achieved in the WSU winter wheat breeding program by implementing different selection strategies either exclusively or in combination.
Collapse
Affiliation(s)
- Dennis N. Lozada
- Crop and Soil Sciences Department, Washington State University, Pullman, WA, United States of America
| | - Brian P. Ward
- USDA-ARS Plant Science Research Unit, Raleigh, NC, United States of America
| | - Arron H. Carter
- Crop and Soil Sciences Department, Washington State University, Pullman, WA, United States of America
| |
Collapse
|
48
|
Al-Ashkar I, Alderfasi A, Ben Romdhane W, Seleiman MF, El-Said RA, Al-Doss A. Morphological and Genetic Diversity within Salt Tolerance Detection in Eighteen Wheat Genotypes. PLANTS (BASEL, SWITZERLAND) 2020; 9:E287. [PMID: 32106488 PMCID: PMC7154827 DOI: 10.3390/plants9030287] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 01/24/2023]
Abstract
Salinity is a major obstacle to wheat production worldwide. Salt-affected soils could be used by improving salt-tolerant genotypes depending upon the genetic variation and salt stress response of adapted and donor wheat germplasm. We used a comprehensive set of morpho-physiological and biochemical parameters and simple sequence repeat (SSR) marker technique with multivariate analysis to accurately demonstrate the phenotypic and genetic variation of 18 wheat genotypes under salinity stress. All genotypes were evaluated without NaCl as a control and with 150 mM NaCl, until the onset of symptoms of death in the sensitive plant (after 43 days of salinity treatment). The results showed that the relative change of the genetic variation was high for all parameters, heritability (> 60%), and genetic gain (> 20%). Stepwise regression analysis, noting the importance of the root dry matter, relative turgidity, and their respective contributions to the shoot dry matter, indicated their relevance in improving and evaluating the salt-tolerant genotypes of breeding programs. The relative change of the genotypes in terms of the relative turgidity and shoot dry matter during salt stress was verified using clustering methods. For cluster analysis, the genotypes were classified into three groups: tolerant, intermediate, and sensitive, representing five, six, and seven genotypes, respectively. The morphological and genetic distances were significantly correlated based on the Mantel test. Of the 23 SSR markers that showed polymorphism, 17 were associated with almost all examined parameters. Therefore, based on the observed molecular marker-phenotypic trait association, the markers were highly useful in detecting tolerant and sensitive genotypes. Thus, it considers a helpful tool for salt tolerance through marker-assisted selection.
Collapse
Affiliation(s)
- Ibrahim Al-Ashkar
- Plant Production, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.); (W.B.R.); or (M.F.S.); (A.A.-D.)
- Agronomy Department, Faculty of Agriculture, Al-Azhar University, Cairo 11651, Egypt
| | - Ali Alderfasi
- Plant Production, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.); (W.B.R.); or (M.F.S.); (A.A.-D.)
| | - Walid Ben Romdhane
- Plant Production, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.); (W.B.R.); or (M.F.S.); (A.A.-D.)
| | - Mahmoud F. Seleiman
- Plant Production, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.); (W.B.R.); or (M.F.S.); (A.A.-D.)
- Department of Crop Sciences, Faculty of Agriculture, Menoufia University, Shibin El-kom 32514, Egypt
| | - Rania A. El-Said
- Biological and Ecological Department, Faculty of Home Economic, Al-Azhar University, Tanta 31732, Egypt;
| | - Abdullah Al-Doss
- Plant Production, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.); (W.B.R.); or (M.F.S.); (A.A.-D.)
| |
Collapse
|