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Xu X, Su Y, Yang J, Li J, Gao Y, Li C, Wang X, Gou L, Zheng Z, Xie C, Ma J, Ma J. A novel QTL conferring Fusarium crown rot resistance on chromosome 2A in a wheat EMS mutant. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:49. [PMID: 38349579 DOI: 10.1007/s00122-024-04557-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024]
Abstract
KEY MESSAGE A novel QTL on chromosome 2A for Fusarium crown rot resistance was identified and validated in wheat. Fusarium crown rot (FCR) is a fungal disease that causes significant yield losses in many cereal growing regions in the world. In this study, genetic analysis was conducted for a wheat EMS mutant C549 which showed stable resistance to FCR at seedling stage. A total of 10 QTL were detected on chromosomes 1A, 2A, 3B, 4A, 6B, and 7B using a population of 138 F7 recombinant inbred lines (RILs) derived from a cross between C549 and a Chinese germplasm 3642. A novel locus Qfcr.cau-2A, which accounted for up to 24.42% of the phenotypic variation with a LOD value of 12.78, was consistently detected across all six trials conducted. Furthermore, possible effects of heading date (HD) and plant height on FCR severity were also investigated in the mapping population. While plant height had no effects on FCR resistance, a weak and negative association between FCR resistance and HD was observed. A QTL for HD (Qhd.cau-2A.2) was coincident with Qfcr.cau-2A. Conditional QTL mapping indicated that although Qfcr.cau-2A and Qhd.cau-2A.2 had significant interactions, Qfcr.cau-2A remained significant after the effects of HD was removed. It is unlikely that genes underlying these two loci are same. Nevertheless, the stable expression of Qfcr.cau-2A in the validation population of 148 F7 RILs developed between C549 and its wild parent Chuannong 16 demonstrated the potential value of this locus in FCR resistance breeding programs.
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Affiliation(s)
- Xiangru Xu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yuqing Su
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jiatian Yang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jinlong Li
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yutian Gao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xingyi Wang
- College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Lulu Gou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhi Zheng
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Chaojie Xie
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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Ali S, Zhang T, Lambing C, Wang W, Zhang P, Xie L, Wang J, Khan N, Zhang Q. Loss of chromatin remodeler DDM1 causes segregation distortion in Arabidopsis thaliana. PLANTA 2021; 254:107. [PMID: 34694462 DOI: 10.1007/s00425-021-03763-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
In ddm1 mutants, the DNA methylation is primarily affected in the heterochromatic region of the chromosomes, which is associated with the segregation distortion of SNPs in the F2 progenies. Segregation distortion (SD) is common in most genetic mapping experiments and a valuable resource to determine how gene loci induce deviation. Meiotic DNA crossing over and SD are under the control of several types of epigenetic modifications. DNA methylation is an important regulatory epigenetic modification that is inherited across generations. In the present study, we investigated the relationship between SD and DNA methylation. The ecotypes Col-0/C24 and chromatin remodeler mutants ddm1-10/Col and ddm1-15/C24 were reciprocally crossed to obtain F2 generations. A total of 300 plants for each reciprocally crossed plant in the F2 generations were subjected to next-generation sequencing to detect the single-nucleotide polymorphisms (SNPs) as DNA markers. All SNPs were analyzed using the Chi-square test method to determine their segregation ratio in F2 generations. Through the segregation ratio, whole-genome SNPs were classified into 16 classes. In class 10, the SNPs in the reciprocal crosses of wild type showed the expected Mendelian ratio of 1:2:1, while those in the reciprocal crosses of ddm1 mutants showed distortion. In contrast, all SNPs in class 16 displayed a normal 1:2:1 ratio, and class 1 showed SD, regardless of wild type or mutants, as assessed using CAPS (cleaved amplified polymorphic sequences) marker analysis to confirm the next-generation sequencing. In ddm1 mutants, the DNA methylation is highly reduced throughout the whole genome and more significantly in the heterochromatic regions of chromosomes. Our results showed that the ddm1 mutants exhibit low levels of DNA methylation, which facilitates the SD of SNPs primarily located in the heterochromatic region of chromosomes by reducing the heterozygous ratio. The present study will provide a strong base for future research focusing on the impact of DNA methylation on trait segregation and plant evolution.
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Affiliation(s)
- Shahid Ali
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | | | - Wanpeng Wang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Peng Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Linan Xie
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Jiang Wang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
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3
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Nyouma A, Bell JM, Jacob F, Riou V, Manez A, Pomiès V, Nodichao L, Syahputra I, Affandi D, Cochard B, Durand-Gasselin T, Cros D. Genomic predictions improve clonal selection in oil palm (Elaeis guineensis Jacq.) hybrids. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110547. [PMID: 32900451 DOI: 10.1016/j.plantsci.2020.110547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/14/2020] [Accepted: 06/01/2020] [Indexed: 05/14/2023]
Abstract
The prediction of clonal genetic value for yield is challenging in oil palm (Elaeis guineensis Jacq.). Currently, clonal selection involves two stages of phenotypic selection (PS): ortet preselection on traits with sufficient heritability among a small number of individuals in the best crosses in progeny tests, and final selection on performance in clonal trials. The present study evaluated the efficiency of genomic selection (GS) for clonal selection. The training set comprised almost 300 Deli × La Mé crosses phenotyped for eight palm oil yield components and the validation set 42 Deli × La Mé ortets. Genotyping-by-sequencing (GBS) revealed 15,054 single nucleotide polymorphisms (SNP). The effects of the SNP dataset (density and percentage of missing data) and two GS modeling approaches, ignoring (ASGM) and considering (PSAM) the parental origin of alleles, were assessed. The results showed prediction accuracies ranging from 0.08 to 0.70 for ortet candidates without data records, depending on trait, SNP dataset and modeling. ASGM was better (on average slightly more accurate, less sensitive to SNP dataset and simpler), although PSAM appeared interesting for a few traits. With ASGM, the number of SNPs had to reach 7,000, while the percentage of missing data per SNP was of secondary importance, and GS prediction accuracies were higher than those of PS for most of the traits. Finally, this makes possible two practical applications of GS, that will increase genetic progress by improving ortet preselection before clonal trials: (1) preselection at the mature stage on all yield components jointly using ortet genotypes and phenotypes, and (2) genomic preselection on more yield components than PS, among a large population of the best possible crosses at nursery stage.
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Affiliation(s)
- Achille Nyouma
- Department of Plant Biology, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon; CETIC (African Center of Excellence in Information and Communication Technologies), University of Yaoundé 1, Yaoundé, Cameroon
| | - Joseph Martin Bell
- Department of Plant Biology, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | | | - Virginie Riou
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France; AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aurore Manez
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France; AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Virginie Pomiès
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France; AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Leifi Nodichao
- AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France; INRAB, CRA-PP, Pobè, Benin
| | | | | | | | | | - David Cros
- CETIC (African Center of Excellence in Information and Communication Technologies), University of Yaoundé 1, Yaoundé, Cameroon; CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France; AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.
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Dhariwal R, Henriquez MA, Hiebert C, McCartney CA, Randhawa HS. Mapping of Major Fusarium Head Blight Resistance from Canadian Wheat cv. AAC Tenacious. Int J Mol Sci 2020; 21:E4497. [PMID: 32599868 PMCID: PMC7350018 DOI: 10.3390/ijms21124497] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 01/22/2023] Open
Abstract
Fusarium head blight (FHB) is one of the most devastating wheat disease due to its direct detrimental effects on grain-yield, quality and marketability. Resistant cultivars offer the most effective approach to manage FHB; however, the lack of different resistance resources is still a major bottleneck for wheat breeding programs. To identify and dissect FHB resistance, a doubled haploid wheat population produced from the Canadian spring wheat cvs AAC Innova and AAC Tenacious was phenotyped for FHB response variables incidence and severity, visual rating index (VRI), deoxynivalenol (DON) content, and agronomic traits days to anthesis (DTA) and plant height (PHT), followed by single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker genotyping. A high-density map was constructed consisting of 10,328 markers, mapped on all 21 chromosomes with a map density of 0.35 cM/marker. Together, two major quantitative trait loci for FHB resistance were identified on chromosome 2D from AAC Tenacious; one of these loci on 2DS also colocated with loci for DTA and PHT. Another major locus for PHT, which cosegregates with locus for low DON, was also identified along with many minor and epistatic loci. QTL identified from AAC Tenacious may be useful to pyramid FHB resistance.
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Affiliation(s)
- Raman Dhariwal
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada;
| | - Maria A. Henriquez
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB R6M 1Y5, Canada; (M.A.H.); (C.H.); (C.A.M.)
| | - Colin Hiebert
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB R6M 1Y5, Canada; (M.A.H.); (C.H.); (C.A.M.)
| | - Curt A. McCartney
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB R6M 1Y5, Canada; (M.A.H.); (C.H.); (C.A.M.)
| | - Harpinder S. Randhawa
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada;
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Wu X, Alexander LW. Genome-wide association studies for inflorescence type and remontancy in Hydrangea macrophylla. HORTICULTURE RESEARCH 2020; 7:27. [PMID: 32140236 PMCID: PMC7049302 DOI: 10.1038/s41438-020-0255-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/31/2019] [Accepted: 01/04/2020] [Indexed: 05/28/2023]
Abstract
Inflorescence type and remontancy are two valuable traits in bigleaf hydrangea (Hydrangea macrophylla L.) and both are recessively inherited. Molecular marker-assisted selection (MAS) can greatly reduce the time necessary to breed cultivars with desired traits. In this study, a genome-wide association study (GWAS) using 5803 single-nucleotide polymorphisms (SNPs) was performed using a panel of 82 bigleaf hydrangea cultivars. One SNP locus (Hy_CAPS_Inflo) associated with inflorescence type was identified with general linear model (GLM) and mixed linear model (MLM) methods that explained 65.5% and 36.1% of the phenotypic variations, respectively. Twenty-three SNPs associated with remontancy were detected in GLM whereas no SNP was detected in MLM. The SNP locus (Hy_CAPS_Inflo) was converted to a cleaved amplified polymorphic sequence (CAPS) marker that showed absolute identification accuracy (100%) of inflorescence type in a validation panel consisting of eighteen H. macrophylla cultivars. The SNP was investigated in 341 F1 progenies using genotyping by sequencing (GBS) and co-segregated with inflorescence type (χ 2 = 0.12; P = 0.73). The SNP was subsequently used for breeding selection using kompetitive allele specific PCR (KASP) technology. Future directions for the use of genomics and MAS in hydrangea breeding improvement are discussed. The results presented in this study provide insights for further research on understanding genetic mechanisms behind inflorescence type and remontancy in H. macrophylla. The CAPS and KASP markers developed here will be immediately useful for applying MAS to accelerate breeding improvement in hydrangea.
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Affiliation(s)
- Xingbo Wu
- Oak Ridge Institute of Science and Technology, Otis L. Floyd Nursery Research Center, 472 Cadillac Lane, McMinnville, TN USA
| | - Lisa W. Alexander
- U.S. Department of Agriculture, Agricultural Research Service, U.S. National Arboretum, Floral and Nursery Plants Research Unit, Otis L. Floyd Nursery Research Center, 472 Cadillac Lane, McMinnville, TN USA
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6
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Coulton A, Przewieslik-Allen AM, Burridge AJ, Shaw DS, Edwards KJ, Barker GLA. Segregation distortion: Utilizing simulated genotyping data to evaluate statistical methods. PLoS One 2020; 15:e0228951. [PMID: 32074141 PMCID: PMC7029859 DOI: 10.1371/journal.pone.0228951] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/26/2020] [Indexed: 11/18/2022] Open
Abstract
Segregation distortion is the phenomenon in which genotypes deviate from expected Mendelian ratios in the progeny of a cross between two varieties or species. There is not currently a widely used consensus for the appropriate statistical test, or more specifically the multiple testing correction procedure, used to detect segregation distortion for high-density single-nucleotide polymorphism (SNP) data. Here we examine the efficacy of various multiple testing procedures, including chi-square test with no correction for multiple testing, false-discovery rate correction and Bonferroni correction using an in-silico simulation of a biparental mapping population. We find that the false discovery rate correction best approximates the traditional p-value threshold of 0.05 for high-density marker data. We also utilize this simulation to test the effect of segregation distortion on the genetic mapping process, specifically on the formation of linkage groups during marker clustering. Only extreme segregation distortion was found to effect genetic mapping. In addition, we utilize replicate empirical mapping populations of wheat varieties Avalon and Cadenza to assess how often segregation distortion conforms to the same pattern between closely related wheat varieties.
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Affiliation(s)
- Alexander Coulton
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom
- * E-mail:
| | | | - Amanda J. Burridge
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom
| | - Daniel S. Shaw
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom
| | - Keith J. Edwards
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom
| | - Gary L. A. Barker
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom
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7
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Mohler V, Schmolke M, Zeller FJ, Hsam SLK. Genetic analysis of Aegilops tauschii-derived seedling resistance to leaf rust in synthetic hexaploid wheat. J Appl Genet 2020; 61:163-168. [PMID: 31981185 PMCID: PMC7148280 DOI: 10.1007/s13353-020-00541-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/19/2019] [Accepted: 01/08/2020] [Indexed: 10/29/2022]
Abstract
Seedling resistance to leaf rust available in the synthetic hexaploid wheat line Syn137 was characterised by means of cytogenetic and linkage mapping. Monosomic analysis located a single dominant gene for leaf rust resistance on chromosome 5D. Molecular mapping not only confirmed this location but also positioned the gene to the distal part of the long arm of chromosome 5D. A test of allelism showed that the gene, tentatively named LrSyn137, is independent but closely linked to Lr1. It appears that Syn137 is occasionally heterogeneous for Lr1 since the analysis of the Lr1-specific marker RGA567-5 in the genetic mapping population indicated the presence of Lr1. Syn137 represents another source of genetic variation that can be useful for the diversification of leaf rust resistance in wheat cultivars.
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Affiliation(s)
- Volker Mohler
- Bayerische Landesanstalt für Landwirtschaft (LfL), Institut für Pflanzenbau und Pflanzenzüchtung (IPZ), Am Gereuth 8, 85354, Freising, Germany.
| | - Michael Schmolke
- Plant Breeding, Centre for Food and Life Sciences Weihenstephan, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Friedrich J Zeller
- Plant Breeding, Centre for Food and Life Sciences Weihenstephan, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Sai L K Hsam
- Plant Breeding, Centre for Food and Life Sciences Weihenstephan, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
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8
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Ruud AK, Dieseth JA, Ficke A, Furuki E, Phan HTT, Oliver RP, Tan KC, Lillemo M. Genome-Wide Association Mapping of Resistance to Septoria Nodorum Leaf Blotch in a Nordic Spring Wheat Collection. THE PLANT GENOME 2019; 12:1-15. [PMID: 33016591 DOI: 10.3835/plantgenome2018.12.0105] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/06/2019] [Indexed: 05/12/2023]
Abstract
First genome-wide association mapping of adult plant Septoria nodorum blotch resistance. Some adult plant resistance loci were shared with seedling resistance loci. Other adult plant resistance loci were significant across environments. Resistant haplotypes were identified, which can be used for breeding. Parastagonospora nodorum is the causal agent of Septoria nodorum leaf blotch (SNB) in wheat (Triticum aestivum L.). It is the most important leaf blotch pathogen in Norwegian spring wheat. Several quantitative trait loci (QTL) for SNB susceptibility have been identified. Some of these QTL are the result of underlying gene-for-gene interactions involving necrotrophic effectors (NEs) and corresponding sensitivity (Snn) genes. A collection of diverse spring wheat lines was evaluated for SNB resistance and susceptibility over seven growing seasons in the field. In addition, wheat seedlings were inoculated and infiltrated with culture filtrates (CFs) from four single spore isolates and infiltrated with semipurified NEs (SnToxA, SnTox1, and SnTox3) under greenhouse conditions. In adult plants, the most stable SNB resistance QTL were located on chromosomes 2B, 2D, 4A, 4B, 5A, 6B, 7A, and 7B. The QTL on chromosome 2D was effective most years in the field. At the seedling stage, the most significant QTL after inoculation were located on chromosomes 1A, 1B, 3A, 4B, 5B, 6B, 7A, and 7B. The QTL on chromosomes 3A and 6B were significant both after inoculation and CF infiltration, indicating the presence of novel NE-Snn interactions. The QTL on chromosomes 4B and 7A were significant in both seedlings and adult plants. Correlations between SnToxA sensitivity and disease severity in the field were significant. To our knowledge, this is the first genome-wide association mapping study (GWAS) to investigate SNB resistance at the adult plant stage under field conditions.
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Affiliation(s)
- Anja Karine Ruud
- Dep. of Plant Sciences, Norwegian Univ. of Life Sciences, Post Box 5003, NO-1432, ÅS, Norway
- Faculty of Science and Technology, Dep. of Molecular Biology and Genetics, Aarhus Univ, 4200, Slagelse, Denmark
| | - Jon Arne Dieseth
- Graminor, AS, Bjørke Gård, Hommelstadvegen 60, NO-2322, Ridabu, Norway
| | - Andrea Ficke
- Division of Biotechnology and Plant Health, Norwegian Inst. of Bioeconomy Research, P.O. Box 115, NO-1431, ÅS, Norway
| | - Eiko Furuki
- Centre for Crop and Disease Management, Dep. of Environment & Agriculture, Curtin Univ., Bentley, Western Australia, Australia
| | - Huyen T T Phan
- Centre for Crop and Disease Management, Dep. of Environment & Agriculture, Curtin Univ., Bentley, Western Australia, Australia
| | - Richard P Oliver
- Centre for Crop and Disease Management, Dep. of Environment & Agriculture, Curtin Univ., Bentley, Western Australia, Australia
| | - Kar-Chun Tan
- Centre for Crop and Disease Management, Dep. of Environment & Agriculture, Curtin Univ., Bentley, Western Australia, Australia
| | - Morten Lillemo
- Dep. of Plant Sciences, Norwegian Univ. of Life Sciences, Post Box 5003, NO-1432, ÅS, Norway
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Farahani S, Maleki M, Mehrabi R, Kanouni H, Scheben A, Batley J, Talebi R. Whole Genome Diversity, Population Structure, and Linkage Disequilibrium Analysis of Chickpea ( Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers. Genes (Basel) 2019; 10:E676. [PMID: 31487948 PMCID: PMC6770975 DOI: 10.3390/genes10090676] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/26/2019] [Accepted: 08/20/2019] [Indexed: 01/09/2023] Open
Abstract
Characterization of genetic diversity, population structure, and linkage disequilibrium is a prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes, including advanced "Kabuli" breeding lines and Iranian landrace "Desi" chickpea genotypes, were genotyped using DArTseq-Based single nucleotide polymorphism (SNP) markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that was covered by SNPs varied from 16,236.36 kbp (LG8) to 67,923.99 kbp (LG5), while LG4 showed a higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6, and LG8 showed higher mean PIC value than average. Unweighted neighbor joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and discriminant analysis of principal component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r2 ≥ 0.8, while 2961 pairs of markers showed complete LD (r2 = 1), and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggest the presence of a high genetic diversity among the studied chickpea genotypes. This study also demonstrates the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits, such as seed yield, abiotic, and biotic stresses, and therefore can be efficiently used in breeding programs to improve chickpea.
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Affiliation(s)
- Somayeh Farahani
- Department of Plant Protection, Varamin-Pishva Branch, Islamic Azad University, Varamin, P.O.Box: 33817-74895, Iran
| | - Mojdeh Maleki
- Department of Plant Protection, Varamin-Pishva Branch, Islamic Azad University, Varamin, P.O.Box: 33817-74895, Iran
| | - Rahim Mehrabi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan P.O. Box: 8415683111, Iran
| | - Homayoun Kanouni
- Kordestan Agricultural and Natural Resources and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Sanandaj, P.O.Box:714, Iran
| | - Armin Scheben
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Reza Talebi
- Department of Agronomy & Plant Breeding, College of Agriculture, Sanandaj Branch, Islamic Azad University, Sanandaj, P.O. Box:618, Iran.
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Huang L, Yan X. Construction of a genetic linkage map in Pyropia yezoensis (Bangiales, Rhodophyta) and QTL analysis of several economic traits of blades. PLoS One 2019; 14:e0209128. [PMID: 30849086 PMCID: PMC6407771 DOI: 10.1371/journal.pone.0209128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/20/2019] [Indexed: 11/18/2022] Open
Abstract
Pyropia yezoensis is an economically important seaweed but its molecular genetics is poorly understood. In the present study, we used a doubled haploid (DH) population that was established in our previous work to construct a genetic linkage map of P. yezoensis and analyze the quantitative trait loci (QTLs) of blades. The DH population was genotyped with fluorescent sequence-related amplified polymorphism (SRAP) markers. A chi-square test identified 301 loci with normal segregation (P ≥ 0.01) and 96 loci (24.18%) with low-level skewed segregation (0.001 ≤ P < 0.01). The genetic map was constructed after a total of 92 loci were assembled into three linkage groups (LGs). The map spanned 557.36 cM covering 93.71% of the estimated genome, with a mean interlocus space of 6.23 cM. Kolmogorov-Smirnov test (α = 5%) showed a uniform distribution of the markers along each LG. On the genetic map, 10 QTLs associated with five economic traits of blades were detected. One QTL was for length, one for width, two for fresh weight, two for specific growth rate of length and four for specific growth rate of fresh weight. These QTLs could explain 2.29–7.87% of the trait variations, indicating that their effects were all minor. The results may serve as a framework for future marker-assisted breeding in P. yezoensis.
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Affiliation(s)
- Linbin Huang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, P. R. China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, P. R. China
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, P. R. China
| | - Xinghong Yan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, P. R. China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, P. R. China
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, P. R. China
- * E-mail:
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Sannemann W, Lisker A, Maurer A, Léon J, Kazman E, Cöster H, Holzapfel J, Kempf H, Korzun V, Ebmeyer E, Pillen K. Adaptive selection of founder segments and epistatic control of plant height in the MAGIC winter wheat population WM-800. BMC Genomics 2018; 19:559. [PMID: 30064354 PMCID: PMC6069784 DOI: 10.1186/s12864-018-4915-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/02/2018] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Multi-parent advanced generation intercross (MAGIC) populations are a newly established tool to dissect quantitative traits. We developed the high resolution MAGIC wheat population WM-800, consisting of 910 F4:6 lines derived from intercrossing eight recently released European winter wheat cultivars. RESULTS Genotyping WM-800 with 7849 SNPs revealed a low mean genetic similarity of 59.7% between MAGIC lines. WM-800 harbours distinct genomic regions exposed to segregation distortion. These are mainly located on chromosomes 2 to 6 of the wheat B genome where founder specific DNA segments were positively or negatively selected. This suggests adaptive selection of individual founder alleles during population development. The application of a genome-wide association study identified 14 quantitative trait loci (QTL) controlling plant height in WM-800, including the known semi-dwarf genes Rht-B1 and Rht-D1 and a potentially novel QTL on chromosome 5A. Additionally, epistatic effects controlled plant height. For example, two loci on chromosomes 2B and 7B gave rise to an additive epistatic effect of 13.7 cm. CONCLUSION The present study demonstrates that plant height in the MAGIC-WHEAT population WM-800 is mainly determined by large-effect QTL and di-genic epistatic interactions. As a proof of concept, our study confirms that WM-800 is a valuable tool to dissect the genetic architecture of important agronomic traits.
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Affiliation(s)
- Wiebke Sannemann
- Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann Straße 3, 06120 Halle, Germany
| | - Antonia Lisker
- Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann Straße 3, 06120 Halle, Germany
| | - Andreas Maurer
- Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann Straße 3, 06120 Halle, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, University of Bonn, Katzenburgweg 5, Bonn, Germany
| | - Ebrahim Kazman
- Syngenta Seeds GmbH, Kroppenstedter Straße 4, 39387 Oschersleben (Bode), Hadmersleben, Germany
| | - Hilmar Cöster
- RAGT 2n, Steinesche 5A, 38855 - Silstedt, Wernigerode, Germany
| | - Josef Holzapfel
- Secobra Saatzucht GmbH, Feldkirchen 3, 85368 Moosburg an der Isar, Germany
| | - Hubert Kempf
- Secobra Saatzucht GmbH, Feldkirchen 3, 85368 Moosburg an der Isar, Germany
| | - Viktor Korzun
- KWS SAAT SE, Grimsehlstraße 31, 37555 Einbeck, Germany
| | - Erhard Ebmeyer
- KWS LOCHOW GMBH, Ferdinand-Lochow-Straße 5, 29303 Bergen/Wohlde, Germany
| | - Klaus Pillen
- Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann Straße 3, 06120 Halle, Germany
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Ando K, Rynearson S, Muleta KT, Gedamu J, Girma B, Bosque-Pérez NA, Chen MS, Pumphrey MO. Genome-wide associations for multiple pest resistances in a Northwestern United States elite spring wheat panel. PLoS One 2018; 13:e0191305. [PMID: 29415008 PMCID: PMC5802848 DOI: 10.1371/journal.pone.0191305] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/01/2018] [Indexed: 12/01/2022] Open
Abstract
Northern areas of the western United States are one of the most productive wheat growing regions in the United States. Increasing productivity through breeding is hindered by several biotic stresses which slow and constrain targeted yield improvement. In order to understand genetic variation for stripe rust (Puccinia striiformis f. sp. tritici), Septoria tritici blotch (Mycosphaerella graminicola), and Hessian fly (Mayetiola destructor) in regional germplasm, a panel of 408 elite spring wheat lines was characterized and genotyped with an Illumina 9K wheat single nucleotide polymorphism (SNP) chip to enable genome-wide association study (GWAS) analyses. Significant marker-trait associations were identified for stripe rust (38 loci), Septoria tritici blotch (8) and Hessian fly (9) resistance. Many of the QTL corresponded with previously reported gene locations or QTL, but we also discovered new resistance loci for each trait. We validated one of the stripe rust resistance loci detected by GWAS in a bi-parental mapping population, which confirmed the detection of Yr15 in the panel. This study elucidated well-defined chromosome regions for multiple pest resistances in elite Northwest germplasm. Newly identified resistance loci, along with SNPs more tightly linked to previously reported genes or QTL will help future breeding and marker assisted selection efforts.
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Affiliation(s)
- Kaori Ando
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Sheri Rynearson
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Kebede T. Muleta
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Jhonatan Gedamu
- Ethiopian Institute of Agricultural Research, Holeta Agricultural Research Center, Holeta, Ethiopia
| | - Bedada Girma
- Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Assela, Ethiopia
| | - Nilsa A. Bosque-Pérez
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, Idaho, United States of America
| | - Ming-Shun Chen
- United States Department of Agriculture–Agricultural Research Service and Department of Entomology, Kansas State University, Manhattan, Kansas, United States of America
| | - Mike O. Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
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Tsai WC, Dievart A, Hsu CC, Hsiao YY, Chiou SY, Huang H, Chen HH. Post genomics era for orchid research. BOTANICAL STUDIES 2017; 58:61. [PMID: 29234904 PMCID: PMC5727007 DOI: 10.1186/s40529-017-0213-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/01/2017] [Indexed: 05/05/2023]
Abstract
Among 300,000 species in angiosperms, Orchidaceae containing 30,000 species is one of the largest families. Almost every habitats on earth have orchid plants successfully colonized, and it indicates that orchids are among the plants with significant ecological and evolutionary importance. So far, four orchid genomes have been sequenced, including Phalaenopsis equestris, Dendrobium catenatum, Dendrobium officinale, and Apostaceae shengen. Here, we review the current progress and the direction of orchid research in the post genomics era. These include the orchid genome evolution, genome mapping (genome-wide association analysis, genetic map, physical map), comparative genomics (especially receptor-like kinase and terpene synthase), secondary metabolomics, and genome editing.
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Affiliation(s)
- Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Anne Dievart
- CIRAD, UMR AGAP, TA A 108/03, Avenue Agropolis, 34398 Montpellier, France
- Present Address: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Life Sciences Building, Room 3-117, Shanghai, 200240 People’s Republic of China
| | - Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Shang-Yi Chiou
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hsin Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hong-Hwa Chen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
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14
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Harnessing Genetic Diversity of Wild Gene Pools to Enhance Wheat Crop Production and Sustainability: Challenges and Opportunities. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040055] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Wild species are extremely rich resources of useful genes not available in the cultivated gene pool. For species providing staple food to mankind, such as the cultivated Triticum species, including hexaploid bread wheat (Triticum aestivum, 6x) and tetraploid durum wheat (T. durum, 4x), widening the genetic base is a priority and primary target to cope with the many challenges that the crop has to face. These include recent climate changes, as well as actual and projected demographic growth, contrasting with reduction of arable land and water reserves. All of these environmental and societal modifications pose major constraints to the required production increase in the wheat crop. A sustainable approach to address this task implies resorting to non-conventional breeding strategies, such as “chromosome engineering”. This is based on cytogenetic methodologies, which ultimately allow for the incorporation into wheat chromosomes of targeted, and ideally small, chromosomal segments from the genome of wild relatives, containing the gene(s) of interest. Chromosome engineering has been successfully applied to introduce into wheat genes/QTL for resistance to biotic and abiotic stresses, quality attributes, and even yield-related traits. In recent years, a substantial upsurge in effective alien gene exploitation for wheat improvement has come from modern technologies, including use of molecular markers, molecular cytogenetic techniques, and sequencing, which have greatly expanded our knowledge and ability to finely manipulate wheat and alien genomes. Examples will be provided of various types of stable introgressions, including pyramiding of different alien genes/QTL, into the background of bread and durum wheat genotypes, representing valuable materials for both species to respond to the needed novelty in current and future breeding programs. Challenging contexts, such as that inherent to the 4x nature of durum wheat when compared to 6x bread wheat, or created by presence of alien genes affecting segregation of wheat-alien recombinant chromosomes, will also be illustrated.
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Jaiswal S, Sheoran S, Arora V, Angadi UB, Iquebal MA, Raghav N, Aneja B, Kumar D, Singh R, Sharma P, Singh GP, Rai A, Tiwari R, Kumar D. Putative Microsatellite DNA Marker-Based Wheat Genomic Resource for Varietal Improvement and Management. FRONTIERS IN PLANT SCIENCE 2017; 8:2009. [PMID: 29234333 PMCID: PMC5712362 DOI: 10.3389/fpls.2017.02009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/10/2017] [Indexed: 05/29/2023]
Abstract
Wheat fulfills 20% of global caloric requirement. World needs 60% more wheat for 9 billion population by 2050 but climate change with increasing temperature is projected to affect wheat productivity adversely. Trait improvement and management of wheat germplasm requires genomic resource. Simple Sequence Repeats (SSRs) being highly polymorphic and ubiquitously distributed in the genome, can be a marker of choice but there is no structured marker database with options to generate primer pairs for genotyping on desired chromosome/physical location. Previously associated markers with different wheat trait are also not available in any database. Limitations of in vitro SSR discovery can be overcome by genome-wide in silico mining of SSR. Triticum aestivum SSR database (TaSSRDb) is an integrated online database with three-tier architecture, developed using PHP and MySQL and accessible at http://webtom.cabgrid.res.in/wheatssr/. For genotyping, Primer3 standalone code computes primers on user request. Chromosome-wise SSR calling for all the three sub genomes along with choice of motif types is provided in addition to the primer generation for desired marker. We report here a database of highest number of SSRs (476,169) from complex, hexaploid wheat genome (~17 GB) along with previously reported 268 SSR markers associated with 11 traits. Highest (116.93 SSRs/Mb) and lowest (74.57 SSRs/Mb) SSR densities were found on 2D and 3A chromosome, respectively. To obtain homozygous locus, e-PCR was done. Such 30 loci were randomly selected for PCR validation in panel of 18 wheat Advance Varietal Trial (AVT) lines. TaSSRDb can be a valuable genomic resource tool for linkage mapping, gene/QTL (Quantitative trait locus) discovery, diversity analysis, traceability and variety identification. Varietal specific profiling and differentiation can supplement DUS (Distinctiveness, Uniformity, and Stability) testing, EDV (Essentially Derived Variety)/IV (Initial Variety) disputes, seed purity and hybrid wheat testing. All these are required in germplasm management as well as also in the endeavor of wheat productivity.
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Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sonia Sheoran
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Vasu Arora
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ulavappa B. Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir A. Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Nishu Raghav
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Bharti Aneja
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Deepender Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Rajender Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - G. P. Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Hussain W, Baenziger PS, Belamkar V, Guttieri MJ, Venegas JP, Easterly A, Sallam A, Poland J. Genotyping-by-Sequencing Derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat. Sci Rep 2017; 7:16394. [PMID: 29180623 PMCID: PMC5703991 DOI: 10.1038/s41598-017-16006-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 11/06/2017] [Indexed: 11/17/2022] Open
Abstract
Winter wheat parents ‘Harry’ (drought tolerant) and ‘Wesley’ (drought susceptible) were used to develop a recombinant inbred population with future goals of identifying genomic regions associated with drought tolerance. To precisely map genomic regions, high-density linkage maps are a prerequisite. In this study genotyping-by- sequencing (GBS) was used to construct the high-density linkage map. The map contained 3,641 markers distributed on 21 chromosomes and spanned 1,959 cM with an average distance of 1.8 cM between markers. The constructed linkage map revealed strong collinearity in marker order across 21 chromosomes with POPSEQ-v2.0, which was based on a high-density linkage map. The reliability of the linkage map for QTL mapping was demonstrated by co-localizing the genes to previously mapped genomic regions for two highly heritable traits, chaff color, and leaf cuticular wax. Applicability of linkage map for QTL mapping of three quantitative traits, flag leaf length, width, and area, identified 21 QTLs in four environments, and QTL expression varied across the environments. Two major stable QTLs, one each for flag leaf length (Qfll.hww-7A) and flag leaf width (Qflw.hww-5A) were identified. The map constructed will facilitate QTL and fine mapping of quantitative traits, map-based cloning, comparative mapping, and in marker-assisted wheat breeding endeavors.
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Affiliation(s)
- Waseem Hussain
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - P Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Mary J Guttieri
- USDA, Agricultural Research Service, Center for Grain and Animal Health Research, Hard Winter Wheat Genetics Research Unit, 1515 College Avenue, Manhattan, KS, 66502, USA
| | - Jorge P Venegas
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Amanda Easterly
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, 71526, Assiut, Egypt
| | - Jesse Poland
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
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17
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Tan CT, Yu H, Yang Y, Xu X, Chen M, Rudd JC, Xue Q, Ibrahim AMH, Garza L, Wang S, Sorrells ME, Liu S. Development and validation of KASP markers for the greenbug resistance gene Gb7 and the Hessian fly resistance gene H32 in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1867-1884. [PMID: 28624908 DOI: 10.1007/s00122-017-2930-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/30/2017] [Indexed: 05/19/2023]
Abstract
Greenbug and Hessian fly are important pests that decrease wheat production worldwide. We developed and validated breeder-friendly KASP markers for marker-assisted breeding to increase selection efficiency. Greenbug (Schizaphis graminum Rondani) and Hessian fly [Mayetiola destructor (Say)] are two major destructive insect pests of wheat (Triticum aestivum L.) throughout wheat production regions in the USA and worldwide. Greenbug and Hessian fly infestation can significantly reduce grain yield and quality. Breeding for resistance to these two pests using marker-assisted selection (MAS) is the most economical strategy to minimize losses. In this study, doubled haploid lines from the Synthetic W7984 × Opata M85 wheat reference population were used to construct linkage maps for the greenbug resistance gene Gb7 and the Hessian fly resistance gene H32 with genotyping-by-sequencing (GBS) and 90K array-based single nucleotide polymorphism (SNP) marker data. Flanking markers were closely linked to Gb7 and H32 and were located on chromosome 7DL and 3DL, respectively. Gb7-linked markers (synopGBS773 and synopGBS1141) and H32-linked markers (synopGBS901 and IWB65911) were converted into Kompetitive Allele Specific PCR (KASP) assays for MAS in wheat breeding. In addition, comparative mapping identified syntenic regions in Brachypodium distachyon, rice (Oryza sativa), and sorghum (Sorghum bicolor) for Gb7 and H32 that can be used for fine mapping and map-based cloning of the genes. The KASP markers developed in this study are the first set of SNPs tightly linked to Gb7 and H32 and will be very useful for MAS in wheat breeding programs and future genetic studies of greenbug and Hessian fly resistance.
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Affiliation(s)
- Chor-Tee Tan
- Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Hangjin Yu
- Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Yan Yang
- Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
- Department of Soil and Crop Science, Texas A&M University, College Station, TX, 77843, USA
| | - Xiangyang Xu
- USDA-ARS Wheat, Peanut and Other Field Crop Research Unit, Stillwater, OK, 74075, USA
| | - Mingshun Chen
- USDA-ARS and Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jackie C Rudd
- Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Qingwu Xue
- Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Amir M H Ibrahim
- Department of Soil and Crop Science, Texas A&M University, College Station, TX, 77843, USA
| | - Lisa Garza
- Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Shichen Wang
- Genomic and Bioinformatics Services, Texas A&M AgriLife Research, College Station, TX, 77845, USA
| | - Mark E Sorrells
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Shuyu Liu
- Texas A&M AgriLife Research, Amarillo, TX, 79106, USA.
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Mihalyov PD, Nichols VA, Bulli P, Rouse MN, Pumphrey MO. Multi-Locus Mixed Model Analysis Of Stem Rust Resistance In Winter Wheat. THE PLANT GENOME 2017; 10. [PMID: 28724061 DOI: 10.3835/plantgenome2017.01.0001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Genome-wide association mapping is a powerful tool for dissecting the relationship between phenotypes and genetic variants in diverse populations. With the improved cost efficiency of high-throughput genotyping platforms, association mapping is a desirable method of mining populations for favorable alleles that hold value for crop improvement. Stem rust, caused by the fungus f. sp. is a devastating disease that threatens wheat ( L.) production worldwide. Here, we explored the genetic basis of stem rust resistance in a global collection of 1411 hexaploid winter wheat accessions genotyped with 5390 single nucleotide polymorphism markers. To facilitate the development of resistant varieties, we characterized marker-trait associations underlying field resistance to North American races and seedling resistance to the races TTKSK (Ug99), TRTTF, TTTTF, and BCCBC. After evaluating several commonly used linear models, a multi-locus mixed model provided the maximum statistical power and improved the identification of loci with direct breeding application. Ten high-confidence resistance loci were identified, including SNP markers linked to and and at least three newly discovered resistance loci that are strong candidates for introgression into modern cultivars. In the present study, we assessed the power of multi-locus association mapping while providing an in-depth analysis for its practical ability to assist breeders with the introgression of rare alleles into elite varieties.
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Zhang P, Yin G, Zhou Y, Qi A, Gao F, Xia X, He Z, Li Z, Liu D. QTL Mapping of Adult-Plant Resistance to Leaf Rust in the Wheat Cross Zhou 8425B/Chinese Spring Using High-Density SNP Markers. FRONTIERS IN PLANT SCIENCE 2017; 8:793. [PMID: 28559910 PMCID: PMC5432574 DOI: 10.3389/fpls.2017.00793] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/27/2017] [Indexed: 05/02/2023]
Abstract
Wheat leaf rust is an important disease worldwide. Growing resistant cultivars is an effective means to control the disease. In the present study, 244 recombinant inbred lines from Zhou 8425B/Chinese Spring cross were phenotyped for leaf rust severities during the 2011-2012, 2012-2013, 2013-2014, and 2014-2015 cropping seasons at Baoding, Hebei province, and 2012-2013 and 2013-2014 cropping seasons in Zhoukou, Henan province. The population was genotyped using the high-density Illumina iSelect 90K SNP assay and SSR markers. Inclusive composite interval mapping identified eight QTL, designated as QLr.hebau-2AL, QLr.hebau-2BS, QLr.hebau-3A, QLr.hebau-3BS, QLr.hebau-4AL, QLr.hebau-4B, QLr.hebau-5BL, and QLr.hebau-7DS, respectively. QLr.hebau-2BS, QLr.hebau-3A, QLr.hebau-3BS, and QLr.hebau-5BL were derived from Zhou 8425B, whereas the other four were from Chinese Spring. Three stable QTL on chromosomes 2BS, 4B and 7DS explained 7.5-10.6%, 5.5-24.4%, and 11.2-20.9% of the phenotypic variance, respectively. QLr.hebau-2BS in Zhou 8425B might be the same as LrZH22 in Zhoumai 22; QLr.hebau-4B might be the residual resistance of Lr12, and QLr.hebau-7DS is Lr34. QLr.hebau-2AL, QLr.hebau-3BS, QLr.hebau-4AL, and QLr.hebau-5BL are likely to be novel QTL for leaf rust. These QTL and their closely linked SNP and SSR markers can be used for fine mapping, candidate gene discovery, and marker-assisted selection in wheat breeding.
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Affiliation(s)
- Peipei Zhang
- College of Plant Protection, Agricultural University of HebeiBaoding, China
| | - Guihong Yin
- Zhoukou Academy of Agricultural SciencesZhoukou, China
| | - Yue Zhou
- Department of Biochemistry, Baoding UniversityBaoding, China
| | - Aiyong Qi
- College of Plant Protection, Agricultural University of HebeiBaoding, China
| | - Fengmei Gao
- Institute of Crop Science, National Wheat Improvement Center – Chinese Academy of Agricultural SciencesBeijing, China
| | - Xianchun Xia
- Institute of Crop Science, National Wheat Improvement Center – Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center – Chinese Academy of Agricultural SciencesBeijing, China
| | - Zaifeng Li
- College of Plant Protection, Agricultural University of HebeiBaoding, China
| | - Daqun Liu
- College of Plant Protection, Agricultural University of HebeiBaoding, China
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Genotyping-by-Sequencing Facilitates a High-Density Consensus Linkage Map for Aegilops umbellulata, a Wild Relative of Cultivated Wheat. G3-GENES GENOMES GENETICS 2017; 7:1551-1561. [PMID: 28364036 PMCID: PMC5427507 DOI: 10.1534/g3.117.039966] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
High-density genetic maps are useful to precisely localize QTL or genes that might be used to improve traits of nutritional and/or economical importance in crops. However, high-density genetic maps are lacking for most wild relatives of crop species, including wheat. Aegilops umbellulata is a wild relative of wheat known for its potential as a source of biotic and abiotic stress resistance genes. In this work, we have developed a framework consensus genetic map using two biparental populations derived from accessions PI 298905, PI 542369, PI 5422375, and PI 554395. The framework map comprised 3009 genotype-by-sequence SNPs with a total map size of 948.72 cM. On average, there were three SNPs per centimorgan for each chromosome. Chromosome 1U was the shortest (66.5 cM), with only 81 SNPs, whereas the remaining chromosomes had between 391 and 591 SNP markers. A total of 2395 unmapped SNPs were added to the linkage maps through a recombination frequency approach, and increased the number of SNPs placed on the consensus map to a total of 5404 markers. Segregation distortion was disproportionally high for chromosome 1U for both populations used to construct component linkage maps, and thus segregation distortion could be one of the probable reasons for the exceptionally reduced linkage size for chromosome 1U. From comparative analysis, Ae. umbellulata chromosomes except 4U showed moderate to strong collinearity with corresponding homeologous chromosomes of hexaploid wheat and barley. The present consensus map may serve as a reference map in QTL mapping and validation projects, and also in genome assembly to develop a reference genome sequence for Ae. umbellulata.
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Abstract
Understanding the genomic complexity of bread wheat is important for unraveling domestication processes, environmental adaptation, and for future of... Understanding the genomic complexity of bread wheat (Triticum aestivum L.) is a cornerstone in the quest to unravel the processes of domestication and the following adaptation of domesticated wheat to a wide variety of environments across the globe. Additionally, it is of importance for future improvement of the crop, particularly in the light of climate change. Focusing on the adaptation after domestication, a nested association mapping (NAM) panel of 60 segregating biparental populations was developed, mainly involving landrace accessions from the core set of the Watkins hexaploid wheat collection optimized for genetic diversity. A modern spring elite variety, “Paragon,” was used as common reference parent. Genetic maps were constructed following identical rules to make them comparable. In total, 1611 linkage groups were identified, based on recombination from an estimated 126,300 crossover events over the whole NAM panel. A consensus map, named landrace consensus map (LRC), was constructed and contained 2498 genetic loci. These newly developed genetics tools were used to investigate the rules underlying genome fluidity or rigidity, e.g., by comparing marker distances and marker orders. In general, marker order was highly correlated, which provides support for strong synteny between bread wheat accessions. However, many exceptional cases of incongruent linkage groups and increased marker distances were also found. Segregation distortion was detected for many markers, sometimes as hot spots present in different populations. Furthermore, evidence for translocations in at least 36 of the maps was found. These translocations fell, in general, into many different translocation classes, but a few translocation classes were found in several accessions, the most frequent one being the well-known T5B:7B translocation. Loci involved in recombination rate, which is an interesting trait for plant breeding, were identified by QTL analyses using the crossover counts as a trait. In total, 114 significant QTL were detected, nearly half of them with increasing effect from the nonreference parents.
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N’Diaye A, Haile JK, Cory AT, Clarke FR, Clarke JM, Knox RE, Pozniak CJ. Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map. PLoS One 2017; 12:e0170941. [PMID: 28135299 PMCID: PMC5279799 DOI: 10.1371/journal.pone.0170941] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/12/2017] [Indexed: 12/30/2022] Open
Abstract
Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pigment colour traits, including the five loci identified by the single marker-based analysis. Furthermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype-based analysis over single marker analysis to detect loci associated with colour traits in durum wheat.
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Affiliation(s)
- Amidou N’Diaye
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Jemanesh K. Haile
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Aron T. Cory
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Fran R. Clarke
- Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - John M. Clarke
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ron E. Knox
- Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Curtis J. Pozniak
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Wen W, He Z, Gao F, Liu J, Jin H, Zhai S, Qu Y, Xia X. A High-Density Consensus Map of Common Wheat Integrating Four Mapping Populations Scanned by the 90K SNP Array. FRONTIERS IN PLANT SCIENCE 2017; 8:1389. [PMID: 28848588 PMCID: PMC5552701 DOI: 10.3389/fpls.2017.01389] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/25/2017] [Indexed: 05/04/2023]
Abstract
A high-density consensus map is a powerful tool for gene mapping, cloning and molecular marker-assisted selection in wheat breeding. The objective of this study was to construct a high-density, single nucleotide polymorphism (SNP)-based consensus map of common wheat (Triticum aestivum L.) by integrating genetic maps from four recombinant inbred line populations. The populations were each genotyped using the wheat 90K Infinium iSelect SNP assay. A total of 29,692 SNP markers were mapped on 21 linkage groups corresponding to 21 hexaploid wheat chromosomes, covering 2,906.86 cM, with an overall marker density of 10.21 markers/cM. Compared with the previous maps based on the wheat 90K SNP chip detected 22,736 (76.6%) of the SNPs with consistent chromosomal locations, whereas 1,974 (6.7%) showed different chromosomal locations, and 4,982 (16.8%) were newly mapped. Alignment of the present consensus map and the wheat expressed sequence tags (ESTs) Chromosome Bin Map enabled assignment of 1,221 SNP markers to specific chromosome bins and 819 ESTs were integrated into the consensus map. The marker orders of the consensus map were validated based on physical positions on the wheat genome with Spearman rank correlation coefficients ranging from 0.69 (4D) to 0.97 (1A, 4B, 5B, and 6A), and were also confirmed by comparison with genetic position on the previously 40K SNP consensus map with Spearman rank correlation coefficients ranging from 0.84 (6D) to 0.99 (6A). Chromosomal rearrangements reported previously were confirmed in the present consensus map and new putative rearrangements were identified. In addition, an integrated consensus map was developed through the combination of five published maps with ours, containing 52,607 molecular markers. The consensus map described here provided a high-density SNP marker map and a reliable order of SNPs, representing a step forward in mapping and validation of chromosomal locations of SNPs on the wheat 90K array. Moreover, it can be used as a reference for quantitative trait loci (QTL) mapping to facilitate exploitation of genes and QTL in wheat breeding.
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Affiliation(s)
- Weie Wen
- College of Agronomy, Xinjiang Agricultural UniversityUrumqi, China
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- International Maize and Wheat Improvement Center (CIMMYT)Beijing, China
| | - Fengmei Gao
- Crop Breeding Institute, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Jindong Liu
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Hui Jin
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Shengnan Zhai
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yanying Qu
- College of Agronomy, Xinjiang Agricultural UniversityUrumqi, China
- *Correspondence: Yanying Qu, Xianchun Xia,
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- *Correspondence: Yanying Qu, Xianchun Xia,
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