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Wu X, Wang J, Wu D, Jiang W, Gao Z, Li D, Wu R, Gao D, Zhang Y. Identification of new resistance loci against wheat sharp eyespot through genome-wide association study. FRONTIERS IN PLANT SCIENCE 2022; 13:1056935. [PMID: 36578345 PMCID: PMC9792169 DOI: 10.3389/fpls.2022.1056935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Wheat sharp eyespot caused by Rhizoctonia cerealis is a serious pathogenic disease affecting plants. The effective strategy for controlling this disease is breeding resistant cultivar. However, to date, no wheat varieties are fully resistant to sharp eyespot, and only a few quantitative trait loci (QTLs) have been shown to be associated with sharp eyespot resistance. METHODS To understand the genetic basis of this disease, a genome-wide association study (GWAS) of sharp eyespot resistance in 262 varieties from all China wheat regions was conducted. RESULTS After cultivation for three years, only 6.5% of the varieties were resistant to sharp eyespot. Notably, the varieties from the middle and lower Yangtze River displayed higher sharp eyespot resistance than those from Huanghuai wheat zone. Only two varieties had the same resistance level to the control Shanhongmai. The results of GWAS showed that 5 single nucleotide polymorphism (SNP) loci were markedly related to sharp eyespot resistance in the three years repeatedly, and two QTLs, qSE-6A and qSE-7B, on chromosome 6A and 7B were identified. Based on the 'CG' haplotypes of significant SNPs, we found that the two QTLs exhibited additive effects on attenuating sharp eyespot resistance. DISCUSSION These results provide novel insights into the genetic basis of sharp eyespot resistance in China wheat varieties. The SNPs related to sharp eyespot resistance can be applied for marker-assisted selection in plant breeding.
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Affiliation(s)
- Xujiang Wu
- Institute of Agricultural Science of the Lixiahe District in Jiangsu Province, Yangzhou, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Low and Middle Yangtze River Valley Wheat Region, Ministry of Agriculture, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Junchan Wang
- Institute of Agricultural Science of the Lixiahe District in Jiangsu Province, Yangzhou, China
| | - Di Wu
- Institute of Agricultural Science of the Lixiahe District in Jiangsu Province, Yangzhou, China
| | - Wei Jiang
- Institute of Agricultural Science of the Lixiahe District in Jiangsu Province, Yangzhou, China
| | - Zhifu Gao
- Institute of Agricultural Science of the Lixiahe District in Jiangsu Province, Yangzhou, China
| | - Dongsheng Li
- Institute of Agricultural Science of the Lixiahe District in Jiangsu Province, Yangzhou, China
| | - Rongling Wu
- Institute of Agricultural Science of the Lixiahe District in Jiangsu Province, Yangzhou, China
| | - Derong Gao
- Institute of Agricultural Science of the Lixiahe District in Jiangsu Province, Yangzhou, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Low and Middle Yangtze River Valley Wheat Region, Ministry of Agriculture, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Yong Zhang
- Institute of Agricultural Science of the Lixiahe District in Jiangsu Province, Yangzhou, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Low and Middle Yangtze River Valley Wheat Region, Ministry of Agriculture, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
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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: 13] [Impact Index Per Article: 4.3] [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.
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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
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Du XX, Park JR, Wang XH, Jang YH, Kim EG, Lee GS, Kim KM. Applying HPLC to Screening QTLs for BLB Resistance in Rice. PLANTS 2021; 10:plants10102145. [PMID: 34685953 PMCID: PMC8537431 DOI: 10.3390/plants10102145] [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: 08/26/2021] [Revised: 09/27/2021] [Accepted: 10/08/2021] [Indexed: 11/28/2022]
Abstract
Bacterial leaf blight (BLB) is caused by Xanthomonas oryzae pv. oryzae and is a major cause of rice yield reductions around the world. When diseased, plants produce a variety of metabolites to resist pathogens. In this study, the various defense metabolites were quantified using high-performance liquid chromatography (HPLC) after Xoo inoculation in a 120 Cheongcheong/Nagdong double haploid (CNDH) population. Quantitative trait locus (QTL) mapping was conducted using the concentration of the plant defense metabolites. HPLC analyzes the concentration of substances according to the severity of disease symptoms. Searching for BLB resistance candidate genes by applying this analysis method is very effective when mapping related genes. These resistance genes can be mapped directly to the causative pathogens. A total of 17 metabolites were detected by means of HPLC analysis after Xoo inoculation in the 120 CNDH population. QTL mapping of the metabolite concentrations resulted in the detection of the BLB resistance candidate gene, OsWRKYq6, in RM3343 of chromosome 6. OsWRKYq6 has a very high homology sequence with WRKY transcription factor 39, and when inoculated with Xoo, the relative expression level of the resistant population was higher than that of the susceptible population. Resistance genes have previously been detected using only phenotypic change data. In this study, resistance candidate genes were detected using the concentration of metabolites produced in plants after inoculation with pathogens. This newly developed analysis method can be used to effectively detect and identify genes directly involved in disease resistance for future studies.
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Affiliation(s)
- Xiao-Xuan Du
- Biosafety Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea;
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Korea;
| | - Jae-Ryoung Park
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Korea;
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (Y.-H.J.); (E.-G.K.)
| | - Xiao-Han Wang
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 55365, Korea;
| | - Yoon-Hee Jang
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (Y.-H.J.); (E.-G.K.)
| | - Eun-Gyeong Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (Y.-H.J.); (E.-G.K.)
| | - Gang-Seob Lee
- Biosafety Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea;
- Correspondence: (G.-S.L.); (K.-M.K.); Tel.: +82-63-238-4714 (G.-S.L.); +82-53-950-5711 (K.-M.K.)
| | - Kyung-Min Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (Y.-H.J.); (E.-G.K.)
- Correspondence: (G.-S.L.); (K.-M.K.); Tel.: +82-63-238-4714 (G.-S.L.); +82-53-950-5711 (K.-M.K.)
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Su J, Zhao J, Zhao S, Li M, Pang S, Kang Z, Zhen W, Chen S, Chen F, Wang X. Genetics of Resistance to Common Root Rot (Spot Blotch), Fusarium Crown Rot, and Sharp Eyespot in Wheat. Front Genet 2021; 12:699342. [PMID: 34249110 PMCID: PMC8260946 DOI: 10.3389/fgene.2021.699342] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/21/2021] [Indexed: 12/05/2022] Open
Abstract
Due to soil changes, high density planting, and the use of straw-returning methods, wheat common root rot (spot blotch), Fusarium crown rot (FCR), and sharp eyespot (sheath blight) have become severe threats to global wheat production. Only a few wheat genotypes show moderate resistance to these root and crown rot fungal diseases, and the genetic determinants of wheat resistance to these devastating diseases are poorly understood. This review summarizes recent results of genetic studies of wheat resistance to common root rot, Fusarium crown rot, and sharp eyespot. Wheat germplasm with relatively higher resistance are highlighted and genetic loci controlling the resistance to each disease are summarized.
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Affiliation(s)
- Jun Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Jiaojie Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Shuqing Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Mengyu Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Shuyong Pang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Wenchao Zhen
- College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Shisheng Chen
- Institute of Advanced Agricultural Sciences, Peking University, Weifang, China
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science, Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
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Haile TA, Walkowiak S, N'Diaye A, Clarke JM, Hucl PJ, Cuthbert RD, Knox RE, Pozniak CJ. Genomic prediction of agronomic traits in wheat using different models and cross-validation designs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:381-398. [PMID: 33135095 DOI: 10.1007/s00122-020-03703-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
Genomic predictions across environments and within populations resulted in moderate to high accuracies but across-population genomic prediction should not be considered in wheat for small population size. Genomic selection (GS) is a marker-based selection suggested to improve the genetic gain of quantitative traits in plant breeding programs. We evaluated the effects of training population (TP) composition, cross-validation design, and genetic relationship between the training and breeding populations on the accuracy of GS in spring wheat (Triticum aestivum L.). Two populations of 231 and 304 spring hexaploid wheat lines that were phenotyped for six agronomic traits and genotyped with the wheat 90 K array were used to assess the accuracy of seven GS models (RR-BLUP, G-BLUP, BayesB, BL, RKHS, GS + de novo GWAS, and reaction norm) using different cross-validation designs. BayesB outperformed the other models for within-population genomic predictions in the presence of few quantitative trait loci (QTL) with large effects. However, including fixed-effect marker covariates gave better performance for an across-population prediction when the same QTL underlie traits in both populations. The accuracy of prediction was highly variable based on the cross-validation design, which suggests the importance to use a design that resembles the variation within a breeding program. Moderate to high accuracies were obtained when predictions were made within populations. In contrast, across-population genomic prediction accuracies were very low, suggesting that the evaluated models are not suitable for prediction across independent populations. On the other hand, across-environment prediction and forward prediction designs using the reaction norm model resulted in moderate to high accuracies, suggesting that GS can be applied in wheat to predict the performance of newly developed lines and lines in incomplete field trials.
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Affiliation(s)
- Teketel A Haile
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sean Walkowiak
- Canadian Grain Commission, Grain Research Laboratory, Winnipeg, MB, Canada
| | - Amidou N'Diaye
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - John M Clarke
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Pierre J Hucl
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Richard D Cuthbert
- Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Ron E Knox
- Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Curtis J Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
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Zhang X, Guo X, Wu C, Li C, Zhang D, Zhu B. Isolation, heterologous expression, and purification of a novel antifungal protein from Bacillus subtilis strain Z-14. Microb Cell Fact 2020; 19:214. [PMID: 33228718 PMCID: PMC7684727 DOI: 10.1186/s12934-020-01475-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/13/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wheat sheath blight, a soil borne fungal disease caused by Rhizoctonia cerealis, is considered as one of the most serious threats to wheat worldwide. Bacillus subtilis Z-14 was isolated from soil sampled from a wheat rhizosphere and was confirmed to have strong antifungal activity against R. cerealis. RESULTS An antifungal protein, termed F2, was isolated from the culture supernatant of Z-14 strain using precipitation with ammonium sulfate, anion exchange chromatography, and reverse phase chromatography. Purified F2 had a molecular mass of approximately 8 kDa, as assessed using sodium dodecyl sulfate polyacrylamide gel electrophoresis. Edman degradation was used to determine the amino acid sequence of the N-terminus, which was NH2ASGGTVGIYGANMRS. This sequence is identical to a hypothetical protein RBAM_004680 (YP_001420098.1) synthesized by B. amyloliquefaciens FZB42. The recombinant F2 protein (rF2) was heterologously expressed in the yeast host Pichia pastoris, purified using a Niaffinity column, and demonstrated significant antifungal activity against R. cerealis. The purified rF2 demonstrated broad spectrum antifungal activity against different varieties of fungi such as Fusarium oxysporum, Verticillium dahliae, Bipolaris papendorfii, and Fusarium proliferatum. rF2 was thermostable, retaining 91.5% of its activity when incubated for 30 min at 100 °C. Meanwhile, rF2 maintained its activity under treatment by proteinase K and trypsin and over a wide pH range from 5 to 10. CONCLUSIONS A novel antifungal protein, F2, was purified from biocontrol Bacillus subtilis Z-14 strain fermentation supernatant and heterologously expressed in Pichia pastoris to verify its antifungal activity against R. cerealis and the validity of the gene encoding F2. Considering its significant antifungal activity and stable characteristics, protein F2 presents an alternative compound to resist fungal infections caused by R. cerealis.
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Affiliation(s)
- Xuechao Zhang
- College of Life Science, Hebei Agricultural University, 289 Lingyusi Road, 071001, Baoding, PR China
| | - Xiaojun Guo
- College of Life Science, Hebei Agricultural University, 289 Lingyusi Road, 071001, Baoding, PR China
| | - Cuihong Wu
- College of Life Science, Hebei Agricultural University, 289 Lingyusi Road, 071001, Baoding, PR China
| | - Chengcui Li
- College of Life Science, Hebei Agricultural University, 289 Lingyusi Road, 071001, Baoding, PR China
| | - Dongdong Zhang
- College of Life Science, Hebei Agricultural University, 289 Lingyusi Road, 071001, Baoding, PR China.
| | - Baocheng Zhu
- College of Life Science, Hebei Agricultural University, 289 Lingyusi Road, 071001, Baoding, PR China.
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Pourbeyrami Hir Y, Yuan S, Torabi Giglou M, Jun M. QTLs position of some important ornamental traits in recently developed OO lily population. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:1419-1434. [PMID: 31736545 PMCID: PMC6825088 DOI: 10.1007/s12298-019-00688-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 05/15/2019] [Accepted: 06/27/2019] [Indexed: 06/10/2023]
Abstract
Lilium L. is a perennial ornamental bulbous species, belonging to Liliaceae family, which consists of about 100 species. One of the most important hybrids in Lilium L. is the Oriental hybrid lily. Different cross combinations have been done in the lily family such as AA (Asiatic × Asiatic), AL (Asiatic × Longiflorum), and OT (Oriental × Trumpet). The OO (Oriental × Oriental) combination is a new one. SSR and AFLP markers were used to overlap each other and the genetic linkage groups were created according to the haploid number of lily chromosomes (12 linkage groups). In this experiment, the final F1 population, which creates a genetic linkage group, was 100 individuals. For map construction, JOINMAP 4.0 software by treating segregation data of markers as a CP (out breeder full-sib family) model was used. After evaluation of ornamental traits, MapQTL 4.0 software was also used to find possible QTLs on these linkage maps. A total of 940 primers were tested and the best ones, which were 172 primer pairs (96 AFLP and 76 SSR markers), were used for map construction and the total of 616 loci (465 loci for AFLP marker and 151 loci for SSR marker) were scored. The entire mapped length was 2144.2 cM. 8 QTLs were obtained for flower number which is an important trait in lily. Each QTL locus explained the phenotypic variation of 2.4-89.5%. The highest amount of LOD (35.21) was found in LG-F1P2 for FN4 QTL. For leaf number, one-QTL was mapped with LOD of 7.08 between 2 markers on the LG-M10 of maternal maps. The QTL for petal length was placed on the LG-F1P2 of the F1 hybrid maps on the E-CGC/M-CGC-4 primer combination. The petal width QTLs also were mapped on the E-CGC/M-CGC-4. Qualitative locus named LN was mapped on the LG-M10 of the maternal maps. PW2 QTL was also localized on the LG-F4 of the paternal maps. In this experiment, 5 QTLs also were mapped for spot number in all F1 hybrids and paternal and maternal maps, and spot size. Moreover, one QTL with the length of 51 cM was measured on the LG-M8 of the maternal maps. Plant height QTL with the LOD of 12.54 was mapped on the primer combination of E-CGC/M-CGC-4 on the LG-F1P2 of the F1 hybrid maps.
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Affiliation(s)
- Younes Pourbeyrami Hir
- Horticultural Department of Agriculture and Natural Resources Faculty, Mohaghegh Ardabili University, Ardabil, Islamic Republic of Iran
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 People’s Republic of China
| | - SuXia Yuan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 People’s Republic of China
| | - Mousa Torabi Giglou
- Horticultural Department of Agriculture and Natural Resources Faculty, Mohaghegh Ardabili University, Ardabil, Islamic Republic of Iran
| | - Ming Jun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 People’s Republic of China
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N’Diaye A, Haile JK, Nilsen KT, Walkowiak S, Ruan Y, Singh AK, Clarke FR, Clarke JM, Pozniak CJ. Haplotype Loci Under Selection in Canadian Durum Wheat Germplasm Over 60 Years of Breeding: Association With Grain Yield, Quality Traits, Protein Loss, and Plant Height. FRONTIERS IN PLANT SCIENCE 2018; 9:1589. [PMID: 30455711 PMCID: PMC6230583 DOI: 10.3389/fpls.2018.01589] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/15/2018] [Indexed: 05/21/2023]
Abstract
Durum wheat was introduced in the southern prairies of western Canada in the late nineteenth century. Breeding efforts have mainly focused on improving quality traits to meet the pasta industry demands. For this study, 192 durum wheat lines were genotyped using the Illumina 90K Infinium iSelect assay, and resulted in a total of 14,324 polymorphic SNPs. Genetic diversity changed over time, declining during the first 20 years of breeding in Canada, then increased in the late 1980s and early 1990s. We scanned the genome for signatures of selection, using the total variance Fst-based outlier detection method (Lositan), the hierarchical island model (Arlequin) and the Bayesian genome scan method (BayeScan). A total of 407 outliers were identified and clustered into 84 LD-based haplotype loci, spanning all 14 chromosomes of the durum wheat genome. The association analysis detected 54 haplotype loci, of which 39% contained markers with a complete reversal of allelic state. This tendency to fixation of favorable alleles corroborates the success of the Canadian durum wheat breeding programs over time. Twenty-one haplotype loci were associated with multiple traits. In particular, hap_4B_1 explained 20.6, 17.9 and 16.6% of the phenotypic variance of pigment loss, pasta b∗ and dough extensibility, respectively. The locus hap_2B_9 explained 15.9 and 17.8% of the variation of protein content and protein loss, respectively. All these pleiotropic haplotype loci offer breeders the unique opportunity for further improving multiple traits, facilitating marker-assisted selection in durum wheat, and could help in identifying genes as functional annotations of the wheat genome become available.
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Affiliation(s)
- Amidou N’Diaye
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jemanesh K. Haile
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kirby T. Nilsen
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sean Walkowiak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yuefeng Ruan
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Fran R. Clarke
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | - John M. Clarke
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Curtis J. Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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Bordat A, Marchand G, Langlade NB, Pouilly N, Muños S, Dechamp-Guillaume G, Vincourt P, Bret-Mestries E. Different genetic architectures underlie crop responses to the same pathogen: the {Helianthus annuus * Phoma macdonaldii} interaction case for black stem disease and premature ripening. BMC PLANT BIOLOGY 2017; 17:167. [PMID: 29052528 PMCID: PMC5649070 DOI: 10.1186/s12870-017-1116-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 10/09/2017] [Indexed: 05/31/2023]
Abstract
BACKGROUND Phoma macdonaldii has been reported as the causal agent of black stem disease (BS) and premature ripening (PR) on sunflower. PR is considered as the most widespread and detrimental disease on sunflower in France. While genetic variability and QTL mapping for partial resistance of sunflower to stem, collar and roots attacks have been reported on plantlets in controlled conditions, this work aims to describe the genetic variability in a subset of a sunflower lines, and for the first time to map QTL involved in PR resistance evaluated in field conditions using controlled inoculation. RESULTS An efficient and reliable method for inoculation used in field experiments induced stem base necrosis on up to 98% of all plants. A significant genetic variability for PR resistance in the field was detected among the 20 inbred lines of the core collection tested across the two years. For QTL mapping, the PR resistance evaluation was performed on two recombinant inbred lines (RIL) populations derived from the crosses XRQxPSC8 and FUxPAZ2 in two different years. QTL analyses were based on a newly developed consensus genetic map comprising 1007 non-redundant molecular markers. In each of the two RIL populations, different QTL involved in PR partial sunflower resistance were detected. The most significant QTL were detected 49 days post infection (DPI) on LG10 (LOD 7.7) and on LG7 (LOD 12.1) in the XRQxPSC8 and FUxPAZ2 RIL population, respectively. In addition, different QTL were detected on both populations for PR resistance measured between 14 and 35 DPI. In parallel, the incidence of natural attack of P. macdonaldii resulting in BS disease was recorded, showing that in these populations, the genetic of resistance to both diseases is not governed by the same factors. CONCLUSION This work provides the first insights on the genetic architecture of sunflower PR resistance in the field. Moreover, the separate studies of symptoms on different organs and in time series allowed the identification of a succession of genetic components involved in the sunflower resistance to PR and BS diseases caused by Phoma macdonaldii along the development of the {plant * pathogen} interaction.
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Affiliation(s)
- Amandine Bordat
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- Present address: INRA, Université de Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, CS 20032, 33882 Villenave d’Ornon, France
| | - Gwenaëlle Marchand
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- Present address: EURALIS Semences, Domaine de Sandreau, 6 Chemin de Panedautes, 31700 Mondonville, France
| | | | - Nicolas Pouilly
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Stéphane Muños
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Grégory Dechamp-Guillaume
- ENSAT, UMR 1248 AGIR, BP52627, F-31326 Castanet-Tolosan, France
- AGIR, Université de Toulouse, INRA, INPT, INP-EI PURPAN, Castanet-Tolosan, France
| | - Patrick Vincourt
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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