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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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Semagn K, Henriquez MA, Iqbal M, Brûlé-Babel AL, Strenzke K, Ciechanowska I, Navabi A, N’Diaye A, Pozniak C, Spaner D. Identification of Fusarium head blight sources of resistance and associated QTLs in historical and modern Canadian spring wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1190358. [PMID: 37680355 PMCID: PMC10482112 DOI: 10.3389/fpls.2023.1190358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/18/2023] [Indexed: 09/09/2023]
Abstract
Fusarium head blight (FHB) is one the most globally destructive fungal diseases in wheat and other small grains, causing a reduction in grain yield by 10-70%. The present study was conducted in a panel of historical and modern Canadian spring wheat (Triticum aestivum L.) varieties and lines to identify new sources of FHB resistance and map associated quantitative trait loci (QTLs). We evaluated 249 varieties and lines for reaction to disease incidence, severity, and visual rating index (VRI) in seven environments by artificially spraying a mixture of four Fusarium graminearum isolates. A subset of 198 them were genotyped with the Wheat 90K iSelect single nucleotide polymorphisms (SNPs) array. Genome-wide association mapping performed on the overall best linear unbiased estimators (BLUE) computed from all seven environments and the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map of 26,449 polymorphic SNPs out of the 90K identified sixteen FHB resistance QTLs that individually accounted for 5.7-10.2% of the phenotypic variance. The positions of two of the FHB resistance QTLs overlapped with plant height and flowering time QTLs. Four of the QTLs (QFhb.dms-3B.1, QFhb.dms-5A.5, QFhb.dms-5A.7, and QFhb.dms-6A.4) were simultaneously associated with disease incidence, severity, and VRI, which accounted for 27.0-33.2% of the total phenotypic variance in the combined environments. Three of the QTLs (QFhb.dms-2A.2, QFhb.dms-2D.2, and QFhb.dms-5B.8) were associated with both incidence and VRI and accounted for 20.5-22.1% of the total phenotypic variance. In comparison with the VRI of the checks, we identified four highly resistant and thirty-three moderately resistant lines and varieties. The new FHB sources of resistance and the physical map of the associated QTLs would provide wheat breeders valuable information towards their efforts in developing improved varieties in western Canada.
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Affiliation(s)
- Kassa Semagn
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, Canada
| | - Maria Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Muhammad Iqbal
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, Canada
| | | | - Klaus Strenzke
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, Canada
| | - Izabela Ciechanowska
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, Canada
| | - Alireza Navabi
- Department of Plant Agriculture, Crop Science Building, University of Guelph, Guelph, ON, Canada
| | - Amidou N’Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Dean Spaner
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, Canada
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Rajpal VR, Singh A, Kathpalia R, Thakur RK, Khan MK, Pandey A, Hamurcu M, Raina SN. The Prospects of gene introgression from crop wild relatives into cultivated lentil for climate change mitigation. FRONTIERS IN PLANT SCIENCE 2023; 14:1127239. [PMID: 36998696 PMCID: PMC10044020 DOI: 10.3389/fpls.2023.1127239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/22/2023] [Indexed: 05/31/2023]
Abstract
Crop wild relatives (CWRs), landraces and exotic germplasm are important sources of genetic variability, alien alleles, and useful crop traits that can help mitigate a plethora of abiotic and biotic stresses and crop yield reduction arising due to global climatic changes. In the pulse crop genus Lens, the cultivated varieties have a narrow genetic base due to recurrent selections, genetic bottleneck and linkage drag. The collection and characterization of wild Lens germplasm resources have offered new avenues for the genetic improvement and development of stress-tolerant, climate-resilient lentil varieties with sustainable yield gains to meet future food and nutritional requirements. Most of the lentil breeding traits such as high-yield, adaptation to abiotic stresses and resistance to diseases are quantitative and require the identification of quantitative trait loci (QTLs) for marker assisted selection and breeding. Advances in genetic diversity studies, genome mapping and advanced high-throughput sequencing technologies have helped identify many stress-responsive adaptive genes, quantitative trait loci (QTLs) and other useful crop traits in the CWRs. The recent integration of genomics technologies with plant breeding has resulted in the generation of dense genomic linkage maps, massive global genotyping, large transcriptomic datasets, single nucleotide polymorphisms (SNPs), expressed sequence tags (ESTs) that have advanced lentil genomic research substantially and allowed for the identification of QTLs for marker-assisted selection (MAS) and breeding. Assembly of lentil and its wild species genomes (~4Gbp) opens up newer possibilities for understanding genomic architecture and evolution of this important legume crop. This review highlights the recent strides in the characterization of wild genetic resources for useful alleles, development of high-density genetic maps, high-resolution QTL mapping, genome-wide studies, MAS, genomic selections, new databases and genome assemblies in traditionally bred genus Lens for future crop improvement amidst the impending global climate change.
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Affiliation(s)
- Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Apekshita Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, U.P., India
| | - Renu Kathpalia
- Department of Botany, Kirori Mal College, University of Delhi, Delhi, India
| | - Rakesh Kr. Thakur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, U.P., India
| | - Mohd. Kamran Khan
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Türkiye
| | - Anamika Pandey
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Türkiye
| | - Mehmet Hamurcu
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Türkiye
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, U.P., India
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Hasseb NM, Sallam A, Karam MA, Gao L, Wang RRC, Moursi YS. High-LD SNP markers exhibiting pleiotropic effects on salt tolerance at germination and seedlings stages in spring wheat. PLANT MOLECULAR BIOLOGY 2022; 108:585-603. [PMID: 35217965 PMCID: PMC8967789 DOI: 10.1007/s11103-022-01248-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 01/25/2022] [Indexed: 06/01/2023]
Abstract
Salt tolerance at germination and seedling growth stages was investigated. GWAS revealed nine genomic regions with pleiotropic effects on salt tolerance. Salt tolerant genotypes were identified for future breeding program. With 20% of the irrigated land worldwide affected by it, salinity is a serious threat to plant development and crop production. While wheat is the most stable food source worldwide, it has been classified as moderately tolerant to salinity. In several crop plants; such as barley, maize and rice, it has been shown that salinity tolerance at seed germination and seedling establishment is under polygenic control. As yield was the ultimate goal of breeders and geneticists, less attention has been paid to understanding the genetic architecture of salt tolerance at early stages. Thus, the genetic control of salt tolerance at these stages is poorly understood relative to the late stages. In the current study, 176 genotypes of spring wheat were tested for salinity tolerance at seed germination and seedling establishment. Genome-Wide Association Study (GWAS) has been used to identify the genomic regions/genes conferring salt tolerance at seed germination and seedling establishment. Salinity stress negatively impacted all germination and seedling development parameters. A set of 137 SNPs showed significant association with the traits of interest. Across the whole genome, 33 regions showed high linkage disequilibrium (LD). These high LD regions harbored 15 SNPs with pleiotropic effect (i.e. SNPs that control more than one trait). Nine genes belonging to different functional groups were found to be associated with the pleiotropic SNPs. Noteworthy, chromosome 2B harbored the gene TraesCS2B02G135900 that acts as a potassium transporter. Remarkably, one SNP marker, reported in an early study, associated with salt tolerance was validated in this study. Our findings represent potential targets of genetic manipulation to understand and improve salinity tolerance in wheat.
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Affiliation(s)
- Nouran M Hasseb
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, 63514, Egypt
| | - Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt.
| | - Mohamed A Karam
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, 63514, Egypt
| | - Liangliang Gao
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State Univ, Manhattan, KS, 66502, USA
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Buxin Road 97, Dapeng-District, Shenzhen, 518120, Guangdong, China
| | - Richard R C Wang
- USDA-ARS Forage and Range Research Lab, Utah State University, Logan, UT, 84322-6300, USA
| | - Yasser S Moursi
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, 63514, Egypt
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5
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Semagn K, Iqbal M, Chen H, Perez-Lara E, Bemister DH, Xiang R, Zou J, Asif M, Kamran A, N'Diaye A, Randhawa H, Beres BL, Pozniak C, Spaner D. Physical mapping of QTL associated with agronomic and end-use quality traits in spring wheat under conventional and organic management systems. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3699-3719. [PMID: 34333664 DOI: 10.1007/s00122-021-03923-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Using phenotypic data of four biparental spring wheat populations evaluated at multiple environments under two management systems, we discovered 152 QTL and 22 QTL hotspots, of which two QTL accounted for up to 37% and 58% of the phenotypic variance, consistently detected in all environments, and fell within genomic regions harboring known genes. Identification of the physical positions of quantitative trait loci (QTL) would be highly useful for developing functional markers and comparing QTL results across multiple independent studies. The objectives of the present study were to map and characterize QTL associated with nine agronomic and end-use quality traits (tillering ability, plant height, lodging, grain yield, grain protein content, thousand kernel weight, test weight, sedimentation volume, and falling number) in hard red spring wheat recombinant inbred lines (RILs) using the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map. We evaluated a total of 698 RILs from four populations derived from crosses involving seven parents at 3-8 conventionally (high N) and organically (low N) managed field environments. Using the phenotypic data combined across all environments per management, and the physical map between 1058 and 6526 markers per population, we identified 152 QTL associated with the nine traits, of which 29 had moderate and 2 with major effects. Forty-nine of the 152 QTL mapped across 22 QTL hotspot regions with each region coincident to 2-6 traits. Some of the QTL hotspots were physically located close to known genes. QSv.dms-1A and QPht.dms-4B.1 individually explained up to 37% and 58% of the variation in sedimentation volume and plant height, respectively, and had very large LOD scores that varied from 19.0 to 35.7 and from 16.7 to 55.9, respectively. We consistently detected both QTL in the combined and all individual environments, laying solid ground for further characterization and possibly for cloning.
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Affiliation(s)
- Kassa Semagn
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Muhammad Iqbal
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Hua Chen
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, Sichuan, China
| | - Enid Perez-Lara
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Darcy H Bemister
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Rongrong Xiang
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Jun Zou
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Muhammad Asif
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Department of Agronomy, 2004 Throckmorton Plant Science Center, Kansas State University, Manhattan, KS, 66506, USA
- Heartland Plant Innovations, Kansas Wheat Innovation Center, 1990 Kimball Avenue, Manhattan, KS, 66502, USA
| | - Atif Kamran
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Department of Botany, Seed Centre, The University of Punjab, New Campus, Lahore, 54590, Pakistan
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Harpinder Randhawa
- Agriculture, and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Brian L Beres
- Agriculture, and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Dean Spaner
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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Semagn K, Iqbal M, Chen H, Perez-Lara E, Bemister DH, Xiang R, Zou J, Asif M, Kamran A, N'Diaye A, Randhawa H, Pozniak C, Spaner D. Physical Mapping of QTL in Four Spring Wheat Populations under Conventional and Organic Management Systems. I. Earliness. PLANTS 2021; 10:plants10050853. [PMID: 33922551 PMCID: PMC8144964 DOI: 10.3390/plants10050853] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/08/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023]
Abstract
In previous studies, we reported quantitative trait loci (QTL) associated with the heading, flowering, and maturity time in four hard red spring wheat recombinant inbred line (RIL) populations but the results are scattered in population-specific genetic maps, which is challenging to exploit efficiently in breeding. Here, we mapped and characterized QTL associated with these three earliness traits using the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map. Our data consisted of (i) 6526 single nucleotide polymorphisms (SNPs) and two traits evaluated at five conventionally managed environments in the 'Cutler' × 'AC Barrie' population; (ii) 3158 SNPs and two traits evaluated across three organic and seven conventional managements in the 'Attila' × 'CDC Go' population; (iii) 5731 SilicoDArT and SNP markers and the three traits evaluated at four conventional and organic management systems in the 'Peace' × 'Carberry' population; and (iv) 1058 SNPs and two traits evaluated across two conventionally and organically managed environments in the 'Peace' × 'CDC Stanley' population. Using composite interval mapping, the phenotypic data across all environments, and the IWGSC RefSeq v2.0 physical maps, we identified a total of 44 QTL associated with days to heading (11), flowering (10), and maturity (23). Fifteen of the 44 QTL were common to both conventional and organic management systems, and the remaining QTL were specific to either the conventional (21) or organic (8) management systems. Some QTL harbor known genes, including the Vrn-A1, Vrn-B1, Rht-A1, and Rht-B1 that regulate photoperiodism, flowering time, and plant height in wheat, which lays a solid basis for cloning and further characterization.
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Affiliation(s)
- Kassa Semagn
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Muhammad Iqbal
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Hua Chen
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang 621010, China
| | - Enid Perez-Lara
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Darcy H Bemister
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Rongrong Xiang
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Jun Zou
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Muhammad Asif
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Department of Agronomy, 2004 Throckmorton Plant Science Center, Kansas State University, Manhattan, KS 66506, USA
- Heartland Plant Innovations, Kansas Wheat Innovation Center, 1990 Kimball Avenue, Manhattan, KS 66502, USA
| | - Atif Kamran
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Seed Centre, Department of Botany, The University of Punjab, New Campus, Lahore 54590, Pakistan
| | - Amidou N'Diaye
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Harpinder Randhawa
- Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1, Canada
| | - Curtis Pozniak
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Dean Spaner
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
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Mapping of QTL for Grain Yield Components Based on a DH Population in Maize. Sci Rep 2020; 10:7086. [PMID: 32341398 PMCID: PMC7184729 DOI: 10.1038/s41598-020-63960-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 04/08/2020] [Indexed: 11/27/2022] Open
Abstract
The elite maize hybrid Zhengdan 958 (ZD958), which has high and stable yield and extensive adaptability, is widely grown in China. To elucidate the genetic basis of yield and its related traits in this elite hybrid, a set of doubled haploid (DH) lines derived from ZD958 were evaluated in four different environments at two locations over two years, and a total of 49 quantitative trait loci (QTL) and 24 pairs of epistatic interactions related to yield and yield components were detected. Furthermore, 21 QTL for six investigated phenotypic traits were detected across two different sites. Combining the results of these QTL in each environment and across both sites, three main QTL hotspots were found in chromosomal bins 2.02, 2.05–2.06, and 6.05 between the simple sequence repeat (SSR) markers umc1165-bnlg1017, umc1065-umc1637, and nc012-bnlg345, respectively. The existence of three QTL hotspots associated with various traits across multiple environments could be explained by pleiotropic QTL or multiple tightly linked QTL. These genetic regions could provide targets for genetic improvement, fine mapping, and marker-assisted selection in future studies.
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8
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Bernardo A, St. Amand P, Le HQ, Su Z, Bai G. Multiplex restriction amplicon sequencing: a novel next-generation sequencing-based marker platform for high-throughput genotyping. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:254-265. [PMID: 31199572 PMCID: PMC6920337 DOI: 10.1111/pbi.13192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/04/2019] [Accepted: 06/11/2019] [Indexed: 05/31/2023]
Abstract
To enable rapid selection of traits in marker-assisted breeding, markers must be technically simple, low-cost, high-throughput and randomly distributed in a genome. We developed such a technology, designated as Multiplex Restriction Amplicon Sequencing (MRASeq), which reduces genome complexity by polymerase chain reaction (PCR) amplification of amplicons flanked by restriction sites. The first PCR primers contain restriction site sequences at 3'-ends, preceded by 6-10 bases of specific or degenerate nucleotide sequences and then by a unique M13-tail sequence which serves as a binding site for a second PCR that adds sequencing primers and barcodes to allow sample multiplexing for sequencing. The sequences of restriction sites and adjacent nucleotides can be altered to suit different species. Physical mapping of MRASeq SNPs from a biparental population of allohexaploid wheat (Triticum aestivum L.) showed a random distribution of SNPs across the genome. MRASeq generated thousands of SNPs from a wheat biparental population and natural populations of wheat and barley (Hordeum vulgare L.). This novel, next-generation sequencing-based genotyping platform can be used for linkage mapping to screen quantitative trait loci (QTL), background selection in breeding and many other genetics and breeding applications of various species.
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Affiliation(s)
- Amy Bernardo
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Hard Winter Wheat Genetics Research UnitUSDA‐ARSManhattanKSUSA
| | - Paul St. Amand
- Hard Winter Wheat Genetics Research UnitUSDA‐ARSManhattanKSUSA
| | - Ha Quang Le
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Zhenqi Su
- Department of AgronomyKansas State UniversityManhattanKSUSA
- China Agricultural UniversityBeijingChina
| | - Guihua Bai
- Hard Winter Wheat Genetics Research UnitUSDA‐ARSManhattanKSUSA
- Department of AgronomyKansas State UniversityManhattanKSUSA
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9
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Desta ZA, Kolano B, Shamim Z, Armstrong SJ, Rewers M, Sliwinska E, Kushwaha SK, Parkin IAP, Ortiz R, de Koning DJ. Field cress genome mapping: Integrating linkage and comparative maps with cytogenetic analysis for rDNA carrying chromosomes. Sci Rep 2019; 9:17028. [PMID: 31745130 PMCID: PMC6863836 DOI: 10.1038/s41598-019-53320-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/30/2019] [Indexed: 11/09/2022] Open
Abstract
Field cress (Lepidium campestre L.), despite its potential as a sustainable alternative oilseed plant, has been underutilized, and no prior attempts to characterize the genome at the genetic or molecular cytogenetic level have been conducted. Genetic maps are the foundation for anchoring and orienting annotated genome assemblies and positional cloning of candidate genes. Our principal goal was to construct a genetic map using integrated approaches of genetic, comparative and cytogenetic map analyses. In total, 503 F2 interspecific hybrid individuals were genotyped using 7,624 single nucleotide polymorphism markers. Comparative analysis demonstrated that ~57% of the sequenced loci in L. campestre were congruent with Arabidopsis thaliana (L.) genome and suggested a novel karyotype, which predates the ancestral crucifer karyotype. Aceto-orcein chromosome staining and fluorescence in situ hybridization (FISH) analyses confirmed that L. campestre, L. heterophyllum Benth. and their hybrids had a chromosome number of 2n = 2x = 16. Flow cytometric analysis revealed that both species possess 2C roughly 0.4 picogram DNA. Integrating linkage and comparative maps with cytogenetic map analyses assigned two linkage groups to their particular chromosomes. Future work could incorporate FISH utilizing A. thaliana mapped BAC clones to allow the chromosomes of field cress to be identified reliably.
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Affiliation(s)
- Zeratsion Abera Desta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundesvagen 10, Box 101, SE-23053, Alnarp, Sweden.
| | - Bozena Kolano
- Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28, 40-032, Katowice, Poland
| | - Zeeshan Shamim
- Mirpur University of Science and Technology (MUST), Mirpur AJK, Pakistan.,School of Biosciences, University of Birmingham, Birmingham, B 15 2TT, United Kingdom
| | - Susan J Armstrong
- School of Biosciences, University of Birmingham, Birmingham, B 15 2TT, United Kingdom
| | - Monika Rewers
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Kaliskiego Ave. 7, 85-789, Bydgoszcz, Poland
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Kaliskiego Ave. 7, 85-789, Bydgoszcz, Poland
| | - Sandeep Kumar Kushwaha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundesvagen 10, Box 101, SE-23053, Alnarp, Sweden
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N0X2, Canada
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundesvagen 10, Box 101, SE-23053, Alnarp, Sweden
| | - Dirk-Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE 75007, Uppsala, Sweden
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10
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Takenaka S, Nitta M, Nasuda S. Population structure and association analyses of the core collection of hexaploid accessions conserved ex situ in the Japanese gene bank NBRP-Wheat. Genes Genet Syst 2018; 93:237-254. [PMID: 30555105 DOI: 10.1266/ggs.18-00041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In this study, we investigated the genetic diversity and population structure of the core collection of hexaploid wheat accessions in the Japanese wheat gene bank NBRP-Wheat. The core collection, consisting of 188 accessions of Triticum aestivum, T. spelta, T. compactum, T. sphaerococcum, T. macha and T. vavilovii, was intensively genotyped by DArTseq markers and consisted of 20,186 SNPs and 60,077 present and absent variations (PAVs). Polymorphic markers were distributed in all chromosomes, with a tendency for smaller numbers on the D-genome chromosomes. We examined the population structure by Bayesian clustering and principal component analysis with a general linear model. Overall, the core collection was divided into seven clusters. Non-admixture accessions in each cluster indicated that the clusters reflect the geographic distribution of the accessions. Both structure analyses strongly suggested that the cluster consisting of T. spelta and T. macha is out-grouped from other hexaploid wheat accessions. We performed genome-wide association analysis pilot studies for nine quantitative and seven qualitative traits and found marker-trait associations for all traits but one, indicating that the current core collection will be useful for detecting uncharacterized QTLs associated with phenotypes of interest.
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Affiliation(s)
- Shotaro Takenaka
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University.,Department of Plant Life Science, Faculty of Agriculture, Ryukoku University
| | - Miyuki Nitta
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University
| | - Shuhei Nasuda
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University
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11
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12
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Tappiban P, Sraphet S, Srisawad N, Smith DR, Triwitayakorn K. Identification and expression of genes in response to cassava bacterial blight infection. J Appl Genet 2018; 59:391-403. [DOI: 10.1007/s13353-018-0457-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 07/08/2018] [Accepted: 07/11/2018] [Indexed: 12/22/2022]
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13
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Zhang X, Mizukoshi M, Zhang H, Tan E, Igarashi Y, Suzuki Y, Mitsuyama S, Kinoshita S, Saito K, Watabe S, Asakawa S. Ultrahigh-Density Linkage Map Construction Using Low-Coverage Whole-Genome Sequencing of a Doubled Haploid Population: Case Study of Torafugu (Takifugu rubripes). Genes (Basel) 2018; 9:genes9030120. [PMID: 29495372 PMCID: PMC5867841 DOI: 10.3390/genes9030120] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/15/2018] [Accepted: 02/20/2018] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing enables genome-wide genotyping of a large population and further facilitates the construction of a genetic linkage map. Low-coverage whole-genome sequencing has been employed for genetic linkage map construction in several species. However, this strategy generally requires available high-quality reference genomes and/or designed inbred pedigree lines, which restrict the scope of application for non-model and unsequenced species. Here, using torafugu (Takifugu rubripes) as a test model, we propose a new strategy for ultrahigh-density genetic linkage map construction using low-coverage whole-genome sequencing of a haploid/doubled haploid (H/DH) population without above requirements. Low-coverage (≈1×) whole-genome sequencing data of 165 DH individuals were used for de novo assembly and further performed single nucleotide polymorphisms (SNPs) calling, resulting in the identification of 1,070,601 SNPs. Based on SNP genotypes and de novo assembly, genotypes were associated with short DNA segments and an ultrahigh-density linkage map was constructed containing information of 802,277 SNPs in 3090 unique positions. Comparative analyses showed near-perfect concordance between the present linkage map and the latest published torafugu genome (FUGU5). This strategy would facilitate ultrahigh-density linkage map construction in various sexually reproducing organisms for which H/DH populations can be generated.
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Affiliation(s)
- Xiang Zhang
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
| | - Misaki Mizukoshi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
| | - Hong Zhang
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
| | - Engkong Tan
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
| | - Yoji Igarashi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.
| | - Susumu Mitsuyama
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
| | - Kazuyoshi Saito
- Akita Prefectural Fisheries Promotion Center, Oga, Akita 010-0531, Japan.
| | - Shugo Watabe
- School of Marine Bioscience, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan.
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
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Nedelkou IP, Maurer A, Schubert A, Léon J, Pillen K. Exotic QTL improve grain quality in the tri-parental wheat population SW84. PLoS One 2017; 12:e0179851. [PMID: 28686676 PMCID: PMC5501409 DOI: 10.1371/journal.pone.0179851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/05/2017] [Indexed: 01/01/2023] Open
Abstract
Developing the tri-parental exotic wheat population SW84 Genetic diversity of cultivated wheat was markedly reduced, first, during domestication and, second, since the onset of modern elite breeding. There is an increasing demand for utilizing genetic resources to increase genetic diversity and, simultaneously, to improve agronomic performance of cultivated wheat. To locate favorable effects of exotic wheat alleles, we developed the tri-parental wheat population SW84. The population was derived from crossing the hexaploid spring wheat cultivars Triso and Devon with one synthetic exotic donor accession, Syn084L, followed by two rounds of backcrossing and three rounds of selfing. SW84 consists of 359 BC2F4 lines, split into two families, D84 (Devon*Syn084L) and T84 (Triso*Syn084L). Studying the genetic control of grain quality in SW84 As a case study, grain quality of SW84 was studied in replicated field trials. Transgressive segregation was observed for all studied grain quality traits by evaluating SW84 for two years at two locations under low and high nitrogen supply. Subsequently, a genome-wide association study (GWAS) was carried out based on genomic data derived from a 90k Infinium iSELECT single nucleotide polymorphism (SNP) array. In total, GWAS yielded 37 marker-trait associations, summarized to 16 quantitative trait loci (QTL). These SNPs indicate genetic regulators of grain protein content, grain hardness, sedimentation value and sedimentation ratio. The majority of exotic QTL alleles (75%) exerted favorable effects, increasing grain protein content and sedimentation value in ten and two cases, respectively. For instance, two exotic QTL alleles were associated with a substantial increase of grain protein content and sedimentation value by 1.09% and 7.31 ml, respectively. This finding confirms the potential of exotic germplasm to improve grain quality in cultivated wheat. So far, the molecular nature of most of the detected QTL is unknown. However, two QTL correspond to known genes controlling grain quality: The major QTL on chromosome 6B, increasing grain protein content by 0.70%, on average, co-localizes with the NAM-B1 gene, known to control grain protein content as well as iron and zinc content. Likewise, the major QTL on chromosome 5D, reducing grain hardness by 8.98%, on average, co-localizes with the gene for puroindoline b (Pinb-D1) at the Ha locus. In total, 13 QTL were detected across families, whereas one and three QTL were exclusively detected in families D84 and T84, respectively. Likewise, ten QTL were detected across nitrogen treatments, whereas one and five QTL were exclusively detected under low and high N treatments, respectively. Our data indicate that most effects in SW84 act across families and N levels. Merging of data from two families or two N treatments may, thus, be considered in association studies to increase sample size and, as a result, QTL detection power. Utilizing favorable exotic QTL alleles in wheat breeding Our study serves as a model how favorable exotic QTL alleles can be located in exotic germplasm of wheat. In future, the localized favorable exotic QTL alleles will be utilized in wheat breeding programs to simultaneously improve grain quality and selectively expand genetic diversity of the elite wheat gene pool.
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Affiliation(s)
- Ioanna-Pavlina Nedelkou
- Martin-Luther-University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Halle, Germany
| | - Andreas Maurer
- Martin-Luther-University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Halle, Germany
| | - Anne Schubert
- University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, Bonn, Germany
| | - Jens Léon
- University of Bonn, Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, Katzenburgweg 5, Bonn, Germany
| | - Klaus Pillen
- Martin-Luther-University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Halle, Germany
- * E-mail:
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15
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Cui F, Zhang N, Fan XL, Zhang W, Zhao CH, Yang LJ, Pan RQ, Chen M, Han J, Zhao XQ, Ji J, Tong YP, Zhang HX, Jia JZ, Zhao GY, Li JM. Utilization of a Wheat660K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number. Sci Rep 2017. [PMID: 28630475 DOI: 10.1038/s41598-017-04028-63] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
In crop plants, a high-density genetic linkage map is essential for both genetic and genomic researches. The complexity and the large size of wheat genome have hampered the acquisition of a high-resolution genetic map. In this study, we report a high-density genetic map based on an individual mapping population using the Affymetrix Wheat660K single-nucleotide polymorphism (SNP) array as a probe in hexaploid wheat. The resultant genetic map consisted of 119 566 loci spanning 4424.4 cM, and 119 001 of those loci were SNP markers. This genetic map showed good collinearity with the 90 K and 820 K consensus genetic maps and was also in accordance with the recently released wheat whole genome assembly. The high-density wheat genetic map will provide a major resource for future genetic and genomic research in wheat. Moreover, a comparative genomics analysis among gramineous plant genomes was conducted based on the high-density wheat genetic map, providing an overview of the structural relationships among theses gramineous plant genomes. A major stable quantitative trait locus (QTL) for kernel number per spike was characterized, providing a solid foundation for the future high-resolution mapping and map-based cloning of the targeted QTL.
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Affiliation(s)
- Fa Cui
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- Genetic Improvement Centre of Agricultural and Forest Crops, College of Agriculture, Ludong Unversity, Yan'tai, 264025, China
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Na Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xiao-Li Fan
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Wei Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China.
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Chun-Hua Zhao
- Genetic Improvement Centre of Agricultural and Forest Crops, College of Agriculture, Ludong Unversity, Yan'tai, 264025, China
| | - Li-Juan Yang
- Xinxiang Academy of Agricultural Sciences, Xinxiang, 453000, China
| | - Rui-Qing Pan
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Mei Chen
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Jie Han
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xue-Qiang Zhao
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun Ji
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi-Ping Tong
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hong-Xia Zhang
- Genetic Improvement Centre of Agricultural and Forest Crops, College of Agriculture, Ludong Unversity, Yan'tai, 264025, China
| | - Ji-Zeng Jia
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guang-Yao Zhao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jun-Ming Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China.
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China.
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16
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Utilization of a Wheat660K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number. Sci Rep 2017. [PMID: 28630475 PMCID: PMC5476560 DOI: 10.1038/s41598-017-04028-6] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
In crop plants, a high-density genetic linkage map is essential for both genetic and genomic researches. The complexity and the large size of wheat genome have hampered the acquisition of a high-resolution genetic map. In this study, we report a high-density genetic map based on an individual mapping population using the Affymetrix Wheat660K single-nucleotide polymorphism (SNP) array as a probe in hexaploid wheat. The resultant genetic map consisted of 119 566 loci spanning 4424.4 cM, and 119 001 of those loci were SNP markers. This genetic map showed good collinearity with the 90 K and 820 K consensus genetic maps and was also in accordance with the recently released wheat whole genome assembly. The high-density wheat genetic map will provide a major resource for future genetic and genomic research in wheat. Moreover, a comparative genomics analysis among gramineous plant genomes was conducted based on the high-density wheat genetic map, providing an overview of the structural relationships among theses gramineous plant genomes. A major stable quantitative trait locus (QTL) for kernel number per spike was characterized, providing a solid foundation for the future high-resolution mapping and map-based cloning of the targeted QTL.
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17
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Arif MAR, Nagel M, Lohwasser U, Börner A. Genetic architecture of seed longevity in bread wheat (Triticum aestivum L.). J Biosci 2017; 42:81-89. [DOI: 10.1007/s12038-016-9661-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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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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Ponyared P, Ponsawat J, Tongsima S, Seresangtakul P, Akkasaeng C, Tantisuwichwong N. ESAP plus: a web-based server for EST-SSR marker development. BMC Genomics 2016; 17:1035. [PMID: 28155670 PMCID: PMC5260030 DOI: 10.1186/s12864-016-3328-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence Tags (ESTs), which can be obtained from the plant mRNA (converted to cDNA), must be utilized. With the advent of high-throughput sequencing technology, huge EST sequence data have been generated and are now accessible from many public databases. However, SSR marker identification from a large in-house or public EST collection requires a computational pipeline that makes use of several standard bioinformatic tools to design high quality EST-SSR primers. Some of these computational tools are not users friendly and must be tightly integrated with reference genomic databases. Results A web-based bioinformatic pipeline, called EST Analysis Pipeline Plus (ESAP Plus), was constructed for assisting researchers to develop SSR markers from a large EST collection. ESAP Plus incorporates several bioinformatic scripts and some useful standard software tools necessary for the four main procedures of EST-SSR marker development, namely 1) pre-processing, 2) clustering and assembly, 3) SSR mining and 4) SSR primer design. The proposed pipeline also provides two alternative steps for reducing EST redundancy and identifying SSR loci. Using public sugarcane ESTs, ESAP Plus automatically executed the aforementioned computational pipeline via a simple web user interface, which was implemented using standard PHP, HTML, CSS and Java scripts. With ESAP Plus, users can upload raw EST data and choose various filtering options and parameters to analyze each of the four main procedures through this web interface. All input EST data and their predicted SSR results will be stored in the ESAP Plus MySQL database. Users will be notified via e-mail when the automatic process is completed and they can download all the results through the web interface. Conclusions ESAP Plus is a comprehensive and convenient web-based bioinformatic tool for SSR marker development. ESAP Plus offers all necessary EST-SSR development processes with various adjustable options that users can easily use to identify SSR markers from a large EST collection. With familiar web interface, users can upload the raw EST using the data submission page and visualize/download the corresponding EST-SSR information from within ESAP Plus. ESAP Plus can handle considerably large EST datasets. This EST-SSR discovery tool can be accessed directly from: http://gbp.kku.ac.th/esap_plus/. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3328-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Piyarat Ponyared
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Jiradej Ponsawat
- Department of Computer Engineering, Faculty of Engineering, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, 12120, Thailand
| | - Pusadee Seresangtakul
- Department of Computer Science, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chutipong Akkasaeng
- Department of Plant Science and Agricultural Resources, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
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Kumar S, Hash CT, Thirunavukkarasu N, Singh G, Rajaram V, Rathore A, Senapathy S, Mahendrakar MD, Yadav RS, Srivastava RK. Mapping Quantitative Trait Loci Controlling High Iron and Zinc Content in Self and Open Pollinated Grains of Pearl Millet [ Pennisetum glaucum (L.) R. Br.]. FRONTIERS IN PLANT SCIENCE 2016; 7:1636. [PMID: 27933068 PMCID: PMC5120122 DOI: 10.3389/fpls.2016.01636] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/17/2016] [Indexed: 05/05/2023]
Abstract
Pearl millet is a multipurpose grain/fodder crop of the semi-arid tropics, feeding many of the world's poorest and most undernourished people. Genetic variation among adapted pearl millet inbreds and hybrids suggests it will be possible to improve grain micronutrient concentrations by selective breeding. Using 305 loci, a linkage map was constructed to map QTLs for grain iron [Fe] and zinc [Zn] using replicated samples of 106 pearl millet RILs (F6) derived from ICMB 841-P3 × 863B-P2. The grains of the RIL population were evaluated for Fe and Zn content using atomic absorption spectrophotometer. Grain mineral concentrations ranged from 28.4 to 124.0 ppm for Fe and 28.7 to 119.8 ppm for Zn. Similarly, grain Fe and Zn in open pollinated seeds ranged between 22.4-77.4 and 21.9-73.7 ppm, respectively. Mapping with 305 (96 SSRs; 208 DArT) markers detected seven linkage groups covering 1749 cM (Haldane) with an average intermarker distance of 5.73 cM. On the basis of two environment phenotypic data, two co-localized QTLs for Fe and Zn content on linkage group (LG) 3 were identified by composite interval mapping (CIM). Fe QTL explained 19% phenotypic variation, whereas the Zn QTL explained 36% phenotypic variation. Likewise for open pollinated seeds, the QTL analysis led to the identification of two QTLs for grain Fe content on LG3 and 5, and two QTLs for grain Zn content on LG3 and 7. The total phenotypic variance for Fe and Zn QTLs in open pollinated seeds was 16 and 42%, respectively. Analysis of QTL × QTL and QTL × QTL × environment interactions indicated no major epistasis.
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Affiliation(s)
- Sushil Kumar
- Plant Biotechnology Centre, Swami Keshwanand Rajasthan Agricultural UniversityBikaner, India; International Crops Research Institute for the Semi-Arid TropicsPatancheru, India; Centre of Excellence in Agricultural Biotechnology, Anand Agricultural UniversityAnand, India
| | - Charles T Hash
- International Crops Research Institute for the Semi-Arid Tropics Niamey, Niger
| | | | - Govind Singh
- Plant Biotechnology Centre, Swami Keshwanand Rajasthan Agricultural University Bikaner, India
| | - Vengaldas Rajaram
- International Crops Research Institute for the Semi-Arid Tropics Patancheru, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics Patancheru, India
| | | | - Mahesh D Mahendrakar
- International Crops Research Institute for the Semi-Arid Tropics Patancheru, India
| | - Rattan S Yadav
- Crop Genetics, Genomics and Breeding Division, Aberystwyth University Aberystwyth, UK
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics Patancheru, India
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Yu K, Liu D, Wu W, Yang W, Sun J, Li X, Zhan K, Cui D, Ling H, Liu C, Zhang A. Development of an integrated linkage map of einkorn wheat and its application for QTL mapping and genome sequence anchoring. THEORETICAL AND APPLIED GENETICS 2016; 130:53-70. [PMID: 27659843 DOI: 10.1007/s00122-016-2791-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/12/2016] [Indexed: 11/26/2022]
Abstract
KEY MESSAGE An integrated genetic map was constructed for einkorn wheat A genome and provided valuable information for QTL mapping and genome sequence anchoring. Wheat is one of the most widely grown food grain crops in the world. The construction of a genetic map is a key step to organize biologically or agronomically important traits along the chromosomes. In the present study, an integrated linkage map of einkorn wheat was developed using 109 recombinant inbred lines (RILs) derived from an inter sub-specific cross, KT1-1 (T. monococcum ssp. boeoticum) × KT3-5 (T. monococcum ssp. monococcum). The map contains 926 molecular markers assigned to seven linkage groups, and covers 1,377 cM with an average marker interval of 1.5 cM. A quantitative trait locus (QTL) analysis of five agronomic traits identified 16 stable QTL on all seven chromosomes, except 6A. The total phenotypic variance explained by these stable QTL using multiple regressions varied across environments from 8.8 to 87.1 % for days to heading, 24.4-63.0 % for spike length, 48.2-79.6 % for spikelet number per spike, 13.1-48.1 % for plant architecture, and 12.2-26.5 % for plant height, revealing that much of the RIL phenotypic variation had been genetically dissected. Co-localizations of closely linked QTL for different traits were frequently observed, especially on 3A and 7A. The QTL on 3A, 5A and 7A were closely associated with Eps-A m 3, Vrn1 and Vrn3 loci, respectively. Furthermore, this genetic map facilitated the anchoring of 237 T. urartu scaffolds onto seven chromosomes with a physical length of 26.15 Mb. This map and the QTL data provide valuable genetic information to dissect important agronomic and developmental traits in diploid wheat and contribute to the genetic ordering of the genome assembly.
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Affiliation(s)
- Kang Yu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, People's Republic of China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Wenying Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Xin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Kehui Zhan
- Collaborative Innovation Center for Grain Crops in Henan, Henan Agricultural University, No. 95 Wenhua Road, Zhengzhou, Henan, 450002, People's Republic of China
| | - Dangqun Cui
- Collaborative Innovation Center for Grain Crops in Henan, Henan Agricultural University, No. 95 Wenhua Road, Zhengzhou, Henan, 450002, People's Republic of China
| | - Hongqing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Chunming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, People's Republic of China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China.
- Collaborative Innovation Center for Grain Crops in Henan, Henan Agricultural University, No. 95 Wenhua Road, Zhengzhou, Henan, 450002, People's Republic of China.
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Perez-Lara E, Semagn K, Chen H, Iqbal M, N’Diaye A, Kamran A, Navabi A, Pozniak C, Spaner D. QTLs Associated with Agronomic Traits in the Cutler × AC Barrie Spring Wheat Mapping Population Using Single Nucleotide Polymorphic Markers. PLoS One 2016; 11:e0160623. [PMID: 27513976 PMCID: PMC4981373 DOI: 10.1371/journal.pone.0160623] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 07/24/2016] [Indexed: 11/30/2022] Open
Abstract
We recently reported three earliness per se quantitative trait loci (QTL) associated with flowering and maturity in a recombinant inbred lines (RILs) population derived from a cross between the spring wheat (Triticum aestivum L.) cultivars ‘Cutler’ and ‘AC Barrie’ using 488 microsatellite and diversity arrays technology (DArT) markers. Here, we present QTLs associated with flowering time, maturity, plant height, and grain yield using high density single nucleotide polymorphic (SNP) markers in the same population. A mapping population of 158 RILs and the two parents were evaluated at five environments for flowering, maturity, plant height and grain yield under field conditions, at two greenhouse environments for flowering, and genotyped with a subset of 1809 SNPs out of the 90K SNP array and 2 functional markers (Ppd-D1 and Rht-D1). Using composite interval mapping on the combined phenotype data across all environments, we identified a total of 19 QTLs associated with flowering time in greenhouse (5), and field (6) conditions, maturity (5), grain yield (2) and plant height (1). We mapped these QTLs on 8 chromosomes and they individually explained between 6.3 and 37.8% of the phenotypic variation. Four of the 19 QTLs were associated with multiple traits, including a QTL on 2D associated with flowering, maturity and grain yield; two QTLs on 4A and 7A associated with flowering and maturity, and another QTL on 4D associated with maturity and plant height. However, only the QTLs on both 2D and 4D had major effects, and they mapped adjacent to well-known photoperiod response Ppd-D1 and height reducing Rht-D1 genes, respectively. The QTL on 2D reduced flowering and maturity time up to 5 days with a yield penalty of 436 kg ha-1, while the QTL on 4D reduced plant height by 13 cm, but increased maturity by 2 days. The high density SNPs allowed us to map eight moderate effect, two major effect, and nine minor effect QTLs that were not identified in our previous study using microsatellite and DArT markers. Results from this study provide additional information to wheat researchers developing early maturing and short stature spring wheat cultivars.
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Affiliation(s)
- Enid Perez-Lara
- Department of Agricultural, Food and Nutritional Science, 4–10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Kassa Semagn
- Department of Agricultural, Food and Nutritional Science, 4–10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Hua Chen
- Department of Agricultural, Food and Nutritional Science, 4–10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Muhammad Iqbal
- Department of Agricultural, Food and Nutritional Science, 4–10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan
| | - Amidou N’Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Atif Kamran
- Seed Centre, Department of Botany, The University of Punjab, New Campus, Lahore, 54590, Pakistan
| | - Alireza Navabi
- Department of Plant Agriculture, Crop Science Building, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Dean Spaner
- Department of Agricultural, Food and Nutritional Science, 4–10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
- * E-mail:
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Muqaddasi QH, Lohwasser U, Nagel M, Börner A, Pillen K, Röder MS. Genome-Wide Association Mapping of Anther Extrusion in Hexaploid Spring Wheat. PLoS One 2016; 11:e0155494. [PMID: 27191600 PMCID: PMC4871436 DOI: 10.1371/journal.pone.0155494] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/01/2016] [Indexed: 01/06/2023] Open
Abstract
In a number of crop species hybrids are able to outperform line varieties. The anthers of the autogamous bread wheat plant are normally extruded post anthesis, a trait which is unfavourable for the production of F1 hybrid grain. Higher anther extrusion (AE) promotes cross fertilization for more efficient hybrid seed production. Therefore, this study aimed at the genetic dissection of AE by genome wide association studies (GWAS) and determination of the main effect QTL. We applied GWAS approach to identify DArT markers potentially linked to AE to unfold its genetic basis in a panel of spring wheat accessions. Phenotypic data were collected for three years and best linear unbiased estimate (BLUE) values were calculated across all years. The extent of the AE correlation between growing years and BLUE values ranged from r = +0.56 (2013 vs 2015) to 0.91 (2014 vs BLUE values). The broad sense heritability was 0.84 across all years. Six accessions displayed stable AE >80% across all the years. Genotyping data included 2,575 DArT markers (with minimum of 0.05 minor allele frequency applied). AE was influenced both by genotype and by the growing environment. In all, 131 significant marker trait associations (MTAs) (|log10 (P)| >FDR) were established for AE. AE behaved as a quantitative trait, with five consistently significant markers (significant across at least two years with a significant BLUE value) contributing a minor to modest proportion (4.29% to 8.61%) of the phenotypic variance and affecting the trait either positively or negatively. For this reason, there is potential for breeding for improved AE by gene pyramiding. The consistently significant markers linked to AE could be helpful for marker assisted selection to transfer AE to high yielding varieties allowing to promote the exploitation of hybrid-heterosis in the key crop wheat.
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Affiliation(s)
- Quddoos H. Muqaddasi
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK-Gatersleben), 06466, Stadt Seeland, Germany
- * E-mail:
| | - Ulrike Lohwasser
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK-Gatersleben), 06466, Stadt Seeland, Germany
| | - Manuela Nagel
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK-Gatersleben), 06466, Stadt Seeland, Germany
| | - Andreas Börner
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK-Gatersleben), 06466, Stadt Seeland, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany
| | - Marion S. Röder
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK-Gatersleben), 06466, Stadt Seeland, Germany
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24
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Perez-Lara E, Semagn K, Chen H, Iqbal M, N'Diaye A, Kamran A, Navabi A, Pozniak C, Spaner D. QTLs Associated with Agronomic Traits in the Cutler × AC Barrie Spring Wheat Mapping Population Using Single Nucleotide Polymorphic Markers. PLoS One 2016. [PMID: 27513976 DOI: 10.1371/journalpone0160623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
We recently reported three earliness per se quantitative trait loci (QTL) associated with flowering and maturity in a recombinant inbred lines (RILs) population derived from a cross between the spring wheat (Triticum aestivum L.) cultivars 'Cutler' and 'AC Barrie' using 488 microsatellite and diversity arrays technology (DArT) markers. Here, we present QTLs associated with flowering time, maturity, plant height, and grain yield using high density single nucleotide polymorphic (SNP) markers in the same population. A mapping population of 158 RILs and the two parents were evaluated at five environments for flowering, maturity, plant height and grain yield under field conditions, at two greenhouse environments for flowering, and genotyped with a subset of 1809 SNPs out of the 90K SNP array and 2 functional markers (Ppd-D1 and Rht-D1). Using composite interval mapping on the combined phenotype data across all environments, we identified a total of 19 QTLs associated with flowering time in greenhouse (5), and field (6) conditions, maturity (5), grain yield (2) and plant height (1). We mapped these QTLs on 8 chromosomes and they individually explained between 6.3 and 37.8% of the phenotypic variation. Four of the 19 QTLs were associated with multiple traits, including a QTL on 2D associated with flowering, maturity and grain yield; two QTLs on 4A and 7A associated with flowering and maturity, and another QTL on 4D associated with maturity and plant height. However, only the QTLs on both 2D and 4D had major effects, and they mapped adjacent to well-known photoperiod response Ppd-D1 and height reducing Rht-D1 genes, respectively. The QTL on 2D reduced flowering and maturity time up to 5 days with a yield penalty of 436 kg ha-1, while the QTL on 4D reduced plant height by 13 cm, but increased maturity by 2 days. The high density SNPs allowed us to map eight moderate effect, two major effect, and nine minor effect QTLs that were not identified in our previous study using microsatellite and DArT markers. Results from this study provide additional information to wheat researchers developing early maturing and short stature spring wheat cultivars.
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Affiliation(s)
- Enid Perez-Lara
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Kassa Semagn
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Hua Chen
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Muhammad Iqbal
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Atif Kamran
- Seed Centre, Department of Botany, The University of Punjab, New Campus, Lahore, 54590, Pakistan
| | - Alireza Navabi
- Department of Plant Agriculture, Crop Science Building, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Dean Spaner
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
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25
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Tyrka M, Tyrka D, Wędzony M. Genetic Map of Triticale Integrating Microsatellite, DArT and SNP Markers. PLoS One 2015; 10:e0145714. [PMID: 26717308 PMCID: PMC4696847 DOI: 10.1371/journal.pone.0145714] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/05/2015] [Indexed: 01/09/2023] Open
Abstract
Triticale (×Triticosecale Wittm) is an economically important crop for fodder and biomass production. To facilitate the identification of markers for agronomically important traits and for genetic and genomic characteristics of this species, a new high-density genetic linkage map of triticale was constructed using doubled haploid (DH) population derived from a cross between cultivars 'Hewo' and 'Magnat'. The map consists of 1615 bin markers, that represent 50 simple sequence repeat (SSR), 842 diversity array technology (DArT), and 16888 DArTseq markers mapped onto 20 linkage groups assigned to the A, B, and R genomes of triticale. No markers specific to chromosome 7R were found, instead mosaic linkage group composed of 1880 highly distorted markers (116 bins) from 10 wheat chromosomes was identified. The genetic map covers 4907 cM with a mean distance between two bins of 3.0 cM. Comparative analysis in respect to published maps of wheat, rye and triticale revealed possible deletions in chromosomes 4B, 5A, and 6A, as well as inversion in chromosome 7B. The number of bin markers in each chromosome varied from 24 in chromosome 3R to 147 in chromosome 6R. The length of individual chromosomes ranged between 50.7 cM for chromosome 2R and 386.2 cM for chromosome 7B. A total of 512 (31.7%) bin markers showed significant (P < 0.05) segregation distortion across all chromosomes. The number of 8 the segregation distorted regions (SDRs) were identified on 1A, 7A, 1B, 2B, 7B (2 SDRs), 5R and 6R chromosomes. The high-density genetic map of triticale will facilitate fine mapping of quantitative trait loci, the identification of candidate genes and map-based cloning.
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Affiliation(s)
- Mirosław Tyrka
- Department of Biochemistry and Biotechnology, Faculty of Chemistry, Rzeszow University of Technology, Rzeszow, Poland
| | - Dorota Tyrka
- Department of Biochemistry and Biotechnology, Faculty of Chemistry, Rzeszow University of Technology, Rzeszow, Poland
| | - Maria Wędzony
- Institute of Biology, Faculty of Geography and Biology, Pedagogical University of Krakow, Krakow, Poland
- Institute of Plant Physiology Polish Academy of Sciences, Krakow, Poland
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26
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Guo J, Zhang X, Hou Y, Cai J, Shen X, Zhou T, Xu H, Ohm HW, Wang H, Li A, Han F, Wang H, Kong L. High-density mapping of the major FHB resistance gene Fhb7 derived from Thinopyrum ponticum and its pyramiding with Fhb1 by marker-assisted selection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015. [PMID: 26220223 DOI: 10.1007/s00122-015-2586-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Wheat lines with shortened Th. ponticum chromatin carrying Fhb7 and molecular markers linked to Fhb7 will accelerate the transfer of Fhb7 to breeding lines and provide an important resource for future map-based cloning of this gene. Fusarium head blight is a major wheat disease globally. A major FHB resistance gene, designated as Fhb7, derived from Thinopyrum ponticum, was earlier transferred to common wheat, but was not used in wheat breeding due to linkage drag. The aims of this study were to (1) saturate this FHB resistance gene region; (2) develop and characterize secondary translocation lines with shortened Thinopyrum segments carrying Fhb7 using ph1b; (3) pyramid Fhb7 and Fhb1 by marker-assisted selection. Fhb7 was mapped in a 1.7 cM interval that was flanked by molecular markers XsdauK66 and Xcfa2240 with SSR, diversity arrays technology, EST-derived and conserved markers. KS24-2 carrying Fhb7 was analyzed with molecular markers and genomic in situ hybridization, confirming it was a 7DS.7el2L Robertsonian translocation. To reduce the Thinopyrum chromatin segments carrying Fhb7, a BC1F2 population (Chinese Spring ph1bph1b*2/KS24-2) was developed and genotyped with the markers linked to Fhb7. Two new translocation lines (SDAU1881 and SDAU1886) carrying Fhb7 on shortened alien segments (approximately 16.1 and 17.3% of the translocation chromosome, respectively) were developed. Furthermore, four wheat lines (SDAU1902, SDAU1903, SDAU1904, and SDAU1906) with the pyramided markers flanking Fhb1 and Fhb7 were developed and the FHB responses indicated lines with mean NDS ranging from 1.3 to 1.6 had successfully combined Fhb7 and Fhb1. Three new molecular markers associated with Fhb7 were identified and validated in 35 common wheat varieties. The translocation lines with shortened alien segments carrying Fhb7 (and Fhb1) and the markers closely linked to Fhb7 will be useful for improving wheat scab resistance.
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Affiliation(s)
- Jun Guo
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018, China
| | - Xiuli Zhang
- College of Life Science, Northeast Forest University, Harbin, 150040, Jilin, China
| | - Yanlin Hou
- State Key Lab of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinjin Cai
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018, China
| | - Xiaorong Shen
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907-1150, USA
| | - Tingting Zhou
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018, China
| | - Huihui Xu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018, China
| | - Herbert W Ohm
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907-1150, USA
| | - Hongwei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018, China
| | - Anfei Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018, China
| | - Fangpu Han
- State Key Lab of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Honggang Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018, China.
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27
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Li H, Vikram P, Singh RP, Kilian A, Carling J, Song J, Burgueno-Ferreira JA, Bhavani S, Huerta-Espino J, Payne T, Sehgal D, Wenzl P, Singh S. A high density GBS map of bread wheat and its application for dissecting complex disease resistance traits. BMC Genomics 2015; 16:216. [PMID: 25887001 PMCID: PMC4381402 DOI: 10.1186/s12864-015-1424-5] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 03/02/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Genotyping-by-sequencing (GBS) is a high-throughput genotyping approach that is starting to be used in several crop species, including bread wheat. Anchoring GBS tags on chromosomes is an important step towards utilizing them for wheat genetic improvement. Here we use genetic linkage mapping to construct a consensus map containing 28644 GBS markers. RESULTS Three RIL populations, PBW343 × Kingbird, PBW343 × Kenya Swara and PBW343 × Muu, which share a common parent, were used to minimize the impact of potential structural genomic variation on consensus-map quality. The consensus map comprised 3757 unique positions, and the average marker distance was 0.88 cM, obtained by calculating the average distance between two adjacent unique positions. Significant variation of segregation distortion was observed across the three populations. The consensus map was validated by comparing positions of known rust resistance genes, and comparing them to wheat reference genome sequences recently published by the International Wheat Genome Sequencing Consortium, Rye and Ae. tauschii genomes. Three well-characterized rust resistance genes (Sr58/Lr46/Yr29, Sr2/Yr30/Lr27, and Sr57/Lr34/Yr18) and 15 published QTLs for wheat rusts were validated with high resolution. Fifty-two per cent of GBS tags on the consensus map were successfully aligned through BLAST to the right chromosomes on the wheat reference genome sequence. CONCLUSION The consensus map should provide a useful basis for analyzing genome-wide variation of complex traits. The identified genes can then be explored as genetic markers to be used in genomic applications in wheat breeding.
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Affiliation(s)
- Huihui Li
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico City, DF, Mexico.
- Institute of Crop Science, CIMMYT-China Office, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Prashant Vikram
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico City, DF, Mexico.
| | - Ravi Prakash Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico City, DF, Mexico.
| | - Andrzej Kilian
- Diversity Array Technologies, DArT, Canberra, Australia.
| | - Jason Carling
- Diversity Array Technologies, DArT, Canberra, Australia.
| | - Jie Song
- Diversity Array Technologies, DArT, Canberra, Australia.
| | | | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico City, DF, Mexico.
| | - Julio Huerta-Espino
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico City, DF, Mexico.
| | - Thomas Payne
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico City, DF, Mexico.
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico City, DF, Mexico.
| | - Peter Wenzl
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico City, DF, Mexico.
| | - Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico City, DF, Mexico.
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Mesterházy A, Lehoczki-Krsjak S, Varga M, Szabó-Hevér Á, Tóth B, Lemmens M. Breeding for FHB Resistance via Fusarium Damaged Kernels and Deoxynivalenol Accumulation as Well as Inoculation Methods in Winter Wheat. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/as.2015.69094] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Li Y, He M. Genetic mapping and QTL analysis of growth-related traits in Pinctada fucata using restriction-site associated DNA sequencing. PLoS One 2014; 9:e111707. [PMID: 25369421 PMCID: PMC4219768 DOI: 10.1371/journal.pone.0111707] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 09/29/2014] [Indexed: 11/19/2022] Open
Abstract
The pearl oyster, Pinctada fucata (P. fucata), is one of the marine bivalves that is predominantly cultured for pearl production. To obtain more genetic information for breeding purposes, we constructed a high-density linkage map of P. fucata and identified quantitative trait loci (QTL) for growth-related traits. One F1 family, which included the two parents, 48 largest progeny and 50 smallest progeny, was sampled to construct a linkage map using restriction site-associated DNA sequencing (RAD-Seq). With low coverage data, 1956.53 million clean reads and 86,342 candidate RAD loci were generated. A total of 1373 segregating SNPs were used to construct a sex-average linkage map. This spanned 1091.81 centimorgans (cM), with 14 linkage groups and an average marker interval of 1.41 cM. The genetic linkage map coverage, Coa, was 97.24%. Thirty-nine QTL-peak loci, for seven growth-related traits, were identified using the single-marker analysis, nonparametric mapping Kruskal-Wallis (KW) test. Parameters included three for shell height, six for shell length, five for shell width, four for hinge length, 11 for total weight, eight for soft tissue weight and two for shell weight. The QTL peak loci for shell height, shell length and shell weight were all located in linkage group 6. The genotype frequencies of most QTL peak loci showed significant differences between the large subpopulation and the small subpopulation (P<0.05). These results highlight the effectiveness of RAD-Seq as a tool for generation of QTL-targeted and genome-wide marker data in the non-model animal, P. fucata, and its possible utility in marker-assisted selection (MAS).
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Affiliation(s)
- Yaoguo Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Maoxian He
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- * E-mail:
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Zeng X, Li W, Wu Y, Liu F, Luo J, Cao Y, Zhu L, Li Y, Li J, You Q, Wu G. Fine mapping of a dominant thermo-sensitive genic male sterility gene (BntsMs) in rapeseed (Brassica napus) with AFLP- and Brassica rapa-derived PCR markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1733-40. [PMID: 24913363 DOI: 10.1007/s00122-014-2335-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 05/20/2014] [Indexed: 05/26/2023]
Abstract
A new thermo-sensitive dominant genic male sterility (TSDGMS) line of Brassica napus was found and mapped in this paper. Our result will greatly accelerate the map-based cloning of the BntsMs gene. TE5A is a thermo-sensitive dominant genic male sterility line originating from spontaneous mutation of the inbred line TE5 in Brassica napus and provides a promising system for the development of hybrid cultivars. Genetic analysis has revealed that the BntsMs mutant is controlled by a single, dominant gene. Here, we describe the fine mapping of BntsMs using amplified fragment length polymorphism (AFLP) and intron polymorphism (IP) methodologies. We screened 1,024 primer combinations and then identified five AFLP markers linked to the BntsMs gene, two of which were successfully converted into sequence-characterised amplified region (SCAR) markers. The linkage of the markers was identified by analysing a large BC2 population of 700 recessive-fertility individuals. Two SCAR markers were found in the flanking region of the BntsMs gene at distance of 3.5 and 4.8 cm. Based on sequence information from the previously screened AFLP markers and on genome organisation comparisons of the A genome of Brassica rapa and Arabidopsis, seven IP markers linked to the BntsMs gene were developed. By analysing the 700 recessive-fertility individuals, two IP markers, IP004 and IP470, were localised to the flanking region of the BntsMs gene at a distance of 0.3 and 0.2 cm, respectively. A comparison of the B. rapa and Arabidopsis genomes revealed 27 genes of B. rapa in the flanking region of these two IP markers. It is likely that the molecular markers developed from these investigations will greatly accelerate the positional cloning of the BntsMs gene.
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Affiliation(s)
- Xinhua Zeng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, No. 2 Xudong Second Road, Wuhan, 430062, People's Republic of China
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Linsell KJ, Rahman MS, Taylor JD, Davey RS, Gogel BJ, Wallwork H, Forrest KL, Hayden MJ, Taylor SP, Oldach KH. QTL for resistance to root lesion nematode (Pratylenchus thornei) from a synthetic hexaploid wheat source. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1409-21. [PMID: 24748126 DOI: 10.1007/s00122-014-2308-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 03/31/2014] [Indexed: 05/22/2023]
Abstract
A whole genome average interval mapping approach identified eight QTL associated with P. thornei resistance in a DH population from a cross between the synthetic-derived wheat Sokoll and cultivar Krichauff. Pratylenchus thornei are migratory nematodes that feed and reproduce within the wheat root cortex, causing cell death (lesions) resulting in severe yield reductions globally. Genotypic selection using molecular markers closely linked to Pratylenchus resistance genes will accelerate the development of new resistant cultivars by reducing the need for laborious and expensive resistance phenotyping. A doubled haploid wheat population (150 lines) from a cross between the synthetic-derived cultivar Sokoll (P. thornei resistant) and cultivar Krichauff (P. thornei moderately susceptible) was used to identify quantitative trait loci (QTL) associated with P. thornei resistance. The resistance identified in the glasshouse was validated in a field trial. A genetic map was constructed using Diversity Array Technology and the QTL regions identified were further targeted with simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers. Six significant and two suggestive P. thornei resistance QTL were detected using a whole genome average interval mapping approach. Three QTL were identified on chromosome 2B, two on chromosome 6D, and a single QTL on each of chromosomes 2A, 2D and 5D. The QTL on chromosomes 2BS and 6DS mapped to locations previously identified to be associated with Pratylenchus resistance. Together, the QTL on 2B (QRlnt.sk-2B.1-2B.3) and 6D (QRlnt.sk-6D.1 and 6D.2) explained 30 and 48 % of the genotypic variation, respectively. Flanking PCR-based markers based on SSRs and SNPs were developed for the major QTL on 2B and 6D and provide a cost-effective high-throughput tool for marker-assisted breeding of wheat with improved P. thornei resistance.
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Affiliation(s)
- Katherine J Linsell
- South Australian Research and Development Institute, University of Adelaide, Molecular Plant Breeding CRC, GPO Box 397, Adelaide, SA, 5001, Australia
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Cui F, Fan X, Zhao C, Zhang W, Chen M, Ji J, Li J. A novel genetic map of wheat: utility for mapping QTL for yield under different nitrogen treatments. BMC Genet 2014; 15:57. [PMID: 24885313 PMCID: PMC4038385 DOI: 10.1186/1471-2156-15-57] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/09/2014] [Indexed: 12/11/2022] Open
Abstract
Background Common wheat (Triticum aestivum L.) is one of the most important food crops worldwide. Wheat varieties that maintain yield (YD) under moderate or even intense nitrogen (N) deficiency can adapt to low input management systems. A detailed genetic map is necessary for both wheat molecular breeding and genomics research. In this study, an F6:7 recombinant inbred line population comprising 188 lines was used to construct a novel genetic map and subsequently to detect quantitative trait loci (QTL) for YD and response to N stress. Results A genetic map consisting of 591 loci distributed across 21 wheat chromosomes was constructed. The map spanned 3930.7 cM, with one marker per 6.7 cM on average. Genomic simple sequence repeat (g-SSR), expressed sequence tag-derived microsatellite (e-SSR), diversity arrays technology (DArT), sequence-tagged sites (STS), sequence-related amplified polymorphism (SRAP), and inter-simple sequence repeat (ISSR) molecular markers were included in the map. The linear relationships between loci found in the present map and in previously compiled physical maps were presented, which were generally in accordance. Information on the genetic and physical positions and allele sizes (when possible) of 17 DArT, 50 e-SSR, 44 SRAP, five ISSR, and two morphological markers is reported here for the first time. Seven segregation distortion regions (SDR) were identified on chromosomes 1B, 3BL, 4AL, 6AS, 6AL, 6BL, and 7B. A total of 22 and 12 QTLs for YD and yield difference between the value (YDDV) under HN and the value under LN were identified, respectively. Of these, QYd-4B-2 and QYddv-4B, two major stable QTL, shared support interval with alleles from KN9204 increasing YD in LN and decreasing YDDV. We probe into the use of these QTLs in wheat breeding programs. Moreover, factors affecting the SDR and total map length are discussed in depth. Conclusions This novel map may facilitate the use of novel markers in wheat molecular breeding programs and genomics research. Moreover, QTLs for YD and YDDV provide useful markers for wheat molecular breeding programs designed to increase yield potential under N stress.
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Affiliation(s)
| | | | | | | | | | | | - Junming Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China.
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Thanh PT, Vladutu CI, Kianian SF, Thanh PT, Ishii T, Nitta M, Nasuda S, Mori N. Molecular Genetic Analysis of Domestication Traits in Emmer Wheat. I: Map Construction and QTL Analysis using an F2Pupulation. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2013.0008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Genetic diversity and population structure analysis of European hexaploid bread wheat (Triticum aestivum L.) varieties. PLoS One 2014; 9:e94000. [PMID: 24718292 PMCID: PMC3981729 DOI: 10.1371/journal.pone.0094000] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 03/11/2014] [Indexed: 12/03/2022] Open
Abstract
Progress in plant breeding is facilitated by accurate information about genetic structure and diversity. Here, Diversity Array Technology (DArT) was used to characterize a population of 94 bread wheat (Triticum aestivum L.) varieties of mainly European origin. In total, 1,849 of 7,000 tested markers were polymorphic and could be used for population structure analysis. Two major subgroups of wheat varieties, GrI and GrII, were identified using the program STRUCTURE, and confirmed by principal component analysis (PCA). These subgroups were largely separated according to origin; GrI comprised varieties from Southern and Eastern Europe, whereas GrII contained mostly modern varieties from Western and Northern Europe. A large proportion of the markers contributing most to the genetic separation of the subgroups were located on chromosome 2D near the Reduced height 8 (Rht8) locus, and PCR-based genotyping suggested that breeding for the Rht8 allele had a major impact on subgroup separation. Consistently, analysis of linkage disequilibrium (LD) suggested that different selective pressures had acted on chromosome 2D in the two subgroups. Our data provides an overview of the allele composition of bread wheat varieties anchored to DArT markers, which will facilitate targeted combination of alleles following DArT-based QTL studies. In addition, the genetic diversity and distance data combined with specific Rht8 genotypes can now be used by breeders to guide selection of crossing parents.
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Cui F, Zhao C, Ding A, Li J, Wang L, Li X, Bao Y, Li J, Wang H. Construction of an integrative linkage map and QTL mapping of grain yield-related traits using three related wheat RIL populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:659-75. [PMID: 24326459 DOI: 10.1007/s00122-013-2249-8] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 11/20/2013] [Indexed: 05/22/2023]
Abstract
A novel high-density consensus wheat genetic map was obtained based on three related RIL populations, and the important chromosomal regions affecting yield and related traits were specified. A prerequisite for mapping quantitative trait locus (QTL) is to build a genetic linkage map. In this study, three recombinant inbred line populations (represented by WL, WY, and WJ) sharing one common parental line were used for map construction and subsequently for QTL detection of yield-related traits. PCR-based and diversity arrays technology markers were screened in the three populations. The integrated genetic map contains 1,127 marker loci, which span 2,976.75 cM for the whole genome, 985.93 cM for the A genome, 922.16 cM for the B genome, and 1,068.65 cM for the D genome. Phenotypic values were evaluated in four environments for populations WY and WJ, but three environments for population WL. Individual and combined phenotypic values across environments were used for QTL detection. A total of 165 putative additive QTL were identified, 22 of which showed significant additive-by-environment interaction effects. A total of 65 QTL (51.5%) were stable across environments, and 23 of these (35.4%) were common stable QTL that were identified in at least two populations. Notably, QTkw-5B.1, QTkw-6A.2, and QTkw-7B.1 were common major stable QTL in at least two populations, exhibiting 11.28-16.06, 5.64-18.69, and 6.76-21.16% of the phenotypic variance, respectively. Genetic relationships between kernel dimensions and kernel weight and between yield components and yield were evaluated. Moreover, QTL or regions that commonly interact across genetic backgrounds were discussed by comparing the results of the present study with those of previous similar studies. The present study provides useful information for marker-assisted selection in breeding wheat varieties with high yield.
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Affiliation(s)
- Fa Cui
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Tai'an Subcenter of National Wheat Improvement Center, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China,
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Singh AK, Knox RE, Clarke JM, Clarke FR, Singh A, DePauw RM, Cuthbert RD. Genetics of pre-harvest sprouting resistance in a cross of Canadian adapted durum wheat genotypes. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 33:919-929. [PMID: 24659906 PMCID: PMC3956934 DOI: 10.1007/s11032-013-0006-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 12/11/2013] [Indexed: 05/06/2023]
Abstract
Severe losses attributable to pre-harvest sprouting (PHS) have been reported in Canada in recent years. The genetics of PHS resistance have been more extensively studied in hexaploid wheat and generally not using combinations of elite agronomic parents. The objective of our research was to understand the genetic nature of PHS resistance in an elite durum cross. A doubled haploid (DH) population and checks were phenotyped in replicated trials for grain yield and PHS traits over 3 years in western Canada. The response of intact spikes to sprouting conditions, sampled over two development time points, was measured in a rain simulation chamber. The DH population was genotyped with simple sequence repeat and Diversity Arrays Technology markers. Genotypes were a significant source of variation for grain yield and PHS resistance traits in each tested environment. Transgressive segregant DH genotypes were identified for grain yield and PHS resistance measurements. Low or no correlation was detected between grain yield and PHS, while correlation between PHS resistance measurements was moderate. The heritability of PHS resistance was moderate and higher than grain yield. Significant quantitative trait loci with small effect were detected on chromosomes 1A, 1B, 5B, 7A and 7B. Both parents contributed to the PHS resistance. Promising DH genotypes with high and stable grain yield as well as PHS resistance were identified, suggesting that grain yield and PHS can be improved simultaneously in elite genetic materials, and that these DH genotypes will be useful parental material for durum breeding programs.
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Affiliation(s)
- A. K. Singh
- Semiarid Prairie Agricultural Research Center, Agriculture and Agri-Food Canada, Swift Current, SK Canada
- Present Address: Department of Agronomy, Iowa State University, Ames, IA USA
| | - R. E. Knox
- Semiarid Prairie Agricultural Research Center, Agriculture and Agri-Food Canada, Swift Current, SK Canada
| | - J. M. Clarke
- University of Saskatchewan, Saskatoon, SK Canada
| | - F. R. Clarke
- Semiarid Prairie Agricultural Research Center, Agriculture and Agri-Food Canada, Swift Current, SK Canada
| | - A. Singh
- Semiarid Prairie Agricultural Research Center, Agriculture and Agri-Food Canada, Swift Current, SK Canada
- Present Address: Department of Agronomy, Iowa State University, Ames, IA USA
| | - R. M. DePauw
- Semiarid Prairie Agricultural Research Center, Agriculture and Agri-Food Canada, Swift Current, SK Canada
| | - R. D. Cuthbert
- Semiarid Prairie Agricultural Research Center, Agriculture and Agri-Food Canada, Swift Current, SK Canada
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Bian M, Zhou M, Sun D, Li C. Molecular approaches unravel the mechanism of acid soil tolerance in plants. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.cj.2013.08.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Liu S, Griffey CA, Hall MD, McKendry AL, Chen J, Brooks WS, Brown-Guedira G, Van Sanford D, Schmale DG. Molecular characterization of field resistance to Fusarium head blight in two US soft red winter wheat cultivars. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2485-98. [PMID: 23832049 PMCID: PMC3782633 DOI: 10.1007/s00122-013-2149-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Accepted: 06/18/2013] [Indexed: 05/21/2023]
Abstract
In the soft red winter wheat (Triticum aestivum L.) regions of the US, Fusarium head blight (FHB, caused by Fusarium spp.) resistance derived from locally adapted germplasm has been used predominantly. Two soft red winter wheat cultivars, Massey and Ernie, have moderate resistance to FHB. Mapping populations derived from Becker/Massey (B/M) and Ernie/MO 94-317 (E/MO) were evaluated for FHB resistance and other traits in multiple environments. Eight QTL in B/M and five QTL in E/MO were associated with FHB variables including incidence, severity (SEV), index (IND), Fusarium damaged kernels (FDK), deoxynivalenol (DON), and morphological traits flowering time and plant height. Four QTL were common to both populations. Three of them were located at or near known genes: Ppd-D1 on chromosome 2DS, Rht-B1 on 4BS, and Rht-D1 on 4DS. Alleles for dwarf plant height (Rht-B1b and Rht-D1b) and photoperiod insensitivity (Ppd-D1a) had pleiotropic effects in reducing height and increasing FHB susceptibility. The other QTL detected for FHB variables were on 3BL in both populations, 1AS, 1DS, 2BL, and 4DL in B/M, and 5AL (B1) and 6AL in E/MO. The additive effects of FHB variables ranged from 0.4 mg kg(-1) of DON to 6.2 % for greenhouse (GH) SEV in B/M and ranged from 0.3 mg kg(-1) of DON to 8.3 % for GH SEV in E/MO. The 4DS QTL had epistasis with Ppd-D1, Qdon.umc-6AL, and Qht.umc-4BS, and additive × additive × environment interactions with the 4BS QTL for SEV, IND, and FDK in E/MO. Marker-assisted selection might be used to enhance FHB resistance through selection of favorable alleles of significant QTL, taking into account genotypes at Rht-B1b, Rht-D1a and Ppd-D1a.
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Affiliation(s)
- Shuyu Liu
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA 24060 USA
- Present Address: Texas A&M AgriLife Research and Extension Center, Texas A&M University System, 6500 Amarillo Blvd W., Amarillo, TX 79106 USA
| | - Carl A. Griffey
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA 24060 USA
| | - Marla D. Hall
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA 24060 USA
- Present Address: Limagrain Cereal Seeds, 6414 N. Sheridan, Wichita, KS 67204 USA
| | - Anne L. McKendry
- Department of Plant Science, University of Missouri, Columbia, MO 65201 USA
| | - Jianli Chen
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA 24060 USA
- Present Address: Department of Agronomy, University of Idaho Aberdeen Research and Extension Center, Aberdeen, ID 83210 USA
| | - Wynse S. Brooks
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA 24060 USA
| | - Gina Brown-Guedira
- Eastern Regional Small Grains Genotyping Lab, USDA-ARS, Raleigh, NC 27695 USA
| | - David Van Sanford
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546 USA
| | - David G. Schmale
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24060 USA
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Olivera PD, Kilian A, Wenzl P, Steffenson BJ. Development of a genetic linkage map for Sharon goatgrass (Aegilops sharonensis) and mapping of a leaf rust resistance gene. Genome 2013; 56:367-76. [PMID: 24099389 DOI: 10.1139/gen-2013-0065] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Aegilops sharonensis (Sharon goatgrass), a diploid wheat relative, is known to be a rich source of disease resistance genes for wheat improvement. To facilitate the transfer of these genes into wheat, information on their chromosomal location is important. A genetic linkage map of Ae. sharonensis was constructed based on 179 F2 plants derived from a cross between accessions resistant (1644) and susceptible (1193) to wheat leaf rust. The linkage map was based on 389 markers (377 Diversity Arrays Technology (DArT) and 12 simple sequence repeat (SSR) loci) and was comprised of 10 linkage groups, ranging from 2.3 to 124.6 cM. The total genetic length of the map was 818.0 cM, with an average interval distance between markers of 3.63 cM. Based on the chromosomal location of 115 markers previously mapped in wheat, the four linkage groups of A, B, C, and E were assigned to Ae. sharonensis (S(sh)) and homoeologous wheat chromosomes 6, 1, 3, and 2. The single dominant gene (designated LrAeSh1644) conferring resistance to leaf rust race THBJ in accession 1644 was positioned on linkage group A (chromosome 6S(sh)) and was flanked by DArT markers wpt-9881 (at 1.9 cM distal from the gene) and wpt-6925 (4.5 cM proximal). This study clearly demonstrates the utility of DArT for genotyping uncharacterized species and tagging resistance genes where pertinent genomic information is lacking.
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Affiliation(s)
- P D Olivera
- a Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
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Czyczyło-Mysza I, Tyrka M, Marcińska I, Skrzypek E, Karbarz M, Dziurka M, Hura T, Dziurka K, Quarrie SA. Quantitative trait loci for leaf chlorophyll fluorescence parameters, chlorophyll and carotenoid contents in relation to biomass and yield in bread wheat and their chromosome deletion bin assignments. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2013; 32:189-210. [PMID: 23794940 PMCID: PMC3684715 DOI: 10.1007/s11032-013-9862-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 03/16/2013] [Indexed: 05/04/2023]
Abstract
Relatively little is known of the genetic control of chlorophyll fluorescence (CF) and pigment traits important in determining efficiency of photosynthesis in wheat and its association with biomass productivity. A doubled haploid population of 94 lines from the wheat cross Chinese Spring × SQ1 was trialled under optimum glasshouse conditions for 4 years to identify quantitative trait loci (QTL) for CF traits including, for the first time in wheat, JIP-test parameters per excited cross section (CSm): ABS/CSm, DIo/CSm, TRo/CSm, RC/CSm and ETo/CSm, key parameters determining efficiency of the photosynthetic apparatus, as well as chlorophyll and carotenoid contents to establish associations with biomass and grain yield. The existing genetic map was extended to 920 loci by adding Diversity Arrays Technology markers. Markers and selected genes for photosynthetic light reactions, pigment metabolism and biomass accumulation were located to chromosome deletion bins. Across all CF traits and years, 116 QTL for CF were located on all chromosomes except 7B, and 39 QTL were identified for pigments on the majority of chromosomes, excluding 1A, 2A, 4A, 3B, 5B, 1D, 2D, 5D, 6D and 7D. Thirty QTL for plant productivity traits were mapped on chromosomes 3A, 5A, 6A, 7A, 1B, 2B, 4B, 6B, 7B, 3D and 4D. A region on chromosome 6B was identified where 14 QTL for CF parameters coincided with QTL for chlorophyll content and grain weight per ear. Thirty-five QTL regions were coincident with candidate genes. The environment was shown to dominate in determining expression of genes for those traits.
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Affiliation(s)
- I. Czyczyło-Mysza
- The F. Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków, Poland
| | - M. Tyrka
- Department of Biochemistry and Biotechnology, Rzeszow University of Technology, Rzeszów, Poland
| | - I. Marcińska
- The F. Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków, Poland
| | - E. Skrzypek
- The F. Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków, Poland
| | - M. Karbarz
- Institute of Applied Biotechnology and Basic Sciences, University of Rzeszow, Rzeszów, Poland
| | - M. Dziurka
- The F. Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków, Poland
| | - T. Hura
- The F. Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków, Poland
| | - K. Dziurka
- The F. Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków, Poland
| | - S. A. Quarrie
- Faculty of Biology, Belgrade University, Belgrade, Serbia
- Newcastle University, Newcastle upon Tyne, UK
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Jakse J, Cerenak A, Radisek S, Satovic Z, Luthar Z, Javornik B. Identification of quantitative trait loci for resistance to Verticillium wilt and yield parameters in hop (Humulus lupulus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1431-43. [PMID: 23423654 DOI: 10.1007/s00122-013-2062-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 02/08/2013] [Indexed: 05/11/2023]
Abstract
Verticillium wilt (VW) can cause substantial yield loss in hop particularly with the outbreaks of the lethal strain of Verticillium albo-atrum. To elucidate genetic control of VW resistance in hop, an F1 mapping population derived from a cross of cultivar Wye Target, with the predicted genetic basis of resistance, and susceptible male breeding line BL2/1 was developed to assess wilting symptoms and to perform QTL mapping. The genetic linkage map, constructed with 203 markers of various types using a pseudo-testcross strategy, formed ten major linkage groups (LG) of the maternal and paternal maps, covering 552.98 and 441.1 cM, respectively. A significant QTL for VW resistance was detected at LOD 7 on a single chromosomal region on LG03 of both parental maps, accounting for 24.2-26.0 % of the phenotypic variance. QTL analysis for alpha-acid content and yield parameters was also performed on this map. QTLs for these traits were also detected and confirmed our previously detected QTLs in a different pedigree and environment. The work provides the basis for exploration of QTL flanking markers for possible use in marker-assisted selection.
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Affiliation(s)
- Jernej Jakse
- University of Ljubljana, Biotechnical Faculty, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
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Semagn K, Beyene Y, Warburton ML, Tarekegne A, Mugo S, Meisel B, Sehabiague P, Prasanna BM. Meta-analyses of QTL for grain yield and anthesis silking interval in 18 maize populations evaluated under water-stressed and well-watered environments. BMC Genomics 2013; 14:313. [PMID: 23663209 PMCID: PMC3751468 DOI: 10.1186/1471-2164-14-313] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/03/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Identification of QTL with large phenotypic effects conserved across genetic backgrounds and environments is one of the prerequisites for crop improvement using marker assisted selection (MAS). The objectives of this study were to identify meta-QTL (mQTL) for grain yield (GY) and anthesis silking interval (ASI) across 18 bi-parental maize populations evaluated in the same conditions across 2-4 managed water stressed and 3-4 well watered environments. RESULTS The meta-analyses identified 68 mQTL (9 QTL specific to ASI, 15 specific to GY, and 44 for both GY and ASI). Mean phenotypic variance explained by each mQTL varied from 1.2 to 13.1% and the overall average was 6.5%. Few QTL were detected under both environmental treatments and/or multiple (>4 populations) genetic backgrounds. The number and 95% genetic and physical confidence intervals of the mQTL were highly reduced compared to the QTL identified in the original studies. Each physical interval of the mQTL consisted of 5 to 926 candidate genes. CONCLUSIONS Meta-analyses reduced the number of QTL by 68% and narrowed the confidence intervals up to 12-fold. At least the 4 mQTL (mQTL2.2, mQTL6.1, mQTL7.5 and mQTL9.2) associated with GY under both water-stressed and well-watered environments and detected up to 6 populations may be considered for fine mapping and validation to confirm effects in different genetic backgrounds and pyramid them into new drought resistant breeding lines. This is the first extensive report on meta-analysis of data from over 3100 individuals genotyped using the same SNP platform and evaluated in the same conditions across a wide range of managed water-stressed and well-watered environments.
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Affiliation(s)
- Kassa Semagn
- International Maize and Wheat Improvement Center, CIMMYT, PO Box 1041, Village Market 00621, Nairobi, Kenya.
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Zhang K, Wang J, Zhang L, Rong C, Zhao F, Peng T, Li H, Cheng D, Liu X, Qin H, Zhang A, Tong Y, Wang D. Association analysis of genomic loci important for grain weight control in elite common wheat varieties cultivated with variable water and fertiliser supply. PLoS One 2013; 8:e57853. [PMID: 23469248 PMCID: PMC3587626 DOI: 10.1371/journal.pone.0057853] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 01/27/2013] [Indexed: 11/18/2022] Open
Abstract
Grain weight, an essential yield component, is under strong genetic control and markedly influenced by the environment. Here, by genome-wide association analysis with a panel of 94 elite common wheat varieties, 37 loci were found significantly associated with thousand-grain weight (TGW) in one or more environments differing in water and fertiliser levels. Five loci were stably associated with TGW under all 12 environments examined. Their elite alleles had positive effects on TGW. Four, two, three, and two loci were consistently associated with TGW in the irrigated and fertilised (IF), rainfed (RF), reduced nitrogen (RN), and reduced phosphorus (RP) environments. The elite alleles of the IF-specific loci enhanced TGW under well-resourced conditions, whereas those of the RF-, RN-, or RP-specific loci conferred tolerance to the TGW decrease when irrigation, nitrogen, or phosphorus were reduced. Moreover, the elite alleles of the environment-independent and -specific loci often acted additively to enhance TGW. Four additional loci were found associated with TGW in specific locations, one of which was shown to contribute to the TGW difference between two experimental sites. Further analysis of 14 associated loci revealed that nine affected both grain length and width, whereas the remaining loci influenced either grain length or width, indicating that these loci control grain weight by regulating kernel size. Finally, the elite allele of Xpsp3152 frequently co-segregated with the larger grain haplotype of TaGW2-6A, suggesting probable genetic and functional linkages between Xpsp3152 and GW2 that are important for grain weight control in cereal plants. Our study provides new knowledge on TGW control in elite common wheat lines, which may aid the improvement of wheat grain weight trait in further research.
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Affiliation(s)
- Kunpu Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Junjun Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Liyi Zhang
- Guizhou Institute of Upland Crops, Guiyang, China
| | - Chaowu Rong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fengwu Zhao
- Dry-Land Farming Institute, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Tao Peng
- Jiyuan Institute of Agricultural Sciences, Jiyuan, China
| | - Huimin Li
- Dry-Land Farming Institute, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Dongmei Cheng
- Jiyuan Institute of Agricultural Sciences, Jiyuan, China
| | - Xin Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Huanju Qin
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Aimin Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yiping Tong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Daowen Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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Lu Q, Lillemo M, Skinnes H, He X, Shi J, Ji F, Dong Y, Bjørnstad A. Anther extrusion and plant height are associated with Type I resistance to Fusarium head blight in bread wheat line 'Shanghai-3/Catbird'. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:317-34. [PMID: 23052019 DOI: 10.1007/s00122-012-1981-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 09/15/2012] [Indexed: 05/20/2023]
Abstract
Fusarium head blight (FHB) is a destructive wheat disease of global importance. Resistance breeding depends heavily on the Fhb1 gene. The CIMMYT line Shanghai-3/Catbird (SHA3/CBRD) is a promising source without this gene. A recombinant inbred line (RIL) population from the cross of SHA3/CBRD with the German spring wheat cv. Naxos was evaluated for FHB resistance and related traits in field trials using spray and spawn inoculation in Norway and point inoculation in China. After spray and spawn inoculation, FHB severities were negatively correlated with both anther extrusion (AE) and plant height (PH). The QTL analysis showed that the Rht-B1b dwarfing allele co-localized with a QTL for low AE and increased susceptibility after spawn and spray inoculation. In general, SHA3/CBRD contributed most of the favorable alleles for resistance to severity after spray and spawn inoculation, while Naxos contributed more favorable alleles for reduction in FDK and DON content and resistance to severity after point inoculation. SHA3/CBRD contributed a major resistance QTL close to the centromere on 2DLc affecting FHB severity and DON after all inoculation methods. This QTL was also associated with AE and PH, with high AE and tall alleles contributed by SHA3/CBRD. Several QTL for AE and PH were detected, and low AE or reduced PH was always associated with increased susceptibility after spawn and spray inoculation. Most of the other minor FHB resistance QTL from SHA3/CBRD were associated with AE or PH, while the QTL from Naxos were mostly not. After point inoculation, no other QTL for FHB traits was associated with AE or PH, except the 2DLc QTL which was common across all inoculation methods. Marker-assisted selection based on the 2DLc QTL from SHA3/CBRD combined with phenotypic selection for AE is recommended for resistance breeding based on this valuable source of resistance.
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Affiliation(s)
- Qiongxian Lu
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway.
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Rauscher G, Simko I. Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes. BMC PLANT BIOLOGY 2013; 13:11. [PMID: 23339733 PMCID: PMC3557189 DOI: 10.1186/1471-2229-13-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 01/08/2013] [Indexed: 05/11/2023]
Abstract
BACKGROUND Lettuce (Lactuca sativa L.) is the major crop from the group of leafy vegetables. Several types of molecular markers were developed that are effectively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly available. We have employed the method of enriched microsatellite libraries to develop 97 genomic SSR markers. RESULTS Testing of newly developed markers on a set of 36 Lactuca accession (33 L. sativa, and one of each L. serriola L., L. saligna L., and L. virosa L.) revealed that both the genetic heterozygosity (UHe = 0.56) and the number of loci per SSR (Na = 5.50) are significantly higher for genomic SSR markers than for previously developed EST-based SSR markers (UHe = 0.32, Na = 3.56). Fifty-four genomic SSR markers were placed on the molecular linkage map of lettuce. Distribution of markers in the genome appeared to be random, with the exception of possible cluster on linkage group 6. Any combination of 32 genomic SSRs was able to distinguish genotypes of all 36 accessions. Fourteen of newly developed SSR markers originate from fragments with high sequence similarity to resistance gene candidates (RGCs) and RGC pseudogenes. Analysis of molecular variance (AMOVA) of L. sativa accessions showed that approximately 3% of genetic diversity was within accessions, 79% among accessions, and 18% among horticultural types. CONCLUSIONS The newly developed genomic SSR markers were added to the pool of previously developed EST-SSRs markers. These two types of SSR-based markers provide useful tools for lettuce cultivar fingerprinting, development of integrated molecular linkage maps, and mapping of genes.
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Affiliation(s)
- Gilda Rauscher
- United States Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA, 93905, USA
- Present address: Agricultural Biotechnology, DuPont Pioneer, Wilmington, Wilmington, DE, 19880, USA
| | - Ivan Simko
- United States Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA, 93905, USA
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Marone D, Laidò G, Gadaleta A, Colasuonno P, Ficco DBM, Giancaspro A, Giove S, Panio G, Russo MA, De Vita P, Cattivelli L, Papa R, Blanco A, Mastrangelo AM. A high-density consensus map of A and B wheat genomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1619-38. [PMID: 22872151 PMCID: PMC3493672 DOI: 10.1007/s00122-012-1939-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 07/03/2012] [Indexed: 05/18/2023]
Abstract
A durum wheat consensus linkage map was developed by combining segregation data from six mapping populations. All of the crosses were derived from durum wheat cultivars, except for one accession of T. ssp. dicoccoides. The consensus map was composed of 1,898 loci arranged into 27 linkage groups covering all 14 chromosomes. The length of the integrated map and the average marker distance were 3,058.6 and 1.6 cM, respectively. The order of the loci was generally in agreement with respect to the individual maps and with previously published maps. When the consensus map was aligned to the deletion bin map, 493 markers were assigned to specific bins. Segregation distortion was found across many durum wheat chromosomes, with a higher frequency for the B genome. This high-density consensus map allowed the scanning of the genome for chromosomal rearrangements occurring during the wheat evolution. Translocations and inversions that were already known in literature were confirmed, and new putative rearrangements are proposed. The consensus map herein described provides a more complete coverage of the durum wheat genome compared with previously developed maps. It also represents a step forward in durum wheat genomics and an essential tool for further research and studies on evolution of the wheat genome.
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Affiliation(s)
- Daniela Marone
- CRA-Cereal Research Centre, SS16 km 675, 71122 Foggia, Italy
| | - Giovanni Laidò
- CRA-Cereal Research Centre, SS16 km 675, 71122 Foggia, Italy
| | - Agata Gadaleta
- Department of Agro-Forestry and Environmental Biology and Chemistry, University of Bari, Via Amendola, 165/A, 70126 Bari, Italy
| | - Pasqualina Colasuonno
- Department of Agro-Forestry and Environmental Biology and Chemistry, University of Bari, Via Amendola, 165/A, 70126 Bari, Italy
| | | | - Angelica Giancaspro
- Department of Agro-Forestry and Environmental Biology and Chemistry, University of Bari, Via Amendola, 165/A, 70126 Bari, Italy
| | - Stefania Giove
- Department of Agro-Forestry and Environmental Biology and Chemistry, University of Bari, Via Amendola, 165/A, 70126 Bari, Italy
| | - Giosué Panio
- CRA-Cereal Research Centre, SS16 km 675, 71122 Foggia, Italy
| | - Maria A. Russo
- CRA-Cereal Research Centre, SS16 km 675, 71122 Foggia, Italy
| | | | - Luigi Cattivelli
- CRA-Cereal Research Centre, SS16 km 675, 71122 Foggia, Italy
- CRA-Genomics Research Centre, Via S. Protaso 302, 29017 Fiorenzuola d’Arda, PC Italy
| | - Roberto Papa
- CRA-Cereal Research Centre, SS16 km 675, 71122 Foggia, Italy
| | - Antonio Blanco
- Department of Agro-Forestry and Environmental Biology and Chemistry, University of Bari, Via Amendola, 165/A, 70126 Bari, Italy
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Tiwari VK, Riera-Lizarazu O, Gunn HL, Lopez K, Iqbal MJ, Kianian SF, Leonard JM. Endosperm tolerance of paternal aneuploidy allows radiation hybrid mapping of the wheat D-genome and a measure of γ ray-induced chromosome breaks. PLoS One 2012; 7:e48815. [PMID: 23144983 PMCID: PMC3492231 DOI: 10.1371/journal.pone.0048815] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 10/01/2012] [Indexed: 11/21/2022] Open
Abstract
Physical mapping and genome sequencing are underway for the ≈17 Gb wheat genome. Physical mapping methods independent of meiotic recombination, such as radiation hybrid (RH) mapping, will aid precise anchoring of BAC contigs in the large regions of suppressed recombination in Triticeae genomes. Reports of endosperm development following pollination with irradiated pollen at dosages that cause embryo abortion prompted us to investigate endosperm as a potential source of RH mapping germplasm. Here, we report a novel approach to construct RH based physical maps of all seven D-genome chromosomes of the hexaploid wheat ‘Chinese Spring’, simultaneously. An 81-member subset of endosperm samples derived from 20-Gy irradiated pollen was genotyped for deletions, and 737 markers were mapped on seven D-genome chromosomes. Analysis of well-defined regions of six chromosomes suggested a map resolution of ∼830 kb could be achieved; this estimate was validated with assays of markers from a sequenced contig. We estimate that the panel contains ∼6,000 deletion bins for D-genome chromosomes and will require ∼18,000 markers for high resolution mapping. Map-based deletion estimates revealed a majority of 1–20 Mb interstitial deletions suggesting mutagenic repair of double-strand breaks in pollen provides a useful resource for RH mapping and map based cloning studies.
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Affiliation(s)
- Vijay K. Tiwari
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| | - Oscar Riera-Lizarazu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India
| | - Hilary L. Gunn
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| | - KaSandra Lopez
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| | - M. Javed Iqbal
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Shahryar F. Kianian
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Jeffrey M. Leonard
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
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Zhang L, Luo JT, Hao M, Zhang LQ, Yuan ZW, Yan ZH, Liu YX, Zhang B, Liu BL, Liu CJ, Zhang HG, Zheng YL, Liu DC. Genetic map of Triticum turgidum based on a hexaploid wheat population without genetic recombination for D genome. BMC Genet 2012; 13:69. [PMID: 22888829 PMCID: PMC3470960 DOI: 10.1186/1471-2156-13-69] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 08/08/2012] [Indexed: 12/13/2022] Open
Abstract
Background A synthetic doubled-haploid hexaploid wheat population, SynDH1, derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from the cross of hybrids Triticum turgidum ssp. durum line Langdon (LDN) and ssp. turgidum line AS313, with Aegilops tauschii ssp. tauschii accession AS60, was previously constructed. SynDH1 is a tetraploidization-hexaploid doubled haploid (DH) population because it contains recombinant A and B chromosomes from two different T. turgidum genotypes, while all the D chromosomes from Ae. tauschii are homogenous across the whole population. This paper reports the construction of a genetic map using this population. Results Of the 606 markers used to assemble the genetic map, 588 (97%) were assigned to linkage groups. These included 513 Diversity Arrays Technology (DArT) markers, 72 simple sequence repeat (SSR), one insertion site-based polymorphism (ISBP), and two high-molecular-weight glutenin subunit (HMW-GS) markers. These markers were assigned to the 14 chromosomes, covering 2048.79 cM, with a mean distance of 3.48 cM between adjacent markers. This map showed good coverage of the A and B genome chromosomes, apart from 3A, 5A, 6A, and 4B. Compared with previously reported maps, most shared markers showed highly consistent orders. This map was successfully used to identify five quantitative trait loci (QTL), including two for spikelet number on chromosomes 7A and 5B, two for spike length on 7A and 3B, and one for 1000-grain weight on 4B. However, differences in crossability QTL between the two T. turgidum parents may explain the segregation distortion regions on chromosomes 1A, 3B, and 6B. Conclusions A genetic map of T. turgidum including 588 markers was constructed using a synthetic doubled haploid (SynDH) hexaploid wheat population. Five QTLs for three agronomic traits were identified from this population. However, more markers are needed to increase the density and resolution of this map in the future study.
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Affiliation(s)
- Li Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, PR China
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Marone D, Panio G, Ficco DBM, Russo MA, De Vita P, Papa R, Rubiales D, Cattivelli L, Mastrangelo AM. Characterization of wheat DArT markers: genetic and functional features. Mol Genet Genomics 2012; 287:741-53. [DOI: 10.1007/s00438-012-0714-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 07/20/2012] [Indexed: 11/30/2022]
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Alheit KV, Maurer HP, Reif JC, Tucker MR, Hahn V, Weissmann EA, Würschum T. Genome-wide evaluation of genetic diversity and linkage disequilibrium in winter and spring triticale (x Triticosecale Wittmack). BMC Genomics 2012; 13:235. [PMID: 22691168 PMCID: PMC3464613 DOI: 10.1186/1471-2164-13-235] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 05/24/2012] [Indexed: 11/10/2022] Open
Abstract
Background Recent advances in genotyping with high-density markers nowadays enable genome-wide genomic analyses in crops. A detailed characterisation of the population structure and linkage disequilibrium (LD) is essential for the application of genomic approaches and consequently for knowledge-based breeding. In this study we used the triticale-specific DArT array to analyze population structure, genetic diversity, and LD in a worldwide set of 161 winter and spring triticale lines. Results The principal coordinate analysis revealed that the first principal coordinate divides the triticale population into two clusters according to their growth habit. The density distributions of the first ten principal coordinates revealed that several show a distribution indicative of population structure. In addition, we observed relatedness within growth habits which was higher among the spring types than among the winter types. The genome-wide analysis of polymorphic information content (PIC) showed that the PIC is variable among and along chromosomes and that especially the R genome of spring types possesses a reduced genetic diversity. We also found that several chromosomes showed regions of high genetic distance between the two growth habits, indicative of divergent selection. Regarding linkage disequilibrium, the A and B genomes showed a similar LD of 0.24 for closely linked markers and a decay within approximately 12 cM. LD in the R genome was lower with 0.19 and decayed within a shorter map distance of approximately 5 cM. The extent of LD was generally higher for the spring types compared to the winter types. In addition, we observed strong variability of LD along the chromosomes. Conclusions Our results confirm winter and spring growth habit are the major contributors to population structure in triticale, and a family structure exists in both growth types. The specific patterns of genetic diversity observed within these types, such as the low diversity on some rye chromosomes of spring habits, provide a basis for targeted broadening of the available breeding germplasm. In addition, the genome-wide analysis of the extent and the pattern of LD will assist scientists and breeders alike in the implementation and the interpretation of association mapping in triticale.
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Affiliation(s)
- Katharina V Alheit
- State Plant Breeding Institute, University of Hohenheim, Stuttgart 70593, Germany
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