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Xue L, Wu H, Chen Y, Li X, Hou J, Lu J, Wei S, Dai X, Olson MS, Liu J, Wang M, Charlesworth D, Yin T. Evidences for a role of two Y-specific genes in sex determination in Populus deltoides. Nat Commun 2020; 11:5893. [PMID: 33208755 PMCID: PMC7674411 DOI: 10.1038/s41467-020-19559-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 10/16/2020] [Indexed: 01/04/2023] Open
Abstract
Almost all plants in the genus Populus are dioecious (i.e. trees are either male or female), but it is unknown whether dioecy evolved in a common ancestor or independently in different subgenera. Here, we sequence the small peritelomeric X- and Y-linked regions of P. deltoides chromosome XIX. Two genes are present only in the Y-linked region. One is a duplication of a non-Y-linked, female-specifically expressed response regulator, which produces siRNAs that block this gene's expression, repressing femaleness. The other is an LTR/Gypsy transposable element family member, which generates long non-coding RNAs. Overexpression of this gene in A. thaliana promotes androecium development. We also find both genes in the sex-determining region of P. simonii, a different poplar subgenus, which suggests that they are both stable components of poplar sex-determining systems. By contrast, only the duplicated response regulator gene is present in the sex-linked regions of P. davidiana and P. tremula. Therefore, findings in our study suggest dioecy may have evolved independently in different poplar subgenera.
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Affiliation(s)
- Liangjiao Xue
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Huaitong Wu
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Yingnan Chen
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Xiaoping Li
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Jing Hou
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Jing Lu
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Suyun Wei
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Xiaogang Dai
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Mingxiu Wang
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK.
| | - Tongming Yin
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China.
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Wang Z, Cheng Y, Yin Y, Yu C, Yang Y, Shi Q, Hao Z, Li H. Genetic linkage map construction and QTL mapping of seedling height, basal diameter and crown width of Taxodium 'Zhongshanshan 302' × T. mucronatum. SPRINGERPLUS 2016; 5:936. [PMID: 27386380 PMCID: PMC4929119 DOI: 10.1186/s40064-016-2617-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/17/2016] [Indexed: 12/13/2022]
Abstract
Taxodium is a genus renowned for its fast growth, good form and tolerance of flooding, salt, alkalinity, disease and strong winds. In this study, a genetic linkage map was constructed using sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR) markers based on an F1 population containing 148 individuals generated from a cross between T. ‘Zhongshanshan 302’ and T. mucronatum. The map has a total length of 976.5 cM, with a mean distance of 7.0 cM between markers, and contains 34 linkage groups with 179 markers (171 SRAPs and 8 SSRs). Quantitative trait loci (QTLs) affecting growth traits, such as seedling height, basal diameter and crown width, were detected based on the constructed linkage map. Four significant QTLs were identified, three of which, namely qtSH-1 for seedling height, qtBD-1 for basal diameter and qtCW-1 for crown width, were located at 2.659 cM of LG7 with logarithm odds values of 3.72, 3.49 and 3.93, respectively, and explained 24.9, 27.0 and 21.7 % of the total variation of the three grown traits, respectively. Another QTL for crown width (qtCW-2) was detected at 1.0 cM on LG13, with a logarithm of odds value of 3.15, and explained 31.7 % of the total variation of crown width. This is the first report on the construction of a genetic linkage map and QTL analysis in Taxodium, laying the groundwork for the construction of a high-density genetic map and QTL mapping in the genus Taxodium.
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Affiliation(s)
- Ziyang Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014 Jiangsu China
| | - Yanli Cheng
- Key Laboratory of Forest Genetics and Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Yunlong Yin
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014 Jiangsu China
| | - Chaoguang Yu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014 Jiangsu China
| | - Ying Yang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014 Jiangsu China
| | - Qin Shi
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014 Jiangsu China
| | - Ziyuan Hao
- Key Laboratory of Forest Genetics and Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Huogen Li
- Key Laboratory of Forest Genetics and Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
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Determination of epigenetic inheritance, genetic inheritance, and estimation of genome DNA methylation in a full-sib family of Cupressus sempervirens L. Gene 2015; 562:180-7. [DOI: 10.1016/j.gene.2015.02.068] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 02/01/2023]
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Lind M, Källman T, Chen J, Ma XF, Bousquet J, Morgante M, Zaina G, Karlsson B, Elfstrand M, Lascoux M, Stenlid J. A Picea abies linkage map based on SNP markers identifies QTLs for four aspects of resistance to Heterobasidion parviporum infection. PLoS One 2014; 9:e101049. [PMID: 25036209 PMCID: PMC4103950 DOI: 10.1371/journal.pone.0101049] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 06/03/2014] [Indexed: 02/05/2023] Open
Abstract
A consensus linkage map of Picea abies, an economically important conifer, was constructed based on the segregation of 686 SNP markers in a F1 progeny population consisting of 247 individuals. The total length of 1889.2 cM covered 96.5% of the estimated genome length and comprised 12 large linkage groups, corresponding to the number of haploid P. abies chromosomes. The sizes of the groups (from 5.9 to 9.9% of the total map length) correlated well with previous estimates of chromosome sizes (from 5.8 to 10.8% of total genome size). Any locus in the genome has a 97% probability to be within 10 cM from a mapped marker, which makes the map suited for QTL mapping. Infecting the progeny trees with the root rot pathogen Heterobasidion parviporum allowed for mapping of four different resistance traits: lesion length at the inoculation site, fungal spread within the sapwood, exclusion of the pathogen from the host after initial infection, and ability to prevent the infection from establishing at all. These four traits were associated with two, four, four and three QTL regions respectively of which none overlapped between the traits. Each QTL explained between 4.6 and 10.1% of the respective traits phenotypic variation. Although the QTL regions contain many more genes than the ones represented by the SNP markers, at least four markers within the confidence intervals originated from genes with known function in conifer defence; a leucoanthocyanidine reductase, which has previously been shown to upregulate during H. parviporum infection, and three intermediates of the lignification process; a hydroxycinnamoyl CoA shikimate/quinate hydroxycinnamoyltransferase, a 4-coumarate CoA ligase, and a R2R3-MYB transcription factor.
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Affiliation(s)
- Mårten Lind
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Thomas Källman
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Xiao-Fei Ma
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jean Bousquet
- Institute for Systems and Integrative Biology, Université Laval, Québec City, Québec, Canada
| | - Michele Morgante
- Dipartimento di Scienze Agrarie e Ambientali, Universita di Udine, Udine, Italy
| | - Giusi Zaina
- Dipartimento di Scienze Agrarie e Ambientali, Universita di Udine, Udine, Italy
| | | | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Abstract
In accordance with pseudo-testcross strategy, the first genetic linkage map of Eucommia ulmoides Oliv. was constructed by an F1 population of 122 plants using amplified fragment length polymorphism (AFLP) markers. A total of 22 AFLP primer combinations generated 363 polymorphic markers. We selected 289 markers segregating as 1:1 and used them for constructing the parent-specific linkage maps. Among the candidate markers, 127 markers were placed on the maternal map LF and 108 markers on the paternal map Q1. The maternal map LF spanned 1116.1 cM in 14 linkage groups with a mean map distance of 8.78 cM; the paternal map Q1 spanned 929.6 cM in 12 linkage groups with an average spacing of 8.61 cM. The estimated coverage of the genome through two methods was 78.5 and 73.9% for LF, and 76.8 and 71.2% for Q1, respectively. This map is the first linkage map of E. ulmoides and provides a basis for mapping quantitative-trait loci and breeding applications.
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Affiliation(s)
- Dawei Wang
- College of Forestry, Northwest A and F University, Yangling, Shaanxi 712100, People's Republic of China.
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de Miguel M, de Maria N, Guevara MA, Diaz L, Sáez-Laguna E, Sánchez-Gómez D, Chancerel E, Aranda I, Collada C, Plomion C, Cabezas JA, Cervera MT. Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers. BMC Genomics 2012; 13:527. [PMID: 23036012 PMCID: PMC3534022 DOI: 10.1186/1471-2164-13-527] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Accepted: 09/26/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. RESULTS We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. CONCLUSIONS This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.
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Affiliation(s)
- Marina de Miguel
- INIA-CIFOR, Departamento de Ecología y Genética Forestal, Madrid, Spain
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Guan L, Shiraishi S. Improved AFLP protocol using dual-suppression PCR and its application to species with large genomes. Mol Ecol Resour 2011; 11:854-61. [PMID: 21676205 DOI: 10.1111/j.1755-0998.2011.03029.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
To improve the amplified fragment length polymorphism assay, dual-suppression PCR was introduced into the preamplification step of the assay. The dual-suppression PCR blocked completely the amplification of fragments with the same sequence (Bsp1407I-Bsp1407I or NlaIII-NlaIII) at both ends and amplified selectively fragments with different adaptor sequences (Bsp1407I-NlaIII) at each end. Two protocols, referred to as A and B, were established for species with medium- and large-sized genomes, respectively. Both protocols incorporated the dual-suppression PCR. Protocol A resulted in high-quality electrophoretic profiles for black cottonwood and rice, which have medium-sized genomes. In protocol B, an intensely selective PCR step was added to protocol A. Protocol B yielded profiles for Japanese black pine and Japanese cedar that were improved significantly relative to protocol A: the number of strong peaks increased and that of low peaks decreased. Japanese black pine and Japanese cedar have large genomes. The optimal profiles were generated with a total of eight or nine selective nucleotides.
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Affiliation(s)
- Lanhua Guan
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 812-8581, Japan
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Kang BY, Major JE, Rajora OP. A high-density genetic linkage map of a black spruce (Picea mariana) × red spruce (Picea rubens) interspecific hybrid. Genome 2011; 54:128-43. [PMID: 21326369 DOI: 10.1139/g10-099] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genetic maps provide an important genomic resource of basic and applied significance. Spruce (Picea) has a very large genome size (between 0.85 × 1010 and 2.4 × 1010 bp; 8.5-24.0 pg/1C, a mean of 17.7 pg/1C ). We have constructed a near-saturated genetic linkage map for an interspecific backcross (BC1) hybrid of black spruce (BS; Picea mariana (Mill.) B.S.P.) and red spruce (RS; Picea rubens Sarg.), using selectively amplified microsatellite polymorphic loci (SAMPL) markers. A total of 2284 SAMPL markers were resolved using 31 SAMPL-MseI selective nucleotide primer combinations. Of these, 1216 SAMPL markers showing Mendelian segregation were mapped, whereas 1068 (46.8%) SAMPL fragments showed segregation distortion at α = 0.05. Maternal, paternal, and consensus maps consistently coalesced into 12 linkage groups, corresponding to the haploid chromosome number (1n = 1x = 12) of 12 in the genus Picea. The maternal BS map consisted of 814 markers distributed over 12 linkage groups, covering 1670 cM, with a mean map distance of 2.1 cM between adjacent markers. The paternal BS × RS map consisted of 773 markers distributed over 12 linkage groups, covering 1563 cM, with a mean map distance of 2.0 cM between adjacent markers. The consensus interspecific hybrid BC1 map consisted of 1216 markers distributed over 12 linkage groups, covering 1865 cM (98% genome coverage), with a mean map distance of 1.5 cM between adjacent markers. The genetic map reported here provides an important genomic resource in Picea, Pinaceae, and conifers.
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Affiliation(s)
- Bum-Yong Kang
- Forest Genetics and Biotechnology Group, Department of Biology, Life Sciences Centre, Dalhousie University, Halifax, NS B3H 4J1, Canada
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Kang BY, Mann IK, Major JE, Rajora OP. Near-saturated and complete genetic linkage map of black spruce (Picea mariana). BMC Genomics 2010; 11:515. [PMID: 20868486 PMCID: PMC2997009 DOI: 10.1186/1471-2164-11-515] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2010] [Accepted: 09/24/2010] [Indexed: 11/17/2022] Open
Abstract
Background Genetic maps provide an important genomic resource for understanding genome organization and evolution, comparative genomics, mapping genes and quantitative trait loci, and associating genomic segments with phenotypic traits. Spruce (Picea) genomics work is quite challenging, mainly because of extremely large size and highly repetitive nature of its genome, unsequenced and poorly understood genome, and the general lack of advanced-generation pedigrees. Our goal was to construct a high-density genetic linkage map of black spruce (Picea mariana, 2n = 24), which is a predominant, transcontinental species of the North American boreal and temperate forests, with high ecological and economic importance. Results We have developed a near-saturated and complete genetic linkage map of black spruce using a three-generation outbred pedigree and amplified fragment length polymorphism (AFLP), selectively amplified microsatellite polymorphic loci (SAMPL), expressed sequence tag polymorphism (ESTP), and microsatellite (mostly cDNA based) markers. Maternal, paternal, and consensus genetic linkage maps were constructed. The maternal, paternal, and consensus maps in our study consistently coalesced into 12 linkage groups, corresponding to the haploid chromosome number (1n = 1x = 12) of 12 in the genus Picea. The maternal map had 816 and the paternal map 743 markers distributed over 12 linkage groups each. The consensus map consisted of 1,111 markers distributed over 12 linkage groups, and covered almost the entire (> 97%) black spruce genome. The mapped markers included 809 AFLPs, 255 SAMPL, 42 microsatellites, and 5 ESTPs. Total estimated length of the genetic map was 1,770 cM, with an average of one marker every 1.6 cM. The maternal, paternal and consensus genetic maps aligned almost perfectly. Conclusion We have constructed the first high density to near-saturated genetic linkage map of black spruce, with greater than 97% genome coverage. Also, this is the first genetic map based on a three-generation outbred pedigree in the genus Picea. The genome length in P. mariana is likely to be about 1,800 cM. The genetic maps developed in our study can serve as a reference map for various genomics studies and applications in Picea and Pinaceae.
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Affiliation(s)
- Bum-Yong Kang
- Department of Biology, Life Sciences Centre, Dalhousie University, Halifax, Canada
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Li S, Chen Y, Gao H, Yin T. Potential chromosomal introgression barriers revealed by linkage analysis in a hybrid of Pinus massoniana and P. hwangshanensis. BMC PLANT BIOLOGY 2010; 10:37. [PMID: 20181290 PMCID: PMC2844070 DOI: 10.1186/1471-2229-10-37] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 02/25/2010] [Indexed: 05/28/2023]
Abstract
BACKGROUND Exploring the genetic mechanisms underlying speciation is a hot topic in modern genetics and evolutionary studies. Distortion of marker transmission ratio is frequently ascribed to selection against alleles that cause hybrid incompatibility. The natural introgression between P. massoniana and P. hwangshanensis and their distribution ranges lead to the emergence of the two species as desirable organisms to study the genetic mechanisms for speciation. RESULTS Using seeds sampled from trees at different elevations, we consistently detected sharp decreases in seed germination rates of trees in the hybrid zone, which might be due largely to the hybrid incompatibility. A genetic map was established using 192 megagametophytes from a single tree in the hybrid zone of the two species. Segregation distortion analysis revealed that the percentage of significant-segregation-distortion (SSD) markers was extremely high, accounting for more than 25% of the segregating markers. The extension range, the distortion direction, and the distortion intensity of SSD markers also varied dramatically on different linkage groups. CONCLUSIONS In this study, we display the potential chromosomal introgression barriers between P. massoniana and P. hwangshanensis. Our study provides a valuable platform for conducting genome-wide association of hybrid incompatible QTLs and/or candidate genes with marker transmission ratio distortion in the hybrid.
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Affiliation(s)
- Shuxian Li
- Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, the Key Lab of Forest Genetics and Biotechnology, Nanjing Forestry University, Nanjing, China
| | - Ying Chen
- Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, the Key Lab of Forest Genetics and Biotechnology, Nanjing Forestry University, Nanjing, China
| | - Handong Gao
- Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, the Key Lab of Forest Genetics and Biotechnology, Nanjing Forestry University, Nanjing, China
| | - Tongming Yin
- Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, the Key Lab of Forest Genetics and Biotechnology, Nanjing Forestry University, Nanjing, China
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Valledor L, Castillejo MA, Lenz C, Rodríguez R, Cañal MJ, Jorrín J. Proteomic Analysis of Pinus radiata Needles: 2-DE Map and Protein Identification by LC/MS/MS and Substitution-Tolerant Database Searching. J Proteome Res 2008; 7:2616-31. [DOI: 10.1021/pr7006285] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luis Valledor
- EPIPHYSAGE Research Group, Área de Fisiología Vegetal, Departamento B.O.S., Universidad de Oviedo, Oviedo, Spain, Instituto Universitario de Biotecnología de Asturias (IUBA), Oviedo, Spain, Proteomics Unit, Servicios Centrales de Apoyo a la Investigación-SCAI, Universidad de Córdoba, Córdoba, Spain, Plant Proteomics-Agricultural and Plant Biochemistry Research Group, Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain, and Applied Biosystems Deutschland, Frankfurter
| | - Maria A. Castillejo
- EPIPHYSAGE Research Group, Área de Fisiología Vegetal, Departamento B.O.S., Universidad de Oviedo, Oviedo, Spain, Instituto Universitario de Biotecnología de Asturias (IUBA), Oviedo, Spain, Proteomics Unit, Servicios Centrales de Apoyo a la Investigación-SCAI, Universidad de Córdoba, Córdoba, Spain, Plant Proteomics-Agricultural and Plant Biochemistry Research Group, Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain, and Applied Biosystems Deutschland, Frankfurter
| | - Christof Lenz
- EPIPHYSAGE Research Group, Área de Fisiología Vegetal, Departamento B.O.S., Universidad de Oviedo, Oviedo, Spain, Instituto Universitario de Biotecnología de Asturias (IUBA), Oviedo, Spain, Proteomics Unit, Servicios Centrales de Apoyo a la Investigación-SCAI, Universidad de Córdoba, Córdoba, Spain, Plant Proteomics-Agricultural and Plant Biochemistry Research Group, Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain, and Applied Biosystems Deutschland, Frankfurter
| | - Roberto Rodríguez
- EPIPHYSAGE Research Group, Área de Fisiología Vegetal, Departamento B.O.S., Universidad de Oviedo, Oviedo, Spain, Instituto Universitario de Biotecnología de Asturias (IUBA), Oviedo, Spain, Proteomics Unit, Servicios Centrales de Apoyo a la Investigación-SCAI, Universidad de Córdoba, Córdoba, Spain, Plant Proteomics-Agricultural and Plant Biochemistry Research Group, Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain, and Applied Biosystems Deutschland, Frankfurter
| | - Maria J. Cañal
- EPIPHYSAGE Research Group, Área de Fisiología Vegetal, Departamento B.O.S., Universidad de Oviedo, Oviedo, Spain, Instituto Universitario de Biotecnología de Asturias (IUBA), Oviedo, Spain, Proteomics Unit, Servicios Centrales de Apoyo a la Investigación-SCAI, Universidad de Córdoba, Córdoba, Spain, Plant Proteomics-Agricultural and Plant Biochemistry Research Group, Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain, and Applied Biosystems Deutschland, Frankfurter
| | - Jesús Jorrín
- EPIPHYSAGE Research Group, Área de Fisiología Vegetal, Departamento B.O.S., Universidad de Oviedo, Oviedo, Spain, Instituto Universitario de Biotecnología de Asturias (IUBA), Oviedo, Spain, Proteomics Unit, Servicios Centrales de Apoyo a la Investigación-SCAI, Universidad de Córdoba, Córdoba, Spain, Plant Proteomics-Agricultural and Plant Biochemistry Research Group, Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain, and Applied Biosystems Deutschland, Frankfurter
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Cerenak A, Satovic Z, Javornik B. Genetic mapping of hop (Humulus lupulus L.) applied to the detection of QTLs for alpha-acid content. Genome 2006; 49:485-94. [PMID: 16767173 DOI: 10.1139/g06-007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The map locations and effects of quantitative trait loci (QTLs) were estimated for alpha-acid content in hop (Humulus lupulus L.) using amplified fragment length polymorphism (AFLP) and microsatellite marker (simple sequence repeat (SSR)) genetic linkage maps constructed from a double pseudotestcross. The mapping population consisted of 111 progeny from a cross between the German hop cultivar 'Magnum', which exhibits high levels of alpha-acids, and a wild Slovene male hop, 2/1. The progeny segregated quantitatively for alpha-acid content determined in 2002, 2003, and 2004. The maternal map consisted of 96 markers mapped on 14 linkage groups defining 661.90 cM of total map distance. The paternal map included 70 markers assigned to 12 linkage groups covering 445.90 cM of hop genome. QTL analysis indicated 4 putative QTLs (alpha1, alpha2, alpha3, and alpha4) on linkage groups (LGs) 03, 01, 09, and 03 of the female map, respectively. QTLs explained 11.9%-24.8% of the phenotypic variance. The most promising QTL to be used in marker-assisted selection is alpha2, the peak of which colocated exactly with the AFLP marker. Three chalcone synthase-like genes (chs2, chs3, and chs4) involved in hop bitter acid synthesis mapped together on LG04 of the female map. Saturation of the maps, particularly the putative QTL regions, will be carried out using SSR markers, and the stability of the QTLs will be tested in the coming years.
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Mehlenbacher SA, Brown RN, Nouhra ER, Gökirmak T, Bassil NV, Kubisiak TL. A genetic linkage map for hazelnut (Corylus avellana L.) based on RAPD and SSR markers. Genome 2006; 49:122-33. [PMID: 16498462 DOI: 10.1139/g05-091] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A linkage map for European hazelnut (Corylus avellana L.) was constructed using random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers and the 2-way pseudotestcross approach. A full-sib population of 144 seedlings from the cross OSU 252.146 x OSU 414.062 was used. RAPD markers in testcross configuration, segregating 1:1, were used to construct separate maps for each parent. Fifty additional RAPD loci were assigned to linkage groups as accessory markers whose exact location could not be determined. Markers in intercross configuration, segregating 3:1, were used to pair groups in one parent with their homologues in the other. Eleven groups were identified for each parent, corresponding to the haploid chromosome number of hazelnut (n = x = 11). Thirty of the 31 SSR loci were able to be assigned to a linkage group. The maternal map included 249 RAPD and 20 SSR markers and spanned a distance of 661 cM. The paternal map included 271 RAPD and 28 SSR markers and spanned a distance of 812 cM. The maps are quite dense, with an average of 2.6 cM between adjacent markers. The S-locus, which controls pollen-stigma incompatibility, was placed on chromosome 5S where 6 markers linked within a distance of 10 cM were identified. A locus for resistance to eastern filbert blight, caused by Anisogramma anomala, was placed on chromosome 6R for which two additional markers tightly linked to the dominant allele were identified and sequenced. These maps will serve as a starting point for future studies of the hazelnut genome, including map-based cloning of important genes. The inclusion of SSR loci on the map will make it useful in other populations.
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Affiliation(s)
- Shawn A Mehlenbacher
- Department of Horticulture, Oregon State University, 4017 Agricultural and Life Sciences Building, Corvallis, OR 97331-7304, USA.
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Pelgas B, Bousquet J, Beauseigle S, Isabel N. A composite linkage map from two crosses for the species complex Picea mariana x Picea rubens and analysis of synteny with other Pinaceae. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1466-88. [PMID: 16215729 DOI: 10.1007/s00122-005-0068-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Accepted: 07/04/2005] [Indexed: 05/04/2023]
Abstract
Four individual linkage maps were constructed from two crosses for the species complex Picea mariana (Mill.) B.S.P. x Picea rubens Sarg in order to integrate their information into a composite map and to compare with other Pinaceae. For all individual linkage maps, 12 major linkage groups were recovered with 306 markers per map on average. Before building the composite linkage map, the common male parent between the two crosses made it possible to construct a reference linkage map to validate the relative position of homologous markers. The final composite map had a length of 2,319 cM (Haldane) and contained a total of 1,124 positioned markers, including 1,014 AFLPs, 3 RAPDs, 53 SSRs, and 54 ESTPs, assembled into 12 major linkage groups. Marker density of the composite map was statistically homogenous and was much higher (one marker every 2.1 cM) than that of the individual linkage maps (one marker every 5.7 to 7.1 cM). Synteny was well conserved between individual, reference, and composite linkage maps and 94% of homologous markers were colinear between the reference and composite maps. The combined information from the two crosses increased by about 24% the number of anchor markers compared to the information from any single cross. With a total number of 107 anchor markers (SSRs and ESTPs), the composite linkage map is a useful starting point for large-scale genome comparisons at the intergeneric level in the Pinaceae. Comparisons of this map with those in Pinus and Pseudotsuga allowed the identification of one breakdown in synteny where one linkage group homologous to both Picea and Pinus corresponded to two linkage groups in Pseudotsuga. Implications for the evolution of the Pinaceae genome are discussed.
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Affiliation(s)
- Betty Pelgas
- Chaire de recherche du Canada en génomique forestière et environnementale, Centre de recherche en biologie forestière, Pavillon Charles-Eugène-Marchand, Université Laval, Sainte-Foy, QC, G1K 7P4, Canada
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Yin TM, DiFazio SP, Gunter LE, Riemenschneider D, Tuskan GA. Large-scale heterospecific segregation distortion in Populus revealed by a dense genetic map. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:451-63. [PMID: 15168022 DOI: 10.1007/s00122-004-1653-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2003] [Accepted: 02/25/2004] [Indexed: 05/07/2023]
Abstract
We report the most complete genetic map to have been constructed for the genus Populus. This map includes 544 markers mapped onto 19 linkage groups, equivalent to the Populus chromosome number, with all markers displaying internally consistent linkage patterns. We estimate the genome length to be between 2,300 and 2,500 cM, based both on the observed number of crossovers in the maternal haplotypes, as well as the total observed map length. Genome coverage was estimated to be greater than 99.9% at 20 cM per marker. We did not detect obvious recombination repression in the maternal tree (a hybrid of Populus trichocarpa Hooker x P. deltoides Marsh.) compared to the paternal tree (pure P. deltoides). Finally, most markers exhibiting segregation distortion were derived from the donor parent in this backcross, and generally occurred in large contiguous blocks on two linkage groups. We hypothesize that divergent selection has occurred on chromosomal scales among the parental species used to create this pedigree, and explore the evolutionary implications of this observation. This genetic linkage map provides the most comprehensive view of the Populus genome reported to date and will prove invaluable for future inquiries into the structural and functional genomics, evolutionary biology, and genetic improvement of this ecologically important model species.
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Affiliation(s)
- T M Yin
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
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Acheré V, Faivre-Rampant P, Jeandroz S, Besnard G, Markussen T, Aragones A, Fladung M, Ritter E, Favre JM. A full saturated linkage map of Picea abies including AFLP, SSR, ESTP, 5S rDNA and morphological markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 108:1602-1613. [PMID: 14991106 DOI: 10.1007/s00122-004-1587-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2003] [Accepted: 12/19/2003] [Indexed: 05/24/2023]
Abstract
Based on an F(1) progeny of 73 individuals, two parental maps were constructed according to the double pseudo-test cross strategy. The paternal map contained 16 linkage groups for a total genetic length of 1,792 cM. The maternal map covered 1,920 cM, and consisted of 12 linkage groups. These parental maps were then integrated using 66 intercross markers. The resulting consensus map covered 2,035 cM and included 755 markers (661 AFLPs, 74 SSRs, 18 ESTPs, the 5S rDNA and the early cone formation trait) on 12 linkage groups, reflecting the haploid number of chromosomes of Picea abies. The average spacing between two adjacent markers was 2.6 cM. The presence of 39 of the SSR and/or ESTP markers from this consensus map on other published maps of different Picea and Pinus species allowed us to establish partial linkage group homologies across three P. abies maps (up to five common markers per linkage group). This first saturated linkage map of P. abies could be therefore used as a support for developing comparative genome mapping in conifers.
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Affiliation(s)
- V Acheré
- UMR INRA/UHP 1136, Tree-Microbe Interactions, Faculté des Sciences, Université Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy, France
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