51
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Chen S, Wang WJ, Su J, Wang CY, Feng AQ, Yang JY, Zeng LX, Zhu XY. Rapid identification of rice blast resistance gene by specific length amplified fragment sequencing. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1159528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Shen Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute, Guangzhou, China
| | - Wen-juan Wang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute, Guangzhou, China
| | - Jing Su
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute, Guangzhou, China
| | - Cong-ying Wang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute, Guangzhou, China
| | - Ai-qing Feng
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute, Guangzhou, China
| | - Jian-yuan Yang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute, Guangzhou, China
| | - Lie-xian Zeng
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute, Guangzhou, China
| | - Xiao-yuan Zhu
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute, Guangzhou, China
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52
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Zhao Z, Gu H, Sheng X, Yu H, Wang J, Huang L, Wang D. Genome-Wide Single-Nucleotide Polymorphisms Discovery and High-Density Genetic Map Construction in Cauliflower Using Specific-Locus Amplified Fragment Sequencing. FRONTIERS IN PLANT SCIENCE 2016; 7:334. [PMID: 27047515 PMCID: PMC4800193 DOI: 10.3389/fpls.2016.00334] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 03/04/2016] [Indexed: 05/19/2023]
Abstract
Molecular markers and genetic maps play an important role in plant genomics and breeding studies. Cauliflower is an important and distinctive vegetable; however, very few molecular resources have been reported for this species. In this study, a novel, specific-locus amplified fragment (SLAF) sequencing strategy was employed for large-scale single nucleotide polymorphism (SNP) discovery and high-density genetic map construction in a double-haploid, segregating population of cauliflower. A total of 12.47 Gb raw data containing 77.92 M pair-end reads were obtained after processing and 6815 polymorphic SLAFs between the two parents were detected. The average sequencing depths reached 52.66-fold for the female parent and 49.35-fold for the male parent. Subsequently, these polymorphic SLAFs were used to genotype the population and further filtered based on several criteria to construct a genetic linkage map of cauliflower. Finally, 1776 high-quality SLAF markers, including 2741 SNPs, constituted the linkage map with average data integrity of 95.68%. The final map spanned a total genetic length of 890.01 cM with an average marker interval of 0.50 cM, and covered 364.9 Mb of the reference genome. The markers and genetic map developed in this study could provide an important foundation not only for comparative genomics studies within Brassica oleracea species but also for quantitative trait loci identification and molecular breeding of cauliflower.
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Affiliation(s)
- Zhenqing Zhao
- Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Xiaoguang Sheng
- Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Huifang Yu
- Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Jiansheng Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Long Huang
- Biomarker Technologies CorporationBeijing, China
| | - Dan Wang
- Biomarker Technologies CorporationBeijing, China
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Li M, Tang Z, Qiu L, Wang Y, Tang S, Fu S. Identification and Physical Mapping of New PCR-Based Markers Specific for the Long Arm of Rye (Secale cereale L.) Chromosome 6. J Genet Genomics 2016; 43:209-16. [PMID: 27090607 DOI: 10.1016/j.jgg.2015.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 11/14/2015] [Accepted: 11/21/2015] [Indexed: 01/15/2023]
Abstract
To effectively use elite genes on the long arm of rye chromosome 6 (the 6RL arm) in wheat breeding programs, precise and fast identification of 6RL chromatin in wheat backgrounds is necessary. PCR-based 6RL-specific markers can facilitate the detection of elite genes on 6RL in wheat breeding. However, only a limited number of 6RL-specific markers have been developed. In the present study, 300 new PCR-based 6RL-specific markers were identified using specific length amplified fragment sequencing (SLAF-seq) technology, and were further physically mapped to four regions on the 6RL arm using 6R and 6RL deletion lines. Interestingly, 127 of the 300 markers were physically localized to a region from the site between 2.3 and 2.5 to the telomere, the same region where the powdery mildew resistance gene was mapped. In addition, 95 of the 300 markers exhibit polymorphisms, which can be used to investigate the diversity of rye 6RL arms. The markers developed in this study can be used to identify given segments of 6RL in wheat backgrounds and accelerate the utilization of elite genes on 6RL in wheat breeding.
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Affiliation(s)
- Meng Li
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China; Agronomy College, Sichuan Agricultural University, Chengdu 611130, China
| | - Zongxiang Tang
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China; Agronomy College, Sichuan Agricultural University, Chengdu 611130, China
| | - Ling Qiu
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China; Agronomy College, Sichuan Agricultural University, Chengdu 611130, China
| | - Yangyang Wang
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China; Agronomy College, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuyao Tang
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China; Agronomy College, Sichuan Agricultural University, Chengdu 611130, China
| | - Shulan Fu
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu 611130, China; Agronomy College, Sichuan Agricultural University, Chengdu 611130, China.
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54
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Qiu L, Tang ZX, Li M, Fu SL. Development of new PCR-based markers specific for chromosome arms of rye (Secale cereale L.). Genome 2016; 59:159-65. [DOI: 10.1139/gen-2015-0154] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
PCR-based rye (Secale cereale L.) chromosome-specific markers can contribute to the effective utilization of elite genes of rye in wheat (Triticum aestivum L.) breeding programs. In the present study, 578 new PCR-based rye-specific markers have been developed by using specific length amplified fragment sequencing (SLAF-seq) technology, and 76 markers displayed different polymorphism among rye Kustro, Imperial, and King II. A total of 427 and 387 markers were, respectively, located on individual chromosomes and chromosome arms of Kustro by using a set of wheat–rye monosomic addition lines and 13 monotelosomic addition lines, which were derived from T. aestivum L. ‘Mianyang11’ × S. cereale L. ‘Kustro’. In addition, two sets of wheat–rye disomic addition lines, which were derived from T. aestivum L. var. Chinese Spring × S. cereale L. var. Imperial and T. aestivum L. ‘Holdfast’ × S. cereale L. var. King II, were used to test the chromosomal specificity of the 427 markers. The chromosomal locations of 281 markers were consistent among the three sets of wheat–rye addition lines. The markers developed in this study can be used to identify a given segment of rye chromosomes in wheat background and accelerate the utilization of elite genes on rye chromosomes in wheat breeding programs.
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Affiliation(s)
- Ling Qiu
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People’s Republic of China
| | - Zong-xiang Tang
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People’s Republic of China
- Institute of Ecological Agricultural, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People’s Republic of China
| | - Meng Li
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People’s Republic of China
| | - Shu-lan Fu
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People’s Republic of China
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Zheng W, Li Z, Zhao J, Zhang Y, Wang C, Lu X, Sun F. Study of the long-distance migration of small brown planthoppers Laodelphax striatellus in China using next-generation sequencing. PEST MANAGEMENT SCIENCE 2016; 72:298-305. [PMID: 25684265 DOI: 10.1002/ps.3992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 02/08/2015] [Accepted: 02/09/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND The small brown planthopper (Laodelphax striatellus) is a widespread insect pest of rice in East Asia. Previous studies have shown the long-distance migrations undertaken by L. striatellus, but have not provided molecular evidence to support this. RESULTS Long-distance immigration has occurred in the north-east coastal rice-growing region of China. Using the specific-locus amplified fragment sequencing technique, sequence data for 2.7 Gb of an abruptly increased population and 13 L. striatellus local populations from a range of regions in China that have serious rice stripe disease were obtained. A total of 2572 single nucleotide polymorphisms (SNPs) and 37 indels were detected, and the genotypes of many polymorphism sites were heterozygous in every sample, which indicated that there were rich genetic differences among the populations, and that the migration of insect pests accelerated the gene flow and increased the heterozygosity of L. striatellus populations. The genetic distance and the polymorphism markers among different populations showed that the abruptly increased population in Liaoning Province is close to several populations from Jiangsu Province and Shandong Province. CONCLUSION The vector that caused rice stripe disease in the north-east of China was an immigrant population; however, the population may be formed from several groups from different areas, such as Jiangsu and Shandong provinces.
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Affiliation(s)
- Wenjing Zheng
- The Crop Molecular Improving Laboratory, Liaoning Innovation Centre, Academy of Agriculture Sciences, Shenyang, China
| | - Zhiqiang Li
- Liaoning Plant Protection Institute, Academy of Agriculture Sciences, Shenyang, China
| | - Jiaming Zhao
- The Crop Molecular Improving Laboratory, Liaoning Innovation Centre, Academy of Agriculture Sciences, Shenyang, China
| | - Yanzhi Zhang
- Liaoning Rice Research Institute, Academy of Agriculture Sciences, Shenyang, China
| | - Changhua Wang
- Liaoning Rice Research Institute, Academy of Agriculture Sciences, Shenyang, China
| | - Xiaochun Lu
- The Crop Molecular Improving Laboratory, Liaoning Innovation Centre, Academy of Agriculture Sciences, Shenyang, China
| | - Fuyu Sun
- Liaoning Plant Protection Institute, Academy of Agriculture Sciences, Shenyang, China
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Rapid Identification of Candidate Genes for Seed Weight Using the SLAF-Seq Method in Brassica napus. PLoS One 2016; 11:e0147580. [PMID: 26824525 PMCID: PMC4732658 DOI: 10.1371/journal.pone.0147580] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/04/2016] [Indexed: 11/30/2022] Open
Abstract
Seed weight is a critical and direct trait for oilseed crop seed yield. Understanding its genetic mechanism is of great importance for yield improvement in Brassica napus breeding. Two hundred and fifty doubled haploid lines derived by microspore culture were developed from a cross between a large-seed line G-42 and a small-seed line 7–9. According to the 1000-seed weight (TSW) data, the individual DNA of the heaviest 46 lines and the lightest 47 lines were respectively selected to establish two bulked DNA pools. A new high-throughput sequencing technology, Specific Locus Amplified Fragment Sequencing (SLAF-seq), was used to identify candidate genes of TSW in association analysis combined with bulked segregant analysis (BSA). A total of 1,933 high quality polymorphic SLAF markers were developed and 4 associated markers of TSW were procured. A hot region of ~0.58 Mb at nucleotides 25,401,885–25,985,931 on ChrA09 containing 91 candidate genes was identified as tightly associated with the TSW trait. From annotation information, four genes (GSBRNA2T00037136001, GSBRNA2T00037157001, GSBRNA2T00037129001 and GSBRNA2T00069389001) might be interesting candidate genes that are highly related to seed weight.
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57
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Hu MJ, Zhang HP, Liu K, Cao JJ, Wang SX, Jiang H, Wu ZY, Lu J, Zhu XF, Xia XC, Sun GL, Ma CX, Chang C. Cloning and Characterization of TaTGW-7A Gene Associated with Grain Weight in Wheat via SLAF-seq-BSA. FRONTIERS IN PLANT SCIENCE 2016; 7:1902. [PMID: 28066462 PMCID: PMC5167734 DOI: 10.3389/fpls.2016.01902] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/01/2016] [Indexed: 05/18/2023]
Abstract
Thousand-grain weight (TGW) of wheat (Triticum aestivum L.) contributes significantly to grain yield. In the present study, a candidate gene associated with TGW was identified through specific-locus amplified fragment sequencing (SLAF-seq) of DNA bulks of recombinant inbred lines (RIL) derived from the cross between Jing 411 and Hongmangchun 21. The gene was located on chromosome 7A, designated as TaTGW-7A with a complete genome sequence and an open reading frame (ORF). A single nucleotide polymorphism (SNP) was present in the first exon between two alleles at TaTGW-7A locus, resulting in a Val to Ala substitution, corresponding to a change from higher to lower TGW. Cleaved amplified polymorphic sequence (CAPS) (TGW7A) and InDel (TG9) markers were developed to discriminate the two alleles TaTGW-7Aa and TaTGW-7Ab for higher and lower TGW, respectively. A major QTL co-segregating with TaTGW-7A explained 21.7-27.1% of phenotypic variance for TGW in the RIL population across five environments. The association of TaTGW-7A with TGW was further validated in a natural population and Chinese mini-core collections. Quantitative real-time PCR revealed higher transcript levels of TaTGW-7Aa than those of TaTGW-7Ab during grain development. High frequencies of the superior allele TaTGW-7Aa for higher TGW in Chinese mini-core collections (65.0%) and 501 wheat varieties (86.0%) indicated a strong and positive selection of this allele in wheat breeding. The molecular markers TGW7A and TG9 can be used for improvement of TGW in breeding programs.
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Affiliation(s)
- Ming-Jian Hu
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Hai-Ping Zhang
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Kai Liu
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Jia-Jia Cao
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Sheng-Xing Wang
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Hao Jiang
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Zeng-Yun Wu
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Xiao F. Zhu
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Xian-Chun Xia
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
- National Wheat Improvement Center/The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Gen-Lou Sun
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
- Department of Biology, Saint Mary’s University, HalifaxNS, Canada
| | - Chuan-Xi Ma
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Cheng Chang
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
- *Correspondence: Cheng Chang,
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Luo C, Shu B, Yao Q, Wu H, Xu W, Wang S. Construction of a High-Density Genetic Map Based on Large-Scale Marker Development in Mango Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq). FRONTIERS IN PLANT SCIENCE 2016; 7:1310. [PMID: 27625670 PMCID: PMC5003885 DOI: 10.3389/fpls.2016.01310] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/16/2016] [Indexed: 05/22/2023]
Abstract
Genetic maps are particularly important and valuable tools for quantitative trait locus (QTL) mapping and marker assisted selection (MAS) of plant with desirable traits. In this study, 173 F1 plants from a cross between Mangifera indica L. "Jin-Hwang" and M. indica L. "Irwin" and their parent plants were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction. After preprocessing, 66.02 Gb of raw data containing 330.64 M reads were obtained. A total of 318,414 SLAFs were detected, of which 156,368 were polymorphic. Finally, 6594 SLAFs were organized into a linkage map consisting of 20 linkage groups (LGs). The total length of the map was 3148.28 cM and the average distance between adjacent markers was 0.48 cM. This map could be considered, to our knowledge, the first high-density genetic map of mango, and might form the basis for fine QTL mapping and MAS of mango.
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Zhu WY, Huang L, Chen L, Yang JT, Wu JN, Qu ML, Yao DQ, Guo CL, Lian HL, He HL, Pan JS, Cai R. A High-Density Genetic Linkage Map for Cucumber (Cucumis sativus L.): Based on Specific Length Amplified Fragment (SLAF) Sequencing and QTL Analysis of Fruit Traits in Cucumber. FRONTIERS IN PLANT SCIENCE 2016; 7:437. [PMID: 27148281 PMCID: PMC4835494 DOI: 10.3389/fpls.2016.00437] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 03/21/2016] [Indexed: 05/10/2023]
Abstract
High-density genetic linkage map plays an important role in genome assembly and quantitative trait loci (QTL) fine mapping. Since the coming of next-generation sequencing, makes the structure of high-density linkage maps much more convenient and practical, which simplifies SNP discovery and high-throughput genotyping. In this research, a high-density linkage map of cucumber was structured using specific length amplified fragment sequencing, using 153 F2 populations of S1000 × S1002. The high-density genetic map composed 3,057 SLAFs, including 4,475 SNP markers on seven chromosomes, and spanned 1061.19 cM. The average genetic distance is 0.35 cM. Based on this high-density genome map, QTL analysis was performed on two cucumber fruit traits, fruit length and fruit diameter. There are 15 QTLs for the two fruit traits were detected.
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Affiliation(s)
- Wen-Ying Zhu
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Long Huang
- Biomarker Technologies CorporationBeijing, China
| | - Long Chen
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Jian-Tao Yang
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Jia-Ni Wu
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Mei-Ling Qu
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | | | - Chun-Li Guo
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Hong-Li Lian
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Huan-Le He
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Jun-Song Pan
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
- *Correspondence: Jun-Song Pan, ; Run Cai,
| | - Run Cai
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
- *Correspondence: Jun-Song Pan, ; Run Cai,
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60
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Wang J, Zhang K, Zhang X, Yan G, Zhou Y, Feng L, Ni Y, Duan X. Construction of Commercial Sweet Cherry Linkage Maps and QTL Analysis for Trunk Diameter. PLoS One 2015; 10:e0141261. [PMID: 26516760 PMCID: PMC4627659 DOI: 10.1371/journal.pone.0141261] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 10/05/2015] [Indexed: 12/03/2022] Open
Abstract
A cross between the sweet cherry (Prunus avium) cultivars ‘Wanhongzhu’ and ‘Lapins’ was performed to create a mapping population suitable for the construction of a linkage map. The specific-locus amplified fragment (SLAF) sequencing technique used as a single nucleotide polymorphism (SNP) discovery platform and generated 701 informative genotypic assays; these, along with 16 microsatellites (SSRs) and the incompatibility (S) gene, were used to build a map which comprised 8 linkage groups (LGs) and covered a genetic distance of 849.0 cM. The mean inter-marker distance was 1.18 cM and there were few gaps > 5 cM in length. Marker collinearity was maintained with the established peach genomic sequence. The map was used to show that trunk diameter (TD) is under the control of 4 loci, mapping to 3 different LGs. Different locus influenced TD at a varying stage of the tree’s development. The high density ‘W×L’ genetic linkage map has the potential to enable high-resolution identification of QTLs of agronomically relevant traits, and accelerate sweet cherry breeding.
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Affiliation(s)
- Jing Wang
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100093, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, P.R. China, Beijing, 100093, China
| | - Kaichun Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100093, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, P.R. China, Beijing, 100093, China
- * E-mail:
| | - Xiaoming Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100093, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, P.R. China, Beijing, 100093, China
| | - Guohua Yan
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100093, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, P.R. China, Beijing, 100093, China
| | - Yu Zhou
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100093, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, P.R. China, Beijing, 100093, China
| | - Laibao Feng
- Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Xiangshan Nanxincun 20, Beijing, 100093, China
| | - Yang Ni
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100093, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, P.R. China, Beijing, 100093, China
| | - Xuwei Duan
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100093, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, P.R. China, Beijing, 100093, China
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Zhu Y, Yin Y, Yang K, Li J, Sang Y, Huang L, Fan S. Construction of a high-density genetic map using specific length amplified fragment markers and identification of a quantitative trait locus for anthracnose resistance in walnut (Juglans regia L.). BMC Genomics 2015; 16:614. [PMID: 26283231 PMCID: PMC4539690 DOI: 10.1186/s12864-015-1822-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 08/07/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Walnut (Juglans regia, 2n = 32, approximately 606 Mb per 1C genome) is an economically important tree crop. Resistance to anthracnose, caused by Colletotrichum gloeosporioides, is a major objective of walnut genetic improvement in China. The recently developed specific length amplified fragment sequencing (SLAF-seq) is an efficient strategy that can obtain large numbers of markers with sufficient sequence information to construct high-density genetic maps and permits detection of quantitative trait loci (QTLs) for molecular breeding. RESULTS SLAF-seq generated 161.64 M paired-end reads. 153,820 SLAF markers were obtained, of which 49,174 were polymorphic. 13,635 polymorphic markers were sorted into five segregation types and 2,577 markers of them were used to construct genetic linkage maps: 2,395 of these fell into 16 linkage groups (LGs) for the female map, 448 markers for the male map, and 2,577 markers for the integrated map. Taking into account the size of all LGs, the marker coverage was 2,664.36 cM for the female map, 1,305.58 cM for the male map, and 2,457.82 cM for the integrated map. The average intervals between two adjacent mapped markers were 1.11 cM, 2.91 cM and 0.95 cM for three maps, respectively. 'SNP_only' markers accounted for 89.25% of the markers on the integrated map. Mapping markers contained 5,043 single nucleotide polymorphisms (SNPs) loci, which corresponded to two SNP loci per SLAF marker. According to the integrated map, we used interval mapping (Logarithm of odds, LOD > 3.0) to detect our quantitative trait. One QTL was detected for anthracnose resistance. The interval of this QTL ranged from 165.51 cM to 176.33 cM on LG14, and ten markers in this interval that were above the threshold value were considered to be linked markers to the anthracnose resistance trait. The phenotypic variance explained by each marker ranged from 16.2 to 19.9%, and their LOD scores varied from 3.22 to 4.04. CONCLUSIONS High-density genetic maps for walnut containing 16 LGs were constructed using the SLAF-seq method with an F1 population. One QTL for walnut anthracnose resistance was identified based on the map. The results will aid molecular marker-assisted breeding and walnut resistance genes identification.
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Affiliation(s)
- Yufeng Zhu
- College of Forestry, Shandong Agricultural University, No.61 Daizong Load, Taian, Shandong Provence, 271018, P. R. China.
| | - Yanfei Yin
- College of Forestry, Shandong Agricultural University, No.61 Daizong Load, Taian, Shandong Provence, 271018, P. R. China.
| | - Keqiang Yang
- College of Forestry, Shandong Agricultural University, No.61 Daizong Load, Taian, Shandong Provence, 271018, P. R. China.
| | - Jihong Li
- College of Forestry, Shandong Agricultural University, No.61 Daizong Load, Taian, Shandong Provence, 271018, P. R. China.
| | - Yalin Sang
- College of Forestry, Shandong Agricultural University, No.61 Daizong Load, Taian, Shandong Provence, 271018, P. R. China.
| | - Long Huang
- Biomarker Technologies Corporation, Beijing, P. R. China.
| | - Shu Fan
- Biomarker Technologies Corporation, Beijing, P. R. China.
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Large-Scale SNP Discovery and Genotyping for Constructing a High-Density Genetic Map of Tea Plant Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq). PLoS One 2015; 10:e0128798. [PMID: 26035838 PMCID: PMC4452719 DOI: 10.1371/journal.pone.0128798] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/30/2015] [Indexed: 11/19/2022] Open
Abstract
Genetic maps are important tools in plant genomics and breeding. The present study reports the large-scale discovery of single nucleotide polymorphisms (SNPs) for genetic map construction in tea plant. We developed a total of 6,042 valid SNP markers using specific-locus amplified fragment sequencing (SLAF-seq), and subsequently mapped them into the previous framework map. The final map contained 6,448 molecular markers, distributing on fifteen linkage groups corresponding to the number of tea plant chromosomes. The total map length was 3,965 cM, with an average inter-locus distance of 1.0 cM. This map is the first SNP-based reference map of tea plant, as well as the most saturated one developed to date. The SNP markers and map resources generated in this study provide a wealth of genetic information that can serve as a foundation for downstream genetic analyses, such as the fine mapping of quantitative trait loci (QTL), map-based cloning, marker-assisted selection, and anchoring of scaffolds to facilitate the process of whole genome sequencing projects for tea plant.
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63
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Meng Y, Huang Y, Wang Q, Wen Q, Jia J, Zhang Q, Huang G, Quan J, Shan W. Phenotypic and genetic characterization of resistance in Arabidopsis thaliana to the oomycete pathogen Phytophthora parasitica. FRONTIERS IN PLANT SCIENCE 2015; 6:378. [PMID: 26074940 PMCID: PMC4445315 DOI: 10.3389/fpls.2015.00378] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/12/2015] [Indexed: 05/28/2023]
Abstract
The interaction between Arabidopsis thaliana and the oomycete pathogen Phytophthora parasitica emerges as a model for exploring the molecular basis and evolution of recognition and host defense. Phenotypic variation and genetic analysis is essential to dissect the underlying mechanisms in plant-oomycete interaction. In this study, the reaction phenotypes of 28 A. thaliana accessions to P. parasitica strain Pp016 were examined using detached leaf infection assay. The results showed the presence of four distinct groups based on host response and disease development. Of all the accessions examined, Zurich (Zu-1) is highly resistant to P. parasitica. Microscopic characterization showed that rapid and severe hypersensitive response at the primary infection epidermal cells is associated with disease resistance. Furthermore, Zu-1 is resistant to a set of 20 diverse P. parasitica strains, which were collected from different host plants and exhibited differential specificities on a set of tobacco cultivars. However, Zu-1 is susceptible to P. parasitica when the root is inoculated, suggesting differential expression of associated resistance genes in the root and foliar tissues. Genetic analysis by crossing Zu-1 and the susceptible accession Landsberg (Ler) showed that the resistance in Zu-1 to P. parasitica is semi-dominant, as shown by infection assays of F1 progenies, and is likely conferred by a single locus, defined as RPPA1 (Zu-1) (for Resistance to P. parasitica 1), as shown by analysis of F2 segregating populations. By employing specific-locus amplified fragment sequencing (SLAF-seq) strategy to identify molecular markers potentially linked to the locus, the strongest associated region was determined to be located between 7.1 and 11.2 Mb in chromosome IV. The future cloning of RPPA1 (Zu-1) locus will facilitate improved understanding of plant broad-spectrum disease resistance to oomycete pathogens.
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Affiliation(s)
- Yuling Meng
- College of Plant Protection, Northwest A&F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Yihua Huang
- College of Plant Protection, Northwest A&F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
- College of Life Sciences, Northwest A&F UniversityYangling, China
| | - Qujiang Wen
- College of Plant Protection, Northwest A&F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Jinbu Jia
- College of Plant Protection, Northwest A&F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Qiang Zhang
- College of Plant Protection, Northwest A&F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Guiyan Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
- College of Life Sciences, Northwest A&F UniversityYangling, China
| | - Junli Quan
- College of Plant Protection, Northwest A&F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Weixing Shan
- College of Plant Protection, Northwest A&F UniversityYangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
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Cai C, Cheng FY, Wu J, Zhong Y, Liu G. The First High-Density Genetic Map Construction in Tree Peony (Paeonia Sect. Moutan) using Genotyping by Specific-Locus Amplified Fragment Sequencing. PLoS One 2015; 10:e0128584. [PMID: 26010095 PMCID: PMC4444326 DOI: 10.1371/journal.pone.0128584] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/28/2015] [Indexed: 11/29/2022] Open
Abstract
Genetic linkage maps, permitting the elucidation of genome structure, are one of most powerful genomic tools to accelerate marker-assisted breeding. However, due to a lack of sufficient user-friendly molecular markers, no genetic linkage map has been developed for tree peonies (Paeonia Sect. Moutan), a group of important horticultural plants worldwide. Specific-locus amplified fragment sequencing (SLAF-seq) is a recent molecular marker development technology that enable the large-scale discovery and genotyping of sequence-based marker in genome-wide. In this study, we performed SLAF sequencing of an F1 population, derived from the cross P. ostti ‘FenDanBai’ × P. × suffruticosa ‘HongQiao’, to identify sufficient high-quality markers for the construction of high-density genetic linkage map in tree peonies. After SLAF sequencing, a total of 78 Gb sequencing data and 285,403,225 pair-end reads were generated. We detected 309,198 high-quality SLAFs from these data, of which 85,124 (27.5%) were polymorphic. Subsequently, 3518 of the polymorphic markers, which were successfully encoded in to Mendelian segregation types, and were in conformity with the criteria of high-quality markers, were defined as effective markers and used for genetic linkage mapping. Finally, we constructed an integrated genetic map, which comprised 1189 markers on the five linkage groups, and spanned 920.699 centiMorgans (cM) with an average inter-marker distance of 0.774 cM. There were 1115 ‘SNP-only’ markers, 18 ‘InDel-only’ markers, and 56 ‘SNP&InDel’ markers on the map. Among these markers, 450 (37.85%) showed significant segregation distortion (P < 0.05). In conclusion, this investigation reported the first large-scale marker development and high-density linkage map construction for tree peony. The results of this study will serve as a solid foundation not only for marker-assisted breeding, but also for genome sequence assembly for tree peony.
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Affiliation(s)
- Changfu Cai
- Landscape Architecture College of Beijing Forestry University, National Flower Engineering Research Centre, Beijing, China
| | - Fang-Yun Cheng
- Landscape Architecture College of Beijing Forestry University, National Flower Engineering Research Centre, Beijing, China
- * E-mail:
| | - Jing Wu
- Landscape Architecture College of Beijing Forestry University, National Flower Engineering Research Centre, Beijing, China
| | - Yuan Zhong
- Landscape Architecture College of Beijing Forestry University, National Flower Engineering Research Centre, Beijing, China
| | - Gaixiu Liu
- National Peony Garden, Luoyang, Henan, China
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65
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Fu S, Chen L, Wang Y, Li M, Yang Z, Qiu L, Yan B, Ren Z, Tang Z. Oligonucleotide Probes for ND-FISH Analysis to Identify Rye and Wheat Chromosomes. Sci Rep 2015; 5:10552. [PMID: 25994088 PMCID: PMC4440213 DOI: 10.1038/srep10552] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 04/17/2015] [Indexed: 11/16/2022] Open
Abstract
Genomic in situ hybridization (GISH) has been widely used to detect rye (Secale cereale L.) chromosomes in wheat (Triticum aestivum L.) introgression lines. The routine procedure of GISH using genomic DNA of rye as a probe is time-consuming and labor-intensive because of the preparation and labeling of genomic DNA of rye and denaturing of chromosomes and probes. In this study, new oligonucleotide probes Oligo-1162, Oligo-pSc200 and Oligo-pSc250 were developed. The three new probes can be used for non-denaturing fluorescence in situ hybridization (ND-FISH) assays and replace genomic DNA of rye as a probe to discriminate rye chromosomes in wheat backgrounds. In addition, previously developed oligonucleotide probes Oligo-pSc119.2-1, Oligo-pSc119.2-2, Oligo-pTa535-1, Oligo-pTa535-2, Oligo-pTa71-2, Oligo-pAWRC.1 and Oligo-CCS1 can also be used for ND-FISH of wheat and rye. These probes have provided an easier, faster and more cost-effective method for the FISH analysis of wheat and hybrids derived from wheat × rye.
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Affiliation(s)
- Shulan Fu
- 1] Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China [2] Agronomy College, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China
| | - Lei Chen
- 1] Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China [2] Agronomy College, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China
| | - Yangyang Wang
- 1] Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China [2] Agronomy College, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China
| | - Meng Li
- 1] Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China [2] Agronomy College, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, Sichuan, People's Republic of China
| | - Ling Qiu
- 1] Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China [2] Agronomy College, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China
| | - Benju Yan
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China
| | - Zhenglong Ren
- 1] Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China [2] Agronomy College, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China
| | - Zongxiang Tang
- 1] Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China [2] Agronomy College, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China
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Rapid identification of major QTLs associated with rice grain weight and their utilization. PLoS One 2015; 10:e0122206. [PMID: 25815721 PMCID: PMC4376791 DOI: 10.1371/journal.pone.0122206] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/08/2015] [Indexed: 11/25/2022] Open
Abstract
To uncover the genetics of rice grain weight, we constructed an RIL population derived from a cross between a large grain accession M201 and a small size variety JY293. Specific Locus Amplified Fragment Sequencing (SLAF-Seq) technology was used to genotype two bulked DNA pools made from individual DNA of the heaviest 30 lines and the lightest 30 lines according to the 1000 grain weight (TGW). Bulked segregant analysis (BSA) was used to identify SLAFs strongly associated with TGW. Two marker-intensive regions at 24,600,000–24,850,000 bp and 25,000,000–25,350,000 bp on chromosome 3 were identified tightly related to the TGW. Then a linkage map of chromosome 3 was constructed with SSR markers and some SLAF derived single nucleotide polymorphisms (SNPs). Quantitative trait locus (QTL) mapping for TGW, grain length, grain width, and grain thickness revealed one major QTL in the second hot-region and two other minor QTLs for grain weight. These three QTLs displayed hierarchical effects on grain length and grain weight in order of qTGW3.2 (qGL3) qTGW3.1 (GS3) qTGW3.3. Multiple comparisons of means among the eight combinations of 3 QTLs revealed that the lines with two of three QTLs deriving from M201 displayed a large grain weight phenotype (TGW 40.2g, average data of three years) and lines with both qTGW3.1 and qTGW3.3 alleles from M201 (42.5g) had similar grain weight to the qTGW3.2 (40.8g) alone. Two strategies with similar effectiveness were proposed to improve grain weight by marker-assisted selection (MAS). One is to introduce the novel qTGW3.2 allele alone, and the other is to pyramid qTGW3.1 and qTGW3.3 alleles together. One new allele of GS3 (39 bp deletion in intron 1) and two SNPs in coding sequence of qGL3 identified in this study from M201 are useful in pyramiding elite alleles for molecular breeding for improvement of rice yield.
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67
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Zhang J, Zhang Q, Cheng T, Yang W, Pan H, Zhong J, Huang L, Liu E. High-density genetic map construction and identification of a locus controlling weeping trait in an ornamental woody plant (Prunus mume Sieb. et Zucc). DNA Res 2015; 22:183-91. [PMID: 25776277 PMCID: PMC4463843 DOI: 10.1093/dnares/dsv003] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/21/2015] [Indexed: 11/14/2022] Open
Abstract
High-density genetic map is a valuable tool for fine mapping locus controlling a specific trait especially for perennial woody plants. In this study, we firstly constructed a high-density genetic map of mei (Prunus mume) using SLAF markers, developed by specific locus amplified fragment sequencing (SLAF-seq). The linkage map contains 8,007 markers, with a mean marker distance of 0.195 cM, making it the densest genetic map for the genus Prunus. Though weeping trees are used worldwide as landscape plants, little is known about weeping controlling gene(s) (Pl). To test the utility of the high-density genetic map, we did fine-scale mapping of this important ornamental trait. In total, three statistic methods were performed progressively based on the result of inheritance analysis. Quantitative trait loci (QTL) analysis initially revealed that a locus on linkage group 7 was strongly responsible for weeping trait. Mutmap-like strategy and extreme linkage analysis were then applied to fine map this locus within 1.14 cM. Bioinformatics analysis of the locus identified some candidate genes. The successful localization of weeping trait strongly indicates that the high-density map constructed using SLAF markers is a worthy reference for mapping important traits for woody plants.
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Affiliation(s)
- Jie Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Weiru Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Junjun Zhong
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Long Huang
- Biomarker Technologies Corporation, Beijing, China
| | - Enze Liu
- Biomarker Technologies Corporation, Beijing, China
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Analysis of the Thinopyrum elongatum Transcriptome under Water Deficit Stress. Int J Genomics 2015; 2015:265791. [PMID: 25722968 PMCID: PMC4334436 DOI: 10.1155/2015/265791] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/13/2015] [Accepted: 01/20/2015] [Indexed: 12/01/2022] Open
Abstract
The transcriptome of Thinopyrum elongatum under water deficit stress was analyzed using RNA-Seq technology. The results showed that genes involved in processes of amplification of stress signaling, reductions in oxidative damage, creation of protectants, and roots development were expressed differently, which played an important role in the response to water deficit. The Th. elongatum transcriptome research highlights the activation of a large set of water deficit-related genes in this species and provides a valuable resource for future functional analysis of candidate genes in the water deficit stress response.
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Lionetti V, Giancaspro A, Fabri E, Giove SL, Reem N, Zabotina OA, Blanco A, Gadaleta A, Bellincampi D. Cell wall traits as potential resources to improve resistance of durum wheat against Fusarium graminearum. BMC PLANT BIOLOGY 2015; 15:6. [PMID: 25597920 PMCID: PMC4298115 DOI: 10.1186/s12870-014-0369-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 12/05/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND Fusarium graminearum, one of the causal agents of Fusarium Head Blight (FHB, scab), leads to severe losses in grain yield and quality due to the production of mycotoxins which are harmful to human and livestock. Different traits for FHB resistance in wheat were identified for common wheat (Triticum aestivum L.) while the sources of FHB resistance in durum wheat (Triticum turgidum ssp. Durum), one of the cereals most susceptible to F. graminearum infection, have not been found. New lines of evidence indicate that content and composition of cell wall polymers affect the susceptibility of the wall to degrading enzymes produced by pathogens during infection and can play a role in the outcome of host-pathogen interactions. The objective of our research is to identify potential cell wall biochemical traits linked to Fusariosis resistance to be transferred from a resistant common wheat to a susceptible durum wheat line. RESULTS A detailed analysis of cell wall composition in spikes isolated from a highly resistant common wheat accession "02-5B-318", a breeding line derived from the FHB-resistant Chinese cv. Sumai-3 and a high susceptible durum wheat cv. Saragolla was performed. Significant differences in lignin monolignols composition, arabinoxylan (AX) substitutions and pectin methylesterification were found between resistant and susceptible plants. We isolated and characterized a pectin methylesterase gene WheatPME1, which we found being down regulated in the FHB-resistant line and induced by fungal infection in the susceptible wheat. CONCLUSIONS Our results indicate cell wall traits differing between the FHB sensitive and resistant wheat genotypes, possibly related to FHB-resistance, and identify the line 02-5B-318R as a potential resource of such traits. Evidence suggests that WheatPME1 is involved in wheat response to F. graminearum.
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Affiliation(s)
- Vincenzo Lionetti
- />Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Angelica Giancaspro
- />Department of Soil, Plant and Food Science (DiSSPA), University of Bari “Aldo Moro”, Via G. Amendola 165/A - 70126, Bari, Italy
| | - Eleonora Fabri
- />Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Stefania L Giove
- />Department of Soil, Plant and Food Science (DiSSPA), University of Bari “Aldo Moro”, Via G. Amendola 165/A - 70126, Bari, Italy
| | - Nathan Reem
- />Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011 USA
| | - Olga A Zabotina
- />Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011 USA
| | - Antonio Blanco
- />Department of Soil, Plant and Food Science (DiSSPA), University of Bari “Aldo Moro”, Via G. Amendola 165/A - 70126, Bari, Italy
| | - Agata Gadaleta
- />Department of Soil, Plant and Food Science (DiSSPA), University of Bari “Aldo Moro”, Via G. Amendola 165/A - 70126, Bari, Italy
| | - Daniela Bellincampi
- />Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
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Guo Y, Shi G, Liu Z, Zhao Y, Yang X, Zhu J, Li K, Guo X. Using specific length amplified fragment sequencing to construct the high-density genetic map for Vitis (Vitis vinifera L. × Vitis amurensis Rupr.). FRONTIERS IN PLANT SCIENCE 2015; 6:393. [PMID: 26089826 PMCID: PMC4454882 DOI: 10.3389/fpls.2015.00393] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/16/2015] [Indexed: 05/04/2023]
Abstract
In this study, 149 F1 plants from the interspecific cross between 'Red Globe' (Vitis vinifera L.) and 'Shuangyou' (Vitis amurensis Rupr.) and the parent were used to construct a molecular genetic linkage map by using the specific length amplified fragment sequencing technique. DNA sequencing generated 41.282 Gb data consisting of 206,411,693 paired-end reads. The average sequencing depths were 68.35 for 'Red Globe,' 63.65 for 'Shuangyou,' and 8.01 for each progeny. In all, 115,629 high-quality specific length amplified fragments were detected, of which 42,279 were polymorphic. The genetic map was constructed using 7,199 of these polymorphic markers. These polymorphic markers were assigned to 19 linkage groups; the total length of the map was 1929.13 cm, with an average distance of 0.28 cm between each maker. To our knowledge, the genetic maps constructed in this study contain the largest number of molecular markers. These high-density genetic maps might form the basis for the fine quantitative trait loci mapping and molecular-assisted breeding of grape.
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Affiliation(s)
| | | | | | - Yuhui Zhao
- *Correspondence: Yuhui Zhao and Xiuwu Guo, College of Horticulture, Shenyang Agricultural University, Dongling Road 120, Shenyang, Liaoning, China ;
| | | | | | | | - Xiuwu Guo
- *Correspondence: Yuhui Zhao and Xiuwu Guo, College of Horticulture, Shenyang Agricultural University, Dongling Road 120, Shenyang, Liaoning, China ;
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Wei Q, Wang Y, Qin X, Zhang Y, Zhang Z, Wang J, Li J, Lou Q, Chen J. An SNP-based saturated genetic map and QTL analysis of fruit-related traits in cucumber using specific-length amplified fragment (SLAF) sequencing. BMC Genomics 2014; 15:1158. [PMID: 25534138 PMCID: PMC4367881 DOI: 10.1186/1471-2164-15-1158] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 12/11/2014] [Indexed: 11/29/2022] Open
Abstract
Background Cucumber, Cucumis sativus L., is an economically important vegetable crop which is processed or consumed fresh worldwide. However, the narrow genetic base in cucumber makes it difficult for constructing high-density genetic maps. The development of massively parallel genotyping methods and next-generation sequencing (NGS) technologies provides an excellent opportunity for developing single nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of horticultural traits. Specific-length amplified fragment sequencing (SLAF-seq) is a recent marker development technology that allows large-scale SNP discovery and genotyping at a reasonable cost. In this study, we constructed a high-density SNP map for cucumber using SLAF-seq and detected fruit-related QTLs. Results An F2 population of 148 individuals was developed from an intra-varietal cross between CC3 and NC76. Genomic DNAs extracted from two parents and 148 F2 individuals were subjected to high-throughput sequencing and SLAF library construction. A total of 10.76 Gb raw data and 75,024,043 pair-end reads were generated to develop 52,684 high-quality SLAFs, out of which 5,044 were polymorphic. 4,817 SLAFs were encoded and grouped into different segregation patterns. A high-resolution genetic map containing 1,800 SNPs was constructed for cucumber spanning 890.79 cM. The average distance between adjacent markers was 0.50 cM. 183 scaffolds were anchored to the SNP-based genetic map covering 46% (168.9 Mb) of the cucumber genome (367 Mb). Nine QTLs for fruit length and weight were detected, a QTL designated fl3.2 explained 44.60% of the phenotypic variance. Alignment of the SNP markers to draft genome scaffolds revealed two mis-assembled scaffolds that were validated by fluorescence in situ hybridization (FISH). Conclusions We report herein the development of evenly dispersed SNPs across cucumber genome, and for the first time an SNP-based saturated linkage map. This 1,800-locus map would likely facilitate genetic mapping of complex QTL loci controlling fruit yield, and the orientation of draft genome scaffolds. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1158) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No,1, Nanjing 210095, China.
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Li B, Tian L, Zhang J, Huang L, Han F, Yan S, Wang L, Zheng H, Sun J. Construction of a high-density genetic map based on large-scale markers developed by specific length amplified fragment sequencing (SLAF-seq) and its application to QTL analysis for isoflavone content in Glycine max. BMC Genomics 2014; 15:1086. [PMID: 25494922 PMCID: PMC4320444 DOI: 10.1186/1471-2164-15-1086] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 11/26/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Quantitative trait locus (QTL) mapping is an efficient approach to discover the genetic architecture underlying complex quantitative traits. However, the low density of molecular markers in genetic maps has limited the efficiency and accuracy of QTL mapping. In this study, specific length amplified fragment sequencing (SLAF-seq), a new high-throughput strategy for large-scale SNP discovery and genotyping based on next generation sequencing (NGS), was employed to construct a high-density soybean genetic map using recombinant inbred lines (RILs, Luheidou2×Nanhuizao, F5:8). With this map, the consistent QTLs for isoflavone content across various environments were identified. RESULTS In total, 23 Gb of data containing 87,604,858 pair-end reads were obtained. The average coverage for each SLAF marker was 11.20-fold for the female parent, 12.51-fold for the male parent, and an average of 3.98-fold for individual RILs. Among the 116,216 high-quality SLAFs obtained, 9,948 were polymorphic. The final map consisted of 5,785 SLAFs on 20 linkage groups (LGs) and spanned 2,255.18 cM in genome size with an average distance of 0.43 cM between adjacent markers. Comparative genomic analysis revealed a relatively high collinearity of 20 LGs with the soybean reference genome. Based on this map, 41 QTLs were identified that contributed to the isoflavone content. The high efficiency and accuracy of this map were evidenced by the discovery of genes encoding isoflavone biosynthetic enzymes within these loci. Moreover, 11 of these 41 QTLs (including six novel loci) were associated with isoflavone content across multiple environments. One of them, qIF20-2, contributed to a majority of isoflavone components across various environments and explained a high amount of phenotypic variance (8.7%-35.3%). This represents a novel major QTL underlying isoflavone content across various environments in soybean. CONCLUSIONS Herein, we reported a high-density genetic map for soybean. This map exhibited high resolution and accuracy. It will facilitate the identification of genes and QTLs underlying essential agronomic traits in soybean. The novel major QTL for isoflavone content is useful not only for further study on the genetic basis of isoflavone accumulation, but also for marker-assisted selection (MAS) in soybean breeding in the future.
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Affiliation(s)
- Bin Li
- />The National Key Facility for Crop Gene Resources and Genetic Improvement, NFCRI, MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Ling Tian
- />The National Key Facility for Crop Gene Resources and Genetic Improvement, NFCRI, MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Jingying Zhang
- />The National Key Facility for Crop Gene Resources and Genetic Improvement, NFCRI, MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Long Huang
- />Biomarker Technologies Corporation, Beijing, 101300 China
| | - Fenxia Han
- />The National Key Facility for Crop Gene Resources and Genetic Improvement, NFCRI, MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Shurong Yan
- />The National Key Facility for Crop Gene Resources and Genetic Improvement, NFCRI, MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Lianzheng Wang
- />The National Key Facility for Crop Gene Resources and Genetic Improvement, NFCRI, MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Hongkun Zheng
- />Biomarker Technologies Corporation, Beijing, 101300 China
| | - Junming Sun
- />The National Key Facility for Crop Gene Resources and Genetic Improvement, NFCRI, MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
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Wu K, Liu H, Yang M, Tao Y, Ma H, Wu W, Zuo Y, Zhao Y. High-density genetic map construction and QTLs analysis of grain yield-related traits in sesame (Sesamum indicum L.) based on RAD-Seq techonology. BMC PLANT BIOLOGY 2014; 14:274. [PMID: 25300176 PMCID: PMC4200128 DOI: 10.1186/s12870-014-0274-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/03/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Sesame (Sesamum indicum L., 2n = 26) is an important oilseed crop with an estimated genome size of 369 Mb. The genetic basis, including the number and locations of quantitative trait loci (QTLs) of sesame grain yield and quality remain poorly understood, due in part to the lack of reliable markers and genetic maps. Here we report on the construction of a hitherto most high-density genetic map of sesame using the restriction-site associated DNA sequencing (RAD-seq) combined with 89 PCR markers, and the identification of grain yield-related QTLs using a recombinant inbred line (RIL) population. RESULT In total, 3,769 single-nucleotide polymorphism (SNP) markers were identified from RAD-seq, and 89 polymorphic PCR markers were identified including 44 expressed sequence tag-simple sequence repeats (EST-SSRs), 10 genomic-SSRs and 35 Insertion-Deletion markers (InDels). The final map included 1,230 markers distributed on 14 linkage groups (LGs) and was 844.46 cM in length with an average of 0.69 cM between adjacent markers. Using this map and RIL population, we detected 13 QTLs on 7 LGs and 17 QTLs on 10 LGs for seven grain yield-related traits by the multiple interval mapping (MIM) and the mixed linear composite interval mapping (MCIM), respectively. Three major QTLs had been identified using MIM with R2 > 10.0% or MCIM with ha 2 > 5.0%. Two co-localized QTL groups were identified that partially explained the correlations among five yield-related traits. CONCLUSION Three thousand eight hundred and four pairs of new DNA markers including SNPs and InDels were developed by RAD-seq, and a so far most high-density genetic map was constructed based on these markers in combination with SSR markers. Several grain yield-related QTLs had been identified using this population and genetic map. We report here the first QTL mapping of yield-related traits with a high-density genetic map using a RIL population in sesame. Results of this study solidified the basis for studying important agricultural traits and implementing marker-assisted selection (MAS) toward genetic improvement in sesame.
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Affiliation(s)
- Kun Wu
- />Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Sesame Genetic Improvement Laboratory, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, Hubei 430062 China
| | - Hongyan Liu
- />Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Sesame Genetic Improvement Laboratory, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, Hubei 430062 China
| | - Minmin Yang
- />Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Sesame Genetic Improvement Laboratory, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, Hubei 430062 China
| | - Ye Tao
- />Shanghai Major Biological Medicine Technology Co., Ltd., Shanghai, 201203 China
| | - Huihui Ma
- />Fuyang Academy of Agricultural Sciences, Fuyang, Anhui 236065 China
| | - Wenxiong Wu
- />Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Sesame Genetic Improvement Laboratory, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, Hubei 430062 China
| | - Yang Zuo
- />Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Sesame Genetic Improvement Laboratory, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, Hubei 430062 China
| | - Yingzhong Zhao
- />Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Sesame Genetic Improvement Laboratory, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, Hubei 430062 China
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Qi Z, Huang L, Zhu R, Xin D, Liu C, Han X, Jiang H, Hong W, Hu G, Zheng H, Chen Q. A high-density genetic map for soybean based on specific length amplified fragment sequencing. PLoS One 2014; 9:e104871. [PMID: 25118194 PMCID: PMC4130620 DOI: 10.1371/journal.pone.0104871] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 07/17/2014] [Indexed: 11/29/2022] Open
Abstract
Soybean is an important oil seed crop, but very few high-density genetic maps have been published for this species. Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for large scale de novo discovery and genotyping of single nucleotide polymorphisms. SLAF-seq was employed in this study to obtain sufficient markers to construct a high-density genetic map for soybean. In total, 33.10 Gb of data containing 171,001,333 paired-end reads were obtained after preprocessing. The average sequencing depth was 42.29 in the Dongnong594, 56.63 in the Charleston, and 3.92 in each progeny. In total, 164,197 high-quality SLAFs were detected, of which 12,577 SLAFs were polymorphic, and 5,308 of the polymorphic markers met the requirements for use in constructing a genetic map. The final map included 5,308 markers on 20 linkage groups and was 2,655.68 cM in length, with an average distance of 0.5 cM between adjacent markers. To our knowledge, this map has the shortest average distance of adjacent markers for soybean. We report here a high-density genetic map for soybean. The map was constructed using a recombinant inbred line population and the SLAF-seq approach, which allowed the efficient development of a large number of polymorphic markers in a short time. Results of this study will not only provide a platform for gene/quantitative trait loci fine mapping, but will also serve as a reference for molecular breeding of soybean.
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Affiliation(s)
- Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China
| | - Long Huang
- Biomarker Technologies Corporation, Beijing, China
| | - Rongsheng Zhu
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China
| | - Chunyan Liu
- The Crop Research and Breeding Center of Land-Reclamation of Heilongjiang Province, Harbin, Heilongjiang, People's Republic of China
| | - Xue Han
- The Crop Research and Breeding Center of Land-Reclamation of Heilongjiang Province, Harbin, Heilongjiang, People's Republic of China
| | - Hongwei Jiang
- The Crop Research and Breeding Center of Land-Reclamation of Heilongjiang Province, Harbin, Heilongjiang, People's Republic of China
| | - Weiguo Hong
- Biomarker Technologies Corporation, Beijing, China
| | - Guohua Hu
- The Crop Research and Breeding Center of Land-Reclamation of Heilongjiang Province, Harbin, Heilongjiang, People's Republic of China
| | | | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China
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Xu X, Xu R, Zhu B, Yu T, Qu W, Lu L, Xu Q, Qi X, Chen X. A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq). FRONTIERS IN PLANT SCIENCE 2014; 5:768. [PMID: 25610449 PMCID: PMC4285734 DOI: 10.3389/fpls.2014.00768] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 12/12/2014] [Indexed: 05/18/2023]
Abstract
High-density genetic map provides an essential framework for accurate and efficient genome assembly and QTL fine mapping. Construction of high-density genetic maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. In this research, a high-density genetic map of cucumber (Cucumis sativus L.) was successfully constructed across an F2 population by a recently developed Specific Length Amplified Fragment sequencing (SLAF-seq) method. In total, 18.69 GB of data containing 93,460,000 paired-end reads were obtained after preprocessing. The average sequencing depth was 44.92 in the D8 (female parent), 42.16 in the Jin5-508 (male parent), and 5.01 in each progeny. 79,092 high-quality SLAFs were detected, of which 6784 SLAFs were polymorphic, and 1892 of the polymorphic markers met the requirements for constructing genetic map. The genetic map spanned 845.87 cm with an average genetic distance of 0.45 cm. It is a reliable linkage map for fine mapping and molecular breeding of cucumber for its high marker density and well-ordered markers.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xuehao Chen
- *Correspondence: Xuehao Chen, Department of Horticulture, School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou 225009, China e-mail:
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