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Current Bioinformatics


ISSN (Print): 1574-8936
ISSN (Online): 2212-392X

Research Article

High-density Genetic Linkage Map Construction in Sunflower (Helianthus annuus L.) Using SNP and SSR Markers

Author(s): Pin Lyu, Jianhua Hou*, Haifeng Yu and Huimin Shi

Volume 15, Issue 8, 2020

Page: [889 - 897] Pages: 9

DOI: 10.2174/1574893615666200324134725

Price: $65


Background: Sunflower (Helianthus annuus L.) is an important oil crop only after soybean, canola and peanuts. A high-quality genetic map is the foundation of marker-assisted selection (MAS). However, for this species, the high-density maps have been reported limitedly.

Objective: In this study, we proposed the construction of a high-density genetic linkage map by the F7 population of sunflowers using SNP and SSR Markers.

Methods: The SLAF-seq strategy was employed to further develop SNP markers with SSR markers to construct the high-density genetic map by the HighMap software.

Results: A total of 1,138 million paired-end reads (226Gb) were obtained and 518,900 SLAFs were detected. Of the polymorphic SLAFs, 2,472,245 SNPs were developed and finally, 5,700 SNPs were found to be ideal to construct a genetic map after filtering. The final high-density genetic map included 4,912 SNP and 93 SSR markers distributed in 17 linkage groups (LGs) and covered 2,425.05 cM with an average marker interval of 0.49 cM.

Conclusion: The final result demonstrated that the SLAF-seq strategy is suitable for SNP markers detection. The genetic map reported in this study can be considered as one of the most highdensity genetic linkage maps of sunflower and could lay a foundation for quantitative trait loci (QTLs) fine mapping or map-based gene cloning.

Keywords: Sunflower (Helianthus annuus L.), Genetic linkage map, High-density, SLAF-seq, SNP, SSR.

Graphical Abstract
Badouin H, Gouzy J, Grassa CJ, et al. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution. Nature 2017; 546(7656): 148-52.
[] [PMID: 28538728]
Gill N, Buti M, Kane N, et al. Sequence-based analysis of structural organization and composition of the cultivated sunflower (Helianthus annuus L.) Genome. Biology (Basel) 2014; 3(2): 295-319.
[] [PMID: 24833511]
Unakıtan G, Aydın B. A comparison of energy use efficiency and economic analysis of wheat and sunflower production in Turkey: a case study in Thrace region. Energy 2018; 149: 279-85.
Harushima Y, Yano M, Shomura A, et al. A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 1998; 148(1): 479-94.
[PMID: 9475757]
Fick GN. Genetics and breeding of sunflower. J Am Oil Chem Soc 1983; 60(7): 1252-3.
Rieseberg LH, Choi H, Chan R, Spore C. Genomic map of a diploid hybrid species. Heredity 1993; 70(3): 285.
Tang S, Yu JK, Slabaugh B, Shintani K, Knapp J. Simple sequence repeat map of the sunflower genome. Theor Appl Genet 2002; 105(8): 1124-36.
[] [PMID: 12582890]
Yu J-K, Tang S, Slabaugh MB, et al. Towards a saturated molecular genetic linkage map for cultivated sunflower. Crop Sci 2003; 43(1): 367-87.
Haddadi P, Ebrahimi A, Langlade NB, et al. Genetic dissection of tocopherol and phytosterol in recombinant inbred lines of sunflower through quanti-tative trait locus analysis and the candidate gene approach. Mol Breed 2011; 29(3): 717-29.
Hatami Maleki H, Darvishzadeh R, Sarrafi A. Genetic linkage map and QTL analysis of partial resistance to black stem in sunflower (Helianthus annuus L.). Australas Plant Pathol 2013; 43(2): 205-13.
Al-Chaarani GR, Gentzbittel L, Wedzony M, Sarrafi A. Identification of QTLs for germination and seedling development in sunflower (Helianthus annuus L.). Plant Sci 2005; 169(1): 221-7.
Talukder ZI, Gong L, Hulke BS, et al. A high-density SNP Map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12. PLoS One 2014; 9(7)e98628
[] [PMID: 25014030]
Brookes AJ. The essence of SNPs. Gene 1999; 234(2): 177-86.
Yang Y, Xie B, Yan J. Application of next-generation sequencing technology in forensic science. Genom Prot Bioinform 2014; 12(5): 190-7.
[] [PMID: 25462152]
Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 2011; 12(7): 499-510.
[] [PMID: 21681211]
Elshire RJ, Glaubitz JC, Sun Q, et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 2011; 6(5)e19379
[] [PMID: 21573248]
Baird NA, Etter PD, Atwood TS, et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 2008; 3(10)e3376
[] [PMID: 18852878]
Sun X, Liu D, Zhang X, et al. SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS One 2013; 8(3)e58700
[] [PMID: 23527008]
Zhang Z, Shang H, Shi Y, et al. Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its appli-cation to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.). BMC Plant Biol 2016; 16: 79.
[] [PMID: 27067834]
Li B, Tian L, Zhang J, et al. 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(1): 1086.
Wang Z, Huai D, Zhang Z, et al. Development of a high-density genetic map based on specific length amplified fragment sequencing and its application in quantitative trait loci analysis for yield-related traits in cultivated peanut. Front Plant Sci 2018; 9: 827.
Yi L, Gao F, Siqin B, et al. Construction of an SNP-based high-density linkage map for flax (Linum usitatissimum L.) using specific length amplified fragment sequencing (SLAF-seq) technology. PLoS One 2017; 12(12)e0189785
Zhou F, Liu Y, Liang C, et al. Construction of a high-density genetic linkage map and QTL mapping of oleic acid content and three agronomic traits in sunflower (Helianthus annuus L.) using specific-locus amplified fragment sequencing (SLAF-seq). Breed Sci 2018; 68(5): 596-605.
[] [PMID: 30697121]
Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24(5): 713-4.
[] [PMID: 18227114]
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25(14): 1754-60.
[] [PMID: 19451168]
DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011; 43(5): 491-8.
[] [PMID: 21478889]
Li H, Handsaker B, Wysoker A, et al. 1000 Genome project data processing subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25(16): 2078-9.
[] [PMID: 19505943]
Lyu P, Yu H, Yu Z, et al. Construction of high-density genetic map and QTL mapping for seed germination traits in sunflower under two water condi-tions. Zuo Wu Xue Bao 2017; 43(1): 19-30.
Liu D, Ma C, Hong W, et al. Construction and analysis of high-density linkage map using high-throughput sequencing data. PLoS One 2014; 9(6)e98855
[] [PMID: 24905985]
VAN Ooijen JW JW VANO. Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Genet Res 2011; 93(5): 343-9.
[] [PMID: 21878144]
Jansen J, De Jong A, Van Ooijen JJT, Genetics A. Constructing dense genetic linkage maps. Theor Appl Genet 2001; 102(6-7): 1113-22.
Zhang Y, Wang L, Xin H, et al. Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing. BMC Plant Biology 2013; 13(1): 141.
van Os H, Stam P, Visser RG, van Eck HJ. SMOOTH: a statistical method for successful removal of genotyping errors from high-density genetic linkage data. Theor Appl Genet 2005; 112(1): 187-94.
[] [PMID: 16258753]
Huang X, Zhao Y, Wei X, et al. Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 2011; 44(1): 32-9.
[] [PMID: 22138690]
Kosambi DD. The estimation of map distances from recombination values. In DD Kosambi. Ann Hum Genet 2012; 12(1): 172-5.
Zhang J, Zhang Q, Cheng T, et al. High-density genetic map construction and identification of a locus controlling weeping trait in an ornamental wo-ody plant (Prunus mume Sieb. et Zucc). DNA Res 2015; 22(3): 183-91.
[] [PMID: 25776277]
Liu T, Guo L, Pan Y, Zhao Q, Wang J, Song Z. Construction of the first high-density genetic linkage map of Salvia miltiorrhiza using specific length amplified fragment (SLAF) sequencing. Sci Rep 2016; 6: 24070.
[] [PMID: 27040179]
Wang L, Li X, Wang L, et al. Construction of a high-density genetic linkage map in pear (Pyrus communis×Pyrus pyrifolia nakai) using SSRs and SNPs developed by SLAF-seq. Sci Hortic (Amsterdam) 2017; 218: 198-204.
Kiani SP, Talia P, Maury P, et al. Genetic analysis of plant water status and osmotic adjustment in recombinant inbred lines of sunflower under two water treatments. Plant Sci 2007; 172(4): 773-87.
Celik I, Bodur S, Frary A, Doganlar S. Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach. Mol Breed 2016; 36(9)
Bowers JE, Bachlava E, Brunick RL, Rieseberg LH, Knapp SJ, Burke JM. Development of a 10,000 locus genetic map of the sunflower genome based on multiple crosses. G3 (Bethesda) 2012; 2(7): 721-9.
[] [PMID: 22870395]
Hulke BS, Grassa CJ, Bowers JE, et al. A unified single nucleotide polymorphism map of sunflower (L.) derived from current genomic resources. Crop Sci 2015; 55(4): 1696-702.
Yang W, Zhu X-J, Huang J, Ding H, Lin H. A brief survey of machine learning methods in protein sub-golgi localization. Curr Bioinform 2019; 14(3): 234-40.
Lv H, Zhang ZM, Li SH, Tan JX, Chen W, Lin H. Evaluation of different computational methods on 5-methylcytosine sites identification. Brief Bioinform 2019; 21(3)bbz048
[PMID: 31157855]
Lai HY, Zhang ZY, Su ZD, et al. iProEP: A computational predictor for predicting promoter. Mol Ther Nucleic Acids 2019; 17: 337-46.
[] [PMID: 31299595]
Manrique-Carpintero NC, Coombs JJ, Veilleux RE, Buell CR, Douches DS. Comparative analysis of regions with distorted segregation in three di-ploid populations of potato. G3 (Bethesda) 2016; 6(8): 2617-28.
[] [PMID: 27342736]
Hussain W, Baenziger PS, Belamkar V, et al. Genotyping-by-sequencing derived high-density linkage map and its application to QTL mapping of flag leaf traits in bread wheat. Sci Rep 2017; 7(1): 16394.
[] [PMID: 29180623]

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