Identification of SNP markers linked to the weeping trait in Prunus mume
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Prunus mume is a traditional ornamental tree with a graceful architecture that blossoms early in spring and presents beautiful flowers with a pleasant fragrance. Recently, the weeping trait has received increasing attention for its ornamental appeal and potential application to agriculture. In this study, we identified the SNPs tightly linked to the weeping trait using a linkage population based on specific-locus amplified fragment sequencing (SLAF-Seq). Six SLAF-derived SNP markers (Marker446598, Marker353041, Marker315769, Marker334902, Marker301243 and Marker311414) were validated as being tightly associated with the weeping phenotype using Sanger sequencing. The Sanger sequencing results of Marker353041 indicated that 100% of the weeping individuals and 73.3% of the upright individuals were homozygous (AA) and heterozygous (AT), respectively. Two genotypes were identified using Marker301243 with allele-specific polymerase chain reaction. All upright individuals were heterozygous (TA) and only 16.7% of the weeping individuals heterozygous (TA) in the F1 segregated population. Two marker combinations led to 89.13% predictability in the cultivars. The results suggest the application of this approach for marker-assisted breeding of P. mume and lay the foundation for the molecular breeding process of the weeping trait in woody ornamental plants.
KeywordsPrunus mume Weeping trait SNP marker Genotyping Ornamental plant
The research was supported by the program for Science and Technology of Beijing (No. Z181100002418006) and Special Fund for Beijing Common Construction Project.
SL and TZ conceived and drafted the manuscript. TZ conceived and designed the experiments. SL and XZ performed the experiments. LL and LQ analysed the data. JW and TC contributed reagents/materials/analysis tools. QZ contributed to the conception of the study and finalized the manuscript. All authors read and approved the final manuscript.
Compliance with ethical standards
Conflict of interest
The authors declare no conflict of interest and this research has been conducted in the absence of any financial or commercial relationships.
- Bakooie M, Pourjam E, Mahmoudi SB, Safaie N, Naderpour M (2018) Development of an SNP marker for sugar beet resistance/susceptible genotyping to root-knot nematode. J Agric Sci Technol 17:443–454Google Scholar
- Bertioli DJ, Cannon SB, Froenicke L, Huang G, Farmer AD, Cannon EK, Liu X, Gao D, Clevenger J, Dash S et al (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat Genet 48:438–446. https://doi.org/10.1038/ng.3517 CrossRefPubMedGoogle Scholar
- Chen J (1996) Chinese mei flowers. Hainan Publishing House, Haikou, pp 51–52Google Scholar
- Chopra R, Burow G, Farmer A, Mudge J, Simpson CE, Wilkins TA, Baring MR, Puppala N, Chamberlin KD, Burow MD (2015) Next-generation transcriptome sequencing, SNP discovery and validation in four market classes of peanut, Arachis hypogaea L.. Mol Genet Genom 290:1169–1180. https://doi.org/10.1007/s00438-014-0976-4 CrossRefGoogle Scholar
- Chopra R, Burow G, Simpson CE, Chagoya J, Mudge J, Burow MD (2016) Transcriptome sequencing of diverse peanut (Arachis) wild species and the cultivated species reveals a wealth of untapped genetic variability. G3 (Bethesda) 6:3825–3836. https://doi.org/10.1534/g3.115.02689810.1534/g3.115.026898CrossRefGoogle Scholar
- Clevenger J, Chu Y, Chavarro C, Agarwal G, Bertioli DJ, Leal-Bertioli SCM, Pandey MK, Vaughn J, Abernathy B, Barkley NA et al (2017) Genome-wide SNP genotyping resolves signatures of selection and tetrasomic recombination in peanut. Mol Plant 10:309–322. https://doi.org/10.1016/j.molp.2016.11.015 CrossRefPubMedPubMedCentralGoogle Scholar
- Hollender CA, Pascal T, Tabb A, Hadiarto T, Srinivasan C, Wang W, Liu Z, Scorza R, Dardick C (2018) Loss of a highly conserved sterile alpha motif domain gene (WEEP) results in pendulous branch growth in peach trees. Proc Natl Acad Sci USA 115:E4690–E4699. https://doi.org/10.1073/pnas.1704515115 CrossRefPubMedGoogle Scholar
- Li B, Tian L, Zhang J, Huang L, Han F, Yan S, Wang L, Zheng H, Sun J (2014) 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 Genom 15:1086CrossRefGoogle Scholar
- Mourad AMI, Sallam A, Belamkar V, Wegulo S, Bowden R, Jin Y, Mahdy E, Bakheit B, El-Wafaa AA, Poland J, Baenziger PS (2018) Genome-wide association study for identification and validation of novel SNP markers for Sr6 stem rust resistance gene in bread wheat. Front Plant Sci 9:380. https://doi.org/10.3389/fpls.2018.00380 CrossRefPubMedPubMedCentralGoogle Scholar
- Schneider K, Kulosa D, Soerensen TR, Möhring S, Heine M, Durstewitz G, Polley A, Weber E, Jamsari Lein J, Hohmann U, Tahiro E, Weisshaar B, Schulz B, Koch G, Jung C, Ganal M (2007) Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes. Theor Appl Genet 115:601–615. https://doi.org/10.1007/s00122-007-0591-4 CrossRefPubMedGoogle Scholar
- Sun X, Liu D, Zhang X, Li W, Liu H, Hong W, Jiang C, Guan N, Ma C, Zeng H, Xu C, Song J, Huang L, Wang C, Shi J, Wang R, Zheng X, Lu C, Wang X, Zheng H (2013b) SLAF-seq: An efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS ONE 8:e58700. https://doi.org/10.1371/journal.pone.0058700 CrossRefPubMedPubMedCentralGoogle Scholar