Hostname: page-component-77c89778f8-rkxrd Total loading time: 0 Render date: 2024-07-18T16:58:39.513Z Has data issue: false hasContentIssue false

Natural allelic variation in blueberry TERMINAL FLOWER 1

Published online by Cambridge University Press:  29 November 2016

Rupesh Gaire
Institute for Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA 30602, USA
H. Dayton Wilde*
Institute for Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA 30602, USA Horticulture Department, University of Georgia, Athens, GA 30602, USA
*Corresponding author. E-mail:


A blueberry (Vaccinium sp.) germplasm collection was screened for allelic variation in TERMINAL FLOWER 1 (TFL1) that could be used in breeding flowering or architecture traits. TFL1 has been found to repress the transition from vegetative to reproductive growth in diverse plant species, with mutations leading to altered flowering and form. The VcTFL1 gene sequence was determined from the draft genome sequence of diploid V. corymbosum line W8520. VcTFL1 is a member of a PEBP gene family and it could be distinguished from its family members by sequence comparison with PEBP family genes from other plants. High-resolution DNA melting analysis of 160 Vaccinium accessions detected VcTFL1 exons that differed in sequence from the W8520 control. DNA sequence analysis confirmed the presence of single nucleotide polymorphisms (SNPs) and identified haplotypes of tetraploid accessions. A total of 18 SNP sites were detected in VcTFL1 coding sequences of the Vaccinium germplasm screened. A SNP causing an alanine-to-valine change in exon 4 (A159V) was determined by multiple bioinformatic tools to be deleterious to VcTFL1 function. A diploid V. corymbosum accession heterozygous for the VcTFL1 mutation was identified as a candidate for breeding novel traits for blueberry.

Research Article
Copyright © NIAB 2016 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)


Adzhubei, IA, Schmidt, S, Peshkin, L, Ramensky, V, Gerasimova, A, Bork, P, Kondrashov, AS and Sunyaev, SR (2010) A method and server for predicting damaging missense mutations. Nature Methods 7: 248249.Google Scholar
Ahn, JH, Miller, D, Winter, VJ, Banfield, MJ, Lee, JH, Yoo, SY, Henz, SR, Brady, RL and Weigel, D (2006) A divergent external loop confers antagonistic activity on floral regulators FT and TFL1. EMBO Journal 25: 605614.Google Scholar
Bairoch, A and Apweiler, R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Research 28: 4548.Google Scholar
Bajaj, D, Srivastava, R, Nath, M, Tripathi, S, Bharadwaj, C, Upadhyaya, HD, Tyagi, AK and Parida, SK (2016) EcoTILLING-based association mapping efficiently delineates functionally relevant natural allelic variants of candidate genes governing agronomic traits in chickpea. Frontiers in Plant Science 7: 450. DOI: 10.3389/fpls.2016.00450.CrossRefGoogle ScholarPubMed
Ballington, JR (2001) Collection, utilization, and preservation of genetic resources in Vaccinium . HortScience 36: 213220.Google Scholar
Bendl, J, Stourac, J, Salanda, O, Pavelka, A, Wieben, ED, Zendulka, J, Brezovsky, J and Damborsky, J (2014) PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations. PLoS Computational Biology 10: e1003440.CrossRefGoogle ScholarPubMed
Bian, Y, Ballington, J, Raja, A, Brouwer, C, Reid, R, Burke, M, Wang, X, Rowland, LJ, Bassil, N and Brown, A (2014) Patterns of simple sequence repeats in cultivated blueberries (Vaccinium section Cyanococcus spp.) and their use in revealing genetic diversity and population structure. Molecular Breeding 34: 675689.CrossRefGoogle Scholar
Boches, P, Bassil, NV and Rowland, L (2006) Genetic diversity in the highbush blueberry evaluated with microsatellite markers. Journal of the American Society for Horticultural Science 131: 674686.Google Scholar
Bradley, D, Ratcliffe, O, Vincent, C, Carpenter, R and Coen, E (1997) Inflorescence commitment and architecture in Arabidopsis . Science 275: 8083.CrossRefGoogle ScholarPubMed
Cheng, J, Randall, A and Baldi, P (2006) Prediction of protein stability changes for single-site mutations using support vector machines. Proteins: Structure, Function, and Bioinformatics 62: 11251132.CrossRefGoogle ScholarPubMed
Choi, Y, Sims, GE, Murphy, S, Miller, JR and Chan, AP (2012) Predicting the functional effect of amino acid substitutions and indels. PLoS ONE 7: e46688.CrossRefGoogle ScholarPubMed
De Koeyer, D, Douglass, K, Murphy, A, Whitney, S, Nolan, L, Song, Y and De Jong, W (2010) Application of high-resolution DNA melting for genotyping and variant scanning of diploid and autotetraploid potato. Molecular Breeding 25: 6790.Google Scholar
Dhanasekar, P and Reddy, KS (2015) A novel mutation in TFL1 homolog affecting determinacy in cowpea (Vigna unguiculata). Molecular Genetics and Genomics 290: 5565.Google Scholar
Die, JV and Rowland, LJ (2013) Advent of genomics in blueberry. Molecular Breeding 32: 493504.Google Scholar
Frerichmann, SL, Kirchhoff, M, Müller, AE, Scheidig, AJ, Jung, C and Kopisch-Obuch, FJ (2013) EcoTILLING in Beta vulgaris reveals polymorphisms in the FLC-like gene BvFL1 that are associated with annuality and winter hardiness. BMC Plant Biology 13: 52. DOI: 10.1186/1471-2229-13-52.Google Scholar
Glaser, F, Pupko, T, Paz, I, Bell, RE, Bechor-Shental, D, Martz, E and Ben-Tal, N (2003) ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19: 163164.Google Scholar
Gnirke, A, Melnikov, A, Maguire, J, Rogov, P, LeProust, EM, Brockman, W, Fennell, T, Giannoukos, G, Fisher, S, Russ, C and Gabriel, S (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature Biotechnology 27: 182189.Google Scholar
Gupta, V, Estrada, AD, Blakley, I, Reid, R, Patel, K, Meyer, MD, Andersen, SU, Brown, AF, Lila, MA and Loraine, AE (2015) RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing. GigaScience 4: 5. DOI 10.1186/s13742-015-0046-9.CrossRefGoogle ScholarPubMed
Han, Y, Kang, Y, Torres-Jerez, I, Cheung, F, Town, CD, Zhao, PX, Udvardi, MK and Monteros, MJ (2011) Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis. BMC Genomics 12: 350.Google Scholar
Han, Y, Khu, DM and Monteros, MJ (2012) High-resolution melting analysis for SNP genotyping and mapping in tetraploid alfalfa (Medicago sativa L.). Molecular Breeding 29: 489501.Google Scholar
Iwata, H, Gaston, A, Remay, A, Thouroude, T, Jeauffre, J, Kawamura, K, Oyant, LH, Araki, T, Denoyes, B and Foucher, F (2012) The TFL1 homologue KSN is a regulator of continuous flowering in rose and strawberry. Plant Journal 69: 116125.Google Scholar
Kearse, M, Moir, R, Wilson, A, Stones-Havas, S, Cheung, M, Sturrock, S, Buxton, S, Cooper, A, Markowitz, S, Duran, C and Thierer, T (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 16471649.Google Scholar
Kiss, MM, Ortoleva-Donnelly, L, Reginald Beer, N, Warner, J, Bailey, CG, Colston, BW, Rothberg, JM, Link, DR and Leamon, JH (2008) High-throughput quantitative polymerase chain reaction in picoliter droplets. Analytical Chemistry 80: 89758981.Google Scholar
Koskela, EA, Sønsteby, A, Flachowsky, H, Heide, OM, Hanke, MV, Elomaa, P and Hytönen, T (2016) TERMINAL FLOWER1 is a breeding target for a novel everbearing trait and tailored flowering responses in cultivated strawberry (Fragaria × ananassa Duch.). Plant Biotechnology Journal 14: 18521861.Google Scholar
Li, B, Krishnan, VG, Mort, ME, Xin, F, Kamati, KK, Cooper, DN, Mooney, SD and Radivojac, P (2009) Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics 25: 27442750.Google Scholar
McGarry, RC and Ayre, BG (2012) Manipulating plant architecture with members of the CETS gene family. Plant Science 188: 7181.Google Scholar
Moose, SP and Mumm, RH (2008) Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiology 147: 969977.CrossRefGoogle ScholarPubMed
Muth, J, Hartje, S, Twyman, RM, Hofferbert, HR, Tacke, E and Prüfer, D (2008) Precision breeding for novel starch variants in potato. Plant Biotechnology Journal 6: 576584.CrossRefGoogle ScholarPubMed
Ng, PC and Henikoff, S (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Research 31: 3812–3214.CrossRefGoogle ScholarPubMed
Pnueli, L, Carmel-Goren, L, Hareven, D, Gutfinger, T, Alvarez, J, Ganal, M, Zamir, D and Lifschitz, E (1998) The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1. Development 125: 19791989.Google Scholar
Porebski, S, Bailey, LG and Baum, BR (1997) Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Molecular Biology Reporter 15: 815.CrossRefGoogle Scholar
Rowland, LJ, Alkharouf, N, Darwish, O, Ogden, EL, Polashock, JJ, Bassil, NV and Main, D (2012) Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation. BMC Plant Biology 12: 46.Google Scholar
Rozen, S and Skaletsky, H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz, S and Misener, S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Totowa, NJ: Humana Press, pp. 365386.Google Scholar
Stanke, M, Steinkamp, R, Waack, S and Morgenstern, B (2004) AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Research 32: W309W312.CrossRefGoogle Scholar
Tamura, K, Stecher, G, Peterson, D, Filipski, A and Kumar, S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular and Biological Evolution 30: 27252729.Google Scholar
Thomas, PD, Campbell, MJ, Kejariwal, A, Mi, H, Karlak, B, Daverman, R, Diemer, K, Muruganujan, A and Narechania, A (2003) PANTHER: a library of protein families and subfamilies indexed by function. Genome Research 13: 21292141.CrossRefGoogle Scholar
Tian, Z, Wang, X, Lee, R, Li, Y, Specht, JE, Nelson, RL, McClean, PE, Qiu, L and Ma, J (2010) Artificial selection for determinate growth habit in soybean. Proceeding of the National Academy of Science of the United States of America 107: 85638568.CrossRefGoogle ScholarPubMed
Till, BJ (2014) Mining genetic resources via Ecotilling. In: Tuberosa, R, Graner, A, Frison, E (eds) Genomics of Plant Genetic Resources. Netherlands: Springer, pp. 349365.CrossRefGoogle Scholar
Uitdewilligen, JG, Wolters, AM, Bjorn, B, Borm, TJ, Visser, RG and van Eck, HJ (2013) A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS ONE 8: e62355.Google Scholar
Vanholme, B, Cesarino, I, Goeminne, G, Kim, H, Marroni, F, Acker, R, Vanholme, R, Morreel, K, Ivens, B, Pinosio, S and Morgante, M (2013) Breeding with rare defective alleles (BRDA): a natural Populus nigra HCT mutant with modified lignin as a case study. New Phytologist 198: 765776.CrossRefGoogle ScholarPubMed
Wang, N, Shi, L, Tian, F, Ning, H, Wu, X, Long, Y and Meng, J (2010) Assessment of FAE1 polymorphisms in three Brassica species using EcoTILLING and their association with differences in seed erucic acid contents. BMC Plant Biology 10: 137. DOI: 10.1186/1471-2229-10-137.Google Scholar
Weng, J, Li, B, Liu, C, Yang, X, Wang, H, Hao, Z, Li, M, Zhang, D, Ci, X, Li, X and Zhang, S (2013) A non-synonymous SNP within the isopentenyl transferase 2 locus is associated with kernel weight in Chinese maize inbreds (Zea mays L.). BMC Plant Biology 13: 1.CrossRefGoogle ScholarPubMed
Yu, S, Liao, F, Wang, F, Wen, W, Li, J, Mei, H and Luo, L (2012) Identification of rice transcription factors associated with drought tolerance using the ecotilling method. PLoS ONE 7: e30765.Google Scholar
Supplementary material: File

Gaire and Wilde supplementary material

Table S1

Download Gaire and Wilde supplementary material(File)
File 153.1 KB
Supplementary material: File

Gaire and Wilde supplementary material

Table S2

Download Gaire and Wilde supplementary material(File)
File 31.2 KB