Updates on Strawberry DNA Testing and Marker-Assisted Breeding at the University of Florida

References

• Akey, J., D. Sosnoski, E. Parra, S. Dios, K. Hiester, B. Su, C. Bonilla, L. Jin, and M. Shriver. 2001. Melting curve analysis of SNPs (McSNP®): A gel-free and inexpensive approach for SNP genotyping. BioTechniques 30(2):358–367. doi: 10.2144/01302tt05.
   PubMed Web of Science ®Google Scholar
• Anciro, A., J. Mangandi, S. Verma, N. Peres, V.M. Whitaker, and S. Lee. 2018. FaRCg1: A quantitative trait locus conferring resistance to Colletotrichum crown rot caused by Colletotrichum gloeosporioides in octoploid strawberry. Theor. Appl. Genet. 131(10):2167–2177. doi: 10.1007/s00122-018-3145-z.
   PubMed Web of Science ®Google Scholar
• Barbey, C.R., M.H. Hogshead, B. Harrison, A.E. Schwartz, S. Verma, Y. Oh, S. Lee, K.M. Folta, and V.M. Whitaker. 2021. Genetic analysis of methyl anthranilate, mesifurane, linalool, and other flavor compounds in cultivated strawberry (Fragaria× ananassa). Front. Plant Sci. 12:615749. doi: 10.3389/fpls.2021.615749.
   PubMed Web of Science ®Google Scholar
• Bassil, N.V., T.M. Davis, H. Zhang, S. Ficklin, M. Mittmann, T. Webster, L. Mahoney, D. Wood, E.S. Alperin, and U.R. Rosyara. 2015. Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria× ananassa. BMC. Genomics 16(1):1–30. doi: 10.1186/s12864-015-1310-1.
   PubMedGoogle Scholar
• Boyd, L.A., C. Ridout, D.M. O’Sullivan, J.E. Leach, and H. Leung. 2013. Plant–pathogen interactions: Disease resistance in modern agriculture. Trends Genet. 29(4):233–240. doi: 10.1016/j.tig.2012.10.011.
   PubMed Web of Science ®Google Scholar
• Capocasa, F., J. Scalzo, B. Mezzetti, and M. Battino. 2008. Combining quality and antioxidant attributes in the strawberry: The role of genotype. Food Chem. 111(4):872–878. doi: 10.1016/j.foodchem.2008.04.068.
   Web of Science ®Google Scholar
• Castillejo, C., V. Waurich, H. Wagner, R. Ramos, N. Oiza, P. Muñoz, J.C. Triviño, J. Caruana, Z. Liu, and N. Cobo. 2020. Allelic variation of MYB10 is the major force controlling natural variation in skin and flesh color in strawberry (Fragaria spp.) fruit. Plant Cell 32(12):3723–3749. doi: 10.1105/tpc.20.00474.
   PubMed Web of Science ®Google Scholar
• Chandler, C.K. 2005. ‘Sweet Charlie’Strawberry. J. Am. Pomol. Soc. 59:67.
   Web of Science ®Google Scholar
• Chandler, C.K., D. Legard, D. Dunigan, T. Crocker, and C. Sims. 2000. ‘Strawberry festival’ strawberry. HortScience. 35(7):1366–1367. doi: 10.21273/HORTSCI.35.7.1366.
   Web of Science ®Google Scholar
• Chandler, C.K., B.M. Santos, N.A. Peres, C. Jouquand, and A. Plotto. 2009. ‘Florida Elyana’Strawberry. HortScience. 44(6):1775–1776. doi: 10.21273/HORTSCI.44.6.1775.
   Web of Science ®Google Scholar
• Chandler, C.K., B.M. Santos, N.A. Peres, C. Jouquand, A. Plotto, and C.A. Sims. 2009. ‘Florida radiance’strawberry. HortScience. 44(6):1769–1770. doi: 10.21273/HORTSCI.44.6.1769.
   Web of Science ®Google Scholar
• Das, G., J.K. Patra, and K.-H. Baek. 2017. Insight into MAS: A molecular tool for development of stress resistant and quality of rice through gene stacking. Front. Plant Sci. 8:985. doi: 10.3389/fpls.2017.00985.
   PubMed Web of Science ®Google Scholar
• Edger, P.P., T.J. Poorten, R. VanBuren, M.A. Hardigan, M. Colle, M. Mr, R.D. Smith, S.J. Teresi, A.D. Nelson, and C.M. Wai. 2019. Origin and evolution of the octoploid strawberry genome. Nat. Genet. 51(3):541–547. doi: 10.1038/s41588-019-0356-4.
   PubMed Web of Science ®Google Scholar
• Fan, Z., T. Hasing, T.S. Johnson, D.M. Garner, M.L. Schwieterman, C.R. Barbey, T.A. Colquhoun, C.A. Sims, M.F. Resende, and V.M. Whitaker. 2021. Strawberry sweetness and consumer preference are enhanced by specific volatile compounds. Hortic. Res. 8(1). doi: 10.1038/s41438-021-00502-5.
   Web of Science ®Google Scholar
• Fan, Z., D.M. Tieman, S.J. Knapp, P. Zerbe, R. Famula, C.R. Barbey, K.M. Folta, R.R. Amadeu, M. Lee, and Y. Oh. 2022. A multi‐omics framework reveals strawberry flavor genes and their regulatory elements. New Phytol. 236(3):1089–1107. doi: 10.1111/nph.18416.
   PubMed Web of Science ®Google Scholar
• Fan, Z., S. Verma, H. Lee, Y.J. Jang, Y. Wang, S. Lee, and V.M. Whitaker. 2023. Strawberry soluble solids QTL with inverse effects on yield. Hortic. Res. 11(2):uhad271. doi: 10.1093/hr/uhad271.
   PubMed Web of Science ®Google Scholar
• Francisco, M., K.D. Lazaruk, M.D. Rhodes, and M.H. Wenz. 2005. Assessment of two flexible and compatible SNP genotyping platforms: TaqMan® SNP genotyping assays and the SNPlex™ genotyping system. Mutat. Res-Fund. Mol 573(1–2):111–135. doi: 10.1016/j.mrfmmm.2005.01.008.
   PubMed Web of Science ®Google Scholar
• Han, H., C.R. Barbey, Z. Fan, S. Verma, V. Whitaker, and S. Lee. 2022. Telomere-to-telomere and haplotype-phased genome assemblies of the heterozygous octoploid′ Florida brilliance′ strawberry (Fragaria× ananassa). BioRxiv. 2022.2010. 2005.509768.
   Google Scholar
• Hardigan, M.A., M.J. Feldmann, A. Lorant, K.A. Bird, R. Famula, C. Acharya, G. Cole, P.P. Edger, and S.J. Knapp. 2020. Genome synteny has been conserved among the octoploid progenitors of cultivated strawberry over millions of years of evolution. Front. Plant Sci. 10:1789. doi: 10.3389/fpls.2019.01789.
   PubMed Web of Science ®Google Scholar
• Hardigan, M.A., M.J. Feldmann, D.D. Pincot, R.A. Famula, M.V. Vachev, M.A. Madera, P. Zerbe, K. Mars, P. Peluso, and D. Rank. 2021. Blueprint for phasing and assembling the genomes of heterozygous polyploids: Application to the octoploid genome of strawberry. BioRxiv. 2021.2011. 2003.467115.
   Google Scholar
• Hasan, N., S. Choudhary, N. Naaz, N. Sharma, and R.A. Laskar. 2021. Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. J. Genet. Eng. Biotechnol. 19(1):1–26. doi: 10.1186/s43141-021-00231-1.
   PubMed Web of Science ®Google Scholar
• Hernández-Martínez, N.R., C. Blanchard, D. Wells, and M.R. Salazar-Gutiérrez. 2023. Current state and future perspectives of commercial strawberry production: A review. Sci. Hortic. 312:111893. doi: 10.1016/j.scienta.2023.111893.
   Web of Science ®Google Scholar
• Jiménez, N.P., M.J. Feldmann, R.A. Famula, D.D. Pincot, M. Bjornson, G.S. Cole, and S.J. Knapp. 2023. Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry. Plant Genome. 16(1):e20275. doi: 10.1002/tpg2.20275.
   PubMed Web of Science ®Google Scholar
• Kalendar, R., A.V. Shustov, I. Akhmetollayev, and U. Kairov. 2022. Designing allele-specific competitive-extension PCR-based assays for high-throughput genotyping and gene characterization. Front. Mol. Biosci. 9:773–956. doi: 10.3389/fmolb.2022.773956.
   Web of Science ®Google Scholar
• Khan, A., B. Shamrez, U. Litaf, A. Zeb, Z. Rehman, R. Naz, S.H. Khan, and A.S. Shah. 2014. Effect of sucrose solution and chemical preservatives on overall quality of strawberry fruit. J. Food Process. Technol 6:2.
   Google Scholar
• Ledda, M., N. Cobo, A. Lorant, M. Hardigan, and S. Knapp (2020) Polyoligo: A bioinformatic platform for identifying target DNA sequences for the development of sub-genome specific DNA markers in polyploid/complex genomes. Annual conference of the American Society of Horticultural Sciences (2019), Las Vegas, NV, USA, p. 21–25
   Google Scholar
• Lee, S., Y.-H. Noh, J.A. Roach, J. Mangandi, S. Verma, V.M. Whitaker, and K.R. Cearley (2016) A high-throughput genotyping system combining rapid DNA extraction and high-resolution melting analysis in allo-octoploid strawberry. Acta. Hortic. 1156:89–94.
   Google Scholar
• Mangandi, J., S. Verma, L. Osorio, N.A. Peres, E. van de Weg, and V.M. Whitaker. 2017. Pedigree-based analysis in a multiparental population of octoploid strawberry reveals QTL alleles conferring resistance to Phytophthora cactorum. G3. Genes, Genomes, Genet. 7(6):1707–1719. doi: 10.1534/g3.117.042119.
   Web of Science ®Google Scholar
• Nelson, J.R., S. Verma, N.V. Bassil, C.E. Finn, J.F. Hancock, G.S. Cole, S.J. Knapp, V.M. Whitaker, and E. Huang. 2021. Discovery of three loci increasing resistance to charcoal rot caused by macrophomina phaseolina in octoploid strawberry. G3 Genes|genomes|genet. 11(3):jkab037. doi: 10.1093/g3journal/jkab037.
   Web of Science ®Google Scholar
• Nelson, R., T. Wiesner-Hanks, R. Wisser, and P. Balint-Kurti. 2018. Navigating complexity to breed disease-resistant crops. Nat. Rev. Genet. 19(1):21–33. doi: 10.1038/nrg.2017.82.
   PubMed Web of Science ®Google Scholar
• Noh, Y.-H., S. Lee, V.M. Whitaker, K.R. Cearley, and J.-S. Cha. 2017. A high-throughput marker-assisted selection system combining rapid DNA extraction high-resolution melting and simple sequence repeat analysis: Strawberry as a model for fruit crops. J. Berry. Res. 7(1):23–31. doi: 10.3233/JBR-160145.
   Web of Science ®Google Scholar
• Oh, Y., C.R. Barbey, S. Chandra, J. Bai, Z. Fan, A. Plotto, J. Pillet, K.M. Folta, V.M. Whitaker, and S. Lee. 2021. Genomic characterization of the fruity aroma gene, FaFAD1, reveals a gene dosage effect on γ-decalactone production in strawberry (Fragaria× ananassa). Front. Plant Sci. 12:639345. doi: 10.3389/fpls.2021.639345.
   PubMed Web of Science ®Google Scholar
• Oh, Y., S. Chandra, and S. Lee. 2020. Development of subgenome-specific markers for FaRXf1 conferring resistance to bacterial angular leaf spot in allo-octoploid strawberry. Int. J. Fruit. Sci. 20(sup2):S198–S210. doi: 10.1080/15538362.2019.1709116.
   Google Scholar
• Oh, Y., J.D. Zurn, N. Bassil, P.P. Edger, S.J. Knapp, V.M. Whitaker, and S. Lee. 2019. The strawberry DNA testing handbook. HortScience. 54(12):2267–2270. doi: 10.21273/HORTSCI14387-19.
   Web of Science ®Google Scholar
• Pincot, D.D., M.J. Feldmann, M.A. Hardigan, M.V. Vachev, P.M. Henry, T.R. Gordon, M. Bjornson, A. Rodriguez, N. Cobo, and R.A. Famula. 2022. Novel Fusarium wilt resistance genes uncovered in natural and cultivated strawberry populations are found on three non-homoeologous chromosomes. Theor. Appl. Genet. 135(6):2121–2145. doi: 10.1007/s00122-022-04102-2.
   PubMed Web of Science ®Google Scholar
• Roach, J.A., S. Verma, N.A. Peres, A.R. Jamieson, W.E. van de Weg, M.C. Bink, N.V. Bassil, S. Lee, and V.M. Whitaker. 2016. FaRXf1: A locus conferring resistance to angular leaf spot caused by Xanthomonas fragariae in octoploid strawberry. Theor. Appl. Genet. 129(6):1191–1201. doi: 10.1007/s00122-016-2695-1.
   PubMed Web of Science ®Google Scholar
• Salinas, N., Z. Fan, N. Peres, S. Lee, and V.M. Whitaker. 2020. FaRCa1 confers moderate resistance to the root necrosis form of strawberry anthracnose caused by Colletotrichum acutatum. HortScience. 55(5):693–698. doi: 10.21273/HORTSCI14807-20.
   Web of Science ®Google Scholar
• Shulaev, V., D.J. Sargent, R.N. Crowhurst, T.C. Mockler, O. Folkerts, A.L. Delcher, P. Jaiswal, K. Mockaitis, A. Liston, and S.P. Mane. 2011. The genome of woodland strawberry (Fragaria vesca). Nat. Genet. 43(2):109–116. doi: 10.1038/ng.740.
   PubMed Web of Science ®Google Scholar
• Verma, S., N.V. Bassil, E. van de Weg, R.J. Harrison, A. Monfort, J.M. Hidalgo, I. Amaya, B. Denoyes, L. Mahoney, T.M. Davis , et al. (2016) Development and evaluation of the Axiom® IStraw35 384HT array for the allo-octoploid cultivated strawberry Fragaria× ananassa. Acta. Hortic. 1156:75–82. doi: 10.17660/ActaHortic.2017.1156.10.
   Google Scholar
• Verma, S., J.D. Zurn, N. Salinas, M.M. Mathey, B. Denoyes, J.F. Hancock, C.E. Finn, N.V. Bassil, and V.M. Whitaker. 2017. Clarifying sub-genomic positions of QTLs for flowering habit and fruit quality in U.S. strawberry (Fragaria×ananassa) breeding populations using pedigree-based QTL analysis. Hortic. Res. 4(1): Res. 4. doi: 10.1038/hortres.2017.62.
   Google Scholar
• Whitaker, V.M. 2011. Applications of molecular markers in strawberry. J. Berry. Res. 1(3):115–127. doi: 10.3233/BR-2011-013.
   Google Scholar
• Whitaker, V.M., C.K. Chandler, N. Peres, M.C. Do Nascimento Nunes, A. Plotto, and C.A. Sims. 2015. Sensation™ ‘Florida127’ strawberry. HortScience. 50(7):1088–1091. doi: 10.21273/HORTSCI.50.7.1088.
   Web of Science ®Google Scholar
• Whitaker, V.M., C. Dalid, L.F. Osorio, N.A. Peres, S. Verma, S. Lee, and A. Plotto. 2023. Florida pearl® ‘FL 16.78-109’ pineberry. HortScience. 58(1):143–146. doi: 10.21273/HORTSCI16951-22.
   Web of Science ®Google Scholar
• Whitaker, V.M., S.J. Knapp, M.A. Hardigan, P.P. Edger, J.P. Slovin, V. Bassil, H.T. N, K.K. Mackenzie, S. Lee, S. Jung, et al. 2020. A roadmap for research in octoploid strawberry. Hortic. Res. 7(1). doi: 10.1038/s41438-020-0252-1.
   Web of Science ®Google Scholar
• Whitaker, V.M., L.F. Osorio, N.A. Peres, Z. Fan, M. Herrington, M.C. Do Nascimento Nunes, A. Plotto, and C.A. Sims. 2017. ‘Florida beauty’strawberry. HortScience. 52:1443–1447. doi: 10.21273/HORTSCI12281-17.
   Web of Science ®Google Scholar
• Whitaker, V.M., N.A. Peres, L.F. Osorio, Z. Fan, M.C. Do Nascimento Nunes, A. Plotto, and C.A. Sims. 2019. ‘Florida brilliance’strawberry. HortScience. 54(11):2073–2077. doi: 10.21273/HORTSCI14327-19.
   Web of Science ®Google Scholar
• Wu, F., Z. Guan, and A.J. Whidden. 2020. An overview of the US and Mexico strawberry industries: FE971, 6/2015. EDIS 2016(1):4–4. doi: 10.32473/edis-fe971-2015.
   Google Scholar
• Zhou, L., J.-K. Wang, Q. Yi, Y.-Z. Wang, Y.-G. Zhu, and Z.-H. Zhang. 2007. Quantitative trait loci for seedling vigor in rice under field conditions. Field Crops Res. 100(2–3):294–301. doi: 10.1016/j.fcr.2006.08.003.
   Web of Science ®Google Scholar