Abstract
Quantitative trait locus (QTL) mapping of sugar yield-related traits can promote the discovery of new sugar yield-related genes. Subsequently, marker-assisted selection (MAS) can be used to breed new high-yield sugar beet varieties. In this study, we observed the F1 population (219 individuals) from a cross of 3a (high-yield, low-sugar, diploid, monogerm, sterile line) and 3b (low-yield, high-sugar, diploid, polyembryonic, pollinated line) parents located in Gaomi City, Shandong Province, China. A total of four traits (root length, root perimeter, root weight, and sugar content) exhibited a normal distribution. Based on a high-density genetic map, including 3287 specific-length amplified fragment markers and nine linkage groups (LGs) with an overall genetic distance of 1554.64 cM, a total of 32 QTLs were identified for the four aforementioned traits. The QTLs were distributed on LG2, LG3, LG5, LG7, and LG9. The root length was mapped to six regions of LG2. The phenotypic variance explained (PVE) ranged from 6.30% to 8.03%. The root perimeter was mapped to five regions of LG5 and 12 regions of LG7. The largest PVE was on LG5 (7.23%). The root weight was mapped to two regions of LG3 and three regions of LG7. The four sugar content-related QTLs located on LG5 and LG9 had a threshold logarithm of odds (LOD) value of 4.35 and a max PVE of 10.13%, indicating a potentially important QTL for future gene cloning. Using trait-based QTL mapping and chromosomal marker distribution data, we identified 3690 candidate genes including 191 root length, 918 root perimeter, 409 root weight, and 2172 sugar content genes. Our results provide valuable information for additional research in fine mapping, gene functional analysis, pyramid breeding, and MAS.
Similar content being viewed by others
References
Barzen, E., W. Mechelke, E. Ritter, J.F. Seitzer, and F. Salamini. 1992. RFLP markers for sugar beet breeding: Chromosomal linkage maps and location of major genes for rhizomania resistance, monogermy and hypocotyl colour. Plant Journal 2: 601–611. https://doi.org/10.1111/j.1365-313X.1992.00601.x.
Barzen, E., W. Mechelke, E. Ritter, E. Schulte-Kappert, and F. Salamini. 1995. An extended map of the sugar beet genome containing RFLP and RAPD loci. Theoretical and Applied Genetics (Theoretische und Angewandte Genetik) 90: 189–193. https://doi.org/10.1007/BF00222201.
Dohm, J.C., A.E. Minoche, D. Holtgräwe, S. Capella-Gutiérrez, F. Zakrzewski, H. Tafer, O. Rupp, T.R. Sörensen, R. Stracke, R. Reinhardt, A. Goesmann, T. Kraft, B. Schulz, P.F. Stadler, T. Schmidt, T. Gabaldón, H. Lehrach, B. Weisshaar, and H. Himmelbauer. 2014. The genome of the recently domesticatedcrop plant sugar beet (Beta vulgaris). Nature 505: 546–549. https://doi.org/10.1038/nature12817.
Gidner, S., B.L. Lennefors, N.O. Nilsson, J. Bensefelt, E. Johansson, U. Gyllenspetz, and T. Kraft. 2005. QTL mapping of BNYVV resistance from the WB41 source in sugar beet. Genome 48: 279–285. https://doi.org/10.1139/g04-108.
Grimmer, M.K., S. Trybush, S. Hanley, S.A. Francis, A. Karp, and M.J.C.J.C. Asher. 2007. An anchored linkage map for sugar beet based on AFLP, SNP and RAPD markers and QTL mapping of a new source of resistance to beet necrotic yellow vein virus. Theoretical and Applied Genetics (Theoretische und Angewandte Genetik) 114: 1151–1160. https://doi.org/10.1007/s00122-007-0507-3.
Grimmer, M.K., T. Kraft, S.A. Francis, and M.J.C. Asher. 2008. QTL mapping of BNYVV resistance from the WB258 source in sugar beet. Plant Breeding 127: 650–652. https://doi.org/10.1111/j.1439-0523.2008.01539.x.
Halldén, C., A. Hjerdin, I.M. Rading, B. Fridlundh, G. Johannisdottir, S. Tuvesson, C. Åkesson, T. Säll, and N.O. Nilsson. 1996. A high density RFLP linkage map of sugar beet. Genome 39: 634–645. https://doi.org/10.1139/g96-081.
Janssen, G.J., M. Nihlgard, and T. Kraft. 2003. Mapping of resistance genes to powdery mildew (Erysiphe betae) in sugar beet. International Sugar Journal 105: 448–451.
Jiang, B., W.R. Liu, D.S. Xie, Q.W. Peng, X.M. He, Y.E. Lin, and Z.J. Liang. 2015. High-density genetic map construction and gene mapping of pericarp color in wax gourd using specific-locus amplified fragment (SLAF) sequencing. BMC Genomics 16: 1035. https://doi.org/10.1186/s12864-015-2220-y.
Kosambi, D.D. 1943. The estimation of map distances from recombination values. Annals of Eugenics 12: 172–175. https://doi.org/10.1111/j.1469-1809.1943.tb02321.x.
Laurent, V., P. Devaux, T. Thiel, F. Viard, S. Mielordt, P. Touzet, and M.C. Quillet. 2007. Comparative effectiveness of sugar beet microsatellite markers isolated from genomic libraries and GenBank ESTs to map the sugar beet genome. Theoretical and Applied Genetics (Theoretische und Angewandte Genetik) 115: 793–805. https://doi.org/10.1007/s00122-007-0609-y.
Li, H., and R. Durbin. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25: 1754–1760. https://doi.org/10.1093/bioinformatics/btp324.
Liu, D.Y., C.X. Ma, W.G. Hong, L. Huang, M. Liu, H. Liu, H.P. Zeng, D.J. Deng, H.G. Xin, J. Song, C.H. Xu, X.W. Sun, X.L. Hou, X.W. Wang, and H.K. Zheng. 2014. Construction and analysis of high-density linkage map using high-throughput sequencing data. PLoS ONE 9: e98855. https://doi.org/10.1371/journal.pone.0098855.
Mao, D.H., L. Yu, D.Z. Chen, L.Y. Li, Y.X. Zhu, Y.Q. Xiao, D.C. Zhang, and C.Y. Chen. 2015. Multiple cold resistance loci confer the high cold tolerance adaptation of Dongxiang wild rice (Oryza rufipogon) to its high-latitude habitat. Theoretical and Applied Genetics (Theoretische und Angewandte Genetik) 128: 1359–1371. https://doi.org/10.1007/s00122-015-2511-3.
Nilsson, N.O., M. Hansen, A.H. Panagopoulos, S. Tuvesson, M. Ehlde, M. Christiansson, I.M. Rading, M. Rissler, and T. Kraft. 1999. QTL analysis of Cercospora leaf spot resistance in sugar beet. Plant Breeding 118: 327–334. https://doi.org/10.1046/j.1439-0523.1999.00390.x.
Pillen, K., G. Steinrücken, G. Wricke, R.G. Herrmann, and C. Jung. 1992. A linkage map of sugar beet (Beta vulgaris L.). Theoretical and Applied Genetics (Theoretische und Angewandte Genetik) 84: 129–135. https://doi.org/10.1007/BF00223992.
Schneider, K., R. Schäfer-Pregl, C. Borchardt, and F. Salamini. 2002. Mapping QTLs for sucrose content, yield and quality in a sugar beet population fingerprinted by EST-related markers. Theoretical and Applied Genetics (Theoretische und Angewandte Genetik) 104: 1107–1113. https://doi.org/10.1007/s00122-002-0890-8.
Schondelmaier, J., G. Steinrucken, and C. Jung. 1996. Integration of AFLP markers into a linkage map of sugar beet (Beta vulgaris L.). Plant Breeding 115: 231–237. https://doi.org/10.1111/j.1439-0523.1996.tb00909.x.
Setiawan, A., G. Koch, S.R. Barnes, and C. Jung. 2000. Mapping quantitative trait loci (QTLs) for resistance to Cercospora leaf spot disease (Cercospora beticola Sacc.) in sugar beet (Beta vulgaris L.). Theoretical and Applied Genetics 100: 1176–1182. https://doi.org/10.1007/s001220051421.
Sun, X.W., D.Y. Liu, X.F. Zhang, W.B. Li, H. Liu, W.G. Hong, C.B. Jiang, N. Guan, C.X. Ma, H.P. Zeng, C.H. Xu, J. Song, L. Huang, C.M. Wang, J.J. Shi, R. Wang, X.H. Zheng, C.Y. Lu, X.W. Wang, and H.K. Zheng. 2013. 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.
Van Geyt, J.P.C., W. Lange, M. Oleo, and T.S.M. De Bock. 1990. Natural variation within the genus Beta and its possible use for breeding sugar beet: A review. Euphytica 49: 57–76. https://doi.org/10.1007/BF00024131.
Van Ooijen, J.W. 2004. MapQTL 5 software for the mapping of quantitative trait loci in experimental populations. Wageningen: Kyazma BV.
van Os, H., P. Stam, R.G.F. Visser, and H.J. van Eck. 2005. Smooth: A statistical method for successful removal of genotyping errors from high-density genetic linkage data. Theoretical and Applied Genetics (Theoretische und Angewandte Genetik) 112: 187–194. https://doi.org/10.1007/s00122-005-0124-y.
Wagner, H., W.E. Weber, and G. Wricke. 1992. Estimating linkage relationship of isozyme markers and morphological markers in sugar beet (Beta vulgaris L.) including families with distorted segregations. Plant Breeding 108: 89–96. https://doi.org/10.1111/j.1439-0523.1992.tb00106.x.
Wang, M.Q., B. Li, and H.Z. Wang. 2014. Construction of molecular genetic linkage map of sugarbeet. Acta Agronomica Sinica 40: 222–230. https://doi.org/10.3724/SP.J.1006.2014.00222.
Wang, J., K.C. Zhang, X.M. Zhang, G.H. Yan, Y. Zhou, L.B. Feng, Y. Ni, and X.W. Duan. 2015. Construction of commercial sweet cherry linkage maps and QTL analysis for trunk diameter. PLoS ONE 10: e0141261. https://doi.org/10.1371/journal.pone.0141261.
Wang, M.Q., B. Li, Z.D. Wu, and H.Z. Wang. 2017. QTL analysis of root yield and sugar content in sugar beet. Chinese Agricultural Science Bulletin 33: 43–47. https://doi.org/10.11924/j.issn.1000-6850.casb16120030.
Wang, M.Q., Y.H. Xu, Z.D. Wu, H.Z. Wang, and H.G. Zhang. 2018. High-density genetic map construction in sugar beet (Beta vulgaris L.) by high-throughput technology. Sugar Tech 20: 212–219. https://doi.org/10.1007/s12355-017-0550-6.
Weber, W.E., D.C. Borchardt, and G. Koch. 1999. Combined linkage maps and QTLs in sugar beet (Beta vulgaris L.) from different populations. Plant Breeding 118: 193–204. https://doi.org/10.1111/j.1439-0523.1999.tb01513.x.
Weber, W.E., D.C. Borchardt, and G. Koch. 2000. Marker analysis for quantitative traits in sugar beet. Plant Breeding 119: 97–106. https://doi.org/10.1046/j.1439-0523.2000.00482.x.
Zhang, Z., H.H. Shang, Y.Z. Shi, L. Huang, J.W. Li, Q. Ge, J.W. Gong, A.Y. Liu, T.T. Chen, D. Wang, Y.L. Wang, K.K. Palanga, J. Muhammad, W.J. Li, Q.W. Lu, X.Y. Deng, Y.N. Tan, W.W. Song, J. Cai, P.T. Li, W.K. Gong, and Y.L. Yuan. 2016. Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to quantitative trait loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum). BMC Plant Biology 16: 79. https://doi.org/10.1186/s12870-016-0741-4.
Zhu, Y.F., Y.F. Yin, K.Q. Yang, J.H. Li, Y.L. Sang, L. Huang, and S. Fan. 2015. 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 16: 614. https://doi.org/10.1186/s12864-015-1822-8.
Zhu, W.Y., L. Huang, L. Chen, J.T. Yang, J.N. Wu, M.L. Qu, D.Q. Yao, C.L. Guo, H.L. Lian, H.L. He, J.S. Pan, and R. Cai. 2016. 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 Plant Science 7: 437. https://doi.org/10.3389/fpls.2016.00437.
Acknowledgements
This work was supported by Fundamental Research Fund for the Provincial Universities Basal Research Project in Heilongjiang Province (KJCXZD201714); Fundamental Research Fund for the Provincial Universities Basal Research Project in Heilongjiang Province (KJCXZD201716); The National Sugar Industrial Technology System Project (CARS-17011306); The National Sugar Industrial Technology System Project (CARS-17011004).
Author information
Authors and Affiliations
Contributions
HZ and HW designed the study and performed the experiments; WX and ZW performed the experiments; MW, WX, and YX analyzed the data and wrote the manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no conflict of interest.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Wang, M., Xu, Y., Wang, W. et al. Quantitative Trait Locus (QTL) Mapping of Sugar Yield-Related Traits in Sugar Beet (Beta vulgaris L.). Sugar Tech 21, 135–144 (2019). https://doi.org/10.1007/s12355-018-0632-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12355-018-0632-0