Genomewide association for sugar yield in sweet sorghum

Crop Science

Volumn 55, Issue 5, 2015, Pages 2138-2148

  Burks, Payne S ^a,b   Kaiser, Chris M ^a   Hawkins, Elizabeth M ^a,c   Brown, Patrick J ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b Chromatin Inc   (United States)

^c PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SORGHUM BICOLOR;

EID: 84939516482     PISSN: 0011183X     EISSN: 14350653     Source Type: Journal    
DOI: 10.2135/cropsci2015.01.0057     Document Type: Article

References (43)

1. Browning, S.R, and B.L. Browning. 2007. Rapid and accurate haplo-type phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81(5):1084-1097. doi:10.1086/521987
2. Burks, P.S, T.J. Felderhoff, H.P. Viator, and W.L. Rooney. 2013. The influence of hybrid maturity and planting date on sweet sorghum productivity during a harvest season. Agron. J. 105(1):263. doi:10.2134/agronj2012.0317
3. Felderhoff, T.J, S.C. Murray, P.E. Klein, A. Sharma, M.T. Hamb-lin, S. Kresovich, W. Vermerris, and W.L. Rooney. 2012. QTLsfor energy-related traits in a sweet X grain sorghum [(L.) Moench] mapping population. Crop Sci. 52(5): 2040. doi:10.2135/crop-sci2011.11.0618
4. Ferraris, R. 1981. Early assessment of sweet sorghum as an agro-industrial crop. I. Varietal evaluation. Anim. Prod. Sci. 21(108):75-82. doi:10.1071/EA9810075
5. Gilmour, A.R, B. Gogel, B. Cullis, R. Thompson, and D. Butler. 2009. ASREML user guide release 3.0.
6. Glaubitz, J.C, T.M. Casstevens, F. Lu, J. Harriman, R.J. Elshire, Q. Sun, and E.S. Buckler. 2014. TASSEL-GBS: A high capacity geno-typing by sequencing analysis pipeline. PLoS ONE. 9(2): E90346.
7. Gnansounou, E, A. Dauriat, and C.E. Wyman. 2005. Refining sweet sorghum to ethanol and sugar: Economic trade-offs in the context of North China. Bioresour. Technol. 96(9):985-1002. doi:10.1016/j.biortech.2004.09.015
8. Gomez, K.A, and A.A. Gomez. 1984. Statistical procedures for agricultural research. Wiley and Son, New York.
9. Guan, Y, H. Wang, L. Qin, H. Zhang, Y. Yang, F. Gao, R. Li, and H. Wang. 2011. QTL mapping of bio-energy related traits in sorghum. Euphytica 182(3):431-440. doi:10.1007/s10681-011-0528-5
10. Gutjahr, S, A. Clement-Vidal, A. Soutiras, N. Sonderegger, S. Bracon-nier, M. Dingkuhn, and D. Luquet. 2013. Grain, sugar and biomass accumulation in photoperiod-sensitive sorghums. II. Biochemical processes at internode level and interaction with phenology. Funct. Plant Biol. 40(4):355. doi:10.1071/FP12177
11. Hamblin, M.T. 2005. Equilibrium processes cannot explain high levels of short-and medium-range linkage disequilibrium in the domesticated grass Sorghum bicolor. Genetics 171(3):1247-1256. doi:10.1534/genetics.105.041566
12. Hart, G.E, K.F. Schertz, Y. Peng, and N.H. Syed. 2001. Genetic mapping of Sorghum bicolor (L.) Moench QTLs that control variation in tillering and other morphological characters. Theor. Appl. Genet. 103(8):1232-1242. doi:10.1007/s001220100582
13. Hilson, G.R. 1916. On the inheritance of certain stem characters insorghum. Agric. J. India 11:150
14. Hoffmann-Thoma, G, K. Hinkel, P. Nicolay, and J. Willenbrink. 1996. Sucrose accumulation in sweet sorghum stem internodes in relation to growth. Physiol. Plant. 97(2):277-284. doi:10.1034/j.1399-3054.1996.970210.x
15. Jackson, P.A. 2005. Breeding for improved sugar content in sugarcane. Field Crops Res. 92(2-3):277-290. doi:10.1016/j.fcr.2005.01.024
16. Langmead, B, and S.L. Salzberg. 2012. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9(4):357-359. doi:10.1038/nmeth.1923
17. Lingle, S.E. 1987. Sucrose metabolism in the primary culm of sweet sorghum during development. Crop Sci. 27(6):1214-1219. doi:10.2135/cropsci1987.0011183X002700060025x
18. Lipka, A.E, F. Tian, Q. Wang, J. Peiffer, M. Li, P.J. Bradbury, M.A. Gore, E.S. Buckler, and Z. Zhang. 2012. GAPIT: Genome association and prediction integrated tool. Bioinformatics 28(18):2397-2399. doi:10.1093/bioinformatics/bts444
19. Lv, P, G. Ji, Y. Han, S. Hou, S. Li, X. Ma, R. Du, and G. Liu. 2013. Association analysis of sugar yield-related traits in sorghum [Sorghum bicolor (L.)]. Euphytica 193(3):419-431. doi:10.1007/s10681-013-0962-7
20. Mace, E.S, K.K. Buhariwalla, H.K. Buhariwalla, and J.H. Crouch. 2003. A high-throughput DNA extraction protocol for tropical molecular breeding programs. Plant Mol. Biol. Rep. 21(4):459-460. doi:10.1007/BF02772596
21. Mace, E.S, and D.R. Jordan. 2010. Location of major effect genes in sorghum [Sorghum bicolor (L.) Moench]. Theor. Appl. Genet. 121(7):1339-1356. doi:10.1007/s00122-010-1392-8
22. Multani, D.S, S.P. Briggs, M.A. Chamberlin, J.J. Blakeslee, A.S. Murphy, and G.S. Johal. 2003. Loss of an MDR transporter in compact stalks of maize br2 and sorghum dw3 mutants. Science 302(5642):81-84. doi:10.1126/science.1086072
23. Murray, S.C, W.L. Rooney, M.T. Hamblin, S.E. Mitchell, and S. Kresovich. 2009. Sweet sorghum genetic diversity and association mapping for Brix and height. Plant Gen. 2(1):48. doi:10.3835/plant-genome2008.10.0011
24. Murray, S.C, W.L. Rooney, S.E. Mitchell, A. Sharma, P.E. Klein, J.E. Mullet, and S. Kresovich. 2008a. Genetic improvement of sorghum as a biofuel feedstock: II. QTL for stem and leaf structural carbohydrates. Crop Sci. 48(6):2180. doi:10.2135/cropsci2008.01.0068
25. Murray, S.C, A. Sharma, W.L. Rooney, P.E. Klein, J.E. Mullet, S.E. Mitchell, and S. Kresovich. 2008b. Genetic improvement of sorghum as a biofuel feedstock: I. QTL for stem sugar and grain non-structural carbohydrates. Crop Sci. 48(6):2165. doi:10.2135/crop-sci2008.01.0016
26. Natoli, A, C. Gorni, F. Chegdani, P. Ajmone Marsan, C. Colombi, C. Lorenzoni, and A. Marocco. 2002. Identification of QTLs associated with sweet sorghum quality. Maydica 47:311-322.
27. Poland, J.A, P.J. Brown, M.E. Sorrells, and J.-L. Jannink. 2012. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE. 7(2): E32253.
28. Prasad, S, A. Singh, N. Jain, and H.C. Joshi. 2007. Ethanol production from sweet sorghum syrup for utilization as automotive fuel in India. Energy Fuels 21(4):2415-2420. doi:10.1021/ef060328z
29. R Core Team. 2014. R: A language and environment for statistical computing. http://www.R-project.org (accessed 24 June 2015).
30. Reddy, B.V, A. Ashok Kumar, and S. Ramesh. 2007. Sweet sorghum: A water saving bio-energy crop. http://oar.icrisat.org/4799/ (accessed 10 Feb. 2014).
31. Reddy, B.V, S. Ramesh, P.S. Reddy, B. Ramaiah, M. Salimath, and R. Kachapur. 2005. Sweet sorghum-A potential alternate raw material for bio-ethanol and bio-energy. Int. Sorghum Millets Newsl. 46:79-86.
32. Ritter, K.B, D.R. Jordan, S.C. Chapman, I.D. Godwin, E.S. Mace, and C. Lynne McIntyre. 2008. Identification of QTL for sugar-related traits in a sweet X grain sorghum [Sorghum bicolor (L.) Moench] recombinant inbred population. Mol. Breed. 22(3):367-384. doi:10.1007/s11032-008-9182-6
33. Rooney, W.L. 2000. Genetics and cytogenetics. In: C.W. Smith and R.A. Frederiksen, editors, Sorghum: Origin, history, technology, and production. Wiley & Sons, New York.
34. Shiringani, A.L, M. Frisch, and W. Friedt. 2010. Genetic mapping of QTLs for sugar-related traits in a RIL population of Sorghum bicolor L. Moench. Theor. Appl. Genet. 121(2):323-336. doi:10.1007/s00122-010-1312-y
35. Smith, G.A, M.O. Bagby, R.T. Lewellan, D.L. Doney, P.H. Moore, F.J. Hills, L.G. Campbell, G.J. Hogaboam, G.E. Coe, and K. Freeman. 1987. Evaluation of sweet sorghum for fermentable sugar production potential. Crop Sci. 27(4):788-793. doi:10.2135/cropsci1987.0011183X002700040037x
36. Srinivas, G, K. Satish, R. Madhusudhana, R. Nagaraja Reddy, S. Murali Mohan, and N. Seetharama. 2009. Identification of quantitative trait loci for agronomically important traits and their association with genic-microsatellite markers in sorghum. Theor. Appl. Genet. 118(8):1439-1454. doi:10.1007/s00122-009-0993-6
37. Tarpley, L, and D.M. Vietor. 2007. Compartmentation of sucrose during radial transfer in mature sorghum culm. BMC Plant Biol. 7(1):33. doi:10.1186/1471-2229-7-33
38. Thurber, C.S, J.M. Ma, R.H. Higgins, and P.J. Brown. 2013. Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production. Genome Biol. 14(6):R68. doi:10.1186/gb-2013-14-6-r68
39. Wang, Y.-H, H.D. Upadhyaya, A.M. Burrell, S.M.E. Sahraeian, R.R. Klein, and P.E. Klein. 2013. Genetic structure and linkage disequilibrium in a diverse, representative collection of the C4 model plant, Sorghum bicolor. G3 GenesGenomesGenetics. 3(5): 783-793.
40. Wang, M.L, C. Zhu, N.A. Barkley, Z. Chen, J.E. Erpelding, S.C. Murray, M.R. Tuinstra, T. Tesso, G.A. Pederson, and J. Yu. 2009. Genetic diversity and population structure analysis of accessions in the US historic sweet sorghum collection. Theor. Appl. Genet. 120(1):13-23. doi:10.1007/s00122-009-1155-6
41. Wu, L, and R.G. Birch. 2007. Doubled sugar content in sugarcane plants modified to produce a sucrose isomer. Plant Biotechnol. J. 5(1):109-117. doi:10.1111/j.1467-7652.2006.00224.x
42. Xu, W, P.K. Subudhi, O.R. Crasta, D.T. Rosenow, J.E. Mullet, and H.T. Nguyen. 2000. Molecular mapping of QTLs conferring stay-green in grain sorghum [Sorghum bicolor (L.) Moench]. Genome 43(3):461-469. doi:10.1139/gen-43-3-461
43. Zegada-Lizarazu, W, and A. Monti. 2012. Are we ready to cultivate sweet sorghum as a bioenergy feedstock? A review on field management practices. Biomass Bioenergy 40:1-12. doi:10.1016/j.biom-bioe.2012.01.048