Abstract
Association mapping is widely used for detecting QTLs in higher plants. In the present study a synthetic sorghum population containing 119 representative samples, including 43 sweet and 76 grain sorghum accessions originating mainly from China, USA and India, were genotyped using 51 simple-sequence repeat (SSR) markers. Linkage disequilibrium (LD) of pair-wise loci and population structure were analyzed, followed by association analysis of SSR loci and 3 sugar yield related traits using the TASSEL general linear model program. Results showed that: (i) different degrees of LD occurred among syntenic markers and also among nonsyntenic markers, indicating historical recombination among sorghum linkage groups; (ii) significant LD extended up to 7.31 cM; (iii) the collection of accessions was composed of three subgroups; (iv) four marker loci were associated with stalk sugar concentration, fresh stalk weight and stalk juice weight measured in different growing environments and could be used, therefore, in future marker assisted breeding programs. Several loci were also associated with two or more traits simultaneously, which might be due to tight linkage between different genes affecting these traits and/or pleiotropy. In addition, some associated markers were located close to QTLs previously mapped in family-based linkage mapping analyses.
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Abbreviations
- LD:
-
Linkage disequilibrium
- SSR:
-
Simple sequence repeat
- QTL:
-
Quantitative trait loci
- FSW:
-
Fresh stalk weight
- SJW:
-
Stalk juice weight
References
Agrama H, Eizenga G, Yan W (2007) Association mapping of yield and its components in rice cultivars. Mol Breed 19:341–356
Bennetzen JL, Subramanian V, Xu J, Salimath SS, Subramanian S, Bhattramakki D, Hart GE (2001) A framewoke genetic map of sorghum containing RFLP, SSR, and morphological markers. In: Phillips RL, Vasil IK (eds) DNA-based markers in plants. Kluwer Academic, Boston
Bian YL, Yazaki S, Inoue M, Cai HW (2006) QTLs for sugar content of stalk in sweet sorghum (Sorghum bicolor L. Moench). Agri Sci China 5:736–744
Bouchet S, Pot D, Deu M, Rami JF, Billot C, Perrier X, Rivallan R, Gardes L, Xia L, Wenzl P (2012) Genetic structure, linkage disequilibrium and signature of selection in sorghum: lessons from physically anchored DArT markers. PLoS ONE 7:e33470
Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635
Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177
Brown P, Klein P, Bortiri E, Acharya C, Rooney W, Kresovich S (2006) Inheritance of inflorescence architecture in sorghum. Theor Appl Genet 113:931–942
Casa AM, Pressoir G, Brown PJ, Mitchell SE, Rooney WL, Tuinstra MR, Franks CD, Kresovich S (2008) Community resources and strategies for association mapping in sorghum. Crop Sci 48:30–40
Corn RJ (2009) Heterosis and composition of sweet sorghum. Dep of Soil and Crop Sci. Texas A&M Univ., College Station, Texas A&M Univ
Doyle J, Doyle J (1987) Genomic plant DNA preparation from fresh tissue-CTAB method. Phytochem Bull 19:11–15
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620
Felderhoff T, Murray S, Klein P, Sharma A, Hamblin M, Kresovich S, Vermerris W, Rooney W (2012) QTLs for energy-related traits in a sweet × grain sorghum [Sorghum bicolor (L.) Moench] mapping population. Crop Sci 52:2040–2049
Gómez G, Álvarez MF, Mosquera T (2011) Association mapping, a method to detect quantitative trait loci: statistical bases. Agronomía Colombiana 29:367–376
Guan Y, Wang H, Qin L, Zhang H, Yang Y, Gao F, Li R (2011) QTL mapping of bio-energy related traits in sorghum. Euphytica 182:431–440
Hall D, Tegström C, Ingvarsson PK (2010) Using association mapping to dissect the genetic basis of complex traits in plants. Briefings Funct Genomics 9:157–165
Hamblin MT, Fernandez MGS, Casa AM, Mitchell SE, Paterson AH, Kresovich S (2005) Equilibrium processes cannot explain high levels of short- and medium-range linkage disequilibrium in the domesticated grass Sorghum bicolor. Genetics 171:1247–1256
Jackson, Arthur MF, Davis M, Kresovich S, Lawhon WT, Lipinsky ES, Price MRA (2008) Research report on development of sweet sorghum as an energy crop, vol 1. Battelle Columbus Labs, Columbus, OH
Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806
Jessup RW (2009) Development and status of dedicated energy crops in the United States. In Vitro Cell Dev-Pl 45:282–290
Kraakman ATW, Niks RE, Van den Berg PMMM, Stam P, Van Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168:435–446
Lekgari AL (2010) Genetic mapping of quantitative trait loci associated with bioenergy traits, and the assessment of genetic variability in sweet sorghum (Sorghum bicolor (L.). Moench). Agronomy and Horticulture. University of Nebraska, Lincoln
McCutchen BF, Avant RV, Baltensperger D (2008) High-tonnage dedicated energy crops:the potential of sorghum and energy cane. Proceedings of the 20th annual conference of the National Agricultural Biotechnology Council, pp 119–122
Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE (2013) Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci USA 110:453–458
Murray SC, Rooney WL, Mitchell SE, Sharma A, Klein PE, Mullet JE, Kresovich S (2008a) Genetic improvement of sorghum as a biofuel feedstock: II. QTL for stem and leaf structural carbohydrates. Crop Sci 48:2180–2193
Murray SC, Sharma A, Rooney WL, Klein PE, Mullet JE, Mitchell SE, Kresovich S (2008b) Genetic improvement of sorghum as a biofuel feedstock: I. QTL for stem sugar and grain nonstructural carbohydrates. Crop Sci 48:2165–2179
Murray SC, Rooney WL, Hamblin MT, Mitchell SE, Kresovich S (2009) Sweet sorghum genetic diversity and association mapping for brix and height. The Plant Genome 2:48
Natoli A, Gorni C, Chegdani F, Ajmone Marsan P, Colombi Lorenzoni CC, Marocco A (2002) Identification of QTLs associated with sweet sorghum quality. Maydica 47:311–322
Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000) Association mapping in structured populations. Am J Hum Genet 67:170
Ritter KB, McIntyre CL, Godwin ID, Jordan DR, Chapman SC (2007) An assessment of the genetic relationship between sweet and grain sorghums, within Sorghum bicolor ssp. bicolor (L.) Moench, using AFLP markers. Euphytica 157:161–176
Shehzad T, Iwata H, Okuno K (2009) Genome-wide association mapping of quantitative traits in sorghum (Sorghum bicolor (L.) Moench) by using multiple models. Breed Sci 59:217–227
Shiringani AL, Frisch M, Friedt W (2010) Genetic mapping of QTLs for sugar-related traits in a RIL population of Sorghum bicolor L. Moench. Theor Appl Genet 121:323–336
Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289
Wang F, Liu CZ (2009) Development of an economic refining strategy of sweet sorghum in the Inner Mongolia Region of China. Energ Fuel 23:4137–4142
Wei X, Jackson PA, McIntyre CL, Aitken KS, Croft B (2006) Associations between DNA markers and resistance to diseases in sugarcane and effects of population substructure. Theor Appl Genet 114:155–164
Wu X, Staggenborg S, Propheter JL, Rooney WL, Yu J, Wang D (2010) Features of sweet sorghum juice and their performance in ethanol fermentation. Ind Crop Prod 31:164–170
Acknowledgments
This work was supported financially by a special fund for Agricultural Science, Technology and Innovation in Hebei, China (No. 2011055001) and China State Industrial System for Agricultural Research (CARS-06-01A).
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Lv, P., Ji, G., Han, Y. et al. Association analysis of sugar yield-related traits in sorghum [Sorghum bicolor (L.)]. Euphytica 193, 419–431 (2013). https://doi.org/10.1007/s10681-013-0962-7
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DOI: https://doi.org/10.1007/s10681-013-0962-7