Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin

Theoretical and Applied Genetics

Volumn 125, Issue 8, 2012, Pages 1687-1696

  Newell, Mark A ^a   Asoro, Franco G ^b   Scott, M Paul ^c   White, Pamela J ^b   Beavis, William D ^b   Jannink, Jean Luc ^d  

^a PLANT BIOLOGY DIVISION   (United States)

^b IOWA STATE UNIVERSITY   (United States)

^c AGRICULTURAL RESEARCH SERVICE   (United States)

^d Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CROPS; PLANTS (BOTANY); RANDOM PROCESSES;

BREEDING PROGRAM; DOUBLED HAPLOID; GENOME-WIDE ASSOCIATION STUDIES; LINKAGE MAPPING; POPULATION STRUCTURES; QUANTITATIVE TRAIT LOCUS; SEQUENCE HOMOLOGY; SOLUBLE DIETARY FIBER;

GENES;

AVENA SATIVA;

EID: 84869087879     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-012-1945-0     Document Type: Article

References (38)

1. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Roy Stat Soc B 57: 289-300.
2. Braaten TJ, Wood PJ, Scott FW, Wolynetz MS, Lowe MK, Bradley-Whyte P (1994) Oat β-glucan reduces blood cholesterol concentration in hypercholesterolemic subjects. Eur J Clin Nutr 48: 465-474.
3. Bradbury P, Parker T, Hamblin MT, Jannink J-L (2011) Assessment of power and false discovery rate in genome-wide association studies using the barley CAP germplasm. Crop Sci 51: 52-59.
4. Burton RA, Fincher GB (2009) (1, 3; 1, 4)-beta-d-glucans in cell walls of the Poaceae, lower plants, and fungi: a tale of two linkages. Mol Plant 2: 873-882.
5. Burton RA, Shirley NJ, King BJ, Harvey AG, Fincher GB (2004) The CesA gene family of barley. Quantitative analysis of transcripts reveals two groups of co-expressed genes. Plant Physiol 134: 224-236.
6. Burton RA, Wilson SM, Hrmova M, Harvey AJ, Shirley NJ, Medhurst A, Stone BA, Newbigin EJ, Bacic A, Fincher GB (2006) Cellulose synthase-like CslF genes mediate the synthesis of cell wall (1, 3; 1, 4)-β-d-glucans. Science 311: 1940-1942.
7. Burton RA, Jobling SA, Harvey AJ, Shirley NJ, Mather DE, Bacic A, Fincher GB (2008) The genetics and transcriptional profiles of the cellulose synthase-like HvCslF gene family in barley. Plant Physiol 146: 1821-1833.
8. Chernyshova AA, White PJ, Scott MP, Jannink J-L (2007) Selection for nutritional function and agronomic performance in oat. Crop Sci 47: 2330-2339.
9. Colleoni-Sirghie M, Fulton B, White PJ (2003) Structural features of water soluble (1-3), (1-4)-β-d-glucan from high-β-glucan and traditional oat lines. Carbohydr Polym 54: 237-249.
10. De Koeyer DL, Tinker NA, Wight CP, Deyl J, Burrows VD, O'Donoughue LS, Lybaert A, Molnar SJ, Armstrong KC, Fedak G, Wesenberg DM, Rossnagel BG, McElroy AR (2004) A molecular linkage map with associated QTLs from a hulless × covered spring oat population. Theor Appl Genet 108: 1285-1298.
11. Endelman JB (2011) Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Genome 4: 250-255.
12. Estrada A, Yun CH, van Kessel A, Li B, Hauta S, Laarveld B (1997) Immunomodulatory activities of oat beta-glucan in vitro and in vivo. Microbiol Immunol 41: 991-998.
13. Fincher GB (2009) Exploring the evolution of (1, 3; 1, 4)-β-d-glucans in plant cell walls: comparative genomics can help! Curr Opin Plant Biol 12: 140-147.
14. Hamblin MT, Close TJ, Bhat PR, Chao S, Kling JG, Abraham KJ, Blake T, Brooks WS, Cooper B, Griffey CA, Hayes PM, Hole DJ, Horsley RD, Obert DE, Smith KP, Ullrich SE, Muehlbauer GJ, Jannink J-L (2010) Population structure and linkage disequilibrium in U. S. barley germplasm: implications for association mapping. Crop Sci 50: 556-566.
15. Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38: 226-231.
16. Izydorczyk MS, Macri LJ, Mac Gregor AW (1998) Structure and physiochemical properties of barley non-starch polysaccharides-I. water-extractable β-glucans and arabinoxylans. Carbohydr Polym 35: 249-258.
17. Jannink J-L, Bink MCAM, Jansen RC (2001) Using complex plant pedigrees to map valuable genes. Trends Plant Sci 6: 337-342.
18. Jenkins AL, Jenkins DJA, Zdravkovic U, Würsch P, Vuksan V (2002) Depression of the glycemic index by high levels of beta-glucan fiber in two functional foods tested in type 2 diabetes. Eur J Clin Nutr 56: 622-628.
19. Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, Eskin E (2008) Efficient control of population structure in model organism association mapping. Genetics 178: 1709-1723.
20. Kearsey MJ, Farquhar AGL (1998) QTL analysis in plants; where are they now? Heredity 80: 137-142.
21. Keenen JM, Pins JJ, Frazel C, Moran A, Turnquist L (2002) Oat ingestion reduces systolic and diastolic blood pressure in patients with mild or borderline hypertension: a pilot study. J Family Pract 51: 369.
22. Kennedy BW, Quinton M, van Arendonk JAM (1992) Estimation of effects of single genes on quantitative traits. J Anim Sci 70: 2000-2012.
23. Kianian SF, Phillips RL, Rines HW, Fulcher RG, Webster FH, Stuthman DD (2000) Quantitative trait loci influencing β-glucan content in oat (Avena sativa, 2n = 6x = 42). Theor Appl Genet 101: 1039-1048.
24. Lande R, Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124: 743-756.
25. Miyagawa T, Nishida N, Ohashi J, Kimura R, Fugimoto A, Kawashima M, Koike A, Sasaki T, Tanii H, Otowa T, Momose Y, Nakahara Y, Gotch J, Okaxaki Y, Tsuji S, Tokunaga K (2008) Appropriate data cleaning methods for genome-wide association study. J Hum Genet 53: 886-893.
26. Newell MA, Cook D, Tinker NA, Jannink J-L (2011) Population structure and linkage disequilibrium in oat (Avena sativa L.): implications for genome-wide association studies. Theor Appl Genet 122: 623-632.
27. Newell MA, Kim HJ, Asoro FG, Lauter A, White PJ, Scott MP, Jannink J-L (2012) Micro-enzymatic evaluation of oat (Avena sativa L.) beta-glucan for high-throughput phenotyping. Cereal Chem. (in review).
28. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35: D883-D887.
29. Robertson A (1960) A theory of limits in artificial selection. Proc Royal Soc London, Series B, Biological Sciences 153: 234-249.
30. R Development Core Team (2009) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. URL http://www. R-project. org.
31. ® 9. 2 User's Guide, SAS Campus Drive, Cary, North Carolina 27513.
32. Stich B, Möhring J, Piepho H-P, Heckenberger M, Buckler ES, Melchinger AE (2008) Comparison of mixed-model approaches for association mapping. Genetics 178: 1745-1754.
33. Sun G, Zhu C, Kramer MH, Yang S-S, Song W, Piepho H-P, Yu J (2010) Variation explained in mixed-model association mapping. Heredity 105: 333-340.
34. Tinker NA, Kilian A, Wight CP, Heller-Uszynska K, Wenzl P, Rines HW, Bjørnstad Å, Howarth CJ, Jannink J-L, Anderson JM, Rossnagel BG, Stuthman DD, Sorrells ME, Jackson EW, Tuvesson S, Kolb RL, Olsson O, Federizzi LC, Carson ML, Ohm HW, Molnar SJ, Scoles GJ, Eckstein PE, Bonman JM, Ceplitis A, Langdon T (2009) New DArT markers for oat provide enhanced map coverage and global germplasm characterization. BMC Genomics 10: 39.
35. Wight CP, Tinker NA, Kianian SF, Sorrells ME, O'Donoughur LS, Hoffman DL, Groh S, Scoles GJ, Li CD, Webster FH, Phillips RL, Rines HW, Livingston SM, Armstrong KC, Fedak G, Molnar SJ (2003) A molecular marker map in 'Kanota' × 'Ogle' hexaploid oat (Avena spp.) enhanced by additional markers and a robust framework. Genome 46: 28-47.
36. Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR, Madden PA, Heath AC, Martin NG, Montgomery GW, Goddard ME, Visscher PM (2010) Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42: 565-569.
37. Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38: 203-208.
38. Zhu C, Gore M, Buckler ES, Yu J (2008) Status and prospects of association mapping in plants. Plant Genome 1: 5-20.