Optimum allocation of resources for QTL detection using a nested association mapping strategy in maize

Theoretical and Applied Genetics

Volumn 120, Issue 3, 2010, Pages 553-561

  Stich, Benjamin ^a   Utz, H Friedrich ^b   Piepho, Hans Peter ^b   Maurer, Hans P ^b   Melchinger, Albrecht E ^b  

^a MAX PLANCK INSTITUTE FOR PLANT BREEDING RESEARCH   (Germany)

^b UNIVERSITY OF HOHENHEIM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION MAPPING; EMPIRICAL DATA; FINANCIAL RESOURCES; FIXED BUDGET; GENETIC COMPLEXITY; GENETIC DIVERSITY; GENOMICS TOOLS; GENOTYPING; INBRED LINE; MAIZE INBREDS; MAPPING POPULATIONS; NESTED DESIGN; OPTIMUM ALLOCATION; OPTIMUM NUMBER; PHENOTYPING; QTL MAPPING; QUANTITATIVE TRAIT LOCUS; QUANTITATIVE TRAITS; RECOMBINANT INBRED LINES; SIMPLE SEQUENCE-REPEAT MARKERS; SINGLE-NUCLEOTIDE POLYMORPHISM MARKERS; TEST ENVIRONMENT; TOTAL BUDGET;

BIOMARKERS; BUDGET CONTROL; COMPUTER SIMULATION; EXPERIMENTS; MAPPING; PLANTS (BOTANY);

POPULATION STATISTICS;

ARTICLE; CHROMOSOME MAP; ECONOMICS; GENETICS; MAIZE; METHODOLOGY; QUANTITATIVE TRAIT LOCUS; REPRODUCIBILITY; RESOURCE ALLOCATION;

PHYSICAL CHROMOSOME MAPPING; QUANTITATIVE TRAIT LOCI; REPRODUCIBILITY OF RESULTS; RESOURCE ALLOCATION; ZEA MAYS;

ZEA MAYS;

EID: 75849163892     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-009-1175-2     Document Type: Article

References (24)

1. Aranzana, MA, Kim S, Zhao K, Bakker E, Horton M, Jacob K, Lister C, Molitor J, Shindo C, Tang C, Toomajia C, Traw B, Zheng H, Bergelson J, Dean C, Marjoram P, Nordborg M (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1: e60.
2. Cho RJ, Mindrinos M, Richards DR, Sapolsky RJ, Anderson M et al (1999) Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat Genet 23: 203-207.
3. Churchill GA, Airey DC, Allayee H, Nagel JM, Attie AD et al (2004) The collaborative cross, a community resource for the genetic analysis of complex traits. Nat Genet 36: 1133-1137.
4. Harjes CE, Rocheford TR, Bai L, Brutnell TP, Kandianis CB et al (2008) Natural Genetic Variation in Lycopene Epsilon Cyclase tapped for maize biofortification. Science 319: 330-333.
5. Knapp SJ, Bridges WC (1990) Using molecular markers to estimate quantitative trait locus parameters: power and genetic variances for unreplicated and replicated progeny. Genetics 126: 769-777.
6. Kraakman ATW, Niks RE, van den Berg PMMM, Stam P, Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivar. Genetics 168: 435-446.
7. Lande R, Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124: 743-756.
8. Liu K, Goodman M, Muse S, Smith JS, Buckler E, Doebley J (2003) Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165: 2117-2128.
9. Longin CFH, Utz HF, Reif JC, Schipprack W, Melchinger AE (2006) Hybrid breeding with doubled haploids: I. One-stage versus two-stage selection for testcross performance. Theor Appl Genet 112: 903-912.
10. Maurer HP, Melchinger AE, Frisch M (2008) Population genetical simulation and data analysis with Plabsoft. Euphytica 161: 133-139.
11. McMullen MD, Kresovich S, Sanchez Villeda H, Bradbuy P, Li H, Sun Qi, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C, Brown P, Browne C, Eller M, Guill K, Harjes C, Kroon D, Lepak N, Mitchell SE, Peterson B, Pressoir G, Romero S, Oropeza Rosas M, Solvo S, Yates H, Hanson M, Jones Elizabeth, Smith S, Glaubitz JC, Goodman M, Ware D, Holland JB, Buckler ES (2009) Genetic properties of the maize nested association mapping population. Science 325: 737-740.
12. Melchinger AE, Utz HF, Schön CC (1998) Quantitative trait locus (QTL) mapping using different testers and independent population samples in maize reveals low power of QTL detection and large bias in estimates of QTL effects. Genetics 149: 383-403.
13. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98: 11479-11484.
14. Schön CC, Utz HF, Groh S, Truberg B, Openshaw S, Melchinger AE (2004) Quantitative trait locus mapping based on resampling in a vast maize testcross experiment and its relevance to quantitative genetics for complex traits. Genetics 167: 485-498.
15. Schwarz G (1978) Estimating the dimension of a model. Ann Stat 6: 461-464.
16. Shendure J, Mitra RD, Varma C, Church GM (2004) Advanced sequencing technologies: methods and goals. Nat Rev Genet 5: 335-344.
17. Stich B, Yu J, Melchinger AE, Piepho H-P, Utz HF, Maurer HP, Buckler ES (2007) Power to detect higher-order epistatic interactions in a metabolic pathway using a new mapping strategy. Genetics 176: 563-570.
18. 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.
19. Tomerius A-M, Miedaner T, Geiger HH (2008) A model calculation approach towards the optimization of a standard scheme of seed-parent line development in hybrid rye breeding. Plant Breed 127: 433-440.
20. Utz HF, Melchinger AE (1996) PLABQTL: a program for composite interval mapping of QTL. J Quant Trait Loci 2: 1-5.
21. Vuylsteke M, Kuiper M, Stam P (2000) Chromosomal regions involved in hybrid performance and heterosis: their AFLP®-based identification and practical use in prediction models. Heredity 85: 208-218.
22. Wilson LM, Whitt SR, Ibáñez AM, Rocheford TR, Goodman MM, Buckler ES (2004) Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell16: 2719-2733.
23. Yu J, Buckler E (2006) Genetic association mapping and genomeorganization of maize. Curr Opin Biotech 17: 155-160.
24. Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178: 539-551.