growth-related traits in tomato. Plant Cell
Environ 41(2):327–341
22. Horton MW et al (2012) Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap
panel. Nat Genet 44(2):212–216
23. Keurentjes JJ et al (2007) Development of a
near-isogenic line population of Arabidopsis
thaliana and comparison of mapping power
with a recombinant inbred line population.
Genetics 175(2):891–905
24. Wei J, Xu S (2016) A random-model approach
to QTL mapping in multiparent advanced generation intercross (MAGIC) populations.
Genetics 202(2):471–486
25. Timm S, Modde K, Bauwe H (2017) Targeted
isolation and characterization of T-DNA
mutants defective in photorespiration. Methods Mol Biol 1653:105–124
26. de Souza LP et al (2017) From chromatogram
to analyte to metabolite. How to pick horses
for courses from the massive web resources for
mass spectral plant metabolomics. Gigascience
6(7):1–20
27. Joseph B, Corwin JA, Kliebenstein DJ (2015)
Genetic variation in the nuclear and organellar
genomes modulates stochastic variation in the
metabolome, growth, and defense. PLoS
Genet 11(1):e1004779
28. Alseekh S et al (2018) Guidelines for sample
normalization to minimize batch variation for
large-scale metabolic profiling of plant natural
genetic variance. Methods Mol Biol
1778:33–46
29. Shimizu T et al (2018) Targeted LC-MS analysis for plant secondary metabolites. Methods
Mol Biol 1778:171–181
30. Allwood JW et al (2011) Plant metabolomics
and its potential for systems biology research:
background concepts, technology, and methodology. In: Jameson D, Verma M, Westerhoff
HV (eds) Methods in enzymology. Methods in
systems biology, vol 500. pp 299–336
31. Kopka J et al (2004) Metabolite profiling in
plant biology: platforms and destinations.
Genome Biol 5(6):831–841
32. Keurentjes JJ et al (2006) The genetics of plant
metabolism. Nat Genet 38(7):842–849
33. Kliebenstein DJ et al (2001) Genetic control of
natural variation in Arabidopsis glucosinolate
accumulation. Plant Physiol 126(2):811–825
34. Chan EK et al (2011) Combining genomewide association mapping and transcriptional
networks to identify novel genes controlling
glucosinolates in Arabidopsis thaliana. PLoS
Biol 9(8):e1001125
35. Wong A, Gehring C (2013) Computational
identification of candidate nucleotide cyclases
in higher plants. Methods Mol Biol
1016:195–205
36. Yamaguchi Y et al (2000) Three Arabidopsis
genes encoding proteins with differential activities for cysteine synthase and betacyanoalanine synthase. Plant Cell Physiol 41
(4):465–476
37. Markert B (1995) Sample preparation (cleaning, drying, homogenization) for trace element
analysis in plant matrices. Sci Total Environ
176(1–3):45–61
38. Osorio S, Do PT, Fernie AR (2012) Profiling
primary metabolites of tomato fruit with gas
chromatography/mass spectrometry. In Hardy
NW, Hall RD (eds) Plant metabolomics: methods and protocols. Humana Press, Totowa, pp
101–109
39. Sehgal D, Singh R, Rajpal VR (2016) Quantitative trait loci mapping in plants: concepts and
approaches. In: Rajpal VR, Rao SR, Raina SN
(eds) Molecular breeding for sustainable crop
improvement, vol 2, pp 31–59
40. Platt A, Vilhjalmsson BJ, Nordborg M (2010)
Conditions under which genome-wide association studies will be positively misleading.
Genetics 186(3):1045–1052
41. Larsson SJ, Lipka AE, Buckler ES (2013) Lessons from dwarf8 on the strengths and weaknesses of structured association mapping. PLoS
Genet 9(2):e1003246
42. Jansen RC (2004) Quantitative trait loci in
inbred lines. In: Handbook of statistical genetics. Wiley
43. Monforte AJ, Tanksley SD (2000) Development of a set of near isogenic and backcross
recombinant inbred lines containing most of
the Lycopersicon hirsutum genome in a
L-esculentum genetic background: a tool for
gene mapping and gene discovery. Genome 43
(5):803–813
44. Jeuken MJW, Lindhout P (2004) The development of lettuce backcross inbred lines (BILs)
for exploitation of the Lactuca saligna (wild
lettuce) germplasm. Theor Appl Genet 109
(2):394–401
45. Blanco A, Simeone R, Gadaleta A (2006)
Detection of QTLs for grain protein content
in durum wheat (vol 112, pg 1195, 2006).
Theor Appl Genet 113(3):563–565
46. Wu S et al (2016) Combined use of genomewide association data and correlation networks
unravels key regulators of primary metabolism
in Arabidopsis thaliana. PLoS Genet 12(10):
e1006363
410
Si Wu et al.
Environ 41(2):327–341
22. Horton MW et al (2012) Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap
panel. Nat Genet 44(2):212–216
23. Keurentjes JJ et al (2007) Development of a
near-isogenic line population of Arabidopsis
thaliana and comparison of mapping power
with a recombinant inbred line population.
Genetics 175(2):891–905
24. Wei J, Xu S (2016) A random-model approach
to QTL mapping in multiparent advanced generation intercross (MAGIC) populations.
Genetics 202(2):471–486
25. Timm S, Modde K, Bauwe H (2017) Targeted
isolation and characterization of T-DNA
mutants defective in photorespiration. Methods Mol Biol 1653:105–124
26. de Souza LP et al (2017) From chromatogram
to analyte to metabolite. How to pick horses
for courses from the massive web resources for
mass spectral plant metabolomics. Gigascience
6(7):1–20
27. Joseph B, Corwin JA, Kliebenstein DJ (2015)
Genetic variation in the nuclear and organellar
genomes modulates stochastic variation in the
metabolome, growth, and defense. PLoS
Genet 11(1):e1004779
28. Alseekh S et al (2018) Guidelines for sample
normalization to minimize batch variation for
large-scale metabolic profiling of plant natural
genetic variance. Methods Mol Biol
1778:33–46
29. Shimizu T et al (2018) Targeted LC-MS analysis for plant secondary metabolites. Methods
Mol Biol 1778:171–181
30. Allwood JW et al (2011) Plant metabolomics
and its potential for systems biology research:
background concepts, technology, and methodology. In: Jameson D, Verma M, Westerhoff
HV (eds) Methods in enzymology. Methods in
systems biology, vol 500. pp 299–336
31. Kopka J et al (2004) Metabolite profiling in
plant biology: platforms and destinations.
Genome Biol 5(6):831–841
32. Keurentjes JJ et al (2006) The genetics of plant
metabolism. Nat Genet 38(7):842–849
33. Kliebenstein DJ et al (2001) Genetic control of
natural variation in Arabidopsis glucosinolate
accumulation. Plant Physiol 126(2):811–825
34. Chan EK et al (2011) Combining genomewide association mapping and transcriptional
networks to identify novel genes controlling
glucosinolates in Arabidopsis thaliana. PLoS
Biol 9(8):e1001125
35. Wong A, Gehring C (2013) Computational
identification of candidate nucleotide cyclases
in higher plants. Methods Mol Biol
1016:195–205
36. Yamaguchi Y et al (2000) Three Arabidopsis
genes encoding proteins with differential activities for cysteine synthase and betacyanoalanine synthase. Plant Cell Physiol 41
(4):465–476
37. Markert B (1995) Sample preparation (cleaning, drying, homogenization) for trace element
analysis in plant matrices. Sci Total Environ
176(1–3):45–61
38. Osorio S, Do PT, Fernie AR (2012) Profiling
primary metabolites of tomato fruit with gas
chromatography/mass spectrometry. In Hardy
NW, Hall RD (eds) Plant metabolomics: methods and protocols. Humana Press, Totowa, pp
101–109
39. Sehgal D, Singh R, Rajpal VR (2016) Quantitative trait loci mapping in plants: concepts and
approaches. In: Rajpal VR, Rao SR, Raina SN
(eds) Molecular breeding for sustainable crop
improvement, vol 2, pp 31–59
40. Platt A, Vilhjalmsson BJ, Nordborg M (2010)
Conditions under which genome-wide association studies will be positively misleading.
Genetics 186(3):1045–1052
41. Larsson SJ, Lipka AE, Buckler ES (2013) Lessons from dwarf8 on the strengths and weaknesses of structured association mapping. PLoS
Genet 9(2):e1003246
42. Jansen RC (2004) Quantitative trait loci in
inbred lines. In: Handbook of statistical genetics. Wiley
43. Monforte AJ, Tanksley SD (2000) Development of a set of near isogenic and backcross
recombinant inbred lines containing most of
the Lycopersicon hirsutum genome in a
L-esculentum genetic background: a tool for
gene mapping and gene discovery. Genome 43
(5):803–813
44. Jeuken MJW, Lindhout P (2004) The development of lettuce backcross inbred lines (BILs)
for exploitation of the Lactuca saligna (wild
lettuce) germplasm. Theor Appl Genet 109
(2):394–401
45. Blanco A, Simeone R, Gadaleta A (2006)
Detection of QTLs for grain protein content
in durum wheat (vol 112, pg 1195, 2006).
Theor Appl Genet 113(3):563–565
46. Wu S et al (2016) Combined use of genomewide association data and correlation networks
unravels key regulators of primary metabolism
in Arabidopsis thaliana. PLoS Genet 12(10):
e1006363
410
Si Wu et al.