Grattapaglia et al. 2012 Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus ESM
Electronic Supplementary Material (ESM)
Table 1. Citations to journal papers (1993-2010) on DNA markers for Myrtaceae with counts of numbers of microsatellites developed de novo for each
genus.
Genera
Eucalyptus
Marker
Type
RFLP
# of Papers
# of Markers
9
RAPD
20
AFLP
11
SSR
43
Citations
(Agrama et al., 2002; Byrne et al., 1994; Byrne et al., 1995; Elliott and
Byrne, 2003; Gion et al., 2000; Glaubitz et al., 2003a; Glaubitz et al.,
2003b; Moran et al., 2000; Wolff et al., 1993)
(Bundock et al., 2000; Delaporte et al., 2001; Gaiotto et al., 1997;
Grattapaglia et al., 1995; Grattapaglia and Sederoff, 1994; Junghans et al.,
2003; Keil and Griffin, 1994; Li, 2000; Neaylon et al., 2001; Nesbitt et al.,
1997; Nesbitt et al., 1995; Rossetto et al., 1997; Sale et al., 1996a;
Shepherd et al., 1999; Skabo et al., 1998; Vaillancourt et al., 2001;
Vaillancourt et al., 1995; Verhaegen and Plomion, 1996; Verhaegen et al.,
1997; Verhaegen et al., 1998)
(Cervera et al., 2000; Kirst et al., 2005a; Kirst et al., 2004; Marcucci-Poltri
et al., 2003; Marques et al., 1998; Marques et al., 2005; Marques et al.,
1999; McKinnon et al., 2008; Myburg et al., 2003; Myburg et al., 2004;
Poltri et al., 2003)
366 (Brondani et al., 2002; Brondani et al., 1998; Brondani and Grattapaglia,
2001; Brondani et al., 2006; Butcher et al., 2009; Butcher et al., 2005;
Byrne et al., 1996; Ceresini et al., 2005; Chaix et al., 2002; Chaix et al.,
2003; Foster et al., 2007; Freeman et al., 2006; Freeman et al., 2008a;
Freeman et al., 2008b; Glaubitz et al., 2001; Glaubitz et al., 2003a;
Glaubitz et al., 2003b; Grattapaglia et al., 2004; Henery et al., 2007;
Holman et al., 2003; Jones et al., 2008; Jones et al., 2002; Kirst et al.,
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Grattapaglia et al. 2012 Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus ESM
Genera
Marker
Type
ISSR
DArT
SNP
Eugenia
Corymbia
Metrosideros
Melaleuca
# of Papers
# of Markers
3
1
6
cpDNA
15
mtDNA
RAPD
AFLP
SSR
cpDNA
SSR
1
1
3
3
1
7
RAPD
AFLP
SSR
cpDNA
RFLP
1
3
3
1
1
Citations
2005b; Le et al., 2009; Marques et al., 2002; McGowen et al., 2001;
Missiaggia et al., 2005; Nevill et al., 2008; Ottewell et al., 2009; Ottewell et
al., 2005; Payn et al., 2008; Rabello et al., 2005; Rathbone et al., 2007;
Sampson and Byrne, 2008; Shepherd and Raymond, 2010; Shepherd et al.,
2010; Smith et al., 2003; Steane et al., 2006; Steane et al., 2001; Stokoe et
al., 2001; Thamarus et al., 2002; Tripiana et al., 2007; Zelener et al., 2005)
(Balasaravanan et al., 2005; Balasaravanan et al., 2006; Okun et al., 2008)
(Sansaloni et al., 2010)
(Kulheim et al., 2009; Novaes et al., 2008; Poke et al., 2003; Sexton et al.,
2010; Thumma et al., 2009; Thumma et al., 2005)
(Byrne and Hines, 2004; Byrne and Macdonald, 2000; Byrne and Moran,
1994; Byrne et al., 1993; Foster et al., 2007; Heinze, 2007; Jackson et al.,
1999; McKinnon et al., 1999; Nevill et al., 2010; Sale et al., 1993; Sale et
al., 1996b; Steane et al., 1998; Steane et al., 2005; Steane et al., 1991;
Wheeler and Byrne, 2006)
(Vaillancourt et al., 2004)
(Trindade and Chaves, 2005)
(Franzon et al., 2010; Margis et al., 2002; Salgueiro et al., 2004)
(Ferreira-Ramos et al., 2008; Zucchi et al., 2002; Zucchi et al., 2003)
(Salgueiro et al., 2004)
28 (Jones et al., 2001; Ochieng et al., 2008a; Ochieng et al., 2008b; Ochieng et
al., 2007; Shepherd et al., 2008; Shepherd et al., 2006; Shepherd et al.,
2007)
(James et al., 2004)
(Broadhurst et al., 2008; Drummond et al., 2000; Kaneko et al., 2008)
24 (Crawford et al., 2008; Harbaugh et al., 2009; Kaneko et al., 2007)
(Drummond et al., 2000)
102 (Broadhurst et al., 2004)
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Grattapaglia et al. 2012 Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus ESM
Genera
Myrtus
Psidium
Calothamnus
Acca
Chamelaucium
Syzygium
Total
Marker
Type
SSR
cpDNA
RAPD
AFLP
SSR
RAPD
SSR
SSR
cpDNA
SSR
# of Papers
# of Markers
Citations
4
1
2
3
1
3
2
1
1
1
152
14
10
13
8
(Miwa et al., 2000; Rossetto et al., 2000; Rossetto et al., 1999a; Rossetto
et al., 1999b)
(Butcher et al., 1995)
(Messaoud et al., 2007; Serce et al., 2008)
(Agrimonti et al., 2007; Albaladejo et al., 2009; Bruna et al., 2007)
(Albaladejo et al., 2010)
(Chen et al., 2007; Perez and Solano, 2007; Prakash et al., 2002)
(Byrne et al., 2007; Elliott and Byrne, 2005)
(Santos et al., 2008)
(Ma et al., 2004)
(Hillyer et al., 2007)
References cited in the table above (not listed in the main article text)
Agrama HA, George TL, Salah SF (2002) Construction of genome map for Eucalyptus camaldulensis DEHN. Silvae Genetica 51:201-206
Balasaravanan T, Chezhian P, Kamalakannan R, et al. (2005) Determination of inter- and intra-species genetic relationships among six Eucalyptus
species based on inter-simple sequence repeats (ISSR). Tree Physiology 25:1295-1302
Balasaravanan T, Chezhian P, Kamalakannan R, et al. (2006) Identification of species-diagnostic ISSR markers for six Eucalyptus species. Silvae Genetica
55:119-122
Butcher PA, Byrne M, Moran GF (1995) Variation within and among the chloroplast genomes of Melaleuca alternifolia and Melaleuca linarifolia
(Myrtaceae). Plant Systematics and Evolution 194:69-81
Butcher PA, Skinner AK, Gardiner CA (2005) Increased inbreeding and inter-species gene flow in remnant populations of the rare Eucalyptus
benthamii. Conservation Genetics 6:213-226
Byrne M, Hines B (2004) Phylogeographical analysis of cpDNA variation in Eucalyptus loxophleba (Myrtaceae). Australian Journal of Botany 52:459-470
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Grattapaglia et al. 2012 Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus ESM
Byrne M, Moran GF, Murrell JC, Tibbits WN (1994) Detection and Inheritance of RFLPs in Eucalyptus nitens. Theoretical and Applied Genetics 89:397402
Ceresini PC, Silva SP, Missio RF, et al. (2005) Satellyptus: Analysis and database of microsatellites from ESTs of Eucalyptus. Genetics and Molecular
Biology 23:589-600
Cervera MT, Remington D, Frigerio JM, et al. (2000) Improved AFLP analysis of tree species. Canadian Journal of Forest Research 30:1608-1616
Chaix G, Chantal I, Poitel M, et al. (2002) Microsatellite primer amplification by multiplexing: A first application to Eucalyptus grandis. Plant Molecular
Biology Reporter 20:67a-67e
Chen TW, Ng CC, Wang CY, Shyu YT (2007) Molecular identification and analysis of Psidium guajava L. from indigenous tribes of Taiwan. Journal of
Food and Drug Analysis 15:82-88
Delaporte KL, Collins GG, Conran JG, Sedgley M (2001) Molecular analysis of an interspecific hybrid ornamental eucalypt for parental identification.
Euphytica 122:165-170
Elliott C, Byrne M (2003) Genetic diversity within and between natural populations of Eucalyptus occidentalis (Myrtaceae). Silvae Genetica 52:169-173
Glaubitz JC, Murrell JC, Moran GF (2003a) Effects of native forest regeneration practices on genetic diversity in Eucalyptus consideniana. Theoretical
and Applied Genetics 107:422-431
Glaubitz JC, Wu HX, Moran GF (2003b) Impacts of silviculture on genetic diversity in the native forest species Eucalyptus sieberi. Conservation
Genetics 4:275-287
Heinze B (2007) A database of PCR primers for the chloroplast genomes of higher plants. Plant Methods 3
Li CY (2000) RAPD analysis of genetic variation in Eucalyptus microtheca F. Muell. populations. Hereditas 132:151-156
Moran GF, Butcher PA, Glaubitz JC (2000) Application of genetic markers in the domestication, conservation and utilisation of genetic resources of
Australasian tree species. Australian Journal of Botany 48:313-320
Neaylon K, Delaporte KL, Sedgley M, Collins GG, Conran JG (2001) Molecular analysis of hybrids among the ornamental eucalypts Eucalyptus
macrocarpa, E. pyriformis, and E. youngiana. Journal of the American Society for Horticultural Science 126:336-339
Nevill PG, Reed A, Bossinger G, et al. (2008) Cross-species amplification of Eucalyptus microsatellite loci. Molecular Ecology Resources 8:1277-1280
Perez DT, Solano JPL (2007) Genetic variability in cultivars of guava (Psidium guajava L.). Revista Fitotecnia Mexicana 30:391-401
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Grattapaglia et al. 2012 Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus ESM
Rabello E, Nunes de Souza A, Saito D, Mui Tsai S (2005) In silico characterisation of microsatellites in Eucalyptus spp.: Abundance, length variation and
transposon associations. Genetics and Molecular Biology 28:582-588
Rossetto M, Lucarotti F, Hopper SD, Dixon KW (1997) DNA fingerprinting of Eucalyptus graniticola: a critically endangered relict species or a rare
hybrid? Heredity 29:310-318
Shepherd M, Pomroy P, Dieters MJ, Lee DJ (2007) Genetic control of propagation traits in a single Corymbia torelliana x C. citriodora spp variegata
family. Canadian Journal of Forest Research 37:2563-2574
Skabo S, Vaillancourt RE, Potts BM (1998) Fine-scale genetic structure of Eucalyptus globulus ssp. globulus forest revealed by RAPDs. Australian
Journal of Botany 46:583-594
Smith S, Hughes J, Wardell-Johnson G (2003) High population differentiation and extensive clonality in a rare mallee eucalypt: Eucalyptus curtisii Conservation genetics of a rare mallee eucalypt. Conservation Genetics 4:289-300
Steane DA, West AK, Potts BM, Ovenden JM, Reid JB (1991) Restriction fragment length polymorphisms in chloroplast DNA from six species of
Eucalyptus. Australian Journal of Botany 39:399-414
Stokoe RL, Shepherd M, Lee D, Nikles DG, Henry RJ (2001) Natural interspecific hybridisation between Eucalyptus acmenoides Schauer and E.
cloeziana F. Muell (Myrtaceae). Annals of Botany 88:563-570
Tripiana V, Bourgeois M, Verhaegen D, Vigneron P, Bouvet JM (2007) Combining microsatellites, growth, and adaptive traits for managing in situ
genetic resources of Eucalyptus urophylla. Canadian Journal of Forest Research 37:773-785
Vaillancourt RE, Boomsma DB, Nicolle D (2001) A disjunct population of Eucalyptus globulus ssp Bicostata from South Australia. Transactions of the
Royal Society of South Australia 125:65-68
Verhaegen D, Plomion C, Poitel M, Costa P, Kremer A (1998) Quantitative trait dissection analysis in Eucalyptus using RAPD markers: 2. Linkage
disequilibrium in a factorial design between E. urophylla and E. grandis. Forest Genetics 5:61-69
Wheeler MA, Byrne M (2006) Congruence between phylogeographic patterns in cpDNA variation in Eucalyptus marginata (Myrtaceae) and
geomorphology of the Darling Plateau, south-west of Western Australia. Australian Journal of Botany 54:17-26
Wolff JLC, Mcdowell SW, Machado MA (1993) Analysis of the Restriction Fragment Length Polymorphism of Eucalyptus urophylla, E.grandis and
E.citriodora. Revista Brasileira de Genetica 16:431-439
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