EST-SSR genetic maps for Citrus sinensis and Poncirus trifoliata

Abstract

The segregation of 141 polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers in an F1 intergeneric citrus population was studied to build the first extensive EST maps for the maternal sweet orange and paternal Poncirus genomes. Of these markers, 122 were found segregating in sweet orange, 59 in Poncirus, and 40 in both. Eleven linkage groups with 113 markers in sweet orange, 8 with 45 markers in Poncirus, and 13 with 123 markers in the cross pollinator (CP) consensus of both, were constructed. About 775.8 cM of sweet orange genome and 425.7 cM of Poncirus genome were covered. Through comparison of shared markers, three cases were found where two linkage groups in one map apparently were colinear with one group of the other map; Poncirus linkages Ar1a and Ar1b and consensus linkages CP1a and CP1b, were both collinear with one sweet orange linkage, Sa1, as were sweet orange Sa3a and Sa3b with Poncirus Ar3 and consensus CP3, and sweet orange Sa7a and Sa7b, and consensus CP7a and CP7b with Poncirus Ar7. These EST-SSR markers are particularly useful for constructing comparative framework maps for related genera because they amplify orthologous genes to provide anchor points across taxa. All SSR primers are freely available to the citrus community.

Multilocus half-tetrad analysis and centromere mapping in citrus: evidence of SDR mechanism for 2n megagametophyte production and partial chiasma interference in mandarin cv ‘Fortune’

“…Thirty-five microsatellite loci were used to analyse the triploid progenies: CAC15, TAA41 (Kijas et al, 1997), CX6F03, CX6F23 (Chen et al, 2007), mest121 , mest56, mest192, mest123 (Aleza et al, 2011), mest104, mest110, mest247, mest488 (François Luro, personal communication; mail to luro@ corse.inra.fr for further information), mCrCIR07F11 (Kamiri et al, 2011), Ci01C07, Ci02B07, Ci08C05, mCrCIR 01E02, mCrCIR01F04a, mCrCIR06A12, mCrCIR06B05, mCrCIR06B07, mCrCIR07E12 and thirteen new designed primers (mCrCIR01C06, mCrCIR0 2A09, mCrCIR02D09, mCrCIR02F12, mCrCIR02G01, mCrC IR02G02, mCrCIR03B07, mCrCIR03C08, mCrCIR03G05, mCrCIR04H06, mCrCIR05A05, mCrCIR07D05, mCrCIR07 D06; Table 1). The polymerase chain reactions (PCRs) were performed with wellRED oligonucleotides (Sigma-Aldrich, St Louis, MO, USA) with the following protocol: Mastercycler epgradient S (Eppendorf Scientific Inc., Westbury, NY, USA); reaction volume 15 ml: 0.8 U Taq polymerase (Fermentas, Burlington, VT, USA), reaction buffer 750 mM Tris-HCl (pH 9), 50 mM KCl, 200 mM (NH 4 ) 2 SO 4 , 0.001% bovine serum albumin, 0.1 mM of each dNTP, 5 mM MgCl 2 , 3 mM of each primer, 30 ng DNA; PCR programme: 94 1C for 5 min; 40 cycles of 30 s at 94 1C, 1 min at 50-55 1C and 30 s at 72 1C; final elongation 10 min at 72 1C).…”

Citrus genomics

“…They were used to develop 79 SSRs for direct anchoring of the Clementine genetic and physical maps . SSR markers have been included in citrus genetic maps (Chen et al 2008a;Lyon et al 2007;Luro et al 2007;Ollitrault et al 2008b;. In addition to genetic mapping, SSRs were used for: the analysis of genetic diversity Corazza-Nunes et al 2002;Barkley et al 2006), discriminating zygotic and nucellar seedlings (Ruiz et al 2000;Oliveira et al 2002;Rao et al 2007), control of the origin of plants obtained by induced gynogenesis (Froelicher et al 2007;Aleza et al 2009), molecular characterization of triploid cultivars (Aleza et al 2010) or somatic hybrids Bassene et al 2009a) and the analysis of the origin of 2n gametes (Luro et al 2004;Chen et al 2008c;Cuenca et al 2009;Ferrante et al 2010).…”

Characterization of Citrus Cultivars and Clones in Cyprus Through Microsatellite and RAPD Analysis

“…in citrus, SSRs and iSSR have been applied for identification of species/cultivars/clones (2,8,12,14,18,20,22,23,25,28,30), for phylogenetic studies (3,13,32) and construction of genetic maps (5,9,21).…”