Tree Genetics & Genomes

, Volume 3, Issue 3, pp 239–249

Development of a new SSR-based linkage map in apricot and analysis of synteny with existing Prunus maps

Authors

    • Dipartimento di Colture ArboreeUniversity of Bologna
  • O. Lain
    • Dipartimento di Scienze agrarie e ambientaliUniversity of Udine
  • F. Geuna
    • Dipartimento di Produzione VegetaleUniversity of Milano
  • R. Banfi
    • Dipartimento di Produzione VegetaleUniversity of Milano
  • F. Gaiotti
    • Dipartimento di Colture ArboreeUniversity of Bologna
  • S. Tartarini
    • Dipartimento di Colture ArboreeUniversity of Bologna
  • D. Bassi
    • Dipartimento di Produzione VegetaleUniversity of Milano
  • R. Testolin
    • Dipartimento di Scienze agrarie e ambientaliUniversity of Udine
Original Paper

DOI: 10.1007/s11295-006-0059-8

Cite this article as:
Dondini, L., Lain, O., Geuna, F. et al. Tree Genetics & Genomes (2007) 3: 239. doi:10.1007/s11295-006-0059-8

Abstract

Linkage maps of the apricot accessions ‘Lito’ and ‘BO 81604311’ were constructed using a total of 185 simple sequence repeat (SSR) markers sampled from those isolated in peach, almond, apricot and cherry; 74 were derived from a new apricot genomic library enriched for AG/CT microsatellite repeats (UDAp series), and in total, 98 had never been mapped in Prunus before. Eight linkage groups putatively corresponding to the eight haploid apricot chromosomes were identified for each parent. The two maps were 504 and 620 cM long, respectively, with 96 anchor markers showing a complete co-linearity between the two genomes. As few as three gaps larger than 15 cM were present in ‘Lito’ and six in the male parent; the maps align well with all the available SSR-based Prunus maps through the many common anchor loci. Only occasionally inverted positions between adjacent markers were found, and this can be explained by the small size of cross populations analysed in these Prunus maps and in those reported in literature. The newly developed apricot SSRs will help saturating the existing Prunus maps and will extend the choice of markers in the development of genetic maps for new breeding populations.

Keywords

Prunus armeniaca L.Genetic mapLinkage mapMolecular markersMicrosatellites

Introduction

The genus Prunus comprises such important fruit crops as almond, apricot, cherry, plum and peach. A better knowledge of the genetics of these species is fundamental for the development of new breeding programmes based on the knowledge of where genes/quantitative trait loci (QTLs) are located and marker-assisted selection (MAS). The first step in this direction is the development of molecular maps to tag genes and to find molecular markers associated with those genes.

In recent years, genetic maps have been produced for several stone-fruit and related species, including almond (Viruel et al. 1995; Joobeur et al. 2000; Ballester et al. 2001), peach and related wild species like Prunus davidiana and Prunus ferganensis (Rajapakse et al. 1995; Dirlewanger et al. 1998, 1999; Lu et al. 1998; Dettori et al. 2001; Yamamoto et al. 2001; Etienne et al. 2002; Foulongne et al. 2003; Decroocq et al. 2005; Verde et al. 2005), apricot (Hurtado et al. 2002; Vilanova et al. 2003; Lambert et al. 2004), myrobalan plum (Dirlewanger et al. 2004b) and cherry (Wang et al. 1998). Maps from two interspecific peach × almond crosses have also been produced (Joobeur et al. 1998; Jáuregui et al. 2001; Bliss et al. 2002; Aranzana et al. 2003), one of which, the F2 ‘Texas’ (almond) × ‘Earlygold’ (peach), coded as ‘TxE’, provided the Prunus reference map (Joobeur et al. 1998; Aranzana et al. 2003). This reference map features, in its latest version, 562 markers, 264 of which are microsatellites. The mean distance between markers is 0.9 cM and the largest gap is 7 cM (Dirlewanger et al. 2004a; Howad et al. 2005).

Several genes/QTLs for important agronomic traits have already been mapped in stone fruit species (reviewed by Dirlewanger et al. 2004a) and MAS has become a routine procedure in some breeding programmes. The comparison of the position of anchor markers [restriction fragment length polymorphisms, simple sequence repeats (SSRs) and isozymes] in the ‘TxE’ reference map and the other 13 maps constructed with Prunus populations showed that the genomes of diploid (2n = 16) species like almond, apricot, sweet cherry, peach, Prunus cerasifera, P. davidiana and P. ferganensis are essentially co-linear (Dirlewanger et al. 2004a). Such co-linearity eases the construction of framework maps and the saturation of chromosomal regions of interest virtually in any cross involving Prunus species by making use of markers of known position.

The first apricot map was based on an F1 progeny (‘Goldrich’ × ‘Valenciano’) segregating for resistance to Sharka, the disease caused by plum pox virus (PPV) (Hurtado et al. 2002). ‘Goldrich’ is known to be tolerant to the pathogen while ‘Valenciano’ was described as susceptible (Martinez-Gomez et al. 2000; Dicenta et al. 2000). The second apricot map based on an F2 population (‘Lito’ selfed) was constructed using amplification fragment length polymorphism and SSR markers (Vilanova et al. 2003). Two important agronomic traits such as PPV (‘D’ strain) resistance and self-incompatibility segregated in this progeny and mapped on linkage groups (LGs) 1 and 6, respectively. The third map from the cross ‘Polonais’ × ‘Stark Earli-Orange’ had a sufficient number of anchor markers to enable the alignment of the eight LGs of apricot with those of the ‘TxE’ reference map (Lambert et al. 2004).

We report the construction of two new apricot genetic maps using the cross ‘Lito’ × ‘BO 81604311’. The new maps include more than 100 SSRs already mapped in other Prunus species and enable the comparison of marker position among all the other maps and studies on synteny. Our new maps also include more than 70 new SSRs developed in apricot and characterised by a high transferability in Prunus (Messina et al. 2004) that will increase the number of SSRs available for the saturation of existing maps and the creation of framework maps in new cross populations.

Materials and methods

Plant material

A cross between the apricot genotypes ‘Lito’ and ‘BO81604311’, the latter being the pollen parent, was adopted as mapping population. ‘Lito’ (‘Stark Earli-Orange’ × ‘Tirynthos’) is reported to be resistant to PPV, strain D, the causal agent of Sharka (Vilanova et al. 2003), while the breeding line ‘BO81604311’ (‘San Castrese’ × ‘Reale di Imola’) is susceptible to it. Other phenotypical traits for which segregation is expected in the progeny are fruit size, firmness, flesh soluble solids and acid content. The mapping population consisted of 125 individuals.

DNA extraction

Genomic DNA was extracted from 200 mg of freeze-dried young leaves collected in spring after Mercado et al. (1999). After extraction in cetyltrimethylammonium bromide buffer, samples were mixed to dichloromethane/isoamyl-alcohol (24:1) and spun for 5 min at 10,000 rpm. Samples were then treated with RNase for 30 min at 37°C and purified again with dichloromethane/isoamyl-alcohol (24:1) as above. DNA quality and yield were assessed by electrophoresis on 1% agarose gel followed by gel image analysis using the Molecular Analyst 1.4.1 software (BioRad, Hercules, CA, USA).

SSR marker analysis

A list of 323 SSRs isolated from different Prunus species in the literature (Table 1) included 44 SSRs from almond (Testolin et al. 2004), 149 from apricot (Lopes et al. 2002; Decroocq et al. 2003; Messina et al. 2004; Hagen et al. 2004), 109 from peach (Cipriani et al. 1999; Sosinski et al. 2000; Dirlewanger et al. 2002; Aranzana et al. 2002), and 21 from sweet cherry (Clarke and Tobutt 2003). The segregation patterns for all SSRs isolated from apricot and for a large number of SSRs isolated from other Prunus species were tested, with preference for those already mapped in stone fruit and related species. The screening was carried out on the two parents and six individuals of the progeny. The analysis was extended to 94 individuals (but 63 SSR markers were analysed on 125) of the progeny for markers that showed a segregation pattern suitable for mapping.
Table 1

SSR markers series used for the F1 ‘Lito’ × ‘BO81604311’ map construction

Species

SSR series

Motif

Author

Available

Tested

Amplifying

Mapped

Loci

% on map

Almond

UDA

AC,AT,CA,CT,GT,TG,TC

Testolin et al. 2004

44

44

19

11

11

25.0

Apricot

AMPA

AC,AG,AAG

Hagen et al. 2004

24

24

22

21

22

87.5

Apricot

PaCITA

AG,CT,CTT,GA,TC

Lopes et al. 2002

21

21

20

15

15

71.4

Apricot

Pac

CA,GA,GGA

Decroocq et al. 2003

10

10

10

5

5

50.0

Apricot

UDAp

AG

Messina et al. 2004

94

94

79

74

84

78.7

Peach

BPPCT

AG

Dirlewanger et al. 2002

38

38

27

27

29

71.1

Peach

CPPCT

CT,GA,TC

Aranzana et al. 2002

35

35

16

11

11

31.4

Peach

pchc(g)ms

AC,AG

Sosinski et al. 2000

10

6

5

5

5

83.3

Peach

UDP

AC,AG,CA,GA,TG

Cipriani et al. 1999; Testolin et al. 2000

26

26

20

14

17

53.8

Sweet cherry

EMPA

AAC,AC,AG,GA,CT

Clarke and Tobutt 2003

21

21

5

4

4

19.0

Total

   

323

319

223

187

203

58.6

Source species, series code, motif, reference and number of markers of the series are reported together with the number tested in the present work and their usefulness in our apricot mapping population.

PCR amplifications were performed according to the standard protocols adopted in each of the three laboratories (Universities of Bologna, Milano and Udine) involved in the study. Three different methods for SSR analysis were used. Part of the SSRs were amplified with standard primers, PCR products separated by electrophoresis on 5% denaturing polyacrylamide gel and fragments visualised by silver staining (Silver Sequencing Kit, Promega, Madison, WI, USA). Other SSRs were amplified with 33P-labelled forward primers, fragments separated as above and visualised by autoradiography. The last set of SSRs was amplified with FAM or HEX dye-labelled forward primers, run on a MegaBACE 500 capillary sequencer (Amersham Biosciences, Piscataway, NJ, USA) and fragments were called and sized using the Fragment Profiler version 1.2 software (Amersham Biosciences). We tried to adapt the PCR annealing temperatures to make multiplex runs. In the case of lack of amplification, we repeated the analysis with the original annealing temperature reported in literature for the specific primer pair.

Linkage analysis

Segregation analysis of individual loci, identification of LGs and linear sequence of markers were done with JoinMap 3.0 (van Ooijen and Voorrips 2002), which allows linkage analysis of markers showing different segregation patterns in the same mapping population. Markers were first grouped using a minimum LOD score of 5; all markers were included even if they showed skewed segregations. Kosambi’s function was used for calculating map distances. Markers creating severe conflicts during ordering were removed from the map and assigned to a LG.

To exclude the possibility that a high total χ2 value was due to mistakes in the map data set, the segregation of each marker was scored three times, and the data indicated by Joinmap as putative double recombinants were checked again. The order of the markers for each LG was also verified on the basis of the recombination frequencies and the LOD values calculated by Joinmap 3.0 among the neighbouring loci. Linkage maps were drawn using the MapChart 2.1 Software (Voorrips 2002).

Results and discussion

Transferability, polymorphism and segregation of SSR markers

Of the 319 microsatellite markers tested in the cross parents and mapping population, 223 (69.9%) gave amplification products and 187 (58.6%) segregated in the progeny and were mapped. Because several primer pairs amplified more than one locus, the total number of loci mapped rose to 203 (Table 1). The percentage of amplified and mapped SSR markers largely depended on the source species (Table 1). The microsatellites isolated from apricot showed on average, as expected, the highest degree of transferability to the cross population and also mapped in high percentages: 78.7% for the UDAp series, 87.5% for the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) series, 71.4% for the PaCITA series and 50% for the Pac series. The Pac series showed the lowest degree of polymorphism among the apricot markers (as evinced by the lowest percentage on map; Table 1). We thought it was because they were isolated from cDNA libraries rather than the genomic libraries, as it was for the first three series. SSRs originated from expressed sequence tag sequences are often reported in literature to be less polymorphic because of the repeat shortness. The length of the Pac SSR repeats was reasonably large (Hagen et al. 2004), so that other features were likely responsible for their relatively low usefulness in our population.

The SSRs isolated from peach showed a variable degree of transferability to our apricot progeny. The best results were found for the pchc(g)ms series with 83.3% of tested SSRs being mapped, followed by the BPPCT (71.1%), the uridine diphosphate (UDP) (53.8%) and the CPCCT series (31.4%). A very low rate of markers that were transferable and suitable for mapping was also found among the SSRs isolated from cherry (19%) and almond (25%) (Table 1).

Map construction

A total of 187 SSR primer pairs segregated in one of the five models enabling the linkage analysis between markers as per the JoinMap software (Table 2). About half of the 203 identified loci showed a co-dominant segregation pattern (Table 2): 38.9% were fully informative (<abxcd> and <abxac>) and another 5% were of the type <abxab>. A further 1.5% of the <abxab> markers showed a 3:1 segregation and were assigned to the LG but not used in map construction. Among the polymorphic SSRs, the percentage of fully informative co-dominant markers did not vary among the different SSR series, especially those from apricot and peach. By contrast, the SSRs derived from almond and cherry evinced a higher percentage of dominant markers, 72.7 and 75%, respectively (Table 2).
Table 2

Amplification and segregation patterns of the mapped SSR loci as per Joinmap 3.0

Species

SSR series

Loci

Dominant

<abxab>

<abxac>

<abxcd>

<abxab> 3:1

n

%

n

%

n

%

n

%

n

%

Almond

UDA

11

8

72.7

0

0.0

2

18.2

1

9.1

0

0.0

Apricot

AMPA

22

12

54.5

2

9.1

4

18.2

3

13.6

1

4.5

Apricot

PaCITA

15

7

46.7

0

0.0

4

26.7

4

26.7

0

0.0

Apricot

Pac

5

2

40.0

0

0.0

1

20.0

2

40.0

0

0.0

Apricot

UDAp

84

44

52.4

4

4.8

17

20.2

19

22.6

0

0.0

Peach

BPPCT

29

17

58.6

2

6.9

5

17.2

4

13.8

1

3.4

Peach

CPPCT

11

5

45.5

2

18.2

2

18.2

2

18.2

0

0.0

Peach

pchc(g)ms

5

2

40.0

0

0.0

2

40.0

0

0.0

1

20.0

Peach

UDP

17

11

64.7

0

0.0

4

23.5

2

11.8

0

0.0

S. cherry

EMPA

4

3

75.0

0

0.0

0

0.0

1

25.0

0

0.0

Total

 

203

111

54.7

10

4.9

41

20.2

38

18.7

3

1.5

For each marker series the number of loci and the segregation type are reported. Markers showing a segregation <abxab> with a ratio 3:1 were assigned to the LG but not used in the map construction.

The frequencies of different segregation patterns for the peach UDP and CPCCT markers (Table 2) were in agreement with those reported by Vilanova et al. (2003). The whole EMPA and UDAp series had never been mapped in Prunus, while the PaCITA and UDA series were never mapped in apricot.

A total of 144 SSR loci were segregating in ‘Lito’ and the same number, although not always the same markers, in the male parent ‘BO81604311’. All markers were assigned to the LGs at LOD ≥ 5.0 to ensure the robustness of the maps. The LGs were named according to the ‘TxE’ reference map. Homologous LGs were identified by means of the many SSR anchor markers shared between our and most of the published linkage maps.

The number of markers for each LG ranged from 8 to 28 in ‘Lito’ and from 4 to 27 in ‘BO81604311’ (Table 3). Apart from LG 8, which contains few SSR markers, as reported in several published Prunus maps (Vilanova et al. 2003; Lambert et al. 2004; Decroocq et al. 2005), the minimum number of loci per LG was 14 in ‘Lito’ and 12 in the male parent.
Table 3

The number of mapped markers, size of the LGs, markers density in cM (mean distance), number of gaps larger than 15 cM and number of SSRs in common with other maps (CS) are reported for each LG. Markers assigned to the LG but not mapped were excluded

Lito

BO81604311

LG

Loci

Length

Mean distance

Gaps >15 cM

CS

LG

Loci

Length

Mean distance

Gaps >15 cM

CS

 

n

cM

cM

n

  

n

cM

cM

n

 

1

28

87

3.1

0

10

1

25

121

4.8

1

13

2

26

67

2.6

0

7

2

27

90

3.3

0

8

3

14

54

3.9

1

6

3

23

70

3.0

0

8

4

14

58

4.1

1

6

4

18

65

3.6

1

11

5

19

62

3.3

0

11

5

17

79

4.6

0

8

6

20

62

3.1

0

10

6

18

80

4.4

1

9

7

15

68

4.5

0

6

7

12

73

6.1

1

6

8

8

46

5.8

1

3

8

4

42

10.5

2

2

Total

144

504

3.5

3

59

 

144

620

4.3

6

65

The total map length was 504 cM in ‘Lito’ and 620 cM in ‘BO81604311’. The difference between the two maps was mainly due to markers that mapped only in the male parent at the ends of the first six LGs. These markers extended the length of their LGs and, in turn, total map length (Fig. 1). The lengths of our maps (and of each LG) are not far from those reported by others in apricot, ranging from 467 cM in ‘Valenciano’ (Hurtado et al. 2002) to 699 cM in ‘Stark Earli-Orange’ (Lambert et al. 2004), as well as in the Prunus reference map, which covers 519 cM (Dirlewanger et al. 2004a).
https://static-content.springer.com/image/art%3A10.1007%2Fs11295-006-0059-8/MediaObjects/11295_2006_59_Fig1a_HTML.gifhttps://static-content.springer.com/image/art%3A10.1007%2Fs11295-006-0059-8/MediaObjects/11295_2006_59_Fig1b_HTML.gif
Fig. 1

a and b Linkage map of ‘Lito’ (L) and ‘BO81604311’ (B). SSRs assigned to a LG but discarded when their segregations caused inconsistencies are reported underneath the relative LG. Markers placed by scoring each allele as dominant are indicated by progressive numbers. Multilocus markers are underlined. Individual loci of multilocus markers are indicated by letters. Markers that were not previously mapped are reported in bold. Markers that identify new loci in the present maps are reported in italics

There are 89 co-dominant markers placed in both maps, and their relative position confirms the robustness of the linear order of the markers and the perfect co-linearity of the genomes of the two parents (Fig. 1). Only a minor inversion was observed in LG 4 (L4–B4) between the two very close (0.5 cM) pchgms 2 and UDAp-480 microsatellites. The reliability of the order of the markers is also confirmed by the high number of SSRs in common with other maps (59 in ‘Lito’ and 65 in ‘BO81604311’; Table 3 and Fig. 2).
https://static-content.springer.com/image/art%3A10.1007%2Fs11295-006-0059-8/MediaObjects/11295_2006_59_Fig2a_HTML.gifhttps://static-content.springer.com/image/art%3A10.1007%2Fs11295-006-0059-8/MediaObjects/11295_2006_59_Fig2b_HTML.gif
Fig. 2

a and b Alignment of different SSR-based Prunus maps: ‘TxE’ F2 almond × peach (Aranzana et al. 2003), ‘Lito’ (L) and ‘BO81604311’ (B) from the present paper, Myrabolan (P2175) and almond × peach (GN22) (Dirlewanger et al. 2004b), (peach × P. ferganensis)× peach (PxF) (Verde et al. 2005), ‘Polonais’ (P) and ‘Stark Earli-Orange’ (SEO) F1 apricot (Lambert et al. 2004), ‘Lito’ apricot selfed (F2L) (Vilanova et al. 2003). The map from Hurtado et al. (2002) was not included due to the limited number of common SSR loci. The orientation of the LGs with just one SSR is tentative

To our knowledge, 98 SSRs (in bold in Fig. 1a,b) had never been mapped before in Prunus species: 74 from the apricot series UDAp (Messina et al. 2004), 4 PaCITA (Lopes et al. 2002), 9 AMPA (Hagen et al. 2004), 4 from the sweet cherry EMPA (Clarke and Tobutt 2003), 6 from almond UDA (Testolin et al. 2004) and 1 from peach BPPCT series (Dirlewanger et al. 2002).

Most of the markers scored as multilocus showed very close loci that mapped in the same LG, e.g. AMPA123, UDAp-412, UDAp-417, UDAp-421 and UDAp-429, with two loci each. The exceptions were BPPCT033 (LG 3 and LG 6) and UDAp-431 (LG 5 and LG 7) in ‘Lito’ and UDAp-435 (LG 1 and LG 6) in the male parent (Fig. 1). UDP-415 amplified six loci in the female and male parents, five of them very close to each other in LG 7, while the sixth locus (UDP-415-5) mapped at the top of LG 3 of ‘BO81604311’ (Fig. 1). Seven SSR primer pairs (Table 4) amplified segregating fragments in both maps and were assigned to different LGs in respect to the other SSR-enriched Prunus maps available (Vilanova et al. 2003; Lambert et al. 2004; Aranzana et al. 2003; Dirlewanger et al. 2004a,b; Verde et al. 2005). Three of these SSRs (BPPCT006, BPPCT019 and BPPCT035) are already known to be multilocus markers; therefore, it is possible that we found an additional locus in the apricot genome.
Table 4

List of multilocus SSR markers and their relative position compared with other Prunus maps

Primer name

Locus name

Map position

BPPCT006

BPPCT006C

LG 3 in (4)

BPPCT006

LG 1 in (2)

BPPCT006

LG 8 in (1) & (2)

BPPCT019

BPPCT019C

LG 1 in (4)

BPPCT019

LG 2 in (2)

BPPCT019

LG 8 in (1) & (2)

BPPCT020

BPPCT020B

LG 2 in (4)

BPPCT020

LG 1 in (1) & (2)

BPPCT033

BPPCT033A

LG 6 in (4)

BPPCT033B

LG 3 in (4)

BPPCT033

LG 6 in (2)

BPPCT035

BPPCT035C

LG 1 in (4)

BPPCT035a & b

LG 4 in (3)

UDA025

UDA025B

LG 1 in (4)

UDA025

LG 2 in (3)

UDP-415

UDP-415-1/2/3/4/6

LG 7 in (4)

UDP-415

LG 7 in (1) & (3)

UDP-415-5

LG 3 in (4)

(1) Aranzana et al. 2003, (2) Dirlewanger et al. 2004b, (3) Verde et al. 2005, (4) the maps herewith reported

Only three gaps of more than 15 cM were still present in ‘Lito’ in the LGs 3, 4 and 8; six in ‘BO81604311’ in the LGs 1, 4, 6 and 7 and two in LG 8. The linear order of markers in all LGs obtained with Joinmap 3.0 represents a ‘first-round map’, the only exception being LG 2 in ‘BO81604311’ obtained at the second round. The marker AMPA 118, included in the second round, did not alter the order of the markers of the LG, although it slightly increased the total mean χ2 of the LG.

Map alignment and synteny among the Prunus species

The SSR marker orders of our apricot maps have been compared with the published maps of apricot (Vilanova et al. 2003; Lambert et al. 2004) and those of peach × almond (Aranzana et al. 2003), myrabolan × (almond × peach) (Dirlewanger et al. 2004a,b) and (peach × P. ferganensis) × peach (Verde et al. 2005) (Fig. 2).

The high number of SSRs in common with different maps allowed us to compare their relative position. The analysis confirms that the order of markers is substantially maintained across the different species (Fig. 2). For instance, comparison of our maps to the ‘TxE’ reference map shows that the only exception to the co-linearity of markers is an inversion in the LG 1 between the two close markers CPPCT026 and CPPCT034. Another severe conflict is created by the position of the UDP-010 marker in the (peach × P. ferganensis) × peach map (‘PxF’) in the LG 6, which contrasts with the map position of the same marker in two different apricot mapping populations (Fig. 2). Verde et al. (2005), the authors of the ‘PxF’ map, reported that the UDP-010 marker showed distorted segregation. Several map conflicts were reported by Dirlewanger et al. (2004a) in their comparison between ‘TxE’ and other maps, but most of those conflicts are between adjacent markers and are likely due to the low resolution of all maps (see also at the web site http://www.mainlab.clemson.edu/gdr/MapView.shtml).

Conclusions

The transferability and the degree of polymorphism in apricot of a large set of SSR markers isolated from different Prunus species was evaluated and reflected the phylogenetic distances between apricot and the source species from which the SSRs were isolated. Our results confirm the rule: the larger the phylogenetic distance, the lower the transferability of markers, with a further source of variability due to the origin of DNA libraries and the goodness of the enrichment/isolation protocols, as reported elsewhere (Cipriani et al. 1999; Sosinski et al. 2000; Dirlewanger et al. 2002; Decroocq et al. 2003; Howad et al. 2005).

Approximately half of the tested microsatellites were mapped in both parents of the cross. The high percentage of SSRs mapped was likely due to the good polymorphism of the markers of different origin, like those isolated in apricot, but also to the choice of the cross parents that were genetically unrelated, as confirmed by the genetic diversity analysis made by Geuna et al. (2003).

The paper provides the map position of 98 previously unmapped SSRs, most of which derive from the UDAp and EMPA series. The high number of loci common to both parents and to other Prunus maps allowed the correct identification and alignment of all eight LGs. Our new apricot maps show a substantial synteny and co-linearity with the ‘TxE’ Prunus reference map and the other SSR-enriched Prunus maps available in literature (Aranzana et al. 2003; Dirlewanger et al. 2004a,b; Lambert et al. 2004; Verde et al. 2005; Vilanova et al. 2003). A few occasional inversions in the marker order were observed mainly when closely placed markers were compared in different taxa. Most conflicts have low impact in genetic studies, as they occur between adjacent markers and are likely due to the low number of informative meioses on which all published Prunus maps rely. The extension of mapping populations to progenies of larger size should likely solve many of those cases. The number of bridge markers is still limited, and very general conclusions cannot yet be drawn. Nevertheless, we do not expect to find large re-arrangements of genome organisation in Prunus in the future. The substantial co-linearity observed in previous works is confirmed. In the future, this will allow a rapid transfer of framework maps from one breeding population to another, and information gathered from one genetic map will help breeders locate the same markers/genes in related taxa.

Acknowledgements

This research work was funded by the Italian Ministry of University, Research and Technology in the framework of project PRIN 2003 ‘Resistance to PPV (Plum Pox Virus) in apricot: fine mapping of genes/QTLs and production of resistant breeding lines’.

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