Genetic mapping of Japanese plum

Genetic mapping of Japanese plum

(Parte 2 de 3)

Construction of genetic maps

Two genetic maps were constructed, one for the cultivar Chatard and the other for Santa Rosa, using the pseudo-testcross strategy (Hemmat et al. 1994, Grattapaglia et al. 1995). In the first phase of the map construction, the parents were used separately, only for the markers that were present in them showing the Mendelian proportion of 1:1 in the progeny. Afterwards the markers that presented distortion of the 1:1 segregation were added to the map. Mapmaker 3.0 (Lincoln et al. 1992) was the software used to construct the genetic linkage maps. Markers were used in the construction of the linkage groups not only in the repulsion, but also in the association phase. For this purpose, the data matrix was duplicated and the duplicated part inverted. First, a framework of the linkage groups was constructed using a LOD of 3.5 and a maximum distance of 25 cM, the marker distance being defined by the Kosambi function (Kosambi 1944). The first grouping was obtained by the command “order”, which was based on the multipoint analysis to establish the best order of the markers within each linkage group. After establishing the framework of the linkage groups, other markers were added using the command “try” under a LOD of 3.0 and a maximum distance of 30 cM. The markers that presented distortions in the 1:1 segregation were added later under the latest stringency parameters.

32 Crop Breeding and Applied Biotechnology 5:29-37, 2005

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Table 2. Number of polymorphic markers detected in the cultivars Chatard and Santa Rosa with the use of 30 combinations of AFLP primers

Each obtained linkage group received a specific name that consisted of the letters ‘F’ (Florianópolis) and ‘P’ (plum) followed by the number of the linkage group. Among the 59 markers generated in cultivar Chatard that segregate in the proportion 1:1, 46 (65%) were mapped into one of the 1 linkage groups along with 10 other markers with distorted segregation (Table 3). Therefore, 13 markers segregating in the proportion 1:1 were not mapped so far. The generated map covered a distance of 905.5 cM, and the proportion of markers linked per group varied from 3.6 to 17.9%. The linkage group sizes varied from 27.9 to 147.6 cM. Among the linkage groups, the average distance between the markers varied from 14 to 2.0 cM (Table 3). Only two intervals between two markers presented distances superior to 30 cM, located in the linkage groups FP2 and FP5. The linkage groups FP1, FP4 and FP5 were the ones that presented the highest number of linked markers: 10, 7 and 7 respectively. The linkage groups FP10 and FP11 consist of two linked markers so far (Table 3 and Figure 1).

Primers

1b 1c 1e 1h 2c 2e 2f 2h 3a 3b 3e 3f 3g 4a 4b 4c 4d 4f 4g 5b 5d 5f 5g 6c 6g 8a 8e 10a 10b 11f Total Mean Standard deviation

Total of markers

Number of markers presentSegregating marker (1:1), P > 0.01

Genetic mapping of Japanese plum

Table 4. Number of markers, size of the linkage groups and average distance between markers in cultivar Santa Rosa

Linkage groups FP1 FP2 FP3 FP4 FP5 FP6 FP7 FP8 FP9 FP10 FP11 FP12 FP13 FP14 Total Mean

Percentage 15.5 15.1 12.0 9.8 9.5 9.3 5.6 5.4 4.1 3.9 3.7 3.2 2.0 0.9 100

Size cM 209.9 203.3 161.7 132.7 128.6 125.3 75.8 73.4 54.8 52.5 49.8 42.8 26.7 12.4 1349.6

Linked % 15.5 17.9 1.9 9.5 8.2 8.2 4.8 4.8 3.6 3.6 3.6 3.6 2.4 2.4 100

Markers Length linkage groups varied from 12.4 cM to 209.8 cM. In the linkage groups, the average distance between the markers varied from 6.2 cM to 19.0 cM. Only four intervals between two markers presented a distance superior to 30 cM, located in the linkage groups FP1 and FP2 and presenting the highest number of markers, i.e. 15 and 13, respectively. The linkage groups FP13 and FP14 consist of two linked markers so far (Table 4 and Figure 2).

Among the 8 polymorphic markers generated in cultivar Santa Rosa that segregated in the proportion 1:1, 67 (76%) were mapped into one of the 14 linkage groups along with 17 other markers with distorted segregation. Thus, 21 markers segregating in the proportion 1:1 were not yet mapped. The generated map covered a distance of 1349.6 cM, and the proportion of markers linked per group varied from 2.4 to 17.9 %. In this map, the sizes of the

Table 3. Number of markers, size of the linkage groups and average distance between markers in cultivar Chatard

Linkage groups

FP1 FP2 FP3 FP4 FP5 FP6 FP7 FP8 FP9 FP10 FP11 Total Mean

Markers Length

34 Crop Breeding and Applied Biotechnology 5:29-37, 2005

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Figure 2. Genetic linkage map of cultivar Santa Rosa; Each linkage group was given a specific name which consists of the letters F (Florianópolis) and P (Plum) followed by the number of the linkage group. Values on the left indicate the distance in relation to the marker of the superior end The AFLP markers are listed on the right of the linkage groups whose terminology is formed by the combination code of primers to which it belongs (Table 1), being followed by the molecular weight of the marker, the codes (a) association configuration and (r) for repulsion configuration. * Markers with distorted segregation

Figure 1. Genetic linkage map of cultivar Chatard; Each linkage group was given a specific name which consists of the letters F (Florianópolis) and P (Plum) followed by the number of the linkage group. Values on the left indicate the distance in relation to the marker of the superior end. The AFLP markers are listed on the right of the linkage groups whose terminology is formed by the combination code of primers to which it belongs (Table 1), being followed by the molecular weight of the marker, the codes (a) association configuration and (r) for repulsion segregation. * Markers with distorted segregation

Genetic mapping of Japanese plum

Comparison with other genetic maps constructed for woody species

The number of molecular markers used to construct the maps varied from 62 in Poncirus trifoliata (Cristofani et al. 1999) to 566 in Populus deltoides (Cervera et al. 2001), demonstrating the small number of markers used for the mapping of the plum tree in the present study, i.e. 56 for cultivar Chatard and 84 for cultivar Santa Rosa (Table 5). The average distance between the linked markers is one of the most important parameters of a linkage genetic map, since it provides the degree of map saturation, which is very important for QTL mapping and the performance of marker-assisted selectio. The average distance of the mapped markers between the compared species (Table 5) varied from 14 cM in Poncirus trifoliata (Cristofani et al. 1999) to 2.3 cM in peach (Dirlewanger et al. 1998). The values found for the plum maps were 16.2 cM for Chatard and 16.1 cM for Santa Rosa, demonstrating the opportunity for saturation.

However, concerning the distance covered by the map, the obtained values of 905.5 cM for cultivar Chatard and 1349.6 cM for cultivar Santa Rosa were very similar to those obtained by the mapping of other Prunaceaes that have a haploid genome of the same size as plum, since these values can vary from 1297.0 cM in peach (Lu et al. 1998) to 415.0 cM in the almond tree (Joobeur et al. 2000).

Table 5. Comparison between the genetic maps of the plum and the ones of the woody species taking into consideration the haploid genome size (pgc), number of markers (NM), number of linkage groups per haploid number of chromosomes (NGL/NhC), size (S) in cM and average distance between linked markers in cM (AD)

Species Plum cv. “Chatard” cv. “Santa rosa” Almond cv. “ferragnés” cv. “Tuono” Citrus Citrus sunki Poncirus trifoliata Apple cv. “White angel” cv. “Rome beuty” Apple cv. “Wycik McIntosh” cv. “Ny 75441-67” cv. “75441-58” Peach x Almond Peach Peach Peach Picea abies Pinus sp. Pinus palustri Pinus elliottii Populos sp. Populus deltoides Populus nigra Populus trichocarpa Grape “Horizon” “Illinois 547-1” pgc

NGL/NhC

S cM

AD cM

Reference (Present results)

(Joobeur et al. 2000)

(Cristofani et al. 1999)

(Hemmat et al. 1994) (Conner et al. 1997)

(Foolad et al. 1995)

(Lu et al. 1998)

(Dirlewanger et al. 2000)

(Shimada et al. 2000) (Paglia et al. 1998) (Kubisiak et al. 1995)

(Cervera et al. 2001)

(Dalbó 2001)

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Mapeamento genético da ameixeira japonesa

RESUMO - Mapas genéticos de ligação de duas cultivares de ameixeiras japonesas, Chatard e Santa Rosa foram construídos com marcadores AFLP utilizando-se a estratégia do pseudo-cruzamento teste. Da população segregante oriunda do cruzamento entre estas duas cultivares, 8 plantas formaram a população de mapeamento, onde estão segregando genes para vários caracteres de interesse agronômico, entre eles, a resistência à escaldadura das folhas. O mapa da cv. Chatard apresentou 56 marcadores ligados em 1 grupos de ligação, cobrindo uma distância de 905,5 cM e apresentando uma distância média entre marcadores de 16,2 cM. O mapa da cv. Santa Rosa apresentou 84 marcadores ligados em 14 grupos de ligação, cobrindo uma distância de 1349,6 cM e apresentando uma distância média entre marcadores de 16,1 cM. Os mapas obtidos no estudo podem ser considerados como mapas básicos da espécie e necessitam ser saturados para terem maior aplicabilidade em programas de melhoramento genético.

Palavras-chave: Prunus; mapeamento genético, AFLP.

(Parte 2 de 3)

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