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Extension of the core map of common bean with EST-SSR, RGA, AFLP, and putative functional markers.

Hanai LR, Santini L, Camargo LE, Fungaro MH, Gepts P, Tsai SM, Vieira ML - Mol. Breed. (2009)

Bottom Line: On average, the polymorphism information content was 0.40 and the mean number of alleles per locus was 2.7.In addition, AFLP and RGA markers based on the NBS-profiling method were developed and a subset of the mapped RGA was sequenced.With the integration of 282 new markers into the common bean core map, we were able to place markers with putative known function in some existing gaps including regions with QTL for resistance to anthracnose and rust.

View Article: PubMed Central - PubMed

ABSTRACT
Microsatellites and gene-derived markers are still underrepresented in the core molecular linkage map of common bean compared to other types of markers. In order to increase the density of the core map, a set of new markers were developed and mapped onto the RIL population derived from the 'BAT93' x 'Jalo EEP558' cross. The EST-SSR markers were first characterized using a set of 24 bean inbred lines. On average, the polymorphism information content was 0.40 and the mean number of alleles per locus was 2.7. In addition, AFLP and RGA markers based on the NBS-profiling method were developed and a subset of the mapped RGA was sequenced. With the integration of 282 new markers into the common bean core map, we were able to place markers with putative known function in some existing gaps including regions with QTL for resistance to anthracnose and rust. The distribution of the markers over 11 linkage groups is discussed and a newer version of the common bean core linkage map is proposed.

No MeSH data available.


Related in: MedlinePlus

Amplification pattern of RGA markers in 6% silver-stained polyacrylamide gel. The DNA was digested with RsaI and amplified using the primers AP and NBSa-F. The parental lines are represented in duplicate (‘BAT 93’, lanes 1 and 2, and ‘Jalo EEP558’, lanes 3 and 4); lanes 6 through 35 correspond to F8 RILs. Arrows indicate polymorphic loci. Lane 5 shows the 25-pb DNA ladder (Invitrogen)
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Fig2: Amplification pattern of RGA markers in 6% silver-stained polyacrylamide gel. The DNA was digested with RsaI and amplified using the primers AP and NBSa-F. The parental lines are represented in duplicate (‘BAT 93’, lanes 1 and 2, and ‘Jalo EEP558’, lanes 3 and 4); lanes 6 through 35 correspond to F8 RILs. Arrows indicate polymorphic loci. Lane 5 shows the 25-pb DNA ladder (Invitrogen)

Mentions: We screened ‘BAT93’ and ‘Jalo EEP558’ for polymorphisms using 156 EST-SSR primer pairs of the PvM series, 16 combinations of restriction enzymes (RsaI, HindIII, AluI and DraI) and NBS primers (Table 1) through the NBS-profiling methodology and 28 combinations of AFLP selective primers. A total of 140 EST-SSR primer pairs amplified scorable loci, of which 50 were polymorphic. Regarding the NBS-profiling method, the restriction enzyme RsaI was chosen because it generated better amplification profiles and more polymorphic RGA loci (data not shown). The four NBS primers in combination with RsaI produced 194 loci, of which 32 were polymorphic (Fig. 2). In addition, the AFLP selective primer combinations (12 from EcoRI/MseI and 16 from PstI/MseI digestions) amplified 1,252 loci, 29% of them being polymorphic. From these, 15 combinations producing 203 polymorphic loci were selected for genotyping the mapping population (Table 3).Fig. 2


Extension of the core map of common bean with EST-SSR, RGA, AFLP, and putative functional markers.

Hanai LR, Santini L, Camargo LE, Fungaro MH, Gepts P, Tsai SM, Vieira ML - Mol. Breed. (2009)

Amplification pattern of RGA markers in 6% silver-stained polyacrylamide gel. The DNA was digested with RsaI and amplified using the primers AP and NBSa-F. The parental lines are represented in duplicate (‘BAT 93’, lanes 1 and 2, and ‘Jalo EEP558’, lanes 3 and 4); lanes 6 through 35 correspond to F8 RILs. Arrows indicate polymorphic loci. Lane 5 shows the 25-pb DNA ladder (Invitrogen)
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2837241&req=5

Fig2: Amplification pattern of RGA markers in 6% silver-stained polyacrylamide gel. The DNA was digested with RsaI and amplified using the primers AP and NBSa-F. The parental lines are represented in duplicate (‘BAT 93’, lanes 1 and 2, and ‘Jalo EEP558’, lanes 3 and 4); lanes 6 through 35 correspond to F8 RILs. Arrows indicate polymorphic loci. Lane 5 shows the 25-pb DNA ladder (Invitrogen)
Mentions: We screened ‘BAT93’ and ‘Jalo EEP558’ for polymorphisms using 156 EST-SSR primer pairs of the PvM series, 16 combinations of restriction enzymes (RsaI, HindIII, AluI and DraI) and NBS primers (Table 1) through the NBS-profiling methodology and 28 combinations of AFLP selective primers. A total of 140 EST-SSR primer pairs amplified scorable loci, of which 50 were polymorphic. Regarding the NBS-profiling method, the restriction enzyme RsaI was chosen because it generated better amplification profiles and more polymorphic RGA loci (data not shown). The four NBS primers in combination with RsaI produced 194 loci, of which 32 were polymorphic (Fig. 2). In addition, the AFLP selective primer combinations (12 from EcoRI/MseI and 16 from PstI/MseI digestions) amplified 1,252 loci, 29% of them being polymorphic. From these, 15 combinations producing 203 polymorphic loci were selected for genotyping the mapping population (Table 3).Fig. 2

Bottom Line: On average, the polymorphism information content was 0.40 and the mean number of alleles per locus was 2.7.In addition, AFLP and RGA markers based on the NBS-profiling method were developed and a subset of the mapped RGA was sequenced.With the integration of 282 new markers into the common bean core map, we were able to place markers with putative known function in some existing gaps including regions with QTL for resistance to anthracnose and rust.

View Article: PubMed Central - PubMed

ABSTRACT
Microsatellites and gene-derived markers are still underrepresented in the core molecular linkage map of common bean compared to other types of markers. In order to increase the density of the core map, a set of new markers were developed and mapped onto the RIL population derived from the 'BAT93' x 'Jalo EEP558' cross. The EST-SSR markers were first characterized using a set of 24 bean inbred lines. On average, the polymorphism information content was 0.40 and the mean number of alleles per locus was 2.7. In addition, AFLP and RGA markers based on the NBS-profiling method were developed and a subset of the mapped RGA was sequenced. With the integration of 282 new markers into the common bean core map, we were able to place markers with putative known function in some existing gaps including regions with QTL for resistance to anthracnose and rust. The distribution of the markers over 11 linkage groups is discussed and a newer version of the common bean core linkage map is proposed.

No MeSH data available.


Related in: MedlinePlus