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Leaf margin phenotype-specific restriction-site-associated DNA-derived markers for pineapple (Ananas comosus L.).

Urasaki N, Goeku S, Kaneshima R, Takamine T, Tarora K, Takeuchi M, Moromizato C, Yonamine K, Hosaka F, Terakami S, Matsumura H, Yamamoto T, Shoda M - Breed. Sci. (2015)

Bottom Line: To explore genome-wide DNA polymorphisms and identify DNA markers for leaf margin phenotypes, a restriction-site-associated DNA sequencing analysis was employed to analyze three bulked DNAs of F1 progeny from a cross between a 'piping-leaf-type' cultivar, 'Yugafu', and a 'spiny-tip-leaf-type' variety, 'Yonekura'.From the analysis, piping-leaf and spiny-tip-leaf gene-specific restriction-site-associated DNA sequencing tags were obtained and designated as PLSTs and STLSTs, respectively.The recombination value between the S locus and STLST loci was 2.4, and STLSTs were located 2.2 cM from the S locus.

View Article: PubMed Central - PubMed

Affiliation: Okinawa Prefectural Agricultural Research Center , 820 Makabe, Itoman, Okinawa 901-0336 , Japan.

ABSTRACT
To explore genome-wide DNA polymorphisms and identify DNA markers for leaf margin phenotypes, a restriction-site-associated DNA sequencing analysis was employed to analyze three bulked DNAs of F1 progeny from a cross between a 'piping-leaf-type' cultivar, 'Yugafu', and a 'spiny-tip-leaf-type' variety, 'Yonekura'. The parents were both Ananas comosus var. comosus. From the analysis, piping-leaf and spiny-tip-leaf gene-specific restriction-site-associated DNA sequencing tags were obtained and designated as PLSTs and STLSTs, respectively. The five PLSTs and two STSLTs were successfully converted to cleaved amplified polymorphic sequence (CAPS) or simple sequence repeat (SSR) markers using the sequence differences between alleles. Based on the genotyping of the F1 with two SSR and three CAPS markers, the five PLST markers were mapped in the vicinity of the P locus, with the closest marker, PLST1_SSR, being located 1.5 cM from the P locus. The two CAPS markers from STLST1 and STLST3 perfectly assessed the 'spiny-leaf type' as homozygotes of the recessive s allele of the S gene. The recombination value between the S locus and STLST loci was 2.4, and STLSTs were located 2.2 cM from the S locus. SSR and CAPS markers are applicable to marker-assisted selection of leaf margin phenotypes in pineapple breeding.

No MeSH data available.


Related in: MedlinePlus

Genetic map of the putative P (left) and S (right) loci in pineapple. In the P locus, the genetic distances and locations between each SSR and CAPS marker and the P locus were calculated from the genotypes of 169 F1 plants from a cross between a ‘piping-leaf-type’ cultivar, ‘Yugafu’, and a ‘spiny-tip-leaf-type’ breeding line, ‘Yonekura’. In the S locus, the genetic distances and locations between each CAPS marker and the S locus were calculated from the genotypes of 57 and 25 F1 plants having spiny-tip and spiny leaves, respectively. The genotypes of these markers are shown in Supplemental Table 4.
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f2-65_276: Genetic map of the putative P (left) and S (right) loci in pineapple. In the P locus, the genetic distances and locations between each SSR and CAPS marker and the P locus were calculated from the genotypes of 169 F1 plants from a cross between a ‘piping-leaf-type’ cultivar, ‘Yugafu’, and a ‘spiny-tip-leaf-type’ breeding line, ‘Yonekura’. In the S locus, the genetic distances and locations between each CAPS marker and the S locus were calculated from the genotypes of 57 and 25 F1 plants having spiny-tip and spiny leaves, respectively. The genotypes of these markers are shown in Supplemental Table 4.

Mentions: Genotypes of PLSTs and STLSTs in 169 F1 plants and 33 pineapple accessions, including the F1 parents, were scored using the SSR and CAPS markers developed (Supplemental Tables 4, 5). In the PLSTs analyses, the recombination value between the P locus and each marker from a PLST was calculated, and the genetic distance (cM) was also estimated from the F1 genotyping results. As a control for the mapping analysis of the P locus, genotypes of SSR_AJ845056 in the 169 F1 plants were also scored (Supplemental Table 4). Consequently, a genetic map surrounding the P locus could be generated (Fig. 2). The five PLSTs were distributed in the vicinity of the P locus, and the closest marker, PLST1, was located 1.5 cM from the P locus (Fig. 2). SSR_AJ845056 was located 12.2 cM from the P locus. The locus had only three recombinants, cultivars ‘Soft Touch’, ‘Okinawa No. 2’, and ‘Okinawa No. 19’; therefore, PLST1_SSR showed the ability to identify leaf margin phenotypes in the tested pineapple resources (Supplemental Table 5).


Leaf margin phenotype-specific restriction-site-associated DNA-derived markers for pineapple (Ananas comosus L.).

Urasaki N, Goeku S, Kaneshima R, Takamine T, Tarora K, Takeuchi M, Moromizato C, Yonamine K, Hosaka F, Terakami S, Matsumura H, Yamamoto T, Shoda M - Breed. Sci. (2015)

Genetic map of the putative P (left) and S (right) loci in pineapple. In the P locus, the genetic distances and locations between each SSR and CAPS marker and the P locus were calculated from the genotypes of 169 F1 plants from a cross between a ‘piping-leaf-type’ cultivar, ‘Yugafu’, and a ‘spiny-tip-leaf-type’ breeding line, ‘Yonekura’. In the S locus, the genetic distances and locations between each CAPS marker and the S locus were calculated from the genotypes of 57 and 25 F1 plants having spiny-tip and spiny leaves, respectively. The genotypes of these markers are shown in Supplemental Table 4.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482178&req=5

f2-65_276: Genetic map of the putative P (left) and S (right) loci in pineapple. In the P locus, the genetic distances and locations between each SSR and CAPS marker and the P locus were calculated from the genotypes of 169 F1 plants from a cross between a ‘piping-leaf-type’ cultivar, ‘Yugafu’, and a ‘spiny-tip-leaf-type’ breeding line, ‘Yonekura’. In the S locus, the genetic distances and locations between each CAPS marker and the S locus were calculated from the genotypes of 57 and 25 F1 plants having spiny-tip and spiny leaves, respectively. The genotypes of these markers are shown in Supplemental Table 4.
Mentions: Genotypes of PLSTs and STLSTs in 169 F1 plants and 33 pineapple accessions, including the F1 parents, were scored using the SSR and CAPS markers developed (Supplemental Tables 4, 5). In the PLSTs analyses, the recombination value between the P locus and each marker from a PLST was calculated, and the genetic distance (cM) was also estimated from the F1 genotyping results. As a control for the mapping analysis of the P locus, genotypes of SSR_AJ845056 in the 169 F1 plants were also scored (Supplemental Table 4). Consequently, a genetic map surrounding the P locus could be generated (Fig. 2). The five PLSTs were distributed in the vicinity of the P locus, and the closest marker, PLST1, was located 1.5 cM from the P locus (Fig. 2). SSR_AJ845056 was located 12.2 cM from the P locus. The locus had only three recombinants, cultivars ‘Soft Touch’, ‘Okinawa No. 2’, and ‘Okinawa No. 19’; therefore, PLST1_SSR showed the ability to identify leaf margin phenotypes in the tested pineapple resources (Supplemental Table 5).

Bottom Line: To explore genome-wide DNA polymorphisms and identify DNA markers for leaf margin phenotypes, a restriction-site-associated DNA sequencing analysis was employed to analyze three bulked DNAs of F1 progeny from a cross between a 'piping-leaf-type' cultivar, 'Yugafu', and a 'spiny-tip-leaf-type' variety, 'Yonekura'.From the analysis, piping-leaf and spiny-tip-leaf gene-specific restriction-site-associated DNA sequencing tags were obtained and designated as PLSTs and STLSTs, respectively.The recombination value between the S locus and STLST loci was 2.4, and STLSTs were located 2.2 cM from the S locus.

View Article: PubMed Central - PubMed

Affiliation: Okinawa Prefectural Agricultural Research Center , 820 Makabe, Itoman, Okinawa 901-0336 , Japan.

ABSTRACT
To explore genome-wide DNA polymorphisms and identify DNA markers for leaf margin phenotypes, a restriction-site-associated DNA sequencing analysis was employed to analyze three bulked DNAs of F1 progeny from a cross between a 'piping-leaf-type' cultivar, 'Yugafu', and a 'spiny-tip-leaf-type' variety, 'Yonekura'. The parents were both Ananas comosus var. comosus. From the analysis, piping-leaf and spiny-tip-leaf gene-specific restriction-site-associated DNA sequencing tags were obtained and designated as PLSTs and STLSTs, respectively. The five PLSTs and two STSLTs were successfully converted to cleaved amplified polymorphic sequence (CAPS) or simple sequence repeat (SSR) markers using the sequence differences between alleles. Based on the genotyping of the F1 with two SSR and three CAPS markers, the five PLST markers were mapped in the vicinity of the P locus, with the closest marker, PLST1_SSR, being located 1.5 cM from the P locus. The two CAPS markers from STLST1 and STLST3 perfectly assessed the 'spiny-leaf type' as homozygotes of the recessive s allele of the S gene. The recombination value between the S locus and STLST loci was 2.4, and STLSTs were located 2.2 cM from the S locus. SSR and CAPS markers are applicable to marker-assisted selection of leaf margin phenotypes in pineapple breeding.

No MeSH data available.


Related in: MedlinePlus