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Association mapping and validation of QTLs for flour yield in the soft winter wheat variety Kitahonami.

Ishikawa G, Nakamura K, Ito H, Saito M, Sato M, Jinno H, Yoshimura Y, Nishimura T, Maejima H, Uehara Y, Kobayashi F, Nakamura T - PLoS ONE (2014)

Bottom Line: The winter wheat variety Kitahonami shows a superior flour yield in comparison to other Japanese soft wheat varieties.In eighteen of these, Kitahonami alleles showed positive effects.Among these, QTLs on chromosomes 3B and 7A showed highly significant and consistent effects across the three populations.

View Article: PubMed Central - PubMed

Affiliation: NARO Tohoku Agricultural Research Center, Morioka, Iwate, Japan.

ABSTRACT
The winter wheat variety Kitahonami shows a superior flour yield in comparison to other Japanese soft wheat varieties. To map the quantitative trait loci (QTL) associated with this trait, association mapping was performed using a panel of lines from Kitahonami's pedigree, along with leading Japanese varieties and advanced breeding lines. Using a mixed linear model corrected for kernel types and familial relatedness, 62 marker-trait associations for flour yield were identified and classified into 21 QTLs. In eighteen of these, Kitahonami alleles showed positive effects. Pedigree analysis demonstrated that a continuous pyramiding of QTLs had occurred throughout the breeding history of Kitahonami. Linkage analyses using three sets of doubled haploid populations from crosses in which Kitahonami was used as a parent were performed, leading to the validation of five of the eight QTLs tested. Among these, QTLs on chromosomes 3B and 7A showed highly significant and consistent effects across the three populations. This study shows that pedigree-based association mapping using breeding materials can be a useful method for QTL identification at the early stages of breeding programs.

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UPGMA dendrogram showing the pattern of genetic diversity among the 164 accessions based on the analysis of 6,042 SNP markers.Open and black circles indicate accessions found in the Association panel. Black circle means accessions in Kitahonami's pedigree. Numbers outside of the dendrogram correspond to accession numbers in Table S1 in File S1.
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pone-0111337-g002: UPGMA dendrogram showing the pattern of genetic diversity among the 164 accessions based on the analysis of 6,042 SNP markers.Open and black circles indicate accessions found in the Association panel. Black circle means accessions in Kitahonami's pedigree. Numbers outside of the dendrogram correspond to accession numbers in Table S1 in File S1.

Mentions: To investigate relationships among accessions, a cladogram was generated based on a distance matrix. Little difference was observed between the marker types, therefore only the cladogram generated from the SNP genotyping was employed here. As shown in Fig. 2, accessions were classified into two main clusters, and most accessions in the association panel into the same cluster. Particularly, clusters within the first four nodes from Kitahonami (Acc. no. 1) displayed relatively short distances and contained 35.4% (23/65) of accessions in the association panel. This indicates that familial relationship should be taken into account for association mapping.


Association mapping and validation of QTLs for flour yield in the soft winter wheat variety Kitahonami.

Ishikawa G, Nakamura K, Ito H, Saito M, Sato M, Jinno H, Yoshimura Y, Nishimura T, Maejima H, Uehara Y, Kobayashi F, Nakamura T - PLoS ONE (2014)

UPGMA dendrogram showing the pattern of genetic diversity among the 164 accessions based on the analysis of 6,042 SNP markers.Open and black circles indicate accessions found in the Association panel. Black circle means accessions in Kitahonami's pedigree. Numbers outside of the dendrogram correspond to accession numbers in Table S1 in File S1.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4215981&req=5

pone-0111337-g002: UPGMA dendrogram showing the pattern of genetic diversity among the 164 accessions based on the analysis of 6,042 SNP markers.Open and black circles indicate accessions found in the Association panel. Black circle means accessions in Kitahonami's pedigree. Numbers outside of the dendrogram correspond to accession numbers in Table S1 in File S1.
Mentions: To investigate relationships among accessions, a cladogram was generated based on a distance matrix. Little difference was observed between the marker types, therefore only the cladogram generated from the SNP genotyping was employed here. As shown in Fig. 2, accessions were classified into two main clusters, and most accessions in the association panel into the same cluster. Particularly, clusters within the first four nodes from Kitahonami (Acc. no. 1) displayed relatively short distances and contained 35.4% (23/65) of accessions in the association panel. This indicates that familial relationship should be taken into account for association mapping.

Bottom Line: The winter wheat variety Kitahonami shows a superior flour yield in comparison to other Japanese soft wheat varieties.In eighteen of these, Kitahonami alleles showed positive effects.Among these, QTLs on chromosomes 3B and 7A showed highly significant and consistent effects across the three populations.

View Article: PubMed Central - PubMed

Affiliation: NARO Tohoku Agricultural Research Center, Morioka, Iwate, Japan.

ABSTRACT
The winter wheat variety Kitahonami shows a superior flour yield in comparison to other Japanese soft wheat varieties. To map the quantitative trait loci (QTL) associated with this trait, association mapping was performed using a panel of lines from Kitahonami's pedigree, along with leading Japanese varieties and advanced breeding lines. Using a mixed linear model corrected for kernel types and familial relatedness, 62 marker-trait associations for flour yield were identified and classified into 21 QTLs. In eighteen of these, Kitahonami alleles showed positive effects. Pedigree analysis demonstrated that a continuous pyramiding of QTLs had occurred throughout the breeding history of Kitahonami. Linkage analyses using three sets of doubled haploid populations from crosses in which Kitahonami was used as a parent were performed, leading to the validation of five of the eight QTLs tested. Among these, QTLs on chromosomes 3B and 7A showed highly significant and consistent effects across the three populations. This study shows that pedigree-based association mapping using breeding materials can be a useful method for QTL identification at the early stages of breeding programs.

Show MeSH