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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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Scatter diagrams of principal component (PC) 1, 2 and 3 values calculated by the PCA function of TASSEL 3.0 using 2,933 DArT (A) and 6,042 SNP (B) markers.
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pone-0111337-g001: Scatter diagrams of principal component (PC) 1, 2 and 3 values calculated by the PCA function of TASSEL 3.0 using 2,933 DArT (A) and 6,042 SNP (B) markers.

Mentions: Array-based marker analyses allowed the identification of 2,933 polymorphic DArT (Dataset S1 in File S2) and 6,042 polymorphic SNP markers (Dataset S2 in File S2) using 151 and 164 accessions, respectively. To obtain an overview of the genetic diversity of the accessions, a PCA was performed with each marker type. With the DArT markers, principal component (PC) 1, PC2 and PC3 explained 9.0, 4.6 and 3.9% of the total variation, while the first three PCs from the SNP markers explained 15.0, 5.2 and 3.5% of the variation. Scatter plots of PC1 and either PC2 or PC3 showed similar distribution patterns for both marker types (Fig. 1). These plots indicated that the accessions were distributed continuously and did not form any clear clusters. For the association panel, most accessions showed high PC1 values, but no clear tendencies were observed with PC2 and PC3 values. Based on the source of the accessions, PC1 represents the axis of earliness or growth habit (data not shown). In the scatter plots of SNP markers, two accessions, U24 (Acc. no. 114) and Gabo (124), showed outlier values in PC2 and PC3. This indicates that the SNP markers used in this study have more power to distinguish lines than the DArT markers.


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)

Scatter diagrams of principal component (PC) 1, 2 and 3 values calculated by the PCA function of TASSEL 3.0 using 2,933 DArT (A) and 6,042 SNP (B) markers.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111337-g001: Scatter diagrams of principal component (PC) 1, 2 and 3 values calculated by the PCA function of TASSEL 3.0 using 2,933 DArT (A) and 6,042 SNP (B) markers.
Mentions: Array-based marker analyses allowed the identification of 2,933 polymorphic DArT (Dataset S1 in File S2) and 6,042 polymorphic SNP markers (Dataset S2 in File S2) using 151 and 164 accessions, respectively. To obtain an overview of the genetic diversity of the accessions, a PCA was performed with each marker type. With the DArT markers, principal component (PC) 1, PC2 and PC3 explained 9.0, 4.6 and 3.9% of the total variation, while the first three PCs from the SNP markers explained 15.0, 5.2 and 3.5% of the variation. Scatter plots of PC1 and either PC2 or PC3 showed similar distribution patterns for both marker types (Fig. 1). These plots indicated that the accessions were distributed continuously and did not form any clear clusters. For the association panel, most accessions showed high PC1 values, but no clear tendencies were observed with PC2 and PC3 values. Based on the source of the accessions, PC1 represents the axis of earliness or growth habit (data not shown). In the scatter plots of SNP markers, two accessions, U24 (Acc. no. 114) and Gabo (124), showed outlier values in PC2 and PC3. This indicates that the SNP markers used in this study have more power to distinguish lines than the DArT markers.

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