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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 predicted and actual FlYd values in DH lines.Regression models were constructed using the three DH populations together (DH_total) (A) or separately (DH_each) (B). KK: Kinuhime/Kitahonami, TK: Tohoku224/Kitahonami, SK: Shunyou/Kitahonami population.
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pone-0111337-g008: Scatter diagrams of predicted and actual FlYd values in DH lines.Regression models were constructed using the three DH populations together (DH_total) (A) or separately (DH_each) (B). KK: Kinuhime/Kitahonami, TK: Tohoku224/Kitahonami, SK: Shunyou/Kitahonami population.

Mentions: Multiple regression analysis showed significant effects in five of the eight markers using the DH_total dataset, which is based on the combination of all three DH populations (Table S9 in File S1). For the DH_each dataset, based on individual DH populations, four, two and three markers were significant in Kinuhime/Kitahonami, Tohoku224/Kitahonami and Shunyou/Kitahonami populations, respectively (Table S9 in File S1). The regression models were used to predict FlYd in the individual DH lines (Dataset S5 in File S2). When we considered all DH lines together, the correlation coefficients between predicted and actual values were 0.479 for DH_total and 0.607 for DH_each (Fig. 8). In each population, prediction accuracies based on the DH_each dataset were consistently higher than those based on the DH_total dataset (Fig. 8).


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 predicted and actual FlYd values in DH lines.Regression models were constructed using the three DH populations together (DH_total) (A) or separately (DH_each) (B). KK: Kinuhime/Kitahonami, TK: Tohoku224/Kitahonami, SK: Shunyou/Kitahonami population.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111337-g008: Scatter diagrams of predicted and actual FlYd values in DH lines.Regression models were constructed using the three DH populations together (DH_total) (A) or separately (DH_each) (B). KK: Kinuhime/Kitahonami, TK: Tohoku224/Kitahonami, SK: Shunyou/Kitahonami population.
Mentions: Multiple regression analysis showed significant effects in five of the eight markers using the DH_total dataset, which is based on the combination of all three DH populations (Table S9 in File S1). For the DH_each dataset, based on individual DH populations, four, two and three markers were significant in Kinuhime/Kitahonami, Tohoku224/Kitahonami and Shunyou/Kitahonami populations, respectively (Table S9 in File S1). The regression models were used to predict FlYd in the individual DH lines (Dataset S5 in File S2). When we considered all DH lines together, the correlation coefficients between predicted and actual values were 0.479 for DH_total and 0.607 for DH_each (Fig. 8). In each population, prediction accuracies based on the DH_each dataset were consistently higher than those based on the DH_total dataset (Fig. 8).

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