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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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Leverage plots of flour yield (FlYd) values.Abbreviations for environments consist of first letter of location and harvest year. K: Kitami, M: Morioka, N: Nagano. For example, K09 means samples of 2008/2009 cropping season at Kitami.
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pone-0111337-g003: Leverage plots of flour yield (FlYd) values.Abbreviations for environments consist of first letter of location and harvest year. K: Kitami, M: Morioka, N: Nagano. For example, K09 means samples of 2008/2009 cropping season at Kitami.

Mentions: The FlYd of lines in each environment and their mean values over the nine environments are provided in Dataset S3 in File S2. The analysis of variance showed significant genetic and environmental variation in FlYd compared to residual errors. Mean squares of accessions and environments were 61.76 (F = 19.65***) and 475.57 (F = 151.26***), respectively. The heritability of FlYd was 38.5%, which was relatively low compared to other traits investigated (Table S5 in File S1). This indicates that environmental factors have strong influence on FlYd. Leverage plots of environment also indicated a significant environmental effect on FlYd (Fig. 3). Samples harvested in 2010 showed a lower mean value for FlYd in all locations, and the lowest mean value was observed in the samples from Morioka in 2010. However, correlations across nine environments ranged from 0.419 to 0.945 (average 0.717), indicating that relative differences among accessions were consistent over the environments (Table 1). Therefore, we considered the mean value from the nine environments as the genotypic value of each accession.


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)

Leverage plots of flour yield (FlYd) values.Abbreviations for environments consist of first letter of location and harvest year. K: Kitami, M: Morioka, N: Nagano. For example, K09 means samples of 2008/2009 cropping season at Kitami.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111337-g003: Leverage plots of flour yield (FlYd) values.Abbreviations for environments consist of first letter of location and harvest year. K: Kitami, M: Morioka, N: Nagano. For example, K09 means samples of 2008/2009 cropping season at Kitami.
Mentions: The FlYd of lines in each environment and their mean values over the nine environments are provided in Dataset S3 in File S2. The analysis of variance showed significant genetic and environmental variation in FlYd compared to residual errors. Mean squares of accessions and environments were 61.76 (F = 19.65***) and 475.57 (F = 151.26***), respectively. The heritability of FlYd was 38.5%, which was relatively low compared to other traits investigated (Table S5 in File S1). This indicates that environmental factors have strong influence on FlYd. Leverage plots of environment also indicated a significant environmental effect on FlYd (Fig. 3). Samples harvested in 2010 showed a lower mean value for FlYd in all locations, and the lowest mean value was observed in the samples from Morioka in 2010. However, correlations across nine environments ranged from 0.419 to 0.945 (average 0.717), indicating that relative differences among accessions were consistent over the environments (Table 1). Therefore, we considered the mean value from the nine environments as the genotypic value of each accession.

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