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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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Relationships between flour yield (FlYd) and flour efficiency (FlEf) (A), FlYd and median diameter of particles (x50) (B) and FlYd and specific surface area of particles (Sv) (C).Accessions could be classified into either soft or hard kernel types based on Pina-D1/Pinb-D1 genotypes. Soft accessions have Pina-D1a and Pinb-D1a, while hard have Pina-D1b or Pinb-D1b.
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pone-0111337-g004: Relationships between flour yield (FlYd) and flour efficiency (FlEf) (A), FlYd and median diameter of particles (x50) (B) and FlYd and specific surface area of particles (Sv) (C).Accessions could be classified into either soft or hard kernel types based on Pina-D1/Pinb-D1 genotypes. Soft accessions have Pina-D1a and Pinb-D1a, while hard have Pina-D1b or Pinb-D1b.

Mentions: Relationships between FlYd and other quality traits were also investigated (TableS6 in File S1). The FlEf (r = 0.511), x50 (0.436), Sv (−0.430) and Fash (0.349) each showed a significant relationship with FlYd, while no relationship with the other traits investigated was observed. It has been reported that x50, Sv and FlEf, as well as FlYd, have strong correlations with soft and hard kernel types (reviewed in Morris [20]). Therefore, the kernel types of 65 accessions were genotyped by Pina-D1/Pinb-D1 markers [21], [22]. All were classified as either soft (48) or hard (17) type. Taking kernel type into consideration, the relationships between FlYd and the other four traits were reanalyzed. This revealed two clear clusters attributable to kernel type, and no correlation with FlYd was detected in either cluster; only FlEf was correlated with kernel type (Fig. 4; TableS6 in File S1). Kitahonami showed the highest FlYd value among accessions in the soft cluster, although its value was considerably lower than the highest value observed in the hard cluster. These results clearly indicate that kernel type is an important element to consider in the association analysis.


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)

Relationships between flour yield (FlYd) and flour efficiency (FlEf) (A), FlYd and median diameter of particles (x50) (B) and FlYd and specific surface area of particles (Sv) (C).Accessions could be classified into either soft or hard kernel types based on Pina-D1/Pinb-D1 genotypes. Soft accessions have Pina-D1a and Pinb-D1a, while hard have Pina-D1b or Pinb-D1b.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111337-g004: Relationships between flour yield (FlYd) and flour efficiency (FlEf) (A), FlYd and median diameter of particles (x50) (B) and FlYd and specific surface area of particles (Sv) (C).Accessions could be classified into either soft or hard kernel types based on Pina-D1/Pinb-D1 genotypes. Soft accessions have Pina-D1a and Pinb-D1a, while hard have Pina-D1b or Pinb-D1b.
Mentions: Relationships between FlYd and other quality traits were also investigated (TableS6 in File S1). The FlEf (r = 0.511), x50 (0.436), Sv (−0.430) and Fash (0.349) each showed a significant relationship with FlYd, while no relationship with the other traits investigated was observed. It has been reported that x50, Sv and FlEf, as well as FlYd, have strong correlations with soft and hard kernel types (reviewed in Morris [20]). Therefore, the kernel types of 65 accessions were genotyped by Pina-D1/Pinb-D1 markers [21], [22]. All were classified as either soft (48) or hard (17) type. Taking kernel type into consideration, the relationships between FlYd and the other four traits were reanalyzed. This revealed two clear clusters attributable to kernel type, and no correlation with FlYd was detected in either cluster; only FlEf was correlated with kernel type (Fig. 4; TableS6 in File S1). Kitahonami showed the highest FlYd value among accessions in the soft cluster, although its value was considerably lower than the highest value observed in the hard cluster. These results clearly indicate that kernel type is an important element to consider in the association analysis.

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