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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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Pedigree analysis of flour yield (FlYd) QTLs.Values indicate frequencies of the same genotype as Kitahonami for each QTL.
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pone-0111337-g006: Pedigree analysis of flour yield (FlYd) QTLs.Values indicate frequencies of the same genotype as Kitahonami for each QTL.

Mentions: For the 18 QTLs that showed positive effects on FlYd when Kitahonami alleles were present, linkage disequilibrium (LD) analyses of the associated loci were performed. Obvious LD blocks were observed in 11 of 18 QTLs (Table 3; Fig. S2). The 3B.1 QTL consisted of two blocks (3B.1.1 and 3B.1.2). The sizes of the blocks ranged from 0.5 to 23.5 cM, with an average size of 7.5 cM. By referencing Kitahonami's pedigree tree (Fig. S1), we investigated the origin and routes of transfer of QTLs into Kitahonami, based on similarities of genotypes in the LD blocks. Results indicated that the QTLs on 2B.1, 2B.2, 3D, 5D.1, 6B, 7B.1, 7B.2 and 7D were derived from the maternal variety, Kitamoe (Acc. no. 2) and 1B.2, 3B.1.1, 3B.1.2, 3B.2, 3B.3 and 4B from the paternal line, Kitakei1660 (Acc. no. 3) (Fig. 6). Since QTLs on 5A, 5D.2, 6A.1, 6A.2 and 7A existed in both parents, it could not be determined which side was the source of these QTLs in Kitahonami. QTLs originating from the maternal donor were further traced back to either Hokushin (Acc. no. 4) (3D, 7B.1, 7B.2 and 7D) or Kitakei1354 (Acc. no. 5) (2B.1, 2B.2 and 5D.1) (Fig. 6). When we attempted to trace the QTLs further back in Kitahonami's lineage, some showed discrepancies with the pedigree record (Fig. S1). However, the origins of several QTLs could be attributed to varieties introduced from abroad: it was concluded that 2B.1, 2B.2, 4B and 7D were from Ibis (Acc. no. 19), 3B.1.1 and 3B.1.2 were from Wichita (Acc. no. 12), and 3D and 5D.1 from Newthach (Acc. no. 24). The QTL on 6B seems to have originated from Norman (Acc. no. 9). The full matrix of similarities within LD blocks is shown in Table S8 in File S1.


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)

Pedigree analysis of flour yield (FlYd) QTLs.Values indicate frequencies of the same genotype as Kitahonami for each QTL.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111337-g006: Pedigree analysis of flour yield (FlYd) QTLs.Values indicate frequencies of the same genotype as Kitahonami for each QTL.
Mentions: For the 18 QTLs that showed positive effects on FlYd when Kitahonami alleles were present, linkage disequilibrium (LD) analyses of the associated loci were performed. Obvious LD blocks were observed in 11 of 18 QTLs (Table 3; Fig. S2). The 3B.1 QTL consisted of two blocks (3B.1.1 and 3B.1.2). The sizes of the blocks ranged from 0.5 to 23.5 cM, with an average size of 7.5 cM. By referencing Kitahonami's pedigree tree (Fig. S1), we investigated the origin and routes of transfer of QTLs into Kitahonami, based on similarities of genotypes in the LD blocks. Results indicated that the QTLs on 2B.1, 2B.2, 3D, 5D.1, 6B, 7B.1, 7B.2 and 7D were derived from the maternal variety, Kitamoe (Acc. no. 2) and 1B.2, 3B.1.1, 3B.1.2, 3B.2, 3B.3 and 4B from the paternal line, Kitakei1660 (Acc. no. 3) (Fig. 6). Since QTLs on 5A, 5D.2, 6A.1, 6A.2 and 7A existed in both parents, it could not be determined which side was the source of these QTLs in Kitahonami. QTLs originating from the maternal donor were further traced back to either Hokushin (Acc. no. 4) (3D, 7B.1, 7B.2 and 7D) or Kitakei1354 (Acc. no. 5) (2B.1, 2B.2 and 5D.1) (Fig. 6). When we attempted to trace the QTLs further back in Kitahonami's lineage, some showed discrepancies with the pedigree record (Fig. S1). However, the origins of several QTLs could be attributed to varieties introduced from abroad: it was concluded that 2B.1, 2B.2, 4B and 7D were from Ibis (Acc. no. 19), 3B.1.1 and 3B.1.2 were from Wichita (Acc. no. 12), and 3D and 5D.1 from Newthach (Acc. no. 24). The QTL on 6B seems to have originated from Norman (Acc. no. 9). The full matrix of similarities within LD blocks is shown in Table S8 in File S1.

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