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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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PCR assays to detect of polymorphic SNPs between Kitahonami and the three other varieties used as parents in the DH populations.White and black arrows indicate bands derived from genome-specific and allele-specific amplicons, respectively. 1: Kitahonami, 2: Kinuhime, 3: Tohoku224, 4: Shunyou.
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pone-0111337-g007: PCR assays to detect of polymorphic SNPs between Kitahonami and the three other varieties used as parents in the DH populations.White and black arrows indicate bands derived from genome-specific and allele-specific amplicons, respectively. 1: Kitahonami, 2: Kinuhime, 3: Tohoku224, 4: Shunyou.

Mentions: For validation of the QTLs detected by association mapping, we performed linkage analysis using three sets of DH populations (Dataset S5 in File S2). The distribution of FlYd among lines in the three DH populations is shown in Fig. S3. For QTL validation, we wished to convert the SNP markers associated with the 11 QTLs into PCR-based markers to reduce the analysis cost involved with using the 9,000 SNP chip detection system. We succeeded in designing primer sets for eight of the 11 QTLs (Table S4 in File S1). Before use of these markers for QTL validation, their genome and allele specificity were confirmed in all four parents used for the DH populations. Based on the design of the primers, two bands were expected if the sample sequence matched with the sequence of the ASP, and a single band if it did not. All amplified products showed the expected band patterns (Fig. 7), indicating the new PCR-based markers were capable of identifying the eight QTLs.


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)

PCR assays to detect of polymorphic SNPs between Kitahonami and the three other varieties used as parents in the DH populations.White and black arrows indicate bands derived from genome-specific and allele-specific amplicons, respectively. 1: Kitahonami, 2: Kinuhime, 3: Tohoku224, 4: Shunyou.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111337-g007: PCR assays to detect of polymorphic SNPs between Kitahonami and the three other varieties used as parents in the DH populations.White and black arrows indicate bands derived from genome-specific and allele-specific amplicons, respectively. 1: Kitahonami, 2: Kinuhime, 3: Tohoku224, 4: Shunyou.
Mentions: For validation of the QTLs detected by association mapping, we performed linkage analysis using three sets of DH populations (Dataset S5 in File S2). The distribution of FlYd among lines in the three DH populations is shown in Fig. S3. For QTL validation, we wished to convert the SNP markers associated with the 11 QTLs into PCR-based markers to reduce the analysis cost involved with using the 9,000 SNP chip detection system. We succeeded in designing primer sets for eight of the 11 QTLs (Table S4 in File S1). Before use of these markers for QTL validation, their genome and allele specificity were confirmed in all four parents used for the DH populations. Based on the design of the primers, two bands were expected if the sample sequence matched with the sequence of the ASP, and a single band if it did not. All amplified products showed the expected band patterns (Fig. 7), indicating the new PCR-based markers were capable of identifying the eight QTLs.

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