Limits...
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.

Show MeSH
Distributions of p- and q-values and impact of kernel type correction on association mapping results for flour yield (FlYd).The distribution was calculated without (w/o) or with (w) employing kernel type as a covariant.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4215981&req=5

pone-0111337-g005: Distributions of p- and q-values and impact of kernel type correction on association mapping results for flour yield (FlYd).The distribution was calculated without (w/o) or with (w) employing kernel type as a covariant.

Mentions: Genotype data obtained with the 3,815 selected markers was used for association mapping (Dataset S4 in File S2). Calculations were performed using a mixed linear model, with and without using kernel type as a covariant. To take into account multiple comparisons, a false discovery rate (q value) was adopted in determining significant marker-trait associations (MTAs). Distributions of q values with and without using kernel type as a covariant are shown in Fig. 5. When the kernel type was not used in the model, the q value was within 0.55–0.85. When kernel type was accounted for, more accurate MTAs were detected, as indicated by q values ranging from 0.09 to 0.93. Therefore, to select reliable markers, kernel type was used as a covariant and the threshold of the q value was set at 0.5. This led to the identification of a total of 62 markers (Table S7 in File S1). Based on the locations of the markers [13], [23], MTAs were classified into 21 QTLs (Table 2), although five MTA locations remained undetermined (Table S7 in File S1). Among the 21 QTLs, 18 had positive effects when the Kitahonami allele was present (Table 2). Since QTLs were classified based on two consensus genetic maps, it is possible that some QTLs overlapped: for example, 3B.3 may represent the same QTL as 3B.1 or 3B.2 (Table 2). Among the 62 MTAs, r2 ranged from 9.2 to 20.5% and effects on FlYd ranged from 1.51 to 2.68 (Table S7 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)

Distributions of p- and q-values and impact of kernel type correction on association mapping results for flour yield (FlYd).The distribution was calculated without (w/o) or with (w) employing kernel type as a covariant.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111337-g005: Distributions of p- and q-values and impact of kernel type correction on association mapping results for flour yield (FlYd).The distribution was calculated without (w/o) or with (w) employing kernel type as a covariant.
Mentions: Genotype data obtained with the 3,815 selected markers was used for association mapping (Dataset S4 in File S2). Calculations were performed using a mixed linear model, with and without using kernel type as a covariant. To take into account multiple comparisons, a false discovery rate (q value) was adopted in determining significant marker-trait associations (MTAs). Distributions of q values with and without using kernel type as a covariant are shown in Fig. 5. When the kernel type was not used in the model, the q value was within 0.55–0.85. When kernel type was accounted for, more accurate MTAs were detected, as indicated by q values ranging from 0.09 to 0.93. Therefore, to select reliable markers, kernel type was used as a covariant and the threshold of the q value was set at 0.5. This led to the identification of a total of 62 markers (Table S7 in File S1). Based on the locations of the markers [13], [23], MTAs were classified into 21 QTLs (Table 2), although five MTA locations remained undetermined (Table S7 in File S1). Among the 21 QTLs, 18 had positive effects when the Kitahonami allele was present (Table 2). Since QTLs were classified based on two consensus genetic maps, it is possible that some QTLs overlapped: for example, 3B.3 may represent the same QTL as 3B.1 or 3B.2 (Table 2). Among the 62 MTAs, r2 ranged from 9.2 to 20.5% and effects on FlYd ranged from 1.51 to 2.68 (Table S7 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