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Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica × indica cross.

Nagata K, Ando T, Nonoue Y, Mizubayashi T, Kitazawa N, Shomura A, Matsubara K, Ono N, Mizobuchi R, Shibaya T, Ogiso-Tanaka E, Hori K, Yano M, Fukuoka S - Breed. Sci. (2015)

Bottom Line: A number of quantitative trait loci (QTLs) for this trait have been identified by using primary F2 mapping populations and recombinant inbred lines, in which QTLs with a small effect are harder to detect than they would be in advanced generations.We compared the ability of these materials to reveal QTLs for grain shape with that of an F2 population.These results strongly suggest that advanced mapping populations can reveal QTLs for agronomic traits under complicated genetic control, and that DNA markers linked with the QTLs are useful for choosing superior allelic combinations to enhance grain shape in the Koshihikari and IR64 genetic backgrounds.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.

ABSTRACT
Grain shape is an important trait for improving rice yield. A number of quantitative trait loci (QTLs) for this trait have been identified by using primary F2 mapping populations and recombinant inbred lines, in which QTLs with a small effect are harder to detect than they would be in advanced generations. In this study, we developed two advanced mapping populations (chromosome segment substitution lines [CSSLs] and BC4F2 lines consisting of more than 2000 individuals) in the genetic backgrounds of two improved cultivars: a japonica cultivar (Koshihikari) with short, round grains, and an indica cultivar (IR64) with long, slender grains. We compared the ability of these materials to reveal QTLs for grain shape with that of an F2 population. Only 8 QTLs for grain length or grain width were detected in the F2 population, versus 47 in the CSSL population and 65 in the BC4F2 population. These results strongly suggest that advanced mapping populations can reveal QTLs for agronomic traits under complicated genetic control, and that DNA markers linked with the QTLs are useful for choosing superior allelic combinations to enhance grain shape in the Koshihikari and IR64 genetic backgrounds.

No MeSH data available.


Chromosome locations of the QTLs for grain length and grain width detected in this study. (A) F2 population (Koshihikari × IR64), (B) IRK-BC4F2 population (see Fig. 1 for details), (C) KSI-BC4F2 (see Fig. 1 for details). Upward-pointing triangles (△, ▲) indicate that the IR64 alleles increase the parameter value, whereas downward-pointing triangles (▽, ▼) indicate that the IR64 alleles decrease the parameter value.
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f2-65_308: Chromosome locations of the QTLs for grain length and grain width detected in this study. (A) F2 population (Koshihikari × IR64), (B) IRK-BC4F2 population (see Fig. 1 for details), (C) KSI-BC4F2 (see Fig. 1 for details). Upward-pointing triangles (△, ▲) indicate that the IR64 alleles increase the parameter value, whereas downward-pointing triangles (▽, ▼) indicate that the IR64 alleles decrease the parameter value.

Mentions: To identify QTLs for grain length and grain width in a primary mapping population, QTL analysis was performed in the F2 population of the cross between Koshihikari and IR64. Five QTLs whose IR64 allele increased grain length and three whose IR64 allele decreased grain width were detected, as expected from the trait values of the parents and the distribution in the F2 population (Fig. 2A, Supplemental Fig. 1). The number of QTLs detected is comparable to that in the previous studies using the F2 (1 to 32, 8.7 on average) (Huang et al. 2013). A QTL for grain length on chromosome 3 accounted for 40% of the phenotypic variation and a QTL for grain width on chromosome 5 accounted for 24% of the phenotypic variation, but the other QTLs had small effects, and each accounted for less than 10% of the phenotypic variation (Table 1).


Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica × indica cross.

Nagata K, Ando T, Nonoue Y, Mizubayashi T, Kitazawa N, Shomura A, Matsubara K, Ono N, Mizobuchi R, Shibaya T, Ogiso-Tanaka E, Hori K, Yano M, Fukuoka S - Breed. Sci. (2015)

Chromosome locations of the QTLs for grain length and grain width detected in this study. (A) F2 population (Koshihikari × IR64), (B) IRK-BC4F2 population (see Fig. 1 for details), (C) KSI-BC4F2 (see Fig. 1 for details). Upward-pointing triangles (△, ▲) indicate that the IR64 alleles increase the parameter value, whereas downward-pointing triangles (▽, ▼) indicate that the IR64 alleles decrease the parameter value.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4542931&req=5

f2-65_308: Chromosome locations of the QTLs for grain length and grain width detected in this study. (A) F2 population (Koshihikari × IR64), (B) IRK-BC4F2 population (see Fig. 1 for details), (C) KSI-BC4F2 (see Fig. 1 for details). Upward-pointing triangles (△, ▲) indicate that the IR64 alleles increase the parameter value, whereas downward-pointing triangles (▽, ▼) indicate that the IR64 alleles decrease the parameter value.
Mentions: To identify QTLs for grain length and grain width in a primary mapping population, QTL analysis was performed in the F2 population of the cross between Koshihikari and IR64. Five QTLs whose IR64 allele increased grain length and three whose IR64 allele decreased grain width were detected, as expected from the trait values of the parents and the distribution in the F2 population (Fig. 2A, Supplemental Fig. 1). The number of QTLs detected is comparable to that in the previous studies using the F2 (1 to 32, 8.7 on average) (Huang et al. 2013). A QTL for grain length on chromosome 3 accounted for 40% of the phenotypic variation and a QTL for grain width on chromosome 5 accounted for 24% of the phenotypic variation, but the other QTLs had small effects, and each accounted for less than 10% of the phenotypic variation (Table 1).

Bottom Line: A number of quantitative trait loci (QTLs) for this trait have been identified by using primary F2 mapping populations and recombinant inbred lines, in which QTLs with a small effect are harder to detect than they would be in advanced generations.We compared the ability of these materials to reveal QTLs for grain shape with that of an F2 population.These results strongly suggest that advanced mapping populations can reveal QTLs for agronomic traits under complicated genetic control, and that DNA markers linked with the QTLs are useful for choosing superior allelic combinations to enhance grain shape in the Koshihikari and IR64 genetic backgrounds.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 , Japan.

ABSTRACT
Grain shape is an important trait for improving rice yield. A number of quantitative trait loci (QTLs) for this trait have been identified by using primary F2 mapping populations and recombinant inbred lines, in which QTLs with a small effect are harder to detect than they would be in advanced generations. In this study, we developed two advanced mapping populations (chromosome segment substitution lines [CSSLs] and BC4F2 lines consisting of more than 2000 individuals) in the genetic backgrounds of two improved cultivars: a japonica cultivar (Koshihikari) with short, round grains, and an indica cultivar (IR64) with long, slender grains. We compared the ability of these materials to reveal QTLs for grain shape with that of an F2 population. Only 8 QTLs for grain length or grain width were detected in the F2 population, versus 47 in the CSSL population and 65 in the BC4F2 population. These results strongly suggest that advanced mapping populations can reveal QTLs for agronomic traits under complicated genetic control, and that DNA markers linked with the QTLs are useful for choosing superior allelic combinations to enhance grain shape in the Koshihikari and IR64 genetic backgrounds.

No MeSH data available.