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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.


Graphical genotypes and positions of the QTLs for grain length that were detected in the region from 30 to 36 Mb on chromosome 2 in the F2 population and in two BC4F2 sub-populations in the genetic background of Koshihikari (IRK) or IR64 (KSI). Black boxes, homozygous for IR64; white, homozygous for Koshihikari; gray, heterozygous. AE, additive effect. Upward-pointing triangles (△) indicate that the IR64 alleles increase values, and downward-pointing triangles (▽) indicate that the IR64 alleles decrease values.
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f5-65_308: Graphical genotypes and positions of the QTLs for grain length that were detected in the region from 30 to 36 Mb on chromosome 2 in the F2 population and in two BC4F2 sub-populations in the genetic background of Koshihikari (IRK) or IR64 (KSI). Black boxes, homozygous for IR64; white, homozygous for Koshihikari; gray, heterozygous. AE, additive effect. Upward-pointing triangles (△) indicate that the IR64 alleles increase values, and downward-pointing triangles (▽) indicate that the IR64 alleles decrease values.

Mentions: All 8 of the QTLs detected in the F2 population were validated in the BC4F2 populations, although 3 of the BC4F2 QTLs were located more than 2.7 Mb from the corresponding QTL in the F2 population (Table 1, footnote b). For example, in the F2 population, a QTL whose IR64 allele increases grain length (additive effect [AE] = −0.02) was detected at 31.20 Mb on chromosome 2. But in IRK-BC4F2, QTL qGL2-3, with the opposite additive effect (AE = 0.09), was detected at the same position, and qGL2-4, whose additive effect was in the same direction (AE = −0.03) as in the F2 population, was detected at 34.69 Mb. The positions of the two QTLs in IRK-BC4F2 were almost same as those in KSI-BC4F2. Notably, the additive effects of qGL2-4 in the KSI-BC4F2 population (AE = −0.24), in which only qGL2-4 is segregating, was 8 times that in the IRK-BC4F2 population (AE = −0.03) and more than 8 times that in the F2 population (AE = −0.02), in which both qGL2-3 and qGL2-4 are segregating (Fig. 5).


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)

Graphical genotypes and positions of the QTLs for grain length that were detected in the region from 30 to 36 Mb on chromosome 2 in the F2 population and in two BC4F2 sub-populations in the genetic background of Koshihikari (IRK) or IR64 (KSI). Black boxes, homozygous for IR64; white, homozygous for Koshihikari; gray, heterozygous. AE, additive effect. Upward-pointing triangles (△) indicate that the IR64 alleles increase values, and downward-pointing triangles (▽) indicate that the IR64 alleles decrease values.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5-65_308: Graphical genotypes and positions of the QTLs for grain length that were detected in the region from 30 to 36 Mb on chromosome 2 in the F2 population and in two BC4F2 sub-populations in the genetic background of Koshihikari (IRK) or IR64 (KSI). Black boxes, homozygous for IR64; white, homozygous for Koshihikari; gray, heterozygous. AE, additive effect. Upward-pointing triangles (△) indicate that the IR64 alleles increase values, and downward-pointing triangles (▽) indicate that the IR64 alleles decrease values.
Mentions: All 8 of the QTLs detected in the F2 population were validated in the BC4F2 populations, although 3 of the BC4F2 QTLs were located more than 2.7 Mb from the corresponding QTL in the F2 population (Table 1, footnote b). For example, in the F2 population, a QTL whose IR64 allele increases grain length (additive effect [AE] = −0.02) was detected at 31.20 Mb on chromosome 2. But in IRK-BC4F2, QTL qGL2-3, with the opposite additive effect (AE = 0.09), was detected at the same position, and qGL2-4, whose additive effect was in the same direction (AE = −0.03) as in the F2 population, was detected at 34.69 Mb. The positions of the two QTLs in IRK-BC4F2 were almost same as those in KSI-BC4F2. Notably, the additive effects of qGL2-4 in the KSI-BC4F2 population (AE = −0.24), in which only qGL2-4 is segregating, was 8 times that in the IRK-BC4F2 population (AE = −0.03) and more than 8 times that in the F2 population (AE = −0.02), in which both qGL2-3 and qGL2-4 are segregating (Fig. 5).

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.