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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.


Development of the plant materials used in this study. CSSL, chromosome segment substitution line; MAS, marker-assisted selection; QTL, quantitative trait locus.
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f1-65_308: Development of the plant materials used in this study. CSSL, chromosome segment substitution line; MAS, marker-assisted selection; QTL, quantitative trait locus.

Mentions: We used three Koshihikari × IR64 populations in this study: an F2 population and advanced reciprocal CSSL and BC4F2 populations (Fig. 1). We began with an F1 population derived from the cross between Koshihikari and IR64 (IRGC66970), and repeatedly backcrossed the progeny with either Koshihikari or IR64 to produce BC4F1 plants. We conducted a whole-genome survey using 150 simple sequence repeat (SSR) markers in each backcrossed generation (BC1F1 to BC4F1) to select target chromosome segments in each CSSL and to minimize non-target chromosome segments from the donor, then selected plants that are homozygous for the target chromosome segments in the self-pollinated progeny (Supplemental Table 1). From BC4F4 or BC4F5 plants, we selected 42 CSSLs with a Koshihikari genetic background (IRK-CSSL) and 40 with an IR64 genetic background (KSI-CSSL), and grew the plants with their parents in 2011 (Fig. 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)

Development of the plant materials used in this study. CSSL, chromosome segment substitution line; MAS, marker-assisted selection; QTL, quantitative trait locus.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1-65_308: Development of the plant materials used in this study. CSSL, chromosome segment substitution line; MAS, marker-assisted selection; QTL, quantitative trait locus.
Mentions: We used three Koshihikari × IR64 populations in this study: an F2 population and advanced reciprocal CSSL and BC4F2 populations (Fig. 1). We began with an F1 population derived from the cross between Koshihikari and IR64 (IRGC66970), and repeatedly backcrossed the progeny with either Koshihikari or IR64 to produce BC4F1 plants. We conducted a whole-genome survey using 150 simple sequence repeat (SSR) markers in each backcrossed generation (BC1F1 to BC4F1) to select target chromosome segments in each CSSL and to minimize non-target chromosome segments from the donor, then selected plants that are homozygous for the target chromosome segments in the self-pollinated progeny (Supplemental Table 1). From BC4F4 or BC4F5 plants, we selected 42 CSSLs with a Koshihikari genetic background (IRK-CSSL) and 40 with an IR64 genetic background (KSI-CSSL), and grew the plants with their parents in 2011 (Fig. 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.