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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.


Related in: MedlinePlus

Grain length and grain width in two sets of CSSLs: (A, B) IRK-CSSLs, with IR64 introgression in a Koshihikari background; (C, D) KSI-CSSLs, with Koshihikari introgression in an IR64 background. Values are means ± SD. Bars labeled with asterisks differed significantly from the means for (A, B) Koshihikari and (C, D) IR64: *, P < 0.05; **, P < 0.01 (two-tailed t-test). Data for SL2119 were excluded from this figure because this line headed too late for us to harvest seeds under natural field conditions.
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f3-65_308: Grain length and grain width in two sets of CSSLs: (A, B) IRK-CSSLs, with IR64 introgression in a Koshihikari background; (C, D) KSI-CSSLs, with Koshihikari introgression in an IR64 background. Values are means ± SD. Bars labeled with asterisks differed significantly from the means for (A, B) Koshihikari and (C, D) IR64: *, P < 0.05; **, P < 0.01 (two-tailed t-test). Data for SL2119 were excluded from this figure because this line headed too late for us to harvest seeds under natural field conditions.

Mentions: To identify putative QTLs and their chromosomal locations in the IRK-CSSLs and KSI-CSSLs developed in the present study, grain length and grain width in these CSSLs and their parents were measured and substitution mapping for these traits was performed. In the IRK-CSSLs, grain lengths ranged from 6.95 to 8.27 mm, versus 7.24 mm in Koshihikari and 9.80 mm in IR64 in 2011 (Fig. 3A). Grain widths ranged from 3.09 to 3.55 mm, versus 3.44 mm in Koshihikari and 2.55 mm in IR64 (Fig. 3B). Twenty-nine IRK-CSSLs differed significantly from ‘Koshihikari’ in grain length (Fig. 3A), and 31 differed in grain width (Fig. 3B). Putative QTLs were assigned at 20 chromosomal regions for grain length and 16 for grain width (Fig. 4A). We could not assign putative QTLs in one line (SL2022) that differed significantly from Koshihikari in grain length and in four lines (SL2012, SL2033, SL2039, and SL2042) that differed in grain width (Fig. 4A). Seven CSSLs carried multiple putative QTLs for either grain length or grain width (Fig. 4A, footnote c).


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)

Grain length and grain width in two sets of CSSLs: (A, B) IRK-CSSLs, with IR64 introgression in a Koshihikari background; (C, D) KSI-CSSLs, with Koshihikari introgression in an IR64 background. Values are means ± SD. Bars labeled with asterisks differed significantly from the means for (A, B) Koshihikari and (C, D) IR64: *, P < 0.05; **, P < 0.01 (two-tailed t-test). Data for SL2119 were excluded from this figure because this line headed too late for us to harvest seeds under natural field conditions.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3-65_308: Grain length and grain width in two sets of CSSLs: (A, B) IRK-CSSLs, with IR64 introgression in a Koshihikari background; (C, D) KSI-CSSLs, with Koshihikari introgression in an IR64 background. Values are means ± SD. Bars labeled with asterisks differed significantly from the means for (A, B) Koshihikari and (C, D) IR64: *, P < 0.05; **, P < 0.01 (two-tailed t-test). Data for SL2119 were excluded from this figure because this line headed too late for us to harvest seeds under natural field conditions.
Mentions: To identify putative QTLs and their chromosomal locations in the IRK-CSSLs and KSI-CSSLs developed in the present study, grain length and grain width in these CSSLs and their parents were measured and substitution mapping for these traits was performed. In the IRK-CSSLs, grain lengths ranged from 6.95 to 8.27 mm, versus 7.24 mm in Koshihikari and 9.80 mm in IR64 in 2011 (Fig. 3A). Grain widths ranged from 3.09 to 3.55 mm, versus 3.44 mm in Koshihikari and 2.55 mm in IR64 (Fig. 3B). Twenty-nine IRK-CSSLs differed significantly from ‘Koshihikari’ in grain length (Fig. 3A), and 31 differed in grain width (Fig. 3B). Putative QTLs were assigned at 20 chromosomal regions for grain length and 16 for grain width (Fig. 4A). We could not assign putative QTLs in one line (SL2022) that differed significantly from Koshihikari in grain length and in four lines (SL2012, SL2033, SL2039, and SL2042) that differed in grain width (Fig. 4A). Seven CSSLs carried multiple putative QTLs for either grain length or grain width (Fig. 4A, footnote c).

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.


Related in: MedlinePlus