Genetic architecture of variation in heading date among Asian rice accessions

Kiyosumi Hori, Yasunori Nonoue, Nozomi Ono, Taeko Shibaya, Kaworu Ebana, Kazuki Matsubara, Eri Ogiso-Tanaka, Takanari Tanabata, Kazuhiko Sugimoto, Fumio Taguchi-Shiobara, Jun ichi Yonemaru, Ritsuko Mizobuchi, Yusaku Uga, Atsunori Fukuda, Tadamasa Ueda, Shin ichi Yamamoto, Utako Yamanouchi, Toshiyuki Takai, Takashi Ikka, Katsuhiko KondoTomoki Hoshino, Eiji Yamamoto, Shunsuke Adachi, Hideki Nagasaki, Ayahiko Shomura, Takehiko Shimizu, Izumi Kono, Sachie Ito, Tatsumi Mizubayashi, Noriyuki Kitazawa, Kazufumi Nagata, Tsuyu Ando, Shuichi Fukuoka, Toshio Yamamoto, Masahiro Yano

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

Background: Heading date, a crucial factor determining regional and seasonal adaptation in rice (Oryza sativa L.), has been a major selection target in breeding programs. Although considerable progress has been made in our understanding of the molecular regulation of heading date in rice during last two decades, the previously isolated genes and identified quantitative trait loci (QTLs) cannot fully explain the natural variation for heading date in diverse rice accessions. Results: To genetically dissect naturally occurring variation in rice heading date, we collected QTLs in advanced-backcross populations derived from multiple crosses of the japonica rice accession Koshihikari (as a common parental line) with 11 diverse rice accessions (5 indica, 3 aus, and 3 japonica) that originate from various regions of Asia. QTL analyses of over 14,000 backcrossed individuals revealed 255 QTLs distributed widely across the rice genome. Among the detected QTLs, 128 QTLs corresponded to genomic positions of heading date genes identified by previous studies, such as Hd1, Hd6, Hd3a, Ghd7, DTH8, and RFT1. The other 127 QTLs were detected in different chromosomal regions than heading date genes. Conclusions: Our results indicate that advanced-backcross progeny allowed us to detect and confirm QTLs with relatively small additive effects, and the natural variation in rice heading date could result from combinations of large- and small-effect QTLs. We also found differences in the genetic architecture of heading date (flowering time) among maize, Arabidopsis, and rice.

Original languageEnglish
Article number115
JournalBMC Plant Biology
Volume15
Issue number1
DOIs
Publication statusPublished - Dec 12 2015
Externally publishedYes

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heading
quantitative trait loci
rice
genes
additive effect
Oryza sativa
Arabidopsis
flowering
genomics
genome
corn
breeding

Keywords

  • Genetic architecture
  • Heading date
  • Natural variation
  • Oryza sativa L
  • QTL

ASJC Scopus subject areas

  • Plant Science

Cite this

Hori, K., Nonoue, Y., Ono, N., Shibaya, T., Ebana, K., Matsubara, K., ... Yano, M. (2015). Genetic architecture of variation in heading date among Asian rice accessions. BMC Plant Biology, 15(1), [115]. https://doi.org/10.1186/s12870-015-0501-x

Genetic architecture of variation in heading date among Asian rice accessions. / Hori, Kiyosumi; Nonoue, Yasunori; Ono, Nozomi; Shibaya, Taeko; Ebana, Kaworu; Matsubara, Kazuki; Ogiso-Tanaka, Eri; Tanabata, Takanari; Sugimoto, Kazuhiko; Taguchi-Shiobara, Fumio; Yonemaru, Jun ichi; Mizobuchi, Ritsuko; Uga, Yusaku; Fukuda, Atsunori; Ueda, Tadamasa; Yamamoto, Shin ichi; Yamanouchi, Utako; Takai, Toshiyuki; Ikka, Takashi; Kondo, Katsuhiko; Hoshino, Tomoki; Yamamoto, Eiji; Adachi, Shunsuke; Nagasaki, Hideki; Shomura, Ayahiko; Shimizu, Takehiko; Kono, Izumi; Ito, Sachie; Mizubayashi, Tatsumi; Kitazawa, Noriyuki; Nagata, Kazufumi; Ando, Tsuyu; Fukuoka, Shuichi; Yamamoto, Toshio; Yano, Masahiro.

In: BMC Plant Biology, Vol. 15, No. 1, 115, 12.12.2015.

Research output: Contribution to journalArticle

Hori, K, Nonoue, Y, Ono, N, Shibaya, T, Ebana, K, Matsubara, K, Ogiso-Tanaka, E, Tanabata, T, Sugimoto, K, Taguchi-Shiobara, F, Yonemaru, JI, Mizobuchi, R, Uga, Y, Fukuda, A, Ueda, T, Yamamoto, SI, Yamanouchi, U, Takai, T, Ikka, T, Kondo, K, Hoshino, T, Yamamoto, E, Adachi, S, Nagasaki, H, Shomura, A, Shimizu, T, Kono, I, Ito, S, Mizubayashi, T, Kitazawa, N, Nagata, K, Ando, T, Fukuoka, S, Yamamoto, T & Yano, M 2015, 'Genetic architecture of variation in heading date among Asian rice accessions', BMC Plant Biology, vol. 15, no. 1, 115. https://doi.org/10.1186/s12870-015-0501-x
Hori K, Nonoue Y, Ono N, Shibaya T, Ebana K, Matsubara K et al. Genetic architecture of variation in heading date among Asian rice accessions. BMC Plant Biology. 2015 Dec 12;15(1). 115. https://doi.org/10.1186/s12870-015-0501-x
Hori, Kiyosumi ; Nonoue, Yasunori ; Ono, Nozomi ; Shibaya, Taeko ; Ebana, Kaworu ; Matsubara, Kazuki ; Ogiso-Tanaka, Eri ; Tanabata, Takanari ; Sugimoto, Kazuhiko ; Taguchi-Shiobara, Fumio ; Yonemaru, Jun ichi ; Mizobuchi, Ritsuko ; Uga, Yusaku ; Fukuda, Atsunori ; Ueda, Tadamasa ; Yamamoto, Shin ichi ; Yamanouchi, Utako ; Takai, Toshiyuki ; Ikka, Takashi ; Kondo, Katsuhiko ; Hoshino, Tomoki ; Yamamoto, Eiji ; Adachi, Shunsuke ; Nagasaki, Hideki ; Shomura, Ayahiko ; Shimizu, Takehiko ; Kono, Izumi ; Ito, Sachie ; Mizubayashi, Tatsumi ; Kitazawa, Noriyuki ; Nagata, Kazufumi ; Ando, Tsuyu ; Fukuoka, Shuichi ; Yamamoto, Toshio ; Yano, Masahiro. / Genetic architecture of variation in heading date among Asian rice accessions. In: BMC Plant Biology. 2015 ; Vol. 15, No. 1.
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AU - Hori, Kiyosumi

AU - Nonoue, Yasunori

AU - Ono, Nozomi

AU - Shibaya, Taeko

AU - Ebana, Kaworu

AU - Matsubara, Kazuki

AU - Ogiso-Tanaka, Eri

AU - Tanabata, Takanari

AU - Sugimoto, Kazuhiko

AU - Taguchi-Shiobara, Fumio

AU - Yonemaru, Jun ichi

AU - Mizobuchi, Ritsuko

AU - Uga, Yusaku

AU - Fukuda, Atsunori

AU - Ueda, Tadamasa

AU - Yamamoto, Shin ichi

AU - Yamanouchi, Utako

AU - Takai, Toshiyuki

AU - Ikka, Takashi

AU - Kondo, Katsuhiko

AU - Hoshino, Tomoki

AU - Yamamoto, Eiji

AU - Adachi, Shunsuke

AU - Nagasaki, Hideki

AU - Shomura, Ayahiko

AU - Shimizu, Takehiko

AU - Kono, Izumi

AU - Ito, Sachie

AU - Mizubayashi, Tatsumi

AU - Kitazawa, Noriyuki

AU - Nagata, Kazufumi

AU - Ando, Tsuyu

AU - Fukuoka, Shuichi

AU - Yamamoto, Toshio

AU - Yano, Masahiro

PY - 2015/12/12

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N2 - Background: Heading date, a crucial factor determining regional and seasonal adaptation in rice (Oryza sativa L.), has been a major selection target in breeding programs. Although considerable progress has been made in our understanding of the molecular regulation of heading date in rice during last two decades, the previously isolated genes and identified quantitative trait loci (QTLs) cannot fully explain the natural variation for heading date in diverse rice accessions. Results: To genetically dissect naturally occurring variation in rice heading date, we collected QTLs in advanced-backcross populations derived from multiple crosses of the japonica rice accession Koshihikari (as a common parental line) with 11 diverse rice accessions (5 indica, 3 aus, and 3 japonica) that originate from various regions of Asia. QTL analyses of over 14,000 backcrossed individuals revealed 255 QTLs distributed widely across the rice genome. Among the detected QTLs, 128 QTLs corresponded to genomic positions of heading date genes identified by previous studies, such as Hd1, Hd6, Hd3a, Ghd7, DTH8, and RFT1. The other 127 QTLs were detected in different chromosomal regions than heading date genes. Conclusions: Our results indicate that advanced-backcross progeny allowed us to detect and confirm QTLs with relatively small additive effects, and the natural variation in rice heading date could result from combinations of large- and small-effect QTLs. We also found differences in the genetic architecture of heading date (flowering time) among maize, Arabidopsis, and rice.

AB - Background: Heading date, a crucial factor determining regional and seasonal adaptation in rice (Oryza sativa L.), has been a major selection target in breeding programs. Although considerable progress has been made in our understanding of the molecular regulation of heading date in rice during last two decades, the previously isolated genes and identified quantitative trait loci (QTLs) cannot fully explain the natural variation for heading date in diverse rice accessions. Results: To genetically dissect naturally occurring variation in rice heading date, we collected QTLs in advanced-backcross populations derived from multiple crosses of the japonica rice accession Koshihikari (as a common parental line) with 11 diverse rice accessions (5 indica, 3 aus, and 3 japonica) that originate from various regions of Asia. QTL analyses of over 14,000 backcrossed individuals revealed 255 QTLs distributed widely across the rice genome. Among the detected QTLs, 128 QTLs corresponded to genomic positions of heading date genes identified by previous studies, such as Hd1, Hd6, Hd3a, Ghd7, DTH8, and RFT1. The other 127 QTLs were detected in different chromosomal regions than heading date genes. Conclusions: Our results indicate that advanced-backcross progeny allowed us to detect and confirm QTLs with relatively small additive effects, and the natural variation in rice heading date could result from combinations of large- and small-effect QTLs. We also found differences in the genetic architecture of heading date (flowering time) among maize, Arabidopsis, and rice.

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KW - Heading date

KW - Natural variation

KW - Oryza sativa L

KW - QTL

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