Isolation of a novel mutant gene for soil-surface rooting in rice (Oryza sativa L.)

Eiko Hanzawa, Kazuhiro Sasaki, Shinsei Nagai, Mitsuhiro Obara, Yoshimichi Fukuta, Yusaku Uga, Akio Miyao, Hirohiko Hirochika, Atsushi Higashitani, Masahiko Maekawa, Tadashi Sato

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Background: Root system architecture is an important trait affecting the uptake of nutrients and water by crops. Shallower root systems preferentially take up nutrients from the topsoil and help avoid unfavorable environments in deeper soil layers. We have found a soil-surface rooting mutant from an M2 population that was regenerated from seed calli of a japonica rice cultivar, Nipponbare. In this study, we examined the genetic and physiological characteristics of this mutant. Results: The primary roots of the mutant showed no gravitropic response from the seedling stage on, whereas the gravitropic response of the shoots was normal. Segregation analyses by using an F2 population derived from a cross between the soil-surface rooting mutant and wild-type Nipponbare indicated that the trait was controlled by a single recessive gene, designated as sor1. Fine mapping by using an F2 population derived from a cross between the mutant and an indica rice cultivar, Kasalath, revealed that sor1 was located within a 136-kb region between the simple sequence repeat markers RM16254 and 2935-6 on the terminal region of the short arm of chromosome 4, where 13 putative open reading frames (ORFs) were found. We sequenced these ORFs and detected a 33-bp deletion in one of them, Os04g0101800. Transgenic plants of the mutant transformed with the genomic fragment carrying the Os04g0101800 sequence from Nipponbare showed normal gravitropic responses and no soil-surface rooting. Conclusion: These results suggest that sor1, a rice mutant causing soil-surface rooting and altered root gravitropic response, is allelic to Os04g0101800, and that a 33-bp deletion in the coding region of this gene causes the mutant phenotypes.

Original languageEnglish
Pages (from-to)1-11
Number of pages11
JournalRice
Volume6
Issue number1
DOIs
Publication statusPublished - 2013

Fingerprint

rooting
Oryza sativa
soil surface
rice
mutants
gene
soil
genes
root system
root systems
open reading frames
cultivar
transgenic plant
mutant
nutrient
recessive genes
cultivars
water uptake
nutrient uptake
topsoil

Keywords

  • Gene isolation
  • Gravitropic response
  • Root system architecture
  • Shallow rooting
  • Soil-surface rooting

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Plant Science
  • Soil Science

Cite this

Hanzawa, E., Sasaki, K., Nagai, S., Obara, M., Fukuta, Y., Uga, Y., ... Sato, T. (2013). Isolation of a novel mutant gene for soil-surface rooting in rice (Oryza sativa L.). Rice, 6(1), 1-11. https://doi.org/10.1186/1939-8433-6-30

Isolation of a novel mutant gene for soil-surface rooting in rice (Oryza sativa L.). / Hanzawa, Eiko; Sasaki, Kazuhiro; Nagai, Shinsei; Obara, Mitsuhiro; Fukuta, Yoshimichi; Uga, Yusaku; Miyao, Akio; Hirochika, Hirohiko; Higashitani, Atsushi; Maekawa, Masahiko; Sato, Tadashi.

In: Rice, Vol. 6, No. 1, 2013, p. 1-11.

Research output: Contribution to journalArticle

Hanzawa, E, Sasaki, K, Nagai, S, Obara, M, Fukuta, Y, Uga, Y, Miyao, A, Hirochika, H, Higashitani, A, Maekawa, M & Sato, T 2013, 'Isolation of a novel mutant gene for soil-surface rooting in rice (Oryza sativa L.)', Rice, vol. 6, no. 1, pp. 1-11. https://doi.org/10.1186/1939-8433-6-30
Hanzawa, Eiko ; Sasaki, Kazuhiro ; Nagai, Shinsei ; Obara, Mitsuhiro ; Fukuta, Yoshimichi ; Uga, Yusaku ; Miyao, Akio ; Hirochika, Hirohiko ; Higashitani, Atsushi ; Maekawa, Masahiko ; Sato, Tadashi. / Isolation of a novel mutant gene for soil-surface rooting in rice (Oryza sativa L.). In: Rice. 2013 ; Vol. 6, No. 1. pp. 1-11.
@article{191a13990c77487ca770c0dfcb26662e,
title = "Isolation of a novel mutant gene for soil-surface rooting in rice (Oryza sativa L.)",
abstract = "Background: Root system architecture is an important trait affecting the uptake of nutrients and water by crops. Shallower root systems preferentially take up nutrients from the topsoil and help avoid unfavorable environments in deeper soil layers. We have found a soil-surface rooting mutant from an M2 population that was regenerated from seed calli of a japonica rice cultivar, Nipponbare. In this study, we examined the genetic and physiological characteristics of this mutant. Results: The primary roots of the mutant showed no gravitropic response from the seedling stage on, whereas the gravitropic response of the shoots was normal. Segregation analyses by using an F2 population derived from a cross between the soil-surface rooting mutant and wild-type Nipponbare indicated that the trait was controlled by a single recessive gene, designated as sor1. Fine mapping by using an F2 population derived from a cross between the mutant and an indica rice cultivar, Kasalath, revealed that sor1 was located within a 136-kb region between the simple sequence repeat markers RM16254 and 2935-6 on the terminal region of the short arm of chromosome 4, where 13 putative open reading frames (ORFs) were found. We sequenced these ORFs and detected a 33-bp deletion in one of them, Os04g0101800. Transgenic plants of the mutant transformed with the genomic fragment carrying the Os04g0101800 sequence from Nipponbare showed normal gravitropic responses and no soil-surface rooting. Conclusion: These results suggest that sor1, a rice mutant causing soil-surface rooting and altered root gravitropic response, is allelic to Os04g0101800, and that a 33-bp deletion in the coding region of this gene causes the mutant phenotypes.",
keywords = "Gene isolation, Gravitropic response, Root system architecture, Shallow rooting, Soil-surface rooting",
author = "Eiko Hanzawa and Kazuhiro Sasaki and Shinsei Nagai and Mitsuhiro Obara and Yoshimichi Fukuta and Yusaku Uga and Akio Miyao and Hirohiko Hirochika and Atsushi Higashitani and Masahiko Maekawa and Tadashi Sato",
year = "2013",
doi = "10.1186/1939-8433-6-30",
language = "English",
volume = "6",
pages = "1--11",
journal = "Rice",
issn = "1939-8425",
publisher = "Springer Publishing Company",
number = "1",

}

TY - JOUR

T1 - Isolation of a novel mutant gene for soil-surface rooting in rice (Oryza sativa L.)

AU - Hanzawa, Eiko

AU - Sasaki, Kazuhiro

AU - Nagai, Shinsei

AU - Obara, Mitsuhiro

AU - Fukuta, Yoshimichi

AU - Uga, Yusaku

AU - Miyao, Akio

AU - Hirochika, Hirohiko

AU - Higashitani, Atsushi

AU - Maekawa, Masahiko

AU - Sato, Tadashi

PY - 2013

Y1 - 2013

N2 - Background: Root system architecture is an important trait affecting the uptake of nutrients and water by crops. Shallower root systems preferentially take up nutrients from the topsoil and help avoid unfavorable environments in deeper soil layers. We have found a soil-surface rooting mutant from an M2 population that was regenerated from seed calli of a japonica rice cultivar, Nipponbare. In this study, we examined the genetic and physiological characteristics of this mutant. Results: The primary roots of the mutant showed no gravitropic response from the seedling stage on, whereas the gravitropic response of the shoots was normal. Segregation analyses by using an F2 population derived from a cross between the soil-surface rooting mutant and wild-type Nipponbare indicated that the trait was controlled by a single recessive gene, designated as sor1. Fine mapping by using an F2 population derived from a cross between the mutant and an indica rice cultivar, Kasalath, revealed that sor1 was located within a 136-kb region between the simple sequence repeat markers RM16254 and 2935-6 on the terminal region of the short arm of chromosome 4, where 13 putative open reading frames (ORFs) were found. We sequenced these ORFs and detected a 33-bp deletion in one of them, Os04g0101800. Transgenic plants of the mutant transformed with the genomic fragment carrying the Os04g0101800 sequence from Nipponbare showed normal gravitropic responses and no soil-surface rooting. Conclusion: These results suggest that sor1, a rice mutant causing soil-surface rooting and altered root gravitropic response, is allelic to Os04g0101800, and that a 33-bp deletion in the coding region of this gene causes the mutant phenotypes.

AB - Background: Root system architecture is an important trait affecting the uptake of nutrients and water by crops. Shallower root systems preferentially take up nutrients from the topsoil and help avoid unfavorable environments in deeper soil layers. We have found a soil-surface rooting mutant from an M2 population that was regenerated from seed calli of a japonica rice cultivar, Nipponbare. In this study, we examined the genetic and physiological characteristics of this mutant. Results: The primary roots of the mutant showed no gravitropic response from the seedling stage on, whereas the gravitropic response of the shoots was normal. Segregation analyses by using an F2 population derived from a cross between the soil-surface rooting mutant and wild-type Nipponbare indicated that the trait was controlled by a single recessive gene, designated as sor1. Fine mapping by using an F2 population derived from a cross between the mutant and an indica rice cultivar, Kasalath, revealed that sor1 was located within a 136-kb region between the simple sequence repeat markers RM16254 and 2935-6 on the terminal region of the short arm of chromosome 4, where 13 putative open reading frames (ORFs) were found. We sequenced these ORFs and detected a 33-bp deletion in one of them, Os04g0101800. Transgenic plants of the mutant transformed with the genomic fragment carrying the Os04g0101800 sequence from Nipponbare showed normal gravitropic responses and no soil-surface rooting. Conclusion: These results suggest that sor1, a rice mutant causing soil-surface rooting and altered root gravitropic response, is allelic to Os04g0101800, and that a 33-bp deletion in the coding region of this gene causes the mutant phenotypes.

KW - Gene isolation

KW - Gravitropic response

KW - Root system architecture

KW - Shallow rooting

KW - Soil-surface rooting

UR - http://www.scopus.com/inward/record.url?scp=84891375972&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84891375972&partnerID=8YFLogxK

U2 - 10.1186/1939-8433-6-30

DO - 10.1186/1939-8433-6-30

M3 - Article

VL - 6

SP - 1

EP - 11

JO - Rice

JF - Rice

SN - 1939-8425

IS - 1

ER -