Isolation of a novel mutant gene for soil-surface rooting in rice (Oryza sativa L.)
Eiko Hanzawa
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2
Kazuhiro Sasaki
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2
Shinsei Nagai
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2
Mitsuhiro Obara
2
Yoshimichi Fukuta
2
Yusaku Uga
2
Akio Miyao
2
Hirohiko Hirochika
2
Atsushi Higashitani
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2
Masahiko Maekawa
2
Tadashi Sato
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1
2
0
Graduate School of Life Sciences, Tohoku University
, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577,
Japan
1
RIKEN Innovation Center, Ion Beam Breeding Laboratory
, 2-1 Hirosawa,
Wako, Saitama 351-0198, Japan
2
Center, Ion Beam Breeding Laboratory
, 2-1 Hirosawa,
Wako, Saitama 351-0198, Japan
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.
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Background
Root system architecture is an important trait for plant
growth and crop yield because it affects the uptake of
nutrients and water, which are unevenly distributed in
the soil. Diversity of the vertical distribution of the root
systems of different species allows efficient maximization
of plant growth and crop yields in unfavorable
environments with poor resource mobility, such as infertile or
arid fields (Hodge et al. 2009; Rich and Watt 2013).
Shallow root systems enhance phosphorus acquisition in
common bean (Ge et al. 2000; Liao et al. 2004; Lynch 2011)
and wheat (Manske et al. 2000). Phosphorus-efficient bean
cultivars have shallower basal roots and more adventitious
rooting in the topsoil than other bean cultivars (Lynch and
Brown 2001). In teosintes, adventitious root formation at
the soil surface may provide an alternative growth strategy
to cope with soil flooding or waterlogging (Mano et al.
2005). Therefore, shallower root systems preferentially take
up nutrients from the topsoil and help to avoid unfavorable
environments in deeper soil layers.
When submerged, Indonesian rice (Oryza sativa L.)
cultivars that belong to the Bulu ecotype develop thick
primary roots above and near the soil surface (Lafitte
et al. 2001; Ueno and Sato 1989, 1992). These authors
suggested that soil-surface and shallow roots contribute
to the avoidance of hypoxic soils in rice. Rice superficial
roots develop near the soil surface from the beginning of
the spikelet differentiation stage to the fully ripe stage
(Morita and Yamazaki 1993). The fresh weight of
superficial roots is positively correlated with yields in paddy
fields (Morita and Yamazaki 1993). Thus, soil-surface and
shallow roots may contribute to the avoidance of hypoxic
environments and promote rice growth.
Genetic analyses of root system architecture have been
performed in a variety of rice lines; however, no genes
controlling soil-surface rooting have been isolated by using
natural variation. A study of 81 diverse genotypes in rice
revealed two DNA molecular markers associated with
shallow and deep rooting on chromosomes 9 and 10,
respectively (Chaitra et al. 2006). Uga et al. (2012) identified
four quantitative trait loci (QTLs) for soil-surface rooting
on chromosomes 3, 4, 6, and 7 by using recombinant
inbred lines derived from a cross between an Indonesian
rice cultivar with soil-surface roots and a Japanese cultivar
without such roots. The use of mutants is an alternative
approach to isolate causal genes for traits of interest. Rice
mutants have been isolated for the following root
morphological characteristics: inhibition of root growth,
absence of crown roots, short lateral roots or absence of
lateral roots, short root hairs, and hairless roots (Chh (...truncated)