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

Rice, Nov 2013

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

Eiko Hanzawa 0 2 Kazuhiro Sasaki 0 2 Shinsei Nagai 0 2 Mitsuhiro Obara 2 Yoshimichi Fukuta 2 Yusaku Uga 2 Akio Miyao 2 Hirohiko Hirochika 2 Atsushi Higashitani 0 2 Masahiko Maekawa 2 Tadashi Sato 0 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. - 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)


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Eiko Hanzawa, Kazuhiro Sasaki, Shinsei Nagai, Mitsuhiro Obara, Yoshimichi Fukuta, Yusaku Uga, Akio Miyao, Hirohiko Hirochika, Atsushi Higashitani, Masahiko Maekawa, Tadashi Sato. Isolation of a novel mutant gene for soil-surface rooting in rice (Oryza sativa L.), Rice, 2013, pp. 30, Volume 6, Issue 1, DOI: 10.1186/1939-8433-6-30