Keiji Motomura

Genetic analysis of root elongation induced by phosphorus deficiency in rice (Oryza sativa L.): fine QTL mapping and multivariate analysis of related traits

Root elongation induced by phosphorus deficiency has been reported as one of the adaptive mechanisms in plants. Genetic differences were found in rice for the root elongation under phosphorus deficiency (REP), for which a distinct quantitative trait locus (QTL) was detected on the long arm of chromosome 6. Subsequently, the effect and position of the QTL, designated as qREP-6, were confirmed using chromosome segment substitution lines (CSSLs), in which the background of a japonica cultivar, ‘Nipponbare’ with non-REP, was partially substituted by chromosomal segments from an indica cultivar, ‘Kasalath’ with remarkable REP. Out of 54 CSSLs, two lines (CSSL28 and CSSL29) that retain a common ‘Kasalath’-derived segment on the long arm of chromosome 6 showed a significantly high REP. The high REP lines also showed high adaptabilities such as enhanced tillering ability and shoot phosphorus content. Accordingly, conditional dependencies between the related traits were assessed using a graphical Gaussian model (GGM). Direct interactions between REP and root length, and between root length and tiller number were detected under P deficiency in CSSLs. Furthermore, qREP-6 for REP and qTNP-6 for tiller number under P deficiency were fine-mapped with an F2 population of a cross between Nipponbare and CSSL29. A region containing qREP-6 accounted for more than half of the phenotypic variance, the most plausible interval of which contained 37 candidate genes. The result provides a foundation for cloning of the qREP-6 gene which will be applicable to study P deficiency-dependent response and to improve rice’s adaptability to P deficiency stress.

Whole genomic sequencing of RT98 mitochondria derived from Oryza rufipogon and northern blot analysis to uncover a cytoplasmic male sterility-associated gene

Cytoplasmic male sterility (CMS) is a maternally inherited trait resulting in the failure to produce functional pollen and is often observed when an alien cytoplasm is transferred into a cultivated species. An RT98A CMS line and an RT98C fertility restorer line were obtained by successive backcrossing between Oryza rufipogon W1109 and Oryza sativa cultivar Taichung 65. To uncover the CMS-associated mitochondrial genes, we determined the complete sequence of the RT98-CMS mitochondrial genome using next-generation pyrosequencing, and searched new open reading frames (orfs) absent in a reported mitochondrial genome of O. sativa Nipponbare. Then, six candidates were selected for the CMS-associated genes based on the criteria in which they were chimeric in structure or encoded a peptide with transmembrane domains. One of the candidates, orf113, showed different transcript sizes between RT98A and RT98C on Northern blot analysis. The orf113 gene was shown to be co-transcribed with atp4 and cox3 encoding ATP synthase F0 subunit 4 and Cyt c oxidase subunit 3, respectively, and their transcripts were distinctly processed in the presence of a fertility restorer gene. Our results indicate that orf113 is a CMS-associated gene of RT98-CMS.

Effects of Planting Pattern and Planting Distance on Growth and Yield of Turmeric (Curcuma longa L.)

Abstract The effects of planting pattern and planting distance on the growth and yield of turmeric (Curcuma longa L.) were examined in Okinawa Prefecture situated in southern Japan. The dry weights of shoot and rhizome (yield) of turmeric planted in a triangular pattern were heavier than those planted in a quadrate pattern. A 30-cm-triangular planting resulted in the heaviest shoot and rhizome yield among the planting patterns examined. Dry weight of shoot per unit land area (m2) was significantly heavier when planted at a 20- and 30-cm spacing than when planted with a larger spacing, whereas the highest yield was obtained when planted at a 30-cm spacing followed by 20- and 40-cm spacing. When turmeric was planted at a 20-cm spacing, rhizome could not expand properly, which ultimately resulted in the smaller rhizome compared with that planted with a larger spacing. The highest turmeric yield coupled with the lowest weed biomass was obtained on the two-row ridge in a 75-100 cm width compared with a one- or two-row ridge in a larger or smaller width. This study indicates that for reducing weed interference and obtaining higher yield, turmeric should be planted in a 30-cm-triangular pattern on two-row ridge in a 75-100 cm width.

Whole Mitochondrial Genome Sequencing and Transcriptional Analysis to Uncover an RT102-Type Cytoplasmic Male Sterility-Associated Candidate Gene Derived from Oryza rufipogon

Cytoplasmic male sterility (CMS) is a maternally inherited trait in which plants fail to produce functional pollen and is associated with the expression of a novel open reading frame (orf) gene encoded by the mitochondrial genome. An RT102A CMS line and an RT102C fertility restorer line were obtained by successive backcrossing between Oryza rufipogon W1125 and O. sativa Taichung 65. Using next-generation pyrosequencing, we determined whole-genome sequences of the mitochondria in RT102-CMS cytoplasm. To identify candidates for the CMS-associated gene in RT102 mitochondria, we screened the mitochondrial genome for the presence of specific orf genes that were chimeric or whose products carried predicted transmembrane domains. One of these orf genes, orf352, which showed different transcript sizes depending on whether the restorer of fertility (Rf) gene was present or not, was identified. The orf352 gene was co-transcribed with the ribosomal protein gene rpl5, and the 2.8 kb rpl5-orf352 transcripts were processed into 2.6 kb transcripts with a cleavage at the inside of the orf352 coding region in the presence of the Rf gene. The orf352 gene is an excellent candidate for the CMS-associated gene for RT102-CMS.

Effects of Seed Rhizome Size on Growth and Yield of Turmeric (Curcuma longa L.)

Abstract Turmeric (Curcuma longa L ) plant species produces different sizes of daughter rhizomes (R) and mother rhizomes (MR), which are the only propagules (seed) for its cultivation. Here, we evaluated the effects of seed rhizome size on growth and yield of turmeric. Daughter rhizomes of 5-50 g (R-5 g~R-50 g) and mother rhizomes of 48-52 g (MR) were tested. The heavier the R up to 40 g, the better the plant growth, and the plants from the R-30 g, R-40 g, R-50 g and MR grew similarly well. The seed rhizomes with a greater diameter developed vigorous seedlings. The plants grown from R-30 g, R-40 g and R-50 g had a similar plant height, tiller number and leaf number, which were significantly higher than those from lighter R. The plants from R-30 g, R-40 g and R-50 g had a significantly larger shoot biomass and higher yield than those from smaller R in both the greenhouse and field experiments. R-50 g was easily broken at the time of planting, and had secondary and tertiary daughter rhizomes, which developed thinner plants and resulted in a lower yield. The shoot biomass and yield were highest in the plants grown directly from MR, and lower in the plants grown from daughter rhizomes attached to MR. This study indicates that the turmeric seed rhizome should be 30-40 g with a larger diameter, and seed mother rhizome should be free from daughter rhizomes.

Sterility of Thermo-Sensitive Genic Male Sterile Line, Heterosis for Grain Yield and Related Characters in F1 Hybrid Rice (Oryza sativa L.)

Abstract The thermo-sensitive genic male sterile (TGMS) T29s line was sterile when exposed to daily mean temperatures of 24.1°C or above during the critical stage (from 15 to 11 days before heading). It was completely sterile for both pollen and spikelet when the plant headed from June 16 to November 7 in Okinawa, because the temperature exceeded 24.1°C. The heterosis of the F1 hybrids between the T29s line and seven indica cultivars was examined. Most of the F1 hybrids showed positive heterosis over the male parent for grain yield per plant and the number of spikelets per panicle, and one of them manifested heterosis for grain yield over a F1 hybrid from a cytoplasmic male sterile (CMS) line. Dry matter accumulation per plant at the panicle initiation stage in most F1 hybrids was higher than that in the respective male parent or mid-parent, and it was correlated with a larger number of tillers and leaf area per plant. All F1 hybrids produced a larger number of panicles per plant than their respective male parent. Positive heterosis over the male parent for the number of filled grains per panicle, 1000-grain weight and harvest index was obtained in several F1 hybrids. A positive correlation was found between grain yield and the dry matter accumulation per plant in F1 hybrids. Both the larger number of panicles per plant and the larger number of spikelets per panicle were more important for the positive heterosis for grain yield in F1 hybrids rather than the higher 1000-grain weight. Among the yield attributes, a larger number of filled grains per panicle mainly contributed to a higher grain yield of F1 hybrids.

Trisomic analysis of new gene for late heading in rice, Oryza sativa L

A near isogenic line, T65-LH7 bred from a rice variety, Ketan Nangka by five times of successive backcrossing with Taichung 65 (T65) as recurrent parent was found to carry a recessive lateness gene tentatively designated as ef6(t). The present study was performed to investigate the allelic relationships between ef6(t) and other heading time genes, Ef1, Efx, ef2(t), ef3(t), ef4(t) and ef5 by allelism test and to locate the chromosomal location of ef6(t) by trisomic analysis. In allelism test, six testers carrying each of heading time genes, Ef1, Efx, ef2(t), ef3(t), ef4(t) and ef5 were used. Those testers were the near isogenic lines of T65. T65-LH7 was crossed with respective testers. Heading times in F2 and/or B1F1 plants were examined. All F2 and/or B1F1 populations derived from those crosses exhibited digenic segregations, respectively. These results suggested that ef6(t) was independent of Ef1, Efx, ef2(t), ef3(t), ef4(t) and ef5. Sub sequently, trisomic analysis of ef6(t) was performed using seven Triplo lines having extra chromosomes, 2, 4, 5, 7, 9, 10 and 12. These Triplo lines were the near isogenic lines of T65. They were used as maternal parent to cross with T65-LH7. Heading times in F2 plants obtained from self-pollination of F1 plants were observed. Among F2 plants examined only those derived from a cross between Triplo-7 and T65-LH7 showed a typical trisomic segregation manner, suggesting that ef6(t) was located on chromosome 7. Consequently, the nomenclature of the present gene should be designated as ef6.