Natural Variation in the Flag Leaf Morphology of Rice Due to a Mutation of the NARROW LEAF 1 Gene in Oryza sativa L.

We investigated the natural variations in the flag leaf morphology of rice. We conducted a principal component analysis based on nine flag leaf morphology traits using 103 accessions from the National Institute of Agrobiological Sciences Core Collection. The first component explained 39% of total variance, and the variable with highest loading was the width of the flag leaf (WFL). A genome-wide association analysis of 102 diverse Japanese accessions revealed that marker RM6992 on chromosome 4 was highly associated with WFL. In analyses of progenies derived from a cross between Takanari and Akenohoshi, the most significant quantitative trait locus (QTL) for WFL was in a 10.3-kb region containing the NARROW LEAF 1 (NAL1) gene, located 0.4 Mb downstream of RM6992. Analyses of chromosomal segment substitution lines indicated that a mutation (G1509A single-nucleotide mutation, causing an R233H amino acid substitution in NAL1) was present at the QTL. This explained 13 and 20% of total variability in WFL and the distance between small vascular bundles, respectively. The mutation apparently occurred during rice domestication and spread into japonica, tropical japonica, and indica subgroups. Notably, one accession, Phulba, had a NAL1 allele encoding only the N-terminal, or one-fourth, of the wild-type peptide. Given that the Phulba allele and the histidine-type allele showed essentially the same phenotype, the histidine-type allele was regarded as malfunctional. The phenotypes of transgenic plants varied depending on the ratio of histidine-type alleles to arginine-type alleles, raising the possibility that H(233)-type products function differently from and compete with R(233)-type products

A reference-grade wild soybean genome

Wild relatives of crop plants are invaluable germplasm for genetic improvement. Here, Xie et al. report a reference-grade wild soybean genome and show that it can be used to identify structural variation and refine quantitative trait loci

A reference-grade wild soybean genome

Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs

Phytochrome-mediated growth inhibition of seminal roots in rice seedlings

In rice (Oryza sativa) seedlings, continuous white-light irradiation inhibited the growth of seminal roots but promoted the growth of crown roots. Here, we examined the mechanisms of photoinhibition of seminal root growth. Photoinhibition occurred in the absence of nitrogen, but increased with increasing nitrogen concentrations. In the presence of nitrogen, photoinhibition was correlated with coiling of the root tips. The seminal roots were most photosensitive 48-72 h after germination during the 7-d period after germination. White-light irradiation for at least 6 h was required for photoinhibition, and the Bunsen-Roscoe law of reciprocity was not observed. Experiments with phytochrome mutants showed that far-red light was perceived exclusively by phyA, that red light was perceived by both phyA and phyB, and phyC had little or no role in growth inhibition or coiling of the seminal roots. Fluence-response curve analyses also showed that phyA and phyB control very low fluence response and low fluence response, respectively, in the seminal roots. This was essentially the same as the growth inhibition previously observed at the late stage of coleoptile development (80 h after germination). These results also suggest that other blue-light photoreceptors are involved in growth inhibition of the seminal roots. The photoperceptive site for the root growth inhibition appeared to be the roots themselves. All three phytochrome species of rice were detected immunochemically in roots

Effect of Nitrate on Nodule and Root Growth of Soybean (Glycine max (L.) Merr.)

The application of combined nitrogen, especially nitrate, to soybean plants is known to strongly inhibit nodule formation, growth and nitrogen fixation. In the present study, we measured the effects of supplying 5 mM nitrate on the growth of nodules, primary root, and lateral roots under light at 28 °C or dark at 18 °C conditions. Photographs of the nodulated roots were periodically taken by a digital camera at 1-h intervals, and the size of the nodules was measured with newly developed computer software. Nodule growth was depressed approximately 7 h after the addition of nitrate under light conditions. The nodule growth rate under dark conditions was almost half that under light conditions, and nodule growth was further suppressed by the addition of 5 mM nitrate. Similar results were observed for the extending growth rate of the primary root as those for nodule growth supplied with 5 mM nitrate under light/dark conditions. In contrast, the growth of lateral roots was promoted by the addition of 5 mM nitrate. The 2D-PAGE profiles of nodule protein showed similar patterns between the 0 and 5 mM nitrate treatments, which suggested that metabolic integrity may be maintained with the 5 mM nitrate treatment. Further studies are required to confirm whether light or temperature condition may give the primary effect on the growth of nodules and roots

Differences in lamina joint anatomy cause cultivar differences in leaf inclination angle of rice

Leaf erectness is an important agronomic trait for improving canopy photosynthesis in rice. It is well known that leaf inclination angle (LIA) decreases after expansion during ripening. However, the high-yielding indica cultivar ‘Takanari’ retains a greater LIA during ripening than the high-quality japonica cultivar ‘Koshihikari’. To clarify the cause of the cultivar difference in LIA, we investigated anatomical characteristics of the lamina joint of a flag leaf. We found a close linear correlation between LIA at the centre and at the base of the leaf blade in both cultivars during ripening. The length of the lamina joint increased significantly more on the adaxial side of a leaf (the margin of the collar) than on the abaxial side (the abaxial side of the central part of the collar) in ‘Koshihikari’ after leaf expansion, but there was no clear difference in ‘Takanari’. We found a close linear correlation between the ratio of lamina joint length on the adaxial to abaxial sides and LIA in ‘Koshihikari’ and ‘Takanari’ during ripening. In ‘Koshihikari’, the average length of cells on the adaxial side increased significantly after leaf expansion, with no significant increase in that on the abaxial side and no significant change in cell number on either side. In ‘Takanari’, cell length and cell number showed no significant changes on either side of the lamina joint. We conclude that the cultivar difference in LIA during ripening is caused mainly by cell elongation on the adaxial side of the lamina joint. List of Abbreviations: k: light extinction coefficient; LIA: leaf inclination angle; QTL: quantitative trait locu

Isolation of a major genetic interaction associated with an extreme phenotype using assorted F2 populations in rice

Detection of quantitative trait loci (QTLs) is dependent on the materials used in the analysis, as different combinations of parental materials may lead to different outcomes in QTLs for the same trait. On the other hand, an extreme phenotype associated with a given trait implies the potential involvement of a particular allele in various allelic interactions. A genetic factor associated with such an extreme phenotype may frequently be identified from various genetic populations consisting of different parental combinations. In this study, we attempted to uncover the genetic factor associated with extremely early heading date in rice, using various F2 populations. Heading date in rice has been characterized by at least 19 QTLs, from which 12 genes have been identified. A58, a rice strain with an extremely early heading date, is adapted to Hokkaido, the northernmost limit of rice cultivation. Six F2 populations derived from crosses of A58 with six other strains displayed a range of heading dates. Genotyping using 19 QTL markers indicated that the A58 allele of the Ghd7 locus was present in most F2 individuals exhibiting extremely early heading dates. This analysis also demonstrated that when the wild-type Ehd1 allele was present, the Ghd7 allele from A58 accelerated floral induction. The results of this study demonstrate that assorted F2 populations are valuable materials for comprehensive genotyping to explore major genetic factors for extreme phenotypes, and that this methodology is broadly applicable to other unknown traits