Rosalyn B. Angeles-Shim

Isolation and characterization of dominant dwarf mutants, Slr1-d, in rice.

Abstractsd1 is known as the ‘green revolution’ gene in rice because its application in rice breeding has dramatically increased rice yield. Since the ‘green revolution,’ sd1 has been extensively used to produce modern semi-dwarf varieties. The extensive use of limited dwarfing sources may, however, cause a bottleneck effect in the genetic background of rice varieties. To circumvent this problem, novel and useful sources of dwarf genes must be identified. In this study, we identified three semi-dominant dwarf mutants. These mutants were categorized as dn-type dwarf mutants according to the elongation pattern of internodes. Gibberellin (GA) response tests showed that the mutants were still responsive to GA, although at a reduced rate. Map-based cloning revealed that the dwarf phenotype in these mutants was caused by gain-of-function mutations in the N-terminal region of SLR1. Degradation of the SLR1 protein in these mutants occurred later than in the wild type. Reduced interaction abilities of the SLR1 protein in these mutants with GID1 were also observed using the yeast two-hybrid system. Crossing experiments indicated that with the use of an appropriate genetic background, the semi-dominant dwarf alleles identified in this study could be used to alleviate the deficiency of dwarfing genes for breeding applications.

Gibberellin biosynthesis and signal transduction is essential for internode elongation in deepwater rice

Under flooded conditions, the leaves and internodes of deepwater rice can elongate above the water surface to capture oxygen and prevent drowning. Our previous studies showed that three major quantitative trait loci (QTL) regulate deepwater-dependent internode elongation in deepwater rice. In this study, we investigated the age-dependent internode elongation in deepwater rice. We also investigated the relationship between deepwater-dependent internode elongation and the phytohormone gibberellin (GA) by physiological and genetic approach using a QTL pyramiding line (NIL-1 + 3 + 12). Deepwater rice did not show internode elongation before the sixth leaf stage under deepwater condition. Additionally, deepwater-dependent internode elongation occurred on the sixth and seventh internodes during the sixth leaf stage. These results indicate that deepwater rice could not start internode elongation until the sixth leaf stage. Ultra-performance liquid chromatography tandem mass-spectrometry (UPLC-MS/MS) method for the phytohormone contents showed a deepwater-dependent GA1 and GA4 accumulation in deepwater rice. Additionally, a GA inhibitor abolished deepwater-dependent internode elongation in deepwater rice. On the contrary, GA feeding mimicked internode elongation under ordinary growth conditions. However, mutations in GA biosynthesis and signal transduction genes blocked deepwater-dependent internode elongation. These data suggested that GA biosynthesis and signal transduction are essential for deepwater-dependent internode elongation in deepwater rice. Deepwater rice obtained the ability for rapid internode elongation to avoid drowning and adapt to flooded condition. How does it regulate internode elongation? Using both physiological and genetic approach, this paper shows that the plant hormone, gibberellin (GA) regulates internode elongation.

Development and evaluation of chromosome segment substitution lines (CSSLs) carrying chromosome segments derived from Oryza rufipogon in the genetic background of Oryza sativa L.

The wild relatives of rice (Oryza sativa L.) are useful sources of alleles that have evolved to adapt in diverse environments around the world. Oryza rufipogon, the known progenitor of the cultivated rice, harbors genes that have been lost in cultivated varieties through domestication or evolution. This makes O. rufipogon an ideal source of value-added traits that can be utilized to improve the existing rice cultivars. To explore the potential of the rice progenitor as a genetic resource for improving O. sativa, 33 chromosome segment substitution lines (CSSLs) of O. rufipogon (W0106) in the background of the elite japonica cultivar Koshihikari were developed and evaluated for several agronomic traits. Over 90% of the entire genome was introgressed from the donor parent into the CSSLs. A total of 99 putative QTLs were detected, of which 15 were identified as major effective QTLs that have significantly large effects on the traits examined. Among the 15 major effective QTLs, a QTL on chromosome 10 showed a remarkable positive effect on the number of grains per panicle. Comparison of the putative QTLs identified in this study and previous studies indicated a wide genetic diversity between O. rufipogon accessions.

Two novel QTLs regulate internode elongation in deepwater rice during the early vegetative stage.

Deepwater rice possesses internode elongation ability to avoid drowning under deepwater conditions. Previous studies identified three QTLs regulating internode elongation ability on chromosomes 1, 3 and 12 using different populations. However, these QTLs only induce internode elongation in response to deepwater conditions from the 7-leaf stage and not during the early leaf stage. In this study, we detected two novel QTLs, qTIL2 and qTIL4 regulating deepwater response at the early leaf stage using an F2 population derived from the cross between NIL1-3-12 carrying the three QTLs regulating deepwater response in T65 (O. sativa ssp. japonica) genetic background and C9285 (O. sativa ssp. indica, deepwater rice). Plants of the BC2F2 population derived from NIL1-3-12/C9285 and the RILs of T65/Bhadua (O. sativa ssp. indica, deepwater rice) possessing these QTLs as well as the three QTLs previously identified also showed internode elongation during the early leaf stage. These results indicate that qTIL2 and qTIL4 regulate early internode elongation and function in coordination with the three major QTLs under deepwater conditions. The results presented here would not only help define the mechanism of deepwater response in rice but also contribute in the breeding of deepwater tolerant rice that is adapted to various water depths.

Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice.

Significance This study investigates a previously unidentified cysteine-rich peptide (CRP). CRPs have diverse roles in plant growth and development, such as control of stomata density and guidance of pollen-tube elongation. Despite numerous studies on CRPs in Arabidopsis thaliana, there are still many peptides with unknown function. We identify a previously unidentified rice CRP named Regulator of Awn Elongation 2 (RAE2) and show that it is cleaved specifically in the spikelet to promote awn elongation. We demonstrate that RAE2 was a target of selection during domestication, contributing to loss of awns in Asian but not African rice. The discovery of RAE2 simultaneously deepens our understanding of plant developmental pathways and lends insight into the complex processes underlying cereal domestication. Domestication of crops based on artificial selection has contributed numerous beneficial traits for agriculture. Wild characteristics such as red pericarp and seed shattering were lost in both Asian (Oryza sativa) and African (Oryza glaberrima) cultivated rice species as a result of human selection on common genes. Awnedness, in contrast, is a trait that has been lost in both cultivated species due to selection on different sets of genes. In a previous report, we revealed that at least three loci regulate awn development in rice; however, the molecular mechanism underlying awnlessness remains unknown. Here we isolate and characterize a previously unidentified EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family member named REGULATOR OF AWN ELONGATION 2 (RAE2) and identify one of its requisite processing enzymes, SUBTILISIN-LIKE PROTEASE 1 (SLP1). The RAE2 precursor is specifically cleaved by SLP1 in the rice spikelet, where the mature RAE2 peptide subsequently induces awn elongation. Analysis of RAE2 sequence diversity identified a highly variable GC-rich region harboring multiple independent mutations underlying protein-length variation that disrupt the function of the RAE2 protein and condition the awnless phenotype in Asian rice. Cultivated African rice, on the other hand, retained the functional RAE2 allele despite its awnless phenotype. Our findings illuminate the molecular function of RAE2 in awn development and shed light on the independent domestication histories of Asian and African cultivated rice.

A WUSCHEL-related homeobox 3B gene, depilous (dep), confers glabrousness of rice leaves and glumes

BackgroundGlabrousness is an important agricultural trait for the practical breeding of rice. In this study, depilous (dep), the gene responsible for glabrous leaves and glumes of rice was identified by map-based cloning.ResultsThe dep gene encodes a WUSCHEL-related homeobox 3B that was fine-mapped to a 22-kb region on the short arm of chromosome 5 using progenies derived from crosses between Koshihikari (pubescent) and GLSL15, an Oryza glaberrima chromosome segment substitution line (glabrous). Complementation tests confirmed the conditioning of the glabrous phenotype by the dep gene. Phylogenetic analysis showed that dep groups with the WOX3 family of plant-specific homeobox transcription factors that are involved in regulating lateral organ development. Localization of dep in the nucleus indicates the function of the gene as a transcription factor. Spatial expression of the gene was observed in the base of young shoots, the leaf sheath, midrib, young roots and nodal structures.ConclusionThe identification and cloning of dep will not only provide basis for future research on the elucidation of the molecular mechanisms underlying trichome formation in rice but will also aid in breeding programs for the development of glabrous varieties.

QTL analysis of internode elongation in response to gibberellin in deepwater rice

Gibberellin (GA) is one of the plant hormones which regulates many aspects of plant growth and developmental processes. Rice plants known as deepwater rice can survive during flooding by elongating its internodes to avoid anoxia. Previous studies reported that GA is essential for internode elongation in deepwater rice. However, the interaction between internode elongation and regulator of GA sensitivity is unknown. In this study, we performed a QTL analysis and identified the chromosomal regions that regulate GA responsiveness in deepwater rice. We concluded that deepwater rice could induce internode elongation in response to GA by factors in these regions.

Development of chromosome segment substitution lines (CSSLs) of Oryza longistaminata A. Chev. & Röhr in the background of the elite japonica rice cultivar, Taichung 65 and their evaluation for yield traits

Oryza longistaminata (AA genome) is a wild rice species that is phenotypically inferior to cultivated rice but possesses useful alleles that can be used to improve agronomically important traits. Interspecific hybrids that are derived from cultivated rice and wild rice species with AA genome are important contributors of genetic diversity in rice. To illustrate the potential of wild rice relatives as a source of novel alleles for rice improvement, a total of 40 chromosome segment substitution lines (CSSLs) of O. longistaminata in the background of the elite japonica cultivar Taichung 65 were developed and evaluated for yield and various yield-related traits. A number of CSSLs carrying putative quantitative trait loci (QTLs) controlling different yield-related traits were identified during both dry and wet seasons. In particular, 10 major putative QTLs controlling early heading date, plant height, tiller number, panicle length, number of primary branches per panicle, grain number per panicle, grain width, and grain thickness were identified. Interestingly, one of the CSSL lines, LTSL26, with major putative QTLs on chromosomes 1 and 8 that increase grain number per panicle, showed pleiotropic effects on other traits such as plant height, days to flowering, tiller number, number of branches per panicle, and grain length. These results suggest that O. longistaminata is a good source of new alleles that can be used to improve yield-related traits in cultivated rice varieties.

Construction of a versatile SNP array for pyramiding useful genes of rice.

DNA marker-assisted selection (MAS) has become an indispensable component of breeding. Single nucleotide polymorphisms (SNP) are the most frequent polymorphism in the rice genome. However, SNP markers are not readily employed in MAS because of limitations in genotyping platforms. Here the authors report a Golden Gate SNP array that targets specific genes controlling yield-related traits and biotic stress resistance in rice. As a first step, the SNP genotypes were surveyed in 31 parental varieties using the Affymetrix Rice 44K SNP microarray. The haplotype information for 16 target genes was then converted to the Golden Gate platform with 143-plex markers. Haplotypes for the 14 useful allele are unique and can discriminate among all other varieties. The genotyping consistency between the Affymetrix microarray and the Golden Gate array was 92.8%, and the accuracy of the Golden Gate array was confirmed in 3 F2 segregating populations. The concept of the haplotype-based selection by using the constructed SNP array was proofed.

Convergent Loss of Awn in Two Cultivated Rice Species Oryza sativa and Oryza glaberrima Is Caused by Mutations in Different Loci.

A long awn is one of the distinct morphological features of wild rice species. This organ is thought to aid in seed dispersal and prevent predation by animals. Most cultivated varieties of Oryza sativa and Oryza glaberrima, however, have lost the ability to form long awns. The causal genetic factors responsible for the loss of awn in these two rice species remain largely unknown. Here, we evaluated three sets of chromosome segment substitution lines (CSSLs) in a common O. sativa genetic background (cv. Koshihikari) that harbor genomic fragments from Oryza nivara, Oryza rufipogon, and Oryza glaberrima donors. Phenotypic analyses of these libraries revealed the existence of three genes, Regulator of Awn Elongation 1 (RAE1), RAE2, and RAE3, involved in the loss of long awns in cultivated rice. Donor segments at two of these genes, RAE1 and RAE2, induced long awn formation in the CSSLs whereas an O. sativa segment at RAE3 induced long awn formation in O. glaberrima. These results suggest that the two cultivated rice species, O. sativa and O. glaberrima, have taken independent paths to become awnless.