Characterization of the pp70 protein phosphorylation in the extract of rice young panicle

The endogenous phosphorylation pattern of the extract prepared from rice young panicle has been examined. The extract was phosphorylated in vitro by incubating with [gamma-32p] ATP, and then analyzed by SDS-PAGE and autoradiography. At least eight major phosphoproteins with apparent molecular weights of 70, 60, 52, 40, 33, 30, 20, 16 and 15 kd were detected in the crude extract of rice young panicle. The pp70 which represents the major phosphoprotein in the crude extract of young panicle of rice is a cytosolic protein. Photoaffinity labeling with 8-azido-ATP revealed that a major protein with molecular weight 42,000 dalton but not pp70 can be specifically bound ATP. This suggests that pp70 is not a protein kinase itself, but a substrate of protein kinase. The in vitro phosphorylation of the pp70 occurs at a serine or threonine residue and is time and temperature dependent. The phosphorylation of pp70 does not depend by exogenous Ca++ or cAMP, suggesting that pp70 is a major substrate of an Ca++ or cAMP independent protein kinase in rice young panicle.     

panicle phytomer 1 mutations affect the panicle architecture of rice

 We have characterized three panicle phytomer 1 (pap1) mutations from the phytomer viewpoint. In pap1 mutants, rachis phytomers were strongly affected involving a severe reduction of rachis internode length and an increase in the number of rachis internodes (number of phytomers), resulting in a large number of primary branches. In addition, bracts were frequently over-developed. By contrast, pap1 differently affected primary branch phytomers resulting in a reduction in both the number and length of internodes. Spikelets were also modified. Rudimentary and empty glumes were frequently elongated. Floral organs were mostly normal. However, a double mutation between pap1 and fon1 markedly increased the number of floral organs compared with the single fon1 mutation, suggesting that PAP1 has a distinct role in the differentiation of floral organs. The functions of PAP1 on panicle architecture are: (1) the negative regulation of the number of phytomers on the rachis but a positive regulation of the number on primary branches, (2) an elongation of internodes, and (3) the negative regulation of bract development. Received: 5 October 1997 / Accepted: 27 January 1998     

Tillering and panicle branching genes in rice

Rice (Oryza sativa L.) is one of the most important staple food crops in the world, and rice tillering and panicle branching are important traits determining grain yield. Since the gene MONOCULM 1 (MOC 1) was first characterized as a key regulator in controlling rice tillering and branching, great progress has been achieved in identifying important genes associated with grain yield, elucidating the genetic basis of yield-related traits. Some of these important genes were shown to be applicable for molecular breeding of high-yielding rice. This review focuses on recent advances, with emphasis on rice tillering and panicle branching genes, and their regulatory networks.     

Characterization of Imcrop, a Mutator-like MITE family in the rice genome

Sequence comparisons of ammonium transporter 1?C2 genes (OsAMT1-2) in different rice accessions revealed a MITE insertion in the upstream region of the gene. The 391-bp MITE, classified as a Mutator superfamily member and named Imcrop, included terminal inverted repeat (TIR) and 9-bp target site duplication (TSD) sequences. We identified 151 Imcrop elements dispersed on 12 chromosomes of the japonica reference genome. Of these, 12.6% were found in genic regions and 33.1% were located within 1.5 kb of annotated rice genes. We constructed comparative insertion maps with 111 and 102 intact Imcrop elements in the japonica and indica reference genomes, respectively. The Imcrop elements showed relatively even distribution across all chromosomes although their frequency was higher on chromosomes 1, 3, and 4 in both genomes. Seventy seven Imcrop elements were detected in both subspecies, whereas 34 and 25 insertions were found only in the japonica or indica genome, respectively. We compared insertion polymorphisms of 19 Imcrop elements found inside genes in 48 Korean rice cultivars, consisting of 42 japonica and six Tongil-types (indica-japonica cross). Thirteen insertions were common to all cultivars indicating these elements were present before indica-japonica divergence. The six other elements showed insertion polymorphisms among accessions, showing their recent insertion history or no critical positive effect of their insertion on the rice genome.     

Molecular tagging and mapping of the erect panicle gene in rice

Erect panicle (EP) is one of the more important traits of the proposed ideotype of high-yielding rice. Several rice cultivars with the EP phenotype, which has been reported to be controlled by a dominant gene, have been successfully developed and released for commercial production in North China. To analyze the inheritance of the EP trait, we generated segregating F₂ and BC₁F₁ populations by crossing an EP-type variety, Liaojing 5, and a curved-panicle-type variety, Fengjin. Our results confirmed that a dominant gene controls the EP trait. Simple-sequence repeat (SSR) and bulked segregant analyses of the F₂ population revealed that the EP gene is located on chromosome 9, between two newly developed SSR markers, RM5833-11 and RM5686-23, at a genetic distance of 1.5 and 0.9 cM, respectively. Markers closer to the EP gene were developed by amplified fragment length polymorphism (AFLP) analysis with 128 AFLP primer combinations. Three AFLP markers were found to be linked to the EP gene, and the nearest marker, E-TA/M-CTC₂₀₀, was mapped to the same location as SSR marker RM5686-23, 1.5 cM from the EP gene. A local map around the EP gene comprising nine SSR and one AFLP marker was constructed. These markers will be useful for marker-assisted selection (MAS) for the EP trait in rice breeding programs.     

Decoding the rice genome

Rice cultivation is one of the most important agricultural activities on earth, with nearly 90% of it being produced in Asia. It belongs to the family of crops that includes wheat, maize and barley, and it supplies more than 50% of calories consumed by the world population. Its immense economic value and a relatively small genome size makes it a focal point for scientific investigations, so much so that four whole genome sequence drafts with varying qualities have been generated by both public and privately funded ventures. The availability of a complete and high-quality map-based sequence has provided the opportunity to study genome organization and evolution. Most importantly, the order and identity of 37,544 genes of rice have been unraveled. The sequence provides the required ingredients for functional genomics and molecular breeding programs aimed at unraveling intricate cellular processes and improving rice productivity.     

Characterization and expression profiles of miRNAs in rice seeds

Small RNAs (sRNAs) are common and effective modulators of gene expression in eukaryotic organisms. To characterize the sRNAs expressed during rice seed development, massively parallel signature sequencing (MPSS) was performed, resulting in the obtainment of 797 399 22-nt sequence signatures, of which 111 161 are distinct ones. Analysis on the distributions of sRNAs on chromosomes showed that most sRNAs originate from interspersed repeats that mainly consist of transposable elements, suggesting the major function of sRNAs in rice seeds is transposon silencing. Through integrative analysis, 26 novel miRNAs and 12 miRNA candidates were identified. Further analysis on the expression profiles of the known and novel miRNAs through hybridizing the generated chips revealed that most miRNAs were expressed preferentially in one or two rice tissues. Detailed comparison of the expression patterns of miRNAs and corresponding target genes revealed the negative correlation between them, while few of them are positively correlated. In addition, differential accumulations of miRNAs and corresponding miRNA*s suggest the functions of miRNA*s other than being passenger strands of mature miRNAs, and in regulating the miRNA functions.     

Specific panicle responses resulting from MSMA-induced straighthead sterility in rice

Straighthead is a physiological disorder of rice causing sterility. A particular characteristic of straighthead is panicles that remain upright because of the light weight of the unfilled grains, the hulls of which may be distorted into a crescent or parrot-beak shape. Monosodium methanearsenate (MSMA) was used in this study, to induce straighthead-like sterility symptoms in rice. Rating scales were developed to quantify the specific symptoms of straighthead (grain distortion, rachis curvature, panicle exsertion, and panicle weight), which were used to examine MSMA-induced straighthead in a greenhouse setting. Different rice cultivars were surveyed for their specific responses to MSMA, to identify targets for focus in rice breeding that differ in their responses. MSMA altered the pattern of anthesis so that flowering continued for a longer period of time although the initial flowering time and total panicle number were not affected. Early flowering panicles were less affected by MSMA than later flowering panicles. While all previous studies of MSMA-induced straighthead used MSMA applied at or before planting, a time course of MSMA application showed a time point for application at about the V4 (4-leaf) stage when the sterility symptoms were reduced and then an interval of time from about V6 to V8 when applications resulted in symptoms more severe than application at planting. A greenhouse temperature study demonstrated that lowering the temperature of the roots reduced the severity of the responses. MSMA is valuable as a trigger to induce a set of sterility symptoms so that the underlying physiological, biochemical, and genetic causes can be studied, and which may have implications for other sterility conditions.     

Whole-mtDNA genome sequence analysis of ancient African lineages

Studies of human mitochondrial (mt) DNA genomes demonstrate that the root of the human phylogenetic tree occurs in Africa. Although 2 mtDNA lineages with an African origin (haplogroups M and N) were the progenitors of all non-African haplogroups, macrohaplogroup L (including haplogroups L0-L6) is limited to sub-Saharan Africa. Several L haplogroup lineages occur most frequently in eastern Africa (e.g., L0a, L0f, L5, and L3g), but some are specific to certain ethnic groups, such as haplogroup lineages L0d and L0k that previously have been found nearly exclusively among southern African "click" speakers. Few studies have included multiple mtDNA genome samples belonging to haplogroups that occur in eastern and southern Africa but are rare or absent elsewhere. This lack of sampling in eastern Africa makes it difficult to infer relationships among mtDNA haplogroups or to examine events that occurred early in human history. We sequenced 62 complete mtDNA genomes of ethnically diverse Tanzanians, southern African Khoisan speakers, and Bakola Pygmies and compared them with a global pool of 226 mtDNA genomes. From these, we infer phylogenetic relationships amongst mtDNA haplogroups and estimate the time to most recent common ancestor (TMRCA) for haplogroup lineages. These data suggest that Tanzanians have high genetic diversity and possess ancient mtDNA haplogroups, some of which are either rare (L0d and L5) or absent (L0f) in other regions of Africa. We propose that a large and diverse human population has persisted in eastern Africa and that eastern Africa may have been an ancient source of dispersion of modern humans both within and outside of Africa.     

水稻基因组加倍对籽粒大小调控基因表达的影响

水稻是最重要的粮食作物之一,提高水稻产量一直是育种的主要目标。水稻四倍体相对于二倍体具有籽粒变大、粒重增加的特点,研究基因组加倍后籽粒大小基因的调控模式,在育种应用方面具有十分重要的意义。本文以二倍体 -四倍体水稻为材料,分析6个控制籽粒大小基因在幼穗发育中的表达差异,同时结合转基因实验,探讨基因剂量增加对基因表达水平和籽粒大小的影响。结果发现：基因组加倍后,水稻的发育进程不变,但株高增加,叶片变宽,籽粒变大,增大后的籽粒在籼稻表现为长、宽均增加显著,而在粳稻中长度比宽度增加更为明显。进一步分析控制籽粒大小基因的表达差异情况,发现这些基因的表达不仅受发育时期的影响,在籼粳亚种间也明显不同,即受遗传背景的影响。在基因组加倍的情况下,正调控基因GS5、HGW的表达普遍高于对应的二倍体;负调控基因GS3在籼稻D9311中趋于下调或沉默,而在粳稻DBl中趋于上调,GW2在D9311中上调,而在DBl中趋于沉默。通过转基因实验分析负调控基因GW2在二倍体Bl中的表达趋势,发现其在基因剂量线性增加的情况下,表达水平高于二倍体和四倍体,导致其籽粒变小。本研究结果有助于了解水稻中控制籽粒大小的基因在二倍体和四倍体中的表达模式,为高产育种提供理论依据。     

Gene expression profiling in rice young panicle and vegetative organs and identification of panicle-specific genes through known gene functions

In rice, at the stage from pistil and stamen primordia formation to microsporocyte meiosis, the young panicle organs (YPO) make a great contribution to grain productivity. This period corresponds to the onset of meiosis and marks the transition from vegetative to reproductive stages. By comparing gene expression profiling of YPO with that of rice aerial vegetative organs (AVO), it is possible to gain further molecular insight into this period that is developmentally and functionally important. In this report, a total of 92,582 high-quality ESTs from 5′-end sequencing, including 44,247 from YPO and 48,335 from AVO, were obtained and classified. There were 12,884 (29.12%) ESTs from YPO and 16,304 (33.73%) ESTs from AVO matched to known genes, which generated 1,667 and 2,172 known genes, respectively, after integration of these ESTs. From the functions of known homologous genes, we identified some tissue- and developmental-stage-specified genes in YPO. The expression of these genes clearly reflected the unique functional characteristics of YPO. Furthermore, we estimated that there are about 10,000 mRNAs specifically expressed in rice YPO. Jiabin Tang and Hong’ai Xia contributed equally to this work