Intron length polymorphisms (ILPs) have been used as genetic markers in some studies. However, a systematic investigation and large-scale exploitation of ILP markers has not been reported. In this study, we performed a genome-wide search of ILPs between two subspecies (indica and japonica) in rice using the draft genomic sequences of cultivars 93-11 (indica) and Nipponbare (japonica) and 32,127...

Indica and japonica are two main subspecies of Asian cultivated rice (Oryza sativa L.) that differ clearly in morphological and agronomic traits, in physiological and biochemical characteristics and in their genomic structure. However, the proteins and genes responsible for these differences remain poorly characterized. In this study, proteomic tools, including two-dimensional electrophoresis a...

Having a deep genetic structure evolved during its domestication and adaptation, the Asian cultivated rice (Oryza sativa) displays considerable physiological and morphological variations. Here, we describe deep whole-genome sequencing of the aus rice cultivar Kasalath by using the advanced next-generation sequencing (NGS) technologies to gain a better understanding of the sequence and structura...

A new locus responsible for increased yield potential across the genetic background in rice (Oryza sativa L.) was identified and evaluated. Quantitative trait loci (QTLs) were analysed for the ratio of filled grains, a yield component, in backcrossed inbred lines of a japonica 'Nipponbare'xindica 'Kasalath' cross for 3 years. Only one QTL (rg5), with a positive Kasalath allele, was detected acr...

Seedlings of three rice (Oryza sativa L.) varieties (one indica, ARC5955; and two japonica, Nipponbare and Koshihikari) with or without pre-colonization by the arbuscular mycorrhizal fungus Funneliformis mosseae were transplanted into an upland field and grown to maturity. Pre-colonization had no effect on the yield of Nipponbare or Koshihikari. However, pre-colonized ARC5955 exhibited a strong...

Single nucleotide polymorphisms (SNPs) are known as the most detectable variations among related genomes. We estimated the SNPs between Tainung 67 (TNG67), an elite cultivar of rice (Oryza sativa) in Taiwan, and Nipponbare, the cultivar used for rice genome sequencing by the international consortium. More than 6,000 expressed sequence tag (EST) sequences from developing panicles of TNG67 were c...

Although quantitative traits loci (QTL) analysis has been widely performed to isolate agronomically important genes, it has been difficult to obtain molecular markers between individuals with similar phenotypes (assortative mating). Recently, the miniature inverted-repeat transposable element mPing was shown to be active in the japonica strain Gimbozu EG4 where it had accumulated more than 1000...

Hd6 is a quantitative trait locus involved in rice photoperiod sensitivity. It was detected in backcross progeny derived from a cross between the japonica variety Nipponbare and the indica variety Kasalath. To isolate a gene at Hd6, we used a large segregating population for the high-resolution and fine-scale mapping of Hd6 and constructed genomic clone contigs around the Hd6 region. Linkage an...

Miniature inverted-repeat transposable elements (MITEs) are ubiquitous in high eukaryotic genomes. More than 178,000 MITE sequences of 338 families are present in the genome of rice (Oryza sativa) cultivar Nipponbare. Interestingly, only two of the 338 MITE families have homologous sequences in the genome of Brachypodium distachyon, a relative in the grass family. Therefore, the vast majority o...

Alternative splicing creates a diversity of gene products in higher eukaryotes. Twenty-five percent (1,583/ 6,371) of predicted alternatively spliced transcripts can be detected using the NSF45K rice whole-genome oligonucleotide array. We used the NSF45K array to assess differential expression patterns of 507 loci showing at least a twofold change in expression between lightand darkgrown seedli...