Comparative analysis of the genomic regions flanking Xa21 locus in indica and japonica ssp. of rice (Oryza sativa L.)

Abstract Comparative analysis of a 100 kb region flanking of major bacterial blight resistance gene Xa21 (3.57 kb) was performed in the two subspecies of rice Oryza sativa L. ssp. japonica cv. Nipponbare and Oryza sativa L. ssp. indica cv. 93-11 to understand the evolution and divergence of Xa21 locus. A total of 12 genes in japonica and 14 genes in indica were predicted and annotated in this region. Functional annotation revealed the presence of 4 genes and 8 genes in japonica and indica, respectively, which could be putatively associated with disease resistance in the 100 kb region of Xa21 locus. The study also revealed that 50% of japonica genes and 42.8% of indica genes in the genomic region of interest were transposable elements protein coding genes. Analysis of each predicted gene in this region revealed more or less similar GC content in both the subspecies. A total of 109 SSRs have been identified in the region of interest in both indica and japonica. The numbers of repeated motifs were observed to decrease with the increased number of nucleotides. Interestingly, most of the leucine rich repeat (LRR) gene products were predicted to be localized in the plasma membrane and the transposable element related protein coding genes were localized in the nucleus. Phylogenetic tree analysis revealed that the majority of predicted genes with similar functions of both the subspecies were grouped together

Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes

Genealogical patterns in different genomic regions may be different due to the joint influence of gene flow and selection. The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication. We chose 66 accessions from the three rice taxa (about 22 each from Oryza sativa indica, O. sativa japonica, and O. rufipogon) for whole-genome sequencing. In the search for the signature of selection, we focus on low diversity regions (LDRs) shared by both cultivars. We found that the genealogical histories of these overlapping LDRs are distinct from the genomic background. While indica and japonica genomes generally appear to be of independent origin, many overlapping LDRs may have originated only once, as a result of selection and subsequent introgression. Interestingly, many such LDRs contain only one candidate gene of rice domestication, and several known domestication genes have indeed been “rediscovered” by this approach. In summary, we identified 13 additional candidate genes of domestication

いもち病抵抗性遺伝子Pi54座のイネ属における分子進化

Tohoku University東谷篤志課

Genomic organization of chromosomal centromeres in the cultivated rice, Oryza sativa L., and its wild progenitor, O. rufipogon Griff.

Centromeres are responsible for sister-chromatid cohesion, kinetochore formation, and accurate transmission of chromosomes. Rice provides an excellent model for organizational and functional studies of centromeres since several of its chromosomes contain limited amounts of satellite and other repetitive sequences in their centromeres. To facilitate molecular characterization of the centromeres, we screened several BIBAC and BAC libraries of japonica and indica rice, using several centromere-specific repeat elements as probes. The positive clones were identified, fingerprinted and integrated into our whole genome physical map databases of the two rice subspecies. BAC/BIBACbased physical maps were constructed for the centromeric regions of the subspecies. To determine whether the genomic organization of the centromeres has changed since the cultivated rice split from its progenitor and to identify the sequences potentially playing an important role in centromere functions, we constructed a large-insert BIBAC library for the wild progenitor of Asian cultivated rice, O. rufipogon. The library contains 24,192 clones, has an average insert size of 163 kb, and covers 5 x haploid genome of wild rice. We screened the wild rice library with two centromere 8-specific overgo probes designed from the sequences flanking centromere 8 of japonica rice. A BIBACbased map was constructed for wild rice centromere 8. Two of the clones, B43P04 and B15E04, were found to span the entire region of the wild rice centromere and thus selected for sequencing the centromere. By sequencing the B43P09 clone, a 95% genomic sequence of the long arm side of wild rice centromere 8 was obtained. Comparative analysis revealed that the centromeric regions of wild rice have a similar gene content to japonica rice, but the centromeric regions of japonica rice have undergone chromosomal rearrangements at both large scale and nucleotide levels. In addition, although the 155-bp satellite repeats showed dramatic changes at the middle region, they are conserved at the 5' and 3' ends of satellite monomers, suggesting that those regions might have important functional roles for centromeres. These results provide not only new insights into genomic organization and evolution, but also a platform for functional analysis of plant centromeres

Genetic Diversity of Seed Dormancy and Molecular Evolution of Weedy Red Rice

Rice is the grain with the third-highest global production. In the US, Arkansas is the largest rice producing state; however, an estimated 62% of the rice fields in the state are infested with red rice, and can cause up to 80% yield reduction in rice. Among its weedy traits, seed dormancy plays an important role in its persistence, and helps red rice escape weed management techniques thereby increasing the red rice soil seedbank. Red rice also has the potential to hybridize among themselves and with cultivated rice, thus resulting in diverse phenotypes and genotypes. In this study we measured variation in seed dormancy at different after-ripening times, and incubation temperatures; determined the genetic diversity of dormant and non-dormant red rice populations; measured diversity in phenological and morphological traits among and within red rice populations collected across Arkansas; and, determined the genotype-phenotype relationship and population structure of old and recent red rice collections using sequence tagged site (STS) markers. The germination response of red rice to three temperatures (1°C, 15°C, and 35°C) and four after-ripening periods (0, 30, 60, and 90 d), was evaluated. Germination varied among and within red rice populations in response to different temperatures and after-ripening period. Highest variation in germination was observed at 15°C incubation (44-97%). Among the after-ripening periods, the optimum time to release primary dormancy was 90 d. Blackhull red rice ecotypes was more dormant and also showed higher intrapopulation variation in dormancy compared to strawhull ecotypes. To determine the genetic diversity of dormant and non-dormant red rice populations, 25 simple sequence repeat (SSR) markers associated with seed dormancy loci were used. A considerable amount of genetic variation among red rice accessions was found (Nei\u27s gene diversity (h) = 0.355), and blackhull populations (h = 0.398) were more diverse than strawhull populations (h = 0.245). Higher genetic diversity was observed within and among dormant populations than non-dormant red rice populations. Phenological and morphological characteristics were found to significantly vary among 113 strawhull, 71 blackhull, and 24 brownhull red rice accessions. Greater variation was observed among blackhull red rice, the tallest, late flowering, and highly tillering among the ecotypes. Strawhull red rice generally tillered less, but produced higher grain yield. Sequence analysis of 27 old (2002-2003 collection) and 52 recent (2008-2009 collection) red rice accessions, using 48 STS markers revealed a total of 447 SNPs. Recent blackhull red rice accessions had higher nucleotide diversity (Pi = 2.43 per Kb) than the old blackhull accessions (Pi = 1.21 per Kb). Old strawhull had lower sequence polymorphisms than old blackhull red rice. Genetic and phenotypic diversity among and within red rice ecotypes suggests the adoption of diverse weed management techniques in order to successfully control this troublesome weed.

Principles, requirements and prospects of genetic mapping in plants

Genetic mapping (also known as linkage mapping or meiotic mapping) refers to the determination of the relative position and distances between markers along chromosomes. Genetic map distancesbetween two markers are defined as the mean number of recombination events, involving a given chromatid, in that region per meiosis. Genetic map construction requires that the researcher developappropriate mapping population, decide the sample size and type of molecular marker(s) for genotyping, genotype the mapping population with sufficient number of markers, and perform linkageanalyses using statistical programs. The construction of detailed genetic maps with high levels of genome coverage is a first step for localizing genes or quantitative trait loci (QTL) that are associatedwith economically important traits, marker assisted selection, comparative mapping between different species, a framework for anchoring physical maps, and the basis for map-based cloning of genes.Highly reproducible, high throughput, codominant, and transferable molecular markers, especially developed from expressed regions, are sought to increase the utility of genetic maps. This articlereviews the principles, requirements, and future prospects of genetic mapping in plants

Molecular Genetic Analysis of Drought Resistance and Productivity Traits of Rice Genotypes

Rice (Oryza sativa L.) is the staple food for a majority of the world’s population, and uses 30% of the global fresh water during its life cycle. Drought at the reproductive stage is the most important abiotic stress factor limiting grain yield. The United States is the third largest exporter of rice, and Arkansas is the top rice-producing state. The Arkansas rice-growing region in the Lower Mississippi belt is among the 10 areas with the highest risk of water scarcity. Adapted U.S. rice cultivars were screened for drought resistant (DR) traits to find sources for breeding U.S. rice cultivars for a water saving agricultural system. A recombinant inbred line (RIL) population, derived from varieties Kaybonnet (DR) and ZHE733 (drought sensitive), termed K/Z RILs was chosen for genetic analysis of DR traits. The objectives of this research were to 1) analyze the phenotypic and grain yield components of the K/Z RIL rice population for drought-resistance-related traits, 2) evaluate the Abscisic Acid (ABA) response of the K/Z RIL rice population on root architectural traits in relation to drought stress resistance, 3) screen polymorphic molecular markers to identify genes linked to productivity traits of grain yield under drought stress, measured by number of filled grain per panicle using bulk segregant analysis (BSA), and 4) identify QTLs and candidate genes in the K/Z RIL population for drought resistance associated with vegetative morphological traits, grain yield components under drought stress and well-watered conditions, and root architectural traits related to ABA response. The RIL population was screened in the field at Fayetteville (AR) by controlled drought stress (DS) treatment at the reproductive stage, and the effect of DS quantified by measuring drought-related traits. ABA sensitivity was quantified by measuring root architectural traits at the V3 stage. Based on the filled grain per panicle number, 13.13% of K/Z RIL population and parent Kaybonnet were highly drought resistant, while 75.75% of RILs and parent ZHE733 were drought sensitive. Under ABA conditions, Kaybonnet and 48 drought resistant lines exhibit ABA sensitivity, implying regulation of osmotic stress tolerance via ABA-mediated cell signaling. Based on BSA screening, 13 polymorphic markers potentially linked to DR traits were identified. QTL analysis was performed with 4133 SNPs markers by using QTL IciMapping. A total of 213 QTLs and 628 candidate genes within the QTL regions were identified for drought-related traits. The RT-qPCR analysis of the candidate genes revealed that a high number of drought resistance genes were up-regulated in Kaybonnet as the drought-resistant parent. Information from this research will serve an important step towards improvement of adapted Arkansas rice cultivars for higher grain production under DS conditions