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ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations.

S-McCouch PubMed Feed - Wed, 07/25/2012 - 15:45
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ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations.

Bioinformatics. 2010 Dec 1;26(23):2952-60

Authors: Wright MH, Tung CW, Zhao K, Reynolds A, McCouch SR, Bustamante CD

Abstract
MOTIVATION: The development of new high-throughput genotyping products requires a significant investment in testing and training samples to evaluate and optimize the product before it can be used reliably on new samples. One reason for this is current methods for automated calling of genotypes are based on clustering approaches which require a large number of samples to be analyzed simultaneously, or an extensive training dataset to seed clusters. In systems where inbred samples are of primary interest, current clustering approaches perform poorly due to the inability to clearly identify a heterozygote cluster.
RESULTS: As part of the development of two custom single nucleotide polymorphism genotyping products for Oryza sativa (domestic rice), we have developed a new genotype calling algorithm called 'ALCHEMY' based on statistical modeling of the raw intensity data rather than modelless clustering. A novel feature of the model is the ability to estimate and incorporate inbreeding information on a per sample basis allowing accurate genotyping of both inbred and heterozygous samples even when analyzed simultaneously. Since clustering is not used explicitly, ALCHEMY performs well on small sample sizes with accuracy exceeding 99% with as few as 18 samples.
AVAILABILITY: ALCHEMY is available for both commercial and academic use free of charge and distributed under the GNU General Public License at http://alchemy.sourceforge.net/
CONTACT: mhw6@cornell.edu
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID: 20926420 [PubMed - indexed for MEDLINE]

Development of a novel aluminum tolerance phenotyping platform used for comparisons of cereal aluminum tolerance and investigations into rice aluminum tolerance mechanisms.

S-McCouch PubMed Feed - Wed, 07/25/2012 - 15:45
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Development of a novel aluminum tolerance phenotyping platform used for comparisons of cereal aluminum tolerance and investigations into rice aluminum tolerance mechanisms.

Plant Physiol. 2010 Aug;153(4):1678-91

Authors: Famoso AN, Clark RT, Shaff JE, Craft E, McCouch SR, Kochian LV

Abstract
The genetic and physiological mechanisms of aluminum (Al) tolerance have been well studied in certain cereal crops, and Al tolerance genes have been identified in sorghum (Sorghum bicolor) and wheat (Triticum aestivum). Rice (Oryza sativa) has been reported to be highly Al tolerant; however, a direct comparison of rice and other cereals has not been reported, and the mechanisms of rice Al tolerance are poorly understood. To facilitate Al tolerance phenotyping in rice, a high-throughput imaging system and root quantification computer program was developed, permitting quantification of the entire root system, rather than just the longest root. Additionally, a novel hydroponic solution was developed and optimized for Al tolerance screening in rice and compared with the Yoshida's rice solution commonly used for rice Al tolerance studies. To gain a better understanding of Al tolerance in cereals, comparisons of Al tolerance across cereal species were conducted at four Al concentrations using seven to nine genetically diverse genotypes of wheat, maize (Zea mays), sorghum, and rice. Rice was significantly more tolerant than maize, wheat, and sorghum at all Al concentrations, with the mean Al tolerance level for rice found to be 2- to 6-fold greater than that in maize, wheat, and sorghum. Physiological experiments were conducted on a genetically diverse panel of more than 20 rice genotypes spanning the range of rice Al tolerance and compared with two maize genotypes to determine if rice utilizes the well-described Al tolerance mechanism of root tip Al exclusion mediated by organic acid exudation. These results clearly demonstrate that the extremely high levels of rice Al tolerance are mediated by a novel mechanism, which is independent of root tip Al exclusion.

PMID: 20538888 [PubMed - indexed for MEDLINE]

Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome.

S-McCouch PubMed Feed - Wed, 07/25/2012 - 15:45
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Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome.

PLoS One. 2010;5(5):e10780

Authors: Zhao K, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A, Bustamante CD, McCouch SR

Abstract
BACKGROUND: The domestication of Asian rice (Oryza sativa) was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers.
METHODOLOGY/PRINCIPAL FINDINGS: In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV) consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations.
CONCLUSIONS/SIGNIFICANCE: Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species.

PMID: 20520727 [PubMed - indexed for MEDLINE]

Inactivation of the CTD phosphatase-like gene OsCPL1 enhances the development of the abscission layer and seed shattering in rice.

S-McCouch PubMed Feed - Wed, 07/25/2012 - 15:45
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Inactivation of the CTD phosphatase-like gene OsCPL1 enhances the development of the abscission layer and seed shattering in rice.

Plant J. 2010 Jan;61(1):96-106

Authors: Ji H, Kim SR, Kim YH, Kim H, Eun MY, Jin ID, Cha YS, Yun DW, Ahn BO, Lee MC, Lee GS, Yoon UH, Lee JS, Lee YH, Suh SC, Jiang W, Yang JI, Jin P, McCouch SR, An G, Koh HJ

Abstract
Although susceptibility to seed shattering causes severe yield loss during cereal crop harvest, it is an adaptive trait for seed dispersal in wild plants. We previously identified a recessive shattering locus, sh-h, from the rice shattering mutant line Hsh that carries an enhanced abscission layer. Here, we further mapped sh-h to a 34-kb region on chromosome 7 by analyzing 240 F(2) plants and five F(3) lines from the cross between Hsh and Blue&Gundil. Hsh had a point mutation at the 3' splice site of the seventh intron within LOC_Os07g10690, causing a 15-bp deletion of its mRNA as a result of altered splicing. Two transferred DNA (T-DNA) insertion mutants and one point mutant exhibited the enhanced shattering phenotype, confirming that LOC_Os07g10690 is indeed the sh-h gene. RNA interference (RNAi) transgenic lines with suppressed expression of this gene exhibited greater shattering. This gene, which encodes a protein containing a conserved carboxy-terminal domain (CTD) phosphatase domain, was named Oryza sativa CTD phosphatase-like 1 (OsCPL1). Subcellular localization and biochemical analysis revealed that the OsCPL1 protein is a nuclear phosphatase, a common characteristic of metazoan CTD phosphatases involved in cell differentiation. These results demonstrate that OsCPL1 represses differentiation of the abscission layer during panicle development.

PMID: 19807881 [PubMed - indexed for MEDLINE]

The origin and evolution of fragrance in rice (Oryza sativa L.).

S-McCouch PubMed Feed - Wed, 07/25/2012 - 15:45
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The origin and evolution of fragrance in rice (Oryza sativa L.).

Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14444-9

Authors: Kovach MJ, Calingacion MN, Fitzgerald MA, McCouch SR

Abstract
Fragrance in the grain is one of the most highly valued grain quality traits in rice, yet the origin and evolution of the betaine aldehyde dehydrogenase gene (BADH2) underlying this trait remains unclear. In this study, we identify eight putatively nonfunctional alleles of the BADH2 gene and show that these alleles have distinct geographic and genetic origins. Despite multiple origins of the fragrance trait, a single allele, badh2.1, is the predominant allele in virtually all fragrant rice varieties today, including the widely recognized Basmati and Jasmine types. Haplotype analysis allowed us to establish a single origin of the badh2.1 allele within the Japonica varietal group and demonstrate the introgression of this allele from Japonica to Indica. Basmati-like accessions were nearly identical to the ancestral Japonica haplotype across a 5.3-Mb region flanking BADH2 regardless of their fragrance phenotype, demonstrating a close evolutionary relationship between Basmati varieties and the Japonica gene pool. These results clarify the relationships among fragrant rice varieties and challenge the traditional assumption that the fragrance trait arose in the Indica varietal group.

PMID: 19706531 [PubMed - indexed for MEDLINE]

Gramene QTL database: development, content and applications.

S-McCouch PubMed Feed - Wed, 07/25/2012 - 15:45
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Gramene QTL database: development, content and applications.

Database (Oxford). 2009;2009:bap005

Authors: Ni J, Pujar A, Youens-Clark K, Yap I, Jaiswal P, Tecle I, Tung CW, Ren L, Spooner W, Wei X, Avraham S, Ware D, Stein L, McCouch S

Abstract
Gramene is a comparative information resource for plants that integrates data across diverse data domains. In this article, we describe the development of a quantitative trait loci (QTL) database and illustrate how it can be used to facilitate both the forward and reverse genetics research. The QTL database contains the largest online collection of rice QTL data in the world. Using flanking markers as anchors, QTLs originally reported on individual genetic maps have been systematically aligned to the rice sequence where they can be searched as standard genomic features. Researchers can determine whether a QTL co-localizes with other QTLs detected in independent experiments and can combine data from multiple studies to improve the resolution of a QTL position. Candidate genes falling within a QTL interval can be identified and their relationship to particular phenotypes can be inferred based on functional annotations provided by ontology terms. Mutations identified in functional genomics populations and association mapping panels can be aligned with QTL regions to facilitate fine mapping and validation of gene-phenotype associations. By assembling and integrating diverse types of data and information across species and levels of biological complexity, the QTL database enhances the potential to understand and utilize QTL information in biological research.

PMID: 20157478 [PubMed - as supplied by publisher]

Dissection of a QTL reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice.

S-McCouch PubMed Feed - Wed, 07/25/2012 - 15:45
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Dissection of a QTL reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice.

Theor Appl Genet. 2010 Mar;120(5):895-908

Authors: Maas LF, McClung A, McCouch S

Abstract
A days to heading QTL (dth1.1) located on the short arm of rice chromosome 1 was sub-divided into eight sub-introgression lines (SILs) to analyze the genetic basis of transgressive variation for flowering time. Each SIL contained one or more introgression(s) from O. rufipogon in the genetic background of the elite Oryza sativa cultivar, Jefferson. Each introgression was defined at high resolution using molecular markers and those in the dth1.1 region were associated with the presence of one or more flowering time genes (GI, SOC1, FT-L8, EMF1, and PNZIP). SILs and controls were evaluated for flowering time under both short- and long-day growing conditions. Under short-day lengths, lines with introgressions carrying combinations of linked flowering time genes (GI/SOC1, SOC1/FT-L8, GI/SOC1/FT-L8 and EMF1/PNZIP) from the late parent, O. rufipogon, flowered earlier than the recurrent parent, Jefferson, while recombinant lines carrying smaller introgressions marked by the presence of GI, SOC1, EMF1 or PNZIP alone no longer flowered early. Under long-day length, lines carrying SOC1/FT-L8, SOC1 or PNZIP flowered early, while those carrying GI or EMF1 delayed flowering. Across all experiments and in the field, only SIL_SOC1/FT-L8 was consistently early. A preliminary yield evaluation indicated that the transgressive early flowering observed in several of the SILs was also associated with a measurable and positive effect on yield. These SILs represent a new source of variation that can be used in breeding programs to manipulate flowering time in rice cultivars without the reduction in yield that is often associated with early maturing phenotypes.

PMID: 19949767 [PubMed - indexed for MEDLINE]

A universal core genetic map for rice.

S-McCouch PubMed Feed - Wed, 07/25/2012 - 15:45
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A universal core genetic map for rice.

Theor Appl Genet. 2010 Feb;120(3):563-72

Authors: Orjuela J, Garavito A, Bouniol M, Arbelaez JD, Moreno L, Kimball J, Wilson G, Rami JF, Tohme J, McCouch SR, Lorieux M

Abstract
To facilitate the creation of easily comparable, low-resolution genetic maps with evenly distributed markers in rice (Oryza sativa L.), we conceived of and developed a Universal Core Genetic Map (UCGM). With this aim, we derived a set of 165 anchors, representing clusters of three microsatellite or simple sequence repeat (SSR) markers arranged into non-recombining groups. Each anchor consists of at least three, closely linked SSRs, located within a distance below the genetic resolution provided by common, segregating populations (<500 individuals). We chose anchors that were evenly distributed across the rice chromosomes, with spacing between 2 and 3.5 Mbp (except in the telomeric regions, where spacing was 1.5 Mbp). Anchor selection was performed using in silico tools and data: the O. sativa cv. Nipponbare rice genome sequence, the CHARM tool, information from the Gramene database and the OrygenesDB database. Sixteen AA-genome accessions of the Oryza genus were used to evaluate polymorphisms for the selected markers, including accessions from O. sativa, O. glaberrima, O. barthii, O. rufipogon, O. glumaepatula and O. meridionalis. High levels of polymorphism were found for the tested O. sativa x O. glaberrima or O. sativa x wild rice combinations. We developed Paddy Map, a simple database that is helpful in selecting optimal sets of polymorphic SSRs for any cross that involves the previously mentioned species. Validation of the UCGM was done by using it to develop three interspecific genetic maps and by comparing genetic SSR locations with their physical positions on the rice pseudomolecules. In this study, we demonstrate that the UCGM is a useful tool for the rice genetics and breeding community, especially in strategies based on interspecific hybridisation.

PMID: 19847389 [PubMed - indexed for MEDLINE]

Not just a grain of rice: the quest for quality.

S-McCouch PubMed Feed - Sun, 04/25/2010 - 22:08
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Not just a grain of rice: the quest for quality.

Trends Plant Sci. 2009 Mar;14(3):133-9

Authors: Fitzgerald MA, McCouch SR, Hall RD

A better understanding of the factors that contribute to the overall grain quality of rice (Oryza sativa) will lay the foundation for developing new breeding and selection strategies for combining high quality, with high yield. This is necessary to meet the growing global demand for high quality rice while offering producing countries additional opportunities for generating higher export revenues. Several recent developments in genetics, genomics, metabolomics and phenomics are enhancing our understanding of the pathways that determine several quality traits. New research strategies, as well as access to the draft of the rice genome, will not only advance our understanding of the molecular mechanisms that lead to quality rice but will also pave the way for efficient and targeted grain improvement.

PMID: 19230745 [PubMed - indexed for MEDLINE]

Leaf-level water use efficiency determined by carbon isotope discrimination in rice seedlings: genetic variation associated with population structure and QTL mapping.

S-McCouch PubMed Feed - Sun, 04/25/2010 - 22:08
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Leaf-level water use efficiency determined by carbon isotope discrimination in rice seedlings: genetic variation associated with population structure and QTL mapping.

Theor Appl Genet. 2009 Apr;118(6):1065-81

Authors: Xu Y, This D, Pausch RC, Vonhof WM, Coburn JR, Comstock JP, McCouch SR

Increasing the water use efficiency (WUE) of our major crop species is an important target of agricultural research. Rice is a major water consumer in agriculture and it is also an attractive genetic model. We evaluated leaf-level WUE in young rice seedlings using carbon isotope discrimination (Delta(13)C) as an indicator of the trait. A survey of Delta(13)C was undertaken in 116 diverse germplasm accessions representing O. sativa, O. glaberrima and four wild Oryza species. O. sativa cultivars were classified into sub-populations based on SSR markers, and significant differences in Delta(13)C were observed among the five genetically defined groups. While individual accessions explained a greater proportion of the variation than did sub-population, indica rice varieties had the lowest Delta(13)C values overall, indicating superior WUE, while temperate japonica had the highest Delta(13)C. O sativa accessions had a similar or greater range of Delta(13)C values than wild Oryza species, while domesticated O. glaberrima had a narrower range. Correlation analysis identified leaf morphological and physiological traits that were significantly associated with Delta(13)C, including longer leaves, more drooping leaves, higher tillering ability, and lower leaf nitrogen content. These trait associations were investigated by quantitative trait locus (QTL) mapping using backcross inbred lines derived from a cross between Nipponbare (temperate japonica) and Kasalath (aus). Seven QTL for Delta(13)C were identified using composite interval analysis, located in five chromosomal regions. The QTL with the largest additive effect came from Kasalath and co-localized with QTL for leaf length, tiller number and nitrogen content.

PMID: 19224195 [PubMed - indexed for MEDLINE]

A recommendation for naming transcription factor proteins in the grasses.

S-McCouch PubMed Feed - Sun, 04/25/2010 - 22:08
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A recommendation for naming transcription factor proteins in the grasses.

Plant Physiol. 2009 Jan;149(1):4-6

Authors: Gray J, Bevan M, Brutnell T, Buell CR, Cone K, Hake S, Jackson D, Kellogg E, Lawrence C, McCouch S, Mockler T, Moose S, Paterson A, Peterson T, Rokshar D, Souza GM, Springer N, Stein N, Timmermans M, Wang GL, Grotewold E

PMID: 19126689 [PubMed - indexed for MEDLINE]

A major quantitative trait locus for rice yellow mottle virus resistance maps to a cluster of blast resistance genes on chromosome 12.

S-McCouch PubMed Feed - Sun, 04/25/2010 - 22:08
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A major quantitative trait locus for rice yellow mottle virus resistance maps to a cluster of blast resistance genes on chromosome 12.

Phytopathology. 1997 Dec;87(12):1243-9

Authors: Ghesquière A, Albar L, Lorieux M, Ahmadi N, Fargette D, Huang N, McCouch SR, Notteghem JL

ABSTRACT Two doubled-haploid rice populations, IR64/Azucena and IRAT177/ Apura, were used to identify markers linked to rice yellow mottle virus (RYMV) resistance using core restriction fragment length polymorphism (RFLP) maps. Resistance was measured by mechanical inoculation of 19-day-old seedlings followed by assessment of virus content by enzyme-linked immunosorbent assay tests 15 days after inoculation. IR64/Azucena and IRAT177/Apura populations, 72 and 43 lines, respectively, were evaluated, and resistance was found to be polygenic. Resistance was expressed as a slower virus multiplication, low symptom expression, and limited yield loss when assessed at the field level. Bulked segregant analysis using the IR64/Azucena population identified a single random amplified polymorphic DNA marker that mapped on chromosome 12 and corresponded to a major quantitative trait locus (QTL) evidenced by interval mapping. When pooling RFLP data, integrated mapping of this chromosome revealed that the QTL was common to the two populations and corresponded to a small chromosomal segment known to contain a cluster of major blast resistance genes. This region of the genome also reflected the differentiation observed at the RFLP level between the subspecies indica and japonica of Oryza sativa. This is consistent with the observation that most sources of RYMV resistance used in rice breeding are found in upland rice varieties that typically belong to the japonica subspecies.

PMID: 18945025 [PubMed - in process]

Genetic and functional characterization of the rice bacterial blight disease resistance gene xa5.

S-McCouch PubMed Feed - Sun, 04/25/2010 - 22:08
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Genetic and functional characterization of the rice bacterial blight disease resistance gene xa5.

Phytopathology. 2008 Mar;98(3):289-95

Authors: Iyer-Pascuzzi AS, Jiang H, Huang L, McCouch SR

Xanthomonas oryzae pv. oryzae is the causal agent of rice bacterial blight, a destructive rice disease worldwide. The gene xa5 provides race-specific resistance to X. oryzae pv. oryzae, and encodes the small subunit of transcription factor IIA. How xa5 functions in bacterial blight resistance is not well understood, and its recessive gene action is disputed. Here we show that xa5 is inherited in a completely recessive manner and the susceptible allele Xa5 is fully dominant. In accordance with this, bacterial growth in heterozygous and homozygous susceptible lines is not significantly different. Further, one allele of Xa5 is sufficient to promote disease in previously resistant plants; additional copies are not predictive of increased lesion length. Surprisingly, a resistant nearly isogenic line (NIL) of an indica variety sustains high levels of bacterial populations compared to the susceptible NIL, yet the resistant plants restrict symptom expression. In contrast, in japonica NILs, bacterial population dynamics differ in resistant and susceptible genotypes. However, both resistant indica and japonica plants delay bacterial movement down the leaf. These results support a model in which xa5-mediated recessive resistance is the result of restricted bacterial movement, but not restricted multiplication.

PMID: 18944079 [PubMed - indexed for MEDLINE]

Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages.

S-McCouch PubMed Feed - Sun, 04/25/2010 - 22:08
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Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages.

Comp Funct Genomics. 2005;6(7-8):388-97

Authors: Jaiswal P, Avraham S, Ilic K, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Stevens P, Vincent L, Ware D, Zapata F

The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. A primary goal of the POC is to develop simple yet robust and extensible controlled vocabularies that accurately reflect the biology of plant structures and developmental stages. These provide a network of vocabularies linked by relationships (ontology) to facilitate queries that cut across datasets within a database or between multiple databases. The current version of the ontology integrates diverse vocabularies used to describe Arabidopsis, maize and rice (Oryza sp.) anatomy, morphology and growth stages. Using the ontology browser, over 3500 gene annotations from three species-specific databases, The Arabidopsis Information Resource (TAIR) for Arabidopsis, Gramene for rice and MaizeGDB for maize, can now be queried and retrieved.

PMID: 18629207 [PubMed - in process]

Gramene: development and integration of trait and gene ontologies for rice.

S-McCouch PubMed Feed - Sun, 04/25/2010 - 22:08
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Gramene: development and integration of trait and gene ontologies for rice.

Comp Funct Genomics. 2002;3(2):132-6

Authors: Jaiswal P, Ware D, Ni J, Chang K, Zhao W, Schmidt S, Pan X, Clark K, Teytelman L, Cartinhour S, Stein L, McCouch S

Gramene (http://www.gramene.org/) is a comparative genome database for cereal crops and a community resource for rice. We are populating and curating Gramene with annotated rice (Oryza sativa) genomic sequence data and associated biological information including molecular markers, mutants, phenotypes, polymorphisms and Quantitative Trait Loci (QTL). In order to support queries across various data sets as well as across external databases, Gramene will employ three related controlled vocabularies. The specific goal of Gramene is, first to provide a Trait Ontology (TO) that can be used across the cereal crops to facilitate phenotypic comparisons both within and between the genera. Second, a vocabulary for plant anatomy terms, the Plant Ontology (PO) will facilitate the curation of morphological and anatomical feature information with respect to expression, localization of genes and gene products and the affected plant parts in a phenotype. The TO and PO are both in the early stages of development in collaboration with the International Rice Research Institute, TAIR and MaizeDB as part of the Plant Ontology Consortium. Finally, as part of another consortium comprising macromolecular databases from other model organisms, the Gene Ontology Consortium, we are annotating the confirmed and predicted protein entries from rice using both electronic and manual curation.

PMID: 18628886 [PubMed - in process]

Leveraging natural diversity: back through the bottleneck.

S-McCouch PubMed Feed - Sun, 04/25/2010 - 22:08
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Leveraging natural diversity: back through the bottleneck.

Curr Opin Plant Biol. 2008 Apr;11(2):193-200

Authors: Kovach MJ, McCouch SR

Plant breeders have long recognized the existence of useful genetic variation in the wild ancestors of our domesticated crop species. In cultivated rice (Oryza sativa), crosses between high-yielding elite cultivars and low-yielding wild accessions often give rise to superior offspring, with wild alleles conferring increased performance in the context of the elite cultivar genetic background. Because the breeding value of wild germplasm cannot be determined by examining the performance of wild accessions, a phylogenetic approach is recommended to determine which interspecific combinations are most likely to be useful in a breeding program. As we deepen our understanding of how genetic diversity is partitioned within and between cultivated and wild gene pools of Oryza, breeders will have increased power to make predictions about the most efficient strategies for utilizing wild germplasm for rice improvement.

PMID: 18313975 [PubMed - indexed for MEDLINE]

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.

S-McCouch PubMed Feed - Sun, 04/25/2010 - 22:08
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The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.

Nucleic Acids Res. 2008 Jan;36(Database issue):D449-54

Authors: Avraham S, Tung CW, Ilic K, Jaiswal P, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Stevens P, Vincent L, Zapata F, Ware D

The Plant Ontology Consortium (POC, http://www.plantontology.org) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure (anatomy and morphology) and developmental stages to data types, such as genes and phenotypes, to provide a semantic framework to make meaningful cross-species and database comparisons. The POC builds upon groundbreaking work by the Gene Ontology Consortium (GOC) by adopting and extending the GOC's principles, existing software and database structure. Over the past year, POC has added hundreds of ontology terms to associate with thousands of genes and gene products from Arabidopsis, rice and maize, which are available through a newly updated web-based browser (http://www.plantontology.org/amigo/go.cgi) for viewing, searching and querying. The Consortium has also implemented new functionalities to facilitate the application of PO in genomic research and updated the website to keep the contents current. In this report, we present a brief description of resources available from the website, changes to the interfaces, data updates, community activities and future enhancement.

PMID: 18194960 [PubMed - indexed for MEDLINE]

Evolutionary history of GS3, a gene conferring grain length in rice.

S-McCouch PubMed Feed - Sun, 04/25/2010 - 22:08
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Evolutionary history of GS3, a gene conferring grain length in rice.

Genetics. 2009 Aug;182(4):1323-34

Authors: Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T, Kanamori H, Padhukasahasram B, Bustamante C, Yoshimura A, Doi K, McCouch S

Unlike maize and wheat, where artificial selection is associated with an almost uniform increase in seed or grain size, domesticated rice exhibits dramatic phenotypic diversity for grain size and shape. Here we clone and characterize GS3, an evolutionarily important gene controlling grain size in rice. We show that GS3 is highly expressed in young panicles in both short- and long-grained varieties but is not expressed in leaves or panicles after flowering, and we use genetic transformation to demonstrate that the dominant allele for short grain complements the long-grain phenotype. An association study revealed that a C to A mutation in the second exon of GS3 (A allele) was associated with enhanced grain length in Oryza sativa but was absent from other Oryza species. Linkage disequilibrium (LD) was elevated and there was a 95.7% reduction in nucleotide diversity (theta(pi)) across the gene in accessions carrying the A allele, suggesting positive selection for long grain. Haplotype analysis traced the origin of the long-grain allele to a Japonica-like ancestor and demonstrated introgression into the Indica gene pool. This study indicates a critical role for GS3 in defining the seed morphologies of modern subpopulations of O. sativa and enhances the potential for genetic manipulation of grain size in rice.

PMID: 19506305 [PubMed - indexed for MEDLINE]

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