An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

BACKGROUND: Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees. A dense genetic map that incorporates SSR loci will benefit complete pine genome sequencing, pine population genetics studies, and pine breeding programs. Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map. RESULTS: The updated P. taeda genetic map, with an estimated genome coverage of 1,515 cM((Kosambi)) across 12 linkage groups, incorporated 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers. The average marker interval was 3.1 cM. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs) and 149 were from non-transcribed genomic sequences (genomic-SSRs). Of all 311 mapped cDNA-derived markers, 77% were associated with NCBI Pta UniGene clusters, 67% with RefSeq proteins, and 62% with functional Gene Ontology (GO) terms. Duplicate (i.e., redundant accessory) and paralogous markers were tentatively identified by evaluating marker sequences by their UniGene cluster IDs, clone IDs, and relative map positions. The average gene diversity, H(e), among polymorphic SSR loci, including those that were not mapped, was 0.43 for 94 EST-SSRs and 0.72 for 83 genomic-SSRs. The genetic map can be viewed and queried at http://www.conifergdb.org/pinemap. CONCLUSIONS: Many polymorphic and genetically mapped SSR markers are now available for use in P. taeda population genetics, studies of adaptive traits, and various germplasm management applications. Annotating mapped genes with UniGene clusters and GO terms allowed assessment of redundant and paralogous EST markers and further improved the quality and utility of the genetic map for P. taeda

AGRICULTURE AND BIOLOGY JOURNAL OF NORTH AMERICA Anthracnose disease response in the Burundi sorghum germplasm collection

ABSTRACT The United States National Plant Germplasm System maintains 151 sorghum accessions from Burundi of which 148 accessions were evaluated for resistance to Colletotrichum sublineolum at the Tropical Agriculture Research Station in Isabela, Puerto Rico in replicated evaluations during the 2007 and 2008 growing seasons. For the 2007 experiment, 120 accessions showed a resistant response with 89 of these accessions rated as resistant in 2008. The resistant accessions showed reddening of inoculated leaves with no acervuli development, whereas accessions rated as susceptible showed acervuli development on inoculated leaves. Mean infection severity based on the percentage of infected leaf area for the susceptible accessions was 2% in 2007 and 2.5% for the 2008 experiment. Only four accessions showed an infection severity more than 10% and eight accessions showed a susceptible response across replications and growing seasons. Results of this study indicate that sorghum germplasm from Burundi is an important source of anthracnose resistance for sorghum improvement and that germplasm from regions of high annual rainfall is frequently associated with anthracnose resistance

Respuesta de germoplasma de sorgo de Etiopía a la antracnosis.

Forty-two accessions were randomly selected from the Ethiopian sorghum collection maintained by the USDA-ARS National Plant Germplasm System and were evaluated for anthracnose disease response during the 2004 dry and wet growing seasons in Isabela, Puerto Rico. A resistant response was observed for 20 accessions, with 13 accessions susceptible to the disease for the two growing seasons. This finding would suggest that Ethiopia would be an important source of anthracnose-resistant germplasm for sorghum improvement. Nine accessions showed variation for infection response within and between growing seasons. These accessions also showed low infection severity. Greater infection severity was observed during the dry growing season for the susceptible accessions; however, variation for mean infection severity for these accessions was not significantly different for the two seasons. Approximately 80% of the accessions showed a similar disease response across the two growing seasons.This percentage would suggest that large scale evaluations could be conducted throughout the year in Puerto Rico to screen the more than 7,000 Ethiopian sorghum accessions in the collection for the identification of anthracnose-resistant germplasm.Se seleccionaron al azar 42 accesiones de la colección de sorgo de Etiopía, la cual se mantiene en el Sistema Nacional de Germoplama de Plantas del Servicio de Investigación Agrícola del Departamento de Agricultura de los Estados Unidos (USDA-ARS, NGPS, por sus siglas en inglés). Se evaluó la respuesta de estas accesiones a la antracnosis durante las épocas de lluvia y de sequía en Isabela, Puerto Rico, en el 2004. Se observó resistencia a la enfermedad en 20 accesiones, mientras trece accesiones resultaron susceptibles a la enfermedad en ambas épocas. Estos resultados indican que la colección de sorgo de Etiopía es una fuente importante de germoplasma resistente a la antracnosis para utilizarse en el mejoramiento del sorgo. Nueve accesiones mostraron una variación en la respuesta a la infección dentro y fuera de las épocas de crecimiento. Estas accesiones también mostraron una baja severidad de infección. Las accesiones susceptibles a la enfermedad mostraron una infección mayor durante la época de sequía; sin embargo, la variación promedio de infección de estas accesiones no fue significativamente diferente para las dos épocas. Aproximadamente 80% de las accesiones mostraron una respuesta similar a la enfermedad a través de las dos épocas de crecimiento. Estos resultados indican que en Puerto Rico se pueden llevar a cabo evaluaciones en alta escala a través de todo el año para examinar más de 7,000 accesiones de sorgo de la colección e identificar germoplasma resistente a la antracnosis

Genome-wide association study of Gossypium arboreum resistance to reniform nematode

Abstract Background Reniform nematode (Rotylenchulus reniformis) has emerged as one of the most destructive root pathogens of upland cotton (Gossypium hirsutum) in the United States. Management of R. reniformis has been hindered by the lack of resistant G. hirsutum cultivars; however, resistance has been frequently identified in germplasm accessions from the G. arboreum collection. To determine the genetic basis of reniform nematode resistance, a genome-wide association study (GWAS) was performed using 246 G. arboreum germplasm accessions that were genotyped with 7220 single nucleotide polymorphic (SNP) sequence markers generated from genotyping-by-sequencing. Results Fifteen SNPs representing 12 genomic loci distributed over eight chromosomes showed association with reniform nematode resistance. For 14 SNPs, major alleles were shown to be associated with resistance. From the 15 significantly associated SNPs, 146 genes containing or physically close to these loci were identified as putative reniform nematode resistance candidate genes. These genes are involved in a broad range of biological pathways, including plant innate immunity, transcriptional regulation, and redox reaction that may have a role in the expression of resistance. Eighteen of these genes corresponded to differentially expressed genes identified from G. hirsutum in response to reniform nematode infection. Conclusions The identification of multiple genomic loci associated with reniform nematode resistance would indicate that the G. arboreum collection is a significant resource of novel resistance genes. The significantly associated markers identified from this GWAS can be used for the development of molecular tools for breeding improved reniform nematode resistant upland cotton with resistance introgressed from G. arboreum. Additionally, a greater understanding of the molecular mechanisms of reniform nematode resistance can be determined through genetic structure and functional analyses of candidate genes, which will aid in the pyramiding of multiple resistance genes