Three horticultural races of avocado (Persea americana Mill.) are known: Guatemalan, Mexican, and West Indian. Each race has unique characteristics and current commercial varieties have been selected from within the races or from interracial hybrids. Using 14 microsatellite loci we investigated the genetic variation among 224 accessions (394 plants) maintained at the National Germplasm Repository (NGR) in Miami, Fla., and a set of 34 clones from the University of California South Coast Field Station (SCFS) located in Irvine, Calif. The 14 microsatellite loci had an average of 18.8 alleles per locus and average unbiased genetic diversity was 0.83. The total propagation error in the collection, i.e., plants that had been incorrectly labeled or grafted, was estimated to be 7.0%. Although many unique alleles did exist, no useful race-specific markers were found. A general concordance between the horticultural race and the clusters obtained from molecular data was observed. Principal Coordinate Analysis (PCA) grouped the Guatemalan and Mexican races into two distinct clusters. The West Indian also grouped into a unique major cluster but with an outlying group. Using the PCA a change in the racial designation or interracial hybrid status for 50 accessions (19.7%) is proposed. The unbiased gene diversity estimate was highest in the Mexican and Guatemalan races and lower in the West Indian group. This demonstrates the need to collect more of the West Indian germplasm to broaden the genetic diversity and to emphasize the identification of individuals conferring resistance to Phytophthora Root Rot (PRR).

A heterozygous F1 mapping population of cacao (Theobroma cacao L.) was created and evaluated for resistance to frosty pod [caused by Moniliophthora roreri (Cif. and Par.) Evans et al.], and black pod [caused by Phytophthora palmivora (Butl.) Butl.] and for five horticultural traits at CATIE in Turrialba, Costa Rica. The population consisted of 256 F1 progeny from the cross ‘Pound 7’ × ‘UF 273’. Progeny were used to form a linkage map using 180 markers. The linkage map contained 10 linkage groups (LGs), numbered as the LG in the cacao reference map, and was used to locate putative quantitative trait loci (QTL) for resistance to the aforementioned diseases and five horticultural traits. Resistance to frosty pod was measured by internal and external pod resistance. Five QTLs for frosty pod resistance were found on three LGs, 2, 7, and 8, with UF 273 appearing to be the source of resistance. These alleles are being used for scoring progeny in ongoing cooperative marker‐assisted selection projects, and constitute the first QTLs identified for frosty pod resistance. Three QTLs for black pod resistance were found on LG 4, 8, and 10, with the most favorable alleles coming from Pound 7. One QTL was found on LG 4 for average trunk growth rate, and two QTLs for height of first jorquette were identified on LGs 4 and 6. One QTL each for average trunk diameter growth and pod color was found on LG 4.

In order to study relationships within and among species of the highly complex polyploid genus Saccharum, 30 clones from 5 species (S. barberi, S. officinarum, S. robustum, S. sinense, and S. spontaneum) and 6 cultivated clones were analyzed using 15 sugarcane simple sequence repeat (SSR) markers and two multivariate statistical methods. The origins of two species, S. barberi and S. sinense, are unclear, and it has been hypothesized that they arose from crosses of S. officinarum · S. spontaneum. S. robustum is suggested to be ancestral to S. officinarum, which, when crossed with S. spontaneum, principally comprise the genomes of commercial cultivars. Although our analyses supported S. robustum as being an ancestor of S. officinarum, and show the composition of commercial clones as expected, our results concerning the species S. barberi and S. sinense indicated them to be much less related to the main Saccharum germplasm pool than previous molecular marker investigations, suggesting that introgression from other genera may exist in their ancestry. The differing results of our analysis of S. barberi and S. sinense are likely attributable to more equal and larger numbers of clones studied in each species. Given the extremely high ploidy, the use of only 15 SSR markers enabled clear distinction of Saccharum species and clones, and also identified likely mislabeled accessions. In addition, the replication of DNA extraction, polymerase chain reactions, and fragment electrophoresis increased the robustness of our analysis.

cDNA microarray spot variability arises from many sources, and different systems have varying requirements for achieving the desired level of precision. We determined relative contributions to variance and investigated sequence discrimination using a multiple-array experimental design, with arrays subdivided to determine position and pin effect. Related fragments of 67 resistance gene homologs (RGHs) isolated from Theobroma cacao L. and grouped by sequence similarity were spotted onto arrays, using two of the same RGHs in the fluorescent dye channels (Cy3, Cy5) of the hybridization solution in a "dye-flip" design. A comprehensive statistical model accounted for variability well, giving a coefficient of variation (CV) based on experimental error of 2.12%. Although we were able to separate 85% of RGH group means clearly, some groups more similar to the target were indistinguishable due to nonspecific hybridization. Genetic factors together contributed 72.2% of the total variation, while position and pin effects and their interactions contributed 9.8%. Replication effect was statistically significant. Otherwise, no tests for position effects were significant. The results of the analysis indicate that our Genetic Microsystems 417 arrayer and Affymetrix 428 scanner are performing with sufficient precision, and we produced useful information for planning efficient future experiments.

No abstract