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Ancestral open-pollinated populations of U.S. maize (Zea mays L.) are a resource to broaden the genetic base of modern maize and to ensure long-term gains in maize breeding. We report the extent and distribution of simple sequence repeat (SSR) variation in a comprehensive study of Northern Flints (NFs), Southern Dents (SDs), Corn Belt Dents (CBDs), and historically important inbred lines, and address their implications for maize improvement and conservation. We found that the loss of rare alleles in open-pollinated cultivars from elite gene pools resulted in the divergence of inbred lines as a distinct group apart from their progenitor races. In contrast, the Corn Belt Dent cultivars retained high levels of genetic variation that approximated or exceeded that found in their NF and SD progenitors. Within open-pollinated varieties, the absence of any clear pattern of population differentiation indicates frequent admixture, a relatively recent time of divergence, or poor correlation between the degree of divergence at neutral marker loci and quantitative trait variation. This research suggests that the inbred lines currently used by breeders as the primary genetic resource for line improvement do not represent the genetic variation available in the temperate races from which they are derived: only 56% of the alleles found in the Corn Belt Dents were displayed in a diverse set of inbred lines. Extensive sampling targeted at a limited number of Corn Belt Dent cultivars is a promising approach toward the identification and introgression of rare alleles that were lost during early inbred development or the maintenance of open-pollinated populations., VIRTUALLY ALL U.S. hybrid maize, the bulk of feed corn grown in other temperate regions, and over one-half of the global annual supply of maize are derived from the Corn [...]

Crop species experienced strong selective pressure directed at genes controlling traits of agronomic importance during their domestication and subsequent episodes of selective breeding. Consequently, these genes are expected to exhibit the signature of selection. We screened 501 maize genes for the signature of selection using microsatellites or simple sequence repeats (SSRs). We applied the Ewens-Watterson test, which can reveal deviations from a neutral-equilibrium model, as well as two nonequilibrium tests that incorporate the domestication bottleneck. We investigated two classes of SSRs: those known to be polymorphic in maize (Class I) and those previously classified as monomorphic in maize (Class II). Fifteen SSRs exhibited some evidence for selection in maize and 10 showed evidence under stringent criteria. The genes containing nonneutral SSRs are candidates for agronomically important genes. Because demographic factors can bias our tests, further independent tests of these candidates are necessary. We applied such an additional test to one candidate, which encodes a MADS box transcriptional regulator, and confirmed that this gene experienced a selective sweep during maize domestication. Genomic scans for the signature of selection offer a means of identifying new genes of agronomic importance even when gene function and the phenotype of interest are unknown.

Nuclear DNA content has been estimated using flow cytometry for 17 species and eight cultivars of Malus and for 44 species of 29 other genera within the Rosaceae. Compared to other angiosperms, diploid genome sizes vary little within the family Rosaceae and within the genus Malus. C-values of genera within the subfamilies Spiraeoideae and Rosoideae are among the smallest of flowering plants thus far reported. In general, the Maloideae have the largest diploid genomes of the family, consistent with their higher chromosome numbers and presumed polyploid origin.

DNA markers are being increasingly utilized in cultivar development, quality control of seed production, measurement of genetic diversity for conservation management, varietal identity, and to assist in maintenance of intellectual property protection (IPP). The use of simple sequence repeats (SSRs) for variety profiling can provide high discrimination, with excellent reproducibility at less cost than for restriction fragment length polymorphisms (RFLPs). The objective of this study was to evaluate the potential utility of SSR technology for applications in research, product development, seed production, and genetic resource conservation management for sorghum. Fifty genetically diverse elite sorghum [Sorghum bicolor (L.) Moench] inbreds were used to compare the discrimination abilities of 15 SSR primers with 104 RFLPs and to compare the associations among fines revealed by these molecular data and by pedigrees. RFLP data allowed all lines to be uniquely identified; two lines could not be distinguished by the SSR data. The mean polymorphism information content (PIC) values were 0.62 (RFLPs) and 0.58 (SSRs). Correlations for pairwise molecular profile distances with pedigree distances among the maintainer female (B) lines were 0.52 and 0.53 for RFLP and SSR data, respectively; data for the male parental restorer (R) lines were 0.41 and 0.47. This set of SSRs could be used to help genetic conservation management and to support IPP. Data from additional SSRs that collectively cover more of the genome will be required for applications to assist in breeding., DNA-BASED GENETIC MARKERS are being increasingly utilized in cultivar development, quality control of seed production, measurement of genetic diversity for conservation management, varietal identification, and intellectual property protection (IPP). Previously [...]

Cultivated peanut (Arachis hypogaea I,), an important agronomic crop, exhibits a considerable amount of variability for morphological traits and for resistance to diseases and pests. In contrast, molecular marker assays have detected little variation at the nucleic acid level. Identification of molecular markers would be of great help to peanut breeders, geneticists, and taxonomists. The objectives of this work were to identify simple sequence repeat (SSR) markers in cultivated peanut and to test these markers for their ability to discriminate among accessions. Peanut total genomic DNA libraries were constructed and screened with [.sup.32]P-labeled dinucleotide repeats, [(GT).sub.10] and [(CT).sub.10]. DNA sequences were obtained from the SSR-containing clones and, when possible, primer pairs were designed on the basis of DNA sequences flanking the repeat motif. Primer pairs were tested in polymerase chain reaction (PCR) assays using a collection of 22 peanut DNAs, representing both cultivated peanut and wild species. In all, six SSR markers, five from the library screening procedure and one additional marker obtained from a search of publicly available DNA sequences, detected polymorphisms among the peanut DNAs. Discrimination power was high among the cultivated peanuts, with 17 unique genotypes represented among the 19 accessions tested. From two to 14 DNA fragments were amplified per SSR marker, and as a group, the six markers may amplify up to 10 putive SSR loci. The SSR markers identified in this study were more effective in detecting molecular variation in cultivated peanut than all other DNA-based markers evaluated to date., Cultivated peanut is an important crop internationally for both direct human consumption and as an oilseed crop. Peanuts were domesticated in South America, probably in Southern Bolivia or Northern Argentina [...]

Plant genetic resources conservation is a challenge based on the need to balance acquisition priorities with the constrained level of financial support that is dedicated to long-term maintenance of collections. As such, understanding how variation is partitioned among accessions is essential for effective management. It is generally recognized that most large collections exhibit varying levels of genetic redundancy. To address this issue, all of the sorghum [Sorghum bicolor (L.) Moench] accessions identified as `Orange' presently maintained by the U.S. National Plant Germplasm System (NPGS) were assayed with 15 simple sequence repeat (SSR) markers. Genotyping was performed with fluorescent primers with five primer sets in each of three multiplex polymerase chain reactions (PCRs) and automated allele sizing. A total of 96 individuals were analyzed, five plants from each of 19 Orange accessions and one individual from an elite inbred line, `RTx430'. The SSR markers provided substantial genetic resolution among the Orange entries. Average heterozygosity estimates were low, and phenetic analyses (neighbor-joining dendograms) were generally consistent with known historical relationships among accessions. Most accessions were genetically distinct, but two redundant groups (involving a total of five entries) were found among the 19 Orange accessions evaluated. The molecular variance analysis (AMOVA) showed that 90% of the total genetic variation was partitioned among accessions, while one-tenth of the variation resulted from genetic differences between individual plants within accessions. The variance analysis also indicated that it should be possible to reduce the number of Orange accessions held by NPGS by almost half without seriously jeopardizing the overall amount of genetic variation contained in these holdings. This study demonstrated that a limited number of SSR markers can be used in a cost-efficient manner to rapidly assess variation in accessions of Orange sorghum., Sorghum is an important cereal crop globally, primarily because of its productivity and its tolerance to drought and heat stress (Doggett, 1988). On the basis of intense selection pressure imposed [...]