BackgroundGrapes are one of the most economically important fruit crops. There are about 60 species in the genus Vitis. The phylogenetic relationships among these species are of keen interest for the conservation and use of this germplasm. We selected 309 accessions from 48 Vitis species,varieties, and outgroups, examined ~11 kb (~3.4 Mb total) of aligned nuclear DNA sequences from 27 unlinked genes in a phylogenetic context, and estimated divergence times based on fossil calibrations.ResultsVitis formed a strongly supported clade. There was substantial support for species and less for the higher-level groupings (series). As estimated from extant taxa, the crown age of Vitis was 28 Ma and the divergence of subgenera (Vitis and Muscadinia) occurred at ~18 Ma. Higher clades in subgenus Vitis diverged 16 – 5 Ma with overlapping confidence intervals, and ongoing divergence formed extant species at 12 – 1.3 Ma. Several species had species-specific SNPs. NeighborNet analysis showed extensive reticulation at the core of subgenus Vitis representing the deeper nodes, with extensive reticulation radiating outward. Fitch Parsimony identified North America as the origin of the most recent common ancestor of extant Vitis species.ConclusionsPhylogenetic patterns suggested origination of the genus in North America, fragmentation of an ancestral range during the Miocene, formation of extant species in the late Miocene-Pleistocene, and differentiation of species in the context of Pliocene-Quaternary tectonic and climatic change. Nuclear SNPs effectively resolved relationships at and below the species level in grapes and rectified several misclassifications of accessions in the repositories. Our results challenge current higher-level classifications, reveal the abundance of genetic diversity in the genus that is potentially available for crop improvement, and provide a valuable resource for species delineation, germplasm conservation and use.

The effects of breeding on allele frequency changes at 82 restriction fragment length polymorphism (RFLP) loci were examined in two maize (Zea mays L.) populations undergoing reciprocal recurrent selection, Iowa Stiff Stalk Synthetic and Iowa Corn Borer Synthetic #1. After 12 cycles of selection, approximately 30% of the alleles were extinct and 10% near fixation in each population. A test of selective neutrality identified several loci in each population whose allele frequency changes cannot be explained by genetic drift; interpopulation mean expected heterozygosity increased for that subset of 28 loci but not for the remaining 54 loci. Mean expected heterozygosity within the two subpopulations decreased 39%, while the between-population component of genetic variation increased from 0.5% to 33.4% of the total. Effective population size is a key parameter for discerning allele frequency changes due to genetic drift versus those resulting from selection and genetic hitchhiking. Empirical estimates of effective population size for each population were within the range predicted by the breeding method. KeywordsEffective population size, Selection, Genetic drift, Diversity, Restriction fragment length polymorphism Abstract The effects of breeding on allele frequency changes at 82 restriction fragment length polymorphism (RFLP) loci were examined in two maize (Zea mays L.) populations undergoing reciprocal recurrent selection, Iowa Stiff Stalk Synthetic and Iowa Corn Borer Synthetic #1. After 12 cycles of selection, approximately 30% of the alleles were extinct and 10% near fixation in each population. A test of selective neutrality identified several loci in each population whose allele frequency changes cannot be explained by genetic drift; interpopulation mean expected heterozygosity increased for that subset of 28 loci but not for the remaining 54 loci. Mean expected heterozygosity within the two subpopulations decreased 39%, while the between-population component of genetic variation increased from 0.5% to 33.4% of the total. Effective population size is a key parameter for discerning allele frequency changes due to genetic drift versus those resulting from selection and genetic hitchhiking. Empirical estimates of effective population size for each population were within the range predicted by the breeding method.

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Iowa Stiff Stalk Synthetic (BSSS) and Iowa Corn Borer Synthetic #1 (BSCB1) are undergoing reciprocal recurrent selection as part of Iowa's Federal-State maize (Zea mays L.) breeding program. This study focused on molecular genetic variation in BSSS(R) and BSCBI(R) cycle 0 (CO) and cycle 12 (C12) populations, as well as the inbred progenitor lines (P) used to synthesize BSSS and BSCB1. The objectives were to quantify amounts of genetic variation within populations, to estimate what proportion remained after selection, and to compare genetic diversities between BSSS and BSCB1 populations. Genotypic data for 82 restriction fragment length polymorphism (RFLP) loci were collected from 100 randomly sampled individuals from each CO and C12 population, 16 BSSS(R) progenitors, and 12 BSCBI(R) progenitors. Progenitor lines were highly homozygous as expected. No single progenitor made excessive genetic contributions to CO or C12. The BSSS and BSCB1 progenitor populations were initially genetically similar (Nei's genetic distance = 0.07). After 12 cycles of selection, they substantially diverged (Nei's distance = 0.66). Gene diversity (expected heterozygosity under random mating) across progenitor populations was very broad (mean gene diversity = 0.6) and remained at that level to C12. Within both populations, the polymorphism level decreased from about 99 to 75%, and gene diversity decreased from about 0.6 to 0.3 between P and C12. The mean number of alleles per locus dropped from about four to less than three. Assuming an effective population size as the mean number of selected S1 lines over 12 cycles, the observed loss of variation was consistent with theoretical expectations resulting from genetic drift of neutral alleles.

Troyer, 2000). The Southern Dents, dominant during colonial times in the southeastern USA, were intro-Tens-of-thousands of open-pollinated cultivars of corn (Zea mays duced from Mexican sources via Cuba by Spanish Con-L.) are being maintained in germplasm banks. Knowledge of the amount and distribution of genetic variation within and among acces-quistadors during the 1500s (Doebley et al., 1988; Goodsions can aid end users in choosing among them. We estimated molecu-man and Brown, 1988; Hudson, 1994). Dent corn spread lar genetic variation and looked for influences of pedigree, adaptation, northward from Cuba to Florida in 1539, to South Caroand migration in the genetic makeup of conserved Corn-Belt Dentlina in 1560, and to the Chesapeake Bay area in 1570 related germplasm. Plants sampled from 57 accessions representing (Troyer, 2000). Corn-Belt Dents, Northern Flints, Southern Dents, plus 12 publicBecause flint corn arrived in the USA 2500 yr before inbreds, were genotyped at 20 simple sequence repeat (SSR) loci. For dent, and the two types were isolated for an additional 47 of the accessions, between 5 and 23 plants per accession were 500 yr by flowering time, they became highly genetically genotyped (mean ϭ 9.3). Mean number of alleles per locus was 6.5 differentiated from each other. Today, Northern Flint overall, 3.17 within accessions, and 3.20 within pooled inbreds. Meanand Southern Dent races are considered to be so differgene diversity was 0.53 within accessions and 0.61 within pooled inbreds. Open-pollinated accessions showed a tendency toward inbreed-ent that, relative to the variation found within the wild ing (F IS ϭ 0.09), and 85% of genetic variation was shared among grasses, they would be considered different species and them. A Fitch-Margoliash tree strongly supported the distinctiveness possibly members of different genera (Anderson and of flint from dent germplasm but did not otherwise reveal evidence Brown, 1952). Flint corn carries certain traits for adaptaof genetic structure. Mantel tests revealed significant correlations tion to the cool, moist northeastern climate. The typical between genetic distance and geographical (r ϭ 0.54, P ϭ 0.04) or hard, smooth, and shallow kernels are spaced widely on maturity zone (r ϭ 0.33, P ϭ 0.03) distance only if flint germplasm the ears, allowing them to ripen earlier, be resistant to was included in the analyses. A significant correlation (r ϭ 0.76, P Ͻ molds, dry down quickly, and withstand early fall frosts 0.01) was found between days to pollen shed and maturity zone of without injury so they germinate well the following accession origin. Pedigree, rather than migration or selection, has spring. This is in contrast to dent types that have kernels most influenced the genetic structure of the extant representatives of the open-pollinated cultivars at these SSR loci.