Genetic structure and differentiation in cultivated fig (Ficus carica L.)

Abstract One hundred ninety-four germplasm accessions of fig representing the four fig types, Common, Smyrna, San Pedro, and Caprifig were analyzed for genetic diversity, structure, and differentiation using genetic polymorphism at 15 microsatellite loci. The collection showed considerable polymorphism with observed number of alleles per locus ranging from four for five different loci, MFC4, LMFC14, LMFC22, LMFC31 and LMFC35 to nine for LMFC30 with an average of 4.9 alleles per locus. Seven of the 15 loci included in the genetic structure analyses exhibited significant deviation from panmixia, of which two showed excess and five showed deficiency of heterozygote. The cluster analysis (CA) revealed ten groups with 32 instances of synonymy among cultivars and groups differed significantly for frequency and composition of alleles for different loci. The principal components analysis (PCA) confirmed the results of CA with some groups more differentiated than the others. Further, the model based Bayesian approach clustering suggested a subtle population structure with mixed ancestry for most figs. The gene diversity analysis indicated that much of the total variation is found within groups (H G /H T = 0.853; 85.3%) and the among groups within total component (G GT = 0.147) accounted for the remaining 14.7%, of which *64% accounted for among groups within clusters (G GC = 0.094) and *36% among clusters (G CT = 0.053). The analysis of molecular variance (AMOVA) showed approximately similar results with nearly 87% of variation within groups and *10% among groups within clusters, and *3% among clusters. Overall, the gene pool o

Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials.

BackgroundMutations often accompany DNA replication. Since there may be fewer cell cycles per year in the germlines of long-lived than short-lived angiosperms, the genomes of long-lived angiosperms may be diverging more slowly than those of short-lived angiosperms. Here we test this hypothesis.ResultsWe first constructed a genetic map for walnut, a woody perennial. All linkage groups were short, and recombination rates were greatly reduced in the centromeric regions. We then used the genetic map to construct a walnut bacterial artificial chromosome (BAC) clone-based physical map, which contained 15,203 exonic BAC-end sequences, and quantified with it synteny between the walnut genome and genomes of three long-lived woody perennials, Vitis vinifera, Populus trichocarpa, and Malus domestica, and three short-lived herbs, Cucumis sativus, Medicago truncatula, and Fragaria vesca. Each measure of synteny we used showed that the genomes of woody perennials were less diverged from the walnut genome than those of herbs. We also estimated the nucleotide substitution rate at silent codon positions in the walnut lineage. It was one-fifth and one-sixth of published nucleotide substitution rates in the Medicago and Arabidopsis lineages, respectively. We uncovered a whole-genome duplication in the walnut lineage, dated it to the neighborhood of the Cretaceous-Tertiary boundary, and allocated the 16 walnut chromosomes into eight homoeologous pairs. We pointed out that during polyploidy-dysploidy cycles, the dominant tendency is to reduce the chromosome number.ConclusionSlow rates of nucleotide substitution are accompanied by slow rates of synteny erosion during genome divergence in woody perennials

Patterns of genomic and phenomic diversity in wine and table grapes.

Grapes are one of the most economically and culturally important crops worldwide, and they have been bred for both winemaking and fresh consumption. Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world's largest grape gene banks, the grape germplasm collection of the United States Department of Agriculture. We find that phenological events throughout the growing season are correlated, and quantify the marked difference in size between table and wine grapes. By pairing publicly available historical phenotype data with genome-wide polymorphism data, we identify large effect loci controlling traits that have been targeted during domestication and breeding, including hermaphroditism, lighter skin pigmentation and muscat aroma. Breeding for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited, whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian regions. We uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger berries. Our results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes

cavin-2の発現低下は、口腔癌の成長に寄与する

研究科: 千葉大学大学院医学薬学府学位:千大院医薬博甲第医1120号要約博士(医学)千葉大

Genetic structure and differentiation in cultivated fig (Ficus carica L.)

One hundred ninety-four germplasm accessions of fig representing the four fig types, Common, Smyrna, San Pedro, and Caprifig were analyzed for genetic diversity, structure, and differentiation using genetic polymorphism at 15 microsatellite loci. The collection showed considerable polymorphism with observed number of alleles per locus ranging from four for five different loci, MFC4, LMFC14, LMFC22, LMFC31 and LMFC35 to nine for LMFC30 with an average of 4.9 alleles per locus. Seven of the 15 loci included in the genetic structure analyses exhibited significant deviation from panmixia, of which two showed excess and five showed deficiency of heterozygote. The cluster analysis (CA) revealed ten groups with 32 instances of synonymy among cultivars and groups differed significantly for frequency and composition of alleles for different loci. The principal components analysis (PCA) confirmed the results of CA with some groups more differentiated than the others. Further, the model based Bayesian approach clustering suggested a subtle population structure with mixed ancestry for most figs. The gene diversity analysis indicated that much of the total variation is found within groups (HG/HT = 0.853; 85.3%) and the among groups within total component (GGT = 0.147) accounted for the remaining 14.7%, of which ~64% accounted for among groups within clusters (GGC = 0.094) and ~36% among clusters (GCT = 0.053). The analysis of molecular variance (AMOVA) showed approximately similar results with nearly 87% of variation within groups and ~10% among groups within clusters, and ~3% among clusters. Overall, the gene pool of cultivated fig analyzed possesses substantial genetic polymorphism but exhibits narrow differentiation. It is evident that fig accessions from Turkmenistan are somewhat genetically different from the rest of the Mediterranean and the Caucasus figs. The long history of domestication and cultivation with widespread dispersal of cultivars with many synonyms has resulted in a great deal of confusion in the identification and classification of cultivars in fig

Genecology of Hawaiian Metrosideros

Thesis (Ph. D.)--University of Hawaii at Manoa, 1992.Includes bibliographical references.Microfiche.xix, 279 leaves, bound ill. 29 c

Geographic Survey of Genetic Variation in Kava (Piper methysticum Forst. f. and P. wichmannii C. DC.)

A survey of the genetic resources of kava (Piper methysticum Forst. f. and P. wichmannii C. DC.) was conducted throughout the Pacific. Leaf tissues of more than 300 accessions, collected on 35 islands, were analyzed for isozyme variation in eight enzyme systems including ACO, ALD, DIA, IDH, MDH, ME, PGI, and PGM. Isozymes in P. methysticum cultivars from Polynesia and Micronesia were monomorphic for all enzyme systems examined; however, cultivars from Melanesia were polymorphic for ACO, DIA, MDH, and PGM. The genetic base of this crop is much narrower than previous morphological and biochemical studies suggest. Most of the morphotypes and chemotypes apparently originated through human selection and preservation of somatic mutations in a small number of original clones. Isozymes of P. wichmannii confirmed its status as the wild progenitor of kava. Piper methysticum cultivars and P. wichmannii and P. gibbilimbum C. DC. wild forms were all found to be decaploids with 2n = lOx = 130 chromosomes, but there was no firm evidence that interspecific hybridization has played a role in the origin of P. methysticum

Allozyme variation in spineless pejibaye (Bactris gasipaes Palmae)

Allozyme variation was examined in three pejibaye (Bactris gasipaes) populations introduced into Hawaii for use in heart-of-palm improvement: Benjamin Constant (Putumayo landrace), San Carlos (Guatuso landrace) and Yurimaguas (Pampa Hermosa landrace). Nine enzymes encoded by 16 putative loci with a total of 38 alleles were resolved from meristem extract. Five loci were fixed in all populations, four additional loci were fixed in SC and one additional locus in BC. Six of the 38 alleles were rare, with three unique to BC and one to Y; two moderately high frequency alleles were unique to SC. Mean number of alleles per locus was lowest in SC (44) and highest in Y (69). Observed heterozygosity was lowest in SC (0.051) and BC (0.066) and highest in Y (0.141). Nei's genetic identity was 0.985 between BC and Y and averaged 0.952 between SC and BC-Y. The low heterozygosities are probably due to a long history of selection and inbreeding (sub-mating) during the domestication process, followed by intensive recent selection for spinelessness and more inbreeding. All populations are very closely related, suggesting a single domestication event in Amazonia