ABSTRACT: An investigation into the genetic diversity of in-farm and gene bank cacao resources in Baracoa Region using SNPs derived from ddRADseq technology.
Project description:The genetic diversity of JEV vaccine strains SA14-14-2, SA14-5-3 and SA14-2-8 and the WT parental WT strain they were derived from, SA14, were sequenced using Illumina technology. Passages of the strains were also sequenced to observe changes in genetic diversity.
Project description:Eucalyptus urophylla is a commercially important wood crop plantation species due to its rapid growth, biomass yield, and use as bioenergy feedstock. We characterized the genetic diversity and population structure of 332 E. urophylla individuals from 19 geographically defined E. urophylla populations with a reliability of 14,468 single nucleotide polymorphisms (SNPs). We compared the patterns of genetic variation among these 19 populations. High levels of genetic diversity were observed throughout the 19 E. urophylla populations based on genome-wide SNP data (HE=0.2677 to 0.3487). Analysis with STRUCTURE software, Principal component analysis (PCA) and a neighbor-joining (NJ) tree indicated that E. urophylla populations could be divided into three groups, and moderate and weak population structure was observed with pairwise genetic differentiation (FST) values ranging from −0.09 to 0.074. The low genetic diversity and shallow genetic differentiation found within the 19 populations may be a consequence of their pollination system and seed dispersal mechanism. In addition, 55 core germplasms of E. urophylla were constructed according to the genetic marker data. The genome-wide SNPs we identified will provide a valuable resource for further genetic improvement and effective use of the germplasm resources.
Project description:In the present investigation, the genetic diversity architecture of 96 deep-water rice genotypes of Assam and association mapping strategy was, for the first time, applied to determine the significant SNPsand genes for deep-water rice. These genotypes are known for their unique elongation ability under deep-water condition.The internode elongation under water related genes will be identified here can provide affluent resources for rice breeding especially in flood-prone areas. We investigated the genome-wide association studies (GWAS) using 50 K rice genic SNPchip across 96 deep-water rice genotypes collected from different flood-prone districts/villages of Assam.
Project description:Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation. MethylC-seq from naturally-occurring Arabidopsis accessions
Project description:Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation.
Project description:With the advent of advanced sequencing technology, studies of RNA viruses have shown that genetic diversity contribute to both attenuation and virulence. The differences in genetic diversity of wild-type Asibi virus and 17D-204 vaccine provides an unique opportunity to investigate RNA population theory in the context of a well described live attenuated vaccine. Utilizing infectious clone-derived viruses containing some of the amino acid substitutions that differentiate yellow fever wild-type Asibi strain from 17D vaccine and recovered in a controlled experiment, establishes that the genetic diversity differences that exist between wild-type Asibi and 17D-204 vaccine viruses are not influenced by either different passage history or source of samples, but rather resulted from the attenuation of wild-type Asibi virus to yield the 17D vaccine sub-strains.
Project description:Investigation of the genetic diversity of Emiliania huxleyi, genomic DNA from 15 different strains were compared with the genomic DNA of the sequenced E. huxleyi strain CCMP1516. Gephyrocapsa oceanica and Isochrysis galbana as phylogenetic closely related taxa were used as out-groups.