Genetic diversity analysis of spawner and recaptured populations of Chinese shrimp(Fenneropenaeus chinensis)during stock enhancement in the Bohai Bay based on an SSR marker

Eight microsatellite markers were used to analyze genetic diversity, level of inbreeding, and effective population size of spawner and recaptured populations of Chinese shrimp（Fenneropenaeus chinensis） during stock enhancement in the Bohai Bay in 2013. A total of 254 and 238 alleles were identified in the spawner and recaptured populations, respectively, and the numbers of alleles（N_a） were 8–63 and 6–60, respectively. The numbers of effective alleles（N_e） were 2.52–21.60 and 2.67–20.72, respectively. The polymorphism information content ranged from 0.529 to 0.952. The observed heterozygosity（H_o） values（0.638–0.910 and 0.712–0.927） were lower than the expected heterozygosity（H_e） values（0.603–0.954 and 0.625–0.952）, which indicated that the two populations possessed a rich genetic diversity. In 16 tests（2 populations×8 loci）, 13 tests deviated from the HardyWeinberg equilibrium. F_（is） values were positive at seven loci and the inbreeding coefficients（F） of the two populations estimated by trio ML were 13.234% and 11.603%, suggesting that there was a relatively high degree of inbreeding. A certain level of inbreeding depression had occurred in the Chinese shrimp population. F_（st） values ranged from 0 to 0.059, with a mean of 0.028, displaying a low level of genetic differentiation in the two populations. Effective population sizes（3 060.2 and 3 842.8） were higher than the minimum number suggested for retaining the evolutionary potential to adapt to new environmental conditions. For enhancement activity in 2014,the ideal number of captured shrimp spawners should have ranged from 7 686 to 19 214 to maintain genetic diversity and effective population size. Further strategies to adjust the balance of economic cost, fishing effort and ideal number of shrimp spawners to maintain a satisfactory effective population size for ensuring the sustainability of Chinese shrimp are proposed.

Genetic Diversity and Population Structure in Landraces and Improved Rice Varieties from India

A set of 50 rice genotypes comprising landraces, local selections, and improved varieties were characterized using simple sequence repeat（SSR） and inter simple sequence repeat（ISSR） markers to study genetic diversity and population structure. Following unweighted pair group method with arithmetic mean based clustering using binary data of polymorphic markers, the genotypes were grouped into 5 clusters and 11 sub-clusters, whereas population structure analysis separated 50 rice genotypes into 5 sub-populations. Grouping of rice genotypes showed better resemblance with the pedigree information of the genotypes. Both genetic diversity and population structure analysis separated majority of the improved varieties from landraces and local selections. Some of the SSR markers amplified unique alleles which were specific to a particular genotype and could distinguish them from the rest. The results indicate that these rice genotypes exhibit a higher genetic diversity and can be very useful in rice improvement program.

Genetic diversity of pepper(Capsicum spp.) germplasm resources in China reflects selection for cultivar types and spatial distribution

Pepper（Capsicum spp.） is an important vegetable crop in the world. Now the pepper in China contributes one-third of the world＇s peppers production. Genetic diversity of the pepper germplasm of China is expected interesting to know. To explore the structure of genetic diversity in Chinese pepper germplasm resources and possible relationship with cultivar types or geographic origin, we sampled and compared 372 Gen Bank pepper accessions（local cultivars and landraces） from 31 provinces, autonomous regions and municipalities of China and 31 additional accessions from other countries. These accessions were genotyped using 28 simple sequence repeat（SSR） markers spanning the entire pepper genome. We then investigated the genetic structure of the sampled collection using model-based analysis in STRUCTURE v2.3.4 and examined genetic relationships by the unweighted pair-group method of mathematical averages（UPGMA） in MEGA. In addition to geographic origin, we evaluated eight plant and fruit traits. In total, 363 alleles were amplified using the 28 SSR primers. Gene diversity, polymorphism information content and heterozygosity of the 28 SSR loci were estimated as 0.09–0.92, 0.08–0.92 and 0.01–0.34, respectively. The UPGMA cluster analysis clearly distinguished Capsicum annuum L. from other cultivated pepper species. Population structure analysis of the 368 C. annuum accessions uncovered three genetic groups which also corresponded to distinct cultivar types with respect to the plant and fruit descriptors. The genetic structure was also related to the geographic origin of the landraces. Overall results indicate that genetic diversity of Chinese pepper landraces were structured by migration of genotypes followed by human selection for cultivar types in agreement with consumption modes and adaptation to the highly diversified agro-climatic conditions.

Informative ISSR Markers Help Identify Genetically Distinct Accessions of Oryza rufipogon in Yield Improvement

Inter simple sequence repeat（ISSR） polymorphism was used to determine genetic diversity and phylogenetic relationships in 90 genotypes of wild and cultivated species of Oryza from different geographical regions of the world. In all the 17 primers used in ISSR-PCR, a total of 11 464 bands were amplified at 253 band positions/loci. The primer UBC-809 amplified the maximum bands（1 059） at 21 band positions. UBC-810 and UBC-835 amplified the minimum of 391 bands each at 7 and 14 band positions, respectively. The mean polymorphism information content ranged from 0.44 to 0.84 and resolving power ranged from 8.69 to 23.53. Un-weighted pair group method with arithmetic mean dendrogram and population structure based on the 17 primers separated all genotypes into 4 major clusters with a genetic similarity of 53%–100%. The first two clusters consisted of 30 O. rufipogon accessions each. In the third cluster, O. nivara and O. longistaminata grouped as one sub-cluster and all other O. nivara accessions and cultivars grouped as another sub-cluster. The fourth cluster had only five O. rufipogon accessions which can be a source of new genes. Four sub-populations were identified within O. rufipogon and two sub-populations within O. nivara at K = 7. A subset of six primers with high resolving power values were the most informative and grouped all genotypes almost similarly as the 17 primers did. Use of these six highly informative primers in ISSR-PCR is a cost effective and robust method for assessing genetic diversity in large germplasm collections of wild rice species.

Population transcriptomics reveals a potentially positive role of expression diversity in adaptation

While it is widely accepted that genetic diversity determines the potential of adaptation,the role that gene expression variation plays in adaptation remains poorly known.Here we show that gene expression diversity could have played a positive role in the adaptation of Miscanthus lutarioriparius.RNA-seq was conducted for 80 individuals of the species,with half planted in the energy crop domestication site and the other half planted in the control site near native habitats.A leaf reference transcriptome consisting of 18,503 high-quality transcripts was obtained using a pipeline developed for de novo assembling with population RNA-seq data.The population structure and genetic diversity of M.lutarioriparius were estimated based on 30,609 genic single nucleotide polymorphisms.Population expression（Ep） and expression diversity（Ed）were defined to measure the average level and the magnitude of variation of a gene expression in the population,respectively.It was found that expression diversity increased while genetic Resediversity decreased after the species was transplanted from the native habitats to the harsh domestication site,especially for genes involved in abiotic stress resistance,histone methylation,and biomass synthesis under water limitation.The increased expression diversity could have enriched phenotypic variation directly subject to selections in the new environment.