Genetic relatedness and association mapping of horticulturally valuable traits for the Ceiba plants using ddRAD sequencing

Ceiba species have high ornamental value and are widely cultivated in tropical regions.However,genetic background of cultivated Ceiba plants remains unclear.To understand the genetic relatedness of cultivated Ceiba plants and genetic basis of key horticultural traits,here we explored the genetic relatedness of 153 accessions of Ceiba plants cultivated in Southern China and identified SNPs associated with five horticultural traits,based on 11704 SNPs derived from double-digest restriction-site associated DNA sequencing(ddRAD-seq).Clustering analysis revealed that these accessions were composed of three groups:C.speciosa group,C.insignis group,and hybrid group.The GWAS identified two,four,two,three,and four SNPs related to petal color,petal striation number,flowering time,trunk shape,and prickles on the trunk and branches,respectively.One to two candidate genes were found near the SNPs strongly associated with these traits.This study revealed the genetic relatedness in the Ceiba plants cultivated in Southern China and presented the first GWAS analysis for five horticultural traits for them,laying a foundation for phenotype-related marker selection and molecular breeding.

MethylGenotyper:Accurate Estimation of SNP Genotypes and Genetic Relatedness from DNA Methylation Data

Epigenome-wide association studies(EWAS)are susceptible to widespread confounding caused by population structure and genetic relatedness.Nevertheless,kinship estimation is challenging in EWAS without genotyping data.Here,we proposed MethylGenotyper,a method that for the first time enables accurate genotyping at thousands of single nucleotide polymorphisms(SNPs)directly from commercial DNA methylation microarrays.We modeled the intensities of methylation probes near SNPs with a mixture of three beta distributions corresponding to different genotypes and estimated parameters with an expectation-maximization algorithm.We conducted extensive simulations to demonstrate the performance of the method.When applying MethylGenotyper to the Infinium EPIC array data of 4662 Chinese samples,we obtained genotypes at 4319 SNPs with a concordance rate of 98.26%,enabling the identification of 255 pairs of close relatedness.Furthermore,we showed that MethylGenotyper allows for the estimation of both population structure and cryptic relatedness among 702 Australians of diverse ancestry.We also implemented MethylGenotyper in a publicly available R package(https://github.com/Yi-Jiang/MethylGenotyper)to facilitate future large-scale EWAS.

An estimation of genetic parameters of growth traits in juvenile turbot (Scophthalmus maximus L.) using parental molecular relatedness

The estimation of genetic parameters has played an important role in animal selective breeding for growth traits.Recently studies show that molecular markers can be incorporated into genetic evaluations. In order to improve the performance of an incomplete pedigree（i.e, only parents are known） in the genetic evaluations, 12 microsatellite markers have been applied in the estimation of the genetic parameters for body weight in a farmed population（n=1 890） of juvenile turbot（Scophthalmus maximus L.）. A new relatedness called parental molecular relatedness（PMR） is estimated based on results of genotyping of 48 parents（31 males, 17 females） with microsatellites markers. The feasibility of PMR in estimation of genetic parameters is verified by comparison with pedigree related（PR） which is obtained from a complete pedigree. The results demonstrate that a high correlation（0.872） between them is found. Heritabilities are estimated using the PMR（0.52±0.13） and PR（0.55±0.22） with the same animal model. A cross-validation shows that the predictive abilities of models using the PMR and the PR are identical（0.81）. From that, a conclusion can be made that PMR and PR predicted genetic values equally well in a population of juvenile turbot. Therefore PMR can be applied as an alternative of the PR when only parents are known. However, for a better performance, more markers and more families should be included in a further study.

DNA polymorphisms and genetic relationship among populations of Acacia leucophloea using RAPD markers

RAPD （randomly amplified polymorphic DNA） markers were employed to characterize polymorphisms among 5 provenances of Acacia leucophloea and to detect genetic relatedness of the species with 6 other acacias （A. holosericea, A. auriculiformis, A. mangium, A. dealbata, A. ferruginea, and A. nilotica） widely grown in India. Of 194 markers scored for the provenances, 29.38% exhibited polymorphism. Also, 326 markers were generated among 7 species of Acacia, accounting for 55.82% of the polymorphisms. The fifteen 10-mer primers employed were capable of producing 1-8 polymorphic bands for the provenances, and 6-17 for all seven species of Acacia. The genetic similarity coefficient based on Jaccard＇ s coefficient revealed that provenances Thirumangalam and Dharmapuri were closely related. The dendrogram based on a sequential agglomerative hierarchical non-overlapping （SAHN） clustering analysis grouped 4 provenances of A. leucophloea （Dharapuram, Thirumangalam, Pudukottai and Dharmapuri） into one cluster and the other provenance, Sendurai, into a separate cluster. The genetic similarity matrix for 7 Acacia species showed that A. nilotica and A. dealbata were distantly related, while A. holosericea and A. ferruginea were very closely related. Cluster analysis grouped the species of Acacias into 3 major groups of which A. dealbata alone formed a separate group. The RAPD markers generated 36 provenance-specific markers and 162 species-specific markers that could have strong applications for species identification and tree breeding programs for A. leucophloea and for other Acacia species included in this study.

Genetic analysis of morphological index and its related taxonomic traits for classification of indica

The Cheng index distinguishes indica andjaponica rice based on six taxonomic traits.This index has been widely used for classifi- cation of indica and japonica varieties in China.In this study,a double haploid(DH)popula-tion derived from anther culture of ZYQ8/JX17 F,a typical inter-subspecies hybrid,was used to investigate the six taxonomictraits,i.e.leaf hairiness(LH),color of hullwhen heading(CHH),hairiness of hull(HH),length of the first and second panicle internode(LPI),length/width of grain(L/W),andphenol reaction(PH).The morphological in- dex(MI)was also calculated.Based on themolecular linkage map constructed from this

Blood is not always thicker than water:The limited effect of kin selection on human kinship in the traditional Chinese family

To examine the importance of kin selection in shaping human societies, this study analyzed the kinship system practiced in traditional China for two millennia and teased apart its underlying genetic and other, presumably cultural, components. The results demonstrate that, in the traditional patrilineal Chinese family, both genetic relatedness and the cultural factor of generation were important in determining kinship status for male agnates （genetically related relatives）. For female agnates, however, only genetic relatedness was important. Another surprising finding was that the influence of gender was not as important as genetic relatedness. The most interesting finding in this study, however, was that kin selection and culture （i.e., seniority in generation and age） played vastly different roles in different lineages in the Chinese family： for collateral （indirect） agnates, genetic relatedness was the most important factor in determining their kinship status, but for lineal （direct） agnates, its importance was overridden by seniority in generation and age, a cultural factor. Several other bio-cultural factors also explained a considerable amount of variance in kinship status. Since kinship profoundly affected, and was often the foundation of, the legal and social systems in dynastic China, kin selection, while its strength may differ remarkably between lineal and collateral relatives, could act as a selective force in Chinese families

Long-term overlap of social and genetic structure in free-ranging house mice reveals dynamic seasonal and group size effects

Associating with relatives in social groups can bring benefits such as reduced risk of aggression and increased likelihood of cooperation.Competition among relatives over limited resources,on the other hand,can induce individuals to alter their patterns of association.Population density might further affect the costs and benefits of associating with relatives by altering resource competition or by changing the structure of social groups;preventing easy association with relatives.Consequently,the overlap between genetic and social structure is expected to decrease with increasing population size,as well as during times of increased breeding activity.Here,we use multi-layer network techniques to quantify the similarity between long-term,high resolution genetic,and behavioral data from a large population of free-ranging house mice(Mus musculus domesticus),studied over 10years.We infer how the benefit of associating with genetically similar individuals might fluctuate in relation to breeding behavior and environmental conditions.We found a clear seasonal effect,with decreased overlap between social and genetic structure during summer months,characterized by high temperatures and high breeding activity.Though the effect of overall population size was relatively weak,we found a clear decrease in the overlap between genetic similarity and social associations within larger groups.As well as longer-term within-group changes,these results reveal population-wide short-term shifts in how individuals associate with relatives.Our study suggests that resource competition modifies the trade-off between the costs and benefits of interacting with relatives.

Differential impacts of adult trees on offspring and non-offspring recruits in a subtropical forest

An important mechanism promoting species coexistence is conspecific negative density dependence(CNDD),which inhibits conspecific neighbors by accumulating host-specific enemies near adult trees.Natural enemies may be genotype-specific and regulate offspring dynamics more strongly than non-offspring,which is often neglected due to the difficulty in ascertaining genetic relatedness.Here,we investigated whether offspring and non-offspring of a dominant species,Castanopsis eyrei,suffered from different strength of CNDD based on parentage assignment in a subtropical forest.We found decreased recruitment efficiency(proxy of survival probability)of offspring compared with non-offspring near adult trees during the seedling-sapling transition,suggesting genotype-dependent interactions drive tree demographic dynamics.Furthermore,the genetic similarity between individuals of same cohort decreased in late life history stages,indicating genetic-relatedness-dependent tree mortality throughout ontogeny.Our results demonstrate that within-species genetic relatedness significantly affects the strength of CNDD,implying genotype-specific natural enemies may contribute to population dynamics in natural forests.

Genotypic diversity of a dominant C_(4) grass across a long-term fire frequency gradient

Aims and Methods Diversity-disturbance research has focused on community diversity,but disturbance frequency could impact diversity within species as well,with important consequences for community diversity and ecosystem function.We examined patterns of genetic diversity of a dominant grass species,Andropogon gerardii,in native North American tallgrass prairie sites located in eastern Kansas that have been subjected to a gradient of fire frequency treatments(burned every 1,2,4 or 20 years)since the 1970s.In addition,we were able to assess the relationships between genetic diversity of A.gerardii,species diversity and productivity across this range of fire frequencies.Important Findings We found no significant relationships between genetic diversity of A.gerardii at the local scale(1 m^(2) plot level)and disturbance frequency(burned 2 to 32 times over a 38-year period).However,at the site level(i.e.across all plots sampled within a site,~100 m^(2))there were differences in genotype richness and composition,as well as genomic dissimilarity among individuals of A.gerardii.Genotype richness was greatest for the site burned at an intermediate(4-year)frequency and lowest for the infrequently(20-year)burned site.In addition,genotypes found in the frequently burned sites were more similar from each other than expected by random chance than those found in the infrequently burned sites.Genotype composition of A.gerardii was not significantly different between the frequently burned sites(annual vs.2 year)but did differ between frequently burned and infrequently burned sites(1 and 2 year vs.4 and 20 year,etc.).Together,these results suggest site-level ecological sorting of genotypes in intact prairie across a broad gradient of disturbance frequencies,likely driven by alterations in environmental conditions.Frequent fire promotes the abundance of dominant grass species,reduces plant community diversity and impacts ecosystem processes such as productivity.Our study suggests that genetic diversity within dominant grass species also may be affected by disturbance frequency,which could have important implications for how species are able to respond to disturbance.