Gene flow among wild and cultivated common walnut(Juglans regia)trees in the Qinling Mountains revealed by microsatellite markers

Patterns of gene flow and gene introgres sion can be used to assess the risk of genetic pollution of wild forest trees from widespread cultivated trees.A comprehensive understanding of the genetic relationships and levels of gene flow among wild and cultivated common walnut(Juglans regia)has become an urgent issue.Using twelve microsatellite markers,we investigated the genetic diversity and gene flow between cultivated and wild trees of J.regia in the Qinling Mountains,China.A high level of genetic variation was detected in both cultivated and wild trees.The mean number of alleles per locus was 17.5.Observed heterozygosity(HO)and expected heterozygosity(HE)were 0.777 and 0.800,respectively.Pollination of mother trees was not by nearest neighbors,and a paternity of 60.7%of offspring evaluated could not be assigned to a local,sampled tree.Pollen flow from cultivated trees to wild trees was infrequent(5.4%),and selfing rates ranged from zero to 25.0%.Male parents were located from 0 to 1005 m from their female partners,with an average pollination distance of 285.1 m.These results are discussed in light of the cultivated species’diversity,outlining the frequent spontaneous genetic contributions from the wild to the cultivated compartment.In addition,the pollen flow parameters provide useful information about the dynamics of pollen movement within J.regia populations.

Pan-genome and transcriptome analyses provide insights into genomic variation and differential gene expression profiles related to disease resistance and fatty acid biosynthesis in eastern black walnut (Juglans nigra)

Walnut(Juglans)species are used as nut crops worldwide.Eastern black walnut(EBW,Juglans nigra),a diploid,horticultural important woody species is native to much of eastern North America.Although it is highly valued for its wood and nut,there are few resources for understanding EBW genetics.Here,we present a high-quality genome assembly of J.nigra based on Illumina,Pacbio,and HiC technologies.The genome size was 540.8 Mb,with a scaffold N50 size of 35.1 Mb,and 99.0%of the assembly was anchored to 16 chromosomes.Using this genome as a reference,the resequencing of 74 accessions revealed the effective population size of J.nigra declined during the glacial maximum.A single whole-genome duplication event was identified in the J.nigra genome.Large syntenic blocks among J.nigra,Juglans regia,and Juglans microcarpa predominated,but inversions of more than 600 kb were identified.By comparing the EBW genome with those of J.regia and J.microcarpa,we detected InDel sizes of 34.9 Mb in J.regia and 18.3 Mb in J.microcarpa,respectively.Transcriptomic analysis of differentially expressed genes identified five presumed NBS-LRR(NUCLEOTIDE BINDING SITELEUCINE-RICH REPEAT)genes were upregulated during the development of walnut husks and shells compared to developing embryos.We also identified candidate genes with essential roles in seed oil synthesis,including FAD(FATTY ACID DESATURASE)and OLE(OLEOSIN).Our work advances the understanding of fatty acid bioaccumulation and disease resistance in nut crops,and also provides an essential resource for conducting genomics-enabled breeding in walnut.

The de novo genome assembly of Tapiscia sinensis and the transcriptomic and developmental bases of androdioecy

Tapiscia sinensis(Tapisciaceae)possesses an unusual androdioecious breeding system that has attracted considerable interest from evolutionary biologists.Key aspects of T.sinensis biology,including its biogeography,genomics,and sexlinked genes,are unknown.Here,we report the first de novo assembly of the genome of T.sinensis.The genome size was 410 Mb,with 22,251 predicted genes.Based on whole-genome resequencing of 55 trees from 10 locations,an analysis of population genetic structure indicated that T.sinensis has fragmented into five lineages,with low intrapopulation genetic diversity and little gene flow among populations.By comparing whole-genome scans of male versus hermaphroditic pools,we identified 303 candidate sex-linked genes,79 of which(25.9%)were located on scaffold 25.A 24-kb region was absent in hermaphroditic individuals,and five genes in that region,TsF-box4,TsF-box10,TsF-box13,TsSUT1,and TsSUT4,showed expression differences between mature male and hermaphroditic flowers.The results of this study shed light on the breeding system evolution and conservation genetics of the Tapisciaceae.