Cornell University 




标题:Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus

发表期刊:Nature Communications


主要作者单位:Cornell University

使用Sentieon模块:Sentieon BWA, DNAseq


Transferable DNA markers are essential for breeding and genetics. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked read de novo assemblies and three existing assemblies, adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flankingpoly-morphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%.


Cornell University 




  • 标题:A sorghum practical haplotype graph facilitates genome-wide imputation and cost-effective genomic prediction

  • 发表期刊:The Plant Genome

  • 发表日期:2020年1月4日

  • 主要作者单位:Cornell University

  • 使用Sentieon模块:Sentieon DNAseq


We developed a Sorghum bicolor Practical Haplotype Graph (PHG) pangenome database that stores haplotypes and variant information. The PHG called single nucleotide polymorphisms (SNPs) with 5.9% error at 0.01x coverage—only 3% higher than PHG error when calling SNPs from 8x coverage sequence. Mean prediction accuracies with PHG SNP calls range from .57–.73 and are similar to prediction accuracies obtained with genotyping-by-sequencing or targeted amplicon sequencing (rhAmpSeq) markers. This study demonstrates the use of a sorghum PHG to impute SNPs from low-coverage sequence data and shows that the PHG can unify genotype calls across multiple sequencing platforms.






标题:Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut

发表期刊:Molecular Biology and Evolution



使用Sentieon模块:Sentieon DNAseq, GVCFTyper


The origin of Persian walnut (Juglans regia) has remained mysterious because in phylogenies it occupies an unresolved position between American black walnuts and Asian butternuts. We resequenced the whole genome of 80 individuals from 19 of the 22 species of Juglans and assembled the genome of its relatives Pterocarya stenoptera and Platycarya strobilacea. Using phylogenetic-network analysis of single-copy nuclear genes, genome-wide site pattern probabilities, and Approximate Bayesian Computation, we discovered that J. regia arose as a hybrid between the American and the Asian lineages.


University of Minnesota 




标题:High-resolution crossover mapping reveals similarities anddifferences of male and female recombination in maize

发表期刊:Nature Communications


主要作者单位:University of Minnesota



Although many species exhibit large differences in CO numbers between sexes, sex-specific aspects of CO landscape are particularly poorly elucidated. Here, we conduct high-resolution CO mapping in maize. Our results show that CO numbers as well as their overall distribution are similar in male and female meioses. There are, nevertheless, dissimilarities at local scale. Our data suggest that sex-specific factors not only affect male–female CO number disparities but also cause fine differences in CO positions.