SoySNP618K array:A high-resolution single nucleotide polymorphism platform as a valuable genomic resource for soybean genetics and breeding

Innovations in genomics have enabled the development of low-cost,high-resolution,single nucleotide polymorphism(SNP)genotyping arrays that accelerate breeding progress and support basic research in crop science.Here,we developed and validated the Soy SNP618 K array(618,888 SNPs)for the important crop soybean.The SNPs were selected from whole-genome resequencing data containing 2,214 diverse soybean accessions;29.34%of the SNPs mapped to genic regions representing 86.85%of the 56,044annotated high-confidence genes.Identity-by-state analyses of 318 soybeans revealed 17 redundant accessions,highlighting the potential of the Soy SNP618 K array in supporting gene bank management.The patterns of population stratification and genomic regions enriched through domestication were highly consistent with previous findings based on resequencing data,suggesting that the ascertainment bias in the Soy SNP618 K array was largely compensated for.Genome-wide association mapping in combination with reported quantitative trait loci enabled fine-mapping of genes known to influence flowering time,E2 and Gm PRR3 b,and of a new candidate gene,Gm VIP5.Moreover,genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate(>0.65).Thus,the Soy SNP618 K array is a valuable genomic tool that can be used to address many questions in applied breeding,germplasm management,and basic crop research.

Small Lymphocytic Lymphoma/Chronic Lymphocytic Leukemia with Chromothripsis in an Old Woman

Cell karyotyping in patients with small lymphocytic lymphoma/chronic lymphocytic leukemia （SLL/CLL） is not easy to success, and small genomic lesions （〈5 Mb） are not routinely detected by this method. It is likely that a complete genomic characterization of CLL requires a combination of fluorescence in situ hybridization （FISH）, single nucleotide polymorphism （SNP） array profiling for comprehensive genome-wide analysis of acquired genomic copy number aberrations （aCNAs） and loss-of-heterozygosity （LOH） in dominant clones, and karyotyping for detection of balanced translocations, isochromosomes, and marker chromosomes. SNP array analysis can reveal chromothripsis, a phenomenon by which regions of the cancer genome are shattered and recombined to generate frequent oscillations between the lower and the higher DNA copy number states. This study provided cytogenetic findings in a CLL/SLL patient with v-myc avian myelocytomatosis viral oncogene homolog （C-MYC）-amplification by FISH, in which SNP arrays detected profound genomic upheaval due to chromothripsis that may lead to malignant transformation.