Dataset Information

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

ABSTRACT: Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic 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%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent.

SUBMITTER: Zou C

PROVIDER: S-EPMC6972940 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Zou Cheng C Karn Avinash A Reisch Bruce B Nguyen Allen A Sun Yongming Y Bao Yun Y Campbell Michael S MS Church Deanna D Williams Stephen S Xu Xia X Ledbetter Craig A CA Patel Sagar S Fennell Anne A Glaubitz Jeffrey C JC Clark Matthew M Ware Doreen D Londo Jason P JP Sun Qi Q Cadle-Davidson Lance L

Nature communications 20200121 1

Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of ...[more]

PMID: 31964885

Similar Datasets

Project description:BackgroundBroussonetia papyrifera, B. monoica, and B. kaempferi belong to the genus Broussonetia (Moraceae). These three species hold significant economic and research values. However, few molecular markers have been effectively utilized for resource development and molecular genetic breeding of these species. Sequencing of their genomes allowed us to develop genomic markers (e.g. simple sequence repeats (SSRs)) and construct a high-density physical map.ResultsA total of 369,557, 332,627, and 276,245 SSRs were identified in 13 high-quality assembled pseudochromosomes and their unassembled scaffolds for B. papyrifera, B. monoica, and B. kaempferi, respectively. Among the identified genomic SSRs across the three species, short repeat sequences were more abundant, while long repeat sequences constituted a smaller proportion. Additionally, the predominant repeat motifs in the SSRs of the three Broussonetia species were composed of 'A' and 'T' repeats. Using B. papyrifera genome as a reference, 4,419 common SSRs were identified among these three species, while 2,048 SSRs were specific to B. kaempferi, and 4,285 SSRs were specific to B. monoica. Distribution analysis indicated a notable similarity in the distribution patterns of SSRs across the pseudochromosomes of these three species. Furthermore, of the identified SSRs, 28%, 31%, and 24% were mapped to genes in B. papyrifera, B. kaempferi, and B. monoica, respectively. Genic-mapped SSRs may regulate biological processes by influencing gene activity and protein function. To verify SSRs polymorphism, we selected 30 ones from 10,752 potentially polymorphic SSRs loci for PCR amplification among these three species, all of which were successfully amplified and exhibited polymorphism across these three species.ConclusionsThese findings are helpful for further research on the origin, evolution, and migration of Broussonetia species and also laid the foundation for the precise identification, systematic evaluation, and efficient utilization of the germplasm resources of Broussonetia species.

Project description:Next-generation sequencing technologies promise to dramatically accelerate the use of genetic information for crop improvement by facilitating the genetic mapping of agriculturally important phenotypes. The first step in optimizing the design of genetic mapping studies involves large-scale polymorphism discovery and a subsequent genome-wide assessment of the population structure and pattern of linkage disequilibrium (LD) in the species of interest. In the present study, we provide such an assessment for the grapevine (genus Vitis), the world's most economically important fruit crop. Reduced representation libraries (RRLs) from 17 grape DNA samples (10 cultivated V. vinifera and 7 wild Vitis species) were sequenced with sequencing-by-synthesis technology. We developed heuristic approaches for SNP calling, identified hundreds of thousands of SNPs and validated a subset of these SNPs on a 9K genotyping array. We demonstrate that the 9K SNP array provides sufficient resolution to distinguish among V. vinifera cultivars, between V. vinifera and wild Vitis species, and even among diverse wild Vitis species. We show that there is substantial sharing of polymorphism between V. vinifera and wild Vitis species and find that genetic relationships among V. vinifera cultivars agree well with their proposed geographic origins using principal components analysis (PCA). Levels of LD in the domesticated grapevine are low even at short ranges, but LD persists above background levels to 3 kb. While genotyping arrays are useful for assessing population structure and the decay of LD across large numbers of samples, we suggest that whole-genome sequencing will become the genotyping method of choice for genome-wide genetic mapping studies in high-diversity plant species. This study demonstrates that we can move quickly towards genome-wide studies of crop species using next-generation sequencing. Our study sets the stage for future work in other high diversity crop species, and provides a significant enhancement to current genetic resources available to the grapevine genetic community.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets