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Title: Heterozygous mapping strategy (HetMapps)for high resolution genotyping-by-sequencing markers: a case study in grapevine

Author
item HYMA, KATIE - Cornell University
item BARBA, PAOLA - Cornell University
item WANG, MINGHUI - Cornell University
item Londo, Jason
item ACHARYA, CHARLOTTE - Cornell University
item MITCHELL, SHARON - Cornell University
item SUN, QI - Cornell University
item REISCH, BRUCE - Cornell University
item Cadle-Davidson, Lance

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/21/2015
Publication Date: 8/5/2015
Publication URL: http://doi:10.1371/journal/pone.0134880
Citation: Hyma, K., Barba, P., Wang, M., Londo, J.P., Acharya, C., Mitchell, S., Sun, Q., Reisch, B., Cadle Davidson, L.E. 2015. Heterozygous mapping strategy (HetMapps) for high resolution genotyping-by-sequencing markers: a case study in grapevine. PLoS One. 10(8):e0134880. doi: 10.1371/journal/pone.0134880.

Interpretive Summary: Genotyping by sequencing (GBS) is a new genetic tool to generate high-resolution genetic maps at a low cost. Previously, the technology has not worked well in genetically diverse organisms, like grapes and other specialty crops. To address this, researchers developed a publicly available tool called HetMappS. We used HetMappS to make high resolution maps for five grape families, with 5- to 20-fold more markers than previous grape maps. The genetic order of markers correlated with the grape reference genome. Flower sex was mapped in three of the families, and correctly localized to the sex locus in all cases. HetMappS could have wide application for mapping in diverse species, and its flexible design provides opportunities to adapt portions of HetMappS to other family types, genotyping technologies, or applications.

Technical Abstract: Genotyping by sequencing (GBS) provides opportunities to generate high-resolution genetic maps at a low per-sample genotyping cost, but missing data and under-calling of heterozygotes complicate the creation of GBS linkage maps for highly heterozygous species. To overcome these issues, we developed a publicly available modular approach called HetMappS, which functions independently of parental genotypes and corrects for genotyping errors associated with heterozygosity. For linkage group formation, HetMappS includes both a reference genome-guided synteny pipeline as well as a reference-independent de novo pipeline. The de novo pipeline can be utilized for under-characterized or high diversity families that lack an appropriate reference. We applied HetMappS in four half-sib F1 families involving genetically diverse Vitis spp., using both synteny and de novo pipelines. Starting with at least 116,466 putative SNPs per family, the HetMappS pipelines identified 10,440 to 15,464 phased pseudo-testcross (Pt) markers and generated high-confidence linkage maps. The Pt marker density exceeded biological resolution in all cases, though depending on the family size and pipeline, up to 5,560 non-redundant markers were used to generate parental maps ranging from 1,047 cM to 1,696 cM. The number of markers used was strongly correlated with number of progeny in both de novo and synteny maps (r = 0.92 and 0.91, respectively). Both pipelines generated similar genetic maps, and genetic order was strongly correlated with the reference genome physical order in all cases. Additionally, independently created genetic maps from shared parents exhibited nearly identical results. Flower sex was mapped in three of the families, and correctly localized to the sex locus in all cases. The HetMappS pipeline could have wide application for linkage mapping in highly heterozygous species, and its modularity provides opportunities to adapt portions of the pipeline to other family types, genotyping technologies or applications.