Introduction

To meet the challenges in the increasing food demands and diverse breeding targets in plants and animals, molecular markers have been widely used to reveal polymorphism at the DNA level, and these markers have been further applied to identify marker-trait associations, marker-assisted selection, genomic selection, germplasm characterization, etc. Continuous endeavors have been made to decrease the cost, time and labor in genotyping, and to increase the marker density and accuracy at the same time. Before high-throughput sequencing was available, polymorphism of simple sequence repeats (SSR) and restriction fragment length polymorphism (RFLP) were the most widely used genetic markers. Because these PCR based technologies are labor intensive and time-consuming, and because the number of polymorphism sites across the genome is limited, these methods are only capable of genotyping hundreds to thousands of markers at a time. High-throughput sequencing, mainly capturing the polymorphism in the single nucleotide polymorphisms (SNPs), has increased the efficiently of genotyping by thousands of times. 
Grapes (Vitis vinifera subsp. vinifera) are among the most important horticultural crops in the world. The Vitis genus is an ideal model system to study marker design for the following reasons: (1) The genetic background is highly diverse in the genus Vitis. This genus, which contains approximately sixty species, diverged around 28 million years ago. It is widely distributed in Asia, Europe, North and South America. These locally adapted wild species provide breeders with an abundant resource of germplasm to improve biotic and abiotic tolerance and resistance in cultivated grapes. To make use of wild species, molecular markers that can be used across diverse wild species are essential to the breeding practice. (2) Grapes are a highly heterozygous diploid species. Many economically important plant are highly heterozygous species, including apples\cite{Bianco2016}, pears \cite{wu2013genome}, raspberries \cite{Graham2004}, bananas,  sweet oranges \cite{Jiao2013}, Cassava\cite{Perea2016}, wild potatoes \cite{Leisner2018}, sweet potatoes\cite{Si2016}, and many woody species . Genotyping for highly heterozygous species is challenging in general due to their high genetic diversity and fast linkage disequilibrium decay. The lessons we learn in the Vitis genus can be applied to these highly heterozygous species. (3) In crops, the grape genome size is comparatively small (maize is 2 Gbp, while grape is 450 Mbp). 
Much progress has been made to address the difficulties in genotyping highly diverse and heterozygous species using high-through put sequencing. Resequencing the entire genome is too costly and the marker density exceeds the needs of genetic studies thousand of times. To decrease the genome complexity, restriction enzymes are used to restrict the sequencing in regions that can be digested by the restriction enzymes. However, the missing rate and  XX is high in GBS. One solution has been proposed to further enrich the target region by a capture array \cite{Uitdewilligen2013} .
For example, one approach is that enriching the target region by a capture array and then conduct \cite{Uitdewilligen2013}genotyping-by-sequencing .
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