Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine.
Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine.
复制标题
DOI：
10.1371/journal.pone.0134880
复制
发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Cadle-Davidson L
中科院分区：
文献类型：
--
作者：
Hyma KE;Barba P;Wang M;Londo JP;Acharya CB;Mitchell SE;Sun Q;Reisch B;Cadle-Davidson L
通过测序进行基因分型（GBS）提供了以低基因分型成本生成高分辨率遗传图谱的机会，但是对于高度杂合的物种，缺失数据和杂合子低识别使GBS遗传图谱的创建复杂化。为了克服这些问题，我们开发了一种公开可用的模块化方法，称为HetMappS，其功能独立于父母基因型，并纠正与杂合性相关的基因分型错误。对于连接基团形成，HetMappS包括参考引导的同线性管道和参考独立的从头管道。从头管道可用于缺乏适当参考的特征不足或高度多样性的家庭。我们在涉及遗传多样性葡萄属物种的五个半同胞F1家族中应用了两个HetMappS管道。从每个家族至少116，466个推定的SNP开始，HetMappS管道确定了10，440至17，267个阶段性伪测交（Pt）标记并生成了高置信度地图。在所有情况下，Pt标记密度都超过了交叉分辨率;使用多达5，560个非冗余标记来生成范围从1，047 cM到1，696 cM的亲本图谱。所使用的标记的数量与家族大小在从头和同线性地图（r = 0.92和0.91，分别）。等位基因和标签频率之间的比较表明，许多标记在串联重复序列，并映射为单位点，而标记在两个以上的重复区域被删除在地图策展。这两个管道产生了相似的遗传图谱，在所有情况下，遗传顺序与参考基因组物理顺序密切相关。从共同的父母独立创建的遗传图谱显示出几乎相同的结果。花性别映射在三个家庭和正确定位到已知的性别位点在所有情况下。HetMappS管道可以广泛应用于高度杂合物种的遗传作图，并且其模块化提供了使管道的部分适应其他家族类型、基因分型技术或应用的机会。
Genotyping by sequencing (GBS) provides opportunities to generate high-resolution genetic maps at a low genotyping cost, but for highly heterozygous species, missing data and heterozygote undercalling complicate the creation of GBS genetic maps. 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-guided synteny pipeline and 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 both HetMappS pipelines in five half-sib F1 families involving genetically diverse Vitis spp. Starting with at least 116,466 putative SNPs per family, the HetMappS pipelines identified 10,440 to 17,267 phased pseudo-testcross (Pt) markers and generated high-confidence maps. Pt marker density exceeded crossover resolution in all cases; 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 family size in both de novo and synteny maps (r = 0.92 and 0.91, respectively). Comparisons between allele and tag frequencies suggested that many markers were in tandem repeats and mapped as single loci, while markers in regions of more than two repeats were removed during map curation. Both pipelines generated similar genetic maps, and genetic order was strongly correlated with the reference genome physical order in all cases. Independently created genetic maps from shared parents exhibited nearly identical results. Flower sex was mapped in three families and correctly localized to the known sex locus in all cases. The HetMappS pipeline could have wide application for genetic mapping in highly heterozygous species, and its modularity provides opportunities to adapt portions of the pipeline to other family types, genotyping technologies or applications.