Plant Genome. 2019 Mar;12(1). doi: 10.3835/plantgenome2018.02.0010.
Genotyping-by-sequencing (GBS) was employed to construct a highly saturated genetic linkage map of a tomato ( L.) recombinant inbred line (RIL) population, derived from a cross between cultivar NC EBR-1 and the wild tomato L. accession LA2093. A pipeline was developed to convert single nucleotide polymorphism (SNP) data into genomic bins, which could be used for fine mapping of quantitative trait loci (QTL) and identification of candidate genes. The pipeline, implemented in a python script named SNPbinner, adopts a hidden Markov model approach for calculation of recombination breakpoints followed by genomic bins construction. The total length of the newly developed high-resolution genetic map was 1.2-fold larger than previously estimated based on restriction fragment length polymorphism (RFLP) and polymerase chain reaction (PCR)-based markers. The map was used to verify and refine QTL previously identified for two fruit quality traits in the RIL population, fruit weight (FW) and fruit lycopene content (LYC). Two well-described FW QTL ( and ) were localized precisely at their known underlying causative genes, and the QTL intervals were decreased by two- to tenfold. A major QTL for LYC content () was verified at high resolution and its underlying causative gene was determined to be ζ (). The RIL population, the high resolution genetic map, and the easy-to-use genotyping pipeline, SNPbinner, are made publicly available.
利用测序基因型（GBS）构建了一个来自栽培品种 NC EBR-1 和野生番茄 L. accession LA2093 杂交后代的番茄重组自交系（RIL）群体的高度饱和遗传连锁图谱。开发了一个将单核苷酸多态性（SNP）数据转化为基因组 bin 的管道，可用于数量性状基因座（QTL）的精细定位和候选基因的鉴定。该管道在名为 SNPbinner 的 python 脚本中实现，采用隐马尔可夫模型方法计算重组断点，然后构建基因组 bin。新开发的高分辨率遗传图谱的总长度比以前基于限制性片段长度多态性（RFLP）和聚合酶链反应（PCR）标记估计的长度长 1.2 倍。该图谱用于验证和细化 RIL 群体中两个果实品质性状的先前鉴定的 QTL，果实重量（FW）和果实番茄红素含量（LYC）。两个描述良好的 FW QTL（和）被精确定位在其已知的潜在致病基因上，并且 QTL 间隔缩小了两到十倍。LYC 含量的一个主要 QTL（）在高分辨率下得到验证，其潜在的致病基因被确定为 ζ（）。RIL 群体、高分辨率遗传图谱和易于使用的基因分型管道 SNPbinner 已公开提供。
