Genotyping‐by‐sequencing (GBS) was employed to construct a highly saturated genetic linkage map of a tomato (Solanum lycopersicum L.) recombinant inbred line (RIL) population, derived from a cross between cultivar NC EBR‐1 and the wild tomato S. pimpinellifolium 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 (fw2.2 and fw3.2) 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 (Lyc12.1) was verified at high resolution and its underlying causative gene was determined to be ζ‐carotene isomerase (SlZISO). The RIL population, the high resolution genetic map, and the easy‐to‐use genotyping pipeline, SNPbinner, are made publicly available.

中文翻译：

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基于序列的番茄制图种群的bin图构建，有助于高分辨率定量性状位点的检测。

通过测序进行基因分型（GBS）来构建番茄（Solanum lycopersicum L.）重组近交系（RIL）群体的高度饱和遗传连锁图谱，该图谱来自品种NC EBR-1和野生番茄S的杂交薄荷脑L.登录号LA2093。开发了将单核苷酸多态性（SNP）数据转换为基因组bin的管道，可将其用于定量性状基因座（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，采用隐藏的马尔可夫模型方法来计算重组断点，然后进行基因组仓构建。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）和基于聚合酶链反应（PCR）的标记估计的长度大1.2倍。该图用于验证和完善先前针对RIL群体中两个水果品质性状（水果重量（FW）和水果番茄红素含量（LYC））确定的QTL。两个很好描述的FW QTL（fw2.2和fw3.2）精确定位在其已知的潜在致病基因上，并且QTL间隔减少了2到10倍。LYC含量的主要QTL（Lyc12.1）已在高分辨率下验证，其潜在的致病基因被确定为ζ-胡萝卜素异构酶（SlZISO）。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。