Joint QTL Linkage Mapping for Multiple-Cross Mating Design Sharing One Common Parent

BackgroundNested association mapping (NAM) is a novel genetic mating design that combines the advantages of linkage analysis and association mapping. This design provides opportunities to study the inheritance of complex traits, but also requires more advanced statistical methods. In this paper, we present the detailed algorithm of a QTL linkage mapping method suitable for genetic populations derived from NAM designs. This method is called joint inclusive composite interval mapping (JICIM). Simulations were designed on the detected QTL in a maize NAM population and an Arabidopsis NAM population so as to evaluate the efficiency of the NAM design and the JICIM method. Principal FindingsFifty-two QTL were identified in the maize population, explaining 89% of the phenotypic variance of days to silking, and nine QTL were identified in the Arabidopsis population, explaining 83% of the phenotypic variance of flowering time. Simulations indicated that the detection power of these identified QTL was consistently high, especially for large-effect QTL. For rare QTL having significant effects in only one family, the power of correct detection within the 5 cM support interval was around 80% for 1-day effect QTL in the maize population, and for 3-day effect QTL in the Arabidopsis population. For smaller-effect QTL, the power diminished, e.g., it was around 50% for maize QTL with an effect of 0.5 day. When QTL were linked at a distance of 5 cM, the likelihood of mapping them as two distinct QTL was about 70% in the maize population. When the linkage distance was 1 cM, they were more likely mapped as one single QTL at an intermediary position. ConclusionsBecause it takes advantage of the large genetic variation among parental lines and the large population size, NAM is a powerful multiple-cross design for complex trait dissection. JICIM is an efficient and specialty method for the joint QTL linkage mapping of genetic populations derived from the NAM design.

背景 嵌套关联作图（Nested association mapping, NAM）是一种兼具连锁分析与关联作图优势的新型遗传交配设计。该设计为解析复杂性状的遗传规律提供了可行路径，但同时也对统计分析方法提出了更高要求。本文提出了一种适用于NAM设计衍生遗传群体的数量性状位点（Quantitative Trait Locus, QTL）连锁作图详细算法，即联合包容性复合区间作图（joint inclusive composite interval mapping, JICIM）。本研究通过在玉米NAM群体与拟南芥NAM群体中，针对已检测到的QTL开展模拟实验，以评估NAM设计与JICIM方法的应用效能。

主要研究结果 本研究在玉米群体中共鉴定到52个QTL，可解释抽丝天数89%的表型变异；在拟南芥群体中鉴定到9个QTL，可解释开花时间83%的表型变异。模拟实验结果表明，上述已鉴定QTL的检测效力整体较高，对于效应值较大的QTL尤为显著。对于仅在单个家系中表现出显著效应的稀有QTL，在玉米群体中，效应值为1天的QTL在5 cM置信区间内的正确检测率约为80%；而在拟南芥群体中，效应值为3天的QTL的正确检测率与之相近。对于效应值较小的QTL，其检测效力会出现衰减：例如玉米群体中效应值为0.5天的QTL，检测率约为50%。当两个QTL的连锁距离为5 cM时，在玉米群体中约有70%的概率将其识别为两个独立的QTL；若连锁距离为1 cM，则更倾向于将二者作为位于中间位置的单个QTL进行定位。

研究结论 由于NAM设计充分利用了亲本间丰富的遗传变异与较大的群体规模，因此是一种用于复杂性状解析的高效多亲本交配设计。JICIM是针对NAM设计衍生遗传群体开展联合QTL连锁作图的高效专用方法。