Improving linkage analysis in outcrossed forest trees -: an example from Acacia mangium
Improving linkage analysis in outcrossed forest trees -: an example from Acacia mangium
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DOI：
10.1007/s00122-001-0820-1
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发表时间：
2002-05-01
影响因子：
5.4
通讯作者：
Moran, GF
中科院分区：
文献类型：
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作者：
Butcher, PA;Williams, ER;Moran, GF
森林树木的绘图通常依赖于远交系谱，其中遗传分离是父母双方减数分裂重组的结果。当前可用的作图包对于异型杂交谱系来说并不是最佳的，因为它们要么无法排序阶段模糊数据，要么在对连锁群内的基因座进行排序时仅使用成对信息。已经开发了一个新的软件包 OUTMAP，用于绘制异交树中的共显性基因座。使用来自马占相思两个谱系的连锁数据生成的图谱的比较表明，使用 OUTMAP 生成的标记顺序始终比 JOINMAP 生成的标记顺序具有更高的可能性。此外，可以更有效地生成图谱，无需重新编码数据或对成对重组分数进行详细研究，而这是使用 JOINMAP 选择最佳标记顺序所必需的。标记之间的距离通常与 JOINMAP 计算的距离不同，导致估计的基因组长度增加。 OUTMAP 可与所有分离类型一起使用，以确定阶段并计算替代标记顺序的可能性，并可选择三种优化方法。
Mapping in forest trees generally relies on outbred pedigrees in which genetic segregation is the result of meiotic recombination from both parents. The currently available mapping packages are not optimal for outcrossed pedigrees as they either cannot order phase-ambiguous data or only use pairwise information when ordering loci within linkage groups. A new package, OUTMAP, has been developed for mapping codominant loci in outcrossed trees. A comparison of maps produced using linkage data from two pedigrees of Acacia mangium Willd demonstrated that the marker orders produced using OUTMAP were consistently of higher likelihood than those produced by JOINMAP. In addition, the maps were produced more efficiently, without the need for recoding data or the detailed investigation of pairwise recombination fractions which was necessary to select the optimal marker order Using JOINMAP. Distances between markers often varied from those calculated by JOINMAP, resulting in an increase in the estimated genome length. OUTMAP can be used with all segregation types to determine phase and to calculate the likelihood of alternative marker orders, with a choice of three optimisation methods.