Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps
Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps
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DOI：
10.1139/g08-010
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发表时间：
2008-04-01
期刊：
影响因子：
3.1
通讯作者：
Jackson, Scott
中科院分区：
文献类型：
--
作者：
Shoemaker, Randy C.;Grant, David;Jackson, Scott
大豆Glycine max （L.）全基因组测序稳定。“威廉姆斯82”)使得整合其物理和基因图谱变得非常重要。为了促进图谱的整合，我们从包含Williams 82物理图谱的克隆的BAC端序列中筛选了3290个微卫星（ssr）。对3个作图群体进行ssr筛选。我们发现AAT和ACT基序产生的长度多态性频率最高，分别为17.2% ~ 32.3%和11.8% ~ 33.3%。其他有用的基序包括二核苷酸重复序列AG、AT和AG，其长度多态性频率分别为11.2% ~ 18.4% （AT）、12.4% ~ 20.6% （AG）和11.3% ~ 16.4% （GT）。小于16bp的重复长度通常不如40- 60bp的重复长度有用。至少在一个种群中绘制了265个ssr的遗传图谱。在265个被映射的ssr中，有60个来自尚未被放置到物理图谱中的BAC单基因。其中110个起源于以前没有已知遗传图谱位置的contigs中的bac。95个ssr来自一个或多个其他BACs已经被映射的结构中的BACs。对于这些指纹组（FPC），高比例的标记显示不一致的地图位置。介绍了一种利用大豆全基因组序列的初步4 ×组装来解决物理图谱和遗传图谱不一致的策略。
Whole-genome sequencing of the soybean (Glycine max (L.) Merr. 'Williams 82') has made it important to integrate its physical and genetic maps. To facilitate this integration of maps, we screened 3290 microsatellites (SSRs) identified from BAC end sequences of clones comprising the 'Williams 82' physical map. SSRs were screened against 3 mapping populations. We found the AAT and ACT motifs produced the greatest frequency of length polymorphisms, ranging from 17.2% to 32.3% and from 11.8% to 33.3%, respectively. Other useful motifs include the dinucleotide repeats AG, AT, and AG, with frequency of length polymorphisms ranging from 11.2% to 18.4% (AT), 12.4% to 20.6% (AG), and 11.3% to 16.4% (GT). Repeat lengths less than 16 bp were generally less useful than repeat lengths of 40-60 bp. Two hundred and sixty-five SSRs were genetically mapped in at least one population. Of the 265 mapped SSRs, 60 came from BAC singletons not yet placed into contigs of the physical map. One hundred and ten originated in BACs located in contigs for which no genetic map location was previously known. Ninety-five SSRs came from BACs within contigs for which one or more other BACs had already been mapped. For these fingerprinted contigs (FPC) a high percentage of the mapped markers showed inconsistent map locations. A strategy is introduced by which physical and genetic map inconsistencies can be resolved using the preliminary 4 x assembly of the whole genome sequence of soybean.