Shultz Jeffry L, Kazi Samreen, Bashir Rabia, Afzal Jawaad A, Lightfoot David A
Genomics Core Facility and Center of Excellence in Soybean Research, Teaching and Outreach, and Department of Plant, Soil and Agricultural Systems, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA.
Theor Appl Genet. 2007 Apr;114(6):1081-90. doi: 10.1007/s00122-007-0501-9. Epub 2007 Feb 8.
The composite map of soybean shared among Soybase, LIS and SoyGD (March 2006) contained 3,073 DNA markers in the "Locus" class. Among the markers were 1,019 class I microsatellite markers with 2-3 bp simple sequence repeats (SSRs) of >10 iterations (BARC-SSR markers). However, there were few class II SSRs (2-5 bp repeats with <10 iterations; mostly SIUC-Satt markers). The aims here were to increase the number of classes I and II SSR markers and to integrate bacterial artificial chromosome (BAC) clones onto the soybean physical map using the markers. Used was 10 Mb of BAC-end sequence (BES) derived from 13,473 reads from 7,050 clones constituting minimum tile path 2 of the soybean physical map ( http://www.soybeangenome.siu.edu ; SoyGD). Identified were 1,053 1-6 bp motif, repeat sequences, 333 from class I (>10 repeats) and 720 from class II (<10 repeats). Potential markers were shown on the MTP_SSR track at Gbrowse. Primers were designed as 20-24 bp oligomers that had Tm of 55 +/- 1 C that would generate 100-500 bp amplicons. About 853 useful primer pairs were established. Motifs were not randomly distributed with biases toward AT rich motifs. Strong biases against the GC motif and all tetra-nucleotide repeats were found. The markers discovered were useful. Among the first 135 targeted for use in genetic map improvement about 60% of class II markers and 75% of class I markers were polymorphic among on the parents of four recombinant inbred line (RIL) populations. Many of the BES-based SSRs were located on the soybean genetic map in regions with few BARC-SSR markers. Therefore, BES-based SSRs represent useful tools for genetic map development in soybean. New members of a consortium to map the markers in additional populations are invited.
Soybase、LIS和SoyGD（2006年3月）共享的大豆复合图谱在“基因座”类别中包含3073个DNA标记。这些标记中有1019个I类微卫星标记，具有2 - 3个碱基对的简单序列重复（SSR），重复次数超过10次（BARC - SSR标记）。然而，II类SSR很少（2 - 5个碱基对重复，重复次数小于10次；大多是SIUC - Satt标记）。这里的目标是增加I类和II类SSR标记的数量，并使用这些标记将细菌人工染色体（BAC）克隆整合到大豆物理图谱上。使用了来自大豆物理图谱最小拼接路径2的7050个克隆的13473条读数所衍生的10 Mb BAC末端序列（BES）（http://www.soybeangenome.siu.edu；SoyGD）。鉴定出1053个1 - 6个碱基基序的重复序列，其中333个来自I类（重复次数大于10次），720个来自II类（重复次数小于10次）。潜在标记显示在Gbrowse的MTP_SSR轨迹上。引物设计为20 - 24个碱基的寡聚物，其熔解温度为55±1℃，可产生100 - 500 bp的扩增子。大约建立了853个有用的引物对。基序并非随机分布，偏向于富含AT的基序。发现对GC基序和所有四核苷酸重复序列有强烈偏向。发现的这些标记很有用。在最初用于改进遗传图谱的135个标记中，四个重组自交系（RIL）群体亲本间约60%的II类标记和75%的I类标记具有多态性。许多基于BES的SSR位于大豆遗传图谱上BARC - SSR标记较少的区域。因此，基于BES的SSR是大豆遗传图谱开发的有用工具。欢迎新成员加入联盟，以便在更多群体中对这些标记进行定位。
