Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
Theor Appl Genet. 2011 Mar;122(4):677-86. doi: 10.1007/s00122-010-1477-4. Epub 2010 Oct 27.
Switchgrass, Panicum virgatum L., a native to the tall grass prairies in North America, has been grown for soil conservation and herbage production in the USA and recently widely recognized as a promising dedicated cellulosic bioenergy crop. A large amount of codominant molecular markers including simple sequence repeats (SSRs) are required for the construction of linkage maps and implementation of molecular breeding strategies to develop superior switchgrass cultivars. The objectives of this study were (1) to identify SSR-containing clones and to design PCR primer pairs (PPs) in SSR-enriched genomic libraries, and (2) to validate and characterize the designed SSR PPs. Five genomic SSR enriched libraries were constructed using genomic DNA of 'SL93 7 × 15', a switchgrass genotype selected in an Oklahoma State University (OSU) southern lowland breeding population. A total of 3,046 clones from four libraries enriched in (CA/TG)n, (GA/TC)n, (CAG/CTG)n and (AAG/CTT)n SSR repeats were sequenced at the OSU Core Facility. From the sequences, we isolated 1,300 unique SSR-containing clones, from which we designed 1,398 PPs using SSR Locator V.1 software. Among the designed PPs, 1,030 (73.7%) amplified reproducible and strong bands with expected fragment size, and 802 detected polymorphic alleles, in SL93 7 × 15 and 'NL94 16 × 13', two parents of one mapping population. All of the four libraries contained a high rate of perfect SSR repeat types, ranging from 62.7 to 76.2%. Polymorphism of the effective SSR markers was also tested in two lowland and two upland switchgrass cultivars, encompassing 'Alamo' and 'Kanlow', and 'Blackwell' and 'Dacotah', respectively. The developed SSR markers should be useful in genetic and breeding research in switchgrass.
柳枝稷（Panicum virgatum L.）原产于北美洲的高草草原，在美国被广泛用于土壤保持和草料生产，最近被广泛认为是一种很有前途的专用纤维素生物能源作物。为了构建连锁图谱和实施分子育种策略，以开发优良的柳枝稷品种，需要大量的共显性分子标记，包括简单重复序列（SSR）。本研究的目的是：（1）在 SSR 富集基因组文库中鉴定含 SSR 的克隆，并设计 PCR 引物对（PP）；（2）验证和表征设计的 SSR PP。利用在美国俄克拉荷马州立大学（OSU）南部低地选育群体中选择的柳枝稷基因型‘SL93 7 × 15’的基因组 DNA 构建了 5 个 SSR 富集基因组文库。对四个富含（CA/TG）n、（GA/TC）n、（CAG/CTG）n 和（AAG/CTT）n SSR 重复的文库中的 3046 个克隆进行测序，测序工作在美国俄克拉荷马州立大学核心设施完成。从这些序列中，我们分离出了 1300 个含有 SSR 的克隆，并用 SSR Locator V.1 软件为这些克隆设计了 1398 对 PP。在所设计的 PP 中，有 1030 对（73.7%）能够在 SL93 7 × 15 和一个作图群体的两个亲本之一 NL94 16 × 13 中扩增出可重复和强的预期大小片段，有 802 对检测到多态性等位基因。四个文库都含有很高比例的完美 SSR 重复类型，范围从 62.7%到 76.2%。在两个低地和两个高地柳枝稷品种‘Alamo’和‘Kanlow’，以及‘Blackwell’和‘Dacotah’中也测试了有效 SSR 标记的多态性。所开发的 SSR 标记应该对柳枝稷的遗传和育种研究有用。
