Development of 1,030 genomic SSR markers in switchgrass
Development of 1,030 genomic SSR markers in switchgrass
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DOI：
10.1007/s00122-010-1477-4
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发表时间：
2011-03-01
影响因子：
5.4
通讯作者：
Wu, Y. Q.
中科院分区：
文献类型：
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作者：
Wang, Y. W.;Samuels, T. D.;Wu, Y. Q.
柳枝稷，柳枝稷，原产于北美的高草草原，在美国已被种植用于土壤保护和牧草生产，最近被广泛认为是一种有前途的专用纤维素生物能源作物。为了构建柳枝稷遗传连锁图谱和进行上级柳枝稷分子育种，需要大量的包括SSR在内的共显性分子标记。本研究的目的是（1）在富含SSR的基因组文库中鉴定含SSR的克隆并设计PCR引物对（PP），以及（2）验证和表征所设计的SSR PP。使用“SL 93 7 x 15”的基因组DNA构建了5个基因组SSR富集文库，“SL 93 7 x 15”是在俄克拉荷马州州立大学（OSU）南部低地育种群体中选择的柳枝稷基因型。在OSU Core Facility对来自4个富含（CA/TG）n、（GA/TC）n、（CAG/CTG）n和（AAG/CTT）n SSR重复序列的文库的3，046个克隆进行了测序。从序列中，我们分离出1,300个独特的含SSR的克隆，从中我们使用SSR引物V.1软件设计了1,398个PP。在所设计的PP中，在同一作图群体的两个亲本SL 93 7 × 15和NL 94 16 × 13中，有1,030个（73.7%）扩增出了具有预期片段大小的可重复的强条带，802个检测到多态性等位基因。这4个文库的SSR重复类型完整率都很高，为62.7%~ 76.2%。利用有效SSR标记对两个低地和两个高地柳枝稷品种（分别包括“Alamo”和“Kanlow”，“Blackwell”和“Dacotah”）进行了多态性分析。这些SSR标记为柳枝稷的遗传和育种研究提供了有用的分子标记。
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 x 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 x 15 and 'NL94 16 x 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.