Identification of informative SSR markers capable of distinguishing hybrid rice parental lines and their utilization in seed purity assessment
Identification of informative SSR markers capable of distinguishing hybrid rice parental lines and their utilization in seed purity assessment
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DOI：
10.1007/s10681-007-9630-0
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发表时间：
2008-09-01
期刊：
影响因子：
1.9
通讯作者：
Sarma, N. P.
中科院分区：
文献类型：
--
作者：
Sundaram, R. M.;Naveenkumar, B.;Sarma, N. P.
为了鉴定能够区分水稻杂交种亲本的SSR标记，我们利用一组均匀分布在水稻基因组上的48个超多态性SSR标记对10个细胞质雄性不育系和恢复系沿着10个印度水稻品种进行了鉴定。所有SSR标记均表现出多态性，共扩增出163个等位基因，平均每个位点扩增出3.36 ± 1.3个等位变异。27个SSR标记显示扩增的等位基因，这是非常具体的和独特的特定的亲本线，而不是在任何其他水稻基因型扩增测试。通过多重PCR，SSR标记组合，是唯一的一个特定的亲本系或杂交种也被确定。利用10个SSR标记可以将印度杂交稻及其亲本沿着区分开来。为了有效地利用这些SSR标记检测亲本系中的杂质，设计了涉及20 × 20生长矩阵的二维批量DNA取样策略，并用于检测流行CMS系IR 58025 A的种子批中的杂质。我们还设计了一种多重PCR策略，包括使用2-3个标记进行杂交种子纯度评估的单管分析，并证明其在准确检测杂交种中杂质方面优于单一标记分析。讨论了亲本和杂种特异性SSR标记的影响以及以经济有效的方式利用信息丰富的SSR标记检测污染物的策略。
With the objective of identifying SSR markers that can distinguish parental lines of rice hybrids, we characterized 10 each of cytoplasmic male sterile (CMS) and restorer (R) lines along with 10 popular Indian rice varieties using a set of 48 hyperpolymorphic SSRs distributed uniformly across the rice genome. All the SSR markers were polymorphic, amplifying a total of 163 alleles, with an average of 3.36 +/- 1.3 allelic variants per locus. Twenty-seven SSR markers showed amplification of an allele, which was very specific and unique to a particular parental line and not amplified in any other rice genotype tested. Through multiplex PCR, SSR marker combinations that were unique to a particular parental line or hybrid were also identified. With a set of 10 SSR markers, all the public bred Indian rice hybrids along with their parental lines could be clearly distinguished. To utilize these SSR markers effectively for detection of impurities in parental lines, a two dimensional bulked DNA sampling strategy involving a 20 x 20 grow-out matrix has been designed and used for detection of contaminants in a seed-lot of the popular CMS line IR58025A. We have also designed a multiplex PCR strategy involving single tube analysis using 2-3 markers for hybrid seed purity assessments and demonstrate its superiority over single marker analysis in accurate detection of impurities in hybrids. Implications of parental and hybrid specific SSR markers and strategies to utilize the informative SSR markers for detection of contaminants in a cost effective manner are discussed.