Qu Jingtao, Liu Jian
Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
BMC Res Notes. 2013 Oct 7;6:403. doi: 10.1186/1756-0500-6-403.
Maize (Zea mays ssp. mays L.), as the most important plant for staple food of several million people, animal feed and bioenergy productions, is widely cultivated around the world. Simple sequence repeats (SSRs) are widely used as molecular markers in maize genetics and breeding, but only two thousands pairs of SSRs have been published currently, which hardly satisfies for the increasing needs of geneticists and breeders. Furthermore, the increasing studies have revealed that SSRs also play a vital role in functional regulation and evolution. It is fortunate that the development of sequencing technology and bio-software provides the basis for characterization and development of SSRs in maize.
In this study, MISA was applied to identify overall 179,681 SSRs in maize reference genome B73, with an average distance of 11.46 Kbp. Their distributions within the genome in different regions were non-random, and the density followed in a descending order of UTR, promotor, intron, intergenic and CDS. Meanwhile, 82,694 (46.02%) SSRs with unique flanking sequences were selected, and then applied to analyze the polymorphism of next-generation sequencing data from 345 maize inbred lines and data from maize reference genome B73. There were 58,946 SSRs with length information results in ten or more than ten genomes, accounting for 71.28% of SSRs with unique flanking sequences, while 55,621 SSRs had polymorphism, with an average PIC value of 0.498. 250 pairs of SSR primers in different genomic regions covering all maize chromosomes were randomly chosen for the experimental validation, with an average PIC value of 0.63 in 11 elite maize inbred lines.
Our work provided insight into the non-random distribution spatterns and compositions of SSRs in different regions of maize genome, and also developed more polymorphic SSR markers using next-generation sequencing reads. The genome-wide SSRs polymorphism markers could be useful for genetic analysis and marker-assisted selection in breeding practice, and it was also proved to be high efficient for molecular marker development via next-generation sequencing reads.
玉米（Zea mays ssp. mays L.）作为数百万人主食、动物饲料和生物能源生产的最重要植物，在全球广泛种植。简单序列重复（SSRs）在玉米遗传育种中被广泛用作分子标记，但目前仅公布了两千对SSRs，这几乎无法满足遗传学家和育种者日益增长的需求。此外，越来越多的研究表明，SSRs在功能调控和进化中也起着至关重要的作用。幸运的是，测序技术和生物软件的发展为玉米中SSRs的表征和开发提供了基础。
在本研究中，利用MISA在玉米参考基因组B73中鉴定出总共179,681个SSRs，平均间距为11.46 Kbp。它们在基因组不同区域的分布是非随机的，密度顺序为UTR、启动子、内含子、基因间区域和CDS依次递减。同时，选择了82,694个（46.02%）具有独特侧翼序列的SSRs，然后用于分析来自345个玉米自交系的下一代测序数据以及玉米参考基因组B73的数据。有58,946个具有长度信息的SSRs在十个或十个以上基因组中有结果，占具有独特侧翼序列的SSRs的71.28%，而55,621个SSRs具有多态性，平均PIC值为0.498。随机选择覆盖所有玉米染色体的不同基因组区域的250对SSRs引物进行实验验证，在11个优良玉米自交系中的平均PIC值为0.63。
我们的工作深入了解了玉米基因组不同区域SSRs的非随机分布模式和组成，并且利用下一代测序读数开发了更多多态性SSRs标记。全基因组SSRs多态性标记可用于育种实践中的遗传分析和标记辅助选择，并且也证明了通过下一代测序读数进行分子标记开发是高效的。
