Jayashree B, Punna Ramu, Prasad P, Bantte Kassahun, Hash C Tom, Chandra Subhash, Hoisington David A, Varshney Rajeev K
Bioinformatics and Biometrics Unit, International Crops Research Institute for Semi-Arid Tropics, Patancheru, Andhra Pradesh, India.
In Silico Biol. 2006;6(6):607-20.
Simple sequence repeats (SSRs) or microsatellites are an important class of molecular markers for genome analysis and plant breeding applications. In this paper, the SSR distributions within ESTs from the legumes soybean (Glycine max, representing 135.86 Mb), medicago (Medicago truncatula, 121.1 Mb) and lotus (Lotus japonicus, 45.4 Mb) have been studied relative to the distributions in cereals such as sorghum (Sorghum bicolor, 98.9 Mb), rice (Oryza sativa, 143.9 Mb) and maize (Zea mays, 183.7 Mb). The relative abundance, density, composition and putative annotations of di-, tri-, tetra- and penta-nucleotide repeats have been compared and SSR containing ESTs (SSR-ESTs) have been clustered to give a non-redundant set of EST-SSRs, available in a database. Further, a subset of such candidate EST-SSRs from sorghum have been tested for their ability to detect polymorphism between Striga-susceptible, stay-green drought tolerant mapping population parent 'E 36-1' and its Striga-resistant, non-stay-green counterpart 'N13'. Primer sets for 64% of the EST-SSRs tested produced a clear and specific PCR product band and 34% of these detected scorable polymorphism between the N13 and E 36-1 parental lines. Over half of these markers have been genotyped on 94 RILs from the (N13 x E 36-1)-based mapping population, with 42 markers mapping onto the ten sorghum linkage groups. This establishes the value of this database as a resource of molecular markers for practical applications in cereal and legume genetics and breeding. The primer pairs for non-redundant EST-SSRs have been designed and are freely available through the database (http://intranet.icrisat.org/gt1/ssr/ssrdatabase.html).
简单序列重复（SSRs）或微卫星是用于基因组分析和植物育种应用的一类重要分子标记。本文研究了豆科植物大豆（Glycine max，代表135.86 Mb）、苜蓿（Medicago truncatula，121.1 Mb）和莲（Lotus japonicus，45.4 Mb）的ESTs中的SSR分布，并与高粱（Sorghum bicolor，98.9 Mb）、水稻（Oryza sativa，143.9 Mb）和玉米（Zea mays，183.7 Mb）等谷物中的分布进行了比较。比较了二核苷酸、三核苷酸、四核苷酸和五核苷酸重复的相对丰度、密度、组成和推定注释，并对含SSR的ESTs（SSR-ESTs）进行了聚类，以得到一组非冗余的EST-SSRs，可在数据库中获取。此外，对高粱中此类候选EST-SSRs的一个子集进行了测试，以检测其检测Striga敏感、持绿耐旱作图群体亲本“E 36-1”与其Striga抗性、非持绿对应亲本“N13”之间多态性的能力。所测试的64%的EST-SSRs引物对产生了清晰且特异的PCR产物条带，其中34%的引物对检测到了N13和E 36-1亲本系之间可评分的多态性。这些标记中有一半以上已在基于（N13×E 36-1）的作图群体的94个重组自交系上进行了基因分型，42个标记定位到了高粱的10个连锁群上。这确立了该数据库作为谷物和豆科植物遗传与育种实际应用分子标记资源的价值。已设计了非冗余EST-SSRs的引物对，并可通过数据库（http://intranet.icrisat.org/gt1/ssr/ssrdatabase.html）免费获取。
