Development and characterization of cDNA library based novel EST-SSR marker in radish (Raphanus sativus L.)

• Published in: Scientia horticulturae Vol. 140; pp. 164 - 172
• Main Authors: Jiang, Lina, Wang, Liangju, Liu, Liwang, Zhu, Xianwen, Zhai, Lulu, Gong, Yiqin
• Format: Journal Article
• Language: English
• Published: Amsterdam Elsevier B.V 01.06.2012; Elsevier
• Subjects: Agronomy. Soil science and plant productions; Biological and medical sciences; Expressed sequenced tag (EST); Fundamental and applied biological sciences. Psychology; Generalities. Genetics. Plant material; Genetic diversity analysis; Genetic resources, diversity; Genetics and breeding of economic plants; Plant material; Radish (Raphanus sativus L.); Simple sequence repeats (SSRs); Transferability; Expressed sequenced tag (EST); Genetic diversity analysis; Transferability; Radish (Raphanus sativus L.); Simple sequence repeats (SSRs); Horticulture; Genetic marker; Genetic diversity; Gene library; Raphanus sativus; Vegetable crop; Cruciferae; Dicotyledones; Microsatellite DNA; Angiospermae; Spermatophyta; Radish; Expressed sequence tag
• ISSN: 0304-4238; 1879-1018
• DOI: 10.1016/j.scienta.2012.04.012

► A full-length radish cDNA library was constructed and lots of ESTs were obtained. ► A set of 179 SSRs were detected and well characterized. ► A total of 110 primer pairs could generate unambiguous amplification products. ► Newly developed SSR markers were successfully used for genetic diversity analysis. ► High transferability in Brassicaceae was detected in these EST-SSR markers. To develop novel expressed sequence tags-simple sequence repeats (EST-SSR) markers in radish, a taproot cDNA library was constructed. A total of 10,052 clones from the cDNA library were sequenced and a large number of high quality ESTs was generated. Among these ESTs, a set of 179 SSRs, distributing in 176 unigene sequences, were detected, of which, 50.84% were di-nucleotide, followed by tri- (29.61%), hexa- (9.49%), penta- (6.15%) and tetra-nucleotide (3.91%) repeats, respectively. GA/TC (25.69%) was the most frequent repeat type of all repeat types. Out of 125 primer pairs designed, 110 (88%) could generate unambiguous amplification products. Totally 28 EST-SSR primer pairs were selected for genetic diversity analysis in 32 radish genotypes. It was found that two to seven alleles could be detected with a mean of 3.5 per primer pair and the polymorphism information content (PIC) values of these primers ranged from 0.000 to 0.825 with an average of 0.500. The genotype data were analyzed with NTSYS-pc software, which grouped the 32 accessions into three main clusters at the similarity index value of 0.60, which was mainly in accordance with the different biological characterizations of the accessions. In addition, the 28 EST-SSR primer pairs were further used to test the transferability on 12 accessions from three genera of Raphanus, Brassica and Arabidopsis in Brassicaceae. The results showed that 18 primer pairs (64.2%) could produce target PCR bands in the 12 accessions. The EST-SSR markers developed herein represented a valuable resource for the genetic diversity analysis, genetic mapping and marker-assisted selection in radish.