Development of SSR markers derived from SSR-enriched genomic library of eggplant (Solanum melongena L.)

Abstract

Eggplant (Solanum melongena L.), also known as aubergine or brinjal, is an important vegetable in many countries. Few useful molecular markers have been reported for eggplant. We constructed simple sequence repeat (SSR)-enriched genomic libraries in order to develop SSR markers, and sequenced more than 14,000 clones. From these sequences, we designed 2,265 primer pairs to flank SSR motifs. We identified 1,054 SSR markers from amplification of 1,399 randomly selected primer pairs. The markers have an average polymorphic information content of 0.27 among eight lines of S. melongena. Of the 1,054 SSR markers, 214 segregated in an intraspecific mapping population. We constructed cDNA libraries from several eggplant tissues and obtained 6,144 expressed sequence tag (EST) sequences. From these sequences, we designed 209 primer pairs, 7 of which segregated in the mapping population. On the basis of the segregation data, we constructed a linkage map, and mapped the 236 segregating markers to 14 linkage groups. The linkage map spans a total length of 959.1 cM, with an average marker distance of 4.3 cM. The markers should be a useful resource for qualitative and quantitative trait mapping and for marker-assisted selection in eggplant breeding.

Genetic mapping of a major dominant gene for resistance to Ralstonia solanacearum in eggplant

“…A panel of 835 microsatellite (SSR) primers designed from eggplant (Nunome et al 2003a(Nunome et al , 2009Stagel et al 2008) as well as tomato sequences (SGN) was screened for polymorphism on the mapping parents. A total of 34 SSRs showing polymorphism between the two parents were used to genotype the RIL population.…”

“…Amplified fragment length polymorphism (AFLP) is a good technique for genotyping in such cases, because it generates a large number of genome-wide polymorphic markers. Simple sequence repeat (SSR) markers from eggplant genic and genomic libraries are also described as polymorphic within eggplant germplasm (Nunome et al 2009;Nunome et al 2003a, b). These markers present the advantage of often being transferable between related species.…”

High resolution map of eggplant (Solanum melongena) reveals extensive chromosome rearrangement in domesticated members of the Solanaceae

“…The first molecular linkage map of the eggplant genome was generated by Nunome et al (1998) from an intraspecific cross between the S. melongena cultivars EPL-1 and WCGR112-9. Since that initial effort, several more maps based on the same population and including random amplified polymorphic DNA (RAPD), AFLP markers, and/or simple sequence repeat (SSR) markers have been published (Nunome et al 2001(Nunome et al , 2009). The most recent of these maps (Nunome et al 2009) contains a total of 236 SSR markers encompassing 959 cM and 14 linkage groups with an average of one marker every 4.3 cM.…”

“…Since that initial effort, several more maps based on the same population and including random amplified polymorphic DNA (RAPD), AFLP markers, and/or simple sequence repeat (SSR) markers have been published (Nunome et al 2001(Nunome et al , 2009). The most recent of these maps (Nunome et al 2009) contains a total of 236 SSR markers encompassing 959 cM and 14 linkage groups with an average of one marker every 4.3 cM. Because of the tendency of SSR markers to reside in heterochromatic regions, portions of the genome are not covered by this map.…”

Interspecific Transferability of Watermelon EST-SSRs Assessed by Genetic Relationship Analysis of Cucurbitaceous Crops

“…식물의 유전적 다양성 및 유연관계 분 석을 위해 활용되어 온 분자표지로서는 isozyme (Akashi et al, 2002;Knerr et al, 1989), restriction fragment length polymorphsim(RFLP) (Dijkhuizen et al, 1996;Yi et al, 2006), random amplified polymorphic DNA(RAPD) (Ferriol et al, 2003b;Horejsi et al, 1999;Lee et al, 2003;Levi et al, 2001;Zhuang et al, 2004), amplified fragment length polymorphism (AFLP) (Ferriol et al, 2003a;Garcia-Mas et al, 2000), simple sequence repeat(SSR) (Chung et al, 2006;Katzir et al, 1996;Kwon et al, 2010;Ritschel et al, 2004) 등의 사례들이 있다. 특히 최근에 많이 사용되고 있는 expressed sequence tags (ESTs)은 발현된 유전자 부위에서 나타난 mRNA의 역전사 를 통해 염기서열이 밝혀진 cDNA의 한 부분으로서 가지 (Nunome et al, 2009), 고추 (Yi et al, 2006), 토마토 (D'Agostino et al, 2007), 장미 (Park et al, 2010) …”