Genetic mapping of EST-SSRs, SSR and InDels to improve saturation of genomic regions in a previously developed sunflower map

Paola Talia¹ · Verónica Nishinakamasu¹ · Horacio Esteban Hopp^{1, 2} · Ruth Amelia Heinz^{1, 2} · Norma Paniego*¹

¹Instituto de Biotecnología, CICVyA, CNIA, INTA Castelar, Buenos Aires, Argentina
²Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina

*Corresponding autor: npaniego@cnia.inta.gov.ar

Financial support: This work was supported by INTA-AEBIO1330 /241331, and granted from the Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT/ PAV2004-137), Argentina.

Keywords: EST-SSR, InDels, linkage map, SSR, sunflower.

In order to saturate a sunflower genetic map and facilitate marker-assisted selection (MAS) breeding for stress response, it is necessary to enhance map saturation with molecular markers localized in linkage groups associated to genomic regions involved in these traits. This work describes the identification and characterization of 1,134 simple sequence repeat (SSR) containing expressed sequence tags (ESTs) from unigenes available databases. Twelve of these functional markers as well as 41 public SSR markers were successfully localized in linkage groups, thus contributing to the saturation of specific regions on a reference genetic-linkage-map derived from recombinant inbred lines (RIL) mapping population from the cross between PAC2 x RHA266 lines. The enriched map includes 547 markers (231 SSR, 9 EST-SSR, 3 insertions/deletions (InDels) and 304 amplified fragment length polymorphisms (AFLPs) distributed in 17 linkage groups (LG), spanning genetic size to 1,942.3 cM and improving its mean density to 3.6 cM per locus. As consequence, no gaps longer than 13.2 cM remain uncovered throughout the entire map, which increases the feasibility of detecting genes or traits of agronomic importance in sunflower.