Advancement of cotton (Gossypium) radiation hybrid mapping tools

Abstract

The assembly of a robust structural genomics system requires the development and integration of multiple types of genome maps. This research focused on the development of a relatively new means of plant genome mapping, radiation hybrid mapping, for use in cotton genomics. Simple sequence repeat markers were genotyped onto an existing wide-cross whole-genome radiation hybrid panel for genome mapping of the Gossypium barbadense line ‘3-79’. A new mapping panel was created for genome mapping of the G. hirsutum line ‘TM-1’. Carthagene software was compared to RHMAP and found to be superior in most regards. A total of 92 simple sequence repeat markers were genotyped onto the mapping panel for G. barbadense. Data from 64 of the 92 markers were deemed robust and combined with pre-existing data to develop an expanded framework map, which provides partial coverage of 7 chromosomes and three unidentified linkage groups. A new mapping population was created to allow mapping of the G. hirsutum genome. The population was developed by treatment of TM-1 pollen with 8 krad of radiation, which was used to make more than 1000 controlled cross-pollinations. From these, 979 bolls were harvested and seeds were planted until a population of 115 viable plants was obtained. Of these, 92 were selected at random for inclusion in the mapping panel. Carthagene genome mapping software was evaluated and compared to the previously utilized RHMAP. Carthagene compared favorably in ease of use, calculation speed, and reliability of results. As such, it is recommended for use for the RH mapping project.