Creation of Chromosome Segment Substitution Lines libraries with O. glaberrima introgressions

Population 1: Caiapo x MG12
Background: A BC3F1 population was obtained at CIAT HQs from the cross between Caiapó (an elite tropical japonica from Brazil) and O. glaberrima MG12 (alias IRGC103544) (César P. Martinez). From these lines, anthers were collected and a population of 695 BC3DH lines was obtained through in vitro culture of anthers (Zaida Lentini). A subset of 312 BC3DH lines was genotyped using 200 SSRs. Sixty-four lines covering the whole O. glaberrima genome were selected as candidates for CSSL development by means of the program CSSL Finder using the 125 best markers in terms of their distribution across the twelve rice chromosomes. The average size of the overlapping targeted chromosomal segment was of 10 cM.
Results: New markers have been evaluated to fill in the gaps between RM71 and RM300 (Chr. 2) and between RM185 and RM241 (Chr. 4). A new BC1F1 population has been generated to validate the genetic map and to recover lost segments. This population is currently mapped with polymorphic SSRs selected from the Universal Core Map Genetic of rice developed at CIAT. The population was evaluated at the field level for various agronomic traits at CIAT HQs. Fourteen QTLs for plant height (3), yield (3), tillering (3), 1000-seed weight (2) and sterility (2) located on chromosomes 1, 3, 4 and 6 have been detected. One highly significant QTL for resistance to the Rice Stripe Necrosis Virus (RSNV) could be located on Chr. 11 and fine mapping of this major QTL could be envisaged using BC4F2/F3 lines. All the analyses were performed considering 1) the ANOVA1 F-test value and 2) the graphical genotypes of lines showing extreme phenotypes for the considered trait. The QTLs positions were approximated regarding the IR64 x TOG5681 BC1F1 population developed at CIAT. Moreover, 36 BC3DH lines were selected and backcrossed to both parental accessions, Caiapo and IRGC103544, to provide the materials to study the genetic bases of sterility in interspecific crosses. In order to optimize and to purify the CSSL population, 59 BC3F1DH subsets of the 64 candidates were backcrossed to Caiapo and selfed to obtain 59 BC4F2 families. For each one of these BC4F2 families, a minimum of 60 individuals were planted at CIAT HQs with the aim of identifying plants with the target fragment. These materials (about 3,500 plants) are currently collected for seeds in the field and will be evaluated with microsatellite markers for their genetic background and for the presence of the targeted O. glaberrima segments.
Population 2: IR64 x TOG5681
The genotyping survey of a new BC2F2 population from the cross IR64 x TOG5681 and made of 409 lines was completed. A set of 138 SSR markers from the Universal Core Map and validated by genetic mapping were used. The SSR location validation was reached in mapping all the markers on a newly developed BC1F1 population.
From the graphical genotyping analyses, we could select candidate lines for backcrossing that will allow to fill the few gaps encountered in the first BC2F4/BC3F3 population (that was constituted by 363 lines genotyped with 125 SSR markers).