ARS | Publication request: Use of diversity arrays technology markers for integration into a cotton reference map and anchoring to a recombinant inbred line map

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 15, 2010
Publication Date: April 27, 2011
Citation: Reddy, U.K., Rong, J., Heller-Uszynska, K., Nimmakayala, P., Vajja, G., Rahman, M.A., Yu, J., Soliman, K.M., Kilian, A., Paterson, A.H. 2011. Use of diversity arrays technology markers for integration into a cotton reference map and anchoring to a recombinant inbred line map. Genome. 54:349-359.

Interpretive Summary: A new DNA marker platform called diversity array technology (DArT) markers was developed for cotton and it was compared with other DNA marker systems such as amplified fragment length polymorphism (AFLP). The transferability across the mapping populations was evaluated to improve the map resolution and utility in marker applications. A higher percentage of DNA polymorphism was detected and about 78% of the DArT markers could be genetically mapped. A majority of the new markers had a DNA sequence match with the known genes of cotton species. Further analysis revealed that 794 Arabidopsis genes were homologous with the cotton marker sequences that distributed unevenly among the cotton chromosomes. This study showed the value of the new marker system in cotton genome mapping for cotton improvement.

Technical Abstract: A DArT marker platform is developed for the cotton genome to evaluate the use of DArT markers compared to AFLPs in mapping, and transferability across the mapping populations. We used a reference genetic map of tetraploid Gossypium that already contained ~5000 loci which coalesced into 26 chromosomes, to anchor newly developed DArT and AFLP markers with the aim to further improve its utility and resolution. Our results indicated that the percentage of polymorphic DArT markers that could be genetically mapped (78.15%) was much higher than that of AFLPs (22.28%). Sequence analysis of DArT markers indicated that a majority of them matched with the known EST sequences from tetraploid and diploid Gossypium species. A total of 794 Arabidopsis genes were homologous with various DArT marker sequences. Chromosomes 5(A), 7(A), 19(D), 23(D) and 24(D) had more Arabidopsis synthetic DArT markers than the other chromosomes. Anchoring DArT markers from the reference map to a RIL map indicated that these markers will speed up building maps in de novo RIL populations.