Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/5/2006
Publication Date: 2/20/2007
Citation: Li, J., Klindworth, D.L., Shireen, F., Cai, X., Hu, J., Xu, S.S. 2007. Molecular characterization and chromosome-specific TRAP-marker development for Langdon durum D-genome disomic substitution lines. Genome. 49:1545-1554.
Interpretive Summary: Langdon durum disomic substitution (LDN-DS) lines, where a pair of chromosomes from bread wheat cultivar Chinese Spring (CS) substitute for a chromosome pair in durum wheat cultivar Langdon, are excellent tools for assigning genes and molecular markers to chromosomes in durum wheat and related species. The objective of this study was to develop new molecular markers for a set of 14 newly improved LDN-DS lines. In this study, we developed a total of 310 molecular markers and assigned them to their respective chromosomes. Most of the markers (95.5%) were present on a single chromosome, but 4.5% of the markers mapped to two or more chromosomes. The marker analysis verified the retention of at least 13 pairs of chromosomes from LDN and one pair of chromosomes from CS in each of the LDN-DS lines. The molecular markers developed in this study provide an identity for each of the chromosomes and they will facilitate molecular and genetic characterization of the individual chromosomes in wheat, including genetic mapping and gene identification.
Technical Abstract: Langdon (LDN) durum D-genome disomic substitution (LDN-DS) lines, where a pair of ‘Chinese Spring’ (CS) D-genome chromosomes substitute for a corresponding homoeologous A- or B-genome chromosome pair of LDN, have been widely used for determining chromosomal locations of genes in tetraploid wheat. The objectives of this study were to characterize a set of 14 newly improved LDN-DS and develop chromosome-specific markers using the newly developed TRAP (target region amplification polymorphism) marker technique. A total of 307 polymorphic DNA fragments were amplified from LDN and CS and 302 of them were assigned to individual chromosomes as chromosome-specific markers. Most of the markers (95.5%) were present on a single chromosome, but 4.5% of the markers mapped to two or more chromosomes. The number of markers per chromosome varied from a low of 10 (chromosomes 1A and 6D) to a high of 24 (chromosome 3A). There was an average of 16.6, 16.6, and 15.9 markers per chromosome assigned to the A-, B-, and D-genome chromosomes, respectively, suggesting that TRAP markers were detected at a nearly equal frequency on the three genomes. A comparison of the source of the ESTs used to derive the fixed primers with the chromosomal location of markers revealed that 15.5% of 310 TRAP markers were located on the same chromosomes as the ESTs used to generate the fixed primers. A fixed primer designed from an EST mapped on a chromosome or a homoeologous group amplified at least one fragment specific to that chromosome or group, suggesting that the fixed primers could generate markers from target regions. The TRAP marker analysis verified the retention of at least 13 pairs of A- or B-genome chromosomes from LDN and one pair of D-genome chromosomes from CS in each of the LDN-DS lines. The chromosome-specific markers developed in this study provide an identity for each of the chromosomes and they will facilitate molecular and genetic characterization of the individual chromosomes, including genetic mapping and gene identification.