Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping

Authors: LI, DAWEI - Northwest Agricultural & Forestry University; Weng, Yiqun; CUEVAS, HUGO - University Of Wisconsin; YANG, LUMING - University Of Wisconsin; LI, YUHONG - Northwest Agricultural & Forestry University; GARCIA-MAS, JORDI - Institute De Recerca I Tecnologia Agroalimentaries (IRTA); Zalapa, Juan; Staub, Jack; LUAN, FEISHI - Northeast Agricultural University; REDDY, UMESH - West Virginia State University; HE, XIAOMING - University Of Wisconsin; GONG, ZHENHUI - Northwest Agricultural & Forestry University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/25/2011
Publication Date: 8/5/2011
Citation: Li, D., Weng, Y., Cuevas, H., Yang, L., Li, Y., Garcia-Mas, J., Zalapa, J.E., Staub, J.E., Luan, F., Reddy, U., He, X., Gong, Z. 2011. Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping. Biomed Central (BMC) Genomics. 12:396-409.

Interpretive Summary: Two melon populations, 91 F2 plants from Top Mark × Q3-2-2 and 80 F8 RIL derived from Top Mark × WI 846-1, were employed to construct linkage maps using cucumber microsatellite (SSR) markers. A total of 154 and 127 novel SSR markers were added on previously reported F2- and RIL-based genetic maps, respectively. Subsequently, a consensus melon linkage map was developed through map integration. This consensus map contained 401 co-dominant markers including 199 markers derived exclusively from the cucumber genome. The markers were relegated to 12 linkage groups spanning 1029.0 cM. Associations between markers resident on the consensus melon map and cucumber draft genome scaffolds were established through in silico PCR and/or BLAST-based DNA sequence alignment, which was then used to infer the syntenic relationships between chromosomes of these species. It was determined that cucumber Chromosome 7 was syntenic to melon Chromosome I, where marker loci between these chromosomes were remarkably co-linear. Moreover, cucumber Chromosomes 2 and 6 each contained genomic regions that were syntenic with melon chromosomes III+V+XI and III+VIII+XI, respectively. Likewise, cucumber Chromosomes 1, 3, 4, and 5 each were syntenic with genomic regions of two melon chromosomes previously designated as II+XII, IV+VI, VII+VIII and IX+X, respectively. However, the marker orders in several syntenic blocks on these consensus linkage maps were not co-linear suggesting that more complicated structural changes beyond simple chromosome fusion events have occurred during the evolution of cucumber.

Technical Abstract: Cucumber and melon are two economically important vegetable species. Both species have an Asian origin that diverged approximately nine million years ago. Cucumber is believed to have evolved from melon, where twelve melon chromosomes are thought to have undergone chromosome fusion to result in the current chromosome complement of cucumber. However, the details of this process are largely unknown. In this study, we conducted comparative genetic mapping in melon using cucumber molecular markers. Two melon populations were employed to construct linkage maps using cucumber microsatellite (SSR) markers. A total of 154 and 127 novel SSR markers were added on previously reported F2- and RIL-based genetic maps, respectively. Subsequently, a consensus melon linkage map was developed through map integration. This consensus map contained 401 markers including 199 cucumber markers. Associations between markers resident on the consensus melon map and cucumber draft genome scaffolds were established through in silico PCR and/or BLAST-based DNA sequence alignment. It was determined that cucumber Chromosome 7 was syntenic (conserved) to melon Chromosome I, where marker loci between these chromosomes were remarkably consistent (co-linear). Moreover, cucumber Chromosomes 2 and 6 each contained genomic regions that were syntenic with melon chromosomes III+V+XI and III+VIII+XI, respectively. Likewise, cucumber Chromosomes 1, 3, 4, and 5 each were syntenic with genomic regions of two melon chromosomes previously designated as II+XII, IV+VI, VII+VIII and IX+X, respectively. However, the marker orders in several syntenic blocks on these consensus linkage maps were not co-linear suggesting that more complicated structural changes beyond simple chromosome fusion events have occurred during the evolution of cucumber.