Skip to main content
ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #283798


Location: Corn Insects and Crop Genetics Research

Title: Maize chromosomal knobs are located in gene-dense areas and suppress local recombination

item Ghaffari, Rashin
item Cannon, Ethalinda
item Kanizay, Lisa
item Lawrence, Carolyn
item Dawe, Kelly

Submitted to: Chromosoma
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/9/2012
Publication Date: 3/1/2013
Citation: Ghaffari, R., Cannon, E.K., Kanizay, L.B., Lawrence, C.J., Dawe, K.R. 2013. Maize chromosomal knobs are located in gene-dense areas and suppress local recombination. Chromosoma. 122(1-2):67-75.

Interpretive Summary: The primary method by which beneficial alleles for genes can be stacked to improve corn varieties is though recombination. Some regions of the genome recombine well whereas others do not. This work demonstrates that highly condensed regions of the genome called knobs appear to reduce recombination rates but lie in gene-dense regions, rendering genes in that region potentially recalcitrant to introgression for trait integration.

Technical Abstract: Knobs are conspicuous heterochromatic regions found on the chromosomes of maize and its relatives. The number, locations, and sizes vary dramatically, with most lines containing between four and eight knobs in mid-arm positions. Prior data suggest that some knobs may reduce recombination, but previously comprehensive tests were not possible because the genetic positions of knobs had not been determined systematically. We used fluorescent in situ hybridization and two recombinant inbred populations to map seven knobs and to accurately place three knobs from the B73 inbred on the genomic sequence assembly. The data show that knobs lie in gene-dense regions of the maize genome. Comparisons to 23 other recombinant inbred populations segregating for knobs at the same sites confirm that large knobs can locally reduce crossing over by as much as two fold on a cM/Mb scale. These effects do not extend beyond regions ~10 cM to either side of knobs, and do not appear to affect linkage disequilibrium among genes within and near knob repeat regions of the B73 RefGen_v2 assembly.