Recombination frequency variation in maize as revealed by genomewide single-nucleotide polymorphisms

Farkhari, Md and et al, . (2011) Recombination frequency variation in maize as revealed by genomewide single-nucleotide polymorphisms. Plant Breeding, 130 (5). pp. 533-539. ISSN 1439-0523

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Recombination frequency greatly affects selection efficiency in plant breeding. A high-density single-nucleotide polymorphism (SNP) map integrated with physical map and other molecular maps is very useful for characterizing genetic recombination variation. In this study, recombination frequency in maize was investigated through SNP linkage maps constructed with three recombinant inbred line populations. The integrated map consisted of 1443 molecular markers, including 1155 SNPs, spanning 1346 cM. A 100-fold difference in recombination frequency was observed between different chromosomal regions, ranging from an average of 0.09 cM/Mb for pericentromeric regions to 7.08 cM/Mb for telomeric regions. Recombination suppression in non-centromeric regions identified nine recombination-suppressed regions, one of which likely contained condensed heterochromatin (knobs). Recombination variation along chromosomes was highly predictable for pericentromeric and telomeric regions, but population-specific with 4.5-fold difference for the same marker interval across the three populations or specific chromosome regions because of the presence of knobs. As recombination variation can be identified and well characterized as shown in this study, the related information will facilitate future genetic studies, gene cloning and marker-assisted plant breeding.

Item Type: Article
Uncontrolled Keywords: recombination frequency;integrated linkage map;selection;centromere;maize
Subjects: Others > Maize
Depositing User: Mr Sanat Kumar Behera
Date Deposited: 17 Feb 2012 11:15
Last Modified: 17 Feb 2012 11:15
Official URL:
Funders: Rockefeller Foundation, Bill and Melinda Gates Foundation, European Community, Consultative Group on International Agricultural Research , Goverment of Iran-Ministry of Science, Research and Technology, China Scholarship Council
Acknowledgement: The SNP chips used in this study were developed through a collaborative project between Institute for Genomic Diversity, Cornell University (Ed. Buckler) and CIMMYT (Marilyn Warburton andJianbing Yan). Two RIL populations, �C5� (Ac7643 · Ac7729/ TZSRW) and �C6� (CML444 · Malawi), were developed at CIMMYT for maize DT project (Jean-Marcel Ribaut). Dr Jonathan Crouch provided a comprehensive review on the draft manuscript. We thank Eva Huerta Miranda, Carlos Martinez Flores, Martha Hernandez Rodrı´guez, Alberto Vergara Alva, Maria Asuncio´ n Moreno Ortega and Jose Simon Pastrana Marias for laboratory and field assistance. This work was funded by the Rockefeller Foundation, the Bill and Melinda Gates Foundation, and the European Community, and through other attributed or unrestricted funds provided by donors of the Consultative Group on International Agricultural Research (CGIAR) especially the national governments of USA, Japan and UK. Mohammad Farkhari and Yanli Lu as joint PhD students were partially supported by Ministry of Science, Research and Technology of Iran and China Scholarship Council, respectively, for their research at CIMMYT, Mexico.
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