A High-Density Rice Genetic Linkage Map with 2275 Markers Using a Single F2 Population

TLDR

A 2275‑marker genetic map of rice covering 1521.6 cM was built from 186 F2 plants of a Nipponbare × Kasalath cross, using EST clones and dosage analysis to locate centromeres. The resulting high‑resolution map, the most detailed for any plant, identified 1455 loci (615 with known gene similarity) and revealed limited centromere inhibition of recombination and positive interference across the genome.

Abstract

Abstract A 2275-marker genetic map of rice (Oryza sativa L.) covering 1521.6 cM in the Kosambi function has been constructed using 186 F2 plants from a single cross between the japonica variety Nipponbare and the indica variety Kasalath. The map provides the most detailed and informative genetic map of any plant. Centromere locations on 12 linkage groups were determined by dosage analysis of secondary and telotrisomics using >130 DNA markers located on respective chromosome arms. A limited influence on meiotic recombination inhibition by the centromere in the genetic map was discussed. The main sources of the markers in this map were expressed sequence tag (EST) clones from Nipponbare callus, root, and shoot libraries. We mapped 1455 loci using ESTs; 615 of these loci showed significant similarities to known genes, including single-copy genes, family genes, and isozyme genes. The high-resolution genetic map permitted us to characterize meiotic recombinations in the whole genome. Positive interference of meiotic recombination was detected both by the distribution of recombination number per each chromosome and by the distribution of double crossover interval lengths.