Effect of haplotype structure to linkage analysis on the seedlessness trait in Citrus

Seedlessness is one of the most desirable traits in citrus fruits for consumers. A citrus variety, “Mukaku Kishu” (seedless Kishu; Citrus kinokuni), produces a seedless fruit by aborting the zygote even after pollination. Our previous study on segregation populations suggested that the trait for seedlessness was regulated by a single dominant gene. We have conducted a citrus cross-breeding program in order to introduce the seedlessness trait, and developed several promising lines. Linkage mapping analysis with the SSR marker estimated the loci of the seedlessness trait, and proposed certain DNA markers for marker-assisted selection in cross-bred seedlings. The comparison of the linkage group in this linkage map with those of other linkage maps showed that the region around the loci for seedlessness was less polymorphic among the 22 citrus varieties that have been used for breeding parents; moreover, some of them showed consecutive distribution of the homozygous loci. Linkage analysis also showed that the region harboring the trait could be homozygous after a few crosses. These observations showed that the available number of DNA markers that can be linked to seedlessness for future cross-breeding is limited, and also proposed the need for enriching the available number of DNA markers for this region. Consequently, genome sequence analysis for these varieties is required for high-density mapping. This will lead to increasing the availability of the DNA markers for marker assisted selection.