Genomic diversity in old and recent carrot cultivars and breeding populations at a Japanese seed company

Abstract

Most of the fresh carrots in Japan are domestically produced Kuroda-type and Chantenay-type hybrid cultivars. They are conical or cylindroconical, with root lengths of 16-19 cm and diameters of 4.0-5.5 cm. Uniformity of root shape, root size, and growth habits is among the most important goals in carrot breeding in Japan. At our company, Fujii Seed, Japan, breeders have continuously selected ideal and uniform carrot root shapes and sizes as well as favorite growth habits for several decades. In the present study, to examine the effect of breeding on genomic diversity, we performed double-digest restriction-site-associated DNA sequencing (ddRAD-seq) for our old cultivars bred around 1990, our recent cultivars, and the breeding populations at our company. The ddRAD-seq detected about 13,000 single nucleotide polymorphisms (SNPs) among these 14 cultivars and 3 populations. In the recent cultivars, the whole genome diversity and the number of segregating sites were lower than in the old cultivars and breeding populations. Principal component analysis (PCA) also showed that the recent cultivars have more uniform genomes than the old cultivars and breeding populations. These results showed that genomic diversity within a cultivar has been diminished in recent breeding during the processes of selection for trait uniformity.