Genetic background of the citrus landrace ‘Huarongdao Zhoupigan’ revealed by simple sequence repeat marker and genomic analyses

Abstract

The cultivated landrace ‘Huarongdao Zhoupigan’ originated in China, and it has a history of more than a hundred years. It is widely cultivated for its distinctive pericarp, soft juicy pulp, slight bitter taste, and rich flavonoids and vitamin C (17.2 ± 0.08 mg•mL−1). Morphological observation shows that ‘Huarongdao Zhoupigan’ is mandarin-like in leaf shape, fruit flesh, easy peeling and crumpled pericarp, implying this variety may be a hybrid of orange and mandarin. To reveal the genetic background of ‘Huarongdao Zhoupigan’, 21 citrus accessions were evaluated using nuclear and chloroplast SSR markers and whole-genome SNP information. ‘Huarongdao Zhoupigan’ was grouped with mandarins and closely clustered with ‘Yuanjiang Nanju’ in the nuclear SSR analysis and sub-grouped with ‘Goutou’ sour orange, ‘Dahong’ sweet orange and ‘Newhall’ navel orange in the chloroplast SSR analysis. The genomic sequence similarity rate of ‘Huarongdao Zhoupigan’ with mandarin was 36.09%, with mandarin heterozygosity of 46.50%; the rough ratio of the two main parts was nearly 1:1, except for the unknown (19.11%) and pummelo (1.46%) parts. Thus, ‘Huarongdao Zhoupigan’ may be a natural hybrid with sour orange (a sexual hybrid of pummelo and mandarin) as the seed parent and mandarin as the pollen parent.