Differences in the genetic diversity and genome size between two ecotypes of 𝘐𝘮𝘱𝘦𝘳𝘢𝘵𝘢 𝘤𝘺𝘭𝘪𝘯𝘥𝘳𝘪𝘤𝘢 in Japan

Abstract

Understanding genomic characteristics, such as genetic diversity and genome size, is important because they relate to species and ecotype performance. 𝘐𝘮𝘱𝘦𝘳𝘢𝘵𝘢 𝘤𝘺𝘭𝘪𝘯𝘥𝘳𝘪𝘤𝘢 has two ecotypes, the common type (C-type) and the early-flowering type (E-type), which differ in their ecological characteristics and distribution ranges in Japan. This study aimed to elucidate the genetic diversity of the C-type and E-type ecotypes of 𝘐. 𝘤𝘺𝘭𝘪𝘯𝘥𝘳𝘪𝘤𝘢 throughout Japan, using the multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) method. Genome-wide single-nucleotide polymorphism data analysis revealed that the C-type had greater genetic diversity and clearer isolation by distance than the E-type. Additionally, the C-type exhibited clear genetic differentiation between the southern part of Amami Oshima and other populations, consistent with differences in its life history. The C-type also had a smaller genome than the E-type, which may contribute to faster plant growth and smaller seed mass, as compared with the larger genome of the E-type. These phenomena were consistent with the characteristics of the C-type. These results showed that the two ecotypes differ genetically, highlighting the necessity for different guidelines for each ecotype in their conservation and use for revegetation.