Genome-Wide Development of InDel-SSRs and Association Analysis of Important Agronomic Traits of Taro (Colocasia esculenta) in China

Taro (Colocasia esculenta (L.) Schott) is a tropical tuber crop whose underground corms are used as an important staple food. However, due to a lack of molecular markers, the genetic diversity, germplasm identification, and molecular breeding of taro are greatly limited. In this study, high-density InDel-SSR molecular markers covering the whole genome were developed based on the resequencing data of taro core germplasm. A total of 1,805,634 InDel-SSR loci were identified, and 219 highly polymorphic markers with an average polymorphism information content PIC value of 0.428 were screened. Furthermore, a genetic diversity analysis of 121 taro germplasm resources was conducted based on 219 markers, dividing the resources into three groups. In addition, an association analysis showed that, of the multiple InDel-SSR markers, g13.52 and g12.82 were significantly associated with leaf area and average cormel weight, respectively; the candidate genes CeARF17 (EVM0014444) and CeGA20ox (EVM0001890) were related to cormel expansion; and we excavated the candidate genes CeXXT2 (EVM0016820) and CeLOG1 (EVM0017064), which regulate leaf development. The InDel-SSRs and candidate genes identified in this study are expected to provide important support for genetically improving and breeding new varieties of taro.