A novel set of EST-InDel markers in Eucalyptus L'Herit.: polymorphisms, cross-species amplification, physical positions and genetic mapping

Insertion/deletion (InDel) markers are valuable for genetic applications in plant species, and the public databases of expressed sequence tags (ESTs) have facilitated the development of genic InDel markers. In this study, we developed a novel set of 144 InDel markers in an important tree genus Eucalyptus L'Herit. using the ESTs of GenBank. Amplicon sequencing against two parents of a mapping population (Eucalyptus urophylla S. T. Blake 9 E. tereticornis Smith) revealed that the InDel size ranged from 2 to 44 bases, and the dinucleotide type was the most abundant (37.3 %). The cross-species/subgenus amplification rate ranged from 62.5 % in E. tessellaris F. Muell. (subgenus Blakella) to 99.3 % in E. grandis Hill ex Maiden (subgenus Symphyomyrtus) with an average of 85.4 %. There were 121 EST-InDels (84.0 %) polymorphic among 12 individuals of E. grandis, and the mean number of alleles per polymorphic locus (Na), observed heterozygosity (Ho), expected heterozygosity (He) and polymorphic information content (PIC) were 4.0, 0.278, 0.538 and 0.465, respectively. Physical positions of 143 EST-InDels were predicted on the E. grandis genome sequence. A total of 81 EST-InDels were incorporated into prior dense genetic maps of E. urophylla and E. tereticonis, and extensive synteny and colinearity were observed between E. grandis genome sequence and the mapped EST-InDel markers. These EST-InDels will provide a valuable resource of functional markers for genetic diversity evaluation, genome comparison, QTL mapping and marker-assisted breeding in Eucalyptus.