Screening and characterization of molecular markers for sugarcane (Saccharum officinarum L.) resistance to shoot borer pest

Abstract

Sugarcane (Saccharum officinarum L.) is one of the main crops in Indonesia and is known as a sugar-producing plant. Sugar belongs to one of the 9 essential culinary ingredients in Indonesia. With the high demand for sugar the government in 2017 imported 109,147 tons of sugar or equivalent to IDR 823.8 billion to fulfill the demand. Efforts to increase sugarcane productivity are often constrained by complex pests that attack sugarcane shoots. One way to overcome it is to breed plant varieties that are resistant and of good quality. The purposes of the present study were to screen sugarcane shoot borer resistance gene using the molecular marker SacMPI-Like 3, to determine the phylogenetic relationship between MPI in sugarcane with other species in the family Andropogenae, and to determine the most effective molecular markers for detecting MPI. The primer was designed by using Primer3 Plus. DNA samples of 22 sugarcane varieties derived from the Genetics and Breeding Laboratory, Biology Faculty of Gadjah Mada University were PCR-amplified using 3 selected primer designs. Results showed that all of the 22 samples of sugarcane DNA contained SacMPI-Like 3 ranged from 500 to 600 bp. Some of the samples were sequenced to obtain the arrangement of nucleotide bases for comparison with samples from the NCBI GeneBank. The phylogenetic tree analysis showed that 3 large clusters were formed depended on the presence of MPI. The first cluster consisted of SacMPI1_PS_58, SacMPI1_PS_951, SacMPI2_PS_384, SacMPI2_PS_951, SacMPI3_PS_851, SacMPI3_PS_951, CA282462.1_SHC (Saccharum officinarum L.), XR002447315.1_ SB, XR002447314.1_SB (Sorghum bicolor), XR003227569.1 PH, XR003227568.1_PH (Panicum hallii) EU972719.1_ZM, NM001158424.2_ZM, EU960955.1_ZM, and EU951995.1_ZM (Zea mays). The second cluster consisted of XM024458314.1_BD (Brachypodium distachyon), CT827984.1_OZ, and XM026021872.1_OZ (Oryza sativa).