Development of Tetra-primer ARMS-PCR for Selection and Discrimination of CMD-Resistant Cassava Varieties Used in Thailand
DOI:
https://doi.org/10.14456/thaidoa-agres.2024.18Keywords:
cassava, cassava mosaic disease, molecular marker, single-nucleotide polymorphism (SNP)Abstract
Cassava mosaic disease (CMD) is a major disease that causes damage to cassava production worldwide. CMD-resistant cassava varieties obtained from the International Center for Tropical Agriculture (CIAT) and the International Institute of Tropical Agriculture (IITA), including 7 varieties, namely TME 3, C 33, IITA-TMS-IBA 920057, IITA-TMS-IBA 972205, IITA-TMS-IBA 980505, IITA-TMS-IBA 980581 and TME B 419, are currently being used as parent lines to create hybrids resistant to CMD suitable for cultivation in Thailand. The tetra-primer ARMS-PCR is a technique for single-nucleotide polymorphism (SNP) detection. It has the advantages of amplifying multiple alleles in a single reaction with the inclusion of a control fragment, cost-effectiveness as well as simplicity in operation. The purposes of this research were to develop primer sets using the tetra-primer ARMS-PCR technique to detect SNP markers associated with CMD resistance for the selection of resistant varieties and to develop a primer set for discrimination of variety within 7 CMD-resistant varieties being used in Thailand. The resultant primer sets have been readily developed and optimized condition to detect SNP markers Ex2-78, Ex2-157, Ex3-128, and S12_7926132 on chromosome 12, and can be used to select CMD-resistant varieties. For discrimination of CMD-resistant varieties, a primer set was developed to detect the SNP marker S12_8910428 in the DNA polymerase δ subunit 1 gene, and could distinguish TME B 419 from the remaining six resistant varieties. To our knowledge, this is the first report of using tetra-primer ARMS-PCR, which is cost-effective and simple to operate, in SNP detection for CMD-resistance selection in cassava.
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