Elaeis guineensis is a tropical oil plant with the highest oil yield per unit area in the world. The Tenera hybrid is the most valuable variety for cultivation compared to the parent varieties Dura and Pisifera. It is difficult to select for the morphological characteristics of the oil palm cultivar in oil palm seedlings at the nursery stage; thus, the development of a molecular marker is necessary. In the present study, a sequence characterized amplified region (SCAR) marker was developed that yields 159-bp and 195-bp fragments specific for female and male parents, respectively. Sequence alignment revealed that the 159-bp fragment has a 36-bp deletion. Molecular characterization of the fragments reveals that the sequence is identical to the ALBINO3-like protein 2 (EgALB3.2) and is localized on chromosome 16 of the E. guineensis genome with expression noted in the kernel/endosperm of Tenera fruits only. These markers help in the selection of oil palm hybrids codominantly expressing both fragments; thus, heterozygous individuals can be distinguished from homozygous individuals. The SCAR-specific marker could therefore be used to distinguish oil palm hybrids from their parents by PCR. Moreover, these specific SCAR primers can be used directly to identify the oil palm hybrids without the need for postprocessing steps, and the specific fragments can be detected using an automated sequencer and real-time PCR. This marker-assisted selection is sensitive and suitable for the identification of oil palms in breeding programs.

The viral disease induced by Tomato yellow leaf curl virus (TYLCV) reduces tomato (Solanum lycopersicum) yield significantly in tropical and subtropical regions. A number of loci, including Ty-1 to Ty-5, conferring resistance to TYLCV have been described and introgressed into modern tomato cultivars. The availability of molecular markers linked to these genes would expedite the introgression of TYLCV resistance into commercial cultivars. In the present study, we developed gene-based markers linked to the Ty-3 gene using a segregating population derived from a cross between the TYLCV-resistant line S. lycopersicum ‘A45’ and the susceptible line S. lycopersicum ‘A39’. Agrobacterium-mediated screening was used to test TYLCV resistance of plants in the segregating population, and the resistance was evaluated by a visual scoring method and polymerase chain reaction analysis. By comparing sequences of the Ty-3 genes of the resistant and susceptible lines, two high-resolution melting (HRM) markers (Ty3-HRM1 and Ty3-HRM2) and one sequence characterized amplified region (SCAR) marker (Ty3-SCAR1) were developed. The HRM markers were based on single nucleotide polymorphisms at the 13th exon and the 15th intron, whereas the SCAR marker was based on a 246-bp deletion in the 16th intron. These gene-based markers will be useful tools for marker-assisted selection in breeding programs to improve TYLCV resistance of tomato.

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Amplified fragment length polymorphism (AFLP) is a molecular marker technique based on DNA and is extremely useful in detection of high polymorphism between closely related genotypes like Korean wheat cultivars. Six sequence characterized amplified regions (SCARs) have been developed from inter simple sequence repeat (ISSR) analysis which enabled the identification and differentiation of 13 Korean wheat cultivars from the other cultivars. We used six combinations of primer sets in our AFLP analysis for developing additional cultivar-specific markers in Korean wheat. Fifty-eight of the AFLP bands were isolated from EA-ACG/MA-CAC, EA-AGC/MA-CTG and EA-AGG/MA-CTA primer combinations. Of which 40 bands were selected to design SCAR primer pairs for Korean wheat cultivar identification. Three of 58 amplified primer pairs, KWSM006, KWSM007 and JkSP, enabled wheat cultivar identification. Consequently, 23 of 32 Korean wheat cultivars were classified by eight SCAR marker sets.

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• High-throughput SNP markers for authentication of Korean wheat cultivars based on seven complete plastomes and the nuclear genome
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Inter simple sequence repeat (ISSR) is a technique that leads to the development of novel specific molecular markers and relationship analysis between species. In this study, 54 ISSRs were used to develop cultivar-specific DNA sequence characterized amplified regions (SCARs) for Korean wheat cultivars (Triticum aestivum). Using nine of 54 UBC ISSR primers, 16 cultivar-specific fragments were detected among 32 wheat cultivars. Of the 16 primers, 10 successfully amplified targets in 32 cultivars and six novel cultivar-specific markers were finally selected. A total of 13 Korean wheat cultivars (Ol, Dahong, Namhae, Jinpum, Anbaek, Jopoom, Jokyung, Sinmichal 1, Jeokjoong, Dajung, Goso and Joah) were classified by newly developed six SCAR markers. Cultivar-specific markers can be used not only for cultivar fingerprinting but also for marker-assisted selection in wheat breeding program.

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