| Reference needed? | Complexity reduction | Access to non-coding regions | Cost per sample | Advantage | Disadvantages | Examples |
---|---|---|---|---|---|---|---|
Whole genome resequencing | +++ | Â | ++++ | ++++ | - Complete representation of the genome - Analysis of structure possible | Expensive | Date palm [217], Maize [218], Pepper [99], Rice [208], Sorghum [219], Soybean [220], Tomato [221] |
Exome capture | +++ | ++ | Â | +++ | - Sequence of protein coding regions & functional elements - Known target regions | - Only exons - Prior probe design required | Barley [112], Bread wheat [222], Cotton [223], Pine [224], Rapeseed [225], Soybean [226], Sugarcane [227] |
RNAseq | ++ | ++++ | Â | ++ | - Gene expression analysis possible - Only protein coding regions - Reference-free analysis methods exist | - Only exons - Only protein coding regions - Coverage depends on transcript abundance | African rice[117], Carrot [228] Common bean [229], Cotton [230], Pepper[99], Sunflower[140], Tomato[34] |
Genotyping-by-sequencing | ++ | ++++ | +++ | + | - High-throughput identification of whole-genome markers - Reference-free analysis methods exist | - Sparse marker data - Handling of missing data required | Cassava[138], Chickpea [231], Cotton[69], Cowpea [232], Oat [233], Soybean [234], Watermelon [235] |