Table 2.

Comparison of different resequencing strategies.

	Reference needed?	Complexity reduction	Access to non-coding regions	Cost per sample	Advantage	Disadvantages	Examples
Whole genome resequencing	+++		++++	++++	- 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	+++	++		+++	- 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	++	++++		++	- 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]