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Table 2 Comparison of different resequencing strategies.

From: Genomic approaches for studying crop evolution

 

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]