Table 1.

Comparison of pooled and whole genome sequencing-based trait mapping approaches

Description	Pooled based					Whole population based
	Indel-Seq	Seq-BSA	QTL-seq	MutMap	BSR-seq	WGRS	GBS	SKIM-seq	SNP array	RNA-seq
Cost	Low	Low	Low	Low	Low	High	Medium	Medium	High	Medium
Mapping 1–2 traits at a time	Yes	Yes	Yes	Yes	Yes	No	No	No	No	Yes
Mapping > 2 traits at a time	No	No	No	No	No	Yes	Yes	Yes	Yes	No
DNA/RNA based	DNA	DNA	DNA	DNA	RNA	DNA	DNA	DNA	DNA	RNA
Variants	InDels	SNPs	SNPs	SNPs	SNPs	SNPs	SNPs	SNPs	SNPs	SNPs
Approach	RG = HTP=HTB ≠ LTB	HTP = HTB≠LTB and SNP index	SNP index	SNP frequency	SNPs/FPKM	SNP calls	SNP calls	SNP calls	SNP variation	FPKM
Status of sequencing-based trait mapping in legume crops†	+	+	+++	–	–	++	+++	+	+++	–

RG reference genome, HTP high trait parent, HTB high trait bulk, LTB low trait bulk, FPKM Fragments Per Kilobase of transcript per Million mapped reads

^†+, ++ and +++ signs indicate technologies utilized in moderate, good and excellent quantity in the legume crops, and – sign indicates technologies yet to be utilized in legume crops