DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing

Figures & data

Table 1. Comparison of important characteristics of the most commonly used molecular markers.

Characteristics	RFLP	RAPD	AFLP	ISSR	SSR	SNP	DArT	Retrotransposons
Co-dominant/Dominant	Co-dominant	Dominant	Dominant	Dominant	Co-dominant	Co-dominant	Dominant	Dominant
Reproducibility	High	High	Intermediate	Medium–High	High	High	High	High
Polymorphism level	Medium	very high	High	High	High	High	High	High
Required DNA quality	High	High	High	Low	Low	High	High	High
Required DNA quantity	High	Medium	Low	Low	Low	Low	Low	Low
Marker index	Low	High	Medium	Medium	Medium	High	High	High
Genome abundance	High	Very high	Very high	Medium	Medium	Very high	Very high	High
Cost	High	Less	High	High	High	Variable	Cheapest	Cheapest
Sequencing	Yes	No	No	No	Yes	Yes	Yes	No
Status	Past	Past	Past	Present	Present	Present	Present	Present
PCR requirement	No	Yes	Yes	Yes	Yes	Yes	No	Yes
Visualization	Radioactive	Agarose gel	Agarose gel	Agarose gel	Agarose gel	SNP-VISTA	Microarray	Agarose gel
Required DNA (ng)	10000	20	500–1000	50	50	50	50–100	25–50

Table 2. Advantages and disadvantages of different genetic markers.

Markers	Advantages	Disadvantages	References
Morphological	Easy to use Cheaper Visually characterized	Less polymorphic Influenced by environment Influenced by plant growth stages	[6]
Isozymes	No need of specific instrument Easy to use Co-dominant	Less polymorphic Influenced by environmental factors	[10]
RFLPs	Co-dominant No need of prior sequence information	Time consuming High quantity of pure DNA needed Expensive Time consuming	[12]
RAPD	Easy to use Less quantity of DNA is required Polymorphic	Dominant Highly purified DNA is required. Low reproducibility. Not locus-specific	[5,12]
AFLP	Reliable High reproducibility More informative	Dominant marker Highly purified DNA is required High quantity of pure DNA needed	[12,23,24]
SSRs	Co-dominant marker Less quantity of DNA is required High reproducibility	High developmental cost Presence of more null alleles Occurrence of homoplasy	[30,33,34]
ISSR	Highly polymorphic Simple and easy to use No need of prior sequence information	low reproducibility Pure DNA is required. Fragment are not same sized	[44,47,49]
SRAP	Simple Reliable Easy isolation of bands	Dominant marker Moderate–high throughput ratio	[42,43]
Retrotransposons	Simple and easy to use No need of prior sequence information High reproducibility	Dominant marker	[59,61,62]
SNP	Cost effective Widely distributed in genome No need of prior sequence information High reproducibility Co-dominant marker	High developmental cost	[5,12]
DArT	Cost effective High throughput Highly polymorphic Prior sequence information not needed High reproducibility	Dominant marker High developmental cost	[104–106]

Figure 1. QTL mapping methodology.

Figure 2. Methodology of association mapping.

Figure 3. Some important steps involves in MAS.

Figure 4. Important steps involves in the development of functional markers.

Figure 5. Important steps involved in TILLING.

Figure 6. General methodology of VIGS.

Figure 7. General methodology of genomic selection (GS).

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