**3. Pre-requisites and general activities of marker-assisted breeding**

#### **3.1. Prerequisites for an efficient marker-assisted breeding program**

Compared with conventional breeding approaches, molecular breeding, mainly referred to as DNA marker-assisted breeding, needs more complicated equipment and facilities. In gen‐ eral, the pre-requisites listed below are essential for marker-assisted breeding (MAB) in plants.

	- **•** Ease and low-cost of use and analysis;
	- **•** Small amount of DNA required;
	- **•** Co-dominance;
	- **•** Repeatability/reproducibility of results;
	- **•** High levels of polymorphism; and
	- **•** Occurrence and even distribution genome wide

In addition, another important desirable attribute for the markers to be used is close associa‐ tion with the target gene(s). If the markers are located in close proximity to the target gene or present within the gene, selection of the markers will ensure the success in selection of the gene. Although they can also be used in plant breeding programs, the number of classical markers possessing these features is very small. DNA markers for polymorphism are availa‐ ble throughout the genome, and their presence or absence is not affected by environments and usually do not directly affect the phenotype. DNA markers can be detected at any stage of plant growth, but the detection of classical markers is usually limited to certain growth stages. Therefore, DNA markers are the predominant types of genetic markers for MAB. Each type of markers has advantages and disadvantages for specific purposes. Relatively speaking, SSRs have most of the desirable features and thus are the current marker of choice for many crops. SNPs require more detailed knowledge of the specific, single nucleotide DNA changes responsible for genetic variation among individuals. However, more and more SNPs have become available in many species, and thus they are also considered an im‐ portant type for marker-assisted breeding.

**b.** Quick DNA extraction and high throughput marker detection: For most plant breeding programs, hundreds to thousands of plants/individuals are usually screened for desired marker patterns. In addition, the breeders need the results instantly to make selections in a timely manner. Therefore, a quick DNA extraction technique and a high through‐ put marker detection system are essentially required to handle a large number of tissue samples and a large-scale screening of multiple markers in breeding programs. Extract‐ ing DNA from small tissue samples in 96- or 384-well plates and streamlined operations are adopted in many labs and programs. High throughput PAGE and AGE systems are commonly used for marker detection. Some labs also provide marker detection services using automated detection systems, e.g. SNP chips based on thousands to ten thou‐ sands of markers.


#### **3.2. Activities of marker-assisted breeding**

**3. Pre-requisites and general activities of marker-assisted breeding**

Compared with conventional breeding approaches, molecular breeding, mainly referred to as DNA marker-assisted breeding, needs more complicated equipment and facilities. In gen‐ eral, the pre-requisites listed below are essential for marker-assisted breeding (MAB) in

**a.** Appropriate marker system and reliable markers: For a plant species or crop, a suitable marker system and reliable markers available are critically important to initiate a mark‐ er-assisted breeding program. As discussed above, suitable markers should have fol‐

In addition, another important desirable attribute for the markers to be used is close associa‐ tion with the target gene(s). If the markers are located in close proximity to the target gene or present within the gene, selection of the markers will ensure the success in selection of the gene. Although they can also be used in plant breeding programs, the number of classical markers possessing these features is very small. DNA markers for polymorphism are availa‐ ble throughout the genome, and their presence or absence is not affected by environments and usually do not directly affect the phenotype. DNA markers can be detected at any stage of plant growth, but the detection of classical markers is usually limited to certain growth stages. Therefore, DNA markers are the predominant types of genetic markers for MAB. Each type of markers has advantages and disadvantages for specific purposes. Relatively speaking, SSRs have most of the desirable features and thus are the current marker of choice for many crops. SNPs require more detailed knowledge of the specific, single nucleotide DNA changes responsible for genetic variation among individuals. However, more and more SNPs have become available in many species, and thus they are also considered an im‐

**b.** Quick DNA extraction and high throughput marker detection: For most plant breeding programs, hundreds to thousands of plants/individuals are usually screened for desired marker patterns. In addition, the breeders need the results instantly to make selections in a timely manner. Therefore, a quick DNA extraction technique and a high through‐ put marker detection system are essentially required to handle a large number of tissue samples and a large-scale screening of multiple markers in breeding programs. Extract‐

**3.1. Prerequisites for an efficient marker-assisted breeding program**

plants.

lowing attributes:

54 Plant Breeding from Laboratories to Fields

**•** Co-dominance;

**•** Ease and low-cost of use and analysis;

**•** Repeatability/reproducibility of results;

**•** Occurrence and even distribution genome wide

**•** High levels of polymorphism; and

portant type for marker-assisted breeding.

**•** Small amount of DNA required;

Marker-assisted breeding involves the following activities provided the prerequisites are well equipped or available:

