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Application of Molecular Marker Technology to QA/QC in Plant Breeding

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Molecular markers and QA/QC

In plant breeding, the use of molecular markers in QA and QC can address all aspects of the breeding program. QA and QC can also be improved in the subsequent seed increase and distribution activities through the use of molecular markers

The first step is genetic fingerprinting of the parental germplasm so you know what you have in hand (Genetic fingerprinting or DNA fingerprinting is a method of isolating and making images of sequences of DNA. This technique is useful in parentage detection, diversity analysis, etc). Depending on the goals of your project, you may need to know: how much polymorphism exists between potential parents of future crosses, how much diversity exists in your set of germplasm, or what allele combinations each line has for future identification purposes.  

In order to do that you must determine the number of markers you will need to use.  Three general guidelines are:

  • Minimum number– set of markers which cover all linkage groups with 5 to 10 cM between individual markers
  • Maximum number– all available markers
  • Optimum number of markers to utilize depends on genome size and level of polymorphism

The effective implementation of a molecular marker – based QA/QC program depends on the availability of low-cost, high throughput markers, preferably SNPs, due to their high reproducibility and low cost.

Example of Selection of Markers for Individual Crosses

Iin this case study example we will look at how markers are screened in the parents and then from that group a select number of markers are chosen to be used in verifying later offspring.  This table shows the genotyping results of testing 30 SNP markers on two parental lines. Only six of the markers, highlighted here in yellow, are polymorphic. The other markers are monomorphic (showing no difference) between these two parents, and therefore are not useful. Of the six markers that are polymorphic, any three or more could be used for verification of further crosses. [Data provided by Hamer Paschal]

  • MNC358/PAN127 are the parents
  • 30 markers were tested
  • only 6 are polymorphic in the parents
  • Select any 3 for verification

 

SNP

MNC358

PAN127

BARC-PV-0000055

T:T

A:A

BARC-PV-0000105

C:C

C:C

BARC-PV-0000365

G:G

G:G

BARC-PV-0000468

A:A

A:A

BARC-PV-0000501

T:T

T:T

BARC-PV-0000623

G:G

G:G

BARC-PV-0000669

A:A

A:A

BARC-PV-0000819

A:A

G:G

BARC-PV-0000909

G:G

G:G

BARC-PV-0001361

C:C

C:C

BARC-PV-0001385

C:C

T:T

BARC-PV-0001413

T:T

T:T

BARC-PV-0001591

C:C

T:T

BARC-PV-0001925

T:T

T:T

BARC-PV-0002061

G:G

G:G

BARC-PV-0002064

G:A

G:G

BARC-PV-0002100

G:G

A:A

BARC-PV-0002435

A:A

T:T

BARC-PV-0002440

G:G

G:G

BARC-PV-0002776

C:C

C:C

BARC-PV-0002838

A:A

A:A

BARC-PV-0002848

C:T

C:T

BARC-PV-0002904

T:T

T:T

BARC-PV-0002984

A:A

G:G

BARC-PV-0003025

T:T

T:T

BARC-PV-0003028

T:T

T:T

BARC-PV-0003100

G:G

G:G

BARC-PV-0003108

A:A

A:A

BARC-PV-0003157

C:C

C:C

BARC-PV-0003261

C:A

C:A

 

Table 4: Marker data from an experiment screening two parental lines for polymorphic markers to later be used in subsequent generations.

 

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