Molecular Breeding

Tim Rekayasa Tanaman III

Kompetensi yang diharapkan

• Mahasiswa memahami penerapan marka DNA untuk membantu proses seleksi,

• Mahasiswa mampu memahami pemanfaatan teknologi marka DNA untuk menggabungkan beragam karakter ke dalam suatu kultivar (pyramiding).

Content

• Definition and objectives• Marker assisted selection (MAS) • MAS breeding scheme• Marker assisted backcrossing (MAB)• Case study of MAS• Pyramiding• Combined approach (phenotypic + molecular)

Gambaran: Molecular Breeding- Gen fragrance (aromatic) padi terpaut dg DNA marker RM515

F ‘TAGGACGACCAAAGGGTGAG’R ‘TGGCCTGCTCTCTCTCTCTC’

Example: introgresi gen Xa21 (gen ketahanan thd blas)

Chrom. 11

Tahan, tetua donor

Rentan, recipient

Molecular breeding: Kultivar Resisten dan Rentan

Daftar gen pengendalli karakter (QTL) yang terpaut dengan DNA marker pada padi

Molecular Breeding…?

• Penggunaan teknologi marka DNA yang terpaut atau letaknya berdekatan dengan lokus target tertentu (pengendali karakter) atau marka DNA yang digunakan sebagai alat bantu karakterisasi fenotipe suatu individu.

• Asumsi: marka DNA tersebut dapat diandalkan (reliable)

Tujuan: • membantu proses seleksi (indirect selection: seleksi

berbasis DNA marker- mengeliminasi individu yang tanpa DNA marker).

• meningkatkan efektivitas dan efisiensi seleksi dan penggabungan karakter-karakter yang diinginkan ke dalam suatu kultivar.

Why Molecular breeding ??

• Many traits can be difficult/expensive to measure or are environmentally sensitive, and thus it is difficult to make progress in breeding programs.

• It is difficult to combine numerous important traits simultaneously into cultivars, marker-assisted breeding gives geneticists/breeders a versatile set of tools that can augment, as well as verify, traditional selection techniques

• Mol. Breeding overcomes these limitations by performing an ‘easy’ lab test (DNA extraction- PCR- Electrophoresis-Visualisasi) for indicating the likelihood of having the trait of interest.

Advantages of molecular breeding

Case study: MAS on Jatropha (Jarak pagar) genotyping

In Gh Pu QRIn Gh Pu QR

• 13 primer pairs selected for use in further studies

• These reveal 69/453 polymorphic bands (15.2%)

• Results indicate very little variation between accessions from India, Ghana, Tanzania & Madagascar

Conventional plant breeding

xCross plants, e.g., high oil cultivated with wild disease resistant

Phenotypic screen of all progeny – usually requires mature plants

Limited by number of plants than can be brought to maturity and screened.

Selected progeny then backcrossed with cultivated variety to remove undesirable traits

F2

Marker assisted breeding

Involves creation of a genetic map using ‘Markers’

•Co-inheritance of phenotype and ‘genotype’ reveals linked markers

•These can then be used in fast-track breeding programmes

•Genotype analysis performed at seedling stage

•More rapid, and higher throughput than phenotypic selection

•Plants with correct genotype can then be subjected to phenotypic verification

Var1 h1 ATGTTTGAACGACTTCAA 1 Var1 h2 ATGTTTGAACGACTTCAA 1 Var2 h1 ATGTTTGTACGACTTCAA 2 Var2 h2 ATGTTTGTACGACTTCAA 2 *

Collard & Mackill, 06

Case study: rice

Marker-assisted backcrossing (MAB)

P1 x F1

P1 x P2

CONVENTIONAL BACKCROSSING

BC1F1

VISUAL SELECTION OF BC1 PLANTS THAT MOST CLOSELY RESEMBLE RECURRENT PARENT

BC2

MARKER-ASSISTED BACKCROSSING (breeding)

P1 x F1

P1 x P2

BC1F1

USE ‘BACKGROUND’ MARKERS TO SELECT PLANTS THAT HAVE MOST RP MARKERS AND SMALLEST % OF DONOR GENOME

BC2

Pyramiding:

Pyramiding

Combined approaches (using both phenotypic and molecular marker): Tandem Selection

References

• Collard B & Mackill D. 2008. Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philosophical Transactions of the Royal Society of London Series B 363:557-572.

• Graham I. 2007. Towards the development of new Jatropha varieties: molecular and biochemical analysis of toxic and non-toxic lines. Biology to Benefits Society. Univ of York.

• Semagn K, Bjornstad A and Ndjiondjop MN. 2006. Progress and prospects of marker assisted backcrossing as a tool in crop breeding programs. African Journal of Biotechnology 5:2588-2603.

• Jena KK and Mackil DJ. 2008. Molecular marker s and their use in marker-assisted selection in rice. Crop Science 48:1266-1276.

Quick review

Molecular breeding? Why use molecular breeding?Advantages?Disadvantages?Draw breeding scheme: conventional & MAS

(MAB)?Pyramiding?

Any question left?