The areas of molecular breeding include:
- QTL mapping or gene discovery
- Marker assisted selection and genomic selection 
- Genetic engineering
- Genetic transformation
Marker assisted breeding
- Genotyping and creating molecular maps - genomics
- The commonly used markers include Simple sequence repeats (or microsatellites), single nucleotide polymorphisms (SNP). The process of identification of plant genotypes is known as genotyping.
Development of SNPs has revolutionized the molecular breeding process as it help to create dense markers. The another areas that is developing genotyping by sequencing.
- Phenotyping - phenomics
- To identify genes associated with traits, it is important to measure trait value - known as phenotype. "omics" for measurement of phenotypes is called phenomics. The phenotype can be indicative of measurement of trait itself or an indirectly related or correlated trait.
- QTL mapping or association mapping
- Genes (Quantitative trait loci (abbreviated as QTLs) or quantitative trait genes or minor genes or major genes) involved in controlling trait of interest is identified. The process is known as mapping. Mapping of such genes can be done using molecular markers. QTL mapping can involve single large family, unrelated individuals or multiple families (see: Family based QTL mapping). Basic idea is to identify genes or markers associated with genes that can be used in marker assisted breeding / selection
- Marker assisted selection or genetic selection
- Once genes or markers are identified they can be used for genotyping and selection decision can be made.
- Marker-assisted backcrossing (MABC)
- Backcross is crossing F1 with its parents to transfer a limited number of loci (e.g. transgene, disease resistance loci, etc.) from one genetic background to another. Usually the recipient of such genes is good adopted cultivars otherwise except the gene is to be transferred. So we want to keep genetic background of the recipient genotypes, which is done by 4-6 rounds of repeated backcrosses while selecting for the gene of interest. We can use markers from the whole genome to recover the genome quickly in 2-3 rounds of backcrossing might be good enough in such situation.
- Marker-assisted recurrent selection (MARS)
- MARS include identification and selection of several genomic regions (up to 20 or even more) for complex traits within a single population.
- Genomic selection
- Genomic selection is novel approach to traditional marker-assisted selection where selection are made based on few markers. Rather than seeking to identify individual loci significantly associated with a trait, genomics uses all marker data as predictors of performance and consequently delivers more accurate predictions. Selection can be based on genomic selection predictions, potentially leading to more rapid and lower cost gains from breeding.Genomic prediction combines marker data with phenotypic and pedigree data (when available) in an attempt to increase the accuracy of the prediction of breeding and genotypic values.
Genetic transformation or Genetic engineering
Transfer of genes make it possible for horizontal transfer of genes from one organism to another. Thus plants can receive genes from humans or algae or any other organism. This provides limitless opportunity in breeding crop plants.
- Voosen P (2009) Molecular Breeding Makes Crops Hardier and More Nutritious Markers, knockouts and other technical advances improve breeding without modifying genes, Scientific American
- Stephen P. Moose* and Rita H. Mumm (2008) Molecular Plant Breeding as the Foundation for 21st Century Crop Improvement, Plant Physiology 147:969-977
- Jannink J-L, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genomics 9:166-177
- Heffner EL, Sorrells ME, Jannink JL (2009) Genomic selection for crop improvement. Crop Sci 49:1-12
- Goddard, ME; Hayes, BJ (2007). "Genomic selection". Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie 124 (6): 323–30. doi:10.1111/j.1439-0388.2007.00702.x. PMID 18076469.
- [?] BAKERR, . J., 1986 Selection Indices in Plant Breeding. CRC Press, Bocd Raton, Florida.