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Molecular breeding

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Molecular breeding is the application of molecular biology tools, often in plant breeding[1][2] and animal breeding.[3][4] In the broad sense, molecular breeding can be defined as the use of genetic manipulation performed at the level of DNA to improve traits of interest in plants and animals, and it may also include genetic engineering or gene manipulation, molecular marker-assisted selection, and genomic selection.[5] More often, however, molecular breeding implies molecular marker-assisted breeding (MAB) and is defined as the application of molecular biotechnologies, specifically molecular markers, in combination with linkage maps and genomics, to alter and improve plant or animal traits on the basis of genotypic assays.[6]

The areas of molecular breeding include:

Constituent methods

Marker assisted breeding

Methods in marker assisted breeding include:

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 helps to create dense markers.[clarification needed] Another area that is developing is genotyping by sequencing.[10]

Phenotyping - phenomics

To identify genes associated with traits, it is important to measure the trait value - known as phenotype[dubious – discuss]. The "omics" for measurement of phenotypes is called phenomics. The phenotype can be indicative of the measurement of the trait itself or an indirectly related or correlated trait.

QTL mapping or association mapping

Genes (Quantitative trait loci (abbreviated as QTL) or quantitative trait genes or minor genes or major genes) involved in controlling trait of interest are 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). The basic idea is to identify genes or markers associated with genes that correlate to a phenotypic measurement and 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 decisions can be made.

Marker-assisted backcrossing (MABC)

Backcrossing is crossing an 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 a cultivar that is already well performing - except for the gene that is to be transferred. So we want to keep the 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.[clarification needed]

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 a novel approach to traditional marker-assisted selection where selection is made based on only a few markers.[7] 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.[11]

Genetic transformation or Genetic engineering

Transfer of genes makes possible the 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 opportunities in breeding crop plants.

By organism

Molecular breeding resources (including multiomics data) are available for:

References

  1. ^ Voosen, P. (2009). "Molecular Breeding Makes Crops Hardier and More Nutritious Markers, knockouts and other technical advances improve breeding without modifying genes". Scientific American.
  2. ^ "Stephen P. Moose* and Rita H. Mumm (2008) Molecular Plant Breeding as the Foundation for 21st Century Crop Improvement, Plant Physiology 147:969-977".
  3. ^ Dekkers, Jack C. M.; Hospital, Frédéric (2002). "The use of molecular genetics in the improvement of agricultural populations". Nature Reviews Genetics. 3 (1): 22–32. doi:10.1038/nrg701. PMID 11823788. S2CID 32216266.
  4. ^ C.M. Dekkers, Jack (2012). "Application of Genomics Tools to Animal Breeding". Current Genomics. 13 (3): 207–212. doi:10.2174/138920212800543057. PMC 3382275. PMID 23115522.
  5. ^ Ribaut, J-M; de Vicente, Mc; Delannay, X (April 2010). "Molecular breeding in developing countries: challenges and perspectives". Current Opinion in Plant Biology. 13 (2): 213–218. doi:10.1016/j.pbi.2009.12.011. PMID 20106715.
  6. ^ Hollington, P.A.; Steele, Katherine A. (2007), "Participatory Breeding For Drought and Salt Tolerant Crops", Advances in Molecular Breeding Toward Drought and Salt Tolerant Crops, Dordrecht: Springer Netherlands, pp. 455–478, doi:10.1007/978-1-4020-5578-2_18, ISBN 978-1-4020-5577-5, retrieved 2020-10-02
  7. ^ a b Meuwissen, T. H. E.; Hayes, B. J.; Goddard, M. E. (2001-04-01). "Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps". Genetics. 157 (4): 1819–1829. doi:10.1093/genetics/157.4.1819. ISSN 0016-6731. PMC 1461589. PMID 11290733.
  8. ^ Jannink, Jean-Luc; Lorenz, Aaron J.; Iwata, Hiroyoshi (2010-03-01). "Genomic selection in plant breeding: from theory to practice". Briefings in Functional Genomics. 9 (2): 166–177. doi:10.1093/bfgp/elq001. ISSN 2041-2649. PMID 20156985.
  9. ^ Heffner, Elliot L.; Sorrells, Mark E.; Jannink, Jean-Luc (2009-01-01). "Genomic Selection for Crop Improvement". Crop Science. 49 (1): 1–12. doi:10.2135/cropsci2008.08.0512. ISSN 1435-0653.
  10. ^ "Analysis". bucklerlab.
  11. ^ Goddard, ME; Hayes, BJ (2007). "Genomic selection". Journal of Animal Breeding and Genetics. 124 (6): 323–30. doi:10.1111/j.1439-0388.2007.00702.x. PMID 18076469.
  12. ^ Sun, Min; Yan, Haidong; Zhang, Aling; Jin, Yarong; Lin, Chuang; Luo, Lin; Wu, Bingchao; Fan, Yuhang; Tian, Shilin; Cao, Xiaofang; Wang, Zan; Luo, Jinchan; Yang, Yuchen; Jia, Jiyuan; Zhou, Puding; Tang, Qianzi; Jones, Chris Stephen; Varshney, Rajeev K.; Srivastava, Rakesh K.; He, Min; Xie, Zheni; Wang, Xiaoshan; Feng, Guangyan; Nie, Gang; Huang, Dejun; Zhang, Xinquan; Zhu, Fangjie; Huang, Linkai (2023). "Milletdb: a multi‐omics database to accelerate the research of functional genomics and molecular breeding of millets". doi:10.1111/pbi.14136. PMC 10579705. {{cite journal}}: Cite journal requires |journal= (help)
  13. ^ Sun, Congwei; Hu, Huiting; Cheng, Yongzhen; Yang, Xi; Qiao, Qi; Wang, Canguan; Zhang, Leilei; Chen, Da-Yuan; Zhao, Simin; Dong, Zhongdong; Chen, Feng (2023). "Genomics‐assisted breeding: The next‐generation wheat breeding era". doi:10.1111/pbr.13094. S2CID 258478136. {{cite journal}}: Cite journal requires |journal= (help)

Further reading

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