Fine mapping and gene cloning in the post-NGS era: advances and prospects

Jaganathan, D and Bohra, A and Thudi, M and Varshney, R K (2020) Fine mapping and gene cloning in the post-NGS era: advances and prospects. Theoretical and Applied Genetics (TSI), 133 (5). pp. 1791-1810. ISSN 0040-5752

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Abstract

Improvement in traits of agronomic importance is the top breeding priority of crop improvement programs. Majority of these agronomic traits show complex quantitative inheritance. Identification of quantitative trait loci (QTLs) followed by fine mapping QTLs and cloning of candidate genes/QTLs is central to trait analysis. Advances in genomic technologies revolutionized our understanding of genetics of complex traits, and genomic regions associated with traits were employed in marker-assisted breeding or cloning of QTLs/genes. Next-generation sequencing (NGS) technologies have enabled genomewide methodologies for the development of ultra-high-density genetic linkage maps in different crops, thus allowing placement of candidate loci within few kbs in genomes. In this review, we compare the marker systems used for fine mapping and QTL cloning in the pre- and post-NGS era. We then discuss how different NGS platforms in combination with advanced experimental designs have improved trait analysis and fine mapping. We opine that efficient genotyping/sequencing assays may circumvent the need for cumbersome procedures that were earlier used for fine mapping. A deeper understanding of the trait architectures of agricultural significance will be crucial to accelerate crop improvement.

Item Type:	Article
Divisions:	Research Program : Genetic Gains
CRP:	CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC)
Uncontrolled Keywords:	Genetics, Genomics, Breeding
Subjects:	Others > Plant Breeding Others > Genetics and Genomics
Depositing User:	Mr Arun S
Date Deposited:	04 Sep 2020 17:01
Last Modified:	04 Sep 2020 17:01
URI:	http://oar.icrisat.org/id/eprint/11588
Official URL:	https://doi.org/10.1007/s00122-020-03560-w
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	The authors are thankful to Australia–India Strategic Research Fund (AISRF) project funded by the Department of Science and Technology (DST) and Tropical Legumes I (TLI) project funded by Bill and Melinda Gates Foundation (BMGF) through CGIAR-Generation Challenge Program (GCP; http://www.gener ation cp.org/). The Department of Biotechnology (DBT) is greatly acknowledged for providing the grant and fellowship to the first author. This work has been carried out as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals. ICRISAT is a member of the CGIAR Consortium.
Links:	Google Scholar

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