“Fine mapping and gene cloning: Advances and prospects”

  DNA markers associated with the Quantitative Trait Loci (QTL) region were used for making rapid and accurate selections for introgressing traits in many crop species. The QTLs regions identified by standard mapping procedure often extend several centiMorgans on genetic map and might contain large number of genes and it becomes very difficult to pinpoint causative locus responsible for a specific trait. Therefore, genetic resolution of the mapping procedures should be enhanced to allow QTL placement within the shortest possible genomic region using innovative strategies. This process of refining the QTL region is called as fine mapping¹.

Fine mapping of stable QTL (QTkw-2D) in wheat for thousand kernel weight offers starting point for map-based cloning and functional characterisation³. QTL-Seq, a high resolution mapping technique successfully located the genomic regions on the peanut genome and facilitated discovery of candidate genes and marker development for shelling percentage to use in Genome assisted breeding for faster development of new varieties². Mutation mapping technique, MutMap-Gap was applied to isolate blast resistant gene Pii from the rice cv Hitomebore using mutant lines that have lost Pii function⁴. Other fine mapping techniques, such as Bulk segregant RNA-Seq, MutMap and MutMap+ have been used to fine map complex traits in crop plants which aids in gene cloning.

In recent past, fine mapping of QTL has become less complicated and rapid due to availability of Next Generation Sequencing technologies and with rapid trait mapping approaches. Therefore, fine mapping and QTL cloning are instrumental in dissecting target regions of complex traits with greater precision.

References

1. JAGANATHAN, D., BOHRA, A., THUDI, M. AND VARSHNEY, R. K., 2020, Fine mapping and gene cloning in the post‑NGS era: advances and prospects. Theor. Appl. Genet., 133: 1791-1810.

 

2. LUO, H., PANDEY, M. K., KHAN, A. W.,  GUO, J., WU, B., CAI, Y., HUANG, L., ZHOU, X., CHEN, Y., CHEN, W., LIU, N., LEI, Y., LIAO, B., VARSHNEY, R. K. AND JIANG, H., 2019, Discovery of genomic regions and candidate genes controlling shelling percentage using QTL-seq approach in cultivated peanut (Arachis hypogaea L.). Plant Biotechnol. J., 17: 1248-1260.

 

3. MENG, D., BOTOOL, A., XUAN, YAZHOU., PAN, RUIQING., ZHANG, N., ZHAND, W., ZHI, L., REN, XIAOLI., LI, W., NIU, Y., ZHENG, S., JI, J., SHI, X., WANG, L., LING, H., ZHAO, C., CUI, F., LUI, F., LI, J AND SONG, L., 2023, Fine mapping and validation of stable QTL for thousand kernel weight in wheat (Triticun aestivum L.). Crop J., 23: 23-32.

 

4. TAKAGI, H., UEMURA, A., YAEGASHI, H., TAMIRU, M., ABE, A., MITSUOKA, C., UTSUSHI, H., NATSUME, S., KANZAKI, H, MATSUMURA, H., SAITOH, H., YOSHIDA, K., CANO, L. M., KAMOUN, S. AND TERAUCHI, R., 2013, MutMap-Gap: whole-genome resequencing of mutant F₂ progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii. New Phytol., 200: 276-283.