Reforming cotton genes: From elucidation of DNA structure to genome editing

Authors: MUBARIK, MUHAMMAD SALMAN - University Of Agriculture - Pakistan; MAJEED, SAJID - University Of Agriculture - Pakistan; KHAN, SULTAN HABIBULL - University Of Agriculture - Pakistan; DU, XIONGMING - Chinese Academy Of Agricultural Sciences; Frelichowski, James - Jim; Hinze, Lori; AZHAR, MUHAMMAN TEHSEE - University Of Agriculture - Pakistan

Submitted to: Turkish Journal of Agriculture and Forestry
Publication Type: Review Article
Publication Acceptance Date: 12/4/2021
Publication Date: 4/12/2020
Citation: Mubarik, M., Majeed, S., Khan, S., Du, X., Frelichowski, J.E., Hinze, L.L., Azhar, M. 2020. Reforming cotton genes: From elucidation of DNA structure to genome editing. Turkish Journal of Agriculture and Forestry. 45:691-703. https://doi.org/10.3906/tar-2012-64.

Interpretive Summary: Cotton is a worldwide leading renewable source of fiber for clothing and non-woven products. It is also a significant source of seed oil and protein for secondary food and feed markets. Increasing demands from a rising population and challenges to production from climate changes, drought, heat, insects, diseases, etc. places enormous pressure on plant breeders to sustain high productivity of cotton crops for farmers without increasing costs of inputs. Genetic modification of cotton crops with advanced biotechnology has improved resistance to damaging insect pests. Creation of a new cotton cultivar with present biotechnological methods still takes nearly a decade and still entails significant legal and regulation challenges with the genetically modified seed. Meanwhile genetic researchers discovered a sort of genetic warfare in the natural world of micro-organisms. Closer study revealed the use of many enzymes with capabilities of inserting, replacing, or resequencing genetic sequences on chromosomes, either for the benefit of the invading virus or to correct the genetic damage from them. Careful repackaging of these enzymes resulted in new biotechnological tools for changing existing cotton genes without the need for insertion of foreign genes. This change in tactic creates additional possibilities in creating necessary genes in cotton for better productivity and yield, but also circumvents legal and regulation hurdles involved in the current methods of insertion of foreign recombinant DNA into cotton. This paper contains a basic review of discovery of DNA structure and technologies leading to the evolution of the latest method called Clustered Regularly Interspaced Short Palindromic Repeats, nicknamed 'CRISPR'. It basically enables precise editing of DNA in target organisms. A wide array of uses is described from correction of genetic deficiencies in humans (sickle cell anemia), control of invasive and harmful pests such as pest fruit flies, to designer genes in existing cotton chromosomes. The targeted applications and possibilities in cotton are discussed with priorities on insect control and reducing extensive use of costly and damaging pesticides so that not only are cotton farmers meeting consumer demand but they protect their health and the environment as well.

Technical Abstract: Cotton is an essential fiber producing crop in the world. It also supports additional industries by providing high quality oil and protein in the form of cottonseed cake. Currently, there is a dire need to increase lint yield, fiber quality, and resistance to biotic and abiotic stresses due to rising demand from increased global population pressure and possible supply shortages from the effects of erratic climate changes. Classic plant breeding and transgenic strategies need more genetic breakthroughs to support the increasing demand for fiber quantity and quality. A potential for rapid increases in crop improvement is in various state-of-the-art gene editing technologies. Genetic research in simple micro-organisms revealed novel enzymes involved in natural sequence editing in cells, and they were successfully applied to gene editing in model plants through a system called CRISPR-Cas9. This and other enzymatic systems are heralded as providing numerous possibilities for creating genetic variation for crop breeders. However, gene editing in agriculture is most effective when focused on achieving transmissible changes by inducing targeted mutations in genes involved in yield or quality attributes. The newly emerged CRISPR-Cas variants should accelerate future research in cotton breeding because CRISPR-Cas tools can be utilized efficiently for gene editing without the need for foreign gene insertion through the modification of existing gene regulation, enzymatic activities, epigenetic modifications, insect/pest's gene drive technology, RNA targeting and, more recently, single base and prime editing.