**Abstract**

Conventional breeding interventions in cotton have been successful and these techniques have doubled the productivity of cotton, but it took around 40 years. One of the techniques of molecular biology i.e., genetic engineering has brought significant improvement in productivity within the year of introduction. With cotton genomics maturing, many reference genomes and related genomic resources have been developed. Newer wild species have been discovered and many countries are conserving genetic resources within and between species. This valuable germplasm can be exchanged among countries for increasing cotton productivity. As many as 249 Mapping and Association studies have been carried out and many QTLs have been discovered and it is high time for researchers to get into fine-mapping studies. Techniques of genomic selection hold valuable trust for deciphering quantitative traits like fiber quality and productivity since they take in to account all minor QTLs. There are just two studies involving genomic selection in cotton, underlining its huge prospects in cotton research. Genome editing and transformation techniques have been widely used in cotton with as many as 65 events being developed across various characters, and eight studies carried out using crisper technology. These promising technologies have huge prospects for cotton production sustainability.

**Keywords:** cotton, wild species, reference genomes, markers, QTL mapping, genomic selection, genetic transformation, gene-editing

## **1. Introduction**

Cotton is one among many fiber-producing species, but it is the only major crop cultivated for quenching one of the basic human necessities i.e., clothing. The ancient Harappan civilizations that were discovered in the Indus valley suggested that the first use of cotton was around the 2nd millennium BC [1]. However, the discoveries of cotton fabric at Duweilah in Jordan indicate that cotton was used as early as 4th millennium BC, but the latest discoveries at Mehrgarh in Pakistan suggest that cotton fibers were used as early as 6th millennium BC [2]. Hundreds of years ago cotton was a chief source of clothing and in the future, it would continue to be, because of its unique unparalleled qualities such as comfort, safety and eco-friendly attributes. However, with the revolution in the textile industry, the synthetic fibers were dumped into the markets with the big tag line as "costeffective" as these synthetic fibers can be manufactured at will with the desired

fiber properties to meet the spinning demands. Synthetic fibers were assumed as a major threat to cotton cultivation but sooner than later when people realized the unsustainability, unsafe and less eco-friendly characters of the Petro-chemical based synthetic fibers, cotton is still the most preferred and produced fiber for clothing [3]. It's a big surprise that the majority of us would strictly prefer cottonbased clothing for newborn children but not synthetic fibers, which describes its safety and comfort. Nowadays, the reinforcement of natural fiber by the synthetic fibers has proved excellent in terms of improved properties of the new fiber synthesized [4]. Apart from the primary application as clothing, coarse cotton is widely used in hospitals as cotton swabs. Cotton linters (fiber <3.5 mm) are used in the paper industry along with other pulps to manufacture technical papers, art papers etc. Cotton oil extracted from seed is used in the cosmetics and paint industry, oil can also be used for consumption/cooking if the gossypol content is very low. Cottonseed meal is used as dairy feed. Apart from being economically important, the cotton fiber serves as a powerful single-celled model in studying cell wall and cellulose research. Around 100 million people are involved in cotton production with over 250 million deriving employment in transportation, ginning process, and several million people in textile manufacturing, agriculture inputs sector and cottonseed crushing, among others [5]. The cotton export value during 2017 was around 15.62 billion US\$ (Rice export value; 24.99 billion US\$, Wheat export value: 45.13 billion US\$) [6]. Cotton has around 30% share in world textile fibers [3]. The global textile and apparel market were to the tune of 1.7 trillion US\$ [7], indicating that cotton is a very important crop globally. The world population is booming and it is expected to be 8–10 billion people by 2050 [8] On the contrary, cotton productivity has also seen a rise with few but impactful breeding and molecular breeding interventions such as the introduction of hirsutum, early maturing types, introduction of intra and interspecific hybrids/derivatives and Genetically

**Figure 1.**

*Productivity improvement comparison.*

Modified (GM) crops (pest and herbicide tolerance). However, the trend of increase in productivity of cotton (1961:8.62 q/ha vs. 2018:21.90 q/ha) compared to principal crops such as wheat (1961:10 q/ha vs. 2018: 34.25 q/ha) and rice (1961, 18.69 vs. 2018: 46.78 q/ha) (**Figure 1**) is very low due to less international collaboration and lesser germplasm, technology exchange. In 2050, the cotton production is required to be 94.71 MT of seed cotton (33.15 MT of lint) [9]. To meet the projected demand with the same amount of land i.e., 33 mha, there is a need to boost productivity to 28.7 t/ha of seed cotton. After the era of transgenic introductions, there is no new technological breakthrough to push the stagnant yield plateau to higher peaks. To sustain future demand with available scanty cultivable land with uncertain climatic vulnerabilities, there is a need for a strong, focused and coordinated cotton research among the world cotton research community. There lie huge prospects for molecular breeding to break the yield stagnation. Here we attempt to review the cotton genomics research carried out till date and its ability to meet the future demands.
