**4. Cotton conventional breeding**

Conventional breeding is the base for any trait improvement and without proper knowledge of conventional breeding techniques advanced molecular breeding techniques would surely lead to costly mistakes. Until the advent of molecular marker technologies, conventional breeding was the sole method for genetic improvement. Some of the popular conventional interventions in cotton were the development of determinate growth types. Development of early maturing types (resistant to boll weevils), the inclusion of morphological traits such as fergo bracts, glabrous leaves, nectariless, high gossypol for resistance to boll weevils and bollworms then followed.

Australian Conventional Breeding: American bollworm, Bacterial blight and Verticillium wilt were the major problems in Australia. Okra leaf types were used in an Australian breeding program by Norm Thomson to develop a variety called Siokra1-1 which was the first okra leaf type along with bacterial blight resistance in 1985. Dr. Peter Reid released Verticillium wilt resistance variety which was popular outside Australia [33].

Indian Conventional Breeding: Introduction of *G. hirsutum* during the 1970s and development of first intra-hirsutum hybrid cotton (H4) in India by C T Patel in 1970 [34] and Development of first interspecific hybrid (*G. hirsutum* x *G. barbadense*) in cotton (Varalaxmi) by B.H. Katarki in 1972 [35] led to utilizing hybrid vigour for higher productivity in the Indian subcontinent. Morphological traits such as fergo bracts, glabrous leaves, nectariless, and antibiosis [36–40] were included in the breeding program for bollworm tolerance. Wild species were used widely used through introgression breeding in developing novel varieties like Badnawar-1, Khandwa-1, and Khandwa-2 from *G. hirsutum* x *G. tomentosum* cross, Arogya and PKV081 using *G. hirsutum* x *G. anomalum* cross, Devitej using *G. hirsutum* x *G. herbaceum* cross, SRT-1, Deviraj and Gujarat 67 using *G. hirsutum* x *G. arboreum* cross. MCU2 and MCU5 from *G. hirsutum* x *G. barbadense* cross [41].

US Conventional breeding: Boll weevils were a major threat to cotton cultivation and elimination of boll weevils by developing early maturing short-staple types was one of the significant interventions [20]. To reduce the negative association between yield and fiber quality, exotic germplasm was used in breaking the association and varieties like MD51ne with higher fiber quality were developed [42]. Development of sub okra, smooth leaf, and nectariless for reducing tarnished plant bug populations [43] was another achievement. Some of the private companies like Delta Pine

made huge advances in cotton productivity improvement in cotton. They released mechanical harvest suitable variety called Delta pine smooth leaf which had around 25% US cotton area by 1963, Deltapine-16 with improved disease resistance and better fiber quality had around 28% area in the US by 1972, Delta pine Acala 90 premium quality cotton released was used as parental germplasm in development of many other varieties globally, all these interventions of Delta pine improved cotton production of United States significantly.

Uzbekistan Conventional Breeding: Turkestan Breeding Station established in 1992 with a major emphasis on the collection of cotton germplasm under the leadership of Dr. Zaitsev and Dr. Mauer was a major milestone in realizing the huge germplasm collection of present-day Uzbekistan. Early maturing types AK-Djura and Dehkam by Dr. Zaitsev were an important contribution. Utilizing *G. barbadense* as a resistant source to fusarium wilt and large boll types led to the release of 35-1 and 35-2 cultivars. Termez-14 high yielding cultivar developed by Dr. Ibragimov was another breakthrough. Development of Verticillium wilt resistance variety C-6524 by Dr. Alexander Avtonomov and Dr. Vadim Avtonomov had occupied more than two hundred thousand hectares for fifteen years till 2004 [44].

All these interventions along with production technologies have improved world productivity from 9.65 q/ha in 1960 to 16.20 q/ha in 2000 in the span of 40 years [6]. Conventional breeding methods are effective in transferring the traits but take considerably higher time, resources and uncertainty in the transfer of the trait. A breeding program involving large entries involves more samples needed to be tested for traits like fiber quality/oil content in cotton. We need to put a lot of resources and time to wait for the maturity of cotton. On the contrary, the Bt cotton technology, one of the spin-off technologies of genomics and molecular breeding played a significant role along with other production technologies and has achieved 5 q/ha improvement in just five years (**Figure 4**). Thus, cotton genomics/marker-assisted selection has huge potential in reducing a considerable amount of time, resource and assist conventional breeding in achieving future demands.

### **5. Advances in cotton genome sequencing**

Having a reference genome is a boon since it is possible to characterize gene/ gene families that are species-specific and which are further amenable to functional genomics work [45]. Since the publication "Toward Sequencing Cotton (Gossypium) Genomes" in 2007 by Chen and Co-workers [10], the framework was laid down for genome sequencing of cotton. The initial framework was to get first sequence of D-genome (*G. raimondii*) followed by A and then AD genome. [46] developed the first assembly in cotton (D-Genome). Now, as many as nine assemblies of *G. hirsutum*, four assemblies of *G. barbadense*, three assemblies of *G. arboreum*, three assemblies of *G. raimondii* and one each assembly of wild species such as *G. australe*, *G. darwinii*, *G. longicalyx*, *G. mustelinum*, *G. tomentosum* and *G. turneri* have been documented in CottonGen. The assembly statistics of various Gossypium genomes assembled are presented in **Table 3**. The reference genomes of cotton were used to produce a total of 17,224,361 SNPs that are documented in CottonGen by various researchers, the gene annotations and physical maps provided are valuable information for cotton scientists for various studies like the development of linkage maps, GWAS, validating the linkage maps, expression studies, development of guide RNAs in gene editing, genome-wide characterization studies of gene families etc. Since the sequencing cost is reducing day by day there are huge prospects for developing newer assemblies to catch all the variation



**Table 3.**

*Genome assembly statistics of various cotton species.*

(within and between species) for identifying rare alleles/genes that would help us to sustain future demands in cotton improvement.
