Cotton Gene Bank:

  • The National Centre for Cotton Genetic Resources with more than 9000 accessions of the four cultivated species of Gossypium and over 100 accessions of perennials including wild species and cytogenetic material (in situ in species garden) has been established at CICR, Nagpur. Germplasm lines were screened and a good number of lines with good agronomic base, superior fibre quality and resistant to pests and diseases were identified and distributed to end-users.
  • Seeds of one thousand five hundred seventeen G. hirsutum including 289 exotics and 350 accessions of G. arboreum were sent to NBPGR, New Delhi for long term cold storage, while another set of G. hirsutum and G. arboreum germplasm was kept in Medium Term Cold Storage at CICR, Nagpur .
  • Three genetic stocks of G. arboreum race Cernuum immune to Grey Mildew ( Ramularia areola Atk ) disease viz., 30814 (INGR No. 09117), 30826 (INGR No. 09118) and 30856 (INGR No. 09119) were evaluated and registered with NBPGR, New Delhi.

Varietal Improvement:

  • The Institute has released ten varieties of G.hirsutum (MCU 5 VT, LRA 5166, Supriya, Kanchana, Anjali, CNH36, Arogya, Surabhi, Sumangala and CNH 120 MB), five intra-hirsutum hybrids (Savitha, Surya, Kirthi, Omshankar and CSHH 198), two hirsutum x barbadense (inter- specific) hybrids (HB 224 and Shruthi), and one intra arboreum hybrid (CISAA 2). The variety LRA 5166 occupies the largest acreage in India.
  • The Bt gene has been introgressed in more than thirty genotypes/varieties having good agronomic base through back crossing. The Bt varieties are intended for release in north, central and south zone. The materials are in BC 2 and BC 3 generations.
  • Several multiple adversity resistant (MAR) lines having resistance to grey mildew, altemaria leaf spot and bacteria1leafblight have been developed.
  • Study of different methods of breeding and selection for improvement of seed oil and lint characters resulted in the identification of high yielding early maturing cultures with improved oil content. Biparental selection was found to be ideal for transferring high oil content. Crosses between genetically diverse parents had greater degree of heterosis for oil. .
  • Two promising semi dwarf cultures (CNH 123 and CNH 155) with high yield potential and with amenability to closer spacing have been developed and are in advanced stages of testing in All India Coordinated Cotton Improvement Project trials.
  • Few male sterile plants have been identified in the derivatives of multispecies hybrids involving wild species G.raimondii, G.thurberi and cultivated species G.hirsutum and G.barbadense which are cytomorphologically stable.
  • Maintenance of Male sterile lines : One hundred thirty seven CMS (harknessii), 15 CMS (aridum), 19 GMS and 57 restorer lines were maintained through crossing, sibmating and selfing. For improving the CMS and GMS lines, AK 32 CMS ( aridum) , Rajat CMS ( harknessii) and G 67 (GMS) lines were treated with physical and chemical mutagen (gamma rays and ethyl methane sulphonate). Individual sterile plants were identified and maintained through crossing.
  • Performance of GMS based hybrids CSHG 1862 :   In the AICCIP North Zone trials, based on mean performance of last three years GMS based hybrid CSHG 1862 recorded 13 % increased seed cotton yield and 18 % for lint yield over the conventional check hybrid CSHH 198.
  • Development of Early Duration, Compact Genotype Twelve compact genotypes were evaluated for the third year in succession. Culture HCT 8 recorded the highest yield of 3664 kg/ha followed by HCT 12 with 3355 kg/ha. HCT 7 recorded the highest ginning out turn of 39.7 per cent . The best check Anjali recorded a mean seed cotton yield of 2692 kg/ha. A perusal of three years data also indicated the superiority of HCT 8 and HCT 12 by over 20 per cent as compared to the best check variety Anjali.
  • Development of long and extra long staple G.hirsutum cotton Thirteen long and extra long staple cultures were evaluated in a replicated trial with Surabhi as check for two years. Culture CCH 818 with a mean seed cotton yield of 1957 kg/ha was superior to Surabhi by 30 percent, followed by CCH 820 with 1935 kg/ha.
  • Wild species were used for introgression of useful characters and also for identifying new source of CMS. Elite lines with economic attributes and marker genes were isolated in the inter-specific hybrid derivatives. Gene ,for immunity to bacterial blight was introgressed into G.hirsutum from G.anomalum and dwarf early maturing bacterial blight immune variety NISD-2 was evolved.
  • Factors associated with drought tolerance were assessed and promising drought tolerant cultures CNDTS-2, CNDTS-3, CNDTS-5 and CNDTS 23 were identified.
  • By anatomical and biochemical studies it was deduced that gossypol content in the ovary was the most important deciding factor associated with bollworm tolerance.
  • Different agronomically superior cultivars have been converted into CMS 'A'lines and restorer lines.
  • Triploid hybrids have been developed between cultivated G. hirsutum and wild diploid G. armourianum and the hybridity has been conflrIned through RAPD analysis.
  • Breeder seed production is being taken up in this Institute. Useful information on seed production technology have been generated. Hard seed coat in H 4 was found to have been inherited from female parent. Exposure of seed to 90 °c in water or soaking the seed in ethyl alcohol for 10 minutes helped in overcoming hard seed coat.
  • 20 ppm NAA and 2% DAP sprayed four times during crossing period improved hybrid seed yield. To overcome the adverse effect of injury during emasculation, 50 ppm GA3 application helped in improving boll setting and H 4 seed yield and not in any other hybrid tested.
  • Topping 30 days after square initiation and foliar application of Lihocin 50 ppm improved the seed quality. By crop trimming of parents of GMS based hybrids three crops could be taken up with 30 to 40 % reduction in seed production cost. Higher dose of nitrogen followed by boron and zinc foliar spray improved seed quality and yield. Use of honeybee ~r hybrid seed production was found to be useful.
  • Coating of cotton seeds with Thiram @ 2 g kg -1 + Gypsum @ 60 g kg -1 + Micronutrient @ 20 g kg -1 +Imidacloprid @ 7 g kg -1 + DAP @ 20 g kg -1 in five layers sequentially were found to significantly enhance the viability.


  • Molecular Characterization of cotton germplasm (Core Collection) using DNA markers: A set of 96 core accessions were screened using the informative polymorphic markers. Combination of markers i.e.14 SSR, 17 SRAP and 15 RAPD markers (a total of 46) were employed to access genetic diversity and develop a marker profile. More informative markers are required to be used for reliably understanding the genetic diversity among the core accessions.
  • Bollworm resistant transgenic cotton in tetraploid and diploid cotton : The advanced T4 generation single event G. hirsutum cultivar Anjali (LRK-516) carrying cry 1Ac was raised under contained condition. Plants showing uniformly high concentrations of Cry protein expression were selfed, rouging out the segregating non-Bt plants. CRY protein expression to the extent of 2.70 ppm was recorded. In case of diploid cotton, 848 plants of Gossypium arboreum cv. RG 8 (T6), PA 255 (T4) and PA 402 (T3) containing cry I Ac and cry I Aa3 genes, expression of CRY proteins was determined by ELISA. Bt protein in boll to row progeny of 253 plants of RG 8 ranged from 2.54 to 4.6 ppm. Boll to row progeny of PA 255 culture 366 showed protein up to 3 ppm. In other promising cultures viz., 355, 358 and 365, the protein concentration ranged from 2-3 ppm.
  • Characterization of new transformed events : New transformation events were generated with G. hirsutum cultivars viz., Anjali and LRA 5166 with cry1Ac gene. Total 2076 embryonic explants were subjected to Agrobacterium ?mediated transformation and 11 primary putative transformants were selected in the kanamycin medium. Five cry 1 Ac transformed plants (3-Anjali and 2 LRA) showed integration of gene when checked by PCR. Southern hybridization of 5 plants showed single copy gene integration in two plants. Southern positive T0 plants were hardened and established in the soilrite. In case of diploid G. arboreum , 26 new events (T0) containing cry IAa3 and cry IAc gene were established in cultivars PA 255 and PA 402.
  • Pollen tube pathway transformation : A new method of gene transfer was standardized to overcome limitations associated with recalcitrant, genotype dependent somatic embryogenesis and tissue culture protocols. A number of parameters were standardized. The characteristics of the cry 1F transformants developed through this novel approach, including transformation frequency, transgene expression, copy number integration, stability of gene integration, etc. were studied. The superiority of the new method will be reestablished before filing a patent on the protocol.
  • Genetic Engineering for Abiotic Stress Tolerance in Crops and identification of new genes for high water use efficiency : Elite cultivars viz., LRA 5166 and LRK-516 were subjected to genetic transformation with p ATRD 29A ::AtCBF3/DREB1A+P OsMYB02 ::AtAVP1 gene construct by Agrobacterium –mediated transformation. Putative transformants selected in the antibiotic medium were tested for the presence of transgene by PCR confirmation. The transformation frequency of 0.88% in LRA 5166 and 0.73 % in LRK 516 was recorded.
  • Development of disease resistant transgenic cotton - Cloning of Chitinase genes for fungal resistance Chitinases are known to hydrolyse chitin polymers and are effective against fungi having chitin content in their cell walls. Chitinases belong to group of PR proteins that constitute the second line of plant defense. Using conserved and degenerate primers, a 1.3 kb full length novel class I chitinase gene was amplified and cloned from Gossypium hirsutum variety LRA5166. Analysis of sequence revealed the gene to be unique to upland cotton (GenBank # HM 125506). The gene-specific primers failed to amplify the sequence from G. arboreum lines including cultivar PA255, PA402 and RG-8. Diploid cottons G. arboreum (4-6) did not possess the same. The forward and reverse primers were engineered with Eco RI sites flanking the intitiation and termination codon respectively. Using them the 1.3 kb chitinase gene flanked with Eco RI sites were amplified and cloned in plasmid pGemT (3.0 kb). The recombinant plasmid was subcloned in the binary vector pBInAR and transformed in Agrobacterium tumefaciens strain EHA105, by triparental mating.
  • Identification of Molecular markers and tagging genes for Bacterial blight resistance : Five cotton lines were screened for resistance against race 18 of Xanthomonas axonopodis pv. malvacearum by syringe infiltration of bacterial cell. Gossypium hirsutum cotton Acala 44 and Ganganagar Agethi were highly susceptible against race 18 of X. malvacearum, while G.hirsutum cotton IM216, S295 and 101-102 B were completely resistant to race 18. C rosses were effected using two susceptible lines and three resistant lines viz., IM216, S295 and 101-102B. Susceptible lines were employed as female parents while the resistant lines were used as male parents. The F1s of each of the four crosses viz. Acala-44 X IM216; Ganganagar Agethi X IM216; Ganganagar Agethi X S295; and Ganganagar Agethi X 101-102B, were completely resistant against race 18 of X. malvacearum . The phenotyping of F2 mapping population of 122 plants of a cross between Acala-44 X IM216 by inoculation with Xanthomonas axonopodis pv. Malvacearum showed inheritance of resistance and susceptibility at an expected 3:1 ratio indicating single gene dominance of resistance. Chi-Square analysis was performed for testing independent segregation for bacterial blight resistance and susceptible traits.

CLCuV-resistance transgenic cotton

  • Development of Transgenic Cotton for Cotton Leaf Curl Virus resistance Antisense approach : Southern hybridisation of CLCuV transgenic G. hirsutum HS6 (T1) plants showed integration of the Sense coat protein, antisense coat protein and antisense Rep gene. Three transgenic events one each involving ACP and ARep in HS6 and SCP in H777 proved tolerant against CLCuV when tested in CICR Regional Station at Sirsa with viruliferous whitefly. Fresh transformation events were generated with each of the three gene constructs. The putative transformants were characterized for the presence of genes using gene specific primers.
  • Work is initiated to develop CLCuV resistant transgenic cotton through dsRNAi mediated silencing of viral genes. Plasmids vectors of pKB-Gus (3.9 kb) and pKB-intron developed for generating RNA interference constructs for gene disruption.
  • An RAPD marker associated with CLCuV resistance was identified. The RAPD fragment was converted into a SCAR marker based on which a set of specific primer capable of identifying CLCuV resistance by amplification of a 1.7 kb DNA fragment.

Improvement of fibre strength

  • Attempts are being made to clone cellulose synthase gene (AthA and AthAB) from Arabidopsis which brings about rapid conversion of carbon to UDP glucose to facilitate high fibre strength. cDNA clones were made and the expected amplicons were subjected to sequence analysis and work is in progress.

DNA Finger Printing

  • Molecular Characterization of cotton germplasm (Core Collection) using DNA markers: A set of 96 core accessions were screened using the informative polymorphic markers. Combination of markers i.e.14 SSR, 17 SRAP and 15 RAPD markers (a total of 46) were employed to access genetic diversity and develop a marker profile. More informative markers are required to be used for reliably understanding the genetic diversity among the core accessions.
  • All the wild species available in CICR were characterized by using RAPD and ISSR molecular markers.
  • Eleven cotton hybrids alongwith their parents and 13 cultivars were characterized at the molecular level and specific markers were identified for testing genetic purity
  • SCAR markers and specific primers designed to identify three cotton hybrids Savitha, Shruthi and Surya.
  • Fingerprinting of 56 race 18 strains of Xam with RAPD,IS112,ERIC,Box,Rep-PCR primers and RFLP markers revealed wide genetic variability, grouping them in 10-15 distinct clusters.

Drought Resistance Genes

  • Intensive efforts are underway to clone and characterize native genes from cotton viz., protease inhibitor involved in pest resistance and osmotin and dehydrin genes that govern tolerance of cotton to drought.

Molecular breeding

  • Making framework linkage maps in diploid cotton (A genome) and G.hirsutum has been initiated. Priority is for making fibre quantity traits(QTLs) such as fibre strength ,fibre length and micronaire, oil content and also ginning outturn a major economics trait in diploid and tetraploid cotton. Mapping populations for these traits have been developed in diploid as well as G.hirsutum. The growing information on these aspects will help in Market Assisted Selection (MAS) in cotton.
  • Species specific primers and PCR protocols developed for precise detection and differentiation of four major economically important fungal pathogens of cotton viz., R. areola, R. bataticola, R. solani and A. macrospora.

Nodule Induction in Cotton

  • Cotton plants were subjected to root nodule induction by Rhizobium fredii. Six individual plants of Anjali and two of LRA 5166 produced nodules in their root system. Although bacteriods were present in the nodules, nitrogenase activity was not recorded. The observation opens up the possibility of nodulation and nitrogen fixation by virulent Rhizobia in non-legume plants like cotton.

List of varieties/hybrids released by CICR

Varieties/ hybrids

Year of release

Spinning potential (counts)

Area of adaptability


G. hirsutum

Verticillium wilt prone tracts of Tamil Nadu

Verticillium wilt tolerant
LRA 5166
Rainfed and irrigated tracts of southern cotton zone & Vidarbha (Maharashtra)
Drought tolerant & adaptable to different agro-climatic conditions
Irrigated tracts of southern cotton zone
Whitefly tolerant
Whitefly prone area of southern cotton zone
Whitefly tolerant
Anjali (LRK 516)
Rainfed and irrigated conditions of Maharashtra, Gujarat and south Rajasthan
Early maturing, compact & semidwarf, suited for closer spacing
CNH 36
Irrigated areas of western Maharashtra and southern and middle Gujarat
Dwarf early maturing
Rainfed areas of central Zone
Bacterial blight immune
50s - 60s  
South Zone
Verticillium tolerant extra long staple high yielding than
30s- 40s  
South Zone
CNH 120 MB
Irrigated areas of south zone, also suitable for rainfed condition
compact, early maturing, medium staple with high fiber strength
CISA 310
Irrigated Area of North Zone
Tolerant to fusarium wilt and root-rot
Intraspecific hybrid - Intra-hirsutum
Irrigated tracts of southern cotton zone
Intra-hirsutum hybrids of MCU 5 quality
Kirti (CICR HH1 )
Rainfed areas of Marathwada region of Maharashtra
Early maturing hybrid
Surya (TM 1312)
Southern cotton zone
Presence of genetic marker character
OM- Shankar
Northern cotton belt
Early maturing, high yielding hybrid
CSHH 198
Northern cotton belt
CLCuV resistant
CSHH 238
Irrigated Area of North Zone
CLCuV resistant
CSHH 243
Irrigated Area of North Zone
CLCuV resistant
Interspecific hybrid - G. hirsutum x G. barbadense
HB 224
Irrigated tracts of southern cotton zone
Extra long staple Hybrid
Southern Cotton zone
Compact, short duration hybrid
Intra-arboreum hybrid
Northern cotton zone
GMS based hybrid

some unique cultures/line were registered with NBPGR as Indian National Genetic Resource

Genotype registered with NBPGR

Name of the material/designated material

Genera & species

Race /pedigree

Registration No.

Year of registration/patent

Unique characters

G135-49 Gossypium arboreum L. Bengalense INGR No.00017 Notification date 10.5.2000 Immune to all Grey mildew (Ramularia areola Atk) disease isolates existing in nature at present
30805 Gossypium arboreum L. Cernuum INGR No.00018 Notification date 10.5.2000 -do-
CNO 131 Gossypium hirsutum L. latiofolium INGR No.00010 Notification date 10.5.2000 Earliness and high seed oil content
30838 Gossypium arboreum L. Cernuum INGR No.02020 Notification date 22.5.2002 Immune to all Grey mildew (Ramularia areola Atk) disease isolates existing in nature at present
CNH 123 Gossypium hirsutum L. latiofolium INGR No.02021 Notification date 22.5.2002 Resistant to cotton Leaf curl virus (CLCuV)
LRA 5166 (GMS) Gossypium hirsutum L. latiofolium INGR No.02012 Notification date 22.5.2002 Converted into GMS line
CINA 316 Gossypium arboreum L. Bengalense INGR No.04079 Notification date 31.5.2004 High locule retentivity anad low short fiber content
BNARB-16 Gossypium hirsutum L. G.arboreum Cytoplasm INGR No.05020 Notification date 11.8.2005 Bollworm and Jassid tolerant
BNTOM-277 Gossypium hirsutum L. G.tomentosum Cytoplasm INGR No.05019 Notification date 11.8.2005 Bollworm and Jassid tolerant
CSPFI Gossypium hirsutum L. latiofolium INGR No.07035 Notification date 14.5.2007 Pink colored flower mutant
CPFI Gossypium hirsutum L. latiofolium INGR No.07036 Notification date 14.5.2007 Pink filament mutant
BN Red Gossypium hirsutum L. G.tomentosum Cytoplasm INGR No.07049 Notification date 14.5.2007 Bollworm and Jassid tolerant
BN Okra Gossypium hirsutum L. G.arboreum Cytoplasm INGR No.07050 Notification date 14.5.2007 Bollworm and Jassid tolerant
CNH 301 Gossypium hirsutum L. SRT 1 x 1301 DD in F2 generation INGR No.11061 2011 Drought tolerant nature and yield stability
Vaidehi 95(MSH 53) Gossypium hirsutum L. (G.hirsutum x G.raimondii)2 x (G.barbadense x G.thuberi)2 INGR No.13032 2013 Dark brown lint color
NISC 40 Gossypium hirsutum L. (G.hirsutum x G.raimondii)2 x G.hirsutum INGR No.13033 2013 Jassid tolerant
NISC 43 Gossypium hirsutum L. (G.hirsutum x G.raimondii)2 x G.hirsutum INGR No.13034 2013 Jassid tolerant
NISC 44 Gossypium hirsutum L. (G.hirsutum x G.raimondii)2 x (G.barbadense x G.thuberi)2 INGR No.13035 2013 Jassid tolerant
CNA 5 Gossypium arboreum L G.arboreum race indicum x G.arboreum race burmanicum INGR No.14005 2014 Inter-racial pigmented arboreum
CNH CB 211 Gossypium hirsutum L. Germplasm line (selection) INGR No.14058 2014 Cluster boll bearing habit, deeply palmate leaf lobe
CNH CB 212 Gossypium hirsutum L. Germplasm line (selection) INGR No.14059 2014 Cluster boll bearing habit, zero monopodia and compact habit

Seed Production and Seed Quality Improvement

  • Enhancement of seed germination and vigor : The size graded seeds of G. hirsutum varieties were evaluated to study the effect of seed index on field emergence and seed cotton yield. The seeds with highest index (ranging from 8.5 to 10.0g) gave highest emergence (96%) and seed cotton yield (780 kg/ha). The seed cotton yield from the seeds with lower index (ranging from 7.0 to 8.0g) followed next (662 kg/ha). The seeds with lowest seed index (less than 7.0 g) gave the least seed cotton yield over varieties (530 kg/ha.) Among the seed hardening treatments the controlled hydration of seeds over night was more effective for early and higher emergence under low soil moisture level (at 40%) compared to the control.
  • Development of efficient agro-techniques for enhancing productivity and seed quality in cotton : The application of salicylic acid @ 0.25% at 30 days after flowering gave higher seed cotton yield over control in first picking. However, application of lihocin @100 ppm at flower initiation gave higher seed cotton yield in second picking. The results indicated that salicylic acid application hastened the crop maturity compared to control and lihocin application. Seed index and seedling vigor was significantly superior in all treatments over control.
  • Testing & Documentation of Extant Varieties, hybrids and their Parents for Distinctness, Uniformity & Stability - Implementation of PVP legislation : Distinctiveness, Uniformity and Stability testing of tetraploid cotton genotypes were taken up in two trials comprising 5 and 23 candidate varieties, respectively. Similar trial was conducted for diploid cotton with one candidate and two reference varieties. The complete expression of desired morphological characteristics of seedling, leaf, flower, boll and fibre were measured. The characters were recorded from seedling to maturity adopting the procedure of approved national test guidelines for tetraploid cotton. Registration of extant and new cotton varieties under PPV&FR Act, 2001 was initiated. In the first phase. Sixty one application forms comprising of new and extant cotton varieties were submitted to PPV&FRA through NBPGR. Under the programme of maintenance of reference collection Fifty four G. hirsutum and ten G. barbadense genotypes were maintained. A database on varieties released by CVRC or State Varietal Release committee and in common knowledge/farmer's varieties, etc., was composed.
  • Film coating of cotton seeds with polymers: Seed deterioration can be prevented up to 18 months of storage and can retain the viability of 77% when pre cleaned seeds were coated with seed polymer polykote @ 3ml/kg of seed diluted with 5 ml water combined with carbendazim (Bavistin) @ 2 g /kg and the seeds are stored in cloth bag under ambient condition. Viability can also be retained to 76% by coating the seeds with polykote @ 3ml/kg of seed diluted with 5 ml water combined with carbendazim (Bavistin ) @ 2 g /kg and Imida cloprid @ 7g /kg when seeds are stored in polythene bags.



last updated on 15:06:2015
Information compiled, Page designed and developed by M. Sabesh, CICR, Coimbatore