C. Mahadevaiah

1. Sugarcane Varieties (CVRC/SVRC notified)
2. Co 0212: Associated with development of Co 0212. A midlate maturing sugarcane variety Co 0212 evolved through hybridization and selection from cross Co 7201 × ISH 106. It was released for commercial Tamil Nadu by the State Variety Release Committee during 2015-16.  Co 0212 recorded significantly higher cane yield (150.56 t/ha), CCS % (12.80%) and sugar yield (19.27 t/ha) than the standard variety Co 86032 (131.67 t/ha of cane yield, 12.45% of CCS% and 16.32 t/ha of CCS yield) across eighteen locations. It recorded an average of 14.34 percent improvement for cane yield, 3.06 percent improvement for CCS percent and 18.07 percent improvement for CCS yield
3. Co 06022: Associated with development of Co 06022. New early maturing variety Co 06022 evolved through hybridization and selection from progenies derived from GU 92-275 × Co 86249. It was released for commercial cultivation in Tamil Nadu and Puducherry during 2017-18 by State Variety Release Committee. It is a drought tolerant variety recorded 135.8 tonnes/ha of cane yield, 17.68 t/ha of sugar yield and 13.10 percent of CCS% as compared to early standard varieties CoC 24 and TNAUSi 7.
4. Co 10026: Associated with development of Co 10026. New early maturing variety Co 10026 (Uphaar) and notified for commercial cultivation in peninsular zone by Central Varietal Release Committee during 2018-19. This clone developed through hybridization and selection from progenies derived from Co 86010 × Co 86011. In Peninsular zone, it recorded 11.80 percent improvement for CCS yield (13.85 t/ha) over CoC 671. It recorded the improvement of 20.15, 17.87 and 19.18 percent improvement for cane yield (109.01 t/ha) over CoC 671 (90.73 t/ha), Co 85004 (92.48 t/ha) and Co 94008 (91.47 t/ha) respectively. This variety is moderately resistant to red rot disease and tolerant to drought and salinity.
5. Co 11015: Associated with development of Co 111015. Co 11015 (Atulya) has been notified for cultivation in Tamil Nadu as a short-duration variety in the 83^rd meeting of the Central Sub Committee on Crop Standards, Notification, Government of India. This variety combines high cane yield and high sucrose content right from 8 months to 12 months of crop age. Co 11015 evolved from the cross CoC 671 and Co 86011 at ICAR- Sugarcane Breeding Institute, Coimbatore. The clone showed a remarkably good performance in the clonal trials with clear superiority over the standards Co 86032 and CoC 671. In station trials, it recorded a cane yield of 135.70 t ha^-1, sucrose of 21.46 % and sugar yield of 20.09 t ha^-1 at 360 days.

Genetic Stocks

1. Genetic Stock: Co 85019 (NBPGR Registration No: INGR22183)
            Co 85019 (Genetic Stock: INGR22183) registered for high cane yield and CCS yield under tillering phase drought stress during 2021-22. It is a mid-late maturing clone that performed extremely well in multi location trials conducted under drought conditions in Maharashtra. It recorded the highest cane and sugar yield in the drought experiments (suru season planting) conducted at four locations/R&D farms of sugar factories. Drought stress was imposed during the formative phase by withholding irrigation from March 1st to June 30th (90 days to 150 days) during 2018-19 and 2019-2020. It recorded a cane yield of 99.15 t/ha, sugar yield of 12.87 t/ha and 18.62% sucrose in drought trials and showed an improvement of 27.41%, 27.41% and 1.68%  for cane yield, sugar yield, and sucrose content over Co 86032 and that of  6.17%, 14.26 % and 6.63% improvement in cane yield, sugar yield, and sucrose content over CoM 0265. In the ratoon trial at Kopargaon, the entry Co 85019 showed an improvement of 7.28% and 1.49% for cane yield over the checks Co 86032 and CoM 0265 respectively under severe drought conditions of more than five months. Co 85019 has the ideal plant characters such as millable cane length (221.63 cm), medium thick cane (2.88 cm) and stay green type under drought stress.  The clone is tolerant to drought and salinity conditions, the major yield-limiting abiotic stress in Maharashtra
2. Genetic Stock: Co 98017 (NBPGR Registration No: INGR22184)
           Co 98017 (Genetic Stock: INGR22184) registered for the high number of millable canes under tillering phase drought stress. It is a mid-late maturing clone that recorded superior performance under multilocation conducted under drought conditions in Maharashtra. It is a drought-tolerant clone suitable for cultivation in drought-prone areas of Maharashtra. The drought experiments (suru season planting) were conducted in four locations/R&D farms of sugar factories and formative phase drought stress was imposed by withholding the irrigation from March 1st to June 30th (90 days to 150 days) during 2018-19 and 2019-2020. It recorded a cane yield of 96.43 t/ha, sugar yield of 12.52 t/ha and 18.47% of sucrose in drought trials and showed an improvement of 23.91, 26.11 and 0.89% for cane yield, sugar yield, and sucrose content over Co 86032 and, that of 3.26, 11.08 and 5.79% improvement in cane yield, sugar yield, and sucrose content over CoM 0265. In the ratoon trial at Kopargaon, Co 98017 recorded 82.36 t/ha of cane yield, significantly superior as compared to the checks Co 86032 (52.82 t/ha) and CoM 0265 (45.19 t/ha) respectively under severe drought conditions of more than five months. Co 98017 previously identified for subtropical regions has the ideal plant characters such as the highest number of millable canes (73,700/ha), millable cane length of more than 200 cm and stay green type under drought stress. The clone was identified as drought-tolerant clones, the major yield-limiting abiotic stress in Maharashtra.

PROTOCOL/METHODOLOGY

Standardization of protocol/methodology for androgenesis in sugarcane cultivar Co 86032: Spike/arrow of Co 86032 was sampled at the short blade stage, 5-10 cm between the short blade and symptom leaf. At this stage, most of the microspores in the top 1/3rd of spikes are early to the late uninucleate stage with less starch and tender exine wall. Carbon source: Maltose was found to be optimum for androgenesis as compared to the sucrose content. Chu 6 (N6) media was supplemented with 30 grams of maltose with plant growth regulators such as auxin (2,4-D) and cytokinin (6 Benzyladenine and Kinetin) in the ratio of 3.33 ratio was found to be optimum for androgenesis.  Plants were hardened and three calli viz., callus E, callus 17 and callus 18 showed variation for morphological traits and total DNA content as confirmed by Flow Cytometry analysis

DATABASE

1. Transcriptome Database Bioproject ID: PRJNA716503

          The comparative transcriptome analysis was performed between stressed and control samples of saline-tolerant Eraianthus arundinaceus accession IND99-907 and saline-sensitive sugarcane genotype Co 97010 with three biological replications and data deposited in the Bioproject ID: PRJNA716503. We generated a total of 305, 244, 264, and 263 million raw reads from the stressed and control libraries of IND99-907 and Co 97010 respectively. The pre-processing of raw reads by removal of adapter sequences, rRNA sequences, and ambiguous bases with high-quality sequences with a Phred score of ≥30 (Q30) resulted in 226, 182, 196, and 198 million clean reads from stressed and control libraries of IND99-907 and Co 97010 respectively. We obtained more than 74% of the high-quality clean reads after pre-processing of the raw data resulted in 802 million clean reads which were good enough to perform the RNASeq analysis. The high-quality reads of stressed and control libraries of IND99-907 and Co 97010 were assembled into four de novo assemblies for 907C, 907S, 97010C and 97010S using Trinity v2.8.5. The quality assessment and comparison of assemblies were performed using Quast and BUSCO tools. The Quast analysis revealed the total number of contigs of four assemblies was ranged from 205,717 to 345,745, the highest contig N50 of 1727 bp was observed in 907S assembly and the largest contig of 29724 bp was recorded in 97010S assembly. After unigenes clustering, the number of contigs was ranged from 179304 to 242390 with the highest contig N50 of 2102 bp in 907S unigenes assembly. The merging of control and stressed unigene assemblies for each genotype resulted in the identification of 315611 unigenes with a contig N50 of 2071 bp and 426820 unigenes with N50 of 1800 bp in the clustered unigene assembly of IND99-907 and Co 97010 respectively. The high-quality clustered assemblies of IND99-907 and Co 97010 were used for transcript quantification and annotation processes. The coding DNA sequences were identified from the clustered assemblies of IND99-907 and Co 97010 by using the TransDecoder tool and the transcript quantification was performed by using RSEM v1.2.25. The transcript counts generated by RSEM were used to perform the differential gene expression (DGE) analysis by using DESeq2 for both IND99-907 and Co 97010 separately. The DEGs were identified based on absolute log2FC>2 for upregulated genes and log2FC<-2 for downregulated genes. A total of 7731 DEGs from IND99-907 (Control vs Stress) DEG library and 6159 DEGs from Co 97010 (Control vs Stress) library were obtained at a significance level p<0.05. The FDR corrections were performed through the Benjamini-Hochberg method to reduce the false positives and, a stringent FDR <0.01 was used to further reduce the number of DEGs which yielded a total of 649 DEGs in IND99-907 and among them, 425 genes were upregulated and 197 were downregulated. A total of 501 DEGs were identified in Co 97010 and out of them, 283 genes were upregulated and 213 genes were downregulated. This database serves as resource for sugarcane researchers across the world.

2. Small RNA Seq database BioProject ID: PRJNA888470

           The comparative Small RNA Seq analysis was performed between stressed and control samples of saline-tolerant Eraianthus arundinaceus accession IND99-907 and saline-sensitive sugarcane genotype Co 97010 with three biological replications and data deposited in the Bio project ID: PRJNA888470. a total of 362 known miRNAs belonging to 62 families and 353 miRNAs belonging to 63 families were abundant in IND99-907 and Co 97010 respectively. The miRNA families such as miR156, miR160, miR166, miR167, miR169, miR171, miR395, miR399, miR437 and miR5568 were the most abundant with more than 10 members in both genotypes. The unaligned reads from miRbase were mapped against sugarcane monoploid reference genome using miRDeep2 tool resulting in the identification of 194, 38, 184 and 96 novel miRNAs from 907C, 907S, 97010C and 97010S libraries respectively. The differential expression analysis of miRNA reveals that a total of 221 known miRNAs belonging to 48 families and 130 known miRNAs belonging to 42 families were differentially expressed in IND99-907 and Co 97010 respectively. With regards to miRNA target identification, a total of 12,693 and 7,982 miRNA targets against the monoploid mosaic genome and a total of 15,031 and 12,152 miRNA targets against the de novo transcriptome were identified for differentially expressed 221 and 130 known miRNAs of IND 99-907 and Co 97010 respectively.  The GO enrichment analysis of the miRNA targets revealed that 24, 12 and 14 enriched GO terms (FDR<0.05) for biological process, molecular function and cellular component respectively. The salt-responsive biological processes such as transport, signal transduction, response to abiotic stimulus, response to stress, molecular functions such as binding, transporter activity and hydrolase activity, and cellular components like intracellular and cytoplasmic parts were enriched in our studies. Many miRNAs such as sbi-miR6232, miR6220, sbi-miR5568e and many other miRNAs were abundant and expressed contrastingly in IND99-907 and Co 97010. These miRNAs have many targets which were reported associated regulation of biotic and abiotic stresses. Thus, the genomic resources generated through this study are useful for sugarcane crop improvement through biotechnological and advanced breeding approaches.