Marker-assisted selection (MAS) has been widely used in the last few decades in plant breeding programs for the mapping and introgression of genes for economically important traits, which has enabled the development of a number of superior cultivars in different crops. In sugarcane, which is the most important source for sugar and bioethanol, marker development work was initiated long ago; however, marker-assisted breeding in sugarcane has been lagging, mainly due to its large complex genome, high levels of polyploidy and heterozygosity, varied number of chromosomes, and use of low/medium-density markers. Genomic selection (GS) is a proven technology in animal breeding and has recently been incorporated in plant breeding programs. GS is a potential tool for the rapid selection of superior genotypes and accelerating breeding cycle. However, its full potential could be realized by an integrated approach combining high-throughput phenotyping, genotyping, machine learning, and speed breeding with genomic selection. For better understanding of GS integration, we comprehensively discuss the concept of genetic gain through the breeder’s equation, GS methodology, prediction models, current status of GS in sugarcane, challenges of prediction accuracy, challenges of GS in sugarcane, integrated GS, high-throughput phenotyping (HTP), high-throughput genotyping (HTG), machine learning, and speed breeding followed by its prospective applications in sugarcane improvement.

Sugarcane grown under a wide range of agro-climatic conditions accounts for ~80% of the sugar production worldwide. Since sugarcane productivity is severely affected by abiotic stresses and hence, an experiment was conducted for two consecutive years during 2020 and 2021 on popular sub-tropical sugarcane varieties. The experiment was laid out in two-factorial RBD consisting of nine sugarcane genotypes (Co 98014, Co 0118, Co 0238, Co 05011, Co 06034, Co 09022, Co 12029, Co 15023 and Co 15027) and salinity treatments (Control, EC_iw ~ 4, 8 and 12 dS m⁻¹) in 5 replications. Two budded setts were planted in pots and irrigated with saline water of respective levels till formative phase and observed the build-up in electrical conductivity of soil extract (ECse) from 0.48 (control) to 2.99, 4.81 and 7.08; while further saline irrigation increased the ECse values to 4.48, 6.24 and 9.33 dS m⁻¹ in treatments EC_iw ~ 4, 8 and 12 dS m⁻¹, respectively. Increase in soil EC decreased plant survival by 24.1, 47.0 and 79.6% under continued irrigation of EC_iw ~ 4, 8, 12 dS m⁻¹ with respect to control. Continued saline irrigation caused significant reduction in growth, which was associated with reduction in relative water content (RWC) and gas exchange traits. RWC decreased by 4.91 to 21.9%, chlorophyll content by 8.46 to 32.75%, photosynthetic rate (Pn) by 16.85 to 91.44%, stomatal conductance by 14.96 to 84.25%, transpiration rate by 14.13% to 89.8% and chlorophyll fluorescence by 5.33 to 42.67% from EC_iw ~ 4 to 12 dS m⁻¹, respectively. Significant variations in Na⁺ and K⁺ ion content was observed under elevated saline condition in roots, leaves and juice extract of genotypes. Na⁺/K⁺ ratio, an important trait for screening salinity tolerance, increased in all genotypes as compared to control, the increase was predominant in susceptible varieties. Single cane weight (SCW) was drastically affected by saline irrigation, with a reduction of 36.4, 68.5 and 83.5% at EC_iw ~ 4, 8 and 12 dS m⁻¹, respectively as compared to control, with similar declining trend in juice quality. Based on our results, Co 0238, Co 0118 and Co 98014 were tolerant to salinity stress by maintaining higher Pn, lower leaf Na⁺/K⁺ ratio, higher SCW and higher juice sucrose content.

Additive main effects and multiplicative interaction (AMMI), as well as various AMMI-derived statistics, Genotype, and Genotype × Environment Interaction (GGE) models were employed on 24 sugarcane genotypes planted during two seasons (2017–18, 2018–19) under different induced salinity stress environments using saline water irrigation (iw) viz., E1 (Normal _iw during crop season 2017–18), E2 (Normal _iw during crop season 2018–19), E3 (4 dsm⁻¹ EC_iw during crop season 2017–18), E4 (4 dsm⁻¹ EC_iw during crop season 2018–19), E5 (8 dsm⁻¹ EC_iw during crop season 2017–18), E6 (8 dsm⁻¹ EC_iw during crop season 2018–19), E7 (12 dsm⁻¹ EC_iw during crop season 2017–18) and E8 (12 dsm⁻¹ EC_iw during crop season 2018–19) to assess the genotype by the environment interaction for the cane yield, commercial cane sugar (CCS) yield, number of millable cane (NMC), single cane weight (SCW), and pol % in juice. Individual and interactive effects of the genotype and environment for all the traits were significant. In the expression of total variability, the environmental contribution was higher for the cane yield (66.98%), CCS yield (67.60%), NMC (65.78%), and SCW (43.27%), whereas genotypic contribution was higher in the expression of pol% (82.48%). As per AMMI Stability Value (ASV), G14 (Co 13033), G23 (Co 15026), G7 (Co 05009), G17 (Co 13036), and G2 (Co 15025) were the most stable genotypes for the cane yield. Whereas as per GSI (genotype selection index), genotypes G24 (Co 15027), G21 (Co 15023), G23 (Co 15026), and G17 (Co 13036) were found most stable. The Sustainability Index (SI) of the cane yield (CY) and its contributing and CY-based computed traits were low for most of the genotypes, which indicates the negative impact of increased levels of irrigation-induced salinity in the expression of these traits. In the mean vs stability biplot analysis, G21 (Co 15023), G24 (Co 15027), G16 (Co 13036), G6 (Co 0238), and G20 (Co 14036) were found to be highly productive and stable genotypes for the cane yield. The superior and stable performance of early maturing notified varieties G21 (Co 15023) and G6 (Co 0238) for CY and CCS yield indicates that they will help the farmers to obtain sustainable income in saline soil conditions.