Genomic Selection in Sugarcane: Current Status and Future Prospects

Abstract

Sugarcane is a C4 and agro-industry-based crop with a high potential for biomass production. It serves as raw material for the production of sugar, ethanol, and electricity. Modern sugarcane varieties are derived from the interspecific and intergeneric hybridization between Saccharum officinarum, Saccharum spontaneum, and other wild relatives. Sugarcane breeding programmes are broadly categorized into germplasm collection and characterization, pre-breeding and genetic base-broadening, and varietal development programmes. The varietal identification through the classic breeding programme requires a minimum of 12-14 years. The precise phenotyping in sugarcane is extremely tedious due to the high propensity of lodging and suckering owing to the influence of environmental factors and crop management practices. This kind of phenotyping requires data from both plant crop and ratoon experiments conducted over locations and seasons. In this review, we explored the feasibility of genomic selection schemes for various breeding programmes in sugarcane. The genetic diversity analysis using genome-wide markers helps in the formation of core set germplasm representing the total genomic diversity present in the Saccharum gene bank. The genome-wide association studies and genomic prediction in the Saccharum gene bank are helpful to identify the complete genomic resources for cane yield, commercial cane sugar, tolerances to biotic and abiotic stresses, and other agronomic traits. The implementation of genomic selection in pre-breeding, genetic base-broadening programmes assist in precise introgression of specific genes and recurrent selection schemes enhance the higher frequency of favorable alleles in the population with a considerable reduction in breeding cycles and population size. The integration of environmental covariates and genomic prediction in multi-environment trials assists in the prediction of varietal performance for different agro-climatic zones. This review also directed its focus on enhancing the genetic gain over time, cost, and resource allocation at various stages of breeding programmes.

Keywords: genetic base-broadening; genomic estimated breeding value; genomic selection; multi-environment trials; pre-breeding; sugarcane.

Figure 1

In-depth pedigree analysis of notified sugarcane varieties in India stipulating the total genetic variability present in the field. They are derived from the limited germplasm viz., 17 clones of S Saccharum officinarum and its derivatives (pink color), one clone of Saccharum barberi (orange), two clones of Saccharum spontaneum (gray), one genetic stock IG91-1100 derived from intergeneric hybridization between sugarcane (CoC 772) and Erianthus arundinaceus (blue), and two foreign clones (green). The implementation of genomic prediction in sugarcane germplasm characterization and genomic selection in pre-breeding aids in introgression and augmentation of more favorable alleles, base-broadening of working germplasm, and finally deploying more number of favorable genes into the target environments.

Figure 2

Genomic selection schemes for pre-breeding and genetic base-broadening programmes in sugarcane. The sugarcane pre-breeding requires three or more number of backcrossing with recurrent parents. Wild relatives such as S. spontaneum, Saccharum robustum, and S. barberi are used as male parents and S. officinarum or improved “Co” canes are used as female parents. Cycle 1 requires hybridization between S. officinarum or “Co” canes with wild species and Cycle-2 requires backcrossing progenies derived from cycle-1 with S. officinarum or “Co” canes. The genomic selection schemes are required to be applied in both cycle-1 and cycle-2. The true F_l at Cycle-1 identified by molecular markers and genomic models are required to train at every backcrossing to improve the genomic prediction accuracy.