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.

Evaluation of a Sugarcane (Saccharum spp.) Hybrid F1 Population Phenotypic Diversity and Construction of a Rapid Sucrose Yield Estimation Model for Breeding

“…The relationship between yield (Y) and stalk number (SN), stalk height (SH), and stalk weight (SW) has also been reported by Barreto et al [ 5 ] and Yang et al [ 14 ]. In addition, evidence from genetics also showed that both yield and sucrose were governed by many quantitative trait loci (QTL) or genomic regions [ 14 , 39 ]. These studies also revealed the complexity of high-yield sugarcane breeding and high-sucrose yield breeding.…”

Development of SLAF-Sequence and Multiplex SNaPshot Panels for Population Genetic Diversity Analysis and Construction of DNA Fingerprints for Sugarcane

“…S. spontaneum L., a wild material, is gathered in a single cluster, whereas cultivar materials are distributed among different communities. In the long-term domestic and breeding process, the genetic background of different wild accessions is introduced to the genome of cultivated species [ 60 ]. These sugarcane germplasm exchanges led to an indistinct correlation between the results of population genetic analysis and geographical origin.…”

Recent Advances in Sugarcane Genomics, Physiology, and Phenomics for Superior Agronomic Traits

“…Genetic gain for these traits through phenotypic selection is very low. This is because the accumulation of superior alleles for these traits via phenotypic breeding value is very rare ( Jackson, 2005 ; Mahadevaiah et al, 2021 ). Therefore, it is only possible to accumulate favorable alleles for these traits through recurrent selection schemes ( Lingle et al, 2010 ).…”

“…Additive genetic variance is a proportion of genetic variance inherited in progeny, which is helpful in the selection of desired parental combinations. Non-additive variance, on the other hand, is helpful in the selection of desired plant types during selection from the ground nursery ( Jackson et al, 2016 ; Mahadevaiah et al, 2021 ). As cane yield is reflected by low narrow-sense heritability and CCS has a moderate level of heritability, also governed polygenically ( Hoang et al, 2015 ), both non-additive and additive effects must be taken into account to improve the overall performance of these traits.…”