Genomic Selection in Sugarcane: Current Status and Future Prospects.

Channappa Mahadevaiah,Karen Aitken,Huskur Kumaraswamy Mahadeva Swamy,Palanisamy Vignesh,Giriyapura Shivalingamurthy Suresha,Ramanathan Valarmathi,Bakshi Ram,Chinnaswamy Appunu,Govind Hemaprabha,Ganesh Alagarasan

doi:10.3389/fpls.2021.708233

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.

Highlights

Sugarcane is an important agro-based industrial crop cultivated in tropical and sub-tropical regions; it serves as a raw material for the production of sugar, bioethanol, and bioenergy (Hoang et al, 2015)
The recent review on genomic selection in sugarcane highlighted the recurrent selection schemes (Yadav et al, 2020) and we reviewed the feasibility of genomic selection at various stages of sugarcane breeding programmes, such as germplasm evaluation and formation of core germplasm, pre-breeding and genetic base-broadening programmes, and multi-environmental trails of breeding lines
The genomic prediction models are statistical models, which combines the pedigree data, genotypic data, phenotypic data, and environmental covariates to estimate the genomic estimated breeding values (GEBV) and enhance the prediction accuracies. They are derived from the limited germplasm viz., 17 clones of S Saccharum officinarum and its derivatives, one clone of Saccharum barberi, two clones of Saccharum spontaneum, one genetic stock IG91-1100 derived from intergeneric hybridization between sugarcane (CoC 772) and Erianthus arundinaceus, and two foreign clones

Summary

INTRODUCTION

Sugarcane is an important agro-based industrial crop cultivated in tropical and sub-tropical regions; it serves as a raw material for the production of sugar, bioethanol, and bioenergy (Hoang et al, 2015). The genomic prediction models are statistical models, which combines the pedigree data, genotypic data, phenotypic data, and environmental covariates to estimate the genomic estimated breeding values (GEBV) and enhance the prediction accuracies 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). There were efforts made to utilize the Saccharum germplasm in sugarcane hybridization programme for pre-breeding and base-broadening programmes (Wang et al, 2008; Mohanraj and Nair, 2014; da Silva, 2017; Nair et al, 2017; Cursi et al, 2021), still it was not a complete utilization of Saccharum germplasm or all the favorable alleles contributing to the cane yield and sucrose

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Findings

CONCLUSIONS