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

Abstract

Advances in sugarcane breeding have contributed significantly to improvements in agronomic traits and crop yield. However, the growing global demand for sugar and biofuel in the context of climate change requires further improvements in cane and sugar yields. Attempts to achieve the desired rates of genetic gain in sugarcane by conventional breeding means are difficult as many agronomic traits are genetically complex and polygenic, with each gene exerting small effects. Unlike those of many other crops, the sugarcane genome is highly heterozygous due to its autopolyploid nature, which further hinders the development of a comprehensive genetic map. Despite these limitations, many superior agronomic traits/genes for higher cane yield, sugar production, and disease/pest resistance have been identified through the mapping of quantitative trait loci, genome-wide association studies, and transcriptome approaches. Improvements in traits controlled by one or two loci are relatively easy to achieve; however, this is not the case for traits governed by many genes. Many desirable phenotypic traits are controlled by quantitative trait nucleotides (QTNs) with small and variable effects. Assembling these desired QTNs by conventional breeding methods is time consuming and inefficient due to genetic drift. However, recent developments in genomics selection (GS) have allowed sugarcane researchers to select and accumulate desirable alleles imparting superior traits as GS is based on genomic estimated breeding values, which substantially increases the selection efficiency and genetic gain in sugarcane breeding programs. Next-generation sequencing techniques coupled with genome-editing technologies have provided new vistas in harnessing the sugarcane genome to look for desirable agronomic traits such as erect canopy, leaf angle, prolonged greening, high biomass, deep root system, and the non-flowering nature of the crop. Many desirable cane-yielding traits, such as single cane weight, numbers of tillers, numbers of millable canes, as well as cane quality traits, such as sucrose and sugar yield, have been explored using these recent biotechnological tools. This review will focus on the recent advances in sugarcane genomics related to genetic gain and the identification of favorable alleles for superior agronomic traits for further utilization in sugarcane breeding programs.

Biomass and energy potential of Erianthus arundinaceus and Saccharum spontaneum-derived novel sugarcane hybrids in rainfed environments

“…Cane growth and quality parameters play a crucial role in the success and productivity of sugarcane production [ 44 , 45 ]. Monitoring and understanding these parameters are essential for optimizing cultivation practices, maximizing yield, and ensuring the production of high-quality sugarcane.…”

Comparative Analysis of Sucrose-Regulatory Genes in High- and Low-Sucrose Sister Clones of Sugarcane

“…The sucrose level varies between high- and low-sugar sugarcane genotypes and between immature and mature internodes. Recent advancements in sugarcane breeding have resulted in notable enhancements in agronomic features [ 36 , 37 ]. However, further research is required to fully understand the intricate mechanism of sucrose metabolism in sugarcane [ 9 , 38 , 39 ].…”

Early Detection Cold Markers to Expedite the Sugarcane (Saccharum spp. Hybrids) Breeding

“…Sugarcane has a large genome size and is highly aneuploid, polyploid, and heterozygous . Sugarcane breeding is an expensive, labor-intensive, and time-consuming process.…”

“…Sugarcane has a large genome size and is highly aneuploid, polyploid, and heterozygous. 4 Sugarcane breeding is an expensive, labor-intensive, and time-consuming process. Usually, it takes more than 10 years of testing over several stages and locations.…”