An Updated Overview on Insights into Sugarcane Genome Editing via CRISPR/Cas9 for Sustainable Production

Abstract

Sugarcane crop constitutes one of the most vital sources of sugar and bioenergy globally; however, higher level of polyploidy makes its genome editing an intricate task. Recently, genome editing has become easier with CRISPR/Cas9 system that uses Cas9 to target sequence-specific regions and introduce double-strand breaks into the target region. This technique has been successfully employed to develop new varieties of sugarcane having desired phenotypic and physiological traits. Several genes can be fused with the CRISPR/Cas9 system leading to successful metabolic engineering and biological improvement for ensuring sustainable enhancement in sugarcane production. This simple RNA-guided genome editing technique has become a revolutionary tool and innovative application in biology that might be effectively employed for inducing specified genomic modifications in plant tissues. This review attempts to synthesize fundamentals of genome editing techniques with an ultimate aim to find out opportunities and challenges of sugarcane genome editing. It also tends to summarize the advances and achievements of gene editing via CRISPR-based genome editing technique for numerous field crops. Lastly, the enormous potential of CRISPR/Cas9 for gene editing in sugarcane, major challenges and future perspectives have been objectively elaborated.

Leveraging the sugarcane CRISPR/Cas9 technique for genetic improvement of non-cultivated grasses

“…Moreover, other genetic tools such as site-specific recombinase, base editing ( Yin et al., 2015 ; Zong et al., 2017 ), and transcription activator-like effector nucleases (TALENs) have also been employed for gene’s insertion and/or knocking ( Jung and Altpeter, 2016 ; Kannan et al., 2018 ) in order to acquire desired morphological traits and improve cane yield, sucrose recovery, etc., but these have demonstrated limited efficacy owing to off-targeting ( Peng et al., 2015 ; Ma et al., 2016 ; Zaidi et al., 2017 ). This situation necessitated the development of more advanced genetic tools such as the CRISPR technique ( Aitken and McNeil, 2010 ; Mao et al., 2013 ; Shan et al, 2018 ; Hussin et al., 2022 ) for the gene editing of sugarcane.…”

“…The genome size of sugarcane has been estimated to be over 10 Gbp, wherein genes exist in 10–12 allelic forms. Interestingly, depending on a specific cultivar’s ploidy level, monoploid genome size has been estimated to be approximately 800–900 Mb ( Zhang et al., 2012 ; de Setta et al., 2014 ; Hussin et al., 2022 ). Because of its high polyploidy ( x = 10–13; 2 n = 100–130), interspecific, heterozygous, and aneuploidy nature, the genome of sugarcane tends to decelerate the gene editing attempts intended for crop improvement ( Le Cunff et al., 2008 ; de Setta et al., 2014 ; Oz et al., 2021 ).…”

“…Recently, it has become evident that CRISPR/Cas9 has offered unique efficiency with unmatched precision in gene editing of polyploidy crops like sugarcane ( Bhowmik et al., 2018 ; Hussin et al., 2022 ); however, its application for non-cultivated grasses’ genetic improvement might raise few technical, ethical, and safety concerns. The key technical limitations of CRISPR/Cas9 might include challenges like achieving 100% precision in gene editing ( Ali et al., 2015 ; Zhang et al., 2019 ), because few cells could avoid desired genetic modifications leading to low precision in non-cultivated grass species.…”

“…However, the genome editing of non-cultivated grasses might be initiated by taking sugarcane as a model plant because it is a perennial C-4 grass having exceptional potential for converting solar radiation and farm inputs (nutrients, water, etc.) into chemical harvestable energy (sucrose) ( Hoang et al., 2015 ; Hussin et al., 2022 ). Furthermore, sugarcane has demonstrated intricacy in its genome editing owing to polyploidy and aneuploidy ( Eid et al., 2021 ).…”

CRISPR technology towards genome editing of the perennial and semi-perennial crops citrus, coffee and sugarcane

“…Despite the progress on transformation methodologies in sugarcane ( Figure 5 ), transgene-free genome editing often requires the delivery of RNP complexes or transient expression systems into protoplasts ( González et al., 2021 ; Lin et al., 2022 ; Sidorov et al., 2022 ). However, obtaining regenerated sugarcane plants from protoplasts is indeed a herculean task ( Taylor et al., 1992 ), thus demanding efficient protocols for sugarcane protoplast regeneration ( Hussin et al., 2022 ). Alternatively, delivery of CRISPR reagents directly into plant cells can be conducted via particle bombardment of embryogenic cells and zygotes, as reported in maize ( Svitashev et al., 2016 ), wheat ( Liang et al., 2017 ), and rice ( Toda et al., 2019 ).…”