Background: Plant genomes contain a large number of HAK/KUP/KT transporters, which play important roles in potassium uptake and translocation, osmotic potential regulation, salt tolerance, root morphogenesis and plant development. Potassium deficiency in the soil of a sugarcane planting area is serious. However, the HAK/KUP/KT gene family remains to be characterized in sugarcane (Saccharum). Results: In this study, 30 HAK/KUP/KT genes were identified in Saccharum spontaneum. Phylogenetics, duplication events, gene structures and expression patterns were analyzed. Phylogenetic analysis of the HAK/KUP/KT genes from 15 representative plants showed that this gene family is divided into four groups (clades I-IV). Both ancient whole-genome duplication (WGD) and recent gene duplication contributed to the expansion of the HAK/KUP/KT gene family. Nonsynonymous to synonymous substitution ratio (Ka/Ks) analysis showed that purifying selection was the main force driving the evolution of HAK/KUP/KT genes. The divergence time of the HAK/KUP/KT gene family was estimated to range from 134.8 to 233.7 Mya based on Ks analysis, suggesting that it is an ancient gene family in plants. Gene structure analysis showed that the HAK/KUP/KT genes were accompanied by intron gain/loss in the process of evolution. RNA-seq data analysis demonstrated that the HAK/KUP/KT genes from clades II and III were mainly constitutively expressed in various tissues, while most genes from clades I and IV had no or very low expression in the tested tissues at different developmental stages. The expression of SsHAK1 and SsHAK21 was upregulated in response to low-K⁺ stress. Yeast functional complementation analysis revealed that SsHAK1 and SsHAK21 could rescue K⁺ uptake in a yeast mutant. Conclusions: This study provided insights into the evolutionary history of HAK/KUP/KT genes. HAK7/9/18 were mainly expressed in the upper photosynthetic zone and mature zone of the stem. HAK7/9/18/25 were regulated by sunlight. SsHAK1 and SsHAK21 played important roles in mediating potassium acquisition under limited K⁺ supply. Our results provide valuable information and key candidate genes for further studies on the function of HAK/KUP/KT genes in Saccharum.

Background: Cyclic nucleotide-gated ion channels (CNGCs) are nonselective cation channels that are ubiquitous in eukaryotic organisms. As Ca²⁺ channels, some CNGCs have also proven to be K⁺-permeable and involved in plant development and responses to environmental stimuli. Sugarcane is an important sugar and energy crop worldwide. However, reports on CNGC genes in sugarcane are limited. Results: In this study, 16 CNGC genes and their alleles were identified from Saccharum spontaneum and classified into 5 groups based on phylogenetic analysis. Investigation of gene duplication and syntenic relationships between S. spontaneum and both rice and Arabidopsis demonstrated that the CNGC gene family in S. spontaneum expanded primarily by segmental duplication events. Many SsCNGCs showed variable expression during growth and development as well as in tissues, suggesting functional divergence. Light-responsive cis-acting elements were discovered in the promoters of all the identified SsCNGCs, and the expression of most of the SsCNGCs showed a diurnal rhythm. In sugarcane, the expression of some SsCNGCs was regulated by low-K⁺ treatment. Notably, SsCNGC13 may be involved in both sugarcane development and its response to environmental stimuli, including response to low-K⁺ stress. Conclusion: This study identified the CNGC genes in S. spontaneum and provided insights into the transcriptional regulation of these SsCNGCs during development, circadian rhythm and under low-K⁺ stress. These findings lay a theoretical foundation for future investigations of the CNGC gene family in sugarcane.

Papaya (Carica papaya. L) is widely cultivated in tropical and subtropical regions of China and has high nutritional and medicinal values. More than 11 species of papaya viruses have been recorded in the world, but the most destructive one for papaya production in China is papaya ringspot virus (PRSV) (Li, 2019). In order to control PRSV, a transgenic papaya cultivar, designated as 'Huanong No.1', carrying the nuclear inclusion b (Nib) cistron of PRSV Ys isolate, was successfully commercialized in 2006, and has shown a wide range of resistance to PRSV in China (Li et al. 2007). However, more than 10% of 'Huanong No.1' plants developed different virus-like symptoms on leaves, including mosaic, yellow mottle, and deformation in some plantations of Guangdong Province, China in 2020 (Suppl Figure 1a, b, and c). Based on observation of the symptomatic phenotypes, the field surveys indicated that the disease incidence ranged from 10% to 40%, resulting in significant loss of papaya fruit. The virus particles were purified from symptomatic papaya plants following Gooding and Hebert (1967) and rigid filamentous particles resembling tobacco mosaic virus (TMV) were observed by transmission electron microscopy. Purified virus samples were further utilized to mechanically inoculate healthy seedlings of papaya, Nicotiana glutinosa and N. tabacum K326. At 15 days after inoculation, the obvious symptoms of virus infection on different plants were observed. The diseased plants showed systemic mottling and mosaic in the papaya leaves (Suppl Figure 1d), necrotic spots on the leaves of N. glutinosa (Suppl Figure 1e), mosaic and mottling spots on leaves of N. tabacum K326 (Suppl Figure 1f). These symptoms produced on the hosts were exactly the same caused by TMV. In order to reconfirm the species of the infected virus, the total RNA was extracted from the single leaf of 30 diseased papaya plants using RNAiso Plus kit (Takara, Japan) and reverse transcription--polymerase chain reaction was performed using TMV coat protein cistron specific primers (TMV-CP-R: 5'-TCAAGTTGCAGGACCAGA-3' and TMV-CP-F 5'- ATGTCTTACAGTATCACTAC-3') as described previously (Srivastava et al. 2015). An expected 480-bp fragment was amplified from all of the samples. Sequence analysis revealed that the diseased papaya was infected with TMV, designated as Cpa-TMV. In order to understand the difference among TMV isolates on papaya and other host plants, the whole genomic sequence of TMV from papaya was obtained and analyzed. The total length of the genome of Cpa-TMV was 6395 bp, and the sequence was submitted to the NCBI database (GenBank no. OK149218). A neighbor-joining phylogenetic tree of 19 TMV isolates was constructed using MEGA X software. Phylogenetic analysis indicated that the 19 TMV isolates were divided into Clade I, II and III (Suppl Figure 2). Interestingly, Clade I was composed of 12 Chinese mainland isolates, which further was grouped into IA (Northern China) and IB (Southern China), while 6 isolates from other countries and 1 isolate (pet-TMV) from China Taiwan belong to Clade II and III. It is inferred that the TMV isolates from Chinese mainland are quite different from other countries and China Taiwan. This suggests that geographical differences between Northern and Southern China may lead to the gradual differentiation of TMV isolates and eventually induce those isolates to evolve into two subclades. To our knowledge, this is the first report of TMV infection on papaya under natural conditions. It is necessary to find effective methods to control TMV in transgenic papaya.

Lignocellulosic biomass may play a major role in the production of biofuels, bioplastics, sugar, paper, and various other industrial products. In addition, it is a key trait in plants due to its contribution to lodging resistance. Fiber also shows a significant negative correlation with most yield traits and all sugar traits. As the most harvested crop globally by tonnage, sugarcane is an important resource for both sugar and bioenergy production. In this study, a panel of sugarcane clones was utilized to investigate the fiber content. This panel included 17 core parental lines derived from 11 countries involved in sugarcane cultivation and breeding. It represented the genetic base of commercial sugarcane breeding programs in China and other countries. The objective of this research was to identify molecular markers and candidate genes associated with fiber content in sugarcane using genome-wide association studies (GWASs). By integrating 5,964,084 high-quality single-nucleotide polymorphisms (SNPs) with phenotypic data collected across five different environments, a total of 69 SNPs spanning 41 quantitative trait loci (QTLs) were identified. Based on functional annotations and genomic positions, these QTLs contained 52 candidate genes. These candidate genes encoded the ultraviolet-B receptor (UVR8), leucine-rich repeat receptor-like kinases (LRR-RLKs), serine/threonine kinases (STKs), cellulose synthase (CESA), vegetative cell wall protein glycoproteins1 (gp1), F-box protein, MYB transcription factor, and so on. These genes could directly or indirectly influence the fiber content in sugarcane. Furthermore, according to previous studies, among these candidate genes, five located in four QTL regions were proposed to be the most critical. They included Sspon.02G0041160-2C, encoding CESA; Sspon.03G0039010-1C and Sspon.03G0039030-1C, both encoding gp1; Sspon.06G0023090-1B, encoding an F-box protein; and Sspon.07G0019440-2C, encoding a MYB transcription factor. The genetic basis of the fiber content was explored using elite breeding lines and their derivatives from the Chinese sugarcane breeding program. These candidate genes represent promising targets for future functional studies and may contribute to the development of different types of sugarcane varieties with correspondingly suitable fiber content through marker-assisted selection.

Sugarcane is an essential global industrial cash crop for sugar and bioenergy production, and breeding superior varieties is critical to improving industrial benefits and adapting to changing climatic environments. This review synthesizes the published breeding history, agronomic trial records, juice-quality evaluations, and transcriptomic analyses of the elite sugarcane variety YT93-159, and uses this variety as a model case to discuss the achievements and challenges of sugarcane breeding in South China. YT93-159 was bred through artificial hybridization using YN73-204 as the female parent and CP72-1210 as the male parent. Data compiled from variety-registration archives, peer-reviewed studies, and the authors’ previously published transcriptomic analyses indicate that YT93-159 integrates excellent parental advantages, with prominent early sugar accumulation, high yield, stable stress resistance, and wide adaptability. On the basis of differentially expressed genes identified in published transcriptomic datasets, its superior comprehensive traits may be co-regulated by candidate pathways including carbon fixation, sucrose metabolism, and plant hormone signal transduction; however, several pathway members showed the opposite expression changes, and these mechanisms should be regarded as hypotheses requiring further functional validation. This variety has achieved large-scale popularization in China and possesses excellent functional nutritional values. By clarifying the phenotypic and proposed molecular basis of YT93-159′s superior traits, this review provides a valuable germplasm resource profile and theoretical reference for sugarcane genetic improvement and sustainable industrial development.