Characterization of Nucleotide Binding ­Site-Encoding Genes in Sweetpotato, <b><i>Ipomoea batatas</i></b>(L.) Lam., and Their Response to Biotic and Abiotic Stresses

Abstract

Sweetpotato, &lt;i&gt;Ipomoea batatas&lt;/i&gt; (L.) Lam., is an important and widely grown crop, yet its production is affected severely by biotic and abiotic stresses. The nucleotide binding site (NBS)-encoding genes have been shown to improve stress tolerance in several plant species. However, the characterization of NBS-encoding genes in sweetpotato is not well-documented to date. In this study, a comprehensive analysis of NBS-encoding genes has been conducted on this species by using bioinformatics and molecular biology methods. A total of 315 NBS-encoding genes were identified, and 260 of them contained all essential conserved domains while 55 genes were truncated. Based on domain architectures, the 260 NBS-encoding genes were grouped into 6 distinct categories. Phylogenetic analysis grouped these genes into 3 classes: TIR, CC (I), and CC (II). Chromosome location analysis revealed that the distribution of NBS-encoding genes in chromosomes was uneven, with a number ranging from 1 to 34. Multiple stress-related regulatory elements were detected in the promoters, and the NBS-encoding genes’ expression profiles under biotic and abiotic stresses were obtained. According to the bioinformatics analysis, 9 genes were selected for RT-qPCR analysis. The results revealed that &lt;i&gt;IbNBS75&lt;/i&gt;, &lt;i&gt;IbNBS219&lt;/i&gt;, and &lt;i&gt;IbNBS256&lt;/i&gt; respond to stem nematode infection; &lt;i&gt;Ib­NBS240&lt;/i&gt;, &lt;i&gt;IbNBS90&lt;/i&gt;, and &lt;i&gt;IbNBS80&lt;/i&gt; respond to cold stress, while &lt;i&gt;IbNBS208&lt;/i&gt;, &lt;i&gt;IbNBS71&lt;/i&gt;, and &lt;i&gt;IbNBS159&lt;/i&gt; respond to 30% PEG treatment. We hope these results will provide new insights into the evolution of NBS-encoding genes in the sweetpotato genome and contribute to the molecular breeding of sweetpotato in the future.

A comprehensive overview of omics-based approaches to enhance biotic and abiotic stress tolerance in sweet potato

“…Furthermore, nucleotide-binding sites and leucine-rich repeat domains containing genes are plants’ predominant type of resistance genes. Four NBS encoding genes’ ( IbNBS258 , IbNBS88 , IbNBS10 , and IbNBS20 ) expression were significantly induced in response to stem nematode infection in sweet potato [ 53 ].…”

“…The purple flesh sweet potato (hexaploid) was re-sequenced to dissect the molecular regulation of drought and salinity pathways [ 108 ] and depicted the role of glutathione S-transferases family genes which are involved in the accumulation of mono-caffeoylquinic acids to incorporate resistance against abiotic stress [ 109 ]. The NBS genes IbNBS80 , IbNBS90 , and IbNBS240 were significantly induced under cold stress, while IbNBS71 , IbNBS159 , and IbNBS208 responded to PEG treatment [ 53 ]. Furthermore, the responses of three genes in purple flesh sweet potato were strongly induced ( itb11g07110 , itb11g02640, and itb13g03940 ) by drought and oxidative stresses [ 109 ].…”

“…These findings identify several novel responsive elements that can target the NBS-LRR mediated disease resistance genes and involve the downregulation of SA-mediated defense responsive pathway [ 121 ]. Another genome-wide study was conducted to identify and characterize the nucleotide-binding site (NBS) encoding genes in a wild ancestor of sweet potatoes ( I. trifida ) and found that four NBS genes ( IbNBS258 , IbNBS88 , IbNBS10 , and IbNBS20 ) were significantly induced in response to stem nematode infection, while IbNBS240 , IbNBS90 , and IbNBS80 respond to cold stress, whereas IbNBS208 , IbNBS71 , and IbNBS159 respond to polyethylene glycol (PEG) treatment in sweet potato [ 53 ].…”

Integrated Transcriptome and Metabolome Analyses Reveal Details of the Molecular Regulation of Resistance to Stem Nematode in Sweet Potato

“…Genes encoding nucleotide-binding site (NBS) proteins are a major type of resistance (R) gene that play important roles in biotic stress responses in plants. Si et al [ 7 , 8 ]. recently analyzed the genome and transcriptome data of Ipomoea species and isolated several NBS genes responding to SN infection.…”

Genome-wide comparative analysis of the nucleotide-binding site-encoding genes in four Ipomoea species

“…In recent years, haplotype-based genome assembly of sweet potato was carried out that provides useful information on its complex genome ( Yang et al, 2017 ). Based on the reference genome sequence, 315 NBS-encoded genes were identified recently in sweet potato ( Si et al, 2021 ). The number of NBS-coding genes in sweet potato could be underestimated due to the lack of existing study and research progress ( Wu et al, 2018 ).…”