Origin of a self-compatibility associated MITE in Petota and its application in hybrid potato breeding

Abstract

Introduction

Potato (Solanum tuberosum L.), a staple crop consumed by over 1.3 billion people spanning > 150 countries world-wide, holds paramount significance for global food security (Stokstad, 2019). Currently, commercial potato cultivars are mainly derived from a narrow tetraploid subgroup, S. tuberosum Group stenotomum, which offers advantages such as large tubers and high yield (Spooner et al., 2014; Hardigan et al., 2017). However, there are challenges for traditional tetraploid potato breeding, including genetic variation loss because of the bottleneck effect and prolonged breeding cycles due to complex tetraploid genetics (Zhang et al., 2021; Kardile et al., 2022). Diploid hybrid breeding, using true seeds instead of tubers for propagation, exhibits a much higher reproductive and breeding efficiency than tetraploid breeding. Additionally, c. 70% of the naturally tuber-bearing Solanum section Petota, comprising over 100 species, are diploid, offering a rich genetic resource for breeding (Jansky et al., 2016; Wu et al., 2023). However, self-incompatibility (SI) is observed in most diploids, which hinders the creation of inbred lines essential for hybrid breeding (Ma et al., 2021; Zhang et al., 2021).

Potato exhibits gametophytic SI controlled by the S-locus consisting of pistil-specific S-RNase and a group of pollen-specific S-locus F-box (SLF) genes (Zhang et al., 2009). Generally, SLF interacts weakly with selfS-RNase but strongly with nonself S-RNase, thereby preventing self-fertilization and ensuring SI (Qiao et al., 2004; Hua & Kao, 2006; Kubo et al., 2010; Zhao et al., 2022). Therefore, self-compatibility (SC) diploid potatoes can be achieved by knocking out self S-RNase, selecting naturally occurring low-expressed S-RNase alleles, or overexpressing nonselffunctional SLFs (Ye et al., 2018; Zhang et al., 2021; Zhao et al., 2022). Notably, a nonS-locus F-box gene S-locus inhibitor (Sli) was identified from naturally SC genotypes such as chc525-3 and RH89-039-16 (RH). Sli can interact with multiple self and nonselfS-RNases to overcome SI across different genotypes and thus plays a key role in diploid potato breeding (Hosaka & Hanneman, 1998; Peterson et al., 2016; Clot et al., 2020; Eggers et al., 2021; Ma et al., 2021). Interestingly, the Sli promoter contains a 549 bp miniature inverted transposon element (MITE) insertion (named as Mi-549 hereafter) (Chen et al., 2014). Miniature inverted transposon elements are known to suppress the expression of adjacent genes by altering sequence methylation levels through RNA-directed DNA methylation (RdDM). In this process, CHH (H = A, C or T) methylation is primarily guided by small-interfering RNAs (siRNAs) and catalyzed by the DNA methyltransferase domains rearranged methyltransferase-2 (DRM2) (Cao & Jacobsen, 2002; Calarco et al., 2012). Dicer-like proteins (DCL4, DCL2 and DCL3) generate siRNAs (Axtell, 2013; Wei et al., 2014) that are subsequently incorporated into Argonaute (AGO) proteins, particularly AGO3, AGO4, AGO6 and AGO9 specialized for RdDM-associated siRNAs. The AGO–siRNA complex then mediates the RdDM process, thereby regulating gene expression at multiple levels (Axtell, 2013). Mi-549 may play a crucial role in regulating the pollen-specific expression of Sli and its strict gamete selection in progeny (Chen et al., 2014; Eggers et al., 2021; Ma et al., 2021). However, the mechanism underlying the Mi-549-regulated Sli expression remains largely unknown. Furthermore, what is the evolutionary origin of Mi-549 within the Solanaceae family? Is the rise of Mi-549 accompanied by the SC phenotype in diploid potatoes?

In this study, we revealed that the Mi-549 is associated with a decreased DNA methylation level within the Sli promoter and affects the tissue-specific expression of Sli. In addition, systematic analysis of the whole-genome sequencing (WGS) data of 393 diploid lines showed that Mi-549 originated first in wild relatives and is mostly associated with Sli expression. More importantly, three new SC diploid lines from S. lesteri, S. neocardenasii and S. stenotomum groups were identified from the screening, which expand the current germplasms pool and hold significant value for hybrid potato breeding.