In-silicoidentification of candidate genes for fertility restoration in cytoplasmic male sterile perennial ryegrass (Lolium perenneL.)

Abstract

Perennial ryegrass (Lolium perenne L.) is widely used for forage production in both permanent and temporary grassland systems. To increase yields in perennial ryegrass, recent breeding efforts have been focused on strategies to more efficiently exploit heterosis by hybrid breeding. Cytoplasmic male sterility (CMS) is a widely applied mechanism to control pollination for commercial hybrid seed production and although CMS systems have been identified in perennial ryegrass, they are yet to be fully characterized. Here, we present a bioinformatics pipeline for efficient identification of candidate restorer of fertility (Rf) genes for CMS. From a high-quality draft of the perennial ryegrass genome, 373 pentatricopeptide repeat (PPR) genes were identified and classified, further identifying 25 restorer of fertility-like PPR (RFL) genes through a combination of DNA sequence clustering and comparison to known Rf genes. This extensive gene family was targeted as the majority of Rf genes in higher plants are RFL genes. These RFL genes were further investigated by phylogenetic analyses, identifying three groups of perennial ryegrass RFLs. These three groups likely represent genomic regions of active RFL generation and identify the probable location of perennial ryegrass PPR-Rf genes. This pipeline allows for the identification of candidate PPR-Rf genes from genomic sequence data and can be used in any plant species. Functional markers for PPR-Rf genes will facilitate map-based cloning of Rf genes and enable the use of CMS as an efficient tool to control pollination for hybrid crop production.

Genome-wide Identification of Chile Pepper Pentatricopeptide Repeat Domains Provides Insight into Fertility Restoration

“…form a cluster with closely located PPR genes, whereas other PPR genes are dispersed throughout the genome (Lurin et al, 2004;Wang et al, 2006), and these clustered PPRs share high sequence similarity (Jo et al, 2016). This is all evidence, in conjunction with gene duplication, that the generation of new RFL genes and subsequent loss of nonfunctional RFLs is relatively rapid, and keeps pace with the generation of novel CMS sources (Sykes et al, 2016). It is known that the source of novel CMS mechanisms within the mitochondrial genome has high rates of recombination (Kubo et al, 2011;Sloan et al, 2012).…”

“…It might be expected that the larger the genome the more PPR domains a species might have; however, this is not the case. Although having smaller genomes than chile pepper, arabidopsis (135 Mbp) has 450 PPR domains, rice (430 Mbp) has 477 PPR domains, and perennial ryegrass [Lolium perenne (2.7 Gbp)] has 373 PPR domains (Lurin et al, 2004;O'Toole et al, 2008;Sykes et al, 2016). Greater duckweed (Spirodela polyrhiza), a basal monocot native to aquatic environments with a small genome size (158 Mbp), was found to have 556 The e-value is a parameter that describes the number of hits one can expect to see by random chance when searching a database of a particular size.…”

“…Therefore, RFLs likely serve as a pool from which new Rf genes can emerge (Gaborieau et al, 2016). The likelihood of PPR encoding Rf genes occurring in the regions of active RFL generation is a function of the time required for fertility restoration to become fixed within a population as well as the rate that RFL genes are shuffled throughout the genome (Sykes et al, 2016). It has been suggested that if the rate of fixation is faster than the rate of shuffling, Rf genes will always be found within these RFL clusters (Sykes et al, 2016).…”

Insights into PPR Gene Family in Cajanus Cajan and Other Legume Species

“…Small cluster of RFL PPRs were identified on genome of Glycine, Vigna, Cicer and Phaseolus and allowed us to narrow down the list to 15 potential Rf genes in 4 legumes ( Table 2). Twenty five candidate genes for fertility restoration in CMS perennial reyegrass has been predicted based on homology with known Rf genes and DNA sequence clustering; efficacy of both approaches depending upon the type and quality of input data [30]. Similarly, prediction of RFL PPRs and identification of genomic regions where these are present as clusters on the respective legume genomes is based up on the in silico analysis of draft sequence assemblies.…”

“…RFLs generally constitutes around 10-30 members/plant genome. In silico based approaches to identify RFLs on the basis of phylogenetic analysis and orthologous clustering has been used to identify candidate genes for fertility restoration in perennial ryegrass by Sykes et al [30].…”