PAV markers in Sorghum bicolour: genome pattern, affected genes and pathways, and genetic linkage map construction.

Xin Shen,Yan Xia,Hai-Chun Jing,Zhi-Quan Liu,Anne Mocoeur

doi:10.1007/s00122-015-2458-4

Abstract

Key message 5,511 genic small-size PAVs in sorghum were identified and examined, including the pattern and the function enrichment of PAV genes. 325 PAV markers were developed to construct a genetic map. Presence/absence variants (PAVs) correlate closely to the phenotypic variation, by impacting plant genome sizes and the adaption to the environment. To shed more light on their genome-wide patterns, functions and the possibility of using them as molecular markers, we generated next generation genome sequencing data for four sorghum inbred lines and used associated bioinformatic pipelines to identify small-size PAVs (40–10 kb). Five thousand five hundreds and eleven genic PAVs (40–10 kb) were identified and found to affect 3,238 genes. These PAVs were mainly distributed on the sub-telomeric regions, but the highest proportions occurred in the vicinity of the centromeric regions. One of the prominent features of the PAVs is the high occurrence of long terminal repeats retrotransposons and DNA transposons. PAVs caused various alterations to gene structure, primarily including the coding sequence variants, intron variants, transcript ablation, and initiator codon changes. The genes affected by PAVs were significantly enriched in those involved in stress responses and protein modification. We used 325 PAVs polymorphic between two sorghum inbred lines Ji2731 and E-Tian, together with 49 SSR markers, and constructed a genetic map, which consisted of 10 linkage groups corresponding to the 10 chromosomes of sorghum and spanned 1,430.3 cM in length covering 97 % of the physical genome. The resources reported here should be useful for genetic study and breeding of sorghum and related species.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-015-2458-4) contains supplementary material, which is available to authorized users.

Highlights

Single nucleotide polymorphisms (SNPs) and small insertion/deletion polymorphisms (IDPs) have long been thought to be the only means through which most of genetic variations could arise (Feuk et al 2006)
In maize (Zea mays), it has been reported that 20 % of genome segments were not shared between inbred lines B73 and Mo17 (Morgante et al 2005), while an array of comparative genome hybridization showed that more than 1,000 Presence/absence variants (PAVs) affected at least 180 single copy genes (Springer et al 2009)
We used the available genome resequencing data and identified 5,511 genic small-size PAVs. We showed that these PAVs were preferentially distributed on different parts of chromosome, and the affected 3,238 genes were predominantly involved in stress response and protein modification

Summary

Introduction

Single nucleotide polymorphisms (SNPs) and small insertion/deletion polymorphisms (IDPs) have long been thought to be the only means through which most of genetic variations could arise (Feuk et al 2006). Even since the first description of presence and absence polymorphisms in the RPM1 gene in Arabidopsis (Grant et al 1998), an increasing number of studies indicated that a dominant feature of the PAV genes is the enrichment in genes involved in the stress responses, especially the disease resistance (Shen et al 2006; Ding et al 2007; Ziolkowski et al 2009; Lam et al 2010; McHale et al 2012; Tan et al 2012; Gonzalez et al 2013). We analyzed PAVs with size fragments larger than 30 kb in sorghum and showed that large-size PAVs are widespread in sorghum inbred lines of different origins (Zhang et al 2014) This prompted us to explore further in detail the small-size (40–10 kb) PAVs. Here we reported our study focusing on the genic small-size PAVs, including the distribution over the genome, the function, and the pathway enrichment of genes affected. As a proof of concept, 325 PAV markers from 10 chromosomes were used to construct a genetic map together with 49 SSR markers, which showed the advantages of genome coverage, integration of physical and genetic maps, and a better functionality over maps constructed with other molecular markers used in sorghum

Materials and methods

Results

Discussion

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