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

Abstract

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.

Fig. 1

A diagram to show the designing of primers (a) and representative gel images (b) for the verification of PAVs. Four PAVs between three sorghum lines (Ji2731, E-Tian, and Keller) and BTx623 were presented as examples (Sb04sPAV001, Sb05sPAV005, Sb01sPAV010, Sb05sPAV002). A 100-bp DNA ladder marker was on the left of the gel and used for size measurement of PCR products

Fig. 2

Genome-wide distribution of 5,511 genic small-size PAVs (40–10 kb) discovered from three sorghum lines. The ratio ring shows the ratio between the number of genes with PAVs and the number of total genes in the 300-kb bin of the sorghum genome. The yellow bands denote the centromeric regions. The star symbols stand for the regions with significant enrichment of PAVs by Fisher’s exact test (P value <0.05). The ten chromosomes are drawn by a scale of Mb (color figure online)

Fig. 3

Distributions of PAVs in different variants of gene structure. The x axis represents the frequency of PAVs

Fig. 4

Distributions of PAV genes in the protein families (Pfam). The x axis represents the proportion of PAV genes in total PAV genes with annotated Pfam. The y axis shows the categories of Pfam. The numbers after bars indicate the number of PAV genes

Fig. 5

An integrated genetic linkage map of Sorghum bicolour. The vertical bars represent the chromosomes of Sorghum bicolour. The codes on the left are the PAV marker loci and the SSR marker loci which are labeled with red color, while the corresponding accumulative genetic distances (cM) are on the right. The discrete segments of the vertical chromosomal bars are color-coded according to the allele colors in the figure legends. Heterozygous stands for alleles heterozygous for parents (Ji2731 and E-Tian) alleles. Ji2731(A) is female allele, while E-Tian(B) is male allele. – is missing value (color figure online)

Fig. 6

Colinearity between the physical position and the genetic distance of PAV and SSR markers. The x axis shows the accumulative genetic distance (cM) in the genetic linkage map. The y axis represents the physical positions (bp) obtained by aligning with the reference genome of BTx623