1 Section for Plant and Soil Sciences, Department of Plant and Environmental Sciences, Faculty of Science, Københavns Universitet2 The Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China3 Department of Agriculture & Ecology, Plant and Soil Science, Department of Agriculture & Ecology, Faculty of Life Sciences, Københavns Universitet4 Department of Agriculture & Ecology, Plant and Soil Science, Department of Agriculture & Ecology, Faculty of Life Sciences, Københavns Universitet
genome pattern, affected genes and pathways, and genetic linkage map construction
Abstract Genic presence/absence variants (PAVs) correlate closely to the phenotypic variation, impacting plant genome sizes and the adaption to the environment. To shed more light on their genome-wide patterns, functions and to test the possibility of using them as molecular markers, we analyzed genome sequence data of four sorghum inbred lines for the discovery and validation of small-size PAVs (40bp-10kb). Five thousand five hundreds and eleven (5,511) genic small-size PAVs (40 bp-10 kb) were identified and found to affect 3238 genes. These PAVs were mainly distributed on the sub-telomeric regions, but the highest proportions occurred in the vicinity of the centromeric regions. 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 stress responses and protein modification. We used 325 polymorphic PAVs in 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 1430.3 cM in length covering 97 % of the region of the physical genome. The resources reported here should be useful for genetic study and breeding of sorghum and related species.
Theoretical and Applied Genetics, 2015, Vol 128, Issue 4, p. 623-637