PAV markers in Sorghum bicolour: genome pattern, affected genes and pathways, and genetic linkage map construction
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Le résumé fourni par la source
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.
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Le contrôle bibliographique ouvert
DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.
- Titre Crossref
- PAV markers in Sorghum bicolour: genome pattern, affected genes and pathways, and genetic linkage map construction
- Date Crossref
- 30/01/2015
- Éditeur
- Springer Science and Business Media LLC
- Type
- journal-article
Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude, et il ne compte pas comme une seconde source scientifique indépendante.
Où se fait cette recherche
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Chinese Academy of Sciences pays non établi dans la noticeOrganisme public
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Institute of Botany pays non établi dans la noticeStructure de recherche
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University of Chinese Academy of Sciences pays non établi dans la noticeUniversité ou école supérieure
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Beijing Botanical Garden pays non établi dans la noticeInstitution
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University of Copenhagen pays non établi dans la noticeUniversité ou école supérieure
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Key Laboratory of Plant Resources pays non établi dans la noticeStructure de recherche
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Faculty of Sciences Department of Plant and Environment pays non établi dans la noticeUniversité ou école supérieure
Chinese Academy of Sciences, Institute of Botany et University of Chinese Academy of Sciences, avec 4 autres affiliations.
Une affiliation ne permet pas de déduire la nationalité d’un auteur.