Dataset Information

New development and validation of 50 SSR markers in breadfruit (Artocarpus altilis, Moraceae) by next-generation sequencing.

ABSTRACT: PREMISE OF THE STUDY:Using next-generation sequencing technology, new microsatellite loci were characterized in Artocarpus altilis (Moraceae) and two congeners to increase the number of available markers for genotyping breadfruit cultivars. METHODS AND RESULTS:A total of 47,607 simple sequence repeat loci were obtained by sequencing a library of breadfruit genomic DNA with an Illumina MiSeq system. Among them, 50 single-locus markers were selected and assessed using 41 samples (39 A. altilis, one A. camansi, and one A. heterophyllus). All loci were polymorphic in A. altilis, 44 in A. camansi, and 21 in A. heterophyllus. The number of alleles per locus ranged from two to 19. CONCLUSIONS:The new markers will be useful for assessing the identity and genetic diversity of breadfruit cultivars on a small geographical scale, gaining a better understanding of farmer management practices, and will help to optimize breadfruit genebank management.

SUBMITTER: De Bellis F

PROVIDER: S-EPMC5001855 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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New development and validation of 50 SSR markers in breadfruit (Artocarpus altilis, Moraceae) by next-generation sequencing.

De Bellis Fabien F Malapa Roger R Kagy Valérie V Lebegin Stéphane S Billot Claire C Labouisse Jean-Pierre JP

Applications in plant sciences 20160729 8

<h4>Premise of the study</h4>Using next-generation sequencing technology, new microsatellite loci were characterized in Artocarpus altilis (Moraceae) and two congeners to increase the number of available markers for genotyping breadfruit cultivars.<h4>Methods and results</h4>A total of 47,607 simple sequence repeat loci were obtained by sequencing a library of breadfruit genomic DNA with an Illumina MiSeq system. Among them, 50 single-locus markers were selected and assessed using 41 samples (39 ...[more]

PMID: 27610273

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Project description:BackgroundBreadfruit (Artocarpus altilis) is a traditional staple tree crop throughout the tropics. Through interspecific grafting, a dwarf phenotype with over 50% reduction in plant height was identified when marang (Artocarpus odoratissimus) rootstocks were used. However, the molecular mechanism underlying the rootstock-induced breadfruit dwarfing is poorly understood.ResultsAn RNA-sequencing study of breadfruit scions at 22 months after grafting identified 5409 differentially expressed genes (DEGs) of which 2069 were upregulated and 3339 were downregulated in scion stems on marang rootstocks compared to those on self-graft. The DEGs were predominantly enriched for biological processes involved in carbon metabolism, cell wall organization, plant hormone signal transduction and redox homeostasis. The down-regulation of genes encoding vacuolar acid invertases and alkaline/neutral invertases, was consistent with the decreased activity of both enzymes, accompanying with a higher sucrose but lower glucose and fructose levels in the tissues. Key genes of biosynthetic pathways for amino acids, lipids and cell wall were down regulated, reflecting reduction of sucrose utilisation for stem growth on dwarfing rootstocks. Genes encoding sugar transporters, amino acid transporters, choline transporters, along with large number of potassium channels and aquaporin family members were down-regulated in scion stems on marang rootstocks. Lower activity of plasma membrane H+-ATPase, together with the predominance of genes encoding expansins, wall-associated receptor kinases and key enzymes for biosynthesis and re-modelling of cellulose, xyloglucans and pectins in down-regulated DGEs suggested impairment of cell expansion. Signalling pathways of auxin and gibberellin, along with strigolacton and brassinosteroid biosynthetic genes dominated the down-regulated DEGs. Phenylpropanoid pathway was enriched, with key lignin biosynthetic genes down-regulated, and flavonoid biosynthetic genes upregulated in scions on marang rootstocks. Signalling pathways of salicylic acid, jasmonic acid, ethylene and MAPK cascade were significantly enriched in the upregulated DEGs.ConclusionsRootstock-induced disruption in pathways regulating nutrient transport, sucrose utilisation, cell wall biosynthesis and networks of hormone transduction are proposed to impair cell expansion and stem elongation, leading to dwarf phenotype in breadfruit scions. The information provides opportunity to develop screening strategy for rootstock breeding and selection for breadfruit dwarfing.

Dataset Information

New development and validation of 50 SSR markers in breadfruit (Artocarpus altilis, Moraceae) by next-generation sequencing.

Publications

New development and validation of 50 SSR markers in breadfruit (Artocarpus altilis, Moraceae) by next-generation sequencing.

Similar Datasets

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