Articles
Assessment of genetic diversity and population structure of carrot accessions with DcSto Intron Length Polymorphism markers
Article number
1393_26
Pages
201 – 208
Language
English
Abstract
Carrot is one of the top ten important vegetables in the world, widely consumed due to its high nutritional value.
Carrot cultivars represent immense phenotypic and genotypic diversity.
However, two major gene pools of cultivated carrots are present, i.e., eastern and western carrots.
In the present study, we used markers developed on the basis of Intron Length Polymorphisms (ILPs) which originated from the presence/absence of DcSto miniature inverted-repeat transposable element (MITE) insertions.
Our main objective was to develop a DcS-ILP marker panel suitable to describe the structure of genetic diversity of the eastern carrot gene pool and to validate the ability to differentiate carrot accessions.
We used a total of 84 markers and genotyped 18 accessions, including 14 eastern carrot accessions, of which 10 were Indian cultivars, and 4 were accessions representing western cultivated carrots.
The genetic diversity structure was assessed by STRUCTURE. We also performed principal coordinate analysis (PCoA) with GenAlEx.
The best probable value of K=2 was obtained in STRUCTURE, representing two groups, the western accessions and the eastern accessions along with the Indian cultivars.
At K=3, three groups representing the western accessions, the eastern accessions and the Indian cultivars were revealed.
PCoA showed that the accessions are distributed in the different quadrants of the graph according to their origin.
The total of 48.43% variation was explained by the first three coordinates (27.02, 11.23 and 10.18% by the 1st, 2nd and 3rd coordinates, respectively). The STRUCTURE and PCoA analysis showed the ability of DcS-ILP markers to differentiate the accessions.
These markers can be further used for breeding purposes, e.g., assessment of genetic diversity and germplasm characterization, especially in the eastern carrot gene pool.
Carrot cultivars represent immense phenotypic and genotypic diversity.
However, two major gene pools of cultivated carrots are present, i.e., eastern and western carrots.
In the present study, we used markers developed on the basis of Intron Length Polymorphisms (ILPs) which originated from the presence/absence of DcSto miniature inverted-repeat transposable element (MITE) insertions.
Our main objective was to develop a DcS-ILP marker panel suitable to describe the structure of genetic diversity of the eastern carrot gene pool and to validate the ability to differentiate carrot accessions.
We used a total of 84 markers and genotyped 18 accessions, including 14 eastern carrot accessions, of which 10 were Indian cultivars, and 4 were accessions representing western cultivated carrots.
The genetic diversity structure was assessed by STRUCTURE. We also performed principal coordinate analysis (PCoA) with GenAlEx.
The best probable value of K=2 was obtained in STRUCTURE, representing two groups, the western accessions and the eastern accessions along with the Indian cultivars.
At K=3, three groups representing the western accessions, the eastern accessions and the Indian cultivars were revealed.
PCoA showed that the accessions are distributed in the different quadrants of the graph according to their origin.
The total of 48.43% variation was explained by the first three coordinates (27.02, 11.23 and 10.18% by the 1st, 2nd and 3rd coordinates, respectively). The STRUCTURE and PCoA analysis showed the ability of DcS-ILP markers to differentiate the accessions.
These markers can be further used for breeding purposes, e.g., assessment of genetic diversity and germplasm characterization, especially in the eastern carrot gene pool.
Authors
S. Hadagali, K. Stelmach, A. Macko-Podgórni, S. Cholin, D. Grzebelus
Keywords
Daucus carota, DcSto, MITEs, polymorphism, population structure
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