IDENTIFICATION OF ALLELIC VARIATION IN STRUCTURAL GENES CODING FOR CAROTENOIDS BIOSYNTHESIS IN CARROT

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Date
2016-07
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University of Horticultural Sciences, Bagalkot (COLLEGE OF HORTICULTURE, GKVK POST, BANGALURU)
Abstract
Carrot (Daucuscarota, 2n=18) is an important vegetable crop, providing pro-vitamin A, carotenoids in the human diet. The genes coding for the carotenoid pathway enzymes are evolutionarily conserved, but little information exists about these genes in carrot.This study focused to characterize candidate gene sequence of carotenoid pathway specific genes in orange, black and red carrotsand to identify allelic variations existing in carotenoid biosynthesis genes with respect to carotenoid pigments accumulation in carrot roots. A total of 24 carrot carotenoid biosynthesis pathway genes were investigated.The sequences were retrieved from Genbankdata base and STS primers are designed,synthesized, PCR amplified,PCR product eluted,sequenced, sequences are aligned and variations studied in black,red and orange carrots. Allelic variations are observed like deletions.The three main PSY1 variations differed from each other by 1-2 amino acids positions at 168- 175 postions.PSY1 allelic variations observed at 7 genomic regions, whereas in PSY2 gene;deletions were observed at three gene genomic regions i.e. 137- 139, 504-509, 677, 688 nucleotide regions.Phytoene desaturaseenzyme (PDS) deletions was observed from 308-325gene genomic area in both red and orange carrot, similarly in ζ-Carotene desaturase 2 (ZDS2) more numbers of SNP and deletions are observed in black and red carrots compared to orange carrot at 710, 714, 756 -759. In carotenoid isomerase enzyme (CRTISO) few variations observed in all three colour carrots, in Lycopene β-cyclase (LCYB) a long stretch of deletions from 365-424 observed in black as compared to red and orange carrot. In case of Lycopene ε-cyclase (LCYE) more no. of structural variations are observed in all carrot colour lines. Carotenoid cleavage dioxygenase3 (CCD 3) was also most similar with black, red and orange with respect to sequence. In 9-cis-Epoxycarotenoid dioxygenase1 (NCED1), more variations observed in black and orange compared to red carrot. Similarly (9-cis-Epoxycarotenoid dioxygenase3) NCED3 sequence retrieval very narrow and variation identified.
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