BIOTECHNOLOGICAL STUDIES ON EGYPTIAN DATE PALM

Abstract

In recent years, date palm has been subjected to intensive genome sequencing studies. The advances in bioinformatics have provided the scientists with tools to develop useful SSR markers that help the breeder accelerating their breeding programs.A total of 172,075 SSR motifs was identified in date palm genome sequence with a frequency of 450.97 SSRs per Mbp. Out of these, 130,014 SSRs (75.6%) were located within the intergenic regions. While, only 42,061 SSRs (24.4%) were located within the genic regions. A number of 111,403 of SSR primer pairs were designed, that represent 292.39 SSR primers per Mb. Out of the 111,403 only 31,380 SSR primers were developed in the genic regions, while 80,023 primers were developed in the intergenic regions. A number of 250,507 SNPs were recognized in 84,172 SSR flanking regions, which represent 75.55% of the total SSR flanking regions. Out of 12,274 genes only 463 genes comprising 896 SSR primers were mapped onto 111 pathways using KEGG data base. The most abundant enzymes were identified in the pathway related to the biosynthesis of antibiotics. Validation of the designed SSR primers was conducted using in silico and in vitro PCR. We tested 1031 SSR primers using both publicly available date palm genome sequences as templates in the in silico PCR reactions. When using the date palm genome PDK30 sequence, all the 1031 SSR primer pairs successfully found complementary sequences. However, only 903 SSR primers could successfully hit within the ATBV01 genome. Forin vitro validation, 31 SSR primers among those used in the in silico PCR were synthesized and tested for their ability to detect polymorphism among six Egyptian date palm cultivars. All tested primers have successfully amplified products, but only 16 primers detected polymorphic amplicons among the studied date palm cultivars. Key words: Date palm, SSR, Intergenic regions, Genic regions, SNPs, pathways, KEGG, In vitro PCR, In silico PCR.