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Biology
Evolutionary Biology

Subfamily Relationships and Clustering of Rabbit C Repeats

Profile image of Dan KraneDan Krane

1991

Abstract

C repeats constitute the predominant family of short interspersed repeats (SINES) in the rabbit genome. Determination of the nucleotide sequence 5' to rabbit (- globin genes reveals clusters of C repeats, and analysis of these and other sequenced regions of rabbit chromosomes shows that the C repeats have a strong tendency to insert within or in close proximity to other

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Short interspersed repeats in rabbit DNA can provide functional polyadenylation signals
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Analysis of 37 short repetitive elements (SINES) in rabbit DNA that are known as C repeats has revealed three that contribute functional polyadenylation signals to genes into which they have been inserted. Similar roles have been attributed to particular individual SINES in rodents and primates before, suggesting that these roles may be common to SINES in all mammalian orders. Although most SINES appear to have little influence on the genome individually, the observation that three of 36 rabbit C repeats provide functional sequences suggests a mechanism for the maintenance of SINES within mammalian genomes.

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The importance of DNA and protein applications as powerful tools in breeding programmes is revealed. The inter simple sequence repeats (ISSR) technique was used to characterise and determine phylogenetic relationships among 4 genotypes of rabbit, namely Alexandria (Alex), V line (V), New Zealand White (NZW) and California (Cal). Six out of 7 ISSR primers exhibited sufficient variability and were used to characterise the genetic diversity and relationships among studied genotypes. A total of 141 DNA bands were detected. DNA fragments were generated with 87 (61.7%) being polymorphic, indicating considerable genetic variation among the examined genotypes. While protein electrophoresis provides a precise method for assaying variation in serum proteins which play an important part in productive performance. The results demonstrated 2 specific protein markers in Alexandria rabbits; these specific protein markers may be responsible for the superiority of Alexandria line in weight. Phylogenetic analysis based on Nei and Li unbiased genetic distance illustrated that (Alex & V) and (Cal & V) were genetically closely related. Our results showed that ISSR and protein electrophoresis are useful methods to detect different genetic expressions and understand the variability in some productive traits in rabbits.

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To determine the frequency and clustering of a variety of simple di-and trinucleotide repeats, an Artiodactyl short interspersed element (SINE), an ovine satellite repeat, and a human Alu 1 repeat were used to screen a random selection of cosmids containing inserts of ovine genomic DNA. In total, 197 individual cosmids were digested with EcoRl and the fragments separated on 0.7% agarose gels. Southern blots of these gels were then sequentially probed with (AC)7 , (CT)9, and (CAC)6 oligonucleotides, and the repeats described above. The frequency at which (AC)n , (CT)n, and (CAC) n repeats were found in the cosmids indicated that they occurred at average intervals of 65 kb, 367 kb, and 213 kb respectively within the ovine genome. The Artiodactyl SINE was the most common, occurring at an average interval of 20 kb. No human Alu 1 sequences were detected. There was a significant positive association between the (AC)n and the Artiodactyl SINE. This association is quite strong as there was significant clustering of the two repeats both within cosmids and also within the EcoRI fragments of the digested genomic fragments. With the exception of the sheep satellite sequence, which occurs in tandem arrays, none of the other repeats showed significant clustering within the 41-kb (average size) cosmid inserts. The first 25 ovine microsatellites we characterized had an average polymorphic information content (PIC) of 0.65. The different microsatellite types, containing either perfect, imperfect, or compound repeats, had similar average PICs of 0.64, 0.65, and 0.66 respectively. There was a weak regresz sion relationship (R (adj)% --21.9) between the length of the longest uninterrupted dinucleotide repeat in the largest allele and the PIC of the microsatellite.

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