Abstract
Microsatellites or simple sequence repeats (SSRs) are one of the most popular sources of genetic markers and play a significant role in plant genetics and breeding. In this study, we identified citrus SSRs in the genome of Clementine mandarin and analyzed their frequency and distribution in different genomic regions. A total of 80,708 SSRs were detected in the genome with an overall density of 268 SSRs/Mb. While di-nucleotide repeats were the most frequent microsatellites in genomic DNA sequence, tetra-nucleotides, which had more repeat units than any other SSR types, had the highest cumulative sequence length. We identified 6,834 transcripts as containing 8,989 SSRs in 33,929 Clementine mandarin transcripts, among which, tri-nucleotide motifs (36.0%) were the most common, followed by di-nucleotide (26.9%) and hexa-nucleotide motifs (15.1%). The motif AG (16.7%) was most abundant among these SSRs, while motifs AAG (6.6%), AAT (5.0%), and TAG (2.2%) were most common among tri-nucleotides. Functional categorization of transcripts containing SSRs revealed that 5,879 (86.0%) of such transcripts had homology with known proteins, GO and KEGG annotation revealed that transcripts containing SSRs were those implicated in diverse biological processes in plants, including binding, development, transcription, and protein degradation. When 27 genomic and 78 randomly selected SSRs were tested on Clementine mandarin, 95 SSRs revealed polymorphism. These 95 SSRs were further deployed on 18 genotypes of the three generas of Rutaceae for the genetic diversity assessment, genomic SSRs generally show low transferability in comparison to SSRs developed from expressed sequences. These transcript-markers identified in our study may provide a valuable genetic and genomic tool for further genetic research and varietal development in citrus, such as diversity study, QTL mapping, molecular breeding, comparative mapping and other genetic analyses.
Highlights
Conventional plant breeding is largely dependent on selection of desirable plants which is highly decided by the parents and different environment factors interaction [1]
When 27 genomic and 78 randomly selected SSRs were tested on Clementine mandarin, 95 SSRs revealed polymorphism
The recent release of the Clementine mandarin genome sequence will dramatically enhance the efficiency of functional and comparative genomics research in citrus [18]. This allows researchers studying various agronomic traits related to the perennial trees with a completely new set of tools, including a potentially useful resource for mining SSR markers
Summary
Conventional plant breeding is largely dependent on selection of desirable plants which is highly decided by the parents and different environment factors interaction [1]. During conventional plant breeding genes are mixed and newly assorted This results in non-desired traits being inherited together with the trait of interest. The progress made in the development of DNA based marker systems has advanced including restriction fragment length polymorphisms (RFLPs), random amplification of polymorphic. The SSR information generated by MISA was used for designing primers flanking the repeats. The SSRcontaining transcripts were identified as candidates for SSR marker development if they had sufficient sequences on both sides of the SSR repeats for primer design. For the conventional strategies for SSR isolation, i.e., screening small insert genomic DNA libraries or constructing. The survey was based on genome data, their classification, characterization and comparative analysis in eighteen phylogenetically distant citrus species including deciduous and evergreen citrus trees.
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