SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping

Abstract

BackgroundWith the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers. However, SNP chip data generally suffers from ascertainment biases caused by the SNP discovery and selection process in which a small number of individuals are used as discovery panels. The ongoing International Citrus Genome Consortium sequencing project of the highly heterozygous Clementine and sweet orange genomes will soon result in the release of several hundred thousand SNPs. The primary goals of this study were: (i) to estimate the transferability within the genus Citrus of SNPs discovered from Clementine BACend sequencing (BES), (ii) to estimate bias associated with the very narrow discovery panel, and (iii) to evaluate the usefulness of the Clementine-derived SNP markers for diversity analysis and comparative mapping studies between the different cultivated Citrus species.ResultsFifty-four accessions covering the main Citrus species and 52 interspecific hybrids between pummelo and Clementine were genotyped on a GoldenGate array platform using 1,457 SNPs mined from Clementine BES and 37 SNPs identified between and within C. maxima, C. medica, C. reticulata and C. micrantha. Consistent results were obtained from 622 SNP loci. Of these markers, 116 displayed incomplete transferability primarily in C. medica, C. maxima and wild Citrus species. The two primary biases associated with the SNP mining in Clementine were an overestimation of the C. reticulata diversity and an underestimation of the interspecific differentiation. However, the genetic stratification of the gene pool was high, with very frequent significant linkage disequilibrium. Furthermore, the shared intraspecific polymorphism and accession heterozygosity were generally enough to perform interspecific comparative genetic mapping.ConclusionsA set of 622 SNP markers providing consistent results was selected. Of the markers mined from Clementine, 80.5% were successfully transferred to the whole Citrus gene pool. Despite the ascertainment biases in relation to the Clementine origin, the SNP data confirm the important stratification of the gene pools around C. maxima, C. medica and C. reticulata as well as previous hypothesis on the origin of secondary species. The implemented SNP marker set will be very useful for comparative genetic mapping in Citrus and genetic association in C. reticulata.

A second-generation diagnostic single nucleotide polymorphism (SNP)-based assay, optimized to distinguish among eight poplar (Populus L.) species and their early hybrids

“…This type of result has already been observed when working with distant species because of the presence of unexpected polymorphisms affecting the amplification/hybridization process (e.g., Ollitrault et al 2012). Although fixed null alleles were not included in the counts presented in Table 2, they could be used for diagnostic purposes under certain conditions (see below).…”

Mechanisms of sexual polyploidization and inheritance in triploid citrus populations

“…More recently, the availability of large set of sequencing data has opened the way for insertion-deletion (InDel) and single nucleotide polymorphism (SNP) marker development Ollitrault et al, , 2012bGarcía-Lor et al, 2013b).…”

“…were selected from previous genotyping data obtained on the Illumina GoldenGate® platform (Ollitrault et al, 2012b). These SNPs were also used to test the accuracy of the technique in genotyping repetitions of the same sample over the 'Fortune' × 'Willowleaf' triploid population.…”

“…Genome-wide association studies of pooled DNA samples have been valuable tools in the fast, scalable and economical identification of candidate single nucleotide polymorphisms (SNPs) associated with a phenotype (Brauer et al, 2006;Akhunov et al, 2009;Hyten et al, 2009;Becker et al, 2011;Ricci et al, 2011;Szelinger et al, 2011;Swinnen et al, 2012;Trick et al, 2012). In citrus, very large SNP resources are becoming available from extensive citrus sequencing projects (Terol et al, 2007(Terol et al, , 2008Gmitter et al, 2012;Ollitrault et al, 2012b); meanwhile, new technologies have been developed for very rapidly genotyping large numbers of SNPs in DNA samples. One such technology is the GoldenGate assay from Illumina™ (Fan et al, 2003;Hyten et al, 2009;Yan et al, 2010), which proved useful in citrus by allowing mapping of 677 SNP markers onto the clementine's consensus map (Ollitrault et al, 2012a).…”

“…However, the low availability of SSR markers displaying favourable parental allelic structure that can be used to differentiate male and female contributions to the hybrids limits such studies to just a few areas of the genome. Conversely, large SNP resources have become available from extensive sequencing projects (Terol et al, 2007;Terol et al, 2008;Gmitter et al, 2012;Ollitrault et al, 2012b).…”