Construction of a high-density linkage map and graphical representation of the arrangement of transcriptome-based unigene markers on the chromosomes of onion, Allium cepa L.

Abstract

Background Genomic information for Allium cepa L. is limited as it is heterozygous and its genome is very large. To elucidate potential SNP markers obtained by NGS, we used a complete set of A. fistulosum L.-A. cepa monosomic addition lines (MALs) and doubled haploids (DHs). These were the parental lines of an A. cepa mapping population for transcriptome-based SNP genotyping. Results We mapped the transcriptome sequence reads from a series of A. fistulosum-A. cepa MALs onto the unigene sequence of the doubled haploid shallot A. cepa Aggregatum group (DHA) and compared the MAL genotype call for parental bunching onion and shallot transcriptome mapping data. We identified SNP sites with at least four reads on 25,462 unigenes. They were anchored on eight A. cepa chromosomes. A single SNP site was identified on 3,278 unigenes and multiple SNPs were identified on 22,184 unigenes. The chromosome marker information was made public via the web database Allium TDB (http://alliumtdb.kazusa.or.jp/). To apply transcriptome based genotyping approach for genetic mapping, we gathered RNA sequence data from 96 lines of a DHA × doubled haploid bulb onion A. cepa common onion group (DHC) mapping population. After selecting co-dominant SNP sites, 16,872 SNPs were identified in 5,339 unigenes. Of these, at least two SNPs with identical genotypes were found in 1,435 unigenes. We developed a linkage map using genotype information from these unigenes. All unigene markers mapped onto the eight chromosomes and graphical genotyping was conducted based on the unigene order information. Another 2,963 unigenes were allocated onto the eight chromosomes. To confirm the accuracy of this transcriptome-based genetic linkage map, conventional PCR-based markers were used for linkage analysis. All SNP - and PCR-based markers were mapped onto the expected linkage groups and no inconsistency was found among these chromosomal locations. Conclusions Effective transcriptome analysis with unique Allium resources successfully associated numerous chromosome markers with unigene information and a high-density A. cepa linkage map. The information on these unigene markers is valuable in genome sequencing and useful trait detection in Allium.

Insights from the first genome assembly of Onion (Allium cepa)

“…To further organize our genome assembly, we used three intraspecific genetic linkage maps ( Duangjit et al 2013 ; Choi et al 2020 ; Fujito et al 2021 ) and one interspecific genetic linkage map ( Scholten et al 2016 ) to anchor scaffolds into pseudomolecules using AllMaps ( Tang et al 2015 ). Except for the GBS-based markers from the study of Choi et al (2020) , all markers were developed from transcriptome sequencing.…”

“…With this approach, we were able to anchor 3303 scaffolds (3.6% of the total number of scaffolds) into eight pseudomolecules, with an overall length of 2.4 Gb (15.9% of the assembly size; Supplementary File S6). The pseudomolecules were named after their respective chromosome according to the A. cepa monosomic addition lines ( Shigyo et al 1996 ; Van Heusden et al 2000 ; Fujito et al 2021 ). A subset of 157 scaffolds (0.15 Gb) could be oriented according to the genetic map order.…”

“…This hypothesis is further supported by the results of the synteny analysis with garlic. Not only the 3515 of the 5339 onion unigene derived EST markers ( Fujito et al 2021 ) showed a uniform distribution on the garlic and onion pseudomolecules ( Figure 1 ), also the distribution of transposable elements is uniform over the garlic and onion chromosomes ( Sun et al 2020 ; Supplementary Figure S7). Our hypothesis is in line with previous results in which the mapping of genes on physical chromosomes using molecular cytogenetic methods showed that the genes in Allium are localized in all three regions of the chromosome arms: proximal, interstitial, and distal ( Scholten et al 2007 ; Masamura et al 2012 ; Khrustaleva et al 2016 , 2019a , b ).…”

“…The dovetail scaffolded genome assembly was anchored into pseudomolecules with Allmaps ( Tang et al 2015 ) using four previously published genetic linkage maps ( Duangjit et al 2013 ; Scholten et al 2016 ; Choi et al 2020 ; Fujito et al 2021 ). For the DHAxDHC genetic map ( Fujito et al 2021 ), mean genetic position of the bin was used for all markers in this bin.…”

“…Sequence of EST-based markers from Fujito et al (2021) were blasted to the onion genome and to the garlic genome. A total of 4034 markers had a hit to both genome sequences, of which 519 positioned at unanchored onion scaffolds, leaving 3515 markers positioned at the onion pseudomolecules.…”