Molecular Breeding

, 37:37 | Cite as

Construction of two genetic linkage maps of taro using single nucleotide polymorphism and microsatellite markers

  • Laurent Soulard
  • Pierre Mournet
  • Baptiste Guitton
  • Hâna Chaïr
Article

Abstract

Linkage maps are needed for genetic studies and molecular breeding of taro (Colocasia esculenta). In this study, we used genotyping-by-sequencing (GBS) to identify single nucleotide polymorphism (SNP) loci on two mapping populations: F31 (HLB11 × VU006) composed of 266 progenies and F32 [HLB01 × (VU370×ID316)] composed of 292 progenies. SNP calling generated an initial set of 22,734 SNPs for F31 and 16,744 for F32. A large proportion of individuals and loci were later removed by filtering on the proportion of missing data and segregation distortions. Linkage maps were constructed with filtered SNPs in association with 14 simple sequence repeat (SSR) markers, using the maximum likelihood method. In both populations, loci were successfully grouped into 14 linkage groups (LGs) with an independence logarithm of odds (LOD) threshold of 11.0 and 8.0 for F31 and F32, respectively. LGs ranged in size from 90 to 15 markers for F31 and from 92 to 12 markers for F32. Bridge markers (459 SNPs and 9 SSRs) were identified and revealed homologous groups between families. Although our maps presented unprecedented chromosome coverage, the colinearity between homologous groups was low (except for LG07), and map lengths were globally inflated. Putative effects of missing data, segregation distortion, and genotyping errors on map accuracy are discussed. This research work led to the identification of a reliable set of SNPs potentially useful as a tool for a wide range of genetic studies in taro.

Keywords

Genotyping-by-sequencing Linkage mapping Single nucleotide polymorphism Taro UNEAK 

Supplementary material

11032_2017_646_MOESM1_ESM.docx (13 kb)
Supplementary Table 1Summary of sequencing data. For each mapping family, we give the total, average, minimum and maximum number of good barcoded reads, mapped reads and 3× tags. (DOCX 12 kb)
11032_2017_646_MOESM2_ESM.docx (302 kb)
Supplementary Figure 1Digestion patterns of taro genomic DNA with ApeK1, Pst1 and EcoT221. Fragment size distribution of GBS libraries made with a single DNA sample using three restriction enzymes (top: ApeKI; middle: EcoT22I; bottom: PstI). Libraries were run on an Agilent BioAnalyzer 2100. The x-axis represents elution time and the y-axis shows fluorescence units. Numbers below hatch marks on the x-axis indicate fragment size (bp). Tall peaks at 15 and 1500 bp are size standards, and the small peak at ∼70 bp in all panels represents PCR primer dimers. Adapter dimers (∼128 bp) were not observed. (DOCX 302 kb)
11032_2017_646_MOESM3_ESM.docx (555 kb)
Supplementary Figure 2Neighbor-joining trees constructed with DARwin v5.0.158. Samples and sites were excluded from the analysis due to the extremely high level of missing data. For mapping populations, samples with more than 60% of missing data and individuals with more than 30% of missing data were excluded. As a result, neighbor-joining phylogenetic trees were based on 228 samples and 761 sites for F31 (a), 276 samples and 338 sites for F32 (b). In F31, the replicated samples are colored in green for parent HLB11 and colored in red for parent VU006. In F32, the replicated samples are colored in green for parent VU370 × ID316 and colored in red for parent HLB01. We can notice the same two-group structure for both families. This structure is related to the rate of missing data: one group of samples with low rates of missing data (low %NA) and one group of samples with higher levels (high %NA). (DOCX 554 kb)
11032_2017_646_MOESM4_ESM.docx (334 kb)
Supplementary Figure 3Colinearity of markers between linkage maps of F31 (left) and F32 (right) with a default order. Red lines between linkage groups show homology. Markers with a black label are not shared. SSR markers are shown in black boxes. (DOCX 333 kb)
11032_2017_646_MOESM5_ESM.docx (419 kb)
Supplementary Figure 4Colinearity of markers between linkage maps of F31 (left) and F32 (right) with a fixed order. Red lines between linkage groups show homology. Markers with a black label are not shared. SSR markers are shown in black boxes. (DOCX 418 kb)
11032_2017_646_MOESM6_ESM.docx (202 kb)
Supplementary Figure 5aSNP/SSR linkage map of F31 with a fixed order (DOCX 201 kb)
11032_2017_646_MOESM7_ESM.docx (196 kb)
Supplementary Figure 5bSNP/SSR linkage map of F32 with a fixed order. Specific SNP markers are labeled MXXXX, bridge SNPs are labeled IDKXXXX while SSR markers are shown in black boxes. Asterisks indicate distortion level of markers (*P < 0.05; **P < 0.01; ***P < 0.005; ****P < 0.001, *****P < 0.0005, ******P < 0.0001; *******P < 0.00005). Cumulative distances are indicated to the left of groups in centiMorgan (cM). (DOCX 196 kb)
11032_2017_646_MOESM8_ESM.fasta (99 kb)
Supplementary fasta 1Sequences of all SNPs from linkage map F31 (FASTA 99 kb)
11032_2017_646_MOESM9_ESM.fasta (93 kb)
Supplementary fasta 2Sequences of all SNPs from linkage map F32 (FASTA 92 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  • Laurent Soulard
    • 1
  • Pierre Mournet
    • 1
  • Baptiste Guitton
    • 1
  • Hâna Chaïr
    • 1
  1. 1.CIRAD, UMR AGAPMontpellier Cedex 5France

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