This dataset supports the study:

“Linkage map construction and QTL mapping for morphological traits in Ipomoea trifida, a diploid sweetpotato relative.”

Dataset DOI: https://doi.org/10.5061/dryad.vx0k6dk4w

Overview

This dataset contains phenotypic and genotypic data from an outcrossing mapping population of Ipomoea trifida (2n = 2x = 30), developed from a cross between genotypes M9 × M19.

The data were generated to support linkage map construction and QTL mapping of morphological traits.

Experimental design

The mapping population consists of 188 individuals, including both parents.

• Population type: Full-sib (outcrossing species)
• Cross: M9 × M19
• Location: International Potato Center (CIP), San Ramon, Peru
• Year: 2016
• Conditions: Screen house
• Design: Randomized Complete Block Design (RCBD)
• Replications: 4

Files

M9xM19_screenhouse.csv

• Description: Phenotypic data
• Individuals: 188 (including parents)

all_variants_trifida_merged.vcf

• Description: Genotypic data (SNP markers)
• Format: Variant Call Format (VCF)
• Generated using: GATK pipeline

Data description

Phenotypic data (M9xM19_screenhouse.csv)

Each row represents an individual plant evaluated in a given replication.

• X.Plot: Plot number in the experimental design
• CIPN: Germplasm identifier (CIP code)
• BCODE: Breeding code
• Rep: Replication (block) number
• LEAFSHAP1: Leaf outline
  → Scale: 1–7 (ordinal score)
• LEAFSHAP2: Leaf lobe type
  → Scale: 0–9 (ordinal score)
• LEAFSHAP3: Number of leaf lobes
  → Scale: 1–9 (ordinal score)
• LEAFSHAP4: Shape of the central lobe
  → Scale: 0–9 (ordinal score)
• LEFTPP_TP1: Number of leaves per plant at 12 days
• LEFTPP_TP2: Number of leaves per plant at 30 days
• LEFTPP_TP3: Number of leaves per plant at 58–62 days                                                                                   
• PLANTH_TP1: Plant height at 11 days (cm)
• PLANTH_TP2: Plant height at 30 days (cm)
• VINDIA: Vine internode diameter (mm)
• LFSIZE: Mature leaf size (cm)
• PETIOL: Petiole length
  → Scale: 1–9 (ordinal score)
• LA: Leaf area (mm²)
• SRDW: Storage root dry weight (g)
• SRFW: Storage root fresh weight (g)
• VDW: Vine dry weight (g)
• VFW: Vine fresh weight (g)
• PTRN: Number of pencil-type roots
• PTRFW: Fresh weight of pencil-type roots
• NOSR: Number of storage roots per plant

Variables with suffix _SR: Square root–transformed values of the original trait

Variables with suffix _log: Log10-transformed values of the original trait (log10(x + 1))

Empty cells: Missing values

Genotypic data (all_variants_trifida_merged.vcf)

• Contains SNP markers for all individuals

Code/software

Phenotypic data

Read using base R:

data2016 <- read.csv("M9xM19_screenhouse.csv", header = TRUE, sep = ",")

Genotypic data

Read using the onemap package (v3.0):

vcf <- onemap_read_vcfR(vcf = "all_variants_trifida_merged.vcf",
                        cross = "outcross", 
                        parent1 = "CIP107665.9.merged", 
                        parent2 = "CIP107665.19.merged",
                        only_biallelic = TRUE, 
                        verbose = TRUE)

Acknowledgments

Genotypic data were generated by Dr. Gabriel Gesteira (NCSU) using GATK.