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, 7 (1), 3788

Utilization of a Wheat660K SNP Array-Derived High-Density Genetic Map for High-Resolution Mapping of a Major QTL for Kernel Number

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Utilization of a Wheat660K SNP Array-Derived High-Density Genetic Map for High-Resolution Mapping of a Major QTL for Kernel Number

Fa Cui et al. Sci Rep.

Abstract

In crop plants, a high-density genetic linkage map is essential for both genetic and genomic researches. The complexity and the large size of wheat genome have hampered the acquisition of a high-resolution genetic map. In this study, we report a high-density genetic map based on an individual mapping population using the Affymetrix Wheat660K single-nucleotide polymorphism (SNP) array as a probe in hexaploid wheat. The resultant genetic map consisted of 119 566 loci spanning 4424.4 cM, and 119 001 of those loci were SNP markers. This genetic map showed good collinearity with the 90 K and 820 K consensus genetic maps and was also in accordance with the recently released wheat whole genome assembly. The high-density wheat genetic map will provide a major resource for future genetic and genomic research in wheat. Moreover, a comparative genomics analysis among gramineous plant genomes was conducted based on the high-density wheat genetic map, providing an overview of the structural relationships among theses gramineous plant genomes. A major stable quantitative trait locus (QTL) for kernel number per spike was characterized, providing a solid foundation for the future high-resolution mapping and map-based cloning of the targeted QTL.

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1
Distribution of the 119 566 loci on the 21 wheat chromosomes. The 21 circles indicate the 21 wheat chromosomes, with 7D to 1D, 7B to 1B, and 7A to 1A from inside to outside, respectively. Each chromosome was evenly divided into 100 segments based on the map length, which are shown with different colours. The arc lengths indicate the percentage of markers on each segment (The total number of markers on the corresponding chromosome divided by the number of markers on the segments). The arc in red colour indicates the chromosomal bins near the centromere. The upper left histogram in the circle indicates the distribution of markers on each chromosome; the upper right histogram in the circle indicates the distribution of markers near the centromere on each chromosome; the bottom right histogram in the circle indicates the distribution of map length on each chromosome; the bottom left histogram in the circle indicates the distribution of markers in/near the coding sequences.
Figure 2
Figure 2
The high-density genetic map of wheat developed using an RIL population derived from the cross of cultivars KN9204 and J411. For the redundant loci that showed co-segregation in the 188 KJ-RILs, only one unique informative marker is shown in this figure. The approximate positions of the centromeres are indicated by pink. Short arms are at the top. The positions of the marker loci are indicated using a ruler on the left side of this figure. The names of the marker loci are listed to the right of the corresponding chromosomes. Loci in red were best hits to Chinese Spring (CS) contigs of the short arm of the corresponding chromosomes. Loci in green were best hits to CS contigs of the long arm of the corresponding chromosomes. Loci in black were unknown. Contigs from chromosome 3B were not separated into short/long arm bins, as individual arm datasets were not generated for this chromosome in the Chromosome Survey Sequence (CSS) project.
Figure 3
Figure 3
Schematic representation of the syntenic relationships between any one marker in wheat genetic and physical maps. Gen-1A to Gen-7D represent the 21 wheat chromosomal genetic maps released in this paper; Phy-1A to Phy-7D represent the 21 wheat chromosomal physical maps, which were constructed by assigning 116 261 SNPs to the wheat genome assembly using SNP flanking sequences as the query. For the redundant loci that showed co-segregation in the 188 KJ-RILs, only one unique informative marker is shown in this figure.
Figure 4
Figure 4
Overlapping confidence intervals of QTLs for kernel number per spike (KNPS) based on MapQTL 6.0, IciMapping 4.1 and QTLNetwork 2.0. The segments in red are the overlapping confidence intervals of qKnps-4A, and the overlapping flanking markers of qKnps-4A are indicated by triangles in red, which were detected by QTLNetwork 2.0 based on the combined 10 environmental phenotypic values.
Figure 5
Figure 5
Synteny of the mapped SNPs from the Wheat660K SNP array (in blue) with that from the Wheat90K array (in red) based on their common CSS-assembled contigs.
Figure 6
Figure 6
Synteny of the mapped SNPs from the Wheat660K SNP array (in blue) with that from the Wheat820K array (in green) based on their common CSS-assembled contigs. Notes: The genetic maps of chromosomes 3A, 4B, 5D, 6D and 7B derived from the Wheat820K SNP array are shown in inverted form, with long arms at the top and short arms at the bottom. In this figure, these inversions were corrected.

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