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.
Highlights
High-density genetic linkage maps are essential for genetic and genomic research in crops[1,2,3,4]
An F8:9 recombinant inbred line (RIL) population including 188 lines derived from a cross between Kenong 9204 (KN9204) and Jing 411 (J411), 65 KN9204derived advanced lines/authorized varieties, three parental lines of KN9204, three control varieties from the Winter Wheat Performance Trial of the Northern Huang-Huai Regional Nursery of China, and Chinese Spring (CS) were genotyped using the 630517 single-nucleotide polymorphism (SNP) on the Wheat660K SNP array as probes
The scores for the probes were classified into one of the following six categories according to the cluster patterns produced by the Affymetrix software (Table S1): (i) Poly High Resolution (PHR) (188040; 29.8%); (ii) No Minor Homozygote (NMH) (133246; 21.1%); (iii) Off-Target Variant (OTV) (18471; 3.0%); (iv) Mono High Resolution (MHR) (163308; 25.9%); (v) Call Rate Below Threshold (CRBT) (22635; 3.6%); and (vi) Other (91425, 14.5%)
Summary
The 5175 bin markers were used for linkage analysis based on their scores in the 188 KJ-RILs. In total, 4959 bin markers were mapped to the wheat genetic map. A high-density genetic map with 119566 loci spanning 4424.4 cM was constructed (Table S2) Of these loci, 119001 were SNP markers derived from the Wheat660K SNP array, and the remaining 565 markers were reported previously by Cui et al.[3]. SNP order in the present genetic map was in good agreement with that in the wheat genome assembly, with the exception of chromosome 7DL, in which a segment inversion was identified (Fig. 3; Figure S2; Table S3). Inra.fr/download/iwgsc/IWGSC-WGA_Sequences/), the overlapping confidence intervals of Ax-109844107– Ax-110540586 spanned 3.23 Mb (4 A:680398739–4 A:683638403) in physical position (Figure S7) This region harbours 65 predicted genes in wheat (Figure S8), which might include the candidate gene for qKnps-4A
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