The Wheat 660K SNP array demonstrates great potential for marker‐assisted selection in polyploid wheat

Abstract

Keywords: wheat, marker-assisted breeding, single-nucleotide polymorphisms, Axiomâ Wheat 660K SNP array, Illumina Wheat 90K iSelect SNP genotyping array. AbstractThe rapid development and application of molecular marker assays have facilitated genomic selection and genome-wide linkage and association studies in wheat breeding. Although PCRbased markers (e.g. simple sequence repeats and functional markers) and genotyping by sequencing have contributed greatly to gene discovery and marker-assisted selection, the release of a more accurate and complete bread wheat reference genome has resulted in the design of single-nucleotide polymorphism (SNP) arrays based on different densities or application targets. Here, we evaluated seven types of wheat SNP arrays in terms of their SNP number, distribution, density, associated genes, heterozygosity and application. The results suggested that the Wheat 660K SNP array contained the highest percentage (99.05%) of genome-specific SNPs with reliable physical positions. SNP density analysis indicated that the SNPs were almost evenly distributed across the whole genome. In addition, 229 266 SNPs in the Wheat 660K SNP array were located in 66 834 annotated gene or promoter intervals. The annotated genes revealed by the Wheat 660K SNP array almost covered all genes revealed by the Wheat 35K (97.44%), 55K (99.73%), 90K (86.9%) and 820K (85.3%) SNP arrays. Therefore, the Wheat 660K SNP array could act as a substitute for other 6 arrays and shows promise for a wide range of possible applications. In summary, the Wheat 660K SNP array is reliable and cost-effective and may be the best choice for targeted genotyping and marker-assisted selection in wheat genetic improvement.1354

Identification and validation of quantitative trait loci for kernel traits in common wheat (Triticum aestivum L.)

“…The ‘PuBing3228 × Gao 8901’ RIL population and the two parents were genotyped by the Affymetrix wheat 660 K SNP array [ 64 ]. A total of 101,136 loci showed polymorphisms between P3228 and G8901.…”

Toward the Genetic Basis and Multiple QTLs of Kernel Hardness in Wheat

“…First, the release of several high-quality Triticeae genomes has laid the foundation for performing GWAS analysis, connecting physical and genetic maps and identifying candidate genes within QTL regions [2,[119][120][121][122][123]. Second, a series of high-density SNP genotyping arrays provide versatile scenarios for wheat genotyping for varying costs and applications [126][127][128][142][143][144]. These wheat SNP-genotyping arrays have been comprehensively compared and reviewed [145].…”

High-Resolution Mapping of the Novel Early Leaf Senescence Gene Els2 in Common Wheat

“…The SNP genotyping assays, namely 90K [ 38 ] and 660K [ 42 ], have opened a new way to undertake a more efficient and faster marker saturation of target genes in wheat [ 47 ]. Compared to the 90K SNP chip, the 660K chip has several advantages, such as higher marker density and higher resolution, as well as a better distribution on the chromosomes [ 42 , 44 ]. In the present study, we used the 660K chip to screen candidate markers linked to Els2 and a significant number of polymorphic SNPs were identified ( Figure 3 A,B).…”

“…At present, several kinds of wheat SNP arrays have been reported, such as the Illumina Wheat 9K iSelect SNP array [37], the Illumina Wheat 90K iSelect SNP genotyping array [38], the Axiom®HD Wheat genotyping (820K) array [39], the Wheat Breeders' 35K Axiom array [40], 660K [34] and the Wheat 55K SNP array [41]. The 660K SNP array [42] has been effectively applied to develop Kompetitive allele-specific polymerase chain reaction (KASP) markers for saturation mapping of the target genes. Examples include the molecular mapping of the dwarfing genes Rht12 [43] and Rht24 [44], stripe rust resistances Yr26 [45], YrH62 [46] and Qyrnap.nwafu-2BS [47], and the chlorina mutant gene cn-A1 [48].…”