Utilization of a Wheat660K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number

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.High-density genetic linkage maps are essential for genetic and genomic research in crops 1-4 . Molecular breeding is more effective if the molecular map is dense to provide more choices in the quality and type of markers and to increase the probability of detecting polymorphic markers in important chromosomal intervals. In wheat, the large genome size (17 gigabases), hexaploid nature (AABBDD), high percentage of repetitive regions and low level of polymorphism have complicated the acquisition of high-resolution genetic maps by molecular markers 1-4 . To date, several kinds of molecular markers, including restriction fragment length polymorphism (RFLP) 5,6 , amplified fragment length polymorphism (AFLP) 7 , simple sequence repeats (SSRs) 8,9 , and diversity array technology (DArT) 3, 4, 10, 11 have been used to construct genetic linkage maps in wheat. Information regarding wheat molecular markers and genetic maps is available in some datasets such as GrainGenes 2.0 (https:// wheat.pw.usda.gov/GG3/), URGI (https://urgi.versailles.inra.fr/), etc. Most of these markers are mapped on the telomeric regions, and there is very limited map resolution in proximal part of the chromosomes 3 . Therefore, the density and coverage of the current genetic maps are less than satisfactory.Single-nucleotide polymorphisms (SNPs) are the most abundant type of molecular marker. Accurate and reliable methods have been developed to perform high-throughput genotyping based on SNPs 12 . With the development of new sequencing technologies, increasing numbers of SNPs have been discovered in wheat 1, 2, 13-15 .

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

“…The Wheat 660K SNP array was designed by the Chinese Academy of Agricultural Sciences and is based on hexaploid and tetraploid wheat, emmer wheat and Aegilops tauschii , and has the advantages of being genome‐specific, high‐density, efficient, cost‐effective and with a wide range of possible applications, and has also added numerous markers to the D genome (http://wheat.pw.usda.gov/ggpages/topics/Wheat660_SNP_array_developed_by_CAAS.pdf). The Wheat 660K SNP array has been widely used to identify genetic loci for quality traits, agronomic traits and disease resistance in common wheat (Cui et al , 2017; Jin et al , 2016; Yang et al , 2019).…”

“…Therefore, SNP arrays have been widely used by many breeders in a variety of academic research, including genome‐wide association (Guo et al , 2017; Kidane et al , 2019), linkage map construction and QTL mapping (Cui et al , 2017; Jin et al , 2016), population structure, and phylogenetic analysis (Kidane et al , 2019; Valluru et al , 2017). In the present study, we selected seven widely used high‐throughput wheat arrays (Wheat 9K, 15K, 35K, 55K, 90K, 820K and 660K arrays) and compared their performance in terms of SNP number, distribution, density and associated genes to assess their value and provide guidance for their better application in marker‐assisted breeding at the wheat genome level.…”

“…Of all the papers related to wheat arrays (Figure 1), 80% employed the Wheat 90K array, indicating that the Wheat 90K array was the most widely used in the identification of trait‐related genetic loci over past five years. After the Wheat 660K array was formally utilized in 2017 (Cui et al , 2017), 12 papers employing the 660K array were published in the following two years. Based on SNP density, heterozygosity and distribution on chromosomes, the Wheat 660K array has great potential application in MAS and may be the best choice for the identification of trait‐related genetic loci and MAS in wheat breeding programs.…”

Unraveling the genetic architecture of grain size in einkorn wheat through linkage and homology mapping, and transcriptomic profiling

“…3a, b). This should be attributed to 4 1 7 4AL/5AL/7BS translocations during wheat's evolutionary history (Devos et al, 1995; 4 1 8 King et al, 1994). The translocation between 4A and 5A was observed in einkorn 4 1 9…”

Molecular Mapping of a Recessive Powdery Mildew Resistance Gene in Wheat Cultivar Tian Xuan 45 Using Bulked Segregant Analysis with Polymorphic Single Nucleotide Polymorphism Relative Ratio Distribution

“…According to the results of the distribution of polymorphism SNPs per 1 Mbp in each chromosome, we found that 2B, 4B, and 6A may have higher probability to be the chromosomes that contained PmTx45. 5B and 3B did not show a particularly high enrichment peak under this plot, because the chip had more on the loci of the two chromosomes (Cui et al 2017; Fig. 3C).…”