Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array

Abstract

Polypoid species play significant roles in agriculture and food production. Many crop species are polyploid, such as potato, wheat, strawberry, and sugarcane. Genotyping has been a daunting task for genetic studies of polyploid crops, which lags far behind the diploid crop species. Single nucleotide polymorphism (SNP) array is considered to be one of, high-throughput, relatively cost-efficient and automated genotyping approaches. However, there are significant challenges for SNP identification in complex, polyploid genomes, which has seriously slowed SNP discovery and array development in polyploid species. Ploidy is a significant factor impacting SNP qualities and validation rates of SNP markers in SNP arrays, which has been proven to be a very important tool for genetic studies and molecular breeding. In this review, we (1) discussed the pros and cons of SNP array in general for high throughput genotyping, (2) presented the challenges of and solutions to SNP calling in polyploid species, (3) summarized the SNP selection criteria and considerations of SNP array design for polyploid species, (4) illustrated SNP array applications in several different polyploid crop species, then (5) discussed challenges, available software, and their accuracy comparisons for genotype calling based on SNP array data in polyploids, and finally (6) provided a series of SNP array design and genotype calling recommendations. This review presents a complete overview of SNP array development and applications in polypoid crops, which will benefit the research in molecular breeding and genetics of crops with complex genomes.

Development and evaluation of a genome‐wide Coffee 8.5K SNP array and its application for high‐density genetic mapping and for investigating the origin of Coffea arabica L.

“…Two examples of high-throughput platforms include next-generation sequencing (NGS) (Davey et al, 2011) and the development of DNA microarrays (Gupta et al, 2008). Compared to a whole-genome sequencing methodology, an SNP array approach provides time-effective, low-cost and more straightforward genotyping technology for germplasm screening (You et al, 2018;Yu et al, 2014).…”

Molecular karyotypes of loquat (Eriobotrya japonica) aneuploids can be detected by using SSR markers combined with quantitative PCR irrespective of heterozygosity

“…We first obtained the PCR product amount (ΔRn value) ratios of the 17 LGs in known euploid strains as controls. Known aneuploid strains and unknown loquat strains were then examined and compared with the controls.…”

“…A total of 209 SSRs derived from loquat (16), pear (42), apple (144), peach (5), apricot (1) and plum (1) were used in this study ( Table 2). Some of the SSRs were located in the 17 LGs of bronze loquat [27], and some were also located on genetic linkage maps of the Japanese pears 'Housui' or the European pear 'Bartlett' and 'La France' [28][29][30][31]. Almost all loquat LGs were aligned with the pear consensus map by using at least two apple or pear SSRs [27].…”

“…Quantitative fluorescent polymerase chain reaction (QF-PCR) is widely applied in humans for the prenatal diagnosis of trisomy of chromosomes 21, 18, 13, X, and Y [15,16]. SNP arrays have been used as high-throughput genotyping tools for polyploid wheat, potato, sugarcane, and strawberry crops [17]. Quantitative real-time polymerase chain reaction (qPCR) has also been used for detection of the trisomy of chromosomes 21 (Down syndrome) and 11 [18].…”

“…This approach does not require large numbers of SSR markers or multiple types of fluorescent markers. In addition, this DNAbased qPCR method does not require additional reference genes, and SSR markers in 17 LGs can be selected as cross-references. The approach is also not restricted to heterozygous genotypes.…”