Agricultural SNP Microarray CapitalBio

Customized maize 55K SNP chip microarray test

Maize Molecular Breeding Technology and Application Innovation Team of Institute of Crop Sciences, CAAS cooperated with CapitalBio Technology and Nantong Xinhe Biotechnology Co., Ltd. and jointly developed maize 55K SNP chip by employing Thermo Fisher Axiom platform.The chip has the characteristics of high density, low cost, full coverage and multiple purposes. It can be used for maize genetic mapping, identification of germplasm resources, gene mapping, molecular marker assisted breeding and other relevant researches.

a. Advantages of maize 55K SNP chip

1. High genome coverage probability and evenly distributed testing loci

2. Lower rate of locus deletion and heterozygosity

3. Clearly divided heterotic maize populations in China

4. Clearly divided heterotic maize populations in China

5. Candidate genes that affect important agronomic traits of maize included, open transgenic event tagged site added

6. Stable performance, highly repeatable typing results

b. GWAS on Flowering-related Traits of Maize

The population consisted of 724 hybrid strains derived from 28 temperate maize inbred lines and 23 tropical maize inbred lines.Based on this population, GWAS was conducted using genotyping data and blossom traits generated by 55K SNP chip (days from sowing to tasseling, days from sowing to silking, days from sowing to flowering, as well as flowering-silking interval). Five genomic regions related to flowering traits were identified and used for nucleotide mining of candidate genes and quantitative traits. Besides, 7.9 million SNP markers were obtained by deep re-sequencing of 51 maize inbred lines, which laid the foundation for higher resolution GWAS.

Fig. 5.7 NJ Tree Graph of 51 Parental Inbred Lines and 724 Multi-line Hybrid Populations and LD Attenuation Diagram of the Whole Genome

Fig.5.8 Five Significant Related Regions in the Genome  Obtained through GWAS on Four Flowering Traits of MHP Population

Customized wheat 660K SNP chip microarray test

Professor Jia Jizeng's Research Group comprehensively adopted de novo sequencing, re-sequencing and other strategies for high-throughput sequencing of 118 wheat samples and their related genera and species including 111 common wheat samples, 2 tetraploid wheat samples, 3 A genomes and 2 D genomes, obtained 6Tb data, and used Chinese Spring's survey sequence as the reference sequence to obtain 51.38 million SNPs through bioinformatics analysis as per the strict standard. Through cooperation with Beijing CapitalBio Technology Co., Ltd., wheat 660KSNP chip was formed after bioinformatics screening and chip pre-experiment.

a. Advantages of wheat 660K SNP chip

High polymorphism

The chip was highly polymorphic and high-resolution markers accounted for 58.9%.Among 66 natural populations of common wheat, the SNP of PolyHighResolution, NoNinorHom and OTV accounted for 65.35%.

High efficiency

It can test more than 600,000 SNP loci, and Callrate in hexaploid common wheat is >95%. It is a wheat SNP chip with the most effective testing loci.

High accuracy

After the initial screening, the unclear markers were eliminated.

Clear annotation

Most SNP probes were provided with complete physical and genetic location information, laying a foundation for further study.

Cost effectiveness

The cheapest method for testing SNP markers in wheat

b. GWAS on Black Point of Wheat"

In this research, we used 660K and 90K high-resolution SNP chips to detect the genotypes of 166 important commercial varieties and high generation product series in Huanghuai Wheat Region, and carried out population structure analysis and genome wide association study (GWAS).

Combined with the field phenotypic data under five environments, the classic TasselMLM model and the more rigorous FarmCPU were adopted for GWAS to find the significant association loci of black embryo disease, and the loci existing in the two models were taken as the final results. A total of 25 loci were detected on chromosomes 2A,2B, 3A, 3B(2), 3D, 4B  (2), 5A (3), 5B (3), 6A, 6B, 6D, 7A (5), 7B and 7D (2), respectively interpreting the phenotypic variation from 7.9% to 18.0%. Among the loci found, 13 loci existed in multiple environments and had stable genetic effects, 7 loci were consistent with those in previous researches, and 18 loci were new.

Fig.5.4. Structural Analysis on 166 Wheat Populations

This research not only provided SNP molecular markers and resistance alleles for breeding of wheat resistant to black embryo disease, but also provided new clues for the genetic mechanism of resistance to black embryo discase.

Fig. 5.6 Genome Wide Association Study (GWAS) on Black Point Disease Resistance of 166 Wheat Cultivars by Using the Mixed Linear Model (MLM) of Tasselv5.0 Software