Unveiling the Genomic Landscape: InnoVar’s Groundbreaking Exploration through SNP Analysis and GWAS

Innovar > News > Unveiling the Genomic Landscape: InnoVar’s Groundbreaking Exploration through SNP Analysis and GWAS

InnoVar genomics covers several work areas including transcriptomics, SNP analysis and GWAS exploiting field data for VCU and DUS. All of these tasks will work together to examine plant performance under variable conditions in order to identify desirable traits within the plant genome. Our partners at University of Bologna and University Polytechnic Madrid have been working on the SNP analysis.

All the durum and bread wheat genotypes, 228 and 236 respectively, were then sequenced in North Central Small Grains Genotyping Laboratory USDA- ARS-ETSARC (Fargo, ND, USA) using Illumina iSelect Infinium array SNP 90K Chip. Data were filtered based on SNP correctly mapped on Triticum turgidum cv Svevo reference genome (Maccaferri et al., 2019) and Triticum aestivum cv Chinese Spring v1.0 reference genome (THE INTERNATIONAL WHEAT GENOME SEQUENCING CONSORTIUM (IWGSC) et al., 2018), retaining 39K SNPs for bread wheat and 23K SNPs for durum wheat.

Genotypic data, traits from VCU and DUS and vegetation indexes  from phenomics were merged together to perform genome wide association studies (GWAS), in order to find molecular markers significantly associated with phenotypic variability for each of the measured DUS or VCU character.

The results showed many SNPs significantly associated to different traits, such as heading date, yield, culm and ear glaucosity, corresponding to quantitative trait loci (QTLs). The QTLs intervals identify SNP regions associated to haplotypes, contrasting and recombined between cultivars coming from very different breeding programs and agro-climatic zones (ACZ).

The genotypic characterization of the two panels helped in identifying genetic similarity thresholds (GSV), which better describe differences between genotypes. In addition, the same comparison was performed using DUS traits as morphological markers, reflecting a similar variety group of similarity/dissimilarity as already identified with genotypic data.

Ongoing and future activities will be performed to better describe relationship between varieties with haplotypes. Furthermore, kompetitive allele specific PCR (KASP ®) markers will be developed tagging haplotypes significantly associated with DUS and VCU trait variability (Semagn et al., 2014). Molecular markers and genetic information for each variety will help in augmenting and improving precision and accuracy for DUS and VCU protocol description, breeding programs and variety registration processes.

 

References

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