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Integrating a genome-wide association study with a large-scale transcriptome analysis to predict genetic regions influencing the glycemic index and texture in rice

ABSTRACT: Reliably generating rice varieties with low glycemic index (GI) is an important nutritional intervention given the high rates of Type II diabetes incidences in Asia where rice is staple diet. We integrated a genome-wide association study (GWAS) with a transcriptome-wide association study (TWAS) to determine the genetic basis of the GI in rice. GWAS utilized 305 re-sequenced diverse indica panel comprising ~2.4 million single nucleotide polymorphisms (SNPs) enriched in genic regions. A novel association signal was detected at a synonymous SNP in exon 2 of LOC_Os05g03600 for intermediate-to-high GI phenotypic variation. Another major hotspot region was predicted for contributing intermediate-to-high GI variation, involves 26 genes on chromosome 6 (GI6.1). These set of genes included GBSSI, two hydrolase genes, genes involved in signalling and chromatin modification. The TWAS and methylome sequencing data revealed cis-acting functionally relevant genetic variants with differential methylation patterns in the hot spot GI6.1 region, narrowing the target to 13 genes. Conversely, the promoter region of GBSSI and its alternative splicing allele (G allele of Wxa) explained the intermediate-to-high GI variation. A SNP (C>T) at exon-10 was also highlighted in the preceding analyses to influence final viscosity (FV), which is independent of amylose content/GI. The low GI line with GC haplotype confirmed soft texture, while other two low GI lines with GT haplotype were characterized as hard and cohesive. The low GI lines were further confirmed through clinical in vivo studies. Gene regulatory network analysis highlighted the role of the non‑starch polysaccharide pathway in lowering GI. Overall design: Expression data was obtained from developing grains collected at 16 days after fertilization (DAF) from 195 lines. The grain tissues collected were rapidly frozen in liquid nitrogen, homogenized, subjected to RNA isolation using Qiagen RNeasy Plant Mini Kit, testing the RNA integrity number with 7.0 or above and subjecting it to cDNA synthesis and cRNA labeling using a single-color Low Input Quick Amp Labeling Kit, hybridizing the labeled probe to 60K indica microarrays in SureHyb chamber and scanning the microarrays (with an ozone barrier slide) using SureScan Microarry Scanner following the methods described in Butardo et al., (2017).

INSTRUMENT(S): Agilent-054270 8x60K_O.sativa_ssp_Indica_exp-val_07-2013 054269 (Probe name version)

ORGANISM(S): Oryza sativa Indica Group  

SUBMITTER: Dr.Nese Sreenivasulu  

PROVIDER: GSE123616 | GEO | 2019-02-01


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