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

Autor:	Roslen Anacleto, Nese Sreenivasulu, Trinidad P. Trinidad, Vito M. Butardo, Markus Kuhlmann, Cecilia Acuin, Rosa Paula Cuevas, Saurabh Badoni, Matthew K. Morell, Gopal Misra, Anthony R. Bird, Aida C. Mallillin, Sabiha Parween
Rok vydání:	2019
Předmět:	0106 biological sciences 0301 basic medicine Swine Single-nucleotide polymorphism Genome-wide association study Plant Science Biology Polymorphism Single Nucleotide 01 natural sciences 03 medical and health sciences Exon transcriptome‐wide association study Animals Humans SNP Allele Promoter Regions Genetic Gene Research Articles Genetic Association Studies genome‐wide association study Genetics whole‐genome bisulfite sequencing Gene Expression Profiling gene‐regulatory network analysis Haplotype Oryza Mendelian Randomization Analysis Phenotype 030104 developmental biology Haplotypes glycaemic index Glycemic Index DNA methylation Digestion final viscosity Transcriptome human activities Agronomy and Crop Science Research Article 010606 plant biology & botany Biotechnology
Zdroj:	Plant Biotechnology Journal
ISSN:	1467-7652 1467-7644
DOI:	10.1111/pbi.13051
Popis:	Summary Reliably generating rice varieties with low glycaemic 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 Wx a) 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.
Databáze:	OpenAIRE
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