Genetic dissection of photoperiod response based on GWAS of pre-anthesis phase duration in spring barley

• Published in: PloS one Vol. 9; no. 11; p. e113120
• Main Authors: Alqudah, Ahmad M, Sharma, Rajiv, Pasam, Raj K, Graner, Andreas, Kilian, Benjamin, Schnurbusch, Thorsten
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 24.11.2014; Public Library of Science (PLoS)
• Subjects: Agricultural production; Arabidopsis; Barley; Biology and Life Sciences; Chromosome Mapping; Chromosomes; Chromosomes, Plant - genetics; Circadian rhythm; Crop yield; Developmental stages; Environment, Controlled; Flowers - genetics; Flowers - growth & development; Gene Expression Regulation, Developmental - radiation effects; Gene Expression Regulation, Plant - radiation effects; Gene Regulatory Networks; Genes; Genes, Plant - genetics; Genetic effects; Genetics; Genome, Plant - genetics; Genomes; Genomics; Genotype; Genotyping; Grain; Growth hormone; Haplotypes; Hordeum - genetics; Hordeum - growth & development; Hordeum vulgare; Models, Genetic; Phases; Phenotype; Photoperiod; Plant Proteins - genetics; Polymorphism, Single Nucleotide; Principal Component Analysis; Quantitative genetics; Quantitative trait loci; Quantitative Trait Loci - genetics; Seasons; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Surgery; Time Factors; Triticum
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0113120

Heading time is a complex trait, and natural variation in photoperiod responses is a major factor controlling time to heading, adaptation and grain yield. In barley, previous heading time studies have been mainly conducted under field conditions to measure total days to heading. We followed a novel approach and studied the natural variation of time to heading in a world-wide spring barley collection (218 accessions), comprising of 95 photoperiod-sensitive (Ppd-H1) and 123 accessions with reduced photoperiod sensitivity (ppd-H1) to long-day (LD) through dissecting pre-anthesis development into four major stages and sub-phases. The study was conducted under greenhouse (GH) conditions (LD; 16/8 h; ∼20/∼16°C day/night). Genotyping was performed using a genome-wide high density 9K single nucleotide polymorphisms (SNPs) chip which assayed 7842 SNPs. We used the barley physical map to identify candidate genes underlying genome-wide association scans (GWAS). GWAS for pre-anthesis stages/sub-phases in each photoperiod group provided great power for partitioning genetic effects on floral initiation and heading time. In addition to major genes known to regulate heading time under field conditions, several novel QTL with medium to high effects, including new QTL having major effects on developmental stages/sub-phases were found to be associated in this study. For example, highly associated SNPs tagged the physical regions around HvCO1 (barley CONSTANS1) and BFL (BARLEY FLORICAULA/LEAFY) genes. Based upon our GWAS analysis, we propose a new genetic network model for each photoperiod group, which includes several newly identified genes, such as several HvCO-like genes, belonging to different heading time pathways in barley.