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

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/ OPEN ACCESS Citation: Alqudah AM, Sharma R, Pasam RK, Graner A, Kilian B, et al. (2014) Genetic Dissection of Photoperiod Response Based on GWAS of PreAnthesis Phase Duration in Spring Barley. PLoS ONE 9(11): e113120. doi:10.1371/journal.pone. 0113120 Editor: Chengdao Li, Department of Agriculture and Food Western Australia, Australia Received: June 24, 2014 Accepted: October 23, 2014 Published: November 24, 2014 Copyright: 2014 Alqudah et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability: The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files. Funding: This work was financially supported from DFG (Deutsche Forschungsgemeinschaft) grant number SCHN 768/4-1, and BMBF (German Federal Ministry of Education and Research) GABI-FUTURE Start Program grant number 0315071 to TS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The author has the following affiliation to commercial entities: Bayer CropScience NV; BK has declared that no other competing interests exist. BK has joined Bayer CropScience NV since April 2014. During experiment conducting, data collection and writing the manuscript he was working at IPK. This does not alter the authors’ adherence to PLOS ONE policies on sharing data and materials. PLOS ONE | DOI:10.1371/journal.pone. 0113120 November 24, 2014 1 / 27 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