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

Ahmad M Alqudah, Rajiv Sharma, Raj K Pasam, Andreas Graner, Benjamin Kilian, Thorsten Schnurbusch

Research output: Contribution to journalArticleResearchpeer-review

36 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article numbere113120
JournalPLoS ONE
Volume9
Issue number11
DOIs
Publication statusPrint publication - Nov 2014
Externally publishedYes

Fingerprint

Dissection
Genome-Wide Association Study
spring barley
Photoperiod
Hordeum
heading
photoperiod
Genes
flowering
duration
Single Nucleotide Polymorphism
barley
single nucleotide polymorphism
Polymorphism
Nucleotides
quantitative trait loci
Time and Motion Studies
genes
Genetic Models
genome-wide association study

Keywords

  • Chromosome mapping
  • Chromosomes
  • Controlled environment
  • Flowers
  • Gene expression regulation
  • Genotype
  • Hordeum
  • Phenotype
  • Photoperiod
  • Plant proteins
  • Seasons
  • Time factors

Cite this

Alqudah, Ahmad M ; Sharma, Rajiv ; Pasam, Raj K ; Graner, Andreas ; Kilian, Benjamin ; Schnurbusch, Thorsten. / Genetic dissection of photoperiod response based on GWAS of pre-anthesis phase duration in spring barley. In: PLoS ONE. 2014 ; Vol. 9, No. 11.
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abstract = "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.",
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Genetic dissection of photoperiod response based on GWAS of pre-anthesis phase duration in spring barley. / Alqudah, Ahmad M; Sharma, Rajiv; Pasam, Raj K; Graner, Andreas; Kilian, Benjamin; Schnurbusch, Thorsten.

In: PLoS ONE, Vol. 9, No. 11, e113120, 11.2014.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Genetic dissection of photoperiod response based on GWAS of pre-anthesis phase duration in spring barley

AU - Alqudah, Ahmad M

AU - Sharma, Rajiv

AU - Pasam, Raj K

AU - Graner, Andreas

AU - Kilian, Benjamin

AU - Schnurbusch, Thorsten

PY - 2014/11

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AB - 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.

KW - Chromosome mapping

KW - Chromosomes

KW - Controlled environment

KW - Flowers

KW - Gene expression regulation

KW - Genotype

KW - Hordeum

KW - Phenotype

KW - Photoperiod

KW - Plant proteins

KW - Seasons

KW - Time factors

U2 - 10.1371/journal.pone.0113120

DO - 10.1371/journal.pone.0113120

M3 - Article

VL - 9

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 11

M1 - e113120

ER -