Genome-wide association mapping in a diverse spring barley collection reveals the presence of QTL hotspots and candidate genes for root and shoot architecture traits at seedling stage

Adel H Abdel-Ghani, Rajiv Sharma, Celestine Wabila, Sidram Dhanagond, Saed J Owais, Mahmud A Duwayri, Saddam A Al-Dalain, Christian Klukas, Dijun Chen, Thomas Lübberstedt, Nicolaus von Wirén, Andreas Graner, Benjamin Kilian, Kerstin Neumann

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

BACKGROUND: Adaptation to drought-prone environments requires robust root architecture. Genotypes with a more vigorous root system have the potential to better adapt to soils with limited moisture content. However, root architecture is complex at both, phenotypic and genetic level. Customized mapping panels in combination with efficient screenings methods can resolve the underlying genetic factors of root traits.

RESULTS: A mapping panel of 233 spring barley genotypes was evaluated for root and shoot architecture traits under non-stress and osmotic stress. A genome-wide association study elucidated 65 involved genomic regions. Among them were 34 root-specific loci, eleven hotspots with associations to up to eight traits and twelve stress-specific loci. A list of candidate genes was established based on educated guess. Selected genes were tested for associated polymorphisms. By this, 14 genes were identified as promising candidates, ten remained suggestive and 15 were rejected. The data support the important role of flowering time genes, including HvPpd-H1, HvCry2, HvCO4 and HvPRR73. Moreover, seven root-related genes, HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 are confirmed as promising candidates. For the QTL with the highest allelic effect for root thickness and plant biomass a homologue of the Arabidopsis Trx-m3 was revealed as the most promising candidate.

CONCLUSIONS: This study provides a catalogue of hotspots for seedling growth, root and stress-specific genomic regions along with candidate genes for future potential incorporation in breeding attempts for enhanced yield potential, particularly in drought-prone environments. Root architecture is under polygenic control. The co-localization of well-known major genes for barley development and flowering time with QTL hotspots highlights their importance for seedling growth. Association analysis revealed the involvement of HvPpd-H1 in the development of the root system. The co-localization of root QTL with HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 represents a starting point to explore the roles of these genes in barley. Accordingly, the genes HvHOX2, HsfA2b, HvHAK2, and Dhn9, known to be involved in abiotic stress response, were located within stress-specific QTL regions and await future validation.

Original languageEnglish
Article number216
JournalBMC Plant Biology
Volume19
Issue number1
DOIs
Publication statusPrint publication - 23 May 2019
Externally publishedYes

Fingerprint

spring barley
chromosome mapping
quantitative trait loci
shoots
genome
seedlings
genes
seedling growth
root systems
barley
drought
flowering
genomics
loci
genotype
major genes
osmotic stress
abiotic stress
stress response
Arabidopsis

Keywords

  • Chromosome Mapping
  • Droughts
  • Genome-wide association study
  • Genotype
  • Phenotype
  • Plant roots
  • Polymorphism
  • Quantitative Trait Loci
  • Seedlings

Cite this

Abdel-Ghani, Adel H ; Sharma, Rajiv ; Wabila, Celestine ; Dhanagond, Sidram ; Owais, Saed J ; Duwayri, Mahmud A ; Al-Dalain, Saddam A ; Klukas, Christian ; Chen, Dijun ; Lübberstedt, Thomas ; von Wirén, Nicolaus ; Graner, Andreas ; Kilian, Benjamin ; Neumann, Kerstin. / Genome-wide association mapping in a diverse spring barley collection reveals the presence of QTL hotspots and candidate genes for root and shoot architecture traits at seedling stage. In: BMC Plant Biology. 2019 ; Vol. 19, No. 1.
@article{17d9460e8da04d779e491a2a6d70ec0f,
title = "Genome-wide association mapping in a diverse spring barley collection reveals the presence of QTL hotspots and candidate genes for root and shoot architecture traits at seedling stage",
abstract = "BACKGROUND: Adaptation to drought-prone environments requires robust root architecture. Genotypes with a more vigorous root system have the potential to better adapt to soils with limited moisture content. However, root architecture is complex at both, phenotypic and genetic level. Customized mapping panels in combination with efficient screenings methods can resolve the underlying genetic factors of root traits.RESULTS: A mapping panel of 233 spring barley genotypes was evaluated for root and shoot architecture traits under non-stress and osmotic stress. A genome-wide association study elucidated 65 involved genomic regions. Among them were 34 root-specific loci, eleven hotspots with associations to up to eight traits and twelve stress-specific loci. A list of candidate genes was established based on educated guess. Selected genes were tested for associated polymorphisms. By this, 14 genes were identified as promising candidates, ten remained suggestive and 15 were rejected. The data support the important role of flowering time genes, including HvPpd-H1, HvCry2, HvCO4 and HvPRR73. Moreover, seven root-related genes, HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 are confirmed as promising candidates. For the QTL with the highest allelic effect for root thickness and plant biomass a homologue of the Arabidopsis Trx-m3 was revealed as the most promising candidate.CONCLUSIONS: This study provides a catalogue of hotspots for seedling growth, root and stress-specific genomic regions along with candidate genes for future potential incorporation in breeding attempts for enhanced yield potential, particularly in drought-prone environments. Root architecture is under polygenic control. The co-localization of well-known major genes for barley development and flowering time with QTL hotspots highlights their importance for seedling growth. Association analysis revealed the involvement of HvPpd-H1 in the development of the root system. The co-localization of root QTL with HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 represents a starting point to explore the roles of these genes in barley. Accordingly, the genes HvHOX2, HsfA2b, HvHAK2, and Dhn9, known to be involved in abiotic stress response, were located within stress-specific QTL regions and await future validation.",
keywords = "Chromosome Mapping, Droughts, Genome-wide association study, Genotype, Phenotype, Plant roots, Polymorphism, Quantitative Trait Loci, Seedlings",
author = "Abdel-Ghani, {Adel H} and Rajiv Sharma and Celestine Wabila and Sidram Dhanagond and Owais, {Saed J} and Duwayri, {Mahmud A} and Al-Dalain, {Saddam A} and Christian Klukas and Dijun Chen and Thomas L{\"u}bberstedt and {von Wir{\'e}n}, Nicolaus and Andreas Graner and Benjamin Kilian and Kerstin Neumann",
year = "2019",
month = "5",
day = "23",
doi = "10.1186/s12870-019-1828-5",
language = "English",
volume = "19",
journal = "BMC Plant Biology",
issn = "1471-2229",
publisher = "Springer Verlag",
number = "1",

}

Abdel-Ghani, AH, Sharma, R, Wabila, C, Dhanagond, S, Owais, SJ, Duwayri, MA, Al-Dalain, SA, Klukas, C, Chen, D, Lübberstedt, T, von Wirén, N, Graner, A, Kilian, B & Neumann, K 2019, 'Genome-wide association mapping in a diverse spring barley collection reveals the presence of QTL hotspots and candidate genes for root and shoot architecture traits at seedling stage', BMC Plant Biology, vol. 19, no. 1, 216. https://doi.org/10.1186/s12870-019-1828-5

Genome-wide association mapping in a diverse spring barley collection reveals the presence of QTL hotspots and candidate genes for root and shoot architecture traits at seedling stage. / Abdel-Ghani, Adel H; Sharma, Rajiv; Wabila, Celestine; Dhanagond, Sidram; Owais, Saed J; Duwayri, Mahmud A; Al-Dalain, Saddam A; Klukas, Christian; Chen, Dijun; Lübberstedt, Thomas; von Wirén, Nicolaus; Graner, Andreas; Kilian, Benjamin; Neumann, Kerstin.

In: BMC Plant Biology, Vol. 19, No. 1, 216, 23.05.2019.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Genome-wide association mapping in a diverse spring barley collection reveals the presence of QTL hotspots and candidate genes for root and shoot architecture traits at seedling stage

AU - Abdel-Ghani, Adel H

AU - Sharma, Rajiv

AU - Wabila, Celestine

AU - Dhanagond, Sidram

AU - Owais, Saed J

AU - Duwayri, Mahmud A

AU - Al-Dalain, Saddam A

AU - Klukas, Christian

AU - Chen, Dijun

AU - Lübberstedt, Thomas

AU - von Wirén, Nicolaus

AU - Graner, Andreas

AU - Kilian, Benjamin

AU - Neumann, Kerstin

PY - 2019/5/23

Y1 - 2019/5/23

N2 - BACKGROUND: Adaptation to drought-prone environments requires robust root architecture. Genotypes with a more vigorous root system have the potential to better adapt to soils with limited moisture content. However, root architecture is complex at both, phenotypic and genetic level. Customized mapping panels in combination with efficient screenings methods can resolve the underlying genetic factors of root traits.RESULTS: A mapping panel of 233 spring barley genotypes was evaluated for root and shoot architecture traits under non-stress and osmotic stress. A genome-wide association study elucidated 65 involved genomic regions. Among them were 34 root-specific loci, eleven hotspots with associations to up to eight traits and twelve stress-specific loci. A list of candidate genes was established based on educated guess. Selected genes were tested for associated polymorphisms. By this, 14 genes were identified as promising candidates, ten remained suggestive and 15 were rejected. The data support the important role of flowering time genes, including HvPpd-H1, HvCry2, HvCO4 and HvPRR73. Moreover, seven root-related genes, HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 are confirmed as promising candidates. For the QTL with the highest allelic effect for root thickness and plant biomass a homologue of the Arabidopsis Trx-m3 was revealed as the most promising candidate.CONCLUSIONS: This study provides a catalogue of hotspots for seedling growth, root and stress-specific genomic regions along with candidate genes for future potential incorporation in breeding attempts for enhanced yield potential, particularly in drought-prone environments. Root architecture is under polygenic control. The co-localization of well-known major genes for barley development and flowering time with QTL hotspots highlights their importance for seedling growth. Association analysis revealed the involvement of HvPpd-H1 in the development of the root system. The co-localization of root QTL with HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 represents a starting point to explore the roles of these genes in barley. Accordingly, the genes HvHOX2, HsfA2b, HvHAK2, and Dhn9, known to be involved in abiotic stress response, were located within stress-specific QTL regions and await future validation.

AB - BACKGROUND: Adaptation to drought-prone environments requires robust root architecture. Genotypes with a more vigorous root system have the potential to better adapt to soils with limited moisture content. However, root architecture is complex at both, phenotypic and genetic level. Customized mapping panels in combination with efficient screenings methods can resolve the underlying genetic factors of root traits.RESULTS: A mapping panel of 233 spring barley genotypes was evaluated for root and shoot architecture traits under non-stress and osmotic stress. A genome-wide association study elucidated 65 involved genomic regions. Among them were 34 root-specific loci, eleven hotspots with associations to up to eight traits and twelve stress-specific loci. A list of candidate genes was established based on educated guess. Selected genes were tested for associated polymorphisms. By this, 14 genes were identified as promising candidates, ten remained suggestive and 15 were rejected. The data support the important role of flowering time genes, including HvPpd-H1, HvCry2, HvCO4 and HvPRR73. Moreover, seven root-related genes, HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 are confirmed as promising candidates. For the QTL with the highest allelic effect for root thickness and plant biomass a homologue of the Arabidopsis Trx-m3 was revealed as the most promising candidate.CONCLUSIONS: This study provides a catalogue of hotspots for seedling growth, root and stress-specific genomic regions along with candidate genes for future potential incorporation in breeding attempts for enhanced yield potential, particularly in drought-prone environments. Root architecture is under polygenic control. The co-localization of well-known major genes for barley development and flowering time with QTL hotspots highlights their importance for seedling growth. Association analysis revealed the involvement of HvPpd-H1 in the development of the root system. The co-localization of root QTL with HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 represents a starting point to explore the roles of these genes in barley. Accordingly, the genes HvHOX2, HsfA2b, HvHAK2, and Dhn9, known to be involved in abiotic stress response, were located within stress-specific QTL regions and await future validation.

KW - Chromosome Mapping

KW - Droughts

KW - Genome-wide association study

KW - Genotype

KW - Phenotype

KW - Plant roots

KW - Polymorphism

KW - Quantitative Trait Loci

KW - Seedlings

U2 - 10.1186/s12870-019-1828-5

DO - 10.1186/s12870-019-1828-5

M3 - Article

C2 - 31122195

VL - 19

JO - BMC Plant Biology

JF - BMC Plant Biology

SN - 1471-2229

IS - 1

M1 - 216

ER -