Genome-wide association analysis of aluminum tolerance in cultivated and tibetan wild barley

Shengguan Cai, Dezhi Wu, Zahra Jabeen, Yuqing Huang, Yechang Huang, Guoping Zhang

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

Tibetan wild barley (Hordeum vulgare L ssp. spontaneum), originated and grown in harsh enviroment in Tibet, is well-known for its rich germpalsm with high tolerance to abiotic stresses. However, the genetic variation and genes involved in Al tolerance are not totally known for the wild barley. In this study, a genome-wide association analysis (GWAS) was performed by using four root parameters related with Al tolerance and 469 DArT markers on 7 chromosomes within or across 110 Tibetan wild accessions and 56 cultivated cultivars. Population structure and cluster analysis revealed that a wide genetic diversity was present in Tibetan wild barley. Linkage disequilibrium (LD) decayed more rapidly in Tibetan wild barley (9.30 cM) than cultivated barley (11.52 cM), indicating that GWAS may provide higher resolution in the Tibetan group. Two novel Tibetan group-specific loci, bpb-9458 and bpb-8524 were identified, which were associated with relative longest root growth (RLRG), located at 2H and 7H on barely genome, and could explain 12.9% and 9.7% of the phenotypic variation, respectively. Moreover, a common locus bpb-6949, localized 0.8 cM away from a candidate gene HvMATE, was detected in both wild and cultivated barleys, and showed significant association with total root growth (TRG). The present study highlights that Tibetan wild barley could provide elite germplasm novel genes for barley Al-tolerant improvement.

Original languageEnglish
Article numbere69776
JournalPLoS One
Volume8
Issue number7
DOIs
Publication statusPublished - Jul 26 2013
Externally publishedYes

Fingerprint

Genome-Wide Association Study
Hordeum
Aluminum
aluminum
Genes
barley
root growth
Cluster analysis
Chromosomes
Tibet
genetic variation
loci
genes
genome-wide association study
Chromosomes, Human, Pair 7
linkage disequilibrium
Linkage Disequilibrium
phenotypic variation
Hordeum vulgare
Growth

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Genome-wide association analysis of aluminum tolerance in cultivated and tibetan wild barley. / Cai, Shengguan; Wu, Dezhi; Jabeen, Zahra; Huang, Yuqing; Huang, Yechang; Zhang, Guoping.

In: PLoS One, Vol. 8, No. 7, e69776, 26.07.2013.

Research output: Contribution to journalArticle

Cai, Shengguan ; Wu, Dezhi ; Jabeen, Zahra ; Huang, Yuqing ; Huang, Yechang ; Zhang, Guoping. / Genome-wide association analysis of aluminum tolerance in cultivated and tibetan wild barley. In: PLoS One. 2013 ; Vol. 8, No. 7.
@article{271e9c759dcc45148e0af238c849cf62,
title = "Genome-wide association analysis of aluminum tolerance in cultivated and tibetan wild barley",
abstract = "Tibetan wild barley (Hordeum vulgare L ssp. spontaneum), originated and grown in harsh enviroment in Tibet, is well-known for its rich germpalsm with high tolerance to abiotic stresses. However, the genetic variation and genes involved in Al tolerance are not totally known for the wild barley. In this study, a genome-wide association analysis (GWAS) was performed by using four root parameters related with Al tolerance and 469 DArT markers on 7 chromosomes within or across 110 Tibetan wild accessions and 56 cultivated cultivars. Population structure and cluster analysis revealed that a wide genetic diversity was present in Tibetan wild barley. Linkage disequilibrium (LD) decayed more rapidly in Tibetan wild barley (9.30 cM) than cultivated barley (11.52 cM), indicating that GWAS may provide higher resolution in the Tibetan group. Two novel Tibetan group-specific loci, bpb-9458 and bpb-8524 were identified, which were associated with relative longest root growth (RLRG), located at 2H and 7H on barely genome, and could explain 12.9{\%} and 9.7{\%} of the phenotypic variation, respectively. Moreover, a common locus bpb-6949, localized 0.8 cM away from a candidate gene HvMATE, was detected in both wild and cultivated barleys, and showed significant association with total root growth (TRG). The present study highlights that Tibetan wild barley could provide elite germplasm novel genes for barley Al-tolerant improvement.",
author = "Shengguan Cai and Dezhi Wu and Zahra Jabeen and Yuqing Huang and Yechang Huang and Guoping Zhang",
year = "2013",
month = "7",
day = "26",
doi = "10.1371/journal.pone.0069776",
language = "English",
volume = "8",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "7",

}

TY - JOUR

T1 - Genome-wide association analysis of aluminum tolerance in cultivated and tibetan wild barley

AU - Cai, Shengguan

AU - Wu, Dezhi

AU - Jabeen, Zahra

AU - Huang, Yuqing

AU - Huang, Yechang

AU - Zhang, Guoping

PY - 2013/7/26

Y1 - 2013/7/26

N2 - Tibetan wild barley (Hordeum vulgare L ssp. spontaneum), originated and grown in harsh enviroment in Tibet, is well-known for its rich germpalsm with high tolerance to abiotic stresses. However, the genetic variation and genes involved in Al tolerance are not totally known for the wild barley. In this study, a genome-wide association analysis (GWAS) was performed by using four root parameters related with Al tolerance and 469 DArT markers on 7 chromosomes within or across 110 Tibetan wild accessions and 56 cultivated cultivars. Population structure and cluster analysis revealed that a wide genetic diversity was present in Tibetan wild barley. Linkage disequilibrium (LD) decayed more rapidly in Tibetan wild barley (9.30 cM) than cultivated barley (11.52 cM), indicating that GWAS may provide higher resolution in the Tibetan group. Two novel Tibetan group-specific loci, bpb-9458 and bpb-8524 were identified, which were associated with relative longest root growth (RLRG), located at 2H and 7H on barely genome, and could explain 12.9% and 9.7% of the phenotypic variation, respectively. Moreover, a common locus bpb-6949, localized 0.8 cM away from a candidate gene HvMATE, was detected in both wild and cultivated barleys, and showed significant association with total root growth (TRG). The present study highlights that Tibetan wild barley could provide elite germplasm novel genes for barley Al-tolerant improvement.

AB - Tibetan wild barley (Hordeum vulgare L ssp. spontaneum), originated and grown in harsh enviroment in Tibet, is well-known for its rich germpalsm with high tolerance to abiotic stresses. However, the genetic variation and genes involved in Al tolerance are not totally known for the wild barley. In this study, a genome-wide association analysis (GWAS) was performed by using four root parameters related with Al tolerance and 469 DArT markers on 7 chromosomes within or across 110 Tibetan wild accessions and 56 cultivated cultivars. Population structure and cluster analysis revealed that a wide genetic diversity was present in Tibetan wild barley. Linkage disequilibrium (LD) decayed more rapidly in Tibetan wild barley (9.30 cM) than cultivated barley (11.52 cM), indicating that GWAS may provide higher resolution in the Tibetan group. Two novel Tibetan group-specific loci, bpb-9458 and bpb-8524 were identified, which were associated with relative longest root growth (RLRG), located at 2H and 7H on barely genome, and could explain 12.9% and 9.7% of the phenotypic variation, respectively. Moreover, a common locus bpb-6949, localized 0.8 cM away from a candidate gene HvMATE, was detected in both wild and cultivated barleys, and showed significant association with total root growth (TRG). The present study highlights that Tibetan wild barley could provide elite germplasm novel genes for barley Al-tolerant improvement.

UR - http://www.scopus.com/inward/record.url?scp=84899430549&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84899430549&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0069776

DO - 10.1371/journal.pone.0069776

M3 - Article

C2 - 23922796

AN - SCOPUS:84899430549

VL - 8

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 7

M1 - e69776

ER -