Genetic diversity linked to haplotype variation in the world core collection of Trifolium subterraneum for boron toxicity tolerance provides valuable markers for pasture breeding

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Abstract

In alkaline soils in arid and semi-arid areas toxic concentrations of the micronutrient boron (B) are 17 problematic for many cereal and legume crops. Molecular markers have been developed for B 18 toxicity in cereals and Medicago. There is a need for such tools in clovers – Trifolium. To this end 19 we undertook a genome-wide association study (GWAS) with a diversity panel of subterranean 20 clover (Trifolium subterraneum L.), an established model pasture legume for genetic and genomic 21 analyses for the genus. The panel comprised 124 T. subterraneum genotypes (97 core collection 22 accessions and 27 Australian cultivars). Substantial and useful diversity in B toxicity tolerance was 23 found in T. subterraneum. Such variation was continuously distributed and exhibited a high broadsense heritability H2 24 = 0.92. Among the subspecies of T. subterraneum, ssp. brachycalycinum 25 was most susceptible to B toxicity (P<0.05). From the GWAS the most important discoveries were 26 Single Nucleotide Polymorphisms (SNPs) located on Chr 1, 2 and 3 which mapped to haplotype 27 blocks providing potential genes for a B toxicity tolerance assay and meriting further inverstigation. 28 A SNP identified on Chr 1 aligned with Medicago truncatula respiratory burst oxidase-like protein 29 (TSub_ g2235). This protein is known to respond to abiotic and biotic stimuli. The identification 30 of these novel potential genes and their use to design markers for marker-assisted selection offer a 31 pathway in pasture legumes to manage B toxicity by exploiting B tolerance.
Original languageEnglish
Article number1043
Pages (from-to)1-19
Number of pages20
JournalFrontiers in Plant Science
Volume10
DOIs
Publication statusPublished - 30 Aug 2019

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Trifolium subterraneum
boron
haplotypes
pastures
toxicity
genetic variation
breeding
forage legumes
single nucleotide polymorphism
Medicago
Trifolium
alkaline soils
Medicago truncatula
dietary minerals
marker-assisted selection
heritability
genes
legumes
proteins
genomics

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@article{2049638f58924476a069db9ab29a9e6f,
title = "Genetic diversity linked to haplotype variation in the world core collection of Trifolium subterraneum for boron toxicity tolerance provides valuable markers for pasture breeding",
abstract = "In alkaline soils in arid and semi-arid areas toxic concentrations of the micronutrient boron (B) are 17 problematic for many cereal and legume crops. Molecular markers have been developed for B 18 toxicity in cereals and Medicago. There is a need for such tools in clovers – Trifolium. To this end 19 we undertook a genome-wide association study (GWAS) with a diversity panel of subterranean 20 clover (Trifolium subterraneum L.), an established model pasture legume for genetic and genomic 21 analyses for the genus. The panel comprised 124 T. subterraneum genotypes (97 core collection 22 accessions and 27 Australian cultivars). Substantial and useful diversity in B toxicity tolerance was 23 found in T. subterraneum. Such variation was continuously distributed and exhibited a high broadsense heritability H2 24 = 0.92. Among the subspecies of T. subterraneum, ssp. brachycalycinum 25 was most susceptible to B toxicity (P<0.05). From the GWAS the most important discoveries were 26 Single Nucleotide Polymorphisms (SNPs) located on Chr 1, 2 and 3 which mapped to haplotype 27 blocks providing potential genes for a B toxicity tolerance assay and meriting further inverstigation. 28 A SNP identified on Chr 1 aligned with Medicago truncatula respiratory burst oxidase-like protein 29 (TSub_ g2235). This protein is known to respond to abiotic and biotic stimuli. The identification 30 of these novel potential genes and their use to design markers for marker-assisted selection offer a 31 pathway in pasture legumes to manage B toxicity by exploiting B tolerance.",
author = "Hediyeh Tahghighi and William Erskine and Rick Bennett and Philipp Bayer and {Pazos Navarro}, Maria and Parwinder Kaur",
year = "2019",
month = "8",
day = "30",
doi = "10.3389/fpls.2019.01043",
language = "English",
volume = "10",
pages = "1--19",
journal = "Frontiers in Plant Science",
issn = "1664-462X",
publisher = "Frontiers Media SA",

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TY - JOUR

T1 - Genetic diversity linked to haplotype variation in the world core collection of Trifolium subterraneum for boron toxicity tolerance provides valuable markers for pasture breeding

AU - Tahghighi, Hediyeh

AU - Erskine, William

AU - Bennett, Rick

AU - Bayer, Philipp

AU - Pazos Navarro, Maria

AU - Kaur, Parwinder

PY - 2019/8/30

Y1 - 2019/8/30

N2 - In alkaline soils in arid and semi-arid areas toxic concentrations of the micronutrient boron (B) are 17 problematic for many cereal and legume crops. Molecular markers have been developed for B 18 toxicity in cereals and Medicago. There is a need for such tools in clovers – Trifolium. To this end 19 we undertook a genome-wide association study (GWAS) with a diversity panel of subterranean 20 clover (Trifolium subterraneum L.), an established model pasture legume for genetic and genomic 21 analyses for the genus. The panel comprised 124 T. subterraneum genotypes (97 core collection 22 accessions and 27 Australian cultivars). Substantial and useful diversity in B toxicity tolerance was 23 found in T. subterraneum. Such variation was continuously distributed and exhibited a high broadsense heritability H2 24 = 0.92. Among the subspecies of T. subterraneum, ssp. brachycalycinum 25 was most susceptible to B toxicity (P<0.05). From the GWAS the most important discoveries were 26 Single Nucleotide Polymorphisms (SNPs) located on Chr 1, 2 and 3 which mapped to haplotype 27 blocks providing potential genes for a B toxicity tolerance assay and meriting further inverstigation. 28 A SNP identified on Chr 1 aligned with Medicago truncatula respiratory burst oxidase-like protein 29 (TSub_ g2235). This protein is known to respond to abiotic and biotic stimuli. The identification 30 of these novel potential genes and their use to design markers for marker-assisted selection offer a 31 pathway in pasture legumes to manage B toxicity by exploiting B tolerance.

AB - In alkaline soils in arid and semi-arid areas toxic concentrations of the micronutrient boron (B) are 17 problematic for many cereal and legume crops. Molecular markers have been developed for B 18 toxicity in cereals and Medicago. There is a need for such tools in clovers – Trifolium. To this end 19 we undertook a genome-wide association study (GWAS) with a diversity panel of subterranean 20 clover (Trifolium subterraneum L.), an established model pasture legume for genetic and genomic 21 analyses for the genus. The panel comprised 124 T. subterraneum genotypes (97 core collection 22 accessions and 27 Australian cultivars). Substantial and useful diversity in B toxicity tolerance was 23 found in T. subterraneum. Such variation was continuously distributed and exhibited a high broadsense heritability H2 24 = 0.92. Among the subspecies of T. subterraneum, ssp. brachycalycinum 25 was most susceptible to B toxicity (P<0.05). From the GWAS the most important discoveries were 26 Single Nucleotide Polymorphisms (SNPs) located on Chr 1, 2 and 3 which mapped to haplotype 27 blocks providing potential genes for a B toxicity tolerance assay and meriting further inverstigation. 28 A SNP identified on Chr 1 aligned with Medicago truncatula respiratory burst oxidase-like protein 29 (TSub_ g2235). This protein is known to respond to abiotic and biotic stimuli. The identification 30 of these novel potential genes and their use to design markers for marker-assisted selection offer a 31 pathway in pasture legumes to manage B toxicity by exploiting B tolerance.

U2 - 10.3389/fpls.2019.01043

DO - 10.3389/fpls.2019.01043

M3 - Article

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SN - 1664-462X

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ER -