Genetic Diversity Linked to Haplotype Variation in the World Core Collection of Trifolium subterraneum for Boron Toxicity Tolerance Provides Valuable Markers for Pasture Breeding
In alkaline soils in arid and semi-arid areas toxic concentrations of the micronutrient boron (B) are problematic for many cereal and legume crops. Molecular markers have been developed for B toxicity in cereals and Medicago. There is a need for such tools in clovers—Trifolium. To this end, we under...
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doaj-cf3e0e8f62ac4386b59a319b481b07462020-11-24T21:27:24ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2019-08-011010.3389/fpls.2019.01043453643Genetic Diversity Linked to Haplotype Variation in the World Core Collection of Trifolium subterraneum for Boron Toxicity Tolerance Provides Valuable Markers for Pasture BreedingHediyeh Tahghighi0Hediyeh Tahghighi1William Erskine2William Erskine3Richard G. Bennett4Richard G. Bennett5Philipp E. Bayer6Maria Pazos-Navarro7Maria Pazos-Navarro8Parwinder Kaur9Parwinder Kaur10Centre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Perth, WA, AustraliaInstitute of Agriculture, The University of Western Australia, Perth, WA, AustraliaCentre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Perth, WA, AustraliaInstitute of Agriculture, The University of Western Australia, Perth, WA, AustraliaCentre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Perth, WA, AustraliaInstitute of Agriculture, The University of Western Australia, Perth, WA, AustraliaSchool of Biological Sciences, The University of Western Australia, Perth, WA, AustraliaCentre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Perth, WA, AustraliaInstitute of Agriculture, The University of Western Australia, Perth, WA, AustraliaCentre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Perth, WA, AustraliaInstitute of Agriculture, The University of Western Australia, Perth, WA, AustraliaIn alkaline soils in arid and semi-arid areas toxic concentrations of the micronutrient boron (B) are problematic for many cereal and legume crops. Molecular markers have been developed for B toxicity in cereals and Medicago. There is a need for such tools in clovers—Trifolium. To this end, we undertook a genome-wide association study (GWAS) with a diversity panel of subterranean clover (Trifolium subterraneum L.), an established model pasture legume for genetic and genomic analyses for the genus. The panel comprised 124 T. subterraneum genotypes (97 core collection accessions and 27 Australian cultivars). Substantial and useful diversity in B toxicity tolerance was found in T. subterraneum. Such variation was continuously distributed and exhibited a high broad sense heritability H2 = 0.92. Among the subspecies of T. subterraneum, ssp. brachycalycinum was most susceptible to B toxicity (P < 0.05). From the GWAS, the most important discoveries were single-nucleotide polymorphisms (SNPs) located on Chr 1, 2, and 3, which mapped to haplotype blocks providing potential genes for a B toxicity tolerance assay and meriting further investigation. A SNP identified on Chr 1 aligned with Medicago truncatula respiratory burst oxidase-like protein (TSub_ g2235). This protein is known to respond to abiotic and biotic stimuli. The identification of these novel potential genes and their use to design markers for marker-assisted selection offer a pathway in pasture legumes to manage B toxicity by exploiting B tolerance.https://www.frontiersin.org/article/10.3389/fpls.2019.01043/fullabiotic stressboron toxicitygenome-wide association studyhaplotype analyseshydroponicforage legumes |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Hediyeh Tahghighi Hediyeh Tahghighi William Erskine William Erskine Richard G. Bennett Richard G. Bennett Philipp E. Bayer Maria Pazos-Navarro Maria Pazos-Navarro Parwinder Kaur Parwinder Kaur |
spellingShingle |
Hediyeh Tahghighi Hediyeh Tahghighi William Erskine William Erskine Richard G. Bennett Richard G. Bennett Philipp E. Bayer Maria Pazos-Navarro Maria Pazos-Navarro Parwinder Kaur Parwinder Kaur Genetic Diversity Linked to Haplotype Variation in the World Core Collection of Trifolium subterraneum for Boron Toxicity Tolerance Provides Valuable Markers for Pasture Breeding Frontiers in Plant Science abiotic stress boron toxicity genome-wide association study haplotype analyses hydroponic forage legumes |
author_facet |
Hediyeh Tahghighi Hediyeh Tahghighi William Erskine William Erskine Richard G. Bennett Richard G. Bennett Philipp E. Bayer Maria Pazos-Navarro Maria Pazos-Navarro Parwinder Kaur Parwinder Kaur |
author_sort |
Hediyeh Tahghighi |
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 |
title_short |
Genetic Diversity Linked to Haplotype Variation in the World Core Collection of Trifolium subterraneum for Boron Toxicity Tolerance Provides Valuable Markers for Pasture Breeding |
title_full |
Genetic Diversity Linked to Haplotype Variation in the World Core Collection of Trifolium subterraneum for Boron Toxicity Tolerance Provides Valuable Markers for Pasture Breeding |
title_fullStr |
Genetic Diversity Linked to Haplotype Variation in the World Core Collection of Trifolium subterraneum for Boron Toxicity Tolerance Provides Valuable Markers for Pasture Breeding |
title_full_unstemmed |
Genetic Diversity Linked to Haplotype Variation in the World Core Collection of Trifolium subterraneum for Boron Toxicity Tolerance Provides Valuable Markers for Pasture Breeding |
title_sort |
genetic diversity linked to haplotype variation in the world core collection of trifolium subterraneum for boron toxicity tolerance provides valuable markers for pasture breeding |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Plant Science |
issn |
1664-462X |
publishDate |
2019-08-01 |
description |
In alkaline soils in arid and semi-arid areas toxic concentrations of the micronutrient boron (B) are problematic for many cereal and legume crops. Molecular markers have been developed for B toxicity in cereals and Medicago. There is a need for such tools in clovers—Trifolium. To this end, we undertook a genome-wide association study (GWAS) with a diversity panel of subterranean clover (Trifolium subterraneum L.), an established model pasture legume for genetic and genomic analyses for the genus. The panel comprised 124 T. subterraneum genotypes (97 core collection accessions and 27 Australian cultivars). Substantial and useful diversity in B toxicity tolerance was found in T. subterraneum. Such variation was continuously distributed and exhibited a high broad sense heritability H2 = 0.92. Among the subspecies of T. subterraneum, ssp. brachycalycinum was most susceptible to B toxicity (P < 0.05). From the GWAS, the most important discoveries were single-nucleotide polymorphisms (SNPs) located on Chr 1, 2, and 3, which mapped to haplotype blocks providing potential genes for a B toxicity tolerance assay and meriting further investigation. A SNP identified on Chr 1 aligned with Medicago truncatula respiratory burst oxidase-like protein (TSub_ g2235). This protein is known to respond to abiotic and biotic stimuli. The identification of these novel potential genes and their use to design markers for marker-assisted selection offer a pathway in pasture legumes to manage B toxicity by exploiting B tolerance. |
topic |
abiotic stress boron toxicity genome-wide association study haplotype analyses hydroponic forage legumes |
url |
https://www.frontiersin.org/article/10.3389/fpls.2019.01043/full |
work_keys_str_mv |
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