Climate Clever Clovers: New Paradigm to Reduce the Environmental Footprint of Ruminants by Breeding Low Methanogenic Forages Utilizing Haplotype Variation

Parwinder Kaur, Rudi Appels, Philipp E. Bayer, Gabriel Keeble-Gagnere, Jiankang Wang, Hideki Hirakawa, Kenta Shirasawa, Philip Vercoe, Katia Stefanova, Zoey Durmic, Phillip Nichols, Clinton Revell, Sachiko N. Isobe, David Edwards, William Erskine

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Mitigating methane production by ruminants is a significant challenge to global livestock production. This research offers a new paradigm to reduce methane emissions from ruminants by breeding climate-clever clovers. We demonstrate wide genetic diversity for the trait methanogenic potential in Australia's key pasture legume, subterranean clover (Trifolium subterraneum L.). In a bi-parental population the broadsense heritability in methanogenic potential was moderate (H-2 = 0.4) and allelic variation in a region of Chr 8 accounted for 7.8% of phenotypic variation. In a genome-wide association study we identified four loci controlling methanogenic potential assessed by an in vitro fermentation system. Significantly, the discovery of a single nucleotide polymorphism (SNP) on Chr 5 in a defined haplotype block with an upstream putative candidate gene from a plant peroxidase-like superfamily (TSub_g18548) and a downstream lectin receptor protein kinase (TSub_g18549) provides valuable candidates for an assay for this complex trait. In this way haplotype variation can be tracked to breed pastures with reduced methanogenic potential. Of the quantitative trait loci candidates, the DNA-damage-repair/toleration DRT100-like protein (TSub_g26967), linked to avoid the severity of DNA damage induced by secondary metabolites, is considered central to enteric methane production, as are disease resistance (TSub_g26971, TSub_g26972, and TSub_g18549) and ribonuclease proteins (TSub_g26974, TSub_g26975). These proteins are good pointers to elucidate the genetic basis of in vitro microbial fermentability and enteric methanogenic potential in subterranean clover. The genes identified allow the design of a suite of markers for marker-assisted selection to reduce rumen methane emission in selected pasture legumes. We demonstrate the feasibility of a plant breeding approach without compromising animal productivity to mitigate enteric methane emissions, which is one of the most significant challenges to global livestock production.

Original languageEnglish
Article number1463
Number of pages10
JournalFrontiers in Plant Science
Volume8
DOIs
Publication statusPublished - 5 Sep 2017

Cite this

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title = "Climate Clever Clovers: New Paradigm to Reduce the Environmental Footprint of Ruminants by Breeding Low Methanogenic Forages Utilizing Haplotype Variation",
abstract = "Mitigating methane production by ruminants is a significant challenge to global livestock production. This research offers a new paradigm to reduce methane emissions from ruminants by breeding climate-clever clovers. We demonstrate wide genetic diversity for the trait methanogenic potential in Australia's key pasture legume, subterranean clover (Trifolium subterraneum L.). In a bi-parental population the broadsense heritability in methanogenic potential was moderate (H-2 = 0.4) and allelic variation in a region of Chr 8 accounted for 7.8{\%} of phenotypic variation. In a genome-wide association study we identified four loci controlling methanogenic potential assessed by an in vitro fermentation system. Significantly, the discovery of a single nucleotide polymorphism (SNP) on Chr 5 in a defined haplotype block with an upstream putative candidate gene from a plant peroxidase-like superfamily (TSub_g18548) and a downstream lectin receptor protein kinase (TSub_g18549) provides valuable candidates for an assay for this complex trait. In this way haplotype variation can be tracked to breed pastures with reduced methanogenic potential. Of the quantitative trait loci candidates, the DNA-damage-repair/toleration DRT100-like protein (TSub_g26967), linked to avoid the severity of DNA damage induced by secondary metabolites, is considered central to enteric methane production, as are disease resistance (TSub_g26971, TSub_g26972, and TSub_g18549) and ribonuclease proteins (TSub_g26974, TSub_g26975). These proteins are good pointers to elucidate the genetic basis of in vitro microbial fermentability and enteric methanogenic potential in subterranean clover. The genes identified allow the design of a suite of markers for marker-assisted selection to reduce rumen methane emission in selected pasture legumes. We demonstrate the feasibility of a plant breeding approach without compromising animal productivity to mitigate enteric methane emissions, which is one of the most significant challenges to global livestock production.",
keywords = "greenhouse gas emissions, ruminant enteric methanogenesis, genetic and genomic analyses, forage crops, natural variation, selecting haplotypes, RUMEN MICROBIAL FERMENTATION, TRIFOLIUM-SUBTERRANEUM L., METHANE EMISSIONS, GENUS TRIFOLIUM, PLANT-EXTRACTS, ASSOCIATION, POPULATION, DESIGN, GENOME, STRATEGIES",
author = "Parwinder Kaur and Rudi Appels and Bayer, {Philipp E.} and Gabriel Keeble-Gagnere and Jiankang Wang and Hideki Hirakawa and Kenta Shirasawa and Philip Vercoe and Katia Stefanova and Zoey Durmic and Phillip Nichols and Clinton Revell and Isobe, {Sachiko N.} and David Edwards and William Erskine",
year = "2017",
month = "9",
day = "5",
doi = "10.3389/fpls.2017.01463",
language = "English",
volume = "8",
journal = "Frontiers in Plant Science",
issn = "1664-462X",
publisher = "Frontiers Media SA",

}

Climate Clever Clovers : New Paradigm to Reduce the Environmental Footprint of Ruminants by Breeding Low Methanogenic Forages Utilizing Haplotype Variation. / Kaur, Parwinder; Appels, Rudi; Bayer, Philipp E.; Keeble-Gagnere, Gabriel; Wang, Jiankang; Hirakawa, Hideki; Shirasawa, Kenta; Vercoe, Philip; Stefanova, Katia; Durmic, Zoey; Nichols, Phillip; Revell, Clinton; Isobe, Sachiko N.; Edwards, David; Erskine, William.

In: Frontiers in Plant Science, Vol. 8, 1463, 05.09.2017.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Climate Clever Clovers

T2 - New Paradigm to Reduce the Environmental Footprint of Ruminants by Breeding Low Methanogenic Forages Utilizing Haplotype Variation

AU - Kaur, Parwinder

AU - Appels, Rudi

AU - Bayer, Philipp E.

AU - Keeble-Gagnere, Gabriel

AU - Wang, Jiankang

AU - Hirakawa, Hideki

AU - Shirasawa, Kenta

AU - Vercoe, Philip

AU - Stefanova, Katia

AU - Durmic, Zoey

AU - Nichols, Phillip

AU - Revell, Clinton

AU - Isobe, Sachiko N.

AU - Edwards, David

AU - Erskine, William

PY - 2017/9/5

Y1 - 2017/9/5

N2 - Mitigating methane production by ruminants is a significant challenge to global livestock production. This research offers a new paradigm to reduce methane emissions from ruminants by breeding climate-clever clovers. We demonstrate wide genetic diversity for the trait methanogenic potential in Australia's key pasture legume, subterranean clover (Trifolium subterraneum L.). In a bi-parental population the broadsense heritability in methanogenic potential was moderate (H-2 = 0.4) and allelic variation in a region of Chr 8 accounted for 7.8% of phenotypic variation. In a genome-wide association study we identified four loci controlling methanogenic potential assessed by an in vitro fermentation system. Significantly, the discovery of a single nucleotide polymorphism (SNP) on Chr 5 in a defined haplotype block with an upstream putative candidate gene from a plant peroxidase-like superfamily (TSub_g18548) and a downstream lectin receptor protein kinase (TSub_g18549) provides valuable candidates for an assay for this complex trait. In this way haplotype variation can be tracked to breed pastures with reduced methanogenic potential. Of the quantitative trait loci candidates, the DNA-damage-repair/toleration DRT100-like protein (TSub_g26967), linked to avoid the severity of DNA damage induced by secondary metabolites, is considered central to enteric methane production, as are disease resistance (TSub_g26971, TSub_g26972, and TSub_g18549) and ribonuclease proteins (TSub_g26974, TSub_g26975). These proteins are good pointers to elucidate the genetic basis of in vitro microbial fermentability and enteric methanogenic potential in subterranean clover. The genes identified allow the design of a suite of markers for marker-assisted selection to reduce rumen methane emission in selected pasture legumes. We demonstrate the feasibility of a plant breeding approach without compromising animal productivity to mitigate enteric methane emissions, which is one of the most significant challenges to global livestock production.

AB - Mitigating methane production by ruminants is a significant challenge to global livestock production. This research offers a new paradigm to reduce methane emissions from ruminants by breeding climate-clever clovers. We demonstrate wide genetic diversity for the trait methanogenic potential in Australia's key pasture legume, subterranean clover (Trifolium subterraneum L.). In a bi-parental population the broadsense heritability in methanogenic potential was moderate (H-2 = 0.4) and allelic variation in a region of Chr 8 accounted for 7.8% of phenotypic variation. In a genome-wide association study we identified four loci controlling methanogenic potential assessed by an in vitro fermentation system. Significantly, the discovery of a single nucleotide polymorphism (SNP) on Chr 5 in a defined haplotype block with an upstream putative candidate gene from a plant peroxidase-like superfamily (TSub_g18548) and a downstream lectin receptor protein kinase (TSub_g18549) provides valuable candidates for an assay for this complex trait. In this way haplotype variation can be tracked to breed pastures with reduced methanogenic potential. Of the quantitative trait loci candidates, the DNA-damage-repair/toleration DRT100-like protein (TSub_g26967), linked to avoid the severity of DNA damage induced by secondary metabolites, is considered central to enteric methane production, as are disease resistance (TSub_g26971, TSub_g26972, and TSub_g18549) and ribonuclease proteins (TSub_g26974, TSub_g26975). These proteins are good pointers to elucidate the genetic basis of in vitro microbial fermentability and enteric methanogenic potential in subterranean clover. The genes identified allow the design of a suite of markers for marker-assisted selection to reduce rumen methane emission in selected pasture legumes. We demonstrate the feasibility of a plant breeding approach without compromising animal productivity to mitigate enteric methane emissions, which is one of the most significant challenges to global livestock production.

KW - greenhouse gas emissions

KW - ruminant enteric methanogenesis

KW - genetic and genomic analyses

KW - forage crops

KW - natural variation

KW - selecting haplotypes

KW - RUMEN MICROBIAL FERMENTATION

KW - TRIFOLIUM-SUBTERRANEUM L.

KW - METHANE EMISSIONS

KW - GENUS TRIFOLIUM

KW - PLANT-EXTRACTS

KW - ASSOCIATION

KW - POPULATION

KW - DESIGN

KW - GENOME

KW - STRATEGIES

U2 - 10.3389/fpls.2017.01463

DO - 10.3389/fpls.2017.01463

M3 - Article

VL - 8

JO - Frontiers in Plant Science

JF - Frontiers in Plant Science

SN - 1664-462X

M1 - 1463

ER -