Dataset Information

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 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 H 2 = 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.

SUBMITTER: Tahghighi H

PROVIDER: S-EPMC6729137 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Genetic Diversity Linked to Haplotype Variation in the World Core Collection of Trifolium subterraneum for Boron Toxicity Tolerance Provides Valuable Markers for Pasture Breeding.

Tahghighi Hediyeh H Erskine William W Bennett Richard G RG Bayer Philipp E PE Pazos-Navarro Maria M Kaur Parwinder P

Frontiers in plant science 20190830

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 ...[more]

PMID: 31543883

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Project description:Subterranean clover (Trifolium subterraneum L.) is a diploid self-pollinated annual pasture legume native to the Mediterranean region and widely sown in southern Australia and other countries with Mediterranean-type climates. This study utilised a core collection of 97 lines, representing around 80% of the genetic diversity of the species, to examine morphological diversity within subterranean clover. A total of 23 quantitative agro-morphological and 13 semi-quantitative morphological marker traits were assayed on the core collection and 28 diverse Australian cultivars as spaced plants in a replicated common garden experiment. Relationships between these traits and 24 climatic and edaphic parameters at their sites of origin were also examined within the core collection. Significant diversity was present for all traits. The Australian cultivars had similar levels of diversity to the core collection for several traits. Among the agro-morphological traits, time to flowering, leaf size and petiole diameter in mid-winter, plant area in late winter, maximum stem length, content of the oestogenic isoflavone biochanin A and total isoflavone content, were correlated with seven or more environmental variables. These can be considered highly adaptive, being the result of strong environmental selection pressure over time. For the first time in a clover species, morphological markers, including leaf mark, anthocyanin pigmentation and pubescence traits, have been associated with rainfall and soil parameters. This suggests they either have an adaptive role or the genes controlling them may be linked to other genes controlling adaptive traits. This study demonstrated the value of core collections to examine diversity within much larger global collections. It also identified adaptive traits from wild plants that can be utilised to develop more productive and persistent subterranean clover cultivars. The high heritability of these traits indicates that selection gains can be readily made.

Project description:Subterranean clover (Trifolium subterraneum L., Ts) is a geocarpic, self-fertile annual forage legume with a compact diploid genome (n = x = 8, 544 Mb/1C). Its resilience and climate adaptivity have made it an economically important species in Mediterranean and temperate zones. Using the cultivar Daliak, we generated higher resolution sequence data, created a new genome assembly TSUd_3.0, and conducted molecular diversity analysis for copy number variant (CNV) and single-nucleotide polymorphism (SNP) among 36 cultivars. TSUd_3.0 substantively improves prior genome assemblies with new Hi-C and long-read sequence data, covering 531 Mb, containing 41,979 annotated genes and generating a 94.4% BUSCO score. Comparative genomic analysis among select members of the tribe Trifolieae indicated TSUd 3.0 corrects six assembly-error inversion/duplications and confirmed phylogenetic relationships. Its synteny with T. pratense, T. repens, Medicago truncatula and Lotus japonicus genomes were assessed, with the more distantly related T. repens and M. truncatula showing higher levels of co-linearity with Ts than between Ts and its close relative T. pratense. Resequencing of 36 cultivars discovered 7,789,537 SNPs subsequently used for genomic diversity assessment and sequence-based clustering. Heterozygosity estimates ranged from 1% to 21% within the 36 cultivars and may be influenced by admixture. Phylogenetic analysis supported subspecific genetic structure, although it indicates four or five groups, rather than the three recognized subspecies. Furthermore, there were incidences where cultivars characterized as belonging to a particular subspecies clustered with another subspecies when using genomic data. These outcomes suggest that further investigation of Ts sub-specific classification using molecular and morpho-physiological data is needed to clarify these relationships. This upgraded reference genome, complemented with comprehensive sequence diversity analysis of 36 cultivars, provides a platform for future gene functional analysis of key traits, and genome-based breeding strategies for climate adaptation and agronomic performance. Pangenome analysis, more in-depth intra-specific phylogenomic analysis using the Ts core collection, and functional genetic and genomic studies are needed to further augment knowledge of Trifolium genomes.

Dataset Information

Genetic Diversity Linked to Haplotype Variation in the World Core Collection of Trifolium subterraneum for Boron Toxicity Tolerance Provides Valuable Markers for Pasture Breeding.

Publications

Genetic Diversity Linked to Haplotype Variation in the World Core Collection of <i>Trifolium subterraneum</i> for Boron Toxicity Tolerance Provides Valuable Markers for Pasture Breeding.

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