Dataset Information

Cost-effective detection of genome-wide signatures for 2,4-D herbicide resistance adaptation in red clover.

ABSTRACT: Herbicide resistance is a recurrent evolutionary event that has been reported across many species and for all major herbicide modes of action. The synthetic auxinic herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) has been widely used since the 1940s, however the genetic variation underlying naturally evolving resistance remains largely unknown. In this study, we used populations of the forage legume crop red clover (Trifolium pratense L.) that were recurrently selected for 2,4-D resistance to detect genome-wide signatures of adaptation. Four susceptible and six derived resistant populations were sequenced using a less costly approach by combining targeted sequencing (Capture-Seq) with pooled individuals (Pool-Seq). Genomic signatures of selection were identified using: (i) pairwise allele frequency differences; (ii) genome scan for overly differentiated loci; and (iii) genome-wide association. Fifty significant SNPs were consistently detected, most located in a single chromosome, which can be useful for marker assisted selection. Additionally, we searched for candidate genes at these genomic regions to gain insights into potential molecular mechanisms underlying 2,4-D resistance. Among the predicted functions of candidate genes, we found some related to the auxin metabolism, response to oxidative stress, and detoxification, which are also promising for further functional validation studies.

SUBMITTER: Benevenuto J

PROVIDER: S-EPMC6934753 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Cost-effective detection of genome-wide signatures for 2,4-D herbicide resistance adaptation in red clover.

Benevenuto Juliana J Bhakta Mehul M Lohr Daniel A DA Ferrão Luís Felipe V LFV Resende Marcio F R MFR Kirst Matias M Quesenberry Kenneth K Munoz Patricio P

Scientific reports 20191227 1

Herbicide resistance is a recurrent evolutionary event that has been reported across many species and for all major herbicide modes of action. The synthetic auxinic herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) has been widely used since the 1940s, however the genetic variation underlying naturally evolving resistance remains largely unknown. In this study, we used populations of the forage legume crop red clover (Trifolium pratense L.) that were recurrently selected for 2,4-D resistance to d ...[more]

PMID: 31882573

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Project description:: Detection of selection footprints provides insight into the evolution process and the underlying mechanisms controlling the phenotypic diversity of traits that have been exposed to selection. Selection focused on certain characters, mapping certain genomic regions often shows a loss of genetic diversity with an increased level of homozygosity. Therefore, the runs of homozygosity (ROHs), homozygosity by descent (HBD), and effective population size (Ne) are effective tools for exploring the genetic diversity, understanding the demographic history, foretelling the signature of directional selection, and improving the breeding strategies to use and conserve genetic resources. We characterized the ROH, HBD, Ne, and signature of selection of six Chinese goat populations using single nucleotide polymorphism (SNP) 50K Illumina beadchips. Our results show an inverse relationship between the length and frequency of ROH. A long ROH length, higher level of inbreeding, long HBD segment, and smaller Ne in Guangfeng (GF) goats suggested intensive selection pressure and recent inbreeding in this breed. We identified six reproduction-related genes within the genomic regions with a high ROH frequency, of which two genes overlapped with a putative selection signature. The estimated pair-wise genetic differentiation (FST) among the populations is 9.60% and the inter- and intra-population molecular variations are 9.68% and 89.6%, respectively, indicating low to moderate genetic differentiation. Our selection signatures analysis revealed 54 loci harboring 86 putative candidate genes, with a strong signature of selection. Further analysis showed that several candidate genes, including MARF1, SYCP2,TMEM200C,SF1,ADCY1, and BMP5, are involved in goat fecundity. We identified 11 candidate genes by using cross-population extended haplotype homozygosity (XP-EHH) estimates, of which MARF1 and SF1 are under strong positive selection, as they are differentiated in high and low reproduction groups according to the three approaches used. Gene ontology enrichment analysis revealed that different biological pathways could be involved in the variation of fecundity in female goats. This study provides a new insight into the ROHs patterns for maintenance of within breed diversity and suggests a role of positive selection for genetic variation influencing fecundity in Chinese goat.

Project description:BACKGROUND:The genus Vulpes (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (Vulpes lagopus) which is adapted to the arctic region. A close relative to the Arctic fox, the red fox (Vulpes vulpes), occurs in subarctic to subtropical habitats. To study the genetic basis of their adaptations to different environments, transcriptome sequences from two Arctic foxes and one red fox individual were generated and analyzed for signatures of positive selection. In addition, the data allowed for a phylogenetic analysis and divergence time estimate between the two fox species. RESULTS:The de novo assembly of reads resulted in more than 160,000 contigs/transcripts per individual. Approximately 17,000 homologous genes were identified using human and the non-redundant databases. Positive selection analyses revealed several genes involved in various metabolic and molecular processes such as energy metabolism, cardiac gene regulation, apoptosis and blood coagulation to be under positive selection in foxes. Branch site tests identified four genes to be under positive selection in the Arctic fox transcriptome, two of which are fat metabolism genes. In the red fox transcriptome eight genes are under positive selection, including molecular process genes, notably genes involved in ATP metabolism. Analysis of the three transcriptomes and five Sanger re-sequenced genes in additional individuals identified a lower genetic variability within Arctic foxes compared to red foxes, which is consistent with distribution range differences and demographic responses to past climatic fluctuations. A phylogenomic analysis estimated that the Arctic and red fox lineages diverged about three million years ago. CONCLUSIONS:Transcriptome data are an economic way to generate genomic resources for evolutionary studies. Despite not representing an entire genome, this transcriptome analysis identified numerous genes that are relevant to arctic adaptation in foxes. Similar to polar bears, fat metabolism seems to play a central role in adaptation of Arctic foxes to the cold climate, as has been identified in the polar bear, another arctic specialist.

Dataset Information

Cost-effective detection of genome-wide signatures for 2,4-D herbicide resistance adaptation in red clover.

Publications

Cost-effective detection of genome-wide signatures for 2,4-D herbicide resistance adaptation in red clover.

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