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Genome-wide association study of 29 morphological traits in Aegilops tauschii.

ABSTRACT: Aegilops tauschii is the D-genome progenitor of hexaploid wheat (Triticum aestivum). It is considered to be an important source of genetic variation for wheat breeding, and its genome is an invaluable reference for wheat genomics. We conducted a genome-wide association study using 7,185 single nucleotide polymorphism (SNP) markers across 322 diverse accessions of Ae. tauschii that were systematically phenotyped for 29 morphological traits in order to identify marker-trait associations and candidate genes, assess genetic diversity, and classify the accessions based on phenotypic data and genotypic comparison. Using the general linear model and mixed linear model, we identified a total of 18 SNPs significantly associated with 10 morphological traits. Systematic search of the flanking sequences of trait-associated SNPs in public databases identified several genes that may be linked to variations in phenotypes. Cluster analysis using phenotypic data grouped accessions into four clusters, while accessions in the same cluster were not from the same Ae. tauschii subspecies or from the same area of origin. This work establishes a fundamental research platform for association studies in Ae. tauschii and also provides useful information for understanding the genetic mechanism of agronomic traits in wheat.

SUBMITTER: Liu Y

PROVIDER: S-EPMC4622089 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Genome-wide association study of 29 morphological traits in Aegilops tauschii.

Liu Yaxi Y Wang Lang L Mao Shuangshuang S Liu Kun K Lu Yanli Y Wang Jirui J Wei Yuming Y Zheng Youliang Y

Scientific reports 20151027

Aegilops tauschii is the D-genome progenitor of hexaploid wheat (Triticum aestivum). It is considered to be an important source of genetic variation for wheat breeding, and its genome is an invaluable reference for wheat genomics. We conducted a genome-wide association study using 7,185 single nucleotide polymorphism (SNP) markers across 322 diverse accessions of Ae. tauschii that were systematically phenotyped for 29 morphological traits in order to identify marker-trait associations and candid ...[more]

PMID: 26503608

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Project description:As the post-transcriptional regulators of gene expression, microRNAs or miRNAs comprise an integral part of understanding how genomes function. Although miRNAs have been a major focus of recent efforts, miRNA research is still in its infancy in most plant species. Aegilops tauschii, the D genome progenitor of bread wheat, is a wild diploid grass exhibiting remarkable population diversity. Due to the direct ancestry and the diverse gene pool, A. tauschii is a promising source for bread wheat improvement. In this study, a total of 87 Aegilops miRNA families, including 51 previously unknown, were computationally identified both at the subgenomic level, using flow-sorted A. tauschii 5D chromosome, and at the whole genome level. Predictions at the genomic and subgenomic levels suggested A. tauschii 5D chromosome as rich in pre-miRNAs that are highly associated with Class II DNA transposons. In order to gain insights into miRNA evolution, putative 5D chromosome miRNAs were compared to its modern ortholog, Triticum aestivum 5D chromosome, revealing that 48 of the 58 A. tauschii 5D miRNAs were conserved in orthologous T. aestivum 5D chromosome. The expression profiles of selected miRNAs (miR167, miR5205, miR5175, miR5523) provided the first experimental evidence for miR5175, miR5205 and miR5523, and revealed differential expressional changes in response to drought in different genetic backgrounds for miR167 and miR5175. Interestingly, while miR5523 coding regions were present and expressed as pre-miR5523 in both T. aestivum and A. tauschii, the expression of mature miR5523 was observed only in A. tauschii under normal conditions, pointing out to an interference at the downstream processing of pre-miR5523 in T. aestivum. Overall, this study expands our knowledge on the miRNA catalog of A. tauschii, locating a subset specifically to the 5D chromosome, with ample functional and comparative insight which should contribute to and complement efforts to develop drought tolerant wheat varieties.

Project description:To understand the genetic mechanisms underlying wood anatomical and morphological traits in Populus trichocarpa, we used 869 unrelated genotypes from a common garden in Clatskanie, Oregon that were previously collected from across the distribution range in western North America. Using GEMMA mixed model analysis, we tested for the association of 25 phenotypic traits and nine multitrait combinations with 6.741 million SNPs covering the entire genome. Broad-sense trait heritabilities ranged from 0.117 to 0.477. Most traits were significantly correlated with geoclimatic variables suggesting a role of climate and geography in shaping the variation of this species. Fifty-seven SNPs from single trait GWAS and 11 SNPs from multitrait GWAS passed an FDR threshold of 0.05, leading to the identification of eight and seven nearby candidate genes, respectively. The percentage of phenotypic variance explained (PVE) by the significant SNPs for both single and multitrait GWAS ranged from 0.01% to 6.18%. To further evaluate the potential roles of candidate genes, we used a multi-omic network containing five additional data sets, including leaf and wood metabolite GWAS layers and coexpression and comethylation networks. We also performed a functional enrichment analysis on coexpression nearest neighbors for each gene model identified by the wood anatomical and morphological trait GWAS analyses. Genes affecting cell wall composition and transport related genes were enriched in wood anatomy and stomatal density trait networks. Signaling and metabolism related genes were also common in networks for stomatal density. For leaf morphology traits (leaf dry and wet weight) the networks were significantly enriched for GO terms related to photosynthetic processes as well as cellular homeostasis. The identified genes provide further insights into the genetic control of these traits, which are important determinants of the suitability and sustainability of improved genotypes for lignocellulosic biofuel production.

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Genome-wide association study of 29 morphological traits in Aegilops tauschii.

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Genome-wide association study of 29 morphological traits in Aegilops tauschii.

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