A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives

Sierra Mixe maize is a landrace variety from Oaxaca, Mexico, that utilizes nitrogen derived from the atmosphere via an undefined nitrogen fixation mechanism. The diazotrophic microbiota associated with the plant’s mucilaginous aerial root exudate composed of complex carbohydrates was previously identified and characterized by our group where we found 23 lactococci capable of biological nitrogen fixation (BNF) without containing any of the proposed essential genes for this trait (nifHDKENB). To determine the genes in Lactococcus associated with this phenotype, we selected 70 lactococci from the dairy industry that are not known to be diazotrophic to conduct a comparative population genomic analysis. This showed that the diazotrophic lactococcal genomes were distinctly different from the dairy isolates. Examining the pangenome followed by genome-wide association study and machine learning identified genes with the functions needed for BNF in the maize isolates that were absent from the dairy isolates. Many of the putative genes received an ‘unknown’ annotation, which led to the domain analysis of the 135 homologs. This revealed genes with molecular functions needed for BNF, including mucilage carbohydrate catabolism, glycan-mediated host adhesion, iron/siderophore utilization, and oxidation/reduction control. This is the first report of this pathway in this organism to underpin BNF. Consequently, we proposed a model needed for BNF in lactococci that plausibly accounts for BNF in the absence of the nif operon in this organism.

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Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony

10.21203/rs.3.rs-21864/v1 ◽

2020 ◽

Author(s):

Hojjat Asadollahpour Nanaei ◽

Ali Esmailizadeh ◽

Ahmad Ayatollahi Mehrgardi ◽

Han Jianlin ◽

Dong-Dong Wu ◽

...

Keyword(s):

Body Size ◽

Positive Selection ◽

Nucleotide Diversity ◽

Population Genomics ◽

Small Body ◽

Composite Likelihood ◽

The Body ◽

Fixation Index ◽

Small Body Size ◽

Comparative Population

Abstract Background Body size is considered as one of the most fundamental properties of an organism. Due to intensive breeding and artificial selection throughout the domestication history, horses exhibit striking variations for heights at withers and body sizes. Debao pony (DBP), a famous Chinese horse, is known for its small body size and lives in Guangxi mountains of southern China. In this study, we employed comparative population genomics to study the genetic basis underlying the small body size of DBP breed based on the whole genome sequencing data. To detect genomic signatures of positive selection, we applied three methods based on population comparison, fixation index (FST), cross population composite likelihood ratio (XP-CLR) and nucleotide diversity (Pi), and further analyzed the results to find genomic regions under selection for body size-related traits.Results A number of protein-coding genes with significant (P-value < 0.01) higher FST values (367 genes), XP-CLR scores (681 genes), and a lower value for nucleotide diversity (332 genes) were identified. The most significant signal of positive selection was mapped to the NELL1 gene, probably underlies the body size and development traits, and may also have independently been selected for short stature in the DBP population. In addition, some other loci on different chromosomes were identified to be potentially involved in the development of body size.Conclusions Results of our study identified some positively selected genes across the horse genome, which are possibly involved in body size traits. These novel candidate genes may be useful targets for clarifying our understanding of the molecular basis of body size and as such they should be of great interest for future research into the genetic architecture of relevant traits in horse breeding program.

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Specific genetic markers for wheat, spelt, and four wild relatives: comparison of isozymes, RAPDs, and wheat microsatellites

Genome ◽

10.1139/g01-050 ◽

2001 ◽

Vol 44 (4) ◽

pp. 610-621 ◽

Cited By ~ 22

Author(s):

Roberto Guadagnuolo ◽

Dessislava Savova Bianchi ◽

François Felber

Keyword(s):

Genetic Variation ◽

Wild Species ◽

Wild Relatives ◽

Species Differentiation ◽

Large Set ◽

Strongly Correlated ◽

Aegilops Cylindrica ◽

Elymus Caninus ◽

Set Up ◽

Mantel’S Test

Three types of markersisozymes, RAPDs (random amplified polymorphic DNAs), and wheat microsatelliteswere tested on wheat, spelt, and four wild wheat relatives (Aegilops cylindrica, Elymus caninus, Hordeum marinum, and Agropyron junceum). The aim was to evaluate their capability to provide specific markers for differentiation of the cultivated and wild species. The markers were set up for subsequent detection of hybrids and introgression of wheat DNA into wild relatives. All markers allowed differentiation of the cultivated from the wild species. Wheat microsatellites were not amplified in all the wild relatives, whereas RAPDs and isozymes exhibited polymorphism for all species. The dendrograms obtained with RAPD and isozyme data separated Swiss wheat cultivars from those collected in Austria and England, while no difference was found between Swiss spelt and wheat. RAPD data provided a weak discrimination between English and Austrian E. caninus. The microsatellite-based dendrogram discriminated populations of Ae. cylindrica, but no clear separation of H. marinum from E. caninus was revealed. The similarity matrices based on the three different sets of data were strongly correlated. The highest value was recorded between the matrices based on RAPDs and isozymes (Mantel's test, r = 0.93). Correlations between the similarity matrix based on microsatellites and matrices based on RAPDs and isozymes were lower: 0.74 and 0.68, respectively. While microsatellites are very useful for comparisons of closely related accessions, they are less suitable for studies involving less-related taxa. Isozymes provide interesting markers for species differentiation, but their use seems less appropriate for studies of within-species genetic variation. RAPDs can produce a large set of markers, which can be used for the evaluation of both between- and within-species genetic variation, more rapidly and easily than isozymes and microsatellites.Key words: Triticeae, isozymes, RAPDs, microsatellites, polymorphism.

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