Population genomics of apricots unravels domestication history and adaptive events

AbstractAmong crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding.

Download Full-text

Genomic bases of insularity and ecological divergence in barn owls (Tyto alba) of the Canary Islands

10.1101/2021.12.24.473866 ◽

2021 ◽

Author(s):

Tristan Cumer ◽

Ana Paula Machado ◽

Felipe Siverio ◽

Sidi Imad Cherkaoui ◽

Inês Roque ◽

...

Keyword(s):

Canary Islands ◽

Population Genomics ◽

Small Island ◽

Gene Pools ◽

Tyto Alba ◽

Hot Arid Climate ◽

Barn Owls ◽

Genomics Tools ◽

Genomic Regions ◽

Modern Population

Islands, and the particular organisms that populate them, have long fascinated biologists. Due to their isolation, islands offer unique opportunities to study the effect of neutral and adaptive mechanisms in determining genomic and phenotypical divergence. In the Canary Islands, an archipelago rich in endemics, the barn owl (Tyto alba) is thought to have diverged into a subspecies (T. a. gracilirostris) on the eastern islands, Fuerteventura and Lanzarote. Taking advantage of 40 whole-genomes and modern population genomics tools, we provide the first look at the origin and genetic makeup of barn owls of this archipelago. We show that the Canaries hold diverse, long-standing and monophyletic populations with a neat distinction of gene pools from the different islands. Using new method, less sensitive to structure than classical FST, to detect regions involved in local adaptation to the insular environment, we identified a haplotype-like region likely under positive selection in all Canaries individuals. Genes in this region suggest morphological adaptations to insularity. In the eastern islands, where the subspecies T. a. gracilirostris is present, genomic traces of selection pinpoint signs of locally adapted body proportions and blood pressure, consistent with the smaller size of this population living in a hot arid climate. In turn, genomic regions under selection in the western barn owls from Tenerife showed an enrichment in genes linked to hypoxia, a potential response to inhabiting a small island with a marked altitudinal gradient. Our results illustrate the interplay of neutral and adaptive forces in shaping divergence and early onset speciation.

Download Full-text

Investigating the Features of PDO Green Hams during Salting: Insights for New Markers and Genomic Regions in Commercial Hybrid Pigs

Animals ◽

10.3390/ani11010068 ◽

2021 ◽

Vol 11 (1) ◽

pp. 68

Author(s):

Martina Zappaterra ◽

Paolo Zambonelli ◽

Cristina Schivazappa ◽

Nicoletta Simoncini ◽

Roberta Virgili ◽

...

Keyword(s):

Weight Loss ◽

Salt Content ◽

Phenotypic Traits ◽

Processing Plant ◽

Lean Meat ◽

New Associations ◽

Meat Content ◽

Protected Designation Of Origin ◽

Genomic Regions

Protected Designation of Origin (PDO) dry-cured hams production is greatly dependent on raw meat quality. This study was performed to identify genetic markers associated with the quality of dry-cured ham. Carcass traits of 229 heavy pigs belonging to three commercial genetic lines were registered (weight, EUROP classification). Phenotypic traits (Semimembranosus muscle ultimate pH, ham weight and lean meat content, adsorbed salt) of the corresponding thighs, undergone PDO ham process in three different plants, were measured, using a fast and non-invasive technology. Green ham weight and lean meat percentage influenced the estimated salt content and the weight loss during salting, even if the processing plant greatly affected the variability of the measured ham traits. The genomic data were obtained with the GeneSeek Genomic Profiler (GGP) 70k HD Porcine Array, using the slaughter day and the sex of the animals in the statistical analyses. The phenotypic traits were associated with the genotypes through GenAbel software. The results showed that 18 SNPs located on nine porcine chromosomes were found to be associated with nine phenotypic traits, mainly related to ham weight loss during salting. New associations were found between markers in the genes Neural Precursor Cell Expressed Developmentally Down-Regulated 9 (NEDD9, SSC7), T-Cell Lymphoma Invasion and Metastasis 2 (TIAM2, SSC1), and the ham quality traits. After validation, these SNPs may be useful to improve the quality of thighs for the production of PDO dry-cured hams.

Download Full-text

Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Animals ◽

10.3390/ani10030493 ◽

2020 ◽

Vol 10 (3) ◽

pp. 493

Author(s):

Salvatore Mastrangelo ◽

Filippo Cendron ◽

Gianluca Sottile ◽

Giovanni Niero ◽

Baldassare Portolano ◽

...

Keyword(s):

Genome Wide Association Study ◽

Snp Array ◽

Fixation Index ◽

Phenotypic Traits ◽

Plumage Color ◽

Phenotypic Marker ◽

Genome Wide ◽

A Genome ◽

The Difference ◽

Genomic Regions

Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is an important qualitative trait that can be used as phenotypic marker for breed identification. In order to assess sources of genetic variation related to the Polverara chicken breed plumage colour (black vs. white), we carried out a genome-wide association study (GWAS) and a genome-wide fixation index (FST) scan to uncover the genomic regions involved. A total of 37 animals (17 white and 20 black) were genotyped with the Affymetrix 600 K Chicken single nucleotide polymorphism (SNP) Array. The combination of results from GWAS and FST revealed a total of 40 significant markers distributed on GGA 01, 03, 08, 12 and 21, and located within or near known genes. In addition to the well-known TYR, other candidate genes have been identified in this study, such as GRM5, RAB38 and NOTCH2. All these genes could explain the difference between the two Polverara breeds. Therefore, this study provides the basis for further investigation of the genetic mechanisms involved in plumage color in chicken.

Download Full-text

Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato

10.1101/000208 ◽

2013 ◽

Author(s):

Nicola Nadeau ◽

Mayte Ruiz ◽

Patricio Salazar ◽

Brian Counterman ◽

Jose Alejandro Medina ◽

...

Keyword(s):

Population Genomics ◽

De Novo ◽

Reference Sequence ◽

Colour Pattern ◽

Adaptive Divergence ◽

Population Divergence ◽

Hybrid Zones ◽

Data Alignment ◽

Parallel Hybrid ◽

Genomic Regions

Hybrid zones can be valuable tools for studying evolution and identifying genomic regions responsible for adaptive divergence and underlying phenotypic variation. Hybrid zones between subspecies of Heliconius butterflies can be very narrow and are maintained by strong selection acting on colour pattern. The co-mimetic species H. erato and H. melpomene have parallel hybrid zones where both species undergo a change from one colour pattern form to another. We use restriction associated DNA sequencing to obtain several thousand genome wide sequence markers and use these to analyse patterns of population divergence across two pairs of parallel hybrid zones in Peru and Ecuador. We compare two approaches for analysis of this type of data; alignment to a reference genome and de novo assembly, and find that alignment gives the best results for species both closely (H. melpomene) and distantly (H. erato, ~15% divergent) related to the reference sequence. Our results confirm that the colour pattern controlling loci account for the majority of divergent regions across the genome, but we also detect other divergent regions apparently unlinked to colour pattern differences. We also use association mapping to identify previously unmapped colour pattern loci, in particular the Ro locus. Finally, we identify within our sample a new cryptic population of H. timareta in Ecuador, which occurs at relatively low altitude and is mimetic with H. melpomene malleti.

Download Full-text

Genetic diversity of common bean (Phaseolus vulgaris L.) breeding collection in Serbia

Genetika ◽

10.2298/gensr1901001s ◽

2019 ◽

Vol 51 (1) ◽

pp. 1-15 ◽

Cited By ~ 2

Author(s):

Aleksandra Savic ◽

Milka Brdar-Jokanovic ◽

Miodrag Dimitrijevic ◽

Sofija Petrovic ◽

Milan Zdravkovic ◽

...

Keyword(s):

Common Bean ◽

Gene Pool ◽

Gene Diversity ◽

Principal Component ◽

Molecular Data ◽

Phenotypic Traits ◽

Gene Pools ◽

Vegetable Crops ◽

Novi Sad

The characterization of 41 common bean cultivars and landraces from breeding collection of Institute of Field and Vegetable Crops, Novi Sad, Serbia, was done based on phenotypic traits and microsatellite markers. Phenotypic traits were chosen from Bioversity International descriptor list. In addition, main yield components were investigated. Analysis of phaseolin type revealed affiliation of cultivars and landraces to Mesoamerican or Andean gene pool. Cultivars and landraces demonstrated significant diversity level with regard to studied phenotypic traits. Identified variation showed high potential for developing new cultivars with desirable combination of traits. Principal component analysis based on phenotypic traits separated bean cultivars and landraces in two groups, which corresponded to Mesoamerican and Andean determined according to phaseolin type. Putative hybrids, with combination of traits between gene pools were also identified. Analysis of microsatellite data, using twenty-two SSR primer pairs, showed medium gene diversity in studied material. Microsatellite-based cluster analysis separated genotypes in two discrete clusters and several subclusters. No clear separation according to gene pool was found between the clusters, however grouping according to gene pool and patterns of phenotypic variation, following these gene pools, were observed within subclusters. Knowledge on detailed relationships of cultivars and landraces based on phenotypic and molecular data would facilitate identification of candidates for future breeding.

Download Full-text

Identification and Characterization of Botryosphaeria spp. Causing Gummosis of Peach Trees in Hubei Province, Central China

Plant Disease ◽

10.1094/pdis-12-10-0893 ◽

2011 ◽

Vol 95 (11) ◽

pp. 1378-1384 ◽

Cited By ~ 25

Author(s):

Fan Wang ◽

Lina Zhao ◽

Guohuai Li ◽

Junbin Huang ◽

Tom Hsiang

Keyword(s):

Prunus Persica ◽

Elongation Factor ◽

Fruit Trees ◽

Hubei Province ◽

Central China ◽

Internal Transcribed Spacer Region ◽

Fusicoccum Aesculi ◽

Peach Trees ◽

Production Areas ◽

Genomic Regions

Peach (Prunus persica) is one of the most important and widely grown fruit trees in China; however, perennial gummosis on trunks and branches is a major problem in peach orchards of Hubei Province, one of the most important peach production areas of China. In order to identify the gummosis-causing agents, diseased trunks and branches were collected from 11 peach orchards in Hubei Province. Fungal isolates were obtained from these samples, yielding three species: Botryosphaeria dothidea (anamorph Fusicoccum aesculi), B. rhodina (anamorph Lasiodiplodia theobromae), and B. obtusa (anamorph Diplodia seriata). They were identified based on conidial morphology and cultural characteristics, as well as analyses of nucleotide sequences of three genomic regions: the internal transcribed spacer region, a partial sequence of the β-tubulin gene, and the translation elongation factor 1-α gene. Fusicoccum aesculi was found in all 11 orchards but L. theobromae was found only in Shayang County in the Jingmen region and D. seriata only in Gong'an County in the Jingzhou region. Via artificial inoculation using mycelia on wounded twigs or branches, these three species were all found to be pathogenic, causing dark lesions on the twigs and branches and, sometimes, gum exudation from diseased parts. Isolates of L. theobromae were the most virulent and caused the largest lesions and most copious gummosis, and D. seriata had less gum than the other two species. This report represents the first description of L. theobromae and D. seriata as causal agents of gummosis on peach in China.

Download Full-text

Variability of 21 apricot (Prunus armeniaca L.) cultivars and hybrids in selected traits of fruit and stone

Horticultural Science ◽

10.17221/3868-hortsci ◽

2011 ◽

Vol 30 (No. 3) ◽

pp. 90-97 ◽

Cited By ~ 5

Author(s):

Z. Vachůn

Keyword(s):

Weight Coefficient ◽

Fruit Weight ◽

Prunus Armeniaca ◽

Limit Values ◽

Average Percentage ◽

Positive Trait ◽

Coefficients Of Variation ◽

Selected Traits ◽

One Year ◽

High Level

Weight, height, width and diameter of fruits and stones were evaluated in 21 apricot cultivars and hybrids in 1994–1997. Statistically significant differences between the measured values of traits confirmed their applicability for objective characterization of genotypes. The evaluated traits are genetic dispositions. It was also proved by the rank of genotypes arranged according to the values of particular traits in one year that was highly significantly identical in the other years of the evaluated period (correlation coefficient r = 0.45<sup>++</sup> to 0.87<sup>++</sup>). The relationship between fruit weight and other traits (stone weight, stone height and stone width) is not linear. Fruit weight increases (or decreases) faster towards the limit values of traits. The average percentage proportion of stone weight in fruit weight ranged from 4.9% to 9.6% in the genotypes over the period of four years. A lower proportion of stone in fruit weight is a positive trait for selection of suitable genotypes for direct consumption and flesh processing. This trait can also be a suitable criterion of genotype selection to breed cultivars with a low proportion of inedible part. Promising cultivar Lemeda is an example of the low stone proportion in flesh weight. A high level of variability was found in the values of stone and fruit weight (coefficient of variation v = 19.00% and v = 24.74%, respectively). Coefficients of variation for other traits (fruit and stone height, width and diameter) were by more than a half lower.  

Download Full-text

Genome-wide association analysis for porcine reproductive and respiratory syndrome virus susceptibility traits in two genetic populations of pigs1

Journal of Animal Science ◽

10.1093/jas/skz184 ◽

2019 ◽

Vol 97 (8) ◽

pp. 3253-3261 ◽

Cited By ~ 1

Author(s):

Lianna R Walker ◽

Erin E Jobman ◽

Kylee M Sutton ◽

J’Nan Wittler ◽

Rodger K Johnson ◽

...

Keyword(s):

Specific Antibody ◽

Serum Antibody ◽

Genome Wide Association ◽

Respiratory Syndrome Virus ◽

Coding Region ◽

High Genetic Diversity ◽

Viral Pathogens ◽

Genome Wide ◽

Major Region ◽

Genomic Regions

Abstract Porcine reproductive and respiratory syndrome virus (PRRSV) is an economically important pathogen that continues to threaten swine industry sustainability. The complexity and high genetic diversity of PRRSV has prevented vaccines from conferring adequate protection against disease outbreaks. Genome-wide association analyses of PRRSV experimentally infected pigs representing two genetic lines (n = 174 to 176) revealed two major genomic regions accounting for ~1.2% of the genetic variation in PRRSV-specific antibody level in serum or lung. The major region for serum antibody was mapped to SSC7 near the SLAII complex, which has also been implicated in susceptibility to other swine viral pathogens. Haplotype substitution analysis uncovered potential DQB1 haplotypes associated with divergent effects. A novel major region for lung antibody was mapped to the proximal end of SSC17 with the top SNP overlapping two genes, PRAG1 and LONRF1. Sequencing LONRF1 uncovered polymorphisms within the coding region that may play a role in regulating PRRSV-specific antibody production in lung tissue following PRRSV infection. These data implicate novel host genomic regions (SSC17) that influence PRRSV-specific immune response as well as a common region (SSC7) potentially involved in susceptibility to multiple viral pathogens.

Download Full-text

Genome-wide association mapping of genomic regions associated with phenotypic traits in Canadian western spring wheat

Molecular Breeding ◽

10.1007/s11032-017-0741-6 ◽

2017 ◽

Vol 37 (11) ◽

Cited By ~ 7

Author(s):

Hua Chen ◽

Kassa Semagn ◽

Muhammad Iqbal ◽

Neshat Pazooki Moakhar ◽

Teketel Haile ◽

...

Keyword(s):

Association Mapping ◽

Spring Wheat ◽

Genome Wide Association ◽

Phenotypic Traits ◽

Genome Wide ◽

Genomic Regions

Download Full-text

Genome-wide patterns of divergence during speciation: the lake whitefish case study

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2011.0197 ◽

2012 ◽

Vol 367 (1587) ◽

pp. 354-363 ◽

Cited By ~ 81

Author(s):

S. Renaut ◽

N. Maillet ◽

E. Normandeau ◽

C. Sauvage ◽

N. Derome ◽

...

Keyword(s):

Reproductive Isolation ◽

Genomic Islands ◽

Next Generation Sequencing Data ◽

Adaptive Divergence ◽

Phenotypic Traits ◽

Lake Whitefish ◽

Sequencing Data ◽

Species Pairs ◽

Selective Forces ◽

Genomic Regions

The nature, size and distribution of the genomic regions underlying divergence and promoting reproductive isolation remain largely unknown. Here, we summarize ongoing efforts using young (12 000 yr BP) species pairs of lake whitefish ( Coregonus clupeaformis ) to expand our understanding of the initial genomic patterns of divergence observed during speciation. Our results confirmed the predictions that: (i) on average, phenotypic quantitative trait loci (pQTL) show higher F ST values and are more likely to be outliers (and therefore candidates for being targets of divergent selection) than non-pQTL markers; (ii) large islands of divergence rather than small independent regions under selection characterize the early stages of adaptive divergence of lake whitefish; and (iii) there is a general trend towards an increase in terms of numbers and size of genomic regions of divergence from the least (East L.) to the most differentiated species pair (Cliff L.). This is consistent with previous estimates of reproductive isolation between these species pairs being driven by the same selective forces responsible for environment specialization. Altogether, dwarf and normal whitefish species pairs represent a continuum of both morphological and genomic differentiation contributing to ecological speciation. Admittedly, much progress is still required to more finely map and circumscribe genomic islands of speciation. This will be achieved through the use of next generation sequencing data but also through a better quantification of phenotypic traits moulded by selection as organisms adapt to new environmental conditions.

Download Full-text