scholarly journals Interspecific introgression and natural selection in the evolution of Japanese apricot (Prunus mume)

2020 ◽  
Author(s):  
Koji Numaguchi ◽  
Takashi Akagi ◽  
Yuto Kitamura ◽  
Ryo Ishikawa ◽  
Takashige Ishii
Keyword(s):  
Adaptive Evolution ◽  
Artificial Selection ◽  
Population Differentiation ◽  
List Type ◽  
Nucleotide Polymorphisms ◽  
Prunus Mume ◽  
Japanese Apricot ◽  
Interspecific Introgression ◽  
Genome Wide ◽  
Evolutionary Paths

SummaryDomestication and population differentiation in crops involve considerable phenotypic changes. The logs of these evolutionary paths, including natural/artificial selection, can be found in the genomes of the current populations. However, these profiles have been little studied in tree crops, which have specific characters, such as long generation time and clonal propagation, maintaining high levels of heterozygosity.We conducted exon-targeted resequencing of 129 genomes in the genus Prunus, mainly Japanese apricot (Prunus mume), and apricot (P. armeniaca), plum (P. salicina), and peach (P. persica). Based on their genome-wide single nucleotide polymorphisms merged with published resequencing data of 79 Chinese P. mume cultivars, we inferred complete and ongoing population differentiation in P. mume.Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions between P. mume and related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures of P. mume, suggesting that P. mume has frequently imported advantageous genes from other species in the subgenus Prunus as adaptive evolution.These findings shed light on the complicated nature of adaptive evolution in a tree crop that has undergone interspecific exchange of genome fragments with natural/artificial selection.

scholarly journals Genome-wide Identification and Expression Analysis of NAC Transcription Factor Family Genes during Fruit and Kernel Development in Siberian Apricot

2021 ◽  
pp. 1-22
Author(s):  
Wanyu Xu ◽  
Chen Chen ◽  
Ningning Gou ◽  
Mengzhen Huang ◽  
Tana Wuyun ◽  
...  
Keyword(s):  
Pattern Analysis ◽  
Future Research ◽  
Prunus Mume ◽  
Synteny Analysis ◽  
Transcription Factor Family ◽  
Kernel Development ◽  
Japanese Apricot ◽  
Expression Pattern Analysis ◽  
Genome Wide ◽  
Siberian Apricot

The NAC (NAM, ATAF1/2, and CUC2) family is a group of plant-specific transcription factors that have vital roles in the growth and development of plants, and especially in fruit and kernel development. This study aimed to identify members of the NAC gene (PsNACs) family and investigate their functions in siberian apricot (Prunus sibirica). A total of 102 predicted PsNAC proteins (PsNACs) were divided into 14 clades and the genes were mapped to the eight chromosomes in siberian apricot. The PsNACs of the same clade had similar structures. A synteny analysis showed that the PsNACs had close relationships with the NAC genes of japanese apricot (Prunus mume). An expression pattern analysis of the PsNACs revealed many differences in various tissues and at different stages of fruit and kernel development. All eight PsNACs in clade XI have crucial roles in fruit and kernel development. Seven PsNACs (PsNACs 18, 64, 23, 33, 9, 4, and 50) in clades I, III, VI, VII, and XIII are related to fruit development. Eight PsNACs (PsNACs 6, 13, 46, 51, 41, 67, 37, and 59) in clades I, II, V, VIII, and XIII are involved in fruit ripening. Five PsNACs (PsNACs 6, 94, 41, 32, and 17) in clades I, IV, V, VII, and XI regulated the rapid growth of the kernel. Four PsNACs (PsNACs 50, 4, 67, and 84) in clades I, III, V, and XIII affected the hardening of the kernel. Four PsNACs (PsNACs 17, 82, 13, and 51) in clades II, XI, and IX acted on kernel maturation. We have characterized the NAC genes in siberian apricot during this study. Our results will provide resources for future research of the biological roles of PsNACs in fruit and kernel development in siberian apricot.

scholarly journals Population Differentiation at the HLA Genes

2017 ◽  
Author(s):  
Débora Y. C. Brandt ◽  
Jônatas César ◽  
Jérôme Goudet ◽  
Diogo Meyer
Keyword(s):  
Population Differentiation ◽  
Balancing Selection ◽  
Global Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Hla Genes ◽  
Genome Wide ◽  
Different Populations ◽  
Genomic Regions

ABSTRACTBalancing selection is defined as a class of selective regimes that maintain polymorphism above what is expected under neutrality. Theory predicts that balancing selection reduces population differentiation, as measured by FST. However, balancing selection regimes in which different sets of alleles are maintained in different populations could increase population differentiation. To tackle this issue, we investigated population differentiation at the HLA genes, which constitute the most striking example of balancing selection in humans. We found that population differentiation of single nucleotide polymorphisms (SNPs) at the HLA genes is on average lower than that of SNPs in other genomic regions. However, this result depends on accounting for the differences in allele frequency between selected and putatively neutral sites. Our finding of reduced differentiation at SNPs within HLA genes suggests a predominant role of shared selective pressures among populations at a global scale. However, in pairs of closely related populations, where genome-wide differentiation is low, differentiation at HLA is higher than in other genomic regions. This pattern was reproduced in simulations of overdominant selection. We conclude that population differentiation at the HLA genes is generally lower than genome-wide, but it may be higher for recently diverged population pairs, and that this pattern can be explained by a simple overdominance regime.

scholarly journals Interspecific introgression and natural selection in the evolution of Japanese apricot ( Prunus mume )

2020 ◽  
Vol 104 (6) ◽  
pp. 1551-1567
Author(s):  
Koji Numaguchi ◽  
Takashi Akagi ◽  
Yuto Kitamura ◽  
Ryo Ishikawa ◽  
Takashige Ishii
Keyword(s):  
Natural Selection ◽  
Prunus Mume ◽  
Japanese Apricot ◽  
Interspecific Introgression

scholarly journals Identification of the PmWEEP locus controlling weeping traits in Prunus mume through an integrated genome-wide association study and quantitative trait locus mapping

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Xiaokang Zhuo ◽  
Tangchun Zheng ◽  
Suzhen Li ◽  
Zhiyong Zhang ◽  
Man Zhang ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Regulatory Mechanism ◽  
Lignin Biosynthesis ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Prunus Mume ◽  
Genome Wide ◽  
Trait Locus ◽  
Locus Mapping

AbstractWeeping Prunus mume (mei) has long been cultivated in East Asia for its specific ornamental value. However, little is known about the regulatory mechanism of the weeping trait in mei, which limits molecular breeding for the improvement of weeping-type cultivars. Here, we quantified the weeping trait in mei using nested phenotyping of 214 accessions and 342 F1 hybrids. Two major associated loci were identified from the genome-wide association study (GWAS), which was conducted using 3,014,409 single nucleotide polymorphisms (SNPs) derived from resequencing, and 8 QTLs and 55 epistatic loci were identified from QTL mapping using 7,545 specific lengths amplified fragment (SLAF) markers. Notably, an overlapping PmWEEP major QTL was fine mapped within a 0.29 Mb region on chromosome 7 (Pa7), and a core SNP locus closely associated with the weeping trait was screened and validated. Furthermore, a total of 22 genes in the PmWEEP QTL region were expressed in weeping or upright mei based on RNA-seq analysis. Among them, only a novel gene (Pm024213) containing a thioredoxin (Trx) domain was found to be close to the core SNP and specifically expressed in buds and branches of weeping mei. Co-expression analysis of Pm024213 showed that most of the related genes were involved in auxin and lignin biosynthesis. These findings provide insights into the regulatory mechanism of the weeping trait and effective molecular markers for molecular-assisted breeding in Prunus mume.

scholarly journals Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

2020 ◽  
Vol 11 ◽  
Author(s):  
Waldiodio Seck ◽  
Davoud Torkamaneh ◽  
François Belzile
Keyword(s):  
Root System ◽  
System Architecture ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Primary Root ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide

Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P < 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

EpiPen: An R Package to Investigate Two-Locus Epistatic Models

2014 ◽  
Vol 17 (4) ◽  
Author(s):  
Raymond K. Walters ◽  
Charles Laurin ◽  
Gitta H. Lubke
Keyword(s):  
Power Analysis ◽  
R Package ◽  
Simulation Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Epistatic Interactions ◽  
Model Interpretation ◽  
Genome Wide ◽  
Using Data ◽  
Power Analyses

Epistasis is a growing area of research in genome-wide studies, but the differences between alternative definitions of epistasis remain a source of confusion for many researchers. One problem is that models for epistasis are presented in a number of formats, some of which have difficult-to-interpret parameters. In addition, the relation between the different models is rarely explained. Existing software for testing epistatic interactions between single-nucleotide polymorphisms (SNPs) does not provide the flexibility to compare the available model parameterizations. For that reason we have developed an R package for investigating epistatic and penetrance models, EpiPen, to aid users who wish to easily compare, interpret, and utilize models for two-locus epistatic interactions. EpiPen facilitates research on SNP-SNP interactions by allowing the R user to easily convert between common parametric forms for two-locus interactions, generate data for simulation studies, and perform power analyses for the selected model with a continuous or dichotomous phenotype. The usefulness of the package for model interpretation and power analysis is illustrated using data on rheumatoid arthritis.

scholarly journals Genome-Wide Analysis of Sex Disparities in the Genetic Architecture of Lung and Colorectal Cancers

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 686
Author(s):  
Alireza Nazarian ◽  
Alexander M. Kulminski
Keyword(s):  
Nucleotide Polymorphisms ◽  
Genetic Associations ◽  
Significance Level ◽  
Association Analyses ◽  
Complex Disorders ◽  
Specific Effects ◽  
Genome Wide ◽  
Genetic Mechanisms ◽  
Sex Disparities ◽  
Almost All

Almost all complex disorders have manifested epidemiological and clinical sex disparities which might partially arise from sex-specific genetic mechanisms. Addressing such differences can be important from a precision medicine perspective which aims to make medical interventions more personalized and effective. We investigated sex-specific genetic associations with colorectal (CRCa) and lung (LCa) cancers using genome-wide single-nucleotide polymorphisms (SNPs) data from three independent datasets. The genome-wide association analyses revealed that 33 SNPs were associated with CRCa/LCa at P < 5.0 × 10−6 neither males or females. Of these, 26 SNPs had sex-specific effects as their effect sizes were statistically different between the two sexes at a Bonferroni-adjusted significance level of 0.0015. None had proxy SNPs within their ±1 Mb regions and the closest genes to 32 SNPs were not previously associated with the corresponding cancers. The pathway enrichment analyses demonstrated the associations of 35 pathways with CRCa or LCa which were mostly implicated in immune system responses, cell cycle, and chromosome stability. The significant pathways were mostly enriched in either males or females. Our findings provided novel insights into the potential sex-specific genetic heterogeneity of CRCa and LCa at SNP and pathway levels.

Sign in / Sign up

Export Citation Format

Share Document