scholarly journals Multiple evidences suggest sox2 as the main driver of a young and complex sex determining ZW/ZZ system in turbot (Scophthalmus maximus)

2019 ◽  
Author(s):  
Paulino Martínez ◽  
Diego Robledo ◽  
Xoana Taboada ◽  
Andrés Blanco ◽  
Antonio Gómez-Tato ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Genome Wide Association Study ◽  
Sex Chromosome ◽  
Differentially Expressed Gene ◽  
Scophthalmus Maximus ◽  
Complex Nature ◽  
Recombination Suppression ◽  
Gonad Differentiation ◽  
A Genome ◽  
Main Driver

ABSTRACTA major challenge in evolutionary biology is to find an explanation for the variation in sex-determining (SD) systems across taxa and to understand the mechanisms driving sex chromosome differentiation. We studied the turbot, holding a ZW/ZZ SD system and no sex chromosome heteromorphism, by combining classical genetics and genomics approaches to disentangle the genetic architecture of this trait. RAD-Seq was used to genotype 18,214 SNPs on 1,135 fish from 36 families and a genome wide association study (GWAS) identified a ∼ 6 Mb region on LG5 associated with sex (P < 0.05). The most significant associated markers were located close to sox2, dnajc19 and fxr1 genes. A segregation analysis enabled narrowing down the associated region and evidenced recombination suppression in a region overlapping the candidate genes. A Nanopore/Illumina assembly of the SD region using ZZ and WW individuals identified a single SNP fully associated with Z and W chromosomes. RNA-seq from 5-90 day-old fish detected the expression along the gonad differentiation period of a short non-coding splicing variant (ncRNA) included in a vertebrate-conserved long non-coding RNA overlapping sox2. qPCR showed that sox2 was the only differentially expressed gene between males and females at 50-55 days post fertilization, just prior the beginning of gonad differentiation. More refined information on the involvement of secondary genetic and environmental factors and their interactions on SD was gathered after the analysis of a broad sample of families. Our results confirm the complex nature of SD in turbot and support sox2 as its main driver.

scholarly journals Genome-wide association analysis permits characterization of Stagonospora nodorum blotch (SNB) resistance in hard winter wheat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rami AlTameemi ◽  
Harsimardeep S. Gill ◽  
Shaukat Ali ◽  
Girma Ayana ◽  
Jyotirmoy Halder ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Stagonospora Nodorum ◽  
Complex Nature ◽  
Breeding Programs ◽  
Stagonospora Nodorum Blotch ◽  
Genome Wide ◽  
A Genome

AbstractStagonospora nodorum blotch (SNB) is an economically important wheat disease caused by the necrotrophic fungus Parastagonospora nodorum. SNB resistance in wheat is controlled by several quantitative trait loci (QTLs). Thus, identifying novel resistance/susceptibility QTLs is crucial for continuous improvement of the SNB resistance. Here, the hard winter wheat association mapping panel (HWWAMP) comprising accessions from breeding programs in the Great Plains region of the US, was evaluated for SNB resistance and necrotrophic effectors (NEs) sensitivity at the seedling stage. A genome-wide association study (GWAS) was performed to identify single‐nucleotide polymorphism (SNP) markers associated with SNB resistance and effectors sensitivity. We found seven significant associations for SNB resistance/susceptibility distributed over chromosomes 1B, 2AL, 2DS, 4AL, 5BL, 6BS, and 7AL. Two new QTLs for SNB resistance/susceptibility at the seedling stage were identified on chromosomes 6BS and 7AL, whereas five QTLs previously reported in diverse germplasms were validated. Allele stacking analysis at seven QTLs explained the additive and complex nature of SNB resistance. We identified accessions (‘Pioneer-2180’ and ‘Shocker’) with favorable alleles at five of the seven identified loci, exhibiting a high level of resistance against SNB. Further, GWAS for sensitivity to NEs uncovered significant associations for SnToxA and SnTox3, co-locating with previously identified host sensitivity genes (Tsn1 and Snn3). Candidate region analysis for SNB resistance revealed 35 genes of putative interest with plant defense response-related functions. The QTLs identified and validated in this study could be easily employed in breeding programs using the associated markers to enhance the SNB resistance in hard winter wheat.

scholarly journals A General Model to Explain Repeated Turnovers of Sex Determination in the Salicaceae

2020 ◽  
Author(s):  
Wenlu Yang ◽  
Deyan Wang ◽  
Yiling Li ◽  
Zhiyang Zhang ◽  
Shaofei Tong ◽  
...  
Keyword(s):  
Sex Determination ◽  
General Model ◽  
Genome Wide Association Study ◽  
Sex Chromosome ◽  
Response Regulator ◽  
Single Gene ◽  
Entire Family ◽  
Evolutionary Forces ◽  
A Genome ◽  
Populus Species

Abstract Dioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly in multiple plant lineages. However, the specific mechanisms by which sex systems evolve and their commonalities among plant species remain poorly understood. With both XY and ZW sex systems, the family Salicaceae provides a system to uncover the evolutionary forces driving sex chromosome turnovers. In this study, we performed a genome-wide association study to characterize sex determination in two Populus species, P. euphratica and P. alba. Our results reveal an XY system of sex determination on chromosome 14 of P. euphratica, and a ZW system on chromosome 19 of P. alba. We further assembled the corresponding sex-determination regions, and found that their sex chromosome turnovers may be driven by the repeated translocations of a Helitron-like transposon. During the translocation, this factor may have captured partial or intact sequences that are orthologous to a type-A cytokinin response regulator gene. Based on results from this and other recently published studies, we hypothesize that this gene may act as a master regulator of sex determination for the entire family. We propose a general model to explain how the XY and ZW sex systems in this family can be determined by the same RR gene. Our study provides new insights into the diversification of incipient sex chromosomes in flowering plants by showing how transposition and rearrangement of a single gene can control sex in both XY and ZW systems.

scholarly journals Genome-wide Association Study of Periodontal Pathogen Colonization

2012 ◽  
Vol 91 (7_suppl) ◽  
pp. S21-S28 ◽  
Author(s):  
K. Divaris ◽  
K.L. Monda ◽  
K.E. North ◽  
A.F. Olshan ◽  
E.M. Lange ◽  
...  
Keyword(s):  
Chronic Periodontitis ◽  
Genome Wide Association Study ◽  
Human Microbiome ◽  
Genome Wide Association ◽  
Periodontal Pathogen ◽  
Complex Nature ◽  
Periodontal Pathogens ◽  
Genome Wide ◽  
A Genome ◽  
Pathogen Colonization

Pathological shifts of the human microbiome are characteristic of many diseases, including chronic periodontitis. To date, there is limited evidence on host genetic risk loci associated with periodontal pathogen colonization. We conducted a genome-wide association (GWA) study among 1,020 white participants of the Atherosclerosis Risk in Communities Study, whose periodontal diagnosis ranged from healthy to severe chronic periodontitis, and for whom “checkerboard” DNA-DNA hybridization quantification of 8 periodontal pathogens was performed. We examined 3 traits: “high red” and “high orange” bacterial complexes, and “high” Aggregatibacter actinomycetemcomitans (Aa) colonization. Genotyping was performed on the Affymetrix 6.0 platform. Imputation to 2.5 million markers was based on HapMap II-CEU, and a multiple-test correction was applied (genome-wide threshold of p < 5 × 10−8). We detected no genome-wide significant signals. However, 13 loci, including KCNK1, FBXO38, UHRF2, IL33, RUNX2, TRPS1, CAMTA1, and VAMP3, provided suggestive evidence (p < 5 × 10−6) of association. All associations reported for “red” and “orange” complex microbiota, but not for Aa, had the same effect direction in a second sample of 123 African-American participants. None of these polymorphisms was associated with periodontitis diagnosis. Investigations replicating these findings may lead to an improved understanding of the complex nature of host-microbiome interactions that characterizes states of health and disease.

scholarly journals Partial sex linkage and linkage disequilibrium on the guppy sex chromosome

2022 ◽  
Author(s):  
Suo Qiu ◽  
Lenxob Yong ◽  
Alstair Wilson ◽  
Darrren P Croft ◽  
Chay Graham ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Sex Chromosome ◽  
Natural Populations ◽  
Sex Linkage ◽  
Recombination Suppression ◽  
Genome Region ◽  
A Genome ◽  
Suppressed Recombination ◽  
Male Specific ◽  
New Evidence

The guppy Y chromosome has been considered a model system for the evolution of suppressed recombination between sex chromosomes, and it has been proposed that complete sex-linkage has evolved across about 3 Mb surrounding the sex-determining locus of this fish, followed by recombination suppression across a further 7 Mb of the 23 Mb XY pair, forming younger evolutionary strata. Sequences of the guppy genome show that Y is very similar to the X chromosome, making it important to understand which parts of the Y are completely non-recombining, and whether there is indeed a large completely non-recombining region. Here, we describe new evidence that supports a different interpretation of the data that suggested the presence of such a region. We analysed PoolSeq data in samples from multiple natural populations from Trinidad. This yields evidence for linkage disequilibrium (LD) between sequence variants and the sex-determining locus. Downstream populations have higher diversity than upstream ones (which display the expected signs of bottlenecks). The associations we observe conform to predictions for a genome region with infrequent recombination that carries one or more sexually antagonistic polymorphisms. They also suggest the region in which the sex-determining locus must be located. However, no consistently male-specific variants were found, supporting the suggestion that any completely sex-linked region may be very small.

scholarly journals A general model to explain repeated turnovers of sex determination in the Salicaceae

2020 ◽  
Author(s):  
Wenlu Yang ◽  
Zhiyang Zhang ◽  
Deyan Wang ◽  
Yiling Li ◽  
Shaofei Tong ◽  
...  
Keyword(s):  
Sex Determination ◽  
General Model ◽  
Genome Wide Association Study ◽  
Sex Chromosome ◽  
Response Regulator ◽  
Single Gene ◽  
Entire Family ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
A Genome

AbstractDioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly in multiple plant lineages. However, the specific mechanisms through which sex systems evolve and their commonalities among plant species remain poorly understood. With both XY and ZW sex systems, the family Salicaceae provides a system to uncover the evolutionary forces driving sex chromosome turnovers. In this study, we performed a genome-wide association study to characterize sex determination in two Populus species, P. euphratica and P. alba. Our results reveal an XY system of sex determination on chromosome 14 of P. euphratica, and a ZW system on chromosome 19 of P. alba. We further assembled the corresponding sex determination regions, and found that their sex chromosome turnovers may be driven by the repeated translocations of a Helitron-like transposon. During the translocation, this factor may have captured partial or intact sequences that are orthologous to a type-A cytokinin response regulator gene. Based on results from this and other recently published studies, we hypothesize that this gene may act as a master regulator of sex determination for the entire family. We propose a general model to explain how the XY and ZW sex systems in this family can be determined by the same RR gene. Our study provides new insights into the diversification of incipient sex chromosome in flowering plants by showing how transposition and rearrangement of a single gene can control sex in both XY and ZW systems.

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