Whole-genome Resequencing Data Research Articles

Conservation genomics analysis reveals recent population decline and possible causes in bumblebee Bombus opulentus.

Bumblebees are a genus of pollinators (Bombus) that play important roles in natural ecosystem and agricultural production. Several bumblebee species have been recorded as under population decline, and the proportion of species experiencing population decline within subgenus Thoracobombus is higher than average. Bombus opulentus is 1 species in Thoracobombus, but little is known about its recent population dynamics. Here, we employed conservation genomics methods to investigate the population dynamics of B. opulentus during the recent past and identify the likely environmental factors that may cause population decline. Firstly, we placed the scaffold-level of B. opulentus reference genome sequence onto chromosome-level using Hi-C technique. Then, based on this reference genome and whole-genome resequencing data for 51 B. opulentus samples, we reconstructed the population structure and effective population size (Ne) trajectories of B. opulentus and identified genes that were under positive selection. Our results revealed that the collected B. opulentus samples could be divided into 2 populations, and 1 of them experienced a recent population decline; the declining population also exhibited lower genetic diversity and higher inbreeding levels. Genes related to high-temperature tolerance, immune response, and detoxication showed signals of positive selection in the declining population, suggesting that climate warming and pathogen/pesticide exposures may contribute to the decline of this B. opulentus population. Taken together, our study provided insights into the demography of B. opulentus populations and highlighted that populations of the same bumblebee species could have contrasting Ne trajectories and population decline could be caused by a combination of various stressors.

Morpho-physiological, Genomic, and Transcriptional Diversities in Response to Potassium Deficiency in Rapeseed (Brassica napus L.) Genotypes.

Variations in the resistance to potassium (K) deficiency among rapeseed genotypes emphasize complicated regulatory mechanisms. In this study, a low-K-sensitivity accession (L49) responded to K deficiency with smaller biomasses, severe leaf chlorosis, weaker photosynthesis ability, and deformed stomata morphology compared to a low-K resistant accession (H280). H280 accumulated more K+ than L49 under low K. Whole-genome resequencing (WGS) revealed a total of 5,538,622 single nucleotide polymorphisms (SNPs) and 859,184 insertions/deletions (InDels) between H280 and L49. RNA-seq identified more differentially expressed K+ transporter genes with higher expression in H280 than in L49 under K deficiency. Based on the K+ profiles, differential expression profiling, weighted gene coexpression network analysis, and WGS data between H280 and L49, BnaC4.AKT1 was proposed to be mainly responsible for root K absorption-mediated low K resistance. BnaC4.AKT1 was expressed preferentially in the roots and localized on the plasma membrane. An SNP and an InDel found in the promoter region of BnaC4.AKT1 were proposed to be responsible for its differential expression between rapeseed genotypes. This study identified a gene resource for improving low-K resistance. It also facilitates an integrated knowledge of the differential physiological and transcriptional responses to K deficiency in rapeseed genotypes.

Divergent Selection in Low Recombination Regions Shapes the Genomic Islands in Two Incipient Shorebird Species.

Speciation in the face of gene flow is usually associated with a heterogeneous genomic landscape of divergence in nascent species pairs. However, multiple factors, such as divergent selection and local recombination rate variation, can influence the formation of these genomic islands. Examination of the genomic landscapes of species pairs that are still in the early stages of speciation provides an insight into this conundrum. In this study, population genomic analyses were undertaken using a wide range of sampling and whole-genome resequencing data from 96 unrelated individuals of Kentish plover (Charadrius alexandrinus) and white-faced plover (Charadrius dealbatus). We suggest that the two species exhibit varying levels of population admixture along the Chinese coast and on the Taiwan Island. Genome-wide analyses for introgression indicate that ancient introgression had occurred in Taiwan population, and gene flow is still ongoing in mainland coastal populations. Furthermore, we identified a few genomic regions with significant levels of interspecific differentiation and local recombination suppression, which contain several genes potentially associated with disease resistance, coloration, and regulation of plumage molting and thus may be relevant to the phenotypic and ecological divergence of the two nascent species. Overall, our findings suggest that divergent selection in low recombination regions may be a main force in shaping the genomic islands in two incipient shorebird species.

Ecological Diversification in an Adaptive Radiation of Plants: The Role of De Novo Mutation and Introgression.

Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations versus preexisting variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns of phylogenetic discordance and introgression in Penstemon subgenus Dasanthera, a small and diverse adaptive radiation of plants. We found that magenta hummingbird-adapted flowers have apparently evolved twice from ancestral blue-violet bee-pollinated flowers within this radiation. These shifts in flower color are accompanied by a variety of inactivating mutations to a key anthocyanin pathway enzyme, suggesting that independent de novo loss-of-function mutations underlie the parallel evolution of this trait. Although patterns of introgression and phylogenetic discordance were heterogenous across the genome, a strong effect of gene density suggests that, in general, natural selection opposes introgression and maintains genetic differentiation in gene-rich genomic regions. Our results highlight the importance of both de novo mutation and introgression as sources of evolutionary change and indicate a role for de novo mutation in driving parallel evolution in adaptive radiations.

Whole-genome sequencing of the invasive golden apple snail Pomacea canaliculata from Asia reveals rapid expansion and adaptive evolution.

Pomacea canaliculata, an invasive species native to South America, is recognized for its broad geographic distribution and adaptability to a variety of ecological conditions. The details concerning the evolution and adaptation of P. canaliculate remain unclear due to a lack of whole-genome resequencing data. We examined 173 P. canaliculata genomes representing 17 geographic populations in East and Southeast Asia. Interestingly, P. canaliculata showed a higher level of genetic diversity than other mollusks, and our analysis suggested that the dispersal of P. canaliculata could have been driven by climate changes and human activities. Notably, we identified a set of genes associated with low temperature adaptation, including Csde1, a cold shock protein coding gene. Further RNA sequencing analysis and reverse transcription quantitative polymerase chain reaction experiments demonstrated the gene's dynamic pattern and biological functions during cold exposure. Moreover, both positive selection and balancing selection are likely to have contributed to the rapid environmental adaptation of P. canaliculata populations. In particular, genes associated with energy metabolism and stress response were undergoing positive selection, while a large number of immune-related genes showed strong signatures of balancing selection. Our study has advanced our understanding of the evolution of P. canaliculata and has provided a valuable resource concerning an invasive species.

Genomic insights into endangerment and conservation of the garlic-fruit tree (Malania oleifera), a plant species with extremely small populations

Abstract Background Advanced whole-genome sequencing techniques enable covering nearly all genome nucleotide variations and thus can provide deep insights into protecting endangered species. However, the use of genomic data to make conservation strategies is still rare, particularly for endangered plants. Here we performed comprehensive conservation genomic analysis for Malania oleifera, an endangered tree species with a high amount of nervonic acid. We used whole-genome resequencing data of 165 samples, covering 16 populations across the entire distribution range, to investigate the formation reasons of its extremely small population sizes and to evaluate the possible genomic offsets and changes of ecology niche suitability under future climate change. Results Although M. oleifera maintains relatively high genetic diversity among endangered woody plants (θπ = 3.87 × 10−3), high levels of inbreeding have been observed, which have reduced genetic diversity in 3 populations (JM, NP, and BM2) and caused the accumulation of deleterious mutations. Repeated bottleneck events, recent inbreeding (∼490 years ago), and anthropogenic disturbance to wild habitats have aggravated the fragmentation of M. oleifera and made it endangered. Due to the significant effect of higher average annual temperature, populations distributed in low altitude exhibit a greater genomic offset. Furthermore, ecological niche modeling shows the suitable habitats for M. oleifera will decrease by 71.15% and 98.79% in 2100 under scenarios SSP126 and SSP585, respectively. Conclusions The basic realizations concerning the threats to M. oleifera provide scientific foundation for defining management and adaptive units, as well as prioritizing populations for genetic rescue. Meanwhile, we highlight the importance of integrating genomic offset and ecological niche modeling to make targeted conservation actions under future climate change. Overall, our study provides a paradigm for genomics-directed conservation.

Genome-wide discovery of InDels and validation of PCR-Based InDel markers for earliness in a RIL population and genotypes of lentil (Lens culinaris Medik.).

The systematic identification of insertion/deletion (InDel) length polymorphisms from the entire lentil genome can be used to map the quantitative trait loci (QTL) and also for the marker-assisted selection (MAS) for various linked traits. The InDels were identified by comparing the whole-genome resequencing (WGRS) data of two extreme bulks (early- and late-flowering bulk) and a parental genotype (Globe Mutant) of lentil. The bulks were made by pooling 20 extreme recombinant inbred lines (RILs) each, derived by crossing Globe Mutant (late flowering parent) with L4775 (early flowering parent). Finally, 734,716 novel InDels were identified, which is nearly one InDel per 5,096 bp of lentil genome. Furthermore, 74.94% of InDels were within the intergenic region and 99.45% displayed modifier effects. Of these, 15,732 had insertions or deletions of 20 bp or more, making them amenable to the development of PCR-based markers. An InDel marker I-SP-356.6 (chr. 3; position 356,687,623; positioned 174.5 Kb from the LcFRI gene) was identified as having a phenotypic variance explained (PVE) value of 47.7% for earliness when validated in a RIL population. Thus, I-SP-356.6 marker can be deployed in MAS to facilitate the transfer of the earliness trait to other elite late-maturing cultivars. Two InDel markers viz., I-SP-356.6 and I-SP-383.9 (chr. 3; linked to LcELF3a gene) when tested in 9 lentil genotypes differing for maturity duration, clearly distinguished three early (L4775, ILL7663, Precoz) and four late genotypes (Globe Mutant, MFX, L4602, L830). However, these InDels could not be validated in two genotypes (L4717, L4727), suggesting either absence of polymorphism and/or presence of other loci causing earliness. The identified InDel markers can act as valuable tools for MAS for the development of early maturing lentil varieties.

Cuticular proteins in codling moth (Cydia pomonella) respond to insecticide and temperature stress

The insect cuticle consists of chitin and cuticular proteins (CPs), which stabilize the body shape and provide an effective physical barrier against the external environment. They are also potential target sites for developing environmentally friendly insect management through the utilization of physiology-based methods. The codling moth, Cydia pomonella, is a pest afflicting fruit orchards worldwide. This study used a comparative genomic approach, whole-genome resequencing, and transcriptome data to understand the role that CPs played in the environmental adaptation of the codling moth. A total of 182 putative CPs were identified in the codling moth genome, which were classified into 12 CP families. 119 CPR genes, including 54 RR-1, 60 RR-2, and 5 RR-3 genes were identified and accounted for 65.4% of the total CPs. Eight and seven gene clusters are formed in RR1 and RR2 subfamily and the ancestor-descendant relationship was explained. Five CPAP genes were highly expressed during the egg stage and exposed to high temperature, which indicated their potential role in aiding codling moth eggs in acclimating to varying external heat conditions. Moreover, six CPs belonging to the CPR and CPLCP families were identified in association with insecticide resistance by population resequencing. Their expression levels increased after exposure to insecticides, suggesting they might be involved in codling moth resistance to the insecticides azinphos-methyl or deltamethrin. Our results provide insight into the evolution of codling moth CPs and their association with high temperature adaptation and insecticide resistance, and provide an additional information required for further analysis of CPs in environmental adaptation.

Molecular genetic characterization and meat-use functional gene identification in Jianshui yellow-brown ducks through combined resequencing and transcriptome analysis.

The Jianshui yellow-brown duck is a unique country-specific waterfowl species in Yunnan Province, well known for its tender meat. However, there is a lack of comprehensive systematic research on the molecular genetic characteristics, especially germplasm resources and economic traits, of the Jianshui yellow-brown ducks. This study investigated the molecular genetic characteristics of Jianshui yellow-brown ducks, compared their selection signals with those of ancestral mallard and meat-type Pekin ducks, and identified genes specific to their meat-use performance. Furthermore, this study also evaluated the breeding potential for its meat performance. In this study, phylogenetic trees, PCA and Admixture analysis were used to investigate the population genetic structure among local duck breeds in China; population genetic differentiation index (Fst), nucleotide diversity and Tajima's D were used to detect selected loci and genes in the population of Jianshui yellow-brown ducks; and transcriptome technology was used to screen for differentially expressed genes in the liver, sebum and breast muscle tissues, and finally, the results of the genome selection signals and transcriptome data were integrated to excavate functional genes affecting the meat performance of the Jianshui yellow-brown ducks. The results of the genetic structure of the population showed that Jianshui yellow-brown ducks were clustered into a separate group. Selection signal analysis indicated significant selection pressure on certain genes related to meat characteristics (ELOVL2, ELOVL3, GDF10, VSTM2A, PHOSPHO1, and IGF2BP1) in both Jianshui yellow-brown ducks and mallards. Transcriptomic data analysis suggested that ELOVL3, PHOSPHO1, and GDF10 are vital candidate genes influencing meat production and quality in Jianshui yellow-brown ducks. A comparison of selection signals between Jianshui yellow-brown ducks and Pekin ducks revealed only 21 selected genes in the Jianshui yellow-brown duck population, and no significant genes were related to meat traits. Moreover, whole-genome resequencing data suggested that the Jianshui yellow-brown duck represents a unique category with distinct genetic mechanisms. Through selection signaling and transcriptomic approaches, we successfully screened and identified important candidate genes affecting meat traits in Jianshui yellow-brown ducks. Furthermore, the Jianshui yellow-brown duck has good potential for improved meat performance, highlighting the need for further improvement.

Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing

BackgroundKaryotype, as a basic characteristic of species, provides valuable information for fundamental theoretical research and germplasm resource innovation. However, traditional karyotyping techniques, including fluorescence in situ hybridization (FISH), are challenging and low in efficiency, especially when karyotyping aneuploid and polyploid plants. The use of low coverage whole-genome resequencing (lcWGR) data for karyotyping was explored, but existing methods are complicated and require control samples.ResultsIn this study, a new protocol for molecular karyotype analysis was provided, which proved to be a simpler, faster, and more accurate method, requiring no control. Notably, our method not only provided the copy number of each chromosome of an individual but also an accurate evaluation of the genomic contribution from its parents. Moreover, we verified the method through FISH and published resequencing data.ConclusionsThis method is of great significance for species evolution analysis, chromosome engineering, crop improvement, and breeding.

Whole-genome resequencing to explore genome‑wide single nucleotide polymorphisms and genes associated with avian leukosis virus subgroup J infection in chicken.

Avian leukosis virus subgroup J (ALV-J) is an oncogenic virus that causes serious economic loss in the poultry industry. Currently, no effective vaccine or drug is available against this virus. Therefore, it is imperative to explore and understand the molecular regulatory mechanisms underlying ALV-J infection. In this study, blood samples from 21 ALV-J-infected and 22 ALV-J-uninfected (DZ) chickens (JZ) were analyzed by whole-genome resequencing (WGR). By combining the fixation index (FST) with the nucleotide diversity (π) ratio based on WGR data, 425 candidate genes were identified. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed the top 20 enriched pathways, among which 9 pathways were significantly associated with diseases, including endometrial cancer, Chagas disease, PD-L1 expression and PD-1 checkpoint pathway in cancer, colorectal cancer, endocrine resistance, fluid shear stress, atherosclerosis, basal cell carcinoma, non-small cell lung cancer, and melanoma. Fourteen single nucleotide polymorphisms related to twelve genes showed a notable difference between DZ and JZ group chickens. The genes included COMMD3, PPP1CB, VEGFA, GTF2H1, NOTCH2, ITPR1, FGFR4, GNAS, NECTIN1, WNT2B, PPP1CC, and MRC2. These findings may provide a valuable foundation for further exploration of the pathogenesis of ALV-J in chickens.

Extensive Phylogenomic Discordance and the Complex Evolutionary History of the Neotropical Cat Genus Leopardus.

Even in the genomics era, the phylogeny of Neotropical small felids comprised in the genus Leopardus remains contentious. We used whole-genome resequencing data to construct a time-calibrated consensus phylogeny of this group, quantify phylogenomic discordance, test for interspecies introgression, and assess patterns of genetic diversity and demographic history. We infer that the Leopardus radiation started in the Early Pliocene as an initial speciation burst, followed by another in its subgenus Oncifelis during the Early Pleistocene. Our findings challenge the long-held notion that ocelot (Leopardus pardalis) and margay (L. wiedii) are sister species and instead indicate that margay is most closely related to the enigmatic Andean cat (L. jacobita), whose whole-genome data are reported here for the first time. In addition, we found that the newly sampled Andean tiger cat (L. tigrinus pardinoides) population from Colombia associates closely with Central American tiger cats (L. tigrinus oncilla). Genealogical discordance was largely attributable to incomplete lineage sorting, yet was augmented by strong gene flow between ocelot and the ancestral branch of Oncifelis, as well as between Geoffroy's cat (L. geoffroyi) and southern tiger cat (L. guttulus). Contrasting demographic trajectories have led to disparate levels of current genomic diversity, with a nearly tenfold difference in heterozygosity between Andean cat and ocelot, spanning the entire range of variability found in extant felids. Our analyses improved our understanding of the speciation history and diversity patterns in this felid radiation, and highlight the benefits to phylogenomic inference of embracing the many heterogeneous signals scattered across the genome.

Whole-genome resequencing confirms the genetic effects of dams on an endangered fish Hemibagrus guttatus (Siluriformes: Bagridae): A case study in a tributary of the Pearl River

Dam construction in riverine ecosystems has fragmented natural aquatic habitats and has altered environmental conditions. As a result, damming has been demonstrated to threaten aquatic biodiversity by reducing species distribution ranges and hindering gene exchange, leading to the inability to adapt to environmental changes. Knowledge of the contemporary genetic diversity and genetic structure of fish populations that are separated by dams is vital to developing effective conservation strategies, particularly for endangered fish species. We chose the Lianjiang River, a tributary of the Pearl River, as a case study to assess the effects of dams on the genetic diversity and genetic structure of an endangered fish species, Hemibagrus guttatus, using whole-genome resequencing data from 63 fish samples. The results indicated low levels of genetic diversity, high levels of inbreeding and decreasing trend of effective population size in fragmented H. guttatus populations. In addition, there were significant genetic structure and genetic differentiation among populations, suggesting that the dams might have affected H. guttatus populations. Our findings may benefit management and conservation practices for this endangered species that is currently suffering from the effects of dam construction.

Linking HIF oxygen-sensing system diversity to hypoxia fitness in Eleutheronema: Molecular characterization and transcriptional response to hypoxia exposure

Hypoxia is a mounting environmental problem affecting coastal waters globally, posing severe consequences for biodiversity and marine life. Metazoans respond to hypoxia stress via the hypoxia-inducible factor (HIF) pathway, but few studies have addressed the gene diversity of the functionally important HIF-pathway. Understanding whether functional diversity exists in the HIF-pathway is a key first step in identifying genes that may impact hypoxia fitness. Here, we leveraged whole-genome resequencing data and bioinformatics tools to identify the key members of the HIF-pathway (HIFα/β, EGLN, and VHL) and genetic diversity in the threatened Eleutheronema. Phylogenetic analysis revealed that teleost-specific duplicates of epas1 (epas1a/b) were followed by the loss of one of each hif1α and hif1αl in Eleutheronema species. Strong collinearity and similarity of gene characteristics suggested the functional conservation of the HIF-pathway during Eleutheronema evolution. Purifying selection was the major theme in HIF-pathway evolution, leading to a reduction in genetic diversity. Substantially low nucleotide diversity of the HIF-pathway was observed among populations, which might indicate the loss of hypoxia fitness in Eleutheronema. Additionally, the normoxic presence of the HIF-pathway differed among tissues and was species-dependent, indicating their diverse roles during development. Significant regulation of HIF-pathway expression levels was observed across tissues under hypoxic conditions, suggesting critical roles in the hypoxia stress response. Moreover, variant molecular characters suggested different roles in response to hypoxia of the HIF-pathway, which were reflected in the different expression patterns across tissues. Our present study provides novel insights into the interplay between gene diversity within the HIF-pathway and hypoxia fitness in threatened Eleutheronema. We highlighted the importance of HIF-pathway-mediated transcriptional regulation in response to hypoxia stress, which provided valuable information for the genetic mechanisms underlying hypoxia adaptation in fish. The bioinformatic methods developed here have broad applications for other species.

Genomic evidence for evolutionary history and local adaptation of two endemic apricots: Prunus hongpingensis and P. zhengheensis.

Apricot, belonging to the Armeniaca section of Rosaceae, is one of the economically important crop fruits that has been extensively cultivated. The natural wild apricots offer valuable genetic resources for crop improvement. However, some of them are endemic, with small populations, and are even at risk of extinction. In this study we unveil chromosome-level genome assemblies for two southern China endemic apricots, Prunus hongpingensis (PHP) and P. zhengheensis (PZH). We also characterize their evolutionary history and the genomic basis of their local adaptation using whole-genome resequencing data. Our findings reveal that PHP and PZH are closely related to Prunus armeniaca and form a distinct lineage. Both species experienced a decline in effective population size following the Last Glacial Maximum (LGM), which likely contributed to their current small population sizes. Despite the observed decrease in genetic diversity and heterozygosity, we do not observe an increased accumulation of deleterious mutations in these two endemic apricots. This is likely due to the combined effects of a low inbreeding coefficient and strong purifying selection. Furthermore, we identify a set of genes that have undergone positive selection and are associated with local environmental adaptation in PHP and PZH, respectively. These candidate genes can serve as valuable genetic resources for targeted breeding and improvement of cultivated apricots. Overall, our study not only enriches our comprehension of the evolutionary history of apricot species but also offers crucial insights for the conservation and future breeding of other endemic species amidst rapid climate changes.

Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses.

Copy number variations (CNVs) are crucial structural genomic variants affecting complex traits in humans and livestock animals. The current study was designed to conduct a comprehensive comparative copy number variation analysis among three breeds, Debao (DB), Baise (BS), and Warmblood (WB), with a specific focus on identifying genomic regions associated with miniature features in horses. Using whole-genome next-generation resequencing data, we identified 18,974 CNVs across 31 autosomes. Among the breeds, we found 4279 breed-specific CNV regions (CNVRs). Baise, Debao, and Warmblood displayed 2978, 986, and 895 distinct CNVRs, respectively, with 202 CNVRs shared across all three breeds. After removing duplicates, we obtained 1545 CNVRs from 26 horse genomes. Functional annotation reveals enrichment in biological functions, including antigen processing, cell metabolism, olfactory conduction, and nervous system development. Debao horses have 970 genes overlapping with CNVRs, possibly causing their small size and mountainous adaptations. We also found that the genes GHR, SOX9, and SOX11 may be responsible for the miniature features of the Debao horse by analyzing their overlapping CNVRs. Overall, this study offers valuable insights into the widespread presence of CNVs in the horse genome. The findings contribute to mapping horse CNVs and advance research on unique miniature traits observed in the Debao horse.

Deleterious mutations predicted in the sorghum (Sorghum bicolor) Maturity (Ma) and Dwarf (Dw) genes from whole-genome resequencing

In sorghum [Sorghum bicolor (L.) Moench] the Maturity (Ma1, Ma2, Ma3, Ma4, Ma5, Ma6) and Dwarf (Dw1, Dw2, Dw3, Dw4) loci, encode genes controlling flowering time and plant height, respectively, which are critical for designing sorghum ideotypes for a maturity timeframe and a harvest method. Publicly available whole-genome resequencing data from 860 sorghum accessions was analyzed in silico to identify genomic variants at 8 of these loci (Ma1, Ma2, Ma3, Ma5, Ma6, Dw1, Dw2, Dw3) to identify novel loss of function alleles and previously characterized ones in sorghum germplasm. From ~ 33 million SNPs and ~ 4.4 million InDels, 1445 gene variants were identified within these 8 genes then evaluated for predicted effect on the corresponding encoded proteins, which included newly identified mutations (4 nonsense, 15 frameshift, 28 missense). Likewise, most accessions analyzed contained predicted loss of function alleles (425 ma1, 22 ma2, 40 ma3, 74 ma5, 414 ma6, 289 dw1, 268 dw2 and 45 dw3) at multiple loci, but 146 and 463 accessions had no predicted ma or dw mutant alleles, respectively. The ma and dw alleles within these sorghum accessions represent a valuable source for manipulating flowering time and plant height to develop the full range of sorghum types: grain, sweet and forage/biomass.

Genome-wide association study identifies novel loci associated with feed efficiency traits in Hu lambs1

Feed efficiency (FE) is a crucial economic trait that significantly impacts profitability in intensive sheep production, and can be evaluated by the residual feed intake (RFI) and feed conversion ratio (FCR). However, the underlying genetic mechanisms that underlie FE-related traits in sheep are not fully understood. Herein, we measured the FE-related traits of 1280 Hu sheep and conducted the phenotype statistics and correlation analysis, the result showcase that there was a large variation for FE-related traits, and RFI was significant positive correlation with average daily feed intake (ADFI) and FCR. Moreover, a genome-wide association study (GWAS) was conducted using whole-genome resequencing data to investigate the genetic associations of ADFI, FCR and RFI. For ADFI and FCR traits, two and one single nucleotide polymorphisms (SNPs) exceeded the genome-wide significance threshold, whereas ten and five SNPs exceeded the suggestive significance threshold. For RFI traits, only four SNPs exceeded the suggestive significance threshold. Finally, a total of eight genes (LOC101121953, LOC101110202, CTNNA3, IZUMO3, PPM1E, YIPF7, ZSCAN12 and LOC105603808) were identified as potential candidate genes for FE-related traits. Simultaneously, we further analyzed the effects of two candidate SNPs associated with RFI on growth and FE traits in enlarged experimental population, the results demonstrated that these two SNPs was not significantly associated with growth traits (P > 0.05), but significantly related to RFI traits (P < 0.05). These findings will provide valuable reference data and key genetic variants that can be used to effectively select feed-efficient individual in sheep breeding programs.

Fine-scale environmentally associated spatial structure of lumpfish (Cyclopterus lumpus) across the Northwest Atlantic.

Lumpfish, Cyclopterus lumpus, have historically been harvested throughout Atlantic Canada and are increasingly in demand as a solution to controlling sea lice in Atlantic salmon farms-a process which involves both the domestication and the transfer of lumpfish between geographic regions. At present, little is known regarding population structure and diversity of wild lumpfish in Atlantic Canada, limiting attempts to assess the potential impacts of escaped lumpfish individuals from salmon pens on currently at-risk wild populations. Here, we characterize the spatial population structure and genomic-environmental associations of wild populations of lumpfish throughout the Northwest Atlantic using both 70K SNP array data and whole-genome re-sequencing data (WGS). At broad spatial scales, our results reveal a large environmentally associated genetic break between the southern populations (Gulf of Maine and Bay of Fundy) and northern populations (Newfoundland and the Gulf of St. Lawrence), linked to variation in ocean temperature and ice cover. At finer spatial scales, evidence of population structure was also evident in a distinct coastal group in Newfoundland and significant isolation by distance across the northern region. Both evidence of consistent environmental associations and elevated genome-wide variation in F ST values among these three regional groups supports their biological relevance. This study represents the first extensive description of population structure of lumpfish in Atlantic Canada, revealing evidence of broad and fine geographic scale environmentally associated genomic diversity. Our results will facilitate the commercial use of lumpfish as a cleaner fish in Atlantic salmon aquaculture, the identification of lumpfish escapees, and the delineation of conservation units of this at-risk species throughout Atlantic Canada.

Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus.

Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.