Sugarcane (Saccharum) is the most critical sugar crop worldwide. As one of the most enriched transcription factor families in plants, MYB genes display a great potential to contribute to sugarcane ...improvement by trait modification. We have identified the sugarcane MYB gene family at a whole-genome level through systematic evolution analyses and expression profiling. R2R3-MYB is a large subfamily involved in many plant-specific processes. A total of 202 R2R3-MYB genes (356 alleles) were identified in the polyploid Saccharum spontaneum genomic sequence and classified into 15 subgroups by phylogenetic analysis. The sugarcane MYB family had more members by a comparative analysis in sorghum and significant advantages among most plants, especially grasses. Collinearity analysis revealed that 70% of the SsR2R3-MYB genes had experienced duplication events, logically suggesting the contributors to the MYB gene family expansion. Functional characterization was performed to identify 56 SsR2R3-MYB genes involved in various plant bioprocesses with expression profiling analysis on 60 RNA-seq databases. We identified 22 MYB genes specifically expressed in the stem, of which RT-qPCR validated MYB43, MYB53, MYB65, MYB78, and MYB99. Allelic expression dominance analysis implied the differential expression of alleles might be responsible for the high expression of MYB in the stem. MYB169, MYB181, MYB192 were identified as candidate C.sub.4 photosynthetic regulators by C.sub.4 expression pattern and robust circadian oscillations. Furthermore, stress expression analysis showed that MYB36, MYB48, MYB54, MYB61 actively responded to drought treatment; 19 and 10 MYB genes were involved in response to the sugarcane pokkah boeng and mosaic disease, respectively. This is the first report on genome-wide analysis of the MYB gene family in sugarcane. SsMYBs probably played an essential role in stem development and the adaptation of various stress conditions. The results will provide detailed insights and rich resources to understand the functional diversity of MYB transcription factors and facilitate the breeding of essential traits in sugarcane.
Pathogen‐mediated selection and sexual selection are important drivers of evolution. Both processes are known to target genes of the major histocompatibility complex (MHC), a gene family encoding ...cell‐surface proteins that display pathogen peptides to the immune system. The MHC is also a model for understanding processes such as gene duplication and trans‐species allele sharing. The class II MHC protein is a heterodimer whose peptide‐binding groove is encoded by an MHC‐IIA gene and an MHC‐IIB gene. However, our literature review found that class II MHC papers on infectious disease or sexual selection included IIA data only 18% and 9% of the time, respectively. To assess whether greater emphasis on MHC‐IIA is warranted, we analysed MHC‐IIA sequence data from 50 species of vertebrates (fish, amphibians, birds, mammals) to test for polymorphism and positive selection. We found that the number of MHC‐IIA alleles within a species was often high, and covaried with sample size and number of MHC‐IIA genes assayed. While MHC‐IIA variability tended to be lower than that of MHC‐IIB, the difference was only ~25%, with ~3 fewer IIA alleles than IIB. Furthermore, the unexpectedly high MHC‐IIA variability showed clear signatures of positive selection in most species, and positive selection on MHC‐IIA was stronger in fish than in other surveyed vertebrate groups. Our findings underscore that MHC‐IIA can be an important target of selection. Future studies should therefore expand the characterization of MHC‐IIA at both allelic and genomic scales, and incorporate MHC‐IIA into models of fitness consequences of MHC variation.
Allelic diversity of human leukocyte antigen (HLA) class II genes may help maintain humoral immunity against infectious diseases. In this study, we investigated germline genetic variation in ...classical HLA class II genes and employed a systematic, unbiased approach to explore the relative contribution of this genetic variation in the antibody repertoire to various common pathogens. We leveraged a well-defined cohort of 800 adults representing the general Arab population in which genetic material is shared because of the high frequency of consanguineous unions. By applying a high-throughput method for large-scale antibody profiling to this well-defined cohort, we were able to dissect the overall effect of zygosity for classical HLA class II genes, as well as the effects associated with specific HLA class II alleles, haplotypes and genotypes, on the antimicrobial antibody repertoire breadth and antibody specificity with unprecedented resolution. Our population genetic studies revealed that zygosity of the classical HLA class II genes is a strong predictor of antibody responses to common human pathogens, suggesting that classical HLA class II gene heterozygosity confers a selective advantage. Moreover, we demonstrated that multiple HLA class II alleles can have additive effects on the antibody repertoire to common pathogens. We also identified associations of HLA-DRB1 genotypes with specific antigens. Our findings suggest that HLA class II gene polymorphisms confer specific humoral immunity against common pathogens, which may have contributed to the genetic diversity of HLA class II loci during hominine evolution.
This study assesses the genetic diversity of four different hatchery bred lines of Sydney rock oyster, Saccosstrea glomerata (SRO) after three, five and seven generations of mass selection using ...microsatellite DNA markers and mitochondrial cytochrome C oxidase subunit 1 sequences (COX1). This was achieved using seven newly developed microsatellite markers, along with three published loci. Considering the same number of samples in each line, the number of different alleles in each of the four hatchery lines ranged from 49 to 70 alleles from 10 loci, which was approximate 50% less than the 120 alleles found in the samples from the wild population. However, if we pool all our four hatchery lines together, then their total number of alleles was not significantly different from the wild population. Similar to the patterns found for the DNA microsatellite alleles, mtDNA haplotype numbers were considerably lower in each of the hatchery lines than in the samples from the wild population. Again, pooling the hatchery lines gave a total haplotype number not statistically significantly different from that in the samples from the wild. Considering together the DNA microsatellite alleles and the mtDNA haplotypes, we conclude that there was a substantial loss of genetic diversity within all lines separately over generations of mass selection, and that such mass selection was not sustainable in the long term. However, importantly, these data indicate that for oysters, if multiple independent mass selection lines are kept, then their combined genetic diversity may approach that of the ancestral line or wild population even after many generations of mass selection. These results for oysters, finding preservation of diversity among lines yet loss within them, are similar to recent findings for multiple banana shrimp lines; considering both species together it suggests that one relatively simple option suitable for some farms and industry to maintain genetic diversity during mass selection over many generations of selection is to subdivide their breeding nucleus and keep multiple different and independent lines over generations. It remains to be tested if this approach is general across many aquaculture species and circumstances.
This paper attempts to falsify the published hypothesis set out by Knibb et al., 2014 that “the use of multiple lines under some circumstances may be a hedge against loss of diversity” using a second independent example, namely Sydney rock oysters.
The data of this paper do not refute the generality of the above hypothesis of Knibb et al., 2014 that splitting mass selection lines into multiple sublines preserves genetic variation.
•First assessment of genetic diversity after generations of mass selection for growth and resistance in Sydney rock oysters.•Substantial loss of allelic and haplotypic diversity was evident within each selected line compared with a wild population.•However, considered together, the selected lines had levels of diversity not different to that in the wild population.•The SRO data support published banana shrimp data that genetic variation can be kept by using multiple mass selection lines.
Ahmadi M, Kashiri H, Shabani A, Moghadam AA. 2018. Genetic variability in wild and hatchery populations of commercially important fish: The common carp (Cyprinus carpio). Biodiversitas 19: 1468-1474. ...Common carp, Cyprinus carpio, is considered as one of the most important bony fish with high economic value in the Caspian sea. Since the population size of common carp has decreased during recent decades, restocking of the populations is done through releasing the hatchery-produced larvae into the Caspian Sea. In the present study, the genetic diversity of hatchery and wild populations of C. carpio was investigated using eight microsatellite loci (MFW7, MFW9, MFW13, MFW16, MFW17, MFW20, MFW26 and MFW28). A total of 145 different alleles were observed across all loci, with some of them being unique to each population. Although the allelic and gene diversity of hatchery populations tended to be lower compared to the wild populations, no significant differences (P>0.05) in genetic diversity parameters were observed among the wild and hatchery populations. In most cases, significant departure from Hardy-Weinberg equilibrium was observed, mainly because of the heterozygosity deficiency. Results from FST, RST and UPGMA analysis showed that the hatchery-reared population was the most differentiated and distant group. The results from this study are anticipated to provide important information for setting up more efficient strategies in conservation and restocking of C. carpio.
Summary
The development of improved plant nucleotide‐binding, leucine‐rich repeat (LRR) immune receptors (NLRs) has mostly been based on random mutagenesis or on structural information available for ...specific receptors complexed with the recognized pathogen effector. Here, we use a targeted mutagenesis approach based on the natural diversity of the Pm3 powdery mildew resistance alleles present in different wheat (Triticum aestivum) genotypes. In order to understand the functional importance of the amino acid polymorphisms between the active immune receptor PM3A and the inactive ancestral variant PM3CS, we exchanged polymorphic regions and residues in the LRR domain of PM3A with the corresponding segments of PM3CS. These novel variants were functionally tested for recognition of the corresponding AVRPM3A2/F2 avirulence protein in Nicotiana benthamiana. We identified polymorphic residues in four regions of PM3A that enhance the immune response, but also residues that reduce it or result in complete loss of function. We found that the identified critical residues in PM3A modify its activation threshold towards different protein variants of AVRPM3A2/F2. PM3A variants with a lowered threshold gave a stronger overall response and gained an extended recognition spectrum. One of these variant proteins with a single amino acid change was stably transformed into wheat, where it conferred race‐specific resistance to mildew. This is a proof of concept that improved PM3A variants with an enlarged recognition spectrum can be engineered based on natural diversity by exchanging single or multiple residues that modulate resistance function.
Significance Statement
To engineer plant immune receptors with enhanced and broader recognition specificity, it is essential to identify critical residues for receptor function. Here, we show that natural allelic diversity can be used to determine key residues for specific receptor function. We demonstrate their impact on receptor activity, and use these observations to design an improved immune receptor.
Cicer arietinum
L. (chickpea) is one of the most significant legume crops domesticated in the Fertile Crescent. This study was aimed to characterize a diverse composite set of 384
Cicer
genotypes ...using unlinked simple sequence repeat (SSR) markers. The genotypes grown under the temperate conditions of Western-Himalayas included cultivated and wild relatives from primary (
Cicer reticulatum
Ladiz.), secondary (
Cicer echinospermum
P.H. Davis) and tertiary (
Cicer microphyllum
Benth.) gene pools. The analysis of genotypic data of eight SSR markers from eight linkage groups led to the identification of 63 alleles, ranging from 2 to 6 with an average value of 3.7 alleles per locus. The polymorphic information content of SSR markers ranged from 0.46 to 0.79 with an average value of 0.77 and the gene diversity ranged from 0.47 to 0.79 with an average of 0.64. The clustering of genotypes in the form of dendrogram discriminated all 384 genotypes into four major clusters. The wild genotypes belonging to different gene pools got clustered uniformly in different clusters along with cultivated chickpea genotypes. The analysis of data also led to the selection of core set of 192 genotypes. The core set was found to possess same diversity (63 alleles; average alleles per locus: 3.7; gene diversity: 0.65) as that of composite set of 384 genotypes. The development of core set in chickpea shall prove useful in gene discovery for variety of traits through genome-wide association studies. The results also provide an insight into gene/allele diversity available in our chickpea germplasm collection grown under agro-climatic conditions of the North Western-Himalayas.
Individuals infected with Helicobacter pylori harbor unique and diverse populations of quasispecies, but diversity between and within different regions of the human stomach and the process of ...bacterial adaptation to each location are not yet well understood. We applied whole-genome deep sequencing to characterize the within- and between-stomach region genetic diversity of H. pylori populations from paired antrum and corpus biopsies of 15 patients, along with single biopsies from one region of an additional 3 patients, by scanning allelic diversity. We combined population deep sequencing with more conventional sequencing of multiple H. pylori single colony isolates from individual biopsies to generate a unique dataset. Single colony isolates were used to validate the scanning allelic diversity pipelines. We detected extensive population allelic diversity within the different regions of each patient's stomach. Diversity was most commonly found within non-coding, hypothetical, outer membrane, restriction modification system, virulence, lipopolysaccharide biosynthesis, efflux systems, and chemotaxis-associated genes. Antrum and corpus populations from the same patient grouped together phylogenetically, indicating that most patients were initially infected with a single strain, which then diversified. Single colonies from the antrum and corpus of the same patients grouped into distinct clades, suggesting mechanisms for within-location adaptation across multiple H. pylori isolates from different patients. The comparisons made available by combined sequencing and analysis of isolates and populations enabled comprehensive analysis of the genetic changes associated with H. pylori diversification and stomach region adaptation.
Despite the negative economic and ecological impact of weeds, relatively little is known about the evolutionary mechanisms that influence their persistence in agricultural fields. Here, we use a ...resurrection approach to examine the potential for genotypic and phenotypic evolution in Ipomoea purpurea, an agricultural weed that is resistant to glyphosate, the most widely used herbicide in current‐day agriculture. We found striking reductions in allelic diversity between cohorts sampled nine years apart (2003 vs. 2012), suggesting that populations of this species sampled from agricultural fields have experienced genetic bottleneck events that have led to lower neutral genetic diversity. Heterozygosity excess tests indicate that these bottlenecks may have occurred prior to 2003. A greenhouse assay of individuals sampled from the field as seed found that populations of this species, on average, exhibited modest increases in herbicide resistance over time. However, populations differed significantly between sampling years for resistance: some populations maintained high resistance between the sampling years whereas others exhibited increased or decreased resistance. Our results show that populations of this noxious weed, capable of adapting to strong selection imparted by herbicide application, may lose genetic variation as a result of this or other environmental factors. We probably uncovered only modest increases in resistance on average between sampling cohorts due to a strong and previously identified fitness cost of resistance in this species, along with the potential that nonresistant migrants germinate from the seed bank.
see also the Perspective by Franks
Members of the
complex, includes
(most common fungal infection of the brain) and
(high-impact emerging pathogen worldwide). Currently, the fungal multilocus sequence typing database (Fungal MLST ...Database) constitutes a valuable data repository of the genes used for molecular typing of these pathogens. We analyzed the data available in the Fungal MLST Database for seven housekeeping genes, with the aim to evaluate its contribution in the description of intra-taxa diversity, population genetic structure, and evolutionary patterns. Although the Fungal MLST Database has a greater number of reports for
(
= 487) than for
(
= 344), similar results were obtained for both species in terms of allelic diversity. Phylogenetic reconstructions revealed grouping by molecular type in both species and allowed us to propose differences in evolutionary patterns (gradualism in the case of
and punctuated evolution in the case of
). In addition,
showed a population genetic structure consisting of 37 clonal complexes (CCs; CC1 being predominant), high crosslinking without sequence type (ST) grouping by molecular type, marked divergence events in phylogenetic analysis, and few introgression events (mainly between VNI and VNIV). By contrast,
showed 50 CCs (with greater homogeneity in ST number by CC) and clustering by molecular type with marked crosslinking events in phylogenetic networks being less evident. Understanding relationships at the molecular level for species of the
complex, based on the sequences of the housekeeping genes, provides information for describing the evolutionary history of these emerging pathogens.
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