Molecular Population Genetics and the Search for Adaptive Evolution in Plants

Contrasting levels of transcriptome-wide SNP diversity and adaptive molecular variation among conifers

Adaptive convergence can arise when response to natural selection involves shared molecular or functional mechanisms among multiple taxa. Conifers are archaic species of ancient origin with delayed sexual maturity related to their woody perennial nature. Thus, they represent a relevant plant group to assess if convergence from selection may have become disconnected between molecular and functional levels. In this purpose, transcriptome-wide SNP diversity was assessed in seven partially sympatric and reproductively isolated conifer species (118 individuals from 67 populations) populating the temperate and boreal forests of northeastern North America. SNP diversity was found highly heterogeneous among species, which would relate to variation in species-specific demography and history. Rapidly evolving genes with signatures of positive selection were identified, and their relative abundance among species reflected differences in transcriptome-wide SNP diversity. The analysis of sequence homology also revealed very limited convergence among taxa in spite of sampling same tissues at same age. However, convergence increased gradually at the levels of gene families and biological processes, which were largely related to stress response and regulatory mechanisms in all species. Given their multiple small to large gene families and long time since inception, conifers may have had sufficient gene network flexibility and gene functional redundancy for evolving alternative adaptive genes for similar metabolic responses to environmental selection pressures. Despite a long divergence time of ~350 Mya between conifers and Angiosperms, we also uncovered a set of 17 key genes presumably under positive selection in both lineages.

Comparative Chloroplast Genomics Reveals Intrageneric Divergence in Salix

As the most diverse genus of Salicaceae, Salix is primarily distributed in the temperate zone of the Northern Hemisphere, encompassing 350-500 species worldwide. The genus's evolutionary history is complex due to significant genetic differentiation. Chloroplast genes, being highly conserved, serve as effective tools for studying uniparental inheritance and evolution. In this study, we sequenced and assembled the chloroplast genomes of five representative Salix species. Phylogenetic relationships were constructed using chloroplast genome data, and structural differences among lineages were compared. These Salix chloroplast genomes exhibited a typical quadripartite structure, with lengths ranging from 154,444 to 155,725 bp. We successfully annotated 131 genes, including 88 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. Clade I showed higher variability in the SSC region, identifying five highly variable regions: petA-psbJ, rps16-rps3, ndhD, ccsA-ndhD, and ndhG-ndhI. Two rapidly evolving genes, ndhI and ycf4, were also identified. The total length of insertions and deletions (InDels) in Clade I was 1046 bp. Clade II exhibited greater variability in the LSC region, with four highly variable regions being identified: trnK-trnQ, ndhC-trnV, trnV, and psdE-petL. Four rapidly evolving genes-infA, rpoC1, rps18, and ycf1-were identified. The total length of InDels in Clade II was 1282 bp. Therefore, this study elucidated the chloroplast genome evolution across different Salix lineages, thereby providing deeper insights into intrageneric phylogenetic relationships.

Single-nucleotide polymorphisms and copy number variations drive adaptive evolution to freezing stress in a subtropical evergreen broad-leaved tree: Hexaploid wild Camellia oleifera

Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress, while hexaploid wild Camellia oleifera shows strong freezing tolerance. As a valuable genetic resource of woody oil crop C. oleifera, wild C. oleifera can serve as a case for studying the molecular bases of adaptive evolution to freezing stress. Here, 47 wild C. oleifera from 11 natural distribution sites in China and 4 relative species of C. oleifera were selected for genome sequencing. "Min Temperature of Coldest Month" (BIO6) had the highest comprehensive contribution to wild C. oleifera distribution. The population genetic structure of wild C. oleifera could be divided into two groups: in cold winter (BIO6 ≤ 0 °C) and warm winter (BIO6 > 0 °C) areas. Wild C. oleifera in cold winter areas might have experienced stronger selection pressures and population bottlenecks with lower N e than those in warm winter areas. 155 single-nucleotide polymorphisms (SNPs) were significantly correlated with the key bioclimatic variables (106 SNPs significantly correlated with BIO6). Twenty key SNPs and 15 key copy number variation regions (CNVRs) were found with genotype differentiation > 50% between the two groups of wild C. oleifera. Key SNPs in cis-regulatory elements might affect the expression of key genes associated with freezing tolerance, and they were also found within a CNVR suggesting interactions between them. Some key CNVRs in the exon regions were closely related to the differentially expressed genes under freezing stress. The findings suggest that rich SNPs and CNVRs in polyploid trees may contribute to the adaptive evolution to freezing stress.

Identification of heat stress-related genomic regions by genome-wide association study in Solanum tuberosum

The climate crisis impairs yield and quality of crucial crops like potatoes. We investigated the effects of heat stress on five morpho-physiological parameters in a diverse panel of 178 potato cultivars under glasshouse conditions. Overall, heat stress increased shoot elongation and green fresh weight, but reduced tuber yield, starch content and harvest index. Genomic information was obtained from 258 tetraploid and three diploid cultivars by a genotyping-by-sequencing approach using methylation-sensitive restriction enzymes. This resulted in an enrichment of sequences in gene-rich regions. Population structure analyses using genetic distances and hierarchical clustering revealed strong kinship but weak overall population structure cultivars. A genome-wide association study (GWAS) was conducted with a subset of 20 K stringently filtered SNPs to identify quantitative trait loci (QTL) linked to heat tolerance. We identified 67 QTL and established haploblock boundaries to narrow down the number of candidate genes. Additionally, GO-enrichment analyses provided insights into gene functions. Heritability and genomic prediction were conducted to assess the usability of the collected data for selecting breeding material. The detected QTL might be exploited in marker-assisted selection to develop heat-resilient potato cultivars.

A Dominance Hypothesis Argument for Historical Genetic Gains and the Fixation of Heterosis in Octoploid Strawberry

Heterosis was the catalyst for the domestication of cultivated strawberry (Fragaria × ananassa), an interspecific hybrid species that originated in the 1700s. The hybrid origin was discovered because the phenotypes of spontaneous hybrids transgressed those of their parent species. The transgressions included fruit yield increases and other genetic gains in the twentieth century that sparked the global expansion of strawberry production. The importance of heterosis to the agricultural success of the hybrid species, however, has remained a mystery. Here we show that heterosis has disappeared (become fixed) among improved hybrids within a population (the California population) that has been under long-term selection for increased fruit yield, weight, and firmness. We found that the highest yielding hybrids are among the most highly inbred (59-79%), which seems counterintuitive for a highly heterozygous, outbreeder carrying heavy genetic loads. Although faint remnants of heterosis were discovered, the between-parent allele frequency differences and dispersed favorable dominant alleles necessary for heterosis have decreased nearly genome-wide within the California population. Conversely, heterosis was prevalent and significant among wide hybrids, especially for fruit count, a significant driver of genetic gains for fruit yield. We attributed the disappearance (fixation) of heterosis within the California population to increased homozygosity of favorable dominant alleles and inbreeding associated with selection, random genetic drift, and selective sweeps. Despite historical inbreeding, the highest yielding hybrids reported to-date are estimated to be heterozygous for 20,370-44,280 of 97,000-108,000 genes in the octoploid genome, the equivalent of an entire diploid genome or more.

Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa

Given the escalating impact of climate change on agriculture and food security, gaining insights into the evolutionary dynamics of climatic adaptation and uncovering climate-adapted variation can empower the breeding of climate-resilient crops to face future climate change. Alfalfa (Medicago sativa subsp. sativa), the queen of forages, shows remarkable adaptability across diverse global environments, making it an excellent model for investigating species responses to climate change. In this study, we performed population genomic analyses using genome resequencing data from 702 accessions of 24 Medicago species to unravel alfalfa's climatic adaptation and genetic susceptibility to future climate change. We found that interspecific genetic exchange has contributed to the gene pool of alfalfa, particularly enriching defense and stress-response genes. Intersubspecific introgression between M. sativa subsp. falcata (subsp. falcata) and alfalfa not only aids alfalfa's climatic adaptation but also introduces genetic burden. A total of 1671 genes were associated with climatic adaptation, and 5.7% of them were introgressions from subsp. falcata. By integrating climate-associated variants and climate data, we identified populations that are vulnerable to future climate change, particularly in higher latitudes of the Northern Hemisphere. These findings serve as a clarion call for targeted conservation initiatives and breeding efforts. We also identified pre-adaptive populations that demonstrate heightened resilience to climate fluctuations, illuminating a pathway for future breeding strategies. Collectively, this study enhances our understanding about the local adaptation mechanisms of alfalfa and facilitates the breeding of climate-resilient alfalfa cultivars, contributing to effective agricultural strategies for facing future climate change.

The role of introgressive hybridization in shaping the geographically isolated gene pools of wax palm populations (genus Ceroxylon)

The speciation continuum is the process by which genetic groups diverge until they reach reproductive isolation. It has become common in the literature to show that this process is gradual and flickering, with possibly many instances of secondary contact and introgression after divergence has started. The level of divergence might vary among genomic regions due to, among others, the different forces and roles of selection played by the shared regions. Through hybrid capture, we sequenced ca. 4,000 nuclear regions in populations of six species of wax palms, five of which form a monophyletic group (genus Ceroxylon, Arecaceae: Ceroxyloideae). We show that in this group, the different populations show varying degrees of introgressive hybridization, and two of them are backcrosses of the other three 'pure' species. This is particularly interesting because these three species are dioecious, have a shared main pollinator, and have slightly overlapping reproductive seasons but highly divergent morphologies. Our work supports shows wax palms diverge under positive and background selection in allopatry, and hybridize due to secondary contact and inefficient reproductive barriers, which sustain genetic diversity. Introgressed regions are generally not under positive selection. Peripheral populations are backcrosses of other species; thus, introgressive hybridization is likely modulated by demographic effects rather than selective pressures. In general, these species might function as an 'evolutionary syngameon' where expanding, peripheral, small, and isolated populations maintain diversity by crossing with available individuals of other wax palms. In the Andean context, species can benefit from gained variation from a second taxon or the enhancement of population sizes by recreating a common genetic pool.

Half a Century of Controversy: The Neutralist/Selectionist Debate in Molecular Evolution

The neutral and nearly neutral theories, introduced more than 50 yr ago, have raised and still raise passionate discussion regarding the forces governing molecular evolution and their relative importance. The debate, initially focused on the amount of within-species polymorphism and constancy of the substitution rate, has spread, matured, and now underlies a wide range of topics and questions. The neutralist/selectionist controversy has structured the field and influences the way molecular evolutionary scientists conceive their research.

Genome-wide characterization and expression profiling of GASA gene family in Triticum turgidum ssp. durum (desf.) husn. (Durum wheat) unveils its involvement in environmental stress responses

Family members within the plant-specific gibberellic acid-stimulated Arabidopsis (GASA) gene serve a crucial role in plant growth and development, particularly in flower induction and seed development. Through a genome-wide analysis of Triticum turgidum ssp. Durum (durum wheat), we identified 19 GASA genes, designated as TdGASA1‒19. Moreover, the chromosomal locations, exon-intron distribution and the physiochemical properties of these genes were determined and the subcellular localization of their encoded proteins was estimated. Analyses of their domain structure, motif arrangements, and phylogeny revealed four distinct groups that share a conserved GASA domain. Additionally, a real-time q-PCR analysis revealed differential expression patterns of TdGASA genes in various tissues (including leaves, roots, stems, and seeds) and in response to salinity, osmotic stress, and treatment with exogenous phytohormones (abscisic and gibberellic acid), implying that these genes may play a role in the growth, development, and stress responses of Triticum turgidum. Heterologous expression of TdGASA1, TdGASA4, TdGASA14, and TdGASA19 in Saccharomyces cerevisiae improved its tolerance to salt, osmotic, oxidative, and heat stresses, which suggests the involvement of these genes in abiotic stress tolerance mechanisms. The present study is the first to identify and analyze the expression profile of T. turgidum GASA genes, therefore offering novel insights for their further functional characterization, which may serve as a novel resource for molecular breeding of durum wheat.

Salt stress alters the spectrum of de novo mutation available to selection during experimental adaptation of Chlamydomonas reinhardtii

The genetic basis of adaptation is driven by both selection and the spectrum of available mutations. Given that the rate of mutation is not uniformly distributed across the genome and varies depending on the environment, understanding the signatures of selection across the genome is aided by first establishing what the expectations of genetic change are from mutation. To determine the interaction between salt stress, selection, and mutation across the genome, we compared mutations observed in a selection experiment for salt tolerance in Chlamydomonas reinhardtii to those observed in mutation accumulation (MA) experiments with and without salt exposure. MA lines evolved under salt stress had a single-nucleotide mutation rate of 1.1 × 10 - 9 $1.1 \times 10^{-9}$ , similar to that of MA lines under standard conditions ( 9.6 × 10 - 10 $9.6 \times 10^{-10}$ ). However, we found that salt stress led to an increased rate of indel mutations, but that many of these mutations were removed under selection. Finally, lines adapted to salt also showed excess clustering of mutations in the genome and the co-expression network, suggesting a role for positive selection in retaining mutations in particular compartments of the genome during the evolution of salt tolerance. Our study shows that characterizing mutation rates and spectra expected under stress helps disentangle the effects of environment and selection during adaptation.

Genetic diversity and population dynamic of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow in Central China

Phylogeographic research concerning Central China has been rarely conducted. Population genetic and phylogeography of Ziziphus jujuba var. spinosa (also called sour jujube) were investigated to improve our understanding of plant phylogeographic patterns in Central China. Single-copy nuclear gene markers and complete chloroplast genome data were applied to 328 individuals collected from 21 natural populations of sour jujube in China. Nucleotide variation of sour jujube was relatively high (π = 0.00720, θ w = 0.00925), which resulted from the mating system and complex population dynamics. Analysis of molecular variation analysis revealed that most of the total variation was attributed to variation within populations, and a high level of genetic differentiation among populations was detected (F st = 0.197). Relatively low long-distance dispersal capability and vitality of pollen contributed to high genetic differentiation among populations. Differences in the environmental conditions and long distance among populations further restricted gene flow. Structure clustering analysis uncovered intraspecific divergence between central and marginal populations. Migrate analysis found a high level of gene flow between these two intraspecific groups. Bayesian skyline plot detected population expansion of these two intraspecific groups. Network and phylogeny analysis of chloroplast haplotypes also found intraspecific divergence, and the divergence time was estimated to occur at about 55.86 Ma. Haplotype native to the Loess Plateau was more ancient, and multiple glacial refugia of sour jujube were found to locate at the Loess Plateau, areas adjacent to the Qinling Mountains and Tianmu Mountains. Species distribution model analysis found a typical contraction-expansion model corresponding to the Quaternary climatic oscillations. In the future, the distribution of sour jujube may shift to high-latitude areas. This study provides new insights for phylogeographic research of temperate plant species distributed in Central China and sets a solid foundation for the application of the scientific management strategy of Z. jujuba var. spinosa.

Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection

Gene duplication is increasingly recognized as an important mechanism for the origination of new genes, as revealed by comparative genomic analysis. However, how new duplicate genes contribute to phenotypic evolution remains largely unknown, especially in plants. Here, we identified the new gene EXOV, derived from a partial gene duplication of its parental gene EXOVL in Arabidopsis thaliana. EXOV is a species-specific gene that originated within the last 3.5 million years and shows strong signals of positive selection. Unexpectedly, RNA-sequencing analyses revealed that, despite its young age, EXOV has acquired many novel direct and indirect interactions in which the parental gene does not engage. This observation is consistent with the high, selection-driven substitution rate of its encoded protein, in contrast to the slowly evolving EXOVL, suggesting an important role for EXOV in phenotypic evolution. We observed significant differentiation of morphological changes for all phenotypes assessed in genome-edited and T-DNA insertional single mutants and in double T-DNA insertion mutants in EXOV and EXOVL. We discovered a substantial divergence of phenotypic effects by principal component analyses, suggesting neofunctionalization of the new gene. These results reveal a young gene that plays critical roles in biological processes that underlie morphological evolution in A. thaliana.

Species divergence and phylogeography of Corylus heterophylla Fisch complex (Betulaceae): Inferred from molecular, climatic and morphological data

Historical geo-climatic changes have shaped the geographical distributions and genetic diversity of numerous plant taxa in East Asia, which promote species divergence and ultimately speciation. Here, we integrated multiple approaches, including molecular phylogeography, ecological niche modeling, and morphological traits to examine the nucleotide diversity and interspecific divergence within Corylus heterophylla complex (C. heterophylla, C. kweichowensis, and C. yunnanensis). These three sibling taxa harbored similar high levels of nucleotide diversity at the species level. The molecular data (SCNG and cpDNA) unanimously supported the division of C. heterophylla complex into two major clades, with C. yunnanensis diverged earlier from the complex, whereas C. heterophylla and C. kweichowensis could hardly be separated. The split between the two clades (c. 12.89 Ma) coincided with the formation of Sichuan Basin in the middle Miocene, while the divergence among and within the five subclades (YUN1-YUN3, HK1-HK2) occurred from the late Miocene to the Pleistocene. C. heterophylla of northern China experienced glacial contraction and interglacial expansion during the Quaternary, whereas C. kweichowensis and C. yunnanensis of southern China presented population expansion even during the last glacial maximum. Despite of high levels of genetic admixture between C. heterophylla and C. kweichowensis, significant ecological and morphological discrepancy as well as incomplete geographic isolation indicated that adaptive evolution triggered by divergent selection may have played important roles in incipient ecological speciation.

Landscape Genomics in Tree Conservation Under a Changing Environment

Understanding the genetic basis of how species respond to changing environments is essential to the conservation of species. However, the molecular mechanisms of adaptation remain largely unknown for long-lived tree species which always have large population sizes, long generation time, and extensive gene flow. Recent advances in landscape genomics can reveal the signals of adaptive selection linking genetic variations and landscape characteristics and therefore have created novel insights into tree conservation strategies. In this review article, we first summarized the methods of landscape genomics used in tree conservation and elucidated the advantages and disadvantages of these methods. We then highlighted the newly developed method "Risk of Non-adaptedness," which can predict the genetic offset or genomic vulnerability of species via allele frequency change under multiple scenarios of climate change. Finally, we provided prospects concerning how our introduced approaches of landscape genomics can assist policymaking and improve the existing conservation strategies for tree species under the ongoing global changes.

Rapidly evolving genetic features for desert adaptations in Stipagrostis pennata

BACKGROUND

Stipagrostis pennata is distributed in the mobile and semi-mobile sand dunes which can adapt well to extreme environments such as drought and high temperature. It is a pioneer plant species with potential for stabilizing sand dunes and ecological restoration. It can settle on moving sand dunes earlier than other desert plants. It can effectively improve the stability of sand dunes and help more plants settle down and increase plant diversity. However, despite its important ecological value, the genetic resources available for this species are limited.

RESULTS

We used single-molecule real-time sequencing technology to obtain the complete full-length transcriptome of Stipagrostis pennata, including 90,204 unigenes with an average length of 2624 bp. In addition, the 5436 transcription factors identified in these unigenes are rich in stress resistance genes, such as MYB-related, C3H, bHLH, GRAS and HSF, etc., which may play a role in adapting to desert drought and strong wind stress. Intron retention events are abundant alternative splicing events. Stipagrostis pennata has experienced stronger positive selection, accelerating the fixation of advantageous variants. Thirty-eight genes, such as CPP/TSO1-like gene, have evolved rapidly and may play a role in material transportation, flowering and seed formation.

CONCLUSIONS

The present study captures the complete full-length transcriptome of Stipagrostis pennata and reveals its rapid evolution. The desert adaptation in Stipagrostis pennata is reflected in the regulation of gene expression and the adaptability of gene function. Our findings provide a wealth of knowledge for the evolutionary adaptability of desert grass species.

The promise and deceit of genomic selection component analyses

Selection component analyses (SCA) relate individual genotype to fitness components such as viability, fecundity and mating success. SCA are based on population genetic models and yield selection estimates directly in terms of predicted allele frequency change. This paper explores the statistical properties of gSCA: experiments that apply SCA to genome-wide scoring of SNPs in field sampled individuals. Computer simulations indicate that gSCA involving a few thousand genotyped samples can detect allele frequency changes of the magnitude that has been documented in field experiments on diverse taxa. To detect selection, imprecise genotyping from low-level sequencing of large samples of individuals provides much greater power than precise genotyping of smaller samples. The simulations also demonstrate the efficacy of 'haplotype matching', a method to combine information from a limited collection of whole genome sequence (the reference panel) with the much larger sample of field individuals that are measured for fitness. Pooled sequencing is demonstrated as another way to increase statistical power. Finally, I discuss the interpretation of selection estimates in relation to the Beavis effect, the overestimation of selection intensities at significant loci.

Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach

Marker assisted breeding, facilitated by reference genome assemblies, can help to produce cultivars adapted to changing environmental conditions. However, anomalous linkage disequilibrium (LD), where single markers show high LD with markers on other chromosomes but low LD with adjacent markers, is a serious impediment for genetic studies. We used a LD-correction approach to overcome these drawbacks, correcting the physical position of markers derived from 15 and 135 K arrays in a diversity panel of bread wheat representing 50 years of breeding history. We detected putative mismapping of 11.7% markers and improved the physical alignment of 5.4% markers. Population analysis indicated reduced genetic diversity over time as a result of breeding efforts. By analysis of outlier loci and allele frequency change over time we traced back the 2NS/2AS translocation of Aegilops ventricosa to one cultivar, "Cardos" (registered in 1998) which was the first among the panel to contain this translocation. A "selective sweep" for this important translocation region on chromosome 2AS was found, putatively linked to plant response to biotic stress factors. Our approach helps in overcoming the drawbacks of incorrectly anchored markers on the wheat reference assembly and facilitates detection of selective sweeps for important agronomic traits.

Tapping Diversity From the Wild: From Sampling to Implementation

The diversity observed among crop wild relatives (CWRs) and their ability to flourish in unfavorable and harsh environments have drawn the attention of plant scientists and breeders for many decades. However, it is also recognized that the benefit gained from using CWRs in breeding is a potential rose between thorns of detrimental genetic variation that is linked to the trait of interest. Despite the increased interest in CWRs, little attention was given so far to the statistical, analytical, and technical considerations that should guide the sampling design, the germplasm characterization, and later its implementation in breeding. Here, we review the entire process of sampling and identifying beneficial genetic variation in CWRs and the challenge of using it in breeding. The ability to detect beneficial genetic variation in CWRs is strongly affected by the sampling design which should be adjusted to the spatial and temporal variation of the target species, the trait of interest, and the analytical approach used. Moreover, linkage disequilibrium is a key factor that constrains the resolution of searching for beneficial alleles along the genome, and later, the ability to deplete linked deleterious genetic variation as a consequence of genetic drag. We also discuss how technological advances in genomics, phenomics, biotechnology, and data science can improve the ability to identify beneficial genetic variation in CWRs and to exploit it in strive for higher-yielding and sustainable crops.

A cost-effective barcode system for maize genetic discrimination based on bi-allelic InDel markers

BACKGROUND

Maize is one of the most important cereal crop all over the world with a complex genome of about 2.3 gigabase, and exhibits tremendous phenotypic and molecular diversity among different germplasms. Along with the phenotype identification, molecular markers have been accepted extensively as an alternative tool to discriminate different genotypes.

RESULTS

By using previous re-sequencing data of 205 lines, bi-allelic insertions and deletions (InDels) all over maize genome were screened, and a barcode system was constructed consisting of 37 bi-allelic insertion-deletion markers with high polymorphism information content (PIC) values, large discriminative size among varieties. The barcode system was measured and determined, different maize hybrids and inbreds were clearly discriminated efficiently with these markers, and hybrids responding parents were accurately determined. Compared with microarray data of more than 200 maize lines, the barcode system can discriminate maize varieties with 1.57% of different loci as a threshold. The barcode system can be used in standardized easy and quick operation with very low cost and minimum equipment requirements.

CONCLUSION

A barcode system was constructed for genetic discrimination of maize lines, including 37 InDel markers with high PIC values and user-friendly. The barcode system was measured and determined for efficient identification of maize lines.

A Genomewide Scan for Genetic Structure and Demographic History of Two Closely Related Species, Rhododendron dauricum and R. mucronulatum (Rhododendron, Ericaceae)

Understanding the processes of divergence and speciation is an important task for evolutionary research, and climate oscillations play a pivotal role. We estimated the genetic structure and demographic history of two closely related species of Rhododendron, R. dauricum, and R. mucronulatum, distributed in northeastern China using 664,406 single nucleotide polymorphic loci of specific-locus amplified fragment sequencing (SLAF-seq) and 4 chloroplast DNA (cpDNA) fragments, sampling 376 individuals from 39 populations of these two species across their geographic distributions. The geographical distribution of cpDNA haplotypes revealed that R. dauricum and R. mucronulatum have different spatial genetic structures and haplotype diversity. Analysis of molecular variance (AMOVA) results showed that these two species have significant genetic differentiation and that the phylogeny demonstrates that these two species clustered a monophyletic group based on SLAF data, respectively, but not in cpDNA data. The evidence of significant gene flow was also detected from R. mucronulatum to R. dauricum. A deep divergence between the two species was observed and occurred during the early Oligocene. The niche models showed that the two species have different demographic histories. Thus, our results imply that geography and climate changes played important roles in the evolutionary process of R. dauricum and R. mucronulatum, and although there was an interspecific gene flow, the divergence was maintained by natural selection.

Evolutionary rate variation among genes involved in galactomannan biosynthesis in Coffea canephora

The endosperm cell walls of mature coffee seeds accumulate large amounts of mannan storage polysaccharides, which serve as nutrient reserve for embryo and contribute to beverage quality. Our study investigated the evolutionary patterns of key galactomannan (GM) biosynthesis genes using d N/d S ratio, synteny, and phylogenetic analysis and detected heterogeneity in rate of evolution among gene copies. Selection ratio index revealed evidence of positive selection in the branch editing gene Coffea canephora alpha (α) galactosidase (Cc-alpha Gal) at Cc11_g15950 copy (ω = 1.12), whereas strong purifying selection on deleterious mutations was observed in the Coffea canephora uridine diphosphate (UDP)-glucose 4'-epimerase (Cc-UG4E) and Coffea canephora mannose-1P guanylytransferase (Cc-MGT) genes controlling the crucial nucleotide carbon sugar building blocks flux in the pathway. Relatively low sequence diversity and strong syntenic linkages were detected in all GM pathway genes except in Cc-alpha Gal, which suggests a correlation between selection pressure and nucleotide diversity or synteny analysis. In addition, phylogenetic analysis revealed independent evolution or expansion of GM pathway genes in different plant species, with no obvious inferable clustering patterns according to either gene family or congruent with evolutionary plants lineages tested due to high dynamic nature and specific biochemical cell wall modification requirements. Altogether, our study shows a significant high rate of evolutionary variation among GM pathway genes in the diploid C. canephora and demonstrates the inherent variation in evolution of gene copies and their potential role in understanding selection rates in a homogenously connected metabolic pathway.

Molecular evolution and structural variations in nuclear encoded chloroplast localized heat shock protein 26 (sHSP26) from genetically diverse wheat species

Heat shock proteins are an important class of molecular chaperones known to impart tolerance under high temperature stress. sHSP26, a member of small heat shock protein subfamily is specifically involved in protecting plant's photosynthetic machinery. The present study aimed at identifying and characterizing sequence and structural variations in sHSP26 from genetically diverse progenitor and non-progenitor species of wheat. In silico analysis identified three paralogous copies of TaHSP26 to reside on short arm of chromosome 4A while one homeologue each was localized on long arm of chromosome 4B and 4D of cultivated bread wheat. Wild DD-genome donor Aegilops tauschii carried an additional sHSP26 gene (AET4Gv20569400) which was absent in the cultivated DD genome of bread wheat. In vitro amplification of this novel gene in wild accessions of Ae. tauschii and synthetic hexaploid wheat but not in cultivated bread wheat validated this finding. Further, significant length polymorphism could be identified in exon1 from diverse sHSP26 sequences. Multiple sequence alignment of procured sequences revealed numerous sSNPs and nsSNPs. D3A, P125 L, Q242 K were designated as homeolog specific- while A49 G as non-progenitor specific amino acid replacements. A 9-bp indel in TmHSP26-1(GA) translated into a deletion of SPM amino acid segment in chloroplast specific conserved consensus region III. High degree of divergence in nucleotide sequence between cultivated and wild species appeared in the form of higher ω values (Ka/Ks >1) indicating positive selection during the course of evolution. Phylogenetic analysis elucidated ancestral relationships between wheat sHSP26 proteins and orthologous proteins across plant kingdom. Overall, data mining approach may be employed as an effective pre-breeding strategy to identify and mobilize novel stress responsive genes and distinct allelic variants from wider germplasm collections of wheat to enhance climate resilience of present day elite wheat cultivars.

Comparative sensitivity to gamma radiation at the organismal, cell and DNA level in young plants of Norway spruce, Scots pine and Arabidopsis thaliana

Persistent DNA damage in gamma-exposed Norway spruce, Scots pine and Arabidopsis thaliana, but persistent adverse effects at the organismal and cellular level in the conifers only. Gamma radiation emitted from natural and anthropogenic sources may have strong negative impact on plants, especially at high dose rates. Although previous studies implied different sensitivity among species, information from comparative studies under standardized conditions is scarce. In this study, sensitivity to gamma radiation was compared in young seedlings of the conifers Scots pine and Norway spruce and the herbaceous Arabidopsis thaliana by exposure to ⁶⁰Co gamma dose rates of 1-540 mGy h^-1 for 144 h, as well as 360 h for A. thaliana. Consistent with slightly less prominent shoot apical meristem, in the conifers growth was significantly inhibited with increasing dose rate ≥ 40 mGy h^-1. Post-irradiation, the conifers showed dose-rate-dependent inhibition of needle and root development consistent with increasingly disorganized apical meristems with increasing dose rate, visible damage and mortality after exposure to ≥ 40 mGy h^-1. Regardless of gamma duration, A. thaliana showed no visible or histological damage or mortality, only delayed lateral root development after ≥ 100 mGy h^-1 and slightly, but transiently delayed post-irradiation reproductive development after ≥ 400 mGy h^-1. In all species dose-rate-dependent DNA damage occurred following ≥ 1-10 mGy h^-1 and was still at a similar level at day 44 post-irradiation. In conclusion, the persistent DNA damage (possible genomic instability) following gamma exposure in all species may suggest that DNA repair is not necessarily mobilized more extensively in A. thaliana than in Norway spruce and Scots pine, and the far higher sensitivity at the organismal and cellular level in the conifers indicates lower tolerance to DNA damage than in A. thaliana.

The maintenance of stable yield and high genetic diversity in the agricultural heritage torreya tree system

BACKGROUND

Understanding how traditional agriculture systems have been maintained would help design sustainable agriculture. In this study, we examined how farmers have used two types of local trees (Torreya grandis) for stable yield and maintaining genetic diversity in the "globally important agricultural heritage torreya tree system". The two type of torreya trees are grafted torreya (GT) tree and non-grafted-torreya (NGT) tree. The GT tree has only female and was used to produced seed yields. The NGT tree has both male and female and was used to support GT tree by providing pollens and rootstocks. We first tested the ratio of GT tree to NGT tree, their age groups, ratio of female trees (including GT and NGT trees) to male, and the flowering period of GT and NGT trees. We then tested seed yields and genetic diversity of GT and NGT trees. We further tested gene flow among NGT trees, and the relationship of gene flow with exchange rates of pollens and seeds.

RESULTS

GT and NGT trees (male and female) were planted in a mosaic pattern with a ratio of 4:1 (GT:NGT). In this planting pattern, one NGT male trees provided pollen for 20 female trees of GT and NGT. The trees were classified into four age groups (I = 100-400 years old; II = 400-700 years old; III = 700-1000 years old; and IV = 1000-1300 years old) based on basal diameter. The entire flowering period was longer for NGT trees than for GT trees that ensured GT trees (which lack of males) being exposed to pollens. GT tree had high and stable seed yield that increased with age groups. High genetic diversity has been maintained in both rootstocks of the GT trees and NGT trees. There was a strong gene flow among NGT trees, which positive correlated with the exchange rates of pollens and seeds.

CONCLUSIONS

Our results suggest that farmers obtain stable seed yields, and maintain high genetic diversity by ingeniously using the local GT tree as yield producer and NGT tree as supporter. These GT and NGT trees together ensure sustainable torreya production.

The Genomics of Oryza Species Provides Insights into Rice Domestication and Heterosis

Here, we review recent progress in genetic and genomic studies of the diversity of Oryza species. In recent years, unlocking the genetic diversity of Oryza species has provided insights into the genomics of rice domestication, heterosis, and complex traits. Genome sequencing and analysis of numerous wild rice (Oryza rufipogon) and Asian cultivated rice (Oryza sativa) accessions have enabled the identification of genome-wide signatures of rice domestication and the unlocking of the origin of Asian cultivated rice. Moreover, similar studies on genome variations of African rice (Oryza glaberrima) cultivars and their closely related wild progenitor Oryza barthii accessions have provided strong evidence to support a theory of independent domestication in African rice. Integrated genomic approaches have efficiently investigated many heterotic loci in hybrid rice underlying yield heterosis advantages and revealed the genomic architecture of rice heterosis. We conclude that in-depth unlocking of genetic variations among Oryza species will further enhance rice breeding.

The EIL transcription factor family in soybean: Genome-wide identification, expression profiling and genetic diversity analysis

The ETHYLENE INSENSITIVE3-LIKE (EIL) transcription factor family plays a critical role in the ethylene signaling pathway, which regulates a broad spectrum of plant growth and developmental processes, as well as defenses to myriad stresses. Although genome-wide analysis of this family has been carried out for several plant species, no comprehensive analysis of the EIL gene family in soybean has been reported so far. Furthermore, there are few studies on the functions of EIL genes in soybean. In this study, we identified 12 soybean (Gm) EIL genes, which we divided into three groups based on their phylogenetic relationships. We then detected their duplication status and found that most of the GmEIL genes have duplicated copies derived from two whole-genome duplication events. These duplicated genes underwent strong negative selection during evolution. We further analyzed the transcript profiles of GmEIL genes using the transcriptome data and found that their spatio-temporal and stress expression patterns varied considerably. For example, GmEIL1-GmEIL5 were found to be strongly expressed in almost every sample, while GmEIL8-GmEIL12 exhibited low expression, or were not expressed at all. Additionally, these genes showed different responses to dehydration, salinity and phosphate starvation. Finally, we surveyed genetic variations of these genes in 302 resequenced wild soybeans, landraces and improved soybean cultivars. Our data showed that most GmEIL genes are well conserved, and are not modified in domesticated or improved cultivars. Together, these findings provide a potentially valuable resource for characterizing the GmEIL gene family and lay the basis for further elucidation of their molecular mechanisms.

Exome Resequencing Reveals Evolutionary History, Genomic Diversity, and Targets of Selection in the Conifers Pinus taeda and Pinus elliottii

Loblolly pine (Pinus taeda) and slash pine (Pinus elliottii) are ecologically and economically important pine species that dominate many forest ecosystems in the southern United States, but like all conifers, the study of their genetic diversity and demographic history has been hampered by their large genome size. A small number of studies mainly based on candidate-gene sequencing have been reported for P. taeda to date, whereas none are available for P. elliottii. Targeted exome resequencing has recently enabled population genomics studies for conifers, approach used here to assess genomic diversity, signatures of selection, population structure, and demographic history of P. elliottii and P. taeda. Extensive similarities were revealed between these species: both species feature rapid linkage disequilibrium decay and high levels of genetic diversity. Moreover, genome-wide positive correlations for measures of genetic diversity between the species were also observed, likely due to shared structural genomic constraints. Also, positive selection appears to be targeting a common set of genes in both pines. Demographic history differs between both species, with only P. taeda being affected by a dramatic bottleneck during the last glacial period. The ability of P. taeda to recover from a dramatic reduction in population size while still retaining high levels of genetic diversity shows promise for other pines facing environmental stressors associated with climate change, indicating that these too may be able to adapt successfully to new future conditions even after a drastic population size contraction.

Interspecies evolutionary divergence in Liriodendron, evidence from the nucleotide variations of LcDHN-like gene

Background

Liriodendron is a genus of Magnoliaceae, which consists of two relict species, Liriodendron chinense and L. tulipifera. Although the morphologies are highly similar, the two species exhibit different adaptive capacity. Dehydrins (DHNs) are abiotic stresses resistant proteins in planta, which are associated with adaptive evolution. To better understand the evolution divergence between L. chinense and L. tulipifera and how DHN genes are associated with adaptation evolution, we firstly investigated the DNA polymorphisms of the LcDHN-like gene in 21 L. chinense and 6 L. tulipifera populations.

Results

A 707 bp LcDHN-like gene was cloned, which included a 477 bp open reading frame (ORF) and coding 158 amino acids. 311 LcDHN-like gDNA sequences were obtained from 70 L. chinense and 35 L. tulipifera individuals. The AMOVA and phylogenetic relationship analysis showed significant differences between the two species. A higher genetic diversity was observed in L. tulipifera compared to L. chinense, in consistent with the higher adaptive capacity of L. tulipifera. Our data also suggested that the LcDHN-like genes’ polymorphisms were under neutral mutation and purifying selection model in the L. chinense and L. tulipifera populations, respectively. The distinct expanding range and rate between the two species, haplotypes shared only in L.chinense’s nearby populations, and wide dispersals in L. tulipifera could contribute to the obscure east-west separation in L. chinense and entirely unordered phylogeny in L. tulipifera. The completely separated nonsynonymous substitution at position 875 and the higher range scope of aliphatic index in L. tulipifera populations may be related with its higher adaptive capacity. Taken together, our study suggests LcDHN-like gene is a potential mark gene responsible for adaptive evolution divergence in Liriodendron.

Conclusions

Significant differences and completely distinct haplogroups between L. chinense and L. tulipifera showed that the two species have evolved into different directions. The more widely distribution, earlier haplogroups divergence events, and richer SNPs variations in L. tulipifera could imply its stronger adaptation in this species. And potential effect of the allelic variations in LcDHN-like gene may reflect the difference of water stress and chill tolerance between L. chinense and L. tulipifera, which could provide some information for further adaption evolution studies of Liriodendron.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1318-7) contains supplementary material, which is available to authorized users.

Phylogeographic analyses of a widely distributed Populus davidiana: Further evidence for the existence of glacial refugia of cool-temperate deciduous trees in northern East Asia

Despite several phylogeographic studies had provided evidence to support the existence of glacial refugia of cool-temperate deciduous trees in northeast China, the species used in these studies were limited by the species ranges, which could not exclude the possibility that northern populations were the colonists from southern refugial populations during the last glacial maximum (LGM). Here, we estimated the nucleotide variation in Populus davidiana, a widespread species distributed in Eurasia. Three groups in northeast, central, and southwest China were constructed according to the simulation results from SAMOVA, composition of chloroplast haplotypes and structure results. We revealed that the northeast China had endemic haplotypes, the haplotypes and nucleotide diversity in northern regions were not lower than that in southern China, and this species has not experienced population expansion base on the estimation of Bayesian skyline plots. Ecological niche modeling (ENM) indicated that the northeast China had a high suitability score during the last glacial maximum. The combined evidence clearly demonstrated that northeastern and southwestern refugia were maintained across the current distributional range of P. davidiana during the LGM. The genetic differentiation between these two refugia might be mainly caused by differences of climate among these areas. The phylogeographic analyses of a widely distributed P. davidiana provided robust evidence to clarify the issue of refugia in northeast China, and these results are of great importance for understanding the influence of Quaternary glaciations on the distribution and evolution of species in East Asia.

Biotechnological and Digital Revolution for Climate-Smart Plant Breeding

Climate change, associated with global warming, extreme weather events, and increasing incidence of weeds, pests and pathogens, is strongly influencing major cropping systems. In this challenging scenario, miscellaneous strategies are needed to expedite the rate of genetic gains with the purpose of developing novel varieties. Large plant breeding populations, efficient high-throughput technologies, big data management tools, and downstream biotechnology and molecular techniques are the pillars on which next generation breeding is based. In this review, we describe the toolbox the breeder has to face the challenges imposed by climate change, remark on the key role bioinformatics plays in the analysis and interpretation of big “omics” data, and acknowledge all the benefits that have been introduced into breeding strategies with the biotechnological and digital revolution.

DNA methylation footprints during soybean domestication and improvement

BACKGROUND

In addition to genetic variation, epigenetic variation plays an important role in determining various biological processes. The importance of natural genetic variation to crop domestication and improvement has been widely investigated. However, the contribution of epigenetic variation in crop domestication at population level has rarely been explored.

RESULTS

To understand the impact of epigenetics on crop domestication, we investigate the variation of DNA methylation during soybean domestication and improvement by whole-genome bisulfite sequencing of 45 soybean accessions, including wild soybeans, landraces, and cultivars. Through methylomic analysis, we identify 5412 differentially methylated regions (DMRs). These DMRs exhibit characters distinct from those of genetically selected regions. In particular, they have significantly higher genetic diversity. Association analyses suggest only 22.54% of DMRs can be explained by local genetic variations. Intriguingly, genes in the DMRs that are not associated with any genetic variation are enriched in carbohydrate metabolism pathways.

CONCLUSIONS

This study provides a valuable map of DNA methylation across diverse accessions and dissects the relationship between DNA methylation variation and genetic variation during soybean domestication, thus expanding our understanding of soybean domestication and improvement.

Effects of Geological and Environmental Events on the Diversity and Genetic Divergence of Four Closely Related Pines: Pinus koraiensis, P. armandii, P. griffithii, and P. pumila

The effects of mountain uplift and environmental oscillations on nucleotide variability and species divergence remain largely unknown in East Asia. In this study, based on multiple nuclear DNA markers, we investigated the levels and patterns of nucleotide diversity and interspecific divergence in four closely related pines in China, i.e., Pinus koraiensis, P. armandii, P. griffithii, and P. pumila. The four pine taxa shared low levels of nucleotide polymorphisms at the species level. P. pumila had the highest silent nucleotide diversity (πsil = 0.00661) whereas P. griffithii had the lowest (πsil = 0.00175), while the levels of genetic polymorphism in P. armandii (πsil = 0.00508) and P. koraiensis (πsil = 0.00652) were intermediate between the other two species. Population genetic structure analysis showed that variations primarily existed within populations of the four pine species, presumably due to habitat fragmentation or the island-like distributions of Pinus species. Population divergence (FST) analysis showed that the genetic divergence between P. griffithii and P. koraiensis was much greater than that between P. koraiensis and the other two pines species. Isolation-with-migration analysis suggested that asymmetric gene flow had occurred between any two pairs of pine species. Phylogenetic analyses indicated that the four allied species split into two groups about 1.37 million years ago, where P. armandii and P. pumila were closer and clustered as sister species, whereas P. koraiensis and P. griffithii were clustered on another branch. Our results and those obtained in previous studies suggest that mountain uplift and geological climate oscillations may have led to the patterns of genetic divergence and nucleotide variations in these four pine species.

Evolutionary dynamics of quantitative variation in an adaptive trait at the regional scale: The case of zinc hyperaccumulation in Arabidopsis halleri

Metal hyperaccumulation in plants is an ecological trait whose biological significance remains debated, in particular because the selective pressures that govern its evolutionary dynamics are complex. One of the possible causes of quantitative variation in hyperaccumulation may be local adaptation to metalliferous soils. Here, we explored the population genetic structure of Arabidopsis halleri at fourteen metalliferous and nonmetalliferous sampling sites in southern Poland. The results were integrated with a quantitative assessment of variation in zinc hyperaccumulation to trace local adaptation. We identified a clear hierarchical structure with two distinct genetic groups at the upper level of clustering. Interestingly, these groups corresponded to different geographic subregions, rather than to ecological types (i.e., metallicolous vs. nonmetallicolous). Also, approximate Bayesian computation analyses suggested that the current distribution of A. halleri in southern Poland could be relictual as a result of habitat fragmentation caused by climatic shifts during the Holocene, rather than due to recent colonization of industrially polluted sites. In addition, we find evidence that some nonmetallicolous lowland populations may have actually derived from metallicolous populations. Meanwhile, the distribution of quantitative variation in zinc hyperaccumulation did separate metallicolous and nonmetallicolous accessions, indicating more recent adaptive evolution and diversifying selection between metalliferous and nonmetalliferous habitats. This suggests that zinc hyperaccumulation evolves both ways-towards higher levels at nonmetalliferous sites and lower levels at metalliferous sites. Our results open a new perspective on possible evolutionary relationships between A. halleri edaphic types that may inspire future genetic studies of quantitative variation in metal hyperaccumulation.

Comparative Transcriptome Analysis of Male and Female Conelets and Development of Microsatellite Markers in Pinus bungeana, an Endemic Conifer in China

The sex determination in gymnosperms is still poorly characterized due to the lack of genomic/transcriptome resources and useful molecular genetic markers. To enhance our understanding of the molecular mechanisms of the determination of sexual recognition of reproductive structures in conifers, the transcriptome of male and female conelets were characterized in a Chinese endemic conifer species, Pinus bungeana Zucc. ex Endl. The 39.62 Gb high-throughput sequencing reads were obtained from two kinds of sexual conelets. After de novo assembly of the obtained reads, 85,305 unigenes were identified, 53,944 (63.23%) of which were annotated with public databases. A total of 12,073 differentially expressed genes were detected between the two types of sexes in P. bungeana, and 5766 (47.76%) of them were up-regulated in females. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enriched analysis suggested that some of the genes were significantly associated with the sex determination process of P. bungeana, such as those involved in tryptophan metabolism, zeatin biosynthesis, and cysteine and methionine metabolism, and the phenylpropanoid biosynthesis pathways. Meanwhile, some important plant hormone pathways (e.g., the gibberellin (GA) pathway, carotenoid biosynthesis, and brassinosteroid biosynthesis (BR) pathway) that affected sexual determination were also induced in P. bungeana. In addition, 8791 expressed sequence tag-simple sequence repeats (EST-SSRs) from 7859 unigenes were detected in P. bungeana. The most abundant repeat types were dinucleotides (1926), followed by trinucleotides (1711). The dominant classes of the sequence repeat were A/T (4942) in mononucleotides and AT/AT (1283) in dinucleotides. Among these EST-SSRs, 84 pairs of primers were randomly selected for the characterization of potential molecular genetic markers. Finally, 19 polymorphic EST-SSR primers were characterized. We found low to moderate levels of genetic diversity (N_A = 1.754; H_O = 0.206; H_E = 0.205) across natural populations of P. bungeana. The cluster analysis revealed two distinct genetic groups for the six populations that were sampled in this endemic species, which might be caused by the fragmentation of habitats and long-term geographic isolation among different populations. Taken together, this work provides important insights into the molecular mechanisms of sexual identity in the reproductive organs of P. bungeana. The molecular genetic resources that were identified in this study will also facilitate further studies in functional genomics and population genetics in the Pinus species.

Adaptation in a Fibronectin Binding Autolysin of Staphylococcus saprophyticus

Human-pathogenic bacteria are found in a variety of niches, including free-living, zoonotic, and microbiome environments. Identifying bacterial adaptations that enable invasive disease is an important means of gaining insight into the molecular basis of pathogenesis and understanding pathogen emergence. Staphylococcus saprophyticus, a leading cause of urinary tract infections, can be found in the environment, food, animals, and the human microbiome. We identified a selective sweep in the gene encoding the Aas adhesin, a key virulence factor that binds host fibronectin. We hypothesize that the mutation under selection (aas_2206A>C) facilitates colonization of the urinary tract, an environment where bacteria are subject to strong shearing forces. The mutation appears to have enabled emergence and expansion of a human-pathogenic lineage of S. saprophyticus. These results demonstrate the power of evolutionary genomic approaches in discovering the genetic basis of virulence and emphasize the pleiotropy and adaptability of bacteria occupying diverse niches. IMPORTANCEStaphylococcus saprophyticus is an important cause of urinary tract infections (UTI) in women; such UTI are common, can be severe, and are associated with significant impacts to public health. In addition to being a cause of human UTI, S. saprophyticus can be found in the environment, in food, and associated with animals. After discovering that UTI strains of S. saprophyticus are for the most part closely related to each other, we sought to determine whether these strains are specially adapted to cause disease in humans. We found evidence suggesting that a mutation in the gene aas is advantageous in the context of human infection. We hypothesize that the mutation allows S. saprophyticus to survive better in the human urinary tract. These results show how bacteria found in the environment can evolve to cause disease.

Signatures of soft sweeps across the Dt1 locus underlying determinate growth habit in soya bean [Glycine max (L.) Merr.]

Determinate growth habit is an agronomically important trait associated with domestication in soya bean. Previous studies have demonstrated that the emergence of determinacy is correlated with artificial selection on four nonsynonymous mutations in the Dt1 gene. To better understand the signatures of the soft sweeps across the Dt1 locus and track the origins of the determinate alleles, we examined patterns of nucleotide variation in Dt1 and the surrounding genomic region of approximately 800 kb. Four local, asymmetrical hard sweeps on four determinate alleles, sized approximately 660, 120, 220 and 150 kb, were identified, which constitute the soft sweeps for the adaptation. These variable-sized sweeps substantially reflected the strength and timing of selection and indicated that the selection on the alleles had been completed rapidly within half a century. Statistics of EHH, iHS, H12 and H2/H1 based on haplotype data had the power to detect the soft sweeps, revealing distinct signatures of extensive long-range LD and haplotype homozygosity, and multiple frequent adaptive haplotypes. A haplotype network constructed for Dt1 and a phylogenetic tree based on its extended haplotype block implied independent sources of the adaptive alleles through de novo mutations or rare standing variation in quick succession during the selective phase, strongly supporting multiple origins of the determinacy. We propose that the adaptation of soya bean determinacy is guided by a model of soft sweeps and that this model might be indispensable during crop domestication or evolution.

Identification, genealogical structure and population genetics of S-alleles in Malus sieversii, the wild ancestor of domesticated apple

The self-incompatibility (SI) gene that is specifically expressed in pistils encodes the SI-associated ribonuclease (S-RNase), functioning as the female-specificity determinant of a gametophytic SI system. Despite extensive surveys in Malus domestica, the S-alleles have not been fully investigated for Malus sieversii, the primary wild ancestor of the domesticated apple. Here we screened the M. sieversii S-alleles via PCR amplification and sequencing, and identified 14 distinct alleles in this species. By contrast, nearly 40 are present in its close wild relative, Malus sylvestris. We further sequenced 8 nuclear genes to provide a neutral reference, and investigated the evolution of S-alleles via genealogical and population genetic analyses. Both shared ancestral polymorphism and an excess of non-synonymous substitution were detected in the S-RNases of the tribe Maleae in Rosaceae, indicating the action of long-term balancing selection. Approximate Bayesian Computations based on the reference neutral loci revealed a severe bottleneck in four of the six studied M. sieversii populations, suggesting that the low number of S-alleles found in this species is mainly the result of diversity loss due to a drastic population contraction. Such a bottleneck may lead to ambiguous footprints of ongoing balancing selection detected at the S-locus. This study not only elucidates the constituents and number of S-alleles in M. sieversii but also illustrates the potential utility of S-allele number shifts in demographic inference for self-incompatible plant species.

The Evolutionary Interplay between Adaptation and Self-Fertilization

Genome-wide surveys of nucleotide polymorphisms, obtained from next-generation sequencing, have uncovered numerous examples of adaptation in self-fertilizing organisms, especially regarding changes to climate, geography, and reproductive systems. Yet existing models for inferring attributes of adaptive mutations often assume idealized outcrossing populations, which risks mischaracterizing properties of these variants. Recent theoretical work is emphasizing how various aspects of self-fertilization affects adaptation, yet empirical data on these properties are lacking. We review theoretical and empirical studies demonstrating how self-fertilization alters the process of adaptation, illustrated using examples from current sequencing projects. We propose ideas for how future research can more accurately quantify aspects of adaptation in self-fertilizers, including incorporating the effects of standing variation, demographic history, and polygenic adaptation.

Analysis of large-scale next-generation sequencing datasets are finding more examples of adaptive evolution at the genomic level.

Advances in theoretical work has demonstrated how self-fertilisation affects different aspects of adaptation in these organisms, compared to outcrossers.

Current software and statistical methods do not take different mating systems into account, which risks mischaracterising the presence or strength of adaptive mutations from genome scans.

Development of new mathematical and statistical methods that explicitly consider self-fertilization and associated demographic effects will enable researchers to more accurately quantify adaptation in these organisms.

Distinct patterns of natural selection in Na+/H+ antiporter genes in Populus euphratica and Populus pruinosa

Salt tolerance genes constitute an important class of loci in plant genomes. Little is known about the extent to which natural selection in saline environments has acted upon these loci, and what types of nucleotide diversity such selection has given rise to. Here, we surveyed genetic diversity in three types of Na⁺/H⁺ antiporter gene (SOS, NhaD, and NHX, belonging to the cation/proton antiporter 1 family), which have well‐characterized essential roles in plant salt tolerance. Ten Na⁺/H⁺ antiporter genes and 16 neutral loci randomly selected as controls were sequenced from 17 accessions of two closely related members of the genus Populus, Populus euphratica and Populus pruinosa, section Turanga, which are native to northwest China. The results show that salt tolerance genes are common targets of natural selection in P. euphratica and P. pruinosa. Moreover, the patterns of nucleotide variation across the three types of Na⁺/H⁺ antiporter gene are distinctly different in these two closely related Populus species, and gene flow from P. pruinosa to P. euphratica is highly restricted. Our results suggest that natural selection played an important role in shaping the current distinct patterns of Na⁺/H⁺ antiporter genes, resulting in adaptive evolution in P. euphratica and P. pruinosa.

Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy

Next-generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either 'Landraces' or 'Wild and Weedy' genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP-glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well-characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.

Recent selection for self-compatibility in a population of Leavenworthia alabamica

The evolution of self-compatibility (SC) is the first step in the evolutionary transition in plants from outcrossing enforced by self-incompatibility (SI) to self-fertilization. In the Brassicaceae, SI is controlled by alleles of two tightly linked genes at the S-locus. Despite permitting inbreeding, mutations at the S-locus leading to SC may be selected if they provide reproductive assurance and/or gain a transmission advantage in a population when SC plants self- and outcross. Positive selection can leave a genomic signature in the regions physically linked to the focus of selection when selection has occurred recently. From an SC population of Leavenworthia alabamica with a known nonfunctional mutation at the S-locus, we collected sequence data from a ∼690 Kb region surrounding the S-locus, as well as from regions not linked to the S-locus. To test for recent positive selection acting at the S-locus, we examined polymorphism and the site-frequency spectra. Using forward simulations, we demonstrate that recent selection of the strength expected for SC at a locus formerly under balancing selection can generate patterns similar to those seen in our empirical data.

Genome-Wide Association Study in Arabidopsis thaliana of Natural Variation in Seed Oil Melting Point: A Widespread Adaptive Trait in Plants

Seed oil melting point is an adaptive, quantitative trait determined by the relative proportions of the fatty acids that compose the oil. Micro- and macro-evolutionary evidence suggests selection has changed the melting point of seed oils to covary with germination temperatures because of a trade-off between total energy stores and the rate of energy acquisition during germination under competition. The seed oil compositions of 391 natural accessions of Arabidopsis thaliana, grown under common-garden conditions, were used to assess whether seed oil melting point within a species varied with germination temperature. In support of the adaptive explanation, long-term monthly spring and fall field temperatures of the accession collection sites significantly predicted their seed oil melting points. In addition, a genome-wide association study (GWAS) was performed to determine which genes were most likely responsible for the natural variation in seed oil melting point. The GWAS found a single highly significant association within the coding region of FAD2, which encodes a fatty acid desaturase central to the oil biosynthesis pathway. In a separate analysis of 15 a priori oil synthesis candidate genes, 2 (FAD2 and FATB) were located near significant SNPs associated with seed oil melting point. These results comport with others' molecular work showing that lines with alterations in these genes affect seed oil melting point as expected. Our results suggest natural selection has acted on a small number of loci to alter a quantitative trait in response to local environmental conditions.

Global investigation of the co-evolution of MIRNA genes and microRNA targets during soybean domestication

Although the selection of coding genes during plant domestication has been well studied, the evolution of MIRNA genes (MIRs) and the interaction between microRNAs (miRNAs) and their targets in this process are poorly understood. Here, we present a genome-wide survey of the selection of MIRs and miRNA targets during soybean domestication and improvement. Our results suggest that, overall, MIRs have higher evolutionary rates than miRNA targets. Nonetheless, they do demonstrate certain similar evolutionary patterns during soybean domestication: MIRs and miRNA targets with high expression and duplication status, and with greater numbers of partners, exhibit lower nucleotide divergence than their counterparts without these characteristics, suggesting that expression level, duplication status, and miRNA-target interaction are essential for evolution of MIRs and miRNA targets. Further investigation revealed that miRNA-target pairs that are subjected to strong purifying selection have greater similarities than those that exhibited genetic diversity. Moreover, mediated by domestication and improvement, the similarities of a large number of miRNA-target pairs in cultivated soybean populations were increased compared to those in wild soybeans, whereas a small number of miRNA-target pairs exhibited decreased similarity, which may be associated with the adoption of particular domestication traits. Taken together, our results shed light on the co-evolution of MIRs and miRNA targets during soybean domestication.

Selection for population-specific adaptation shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post-glacial colonization

Spatially varying selection can lead to population-specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location-specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine populations of the perennial herb Arabidopsis lyrata, which has a wide but patchy distribution in temperate and boreal regions of the northern hemisphere. The populations differ in their recent population demographic and colonization histories and current environmental conditions, especially in the growing season length. We searched for population-specific molecular signatures of directional selection by comparing a set of candidate flowering time loci with a genomic reference set within each population using multiple approaches and contrasted the patterns of different populations. The candidate loci possessed approximately 20% of the diversity of the reference loci. On average the flowering time loci had more rare alleles (a smaller Tajima's D) and an excess of highly differentiated sites relative to the reference, suggesting positive selection. The strongest signal of selection was detected in photoperiodic pathway loci in the colonizing populations of Northwestern Europe, whereas no evidence of positive selection was detected in the Central European populations. These findings emphasized the population-specific nature of selection and suggested that photoperiodic adaptation was important during postglacial colonization of the species.