Population genomics has transformed our understanding of how natural selection shapes plant genomes. The explosion of whole-genome resequencing data has enabled estimates of nucleotide diversity across genomes, clarified how selection interacts with recombination and demography, and broadened inference beyond crops and model species to virtually any plant system. Here, we synthesize key lessons and outstanding challenges concerning the action of natural selection on plant genomes. One message is that purifying selection is a pervasive selective force acting against deleterious mutations and structural variants, but its efficacy varies predictably and is often relaxed after demographic contractions, including domestication bottlenecks, range expansions, shifts in mating systems, and polyploid formation. Adaptation also routinely shapes genetic diversity, as evidenced by the detection of selective sweeps. Swept genes have functional biases, but many outstanding questions about adaptive variation remain, including the selection coefficients of adaptive alleles, whether selection typically acts on segregating variants or de novo mutations, and how often selection is polygenic. As with polygenic selection, our knowledge about balancing selection is limited, due in part to challenges in its detection. It is known, however, to act on disease-resistance genes and genes that govern breeding systems. Finally, an emerging theme in plant population genomics is the interplay between introgression and adaptation, but it remains challenging to link introgression confidently to fitness, and further study requires an expanded, multispecies scale. This review reveals the power, and some of the limits, of population genomics to infer the dynamics of selection on plant genomes.

To exploit allelic variation in Hordeum vulgare subsp. spontaneum, the Wild Barley Diversity Collection was subjected to paired-end Illumina sequencing at ∼9 × depth and evaluated for several agronomic traits. We discovered 240.2 million single nucleotide polymorphisms (SNPs) after alignment to the Morex V3 assembly and 24.4 million short (1 to 50 bp) insertions and deletions. A genome-wide association study of lemma color identified one marker-trait association (MTA) on chromosome 1H close to HvBlp, the cloned gene controlling black lemma. Four MTAs were identified for seedling stem rust resistance, including 2 novel loci on chromosomes 1H and 6H and one co-locating to the complex RMRL1-RMRL2 locus on 5H. The whole-genome sequence data described herein will facilitate the identification and utilization of new alleles for barley improvement.

Heat tolerance is an important trait in cowpea, a crop that is the primary protein source for a large portion of the human population in sub-Saharan Africa. Cultivated, landrace, semi-wild, and wild cowpea grow across the region in diverse climatic conditions. This study used environmental association (envGWAS) and allele-frequency outlier approaches across a panel of 580 gene bank accessions to identify genomic regions associated with adaptation to heat and limited precipitation. Allele frequency outliers are detected independent of potential selective factors driving differentiation; we used a ranking-based approach to identify the climate variables most associated with variants among outliers. Precipitation-related variables dominated the signals we identified for envGWAS and allele frequency outliers. We identified variants on all 11 chromosomes that are putatively associated with cowpea adaptation to higher-temperature environments. The overlap between variants associated with low precipitation and high temperature suggests that these traits may be inextricably linked in cowpea. The Sahel region is the source of many accessions with derived variants associated with high temperatures, suggesting that accessions from this region could contribute heat tolerance alleles for cowpea improvement.

Multiple studies have reported genetic evidence of crop-to-wild introgression in phenotypically wild accessions of wild barley (Hordeum vulgare ssp. spontaneum). We examined 318 Wild Barley Diversity Collection (WBDC) accessions for evidence of introgression from domesticated barley. Using SNP genotyping data, we performed local ancestry inference between the WBDC accessions and domesticated barley to identify genomic regions with evidence of introgression. Using the genomic intervals for well-characterised genes involved in domestication and improvement, we examined the evidence for introgression at genomic regions potentially important for maintaining a wild phenotype. Our analysis revealed that nearly 16% (48 of 318) of WBDC accessions showed evidence of introgression from domesticated barley, with up to 16.6% of the genome introgressed. All accessions identified as introgressed based on domestication-related phenotypes show clear genetic evidence of introgression. The size of runs of identity by state and local ancestry inference suggests that most introgression did not occur recently. This study suggests a long history of genetic exchange between wild and domesticated barley, highlighting the potential for introgression to influence the genetic makeup and future adaptation of wild populations, with implications for plant conservation strategies.

Climate change is threatening agricultural production across the globe. Germplasm collections provide an opportunity to explore where variation exists with important crop species. Genome environment association (GEA) is a standard approach for investigating the genetic basis of adaptation to natural environments. While these analyses provide insight into local adaptation, they have not been widely adopted in breeding or conservation programs. This may be attributable to the difficulty in identifying the best individuals for transplantation/relocation in conservation efforts or identification of the best parents in breeding programs. To explore the potential utility in future breeding programs, we used the cereal crop - barley (Hordeum vulgare L.) due to its wide adaptability to different environments and agroecologies, ranging from marginal and low input fields to high-productive farms. Here, we conduct environmental genomic selection (EGS) on 753 landrace barley accessions using a mini-core of 31 landrace accessions and a de-novo core of 100 as the training populations. Since local adaptation to the environment is polygenic, a whole-genome approach is likely to be more accurate for selection. Here we show how an integrative approach coupling environmental genomic selection and species distribution modelling can help identify key parents for adaptation to specific environmental variables.

The nature and effect of mutations are of fundamental importance to the evolutionary process. The generation of mutations with mutagens has also played important roles in genetics. Applications of mutagens include dissecting the genetic basis of trait variation, inducing desirable traits in crops, and understanding the nature of genetic load. Previous studies of sodium azide-induced mutations have reported single nucleotide variants (SNVs) found in individual genes. To characterize the nature of mutations induced by sodium azide, we analyze whole-genome sequencing (WGS) of 11 barley lines derived from sodium azide mutagenesis, where all lines were selected for diminution of plant fitness owing to induced mutations. We contrast observed mutagen-induced variants with those found in standing variation in WGS of 13 barley landraces. Here, we report indels that are two orders of magnitude more abundant than expected based on nominal mutation rates. We found induced SNVs are very specific, with C → T changes occurring in a context followed by another C on the same strand (or the reverse complement). The codons most affected by the mutagen include the sodium azide-specific CC motif (or the reverse complement), resulting in a handful of amino acid changes and few stop codons. The specific nature of induced mutations suggests that mutagens could be chosen based on experimental goals. Sodium azide would not be ideal for gene knockouts but will create many missense mutations with more subtle effects on protein function.

Heat tolerance is an important trait in cowpea, a crop that constitutes the primary protein source for a large portion of the human population in sub-Saharan Africa. Cowpea grows across this region, with cultivated, landrace, semi-wild, and wild cowpeas germplasm growing across diverse climatic conditions. This study used environmental association (envGWAS) and allele frequency outlier approaches in a panel of 580 gene bank accessions to identify genomic regions associated with heat and limited precipitation. Because allele frequency outliers are detected independent of potential selection factors driving differentiation, we used a ranking-based approach to identify the climate variables most associated with variants among outliers. Precipitation-related variables dominated the signals we identified for envGWAS and allele frequency outliers. We found variants on all eleven chromosomes putatively associated with the adaptation of cowpea to higher-temperature environments. The considerable overlap between variants associated with low precipitation and high temperature suggests that these traits may be inextricably linked in cowpea. The Sahel region is the source of many accessions with derived variants associated with high temperature, suggesting the potential for accessions from this region to contribute to heat tolerance alleles for cowpea improvement. ### Competing Interest Statement The authors have declared no competing interest.

The common bean (Phaseolus vulgaris L.) is a crucial legume crop and an ideal evolutionary model to study adaptive diversity in wild and domesticated populations. Here, we present a common bean pan-genome based on five high-quality genomes and whole-genome reads representing 339 genotypes. It reveals similar to 234 Mb of additional sequences containing 6,905 protein-coding genes missing from the reference, constituting 49% of all presence/absence variants (PAVs). More non-synonymous mutations are found in PAVs than core genes, probably reflecting the lower effective population size of PAVs and fitness advantages due to the purging effect of gene loss. Our results suggest pan-genome shrinkage occurred during wild range expansion. Selection signatures provide evidence that partial or complete gene loss was a key adaptive genetic change in common bean populations with major implications for plant adaptation. The pan-genome is a valuable resource for food legume research and breeding for climate change mitigation and sustainable agriculture.

Direct observation is central to our understanding of adaptation, but evolution is rarely documented in a large, multicellular organism for more than a few generations. In this study, we observed evolution across a century-scale competition experiment, barley composite cross II (CCII). CCII was founded in 1929 in Davis, California, with thousands of genotypes, but we found that natural selection has massively reduced genetic diversity, leading to a single lineage constituting most of the population by generation 50. Selection favored alleles originating from climates similar to that of Davis and targeted loci contributing to reproductive development, including the barley diversification loci Vrs1 , HvCEN , Ppd-H1 , and Vrn-H2 . Our findings point to selection as the predominant force shaping genomic variation in one of the world’s oldest biological experiments.

Plant conservation hinges on preserving biodiversity, which is crucial for long-term adaptation. Multiple studies have reported genetic evidence of crop-to-wild introgression in phenotypically wild accessions of wild barley ( Hordeum vulgare ssp. spontaneum ). We examined 318 Wild Barley Diversity Collection (WBDC) accessions for evidence of introgression from cultivated barley. Using SNP genotype and exome capture data, we performed local ancestry inference between the 318 WBDC accessions and cultivated barley to identify genomic regions with evidence of introgression. Using the genomic intervals for well-characterized genes involved in domestication and improvement, we examined the evidence for introgression at genomic regions potentially important for maintaining a wild phenotype. Our analysis revealed that nearly 16% (48 of 318) of WBDC accessions showed evidence of introgression from cultivated barley, and up to 16.6% of the genome has been introgressed. All accessions identified as introgressed based on domestication-related phenotypes show clear genetic evidence of introgression. The size of runs of identity by state and local ancestry inference suggests that most introgression did not occur recently. This study suggests a long history of genetic exchange between wild and cultivated barley, highlighting the potential for introgression to influence the genetic makeup and future adaptation of wild populations, with implications for plant conservation strategies. ### Competing Interest Statement The authors have declared no competing interest.

The genetic basis of adaptation is a fundamental question in evolutionary genetics. Environmental association analysis (EAA) and various allele frequency comparisons in genomic environmental association (GEA) have become standard approaches for investigating the genetic basis of adaptation to natural environments. While these analyses provide insight into local adaptation, they have not been widely adopted in breeding or conservation programs. This may be attributable to the difficulty in identifying the best individuals for transplantation/relocation in conservation efforts or identification of the best parents in breeding programs. To explore the use of EAA and GEA for future breeding programs, we used a cereal crop - barley (Hordeum vulgare L.) as our case-study species due to its wide adaptability to different environments and agro-ecologies, ranging from marginal and low input fields to high-productive farms. Here, we use publicly available data to conduct environmental genomic selection (EGS) on 753 landrace barley accessions using a mini-core of 31 landrace accessions and a de-novo core of 100 as the training populations. Environmental genomic selection is to environmental association analysis (EAA) what genomic selection is to genome-wide association studies (GWAS). Since local adaptation to the environment is polygenic, a whole-genome approach is likely to be more accurate for selecting for environmental adaptation. Here we show distinct genetic background and population differences and how an integrative approach coupling environmental genomic selection and species distribution modelling can help identify key parents for breeding for adaptation to specific environmental variables and geographies to minimize linkage drag. ### Competing Interest Statement The authors have declared no competing interest.

Fusarium head blight (FHB) of barley (Hordeum vulgare) causes yield losses and accumulation of trichothecene mycotoxins (e.g. deoxynivalenol [DON]) in grains. Glucosylation of DON to the nontoxic DON-3-O-glucoside (D3G) is catalyzed by UDP-glucosyltransferases (UGTs), such as barley UGT13248. We explored the natural diversity of UGT13248 in 496 barley accessions and showed that all carried potential functional alleles of UGT13248, as no genotypes showed strongly increased seedling sensitivity to DON. From a TILLING population, we identified 2 mutant alleles (T368I and H369Y) that, based on protein modeling, likely affect the UDP-glucose binding of UGT13248. In DON feeding experiments, DON-to-D3G conversion was strongly reduced in spikes of these mutants compared to controls, and plants overexpressing UGT13248 showed increased resistance to DON and increased DON-to-D3G conversion. Moreover, field-grown plants carrying the T368I or H369Y mutations inoculated with Fusarium graminearum showed increased FHB disease severity and reduced D3G production. Barley is generally considered to have type II resistance that limits the spread of F. graminearum from the infected spikelet to adjacent spikelets. Point inoculation experiments with F. graminearum showed increased infection spread in T368I and H369Y across the spike compared to wild type, while overexpression plants showed decreased spread of FHB symptoms. Confocal microscopy revealed that F. graminearum spread to distant rachis nodes in T368I and H369Y mutants but was arrested at the rachis node of the inoculated spikelet in wild-type plants. Taken together, our data reveal that UGT13248 confers type II resistance to FHB in barley via conjugation of DON to D3G.

Conservation of crop wild relatives is critical for plant breeding and food security. The lack of clarity on the genetic factors that lead to endangered status or extinction create difficulties when attempting to develop concrete recommendations for conserving a citrus wild relative: the wild relatives of crops. Here, we evaluate the conservation of wild kumquat (Fortunella hindsii) using genomic, geographical, environmental, and phenotypic data, and forward simulations. Genome resequencing data from 73 accessions from the Fortunella genus were combined to investigate population structure, demography, inbreeding, introgression, and genetic load. Population structure was correlated with reproductive type (i.e., sexual and apomictic) and with a significant differentiation within the sexually reproducing population. The effective population size for one of the sexually reproducing subpopulations has recently declined to ~1,000, resulting in high levels of inbreeding. In particular, we found that 58% of the ecological niche overlapped between wild and cultivated populations and that there was extensive introgression into wild samples from cultivated populations. Interestingly, the introgression pattern and accumulation of genetic load may be influenced by the type of reproduction. In wild apomictic samples, the introgressed regions were primarily heterozygous, and genome-wide deleterious variants were hidden in the heterozygous state. In contrast, wild sexually reproducing samples carried a higher recessive deleterious burden. Furthermore, we also found that sexually reproducing samples were self-incompatible, which prevented the reduction of genetic diversity by selfing. Our population genomic analyses provide specific recommendations for distinct reproductive types and monitoring during conservation. This study highlights the genomic landscape of a wild relative of citrus and provides recommendations for the conservation of crop wild relatives.

Crop production is becoming an increasing challenge as the global population grows and the climate changes. Modern cultivated crop species are selected for productivity under optimal growth environments and have often lost genetic variants that could allow them to adapt to diverse, and now rapidly changing, environments. These genetic variants are often present in their closest wild relatives, but so are less desirable traits. How to preserve and effectively utilize the rich genetic resources that crop wild relatives offer while avoiding detrimental variants and maladaptive genetic contributions is a central challenge for ongoing crop improvement. This Essay explores this challenge and potential paths that could lead to a solution.

Cowpea, Vigna unguiculata L. Walp., is a diploid warm-season legume of critical importance as both food and fodder in sub-Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America, and East to Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six subpopulations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. In the most complete assembly (IT97K-499-35), 26,026 core and 4963 noncore genes were identified, with 35,436 pan genes when considering all seven accessions. GO terms associated with response to stress and defense response were highly enriched among the noncore genes, while core genes were enriched in terms related to transcription factor activity, and transport and metabolic processes. Over 5 million single nucleotide polymorphisms (SNPs) relative to each assembly and over 40 structural variants >1 Mb in size were identified by comparing genomes. Vu10 was the chromosome with the highest frequency of SNPs, and Vu04 had the most structural variants. Noncore genes harbor a larger proportion of potentially disruptive variants than core genes, including missense, stop gain, and frameshift mutations; this suggests that noncore genes substantially contribute to diversity within domesticated cowpea.

Potato is one of the most important food crops in the world and, in contrast to other staples, has not seen large improvements in yield. Agha, Shannon, and Morrell preview an article recently published in Cell, "Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding,"which advances potato breeding strategies via a genetic approach.

Domesticated crops have been disseminated by humans over vast geographic areas. Common bean ( Phaseolus vulgaris L.) was introduced in Europe after 1492. Here, by combining whole-genome profiling, metabolic fingerprinting and phenotypic characterisation, we show that the first common bean cultigens successfully introduced into Europe were of Andean origin, after Francisco Pizarro’s expedition to northern Peru in 1529. We reveal that hybridisation, selection and recombination have shaped the genomic diversity of the European common bean in parallel with political constraints. There is clear evidence of adaptive introgression into the Mesoamerican-derived European genotypes, with 44 Andean introgressed genomic segments shared by more than 90% of European accessions and distributed across all chromosomes except PvChr11. Genomic scans for signatures of selection highlight the role of genes relevant to flowering and environmental adaptation, suggesting that introgression has been crucial for the dissemination of this tropical crop to the temperate regions of Europe.

SUMMARYThe distribution of recombination events along large cereal chromosomes is uneven and is generally restricted to gene‐rich telomeric ends. To understand how the lack of recombination affects diversity in the large pericentromeric regions, we analysed deep exome capture data from a final panel of 815 Hordeum vulgare (barley) cultivars, landraces and wild barleys, sampled from across their eco‐geographical ranges. We defined and compared variant data across the pericentromeric and non‐pericentromeric regions, observing a clear partitioning of diversity both within and between chromosomes and germplasm groups. Dramatically reduced diversity was found in the pericentromeres of both cultivars and landraces when compared with wild barley. We observed a mixture of completely and partially differentiated single‐nucleotide polymorphisms (SNPs) between domesticated and wild gene pools, suggesting that domesticated gene pools were derived from multiple wild ancestors. Patterns of genome‐wide linkage disequilibrium, haplotype block size and number, and variant frequency within blocks showed clear contrasts among individual chromosomes and between cultivars and wild barleys. Although most cultivar chromosomes shared a single major pericentromeric haplotype, chromosome 7H clearly differentiated the two‐row and six‐row types associated with different geographical origins. Within the pericentromeric regions we identified 22 387 non‐synonymous SNPs, 92 of which were fixed for alternative alleles in cultivar versus wild accessions. Surprisingly, only 29 SNPs found exclusively in the cultivars were predicted to be ‘highly deleterious’. Overall, our data reveal an unconventional pericentromeric genetic landscape among distinct barley gene pools, with different evolutionary processes driving domestication and diversification.

The mutagenic effects of ionizing radiation have been used for decades to create novel variants in experimental populations. Fast neutron (FN) bombardment as a mutagen has been especially widespread in plants, with extensive reports describing the induction of large structural variants, i.e., deletions, insertions, inversions, and translocations. However, the full spectrum of FN-induced mutations is poorly understood. We contrast small insertions and deletions (indels) observed in 27 soybean lines subject to FN irradiation with the standing indels identified in 107 diverse soybean lines. We use the same populations to contrast the nature and context (bases flanking a nucleotide change) of single-nucleotide variants. The accumulation of new single-nucleotide changes in FN lines is marginally higher than expected based on spontaneous mutation. In FN-treated lines and in standing variation, C→T transitions and the corresponding reverse complement G→A transitions are the most abundant and occur most frequently in a CpG local context. These data indicate that most SNPs identified in FN lines are likely derived from spontaneous de novo processes in generations following mutagenesis rather than from the FN irradiation mutagen. However, small indels in FN lines differ from standing variants. Short insertions, from 1 to 6 bp, are less abundant than in standing variation. Short deletions are more abundant and prone to induce frameshift mutations that should disrupt the structure and function of encoded proteins. These findings indicate that FN irradiation generates numerous small indels, increasing the abundance of loss-of-function mutations that impact single genes.