Adaptation and the Geographic Spread of Crop Species

Crops are plant species that were domesticated starting about 11,000 years ago from several centers of origin, most prominently the Fertile Crescent, East Asia, and Mesoamerica. From their domestication centers, these crops spread across the globe and had to adapt to differing environments as a result of this dispersal. We discuss broad patterns of crop spread, including the early diffusion of crops associated with the rise and spread of agriculture, the later movement via ancient trading networks, and the exchange between the Old and New Worlds over the last ∼550 years after the European colonization of the Americas. We also examine the various genetic mechanisms associated with the evolutionary adaptation of crops to their new environments after dispersal, most prominently seasonal adaptation associated with movement across latitudes, as well as altitudinal, temperature, and other environmental factors.

Finding the right balance: The enduring role of florigens during cereal inflorescence development and their influence on fertility

Flowering is a vital process in a plant's lifecycle and variation for flowering-time has helped cereals adapt to diverse environments. Much cereal research has focused on understanding how flowering signals, or florigens, regulate the floral transition and timing of ear emergence. However, flowering genes also perform an enduring role during inflorescence development, with genotypes that elicit a weaker flowering signal producing more elaborately branched inflorescences with extra floret-bearing spikelets. While this outcome indicates that variable expression of flowering genes could boost yield potential, further analysis has shown that dampened florigen levels can compromise fertility, negating the benefit of extra grain-producing sites. Here, we discuss ways that florigens contribute to early and late inflorescence development, including their influence on branch/spikelet architecture and fertility. We propose that a deeper understanding of the role for florigens during inflorescence development could be used to balance the effects of florigens throughout flowering to improve productivity.

Genetic mapping reveals new loci and alleles for flowering time and plant height using the double round-robin population of barley

Flowering time and plant height are two critical determinants of yield potential in barley (Hordeum vulgare). Despite their role in plant physiological regulation, a complete overview of the genetic complexity of flowering time and plant height regulation in barley is still lacking. Using a double round-robin population originated from the crossings of 23 diverse parental inbred lines, we aimed to determine the variance components in the regulation of flowering time and plant height in barley as well as to identify new genetic variants by single and multi-population QTL analyses and allele mining. Despite similar genotypic variance, we observed higher environmental variance components for plant height than flowering time. Furthermore, we detected new QTLs for flowering time and plant height. Finally, we identified a new functional allelic variant of the main regulatory gene Ppd-H1. Our results show that the genetic architecture of flowering time and plant height might be more complex than reported earlier and that a number of undetected, small effect, or low-frequency genetic variants underlie the control of these two traits.

early maturity 7 promotes early flowering by controlling the light input into the circadian clock in barley

Breeding for variation in photoperiod response is crucial to adapt crop plants to various environments. Plants measure changes in day length by the circadian clock, an endogenous timekeeper that allows plants to anticipate changes in diurnal and seasonal light-dark cycles. Here, we describe the early maturity 7 (eam7) locus in barley (Hordeum vulgare), which interacts with PHOTOPERIOD 1 (Ppd-H1) to cause early flowering under non-inductive short days. We identify LIGHT-REGULATED WD 1 (LWD1) as a putative candidate to underlie the eam7 locus in barley as supported by genetic mapping and CRISPR-Cas9-generated lwd1 mutants. Mutations in eam7 cause a significant phase advance and a misregulation of core clock and clock output genes under diurnal conditions. Early flowering was linked to an upregulation of Ppd-H1 during the night and consequent induction of the florigen FLOWERING LOCUS T1 under short days. We propose that EAM7 controls photoperiodic flowering in barley by controlling the light input into the clock and diurnal expression patterns of the major photoperiod response gene Ppd-H1.

Photoperiod sensitivity of Ppd-H1 and ppd-H1 isogenic lines of a spring barley cultivar: exploring extreme photoperiods

Barley is a long-day plant with a major gene (PPD-H1) that determines its photoperiod sensitivity. Under long days (i.e. 16 h), flowering occurs earlier in sensitive (Ppd-H1) than in insensitive (ppd-H1) genotypes, while under short days (i.e. 12 h) both flower late and more or less simultaneously. We hypothesized that (i) the sensitive line should flower later than the insensitive line under very short days (<12 h), and (ii) both the sensitive and insensitive lines should have similar phenology under very long days (>18 h). When comparing a pair of spring isogenic lines for sensitive and insensitive PPD-H1 alleles (introgressing the PPD-H1 allele into the barley cultivar 'WI4441'), we found responses fully in line with expectations for the commonly explored range from 12 to 16-18 h. When the responses were extended to very short days, sensitivity increased noticeably, and time to flowering of the sensitive line was longer than that of the insensitive one. Under very long days, the sensitive line did not respond further (it seemed to have reached its minimum time to flowering under a 16 h period), while the insensitive line continued shortening its time to flowering until c. 21 h. Consequently, both lines flowered similarly under very long days, which opens opportunities to easily test for differences in earliness per se, as in wheat.

Diversity of gene expression responses to light quality in barley

Light quality influence on barley development is poorly understood. We exposed three barley genotypes with either sensitive or insensitive response to two light sources producing different light spectra, fluorescent bulbs, and metal halide lamps, keeping constant light intensity, duration, and temperature. Through RNA-seq, we identified the main genes and pathways involved in the genotypic responses. A first analysis identified genotypic differences in gene expression of development-related genes, including photoreceptors and flowering time genes. Genes from the vernalization pathway of light quality-sensitive genotypes were affected by fluorescent light. In particular, vernalization-related repressors reacted differently: HvVRN2 did not experience relevant changes, whereas HvOS2 expression increased under fluorescent light. To identify the genes primarily related to light quality responses, and avoid the confounding effect of plant developmental stage, genes influenced by development were masked in a second analysis. Quantitative expression levels of PPD-H1, which influenced HvVRN1 and HvFT1, explained genotypic differences in development. Upstream mechanisms (light signaling and circadian clock) were also altered, but no specific genes linking photoreceptors and the photoperiod pathway were identified. The variety of light-quality sensitivities reveals the presence of possible mechanisms of adaptation of winter and facultative barley to latitudinal variation in light quality, which deserves further research.

Origin, variation, and selection of natural alleles controlling flowering and adaptation in wild and cultivated soybean

Soybean (Glycine max) is an economically important crop worldwide, serving as a major source of oil and protein for human consumption and animal feed. Cultivated soybean was domesticated from wild soybean (Glycine soja) which both species are highly sensitive to photoperiod and can grow over a wide geographical range. The extensive ecological adaptation of wild and cultivated soybean has been facilitated by a series of genes represented as quantitative trait loci (QTLs) that control photoperiodic flowering and maturation. Here, we review the molecular and genetic basis underlying the regulation of photoperiodic flowering in soybean. Soybean has experienced both natural and artificial selection during adaptation to different latitudes, resulting in differential molecular and evolutionary mechanisms between wild and cultivated soybean. The in-depth study of natural and artificial selection for the photoperiodic adaptability of wild and cultivated soybean provides an important theoretical and practical basis for enhancing soybean adaptability and yield via molecular breeding. In addition, we discuss the possible origin of wild soybean, current challenges, and future research directions in this important topic.

Sense in sensitivity: difference in the meaning of photoperiod-insensitivity between wheat and barley

The description of long photoperiod sensitivity in wheat and barley is a cause of confusion for researchers working in these crops, usually accustomed to free exchange of physiological and genetic knowledge of such similar crops. Indeed, wheat and barley scientists customarily quote studies of either crop species when researching one of them. Among their numerous similarities the main gene controlling that response is the same in both crops (PPD1; PPD-H1 in barley and PPD-D1 in hexaploid wheat). However, the photoperiod responses are different: (i) the main dominant allele inducing shorter time to anthesis is the insensitive allele in wheat (Ppd-D1a) but the sensitive allele in barley (Ppd-H1) (i.e. sensitivity to photoperiod produces opposite effects on time to heading in wheat and barley), (ii) the main "insensitive" allele in wheat, Ppd-D1a, does confer insensitivity, whilst that of barley reduces the sensitivity but still responds to photoperiod. The different behaviour of PPD1 genes in wheat and barley is put in a common framework based on the similarities and differences of the molecular bases of their mutations, which include polymorphism at gene expression levels, copy number variation, and sequence of coding regions. This common perspective sheds light on a source on confusion for cereal researchers, and prompts us to recommend accounting for the photoperiod sensitivity status of the plant materials when doing research on genetic control of phenology. Finally, we provide advice to facilitate the management of natural PPD1 diversity in breeding programs and suggest targets for further modification through gene editing, based on mutual knowledge on the two crops.

Altered regulation of flowering expands growth ranges and maximizes yields in major crops

Flowering time influences reproductive success in plants and has a significant impact on yield in grain crops. Flowering time is regulated by a variety of environmental factors, with daylength often playing an important role. Crops can be categorized into different types according to their photoperiod requirements for flowering. For instance, long-day crops include wheat (Triticum aestivum), barley (Hordeum vulgare), and pea (Pisum sativum), while short-day crops include rice (Oryza sativa), soybean (Glycine max), and maize (Zea mays). Understanding the molecular regulation of flowering and genotypic variation therein is important for molecular breeding and crop improvement. This paper reviews the regulation of flowering in different crop species with a particular focus on how photoperiod-related genes facilitate adaptation to local environments.

Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding

Rice bean (Vigna umbellata) is an underexploited domesticated legume crop consumed for dietary protein in Asia, yet little is known about the genetic diversity of this species. Here, we present a high-quality reference genome for a rice bean landrace (FF25) built using PacBio long-read data and a Hi-C chromatin interaction map, and assess the phylogenetic position and speciation time of rice bean within the Vigna genus. We sequence 440 landraces (two core collections), and GWAS based on data for growth sites at three widely divergent latitudes reveal loci associated with flowering and yield. Loci harboring orthologs of FUL (FRUITFULL), FT (FLOWERING LOCUS T), and PRR3 (PSEUDO-RESPONSE REGULATOR 3) contribute to the adaptation of rice bean from its low latitude center of origin towards higher latitudes, and the landraces which pyramid early-flowering alleles for these loci display maximally short flowering times. We also demonstrate that copy-number-variation for VumCYP78A6 can regulate seed-yield traits. Intriguingly, 32 landraces collected from a mountainous region in South-Central China harbor a recently acquired InDel in TFL1 (TERMINAL FLOWER1) affecting stem determinacy; these materials also have exceptionally high values for multiple human-desired traits and could therefore substantially advance breeding efforts to improve rice bean.

Rice bean is an underexploited legume crop that has many desirable properties against bio and abiotic stresses. Here, the authors report the genome assembly of this species, conduct population genetics studies and reveal the genetic variations associated with adaptation and yield traits.

The Domestication of the Seasons: The Exploitation of Variations in Crop Seasonality Responses by Later Prehistoric Farmers

Discussions of domestication and its associated genetic traits has focused upon dispersal mechanisms, for example in the rachis structure of cereals. Here we consider another trait of importance to domesticated crops – their seasonality response. We particularly consider flowering response to changing daylength, and how that relates to domesticated species that are carried by farmers considerable distances from their regions of origin. We consider the implications of cultivating crops in regions whose seasonality patterns contrast with those of the crop’s region of origin, and consider the consequent genetic changes. Reference is made to the particular case of barley, and a discussion of archaeogenetic research into its photoperiod response mechanism is provided.

Environment-mediated mutagenetic interference on genetic stabilization and circadian rhythm in plants

Many mortal organisms on this planet have developed the potential to merge all internal as well as external environmental cues to regulate various processes running inside organisms and in turn make them adaptive to the environment through the circadian clock. This moving rotator controls processes like activation of hormonal, metabolic, or defense pathways, initiation of flowering at an accurate period, and developmental processes in plants to ensure their stability in the environment. All these processes that are under the control of this rotating wheel can be changed either by external environmental factors or by an unpredictable phenomenon called mutation that can be generated by either physical mutagens, chemical mutagens, or by internal genetic interruption during metabolic processes, which alters normal functionality of organisms like innate immune responses, entrainment of the clock, biomass reduction, chlorophyll formation, and hormonal signaling, despite its fewer positive roles in plants like changing plant type, loss of vernalization treatment to make them survivable in different latitudes, and defense responses during stress. In addition, with mutation, overexpression of gene components sometimes supresses mutation effect and promote normal circadian genes abundance in the cell, while sometimes it affects circadian functionality by generating arrhythmicity and shows that not only mutation but overexpression also effects normal functional activities of plant. Therefore, this review mainly summarizes the role of each circadian clock genes in regulating rhythmicity, and shows that how circadian outputs are controlled by mutations as well as overexpression phenomenon.

Spatiotemporal Distribution and Geographical Impact Factors of Barley and Wheat during the Late Neolithic and Bronze Age (4000–2300 cal. a BP) in the Gansu–Qinghai Region, Northwest China

During the Late Neolithic and Bronze Age, the spread of Triticeae crops gradually transformed local millet agriculture in the Gansu–Qinghai region. However, few studies focused on the distribution characteristics and geographical factors influencing Triticeae agriculture. Here, geographical data from 65 sites with barley (Hordeum vulgare) and wheat (Triticum aestivum) remains in Gansu–Qinghai region were studied by spatial analysis in ArcGIS. The results showed that spatiotemporal distribution of barley and wheat exhibited three stages: firstly appeared in the central Hexi Corridor at ~4000 cal. a BP, then spread throughout the Hexi Corridor and Qinghai Lake area during 3600–3200 cal. a BP, and continued to move southward to the Hehuang Valley and Weihe River Basin during 3200–2300 cal. a BP. The studied sites were mainly distributed along rivers and certain altitude with suitable climatic conditions. The average distance to the nearest river was ~8 km, with wheat sites ~300 m closer than barley’s. The average elevation was 3500–1500 m, with wheat sites ~200 m lower than barley’s. The variations in spatiotemporal distribution were attributed to greater environmental tolerance of barley. These findings provide important environmental insights into the spatiotemporal distribution and transmission routes of barley and wheat in northwest China.

Spikelet abortion in six-rowed barley is mainly influenced by final spikelet number, with potential spikelet number acting as a suppressor trait

The potential to increase barley grain yield lies in the indeterminate nature of its inflorescence meristem, which produces spikelets, the basic reproductive unit in grasses that are linked to reproductive success. During early reproductive growth, barley spikes pass through the maximum yield potential-a stage after which no new spikelet ridges are produced. Subsequently, spikelet abortion (SA), a phenomenon in which spikelets abort during spike growth, imposes a bottleneck for increasing the grain yield potential. Here, we studied the potential of main culm spikes by counting potential spikelet number (PSN) and final spikelet number (FSN), and computed the corresponding SA (%) in a panel of 417 six-rowed spring barleys. Our phenotypic data analyses showed a significantly large within- and across-years genotypic variation with high broad-sense heritability estimates for all the investigated traits, including SA. Asian accessions displayed the lowest SA, indicating the presence of favourable alleles that may be exploited in breeding programs. A significantly negative Pearson's product-moment correlation was observed between FSN and SA. Our path analysis revealed that PSN and FSN explain 93% of the observed phenotypic variability for SA, with PSN behaving as a suppressor trait that magnifies the effect of FSN. Based on a large set of diverse barley accessions, our results provide a deeper phenotypic understanding of the quantitative genetic nature of SA, its association with traits of high agronomic importance, and a resource for further genetic analyses.

Photoperiod Control of Plant Growth: Flowering Time Genes Beyond Flowering

Fluctuations in environmental conditions greatly influence life on earth. Plants, as sessile organisms, have developed molecular mechanisms to adapt their development to changes in daylength, or photoperiod. One of the first plant features that comes to mind as affected by the duration of the day is flowering time; we all bring up a clear image of spring blossom. However, for many plants flowering happens at other times of the year, and many other developmental aspects are also affected by changes in daylength, which range from hypocotyl elongation in Arabidopsis thaliana to tuberization in potato or autumn growth cessation in trees. Strikingly, many of the processes affected by photoperiod employ similar gene networks to respond to changes in the length of light/dark cycles. In this review, we have focused on developmental processes affected by photoperiod that share similar genes and gene regulatory networks.

Responses of Barley to High Ambient Temperature Are Modulated by Vernalization

Ambient temperatures are increasing due to climate change. Cereal crops development and production will be affected consequently. Flowering time is a key factor for adaptation of small grain cereals and, therefore, exploring developmental responses of barley to rising temperatures is required. In this work, we studied phasic growth, and inflorescence traits related to yield, in eight near isogenic lines of barley (Hordeum vulgare L.) differing at the VRN-H1, VRN-H2 and PPD-H1 genes, representing different growth habits. The lines were grown in contrasting vernalization treatments, under two temperature regimes (18 and 25°C), in long days. Lines with recessive ppd-H1 presented delayed development compared to lines with the sensitive PPD-H1 allele, across the two growth phases considered. High temperature delayed flowering in all unvernalized plants, and in vernalized spring barleys carrying the insensitive ppd-H1 allele, whilst it accelerated flowering in spring barleys with the sensitive PPD-H1 allele. This finding evidenced an interaction between PPD-H1, temperature and vernalization. At the high temperature, PPD-H1 lines in spring backgrounds (VRN-H1-7) yielded more, whereas lines with ppd-H1 were best in vrn-H1 background. Our study revealed new information that will support breeding high-yielding cultivars with specific combinations of major adaptation genes tailored to future climatic conditions.

Transcriptome and Metabolite Insights into Domestication Process of Cultivated Barley in China

The domestication process of cultivated barley in China remains under debate because of the controversial origins of barley. Here, we analyzed transcriptomic and non-targeted metabolic data from 29 accessions together with public resequencing data from 124 accessions to explore the domestication process of cultivated barley in China (Cb-C). These analyses revealed that both Cb-C and Tibetan wild barley (Wb-T) were the descendants of wild barley from the Near East Fertile Crescent (Wb-NE), yielding little support for a local origin of Wb-T. Wb-T was more likely an intermediate in the domestication process from Wb-NE to Cb-C. Wb-T contributed more genetically to Cb-C than Wb-NE, and was domesticated into Cb-C about 3300 years ago. These results together seem to support that Wb-T may be a feralized or hybrid form of cultivated barley from the Near East Fertile Crescent or central Asia. Additionally, the metabolite analysis revealed divergent metabolites of alkaloids and phenylpropanoids and these metabolites were specifically targeted for selection in the evolutionary stages from Wb-NE to Wb-T and from Wb-T to Cb-C. The key missense SNPs in the genes HORVU6Hr1G027650 and HORVU4Hr1G072150 might be responsible for the divergence of metabolites of alkaloids and phenylpropanoids during domestication. Our findings allow for a better understanding of the domestication process of cultivated barley in China.

The Winter-Type Allele of HvCEN Is Associated With Earliness Without Severe Yield Penalty in Icelandic Spring Barley (Hordeum vulgare L.)

Icelandic barley genotypes have shown extreme earliness both in flowering and maturity compared to other north European genotypes, whereas earliness is a key trait in adapting barley to northern latitudes. Four genes were partially re-sequenced, which are Ppd-H1, HvCEN, HvELF3, and HvFT1, to better understand the mechanisms underlying this observed earliness. These genes are all known to play a part in the photoperiod response. The objective of this study is to correlate allelic diversity with flowering time and yield data from Icelandic field trials. The resequencing identified two to three alleles at each locus which resulted in 12 haplotype combinations. One haplotype combination containing the winter-type allele of Ppd-H1 correlated with extreme earliness, however, with a severe yield penalty. A winter-type allele in HvCEN in four genotypes correlated with earliness combined with high yield. Our results open the possibility of marker-assisted pyramiding as a rapid way to develop varieties with a shortened time from sowing to flowering under the extreme Icelandic growing conditions and possibly in other arctic or sub-arctic regions.

Major flowering time genes of barley: allelic diversity, effects, and comparison with wheat

This review summarizes the allelic series, effects, interactions between genes and with the environment, for the major flowering time genes that drive phenological adaptation of barley. The optimization of phenology is a major goal of plant breeding addressing the production of high-yielding varieties adapted to changing climatic conditions. Flowering time in cereals is regulated by genetic networks that respond predominately to day length and temperature. Allelic diversity at these genes is at the basis of barley wide adaptation. Detailed knowledge of their effects, and genetic and environmental interactions will facilitate plant breeders manipulating flowering time in cereal germplasm enhancement, by exploiting appropriate gene combinations. This review describes a catalogue of alleles found in QTL studies by barley geneticists, corresponding to the genetic diversity at major flowering time genes, the main drivers of barley phenological adaptation: VRN-H1 (HvBM5A), VRN-H2 (HvZCCTa-c), VRN-H3 (HvFT1), PPD-H1 (HvPRR37), PPD-H2 (HvFT3), and eam6/eps2 (HvCEN). For each gene, allelic series, size and direction of QTL effects, interactions between genes and with the environment are presented. Pleiotropic effects on agronomically important traits such as grain yield are also discussed. The review includes brief comments on additional genes with large effects on phenology that became relevant in modern barley breeding. The parallelisms between flowering time allelic variation between the two most cultivated Triticeae species (barley and wheat) are also outlined. This work is mostly based on previously published data, although we added some new data and hypothesis supported by a number of studies. This review shows the wide variety of allelic effects that provide enormous plasticity in barley flowering behavior, which opens new avenues to breeders for fine-tuning phenology of the barley crop.

Natural variation and artificial selection of photoperiodic flowering genes and their applications in crop adaptation

Flowering links vegetative growth and reproductive growth and involves the coordination of local environmental cues and plant genetic information. Appropriate timing of floral initiation and maturation in both wild and cultivated plants is important to their fitness and productivity in a given growth environment. The domestication of plants into crops, and later crop expansion and improvement, has often involved selection for early flowering. In this review, we analyze the basic rules for photoperiodic adaptation in several economically important and/or well-researched crop species. The ancestors of rice (Oryza sativa), maize (Zea mays), soybean (Glycine max), and tomato (Solanum lycopersicum) are short-day plants whose photosensitivity was reduced or lost during domestication and expansion to high-latitude areas. Wheat (Triticum aestivum) and barley (Hordeum vulgare) are long-day crops whose photosensitivity is influenced by both latitude and vernalization type. Here, we summarize recent studies about where these crops were domesticated, how they adapted to photoperiodic conditions as their growing area expanded from domestication locations to modern cultivating regions, and how allelic variants of photoperiodic flowering genes were selected during this process. A deeper understanding of photoperiodic flowering in each crop will enable better molecular design and breeding of high-yielding cultivars suited to particular local environments.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-021-00039-0.

Ppd-H1 integrates drought stress signals to control spike development and flowering time in barley

Drought impairs growth and spike development, and is therefore a major cause of yield losses in the temperate cereals barley and wheat. Here, we show that the photoperiod response gene PHOTOPERIOD-H1 (Ppd-H1) interacts with drought stress signals to modulate spike development. We tested the effects of a continuous mild and a transient severe drought stress on developmental timing and spike development in spring barley cultivars with a natural mutation in ppd-H1 and derived introgression lines carrying the wild-type Ppd-H1 allele from wild barley. Mild drought reduced the spikelet number and delayed floral development in spring cultivars but not in the introgression lines with a wild-type Ppd-H1 allele. Similarly, drought-triggered reductions in plant height, and tiller and spike number were more pronounced in the parental lines compared with the introgression lines. Transient severe stress halted growth and floral development; upon rewatering, introgression lines, but not the spring cultivars, accelerated development so that control and stressed plants flowered almost simultaneously. These genetic differences in development were correlated with a differential down-regulation of the flowering promotors FLOWERING LOCUS T1 and the BARLEY MADS-box genes BM3 and BM8. Our findings therefore demonstrate that Ppd-H1 affects developmental plasticity in response to drought in barley.

Genome-Wide DArTSeq Genotyping and Phenotypic Based Assessment of Within and Among Accessions Diversity and Effective Sample Size in the Diverse Sorghum, Pearl Millet, and Pigeonpea Landraces

Germplasm should be conserved in such a way that the genetic integrity of a given accession is maintained. In most genebanks, landraces constitute a major portion of collections, wherein the extent of genetic diversity within and among landraces of crops vary depending on the extent of outcrossing and selection intensity infused by farmers. In this study, we assessed the level of diversity within and among 108 diverse landraces and wild accessions using both phenotypic and genotypic characterization. This included 36 accessions in each of sorghum, pearl millet, and pigeonpea, conserved at ICRISAT genebank. We genotyped about 15 to 25 individuals within each accession, totaling 1,980 individuals using the DArTSeq approach. This resulted in 45,249, 19,052, and 8,211 high-quality single nucleotide polymorphisms (SNPs) in pearl millet, sorghum, and pigeonpea, respectively. Sorghum had the lowest average phenotypic (0.090) and genotypic (0.135) within accession distances, while pearl millet had the highest average phenotypic (0.227) and genotypic (0.245) distances. Pigeonpea had an average of 0.203 phenotypic and 0.168 genotypic within accession distances. Analysis of molecular variance also confirms the lowest variability within accessions of sorghum (26.3%) and the highest of 80.2% in pearl millet, while an intermediate in pigeonpea (57.0%). The effective sample size required to capture maximum variability and to retain rare alleles while regeneration ranged from 47 to 101 for sorghum, 155 to 203 for pearl millet, and 77 to 89 for pigeonpea accessions. This study will support genebank curators, in understanding the dynamics of population within and among accessions, in devising appropriate germplasm conservation strategies, and aid in their utilization for crop improvement.

An Evolutionary Approach to the History of Barley (Hordeum vulgare) Cultivation in the Canary Islands

The Canary Islands are an archipelago that lies about 100 km west of North Africa. Barley (Hordeum vulgare) has been continuously cultivated since the colonization of the islands. To investigate the agricultural history of the islands, the DNA from multiple individuals of six extant landraces of barley was sequenced, and the resulting data were analyzed with ABC modeling. Estimates of separation times of barley populations on the different islands and the mainland were congruent with archaeological dating of the earliest settlements on the islands. The results of the genetic analyses were consistent with the continuous cultivation of barley on Lanzarote island since it was first colonized, but suggested cultivation was carried out at a smaller scale than on Gran Canaria and Tenerife. Contrary to archaeological evidence and early written historical sources, the genetic analyses suggest that barley was cultivated on a larger scale on Tenerife than on Gran Canaria. The genetic analysis of contemporary barley added support to the dating of the colonization of the islands and pointed to the need for more archaeological data concerning barley cultivation on Tenerife.

Evolutionary processes from the perspective of flowering time diversity

Although it is well appreciated that genetic studies of flowering time regulation have led to fundamental advances in the fields of molecular and developmental biology, the ways in which genetic studies of flowering time diversity have enriched the field of evolutionary biology have received less attention despite often being equally profound. Because flowering time is a complex, environmentally responsive trait that has critical impacts on plant fitness, crop yield, and reproductive isolation, research into the genetic architecture and molecular basis of its evolution continues to yield novel insights into our understanding of domestication, adaptation, and speciation. For instance, recent studies of flowering time variation have reconstructed how, when, and where polygenic evolution of phenotypic plasticity proceeded from standing variation and de novo mutations; shown how antagonistic pleiotropy and temporally varying selection maintain polymorphisms in natural populations; and provided important case studies of how assortative mating can evolve and facilitate speciation with gene flow. In addition, functional studies have built detailed regulatory networks for this trait in diverse taxa, leading to new knowledge about how and why developmental pathways are rewired and elaborated through evolutionary time.

Gene-set association and epistatic analyses reveal complex gene interaction networks affecting flowering time in a worldwide barley collection

Single-marker genome-wide association studies (GWAS) have successfully detected associations between single nucleotide polymorphisms (SNPs) and agronomic traits such as flowering time and grain yield in barley. However, the analysis of individual SNPs can only account for a small proportion of genetic variation, and can only provide limited knowledge on gene network interactions. Gene-based GWAS approaches provide enormous opportunity both to combine genetic information and to examine interactions among genetic variants. Here, we revisited a previously published phenotypic and genotypic data set of 895 barley varieties grown in two years at four different field locations in Australia. We employed statistical models to examine gene-phenotype associations, as well as two-way epistasis analyses to increase the capability to find novel genes that have significant roles in controlling flowering time in barley. Genetic associations were tested between flowering time and corresponding genotypes of 174 putative flowering time-related genes. Gene-phenotype association analysis detected 113 genes associated with flowering time in barley, demonstrating the unprecedented power of gene-based analysis. Subsequent two-way epistasis analysis revealed 19 pairs of gene×gene interactions involved in controlling flowering time. Our study demonstrates that gene-based association approaches can provide higher capacity for future crop improvement to increase crop performance and adaptation to different environments.

Environmental Association Identifies Candidates for Tolerance to Low Temperature and Drought

Barley (Hordeum vulgare ssp. vulgare) is cultivated from the equator to the Arctic Circle. The wild progenitor species, Hordeum vulgare ssp. spontaneum, occupies a relatively narrow latitudinal range (∼30 - 40° N) primarily at low elevation (< 1,500 m). Adaptation to the range of cultivation has occurred over ∼8,000 years. The genetic basis of adaptation is amenable to study through environmental association. An advantage of environmental association in a well-characterized crop is that many loci that contribute to climatic adaptation and abiotic stress tolerance have already been identified. This provides the opportunity to determine if environmental association approaches effectively identify these loci of large effect. Using published genotyping from 7,864 SNPs in 803 barley landraces, we examined allele frequency differentiation across multiple partitions of the data and mixed model associations relative to bioclimatic variables. Using newly generated resequencing data from a subset of these landraces, we tested for linkage disequilibrium (LD) between SNPs queried in genotyping and SNPs in neighboring loci. Six loci previously reported to contribute to adaptive differences in flowering time and abiotic stress in barley and six loci previously identified in other plant species were identified in our analyses. In many cases, patterns of LD are consistent with the causative variant occurring in the immediate vicinity of the queried SNP. The identification of barley orthologs to well-characterized genes may provide a new understanding of the nature of adaptive variation and could permit a more targeted use of potentially adaptive variants in barley breeding and germplasm improvement.

Development of a Multiparent Population for Genetic Mapping and Allele Discovery in Six-Row Barley

Germplasm collections hold valuable allelic diversity for crop improvement and genetic mapping of complex traits. To gain access to the genetic diversity within the USDA National Small Grain Collection (NSGC), we developed the Barley Recombinant Inbred Diverse Germplasm Population (BRIDG6), a six-row spring barley multiparent population (MPP) with 88 cultivated accessions crossed to a common parent (Rasmusson). The parents were randomly selected from a core subset of the NSGC that represents the genetic diversity of landrace and breeding accessions. In total, we generated 6160 F5 recombinant inbred lines (RILs), with an average of 69 and a range of 37-168 RILs per family, that were genotyped with 7773 SNPs, with an average of 3889 SNPs segregating per family. We detected 23 quantitative trait loci (QTL) associated with flowering time with five QTL found coincident with previously described flowering time genes. A major QTL was detected near the flowering time gene, HvPpd-H1 which affects photoperiod. Haplotype-based analysis of HvPpd-H1 identified private alleles to families of Asian origin conferring both positive and negative effects, providing the first observation of flowering time-related alleles private to Asian accessions. We evaluated several subsampling strategies to determine the effect of sample size on the power of QTL detection, and found that, for flowering time in barley, a sample size >50 families or 3000 individuals results in the highest power for QTL detection. This MPP will be useful for uncovering large and small effect QTL for traits of interest, and identifying and utilizing valuable alleles from the NSGC for barley improvement.

Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley

Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi-environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype-by-environment (G×E) modelling. Sub-populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock-related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large-effect alleles. Our analysis supports a gene-level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses.

Genetic dissection of grain elements predicted by hyperspectral imaging associated with yield-related traits in a wild barley NAM population

Enhancing the accumulation of essential mineral elements in cereal grains is of prime importance for combating human malnutrition. Biofortification by breeding holds great potential for improving nutrient accumulation in grains. However, conventional breeding approaches require element analysis of many grain samples, which causes high costs. Here we applied hyperspectral imaging to estimate the concentration of 15 grain elements (C, B, Ca, Cd, Cu, Fe, K, Mg, Mn, Mo, N, Na, P, S, Zn) in high-throughput in the wild barley nested association mapping (NAM) population HEB-25, comprising 1,420 BC₁S₃ lines derived from crossing 25 wild barley accessions with the cultivar 'Barke'. Nutrient concentrations varied largely with a multitude of lines having higher micronutrient concentration than 'Barke'. In a genome-wide association study (GWAS), we located 75 quantitative trait locus (QTL) hotspots, whereof many could be explained by major genes such as NO APICAL MERISTEM-1 (NAM-1) and PHOTOPERIOD 1 (Ppd-H1). The GWAS approach revealed exotic alleles that were able to increase grain element concentrations. Remarkably, a QTL linked to GIBBERELLIN 20 OXIDASE 2 (HvGA20ox₂) significantly increased several grain elements without yield loss. We conclude that introgressing promising exotic alleles into elite breeding material can assist in improving the nutritional value of barley grains.

Diversity of a wall-associated kinase gene in wild and cultivated barley

Domestication of barley and other cereals was accompanied by an increase in seed size which has been ascribed to human selection, large seeds being preferred by early farmers or favoured by cultivation practices such as deep sowing. An alternative suggestion is that the increase in seed size was an indirect consequence of selection for plants with more vigorous growth. To begin to address the latter hypothesis we studied the diversity of HvWAK1, a wall-associated kinase gene involved in root proliferation, in 220 wild barley accessions and 200 domesticated landraces. A 3655-bp sequence comprising the gene and upstream region contained 69 single nucleotide polymorphisms (SNPs), one indel and four short tandem repeats. A network of 50 haplotypes revealed a complex evolutionary relationship, but with landraces largely restricted to two parts of the topology. SNPs in the HvWAK1 coding region resulted in nonsynonymous substitutions at nine positions in the translation product, but none of these changes were predicted to have a significant effect on the protein structure. In contrast, the region upstream of the coding sequence contained five SNPs that were invariant in the domesticated population, fixation of these SNPs decreasing the likelihood that the upstream of a pair of TATA boxes and transcription start sites would be used to promote transcription of HvWAK1. The sequence diversity therefore suggests that the cis-regulatory region of HvWAK1 might have been subject to selection during barley domestication. The extent of root proliferation has been linked with traits such as above-ground biomass, so selection for particular cis-regulatory variants of HvWAK1 would be consistent with the hypothesis that seed size increases during domestication were the indirect consequence of selection for plants with increased growth vigour.

Parallelism and convergence in post-domestication adaptation in cereal grasses

The selection of desirable traits in crops during domestication has been well studied. Many crops share a suite of modified phenotypic characteristics collectively known as the domestication syndrome. In this sense, crops have convergently evolved. Previous work has demonstrated that, at least in some instances, convergence for domestication traits has been achieved through parallel molecular means. However, both demography and selection during domestication may have placed limits on evolutionary potential and reduced opportunities for convergent adaptation during post-domestication migration to new environments. Here we review current knowledge regarding trait convergence in the cereal grasses and consider whether the complexity and dynamism of cereal genomes (e.g., transposable elements, polyploidy, genome size) helped these species overcome potential limitations owing to domestication and achieve broad subsequent adaptation, in many cases through parallel means. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.

Barley yield formation under abiotic stress depends on the interplay between flowering time genes and environmental cues

Since the dawn of agriculture, crop yield has always been impaired through abiotic stresses. In a field trial across five locations worldwide, we tested three abiotic stresses, nitrogen deficiency, drought and salinity, using HEB-YIELD, a selected subset of the wild barley nested association mapping population HEB-25. We show that barley flowering time genes Ppd-H1, Sdw1, Vrn-H1 and Vrn-H3 exert pleiotropic effects on plant development and grain yield. Under field conditions, these effects are strongly influenced by environmental cues like day length and temperature. For example, in Al-Karak, Jordan, the day length-sensitive wild barley allele of Ppd-H1 was associated with an increase of grain yield by up to 30% compared to the insensitive elite barley allele. The observed yield increase is accompanied by pleiotropic effects of Ppd-H1 resulting in shorter life cycle, extended grain filling period and increased grain size. Our study indicates that the adequate timing of plant development is crucial to maximize yield formation under harsh environmental conditions. We provide evidence that wild barley alleles, introgressed into elite barley cultivars, can be utilized to support grain yield formation. The presented knowledge may be transferred to related crop species like wheat and rice securing the rising global food demand for cereals.

Genetics of barley tiller and leaf development

In cereals, tillering and leaf development are key factors in the concept of crop ideotype, introduced in the 1960s to enhance crop yield, via manipulation of plant architecture. In the present review, we discuss advances in genetic analysis of barley shoot architecture, focusing on tillering, leaf size and angle. We also discuss novel phenotyping techniques, such as 2D and 3D imaging, that have been introduced in the era of phenomics, facilitating reliable trait measurement. We discuss the identification of genes and pathways that are involved in barley tillering and leaf development, highlighting key hormones involved in the control of plant architecture in barley and rice. Knowledge on genetic control of traits related to plant architecture provides useful resources for designing ideotypes for enhanced barley yield and performance.

Flax latitudinal adaptation at LuTFL1 altered architecture and promoted fiber production

After domestication in the Near East around 10,000 years ago several founder crops, flax included, spread to European latitudes. On reaching northerly latitudes the architecture of domesticated flax became more suitable to fiber production over oil, with longer stems, smaller seeds and fewer axillary branches. Latitudinal adaptations in crops typically result in changes in flowering time, often involving the PEBP family of genes that also have the potential to influence plant architecture. Two PEBP family genes in the flax genome, LuTFL1 and LuTFL2, vary in wild and cultivated flax over latitudinal range with cultivated flax receiving LuTFL1 alleles from northerly wild flax populations. Compared to a background of population structure of flaxes over latitude, the LuTFL1 alleles display a level of differentiation that is consistent with selection for an allele III in the north. We demonstrate through heterologous expression in Arabidopsis thaliana that LuTFL1 is a functional homolog of TFL1 in A. thaliana capable of changing both flowering time and plant architecture. We conclude that specialized fiber flax types could have formed as a consequence of a natural adaptation of cultivated flax to higher latitudes.

Identification of Ideal Allele Combinations for the Adaptation of Spring Barley to Northern Latitudes

The northwards expansion of barley production requires adaptation to longer days, lower temperatures and stronger winds during the growing season. We have screened 169 lines of the current barley breeding gene pool in the Nordic region with regards to heading, maturity, height, and lodging under different environmental conditions in nineteen field trials over 3 years at eight locations in northern and central Europe. Through a genome-wide association scan we have linked phenotypic differences observed in multi-environment field trials (MET) to single nucleotide polymorphisms (SNP). We have identified an allele combination, only occurring among a few Icelandic lines, that affects heat sum to maturity and requires 214 growing degree days (GDD) less heat sum to maturity than the most common allele combination in the Nordic spring barley gene pool. This allele combination is beneficial in a cold environment, where autumn frost can destroy a late maturing harvest. Despite decades of intense breeding efforts relying heavily on the same germplasm, our results show that there still exists considerable variation within the current breeding gene pool and we identify ideal allele combinations for regional adaptation, which can facilitate the expansion of cereal cultivation even further northwards.

Genome-wide association of yield traits in a nested association mapping population of barley reveals new gene diversity for future breeding

To explore wild barley as a source of useful alleles for yield improvement in breeding, we have carried out a genome-wide association scan using the nested association mapping population HEB-25, which contains 25 diverse exotic barley genomes superimposed on an ~70% genetic background of cultivated barley. A total of 1420 HEB-25 lines were trialled for nine yield-related grain traits for 2 years in Germany and Scotland, with varying N fertilizer application. The phenotypic data were related to genotype scores for 5398 gene-based single nucleotide polymorphism (SNP) markers. A total of 96 quantitative trait locus (QTL) regions were identified across all measured traits, the majority of which co-localize with known major genes controlling flowering time (Ppd-H2, HvCEN, HvGI, VRN-H1, and VRN-H3) and spike morphology (VRS3, VRS1, VRS4, and INT-C) in barley. Fourteen QTL hotspots, with at least three traits coinciding, were also identified, several of which co-localize with barley orthologues of genes controlling grain dimensions in rice. Most of the allele effects are specific to geographical location and/or exotic parental genotype. This study shows the existence of beneficial alleles for yield-related traits in exotic barley germplasm and provides candidate alleles for future improvement of these traits by the breeder.

Barley heads east: Genetic analyses reveal routes of spread through diverse Eurasian landscapes

One of the world’s most important crops, barley, was domesticated in the Near East around 11,000 years ago. Barley is a highly resilient crop, able to grown in varied and marginal environments, such as in regions of high altitude and latitude. Archaeobotanical evidence shows that barley had spread throughout Eurasia by 2,000 BC. To further elucidate the routes by which barley cultivation was spread through Eurasia, simple sequence repeat (SSR) analysis was used to determine genetic diversity and population structure in three extant barley taxa: domesticated barley (Hordeum vulgare L. subsp. vulgare), wild barley (H. vulgare subsp. spontaneum) and a six-rowed brittle rachis form (H. vulgare subsp. vulgare f. agriocrithon (Åberg) Bowd.). Analysis of data using the Bayesian clustering algorithm InStruct suggests a model with three ancestral genepools, which captures a major split in the data, with substantial additional resolution provided under a model with eight genepools. Our results indicate that H. vulgare subsp. vulgare f. agriocrithon accessions and Tibetan Plateau H. vulgare subsp. spontaneum are closely related to the H. vulgare subsp. vulgare in their vicinity, and are therefore likely to be feral derivatives of H. vulgare subsp. vulgare. Under the eight genepool model, cultivated barley is split into six ancestral genepools, each of which has a distinct distribution through Eurasia, along with distinct morphological features and flowering time phenotypes. The distribution of these genepools and their phenotypic characteristics is discussed together with archaeological evidence for the spread of barley eastwards across Eurasia.

Contrasting genetic regulation of plant development in wild barley grown in two European environments revealed by nested association mapping

Barley is cultivated more widely than the other major world crops because it adapts well to environmental constraints, such as drought, heat, and day length. To better understand the genetic control of local adaptation in barley, we studied development in the nested association mapping population HEB-25, derived from crossing 25 wild barley accessions with the cultivar 'Barke'. HEB-25 was cultivated in replicated field trials in Dundee (Scotland) and Halle (Germany), differing in regard to day length, precipitation, and temperature. Applying a genome-wide association study, we located 60 and 66 quantitative trait locus (QTL) regions regulating eight plant development traits in Dundee and Halle, respectively. A number of QTLs could be explained by known major genes such as PHOTOPERIOD 1 (Ppd-H1) and FLOWERING LOCUS T (HvFT-1) that regulate plant development. In addition, we observed that developmental traits in HEB-25 were partly controlled via genotype × environment and genotype × donor interactions, defined as location-specific and family-specific QTL effects. Our findings indicate that QTL alleles are available in the wild barley gene pool that show contrasting effects on plant development, which may be deployed to improve adaptation of cultivated barley to future environmental changes.

Association of candidate genes with heading date in a diverse Dactylis glomerata population

Flowering occurs in response to cues from both temperature and photoperiod elicitors in cool-season, long-day forage grasses, and genes involved in sensing the elicitors and inducing downstream flowering responses have been associated with heading date and flowering time in perennial forage grasses as well as cereal grasses. In this study we test for association between orchardgrass (Dactylis glomerata L.) heading date and polymorphisms in the CONSTANS (DgCO1), FLOWERING TIME (DgFT1), a VRN1 like MADS-box (DgMADS), and PHOTOPERIOD (DgPPD1-like) containing genes. A diverse population of 150 genotypes was measured for heading date across three years, genotyped, and candidate genes sequenced. Although pairwise population kinship values were generally low, the genotypes fit into a two-group structure model. Linkage disequilibrium decayed rapidly, reaching r² levels below 0.2 within the 500bp of each gene. SNPs significantly associated with heading date were detected in equal-dose and tetraploid dosage models. The DgCO1 gene had the most significant polymorphisms and those with the largest effects, while DgMADS had several significant polymorphisms in its first intron with smaller effects. These polymorphisms can be used for further validation, selection, and development of breeding lines of orchardgrass.

Journey to the east: Diverse routes and variable flowering times for wheat and barley en route to prehistoric China

Today, farmers in many regions of eastern Asia sow their barley grains in the spring and harvest them in the autumn of the same year (spring barley). However, when it was first domesticated in southwest Asia, barley was grown between the autumn and subsequent spring (winter barley), to complete their life cycles before the summer drought. The question of when the eastern barley shifted from the original winter habit to flexible growing schedules is of significance in terms of understanding its spread. This article investigates when barley cultivation dispersed from southwest Asia to regions of eastern Asia and how the eastern spring barley evolved in this context. We report 70 new radiocarbon measurements obtained directly from barley grains recovered from archaeological sites in eastern Eurasia. Our results indicate that the eastern dispersals of wheat and barley were distinct in both space and time. We infer that barley had been cultivated in a range of markedly contrasting environments by the second millennium BC. In this context, we consider the distribution of known haplotypes of a flowering-time gene in barley, Ppd-H1, and infer that the distributions of those haplotypes may reflect the early dispersal of barley. These patterns of dispersal resonate with the second and first millennia BC textual records documenting sowing and harvesting times for barley in central/eastern China.

Domestication as a model system for the extended evolutionary synthesis

One of the challenges in evaluating arguments for extending the conceptual framework of evolutionary biology involves the identification of a tractable model system that allows for an assessment of the core assumptions of the extended evolutionary synthesis (EES). The domestication of plants and animals by humans provides one such case study opportunity. Here, I consider domestication as a model system for exploring major tenets of the EES. First I discuss the novel insights that niche construction theory (NCT, one of the pillars of the EES) provides into the domestication processes, particularly as they relate to five key areas: coevolution, evolvability, ecological inheritance, cooperation and the pace of evolutionary change. This discussion is next used to frame testable predictions about initial domestication of plants and animals that contrast with those grounded in standard evolutionary theory, demonstrating how these predictions might be tested in multiple regions where initial domestication took place. I then turn to a broader consideration of how domestication provides a model case study consideration of the different ways in which the core assumptions of the EES strengthen and expand our understanding of evolution, including reciprocal causation, developmental processes as drivers of evolutionary change, inclusive inheritance, and the tempo and rate of evolutionary change.

Floral transitions in wheat and barley: interactions between photoperiod, abiotic stresses, and nutrient status

The timing of plant reproduction has a large impact on yield in crop plants. Reproductive development in temperate cereals comprises two major developmental transitions. During spikelet initiation, the identity of the shoot meristem switches from the vegetative to the reproductive stage and spikelet primordia are formed on the apex. Subsequently, floral morphogenesis is initiated, a process strongly affected by environmental variation. Recent studies in cereal grasses have suggested that this later phase of inflorescence development controls floret survival and abortion, and is therefore crucial for yield. Here, we provide a synthesis of the early morphological and the more recent genetic studies on shoot development in wheat and barley. The review explores how photoperiod, abiotic stress, and nutrient signalling interact with shoot development, and pinpoints genetic factors that mediate development in response to these environmental cues. We anticipate that research in these areas will be important in understanding adaptation of cereal grasses to changing climate conditions.

QTLs for earliness and yield-forming traits in the Lubuski × CamB barley RIL population under various water regimes

Drought has become more frequent in Central Europe causing large losses in cereal yields, especially of spring crops. The development of new varieties with increased tolerance to drought is a key tool for improvement of agricultural productivity. Material for the study consisted of 100 barley recombinant inbred lines (RILs) (LCam) derived from the cross between Syrian and European parents. The RILs and parental genotypes were examined in greenhouse experiments under well-watered and water-deficit conditions. During vegetation the date of heading, yield and yield-related traits were measured. RIL population was genotyped with microsatellite and single nucleotide polymorphism markers. This population, together with two other populations, was the basis for the consensus map construction, which was used for identification of quantitative trait loci (QTLs) affecting the traits. The studied lines showed a large variability in heading date. It was noted that drought-treatment negatively affected the yield and its components, especially when applied at the flag leaf stage. In total, 60 QTLs were detected on all the barley chromosomes. The largest number of QTLs was found on chromosome 2H. The main QTL associated with heading, located on chromosome 2H (Q.HD.LC-2H), was identified at SNP marker 5880-2547, in the vicinity of Ppd-H1 gene. SNP 5880-2547 was also the closest marker to QTLs associated with plant architecture, spike morphology and grain yield. The present study showed that the earliness allele from the Syrian parent, as introduced into the genome of an European variety could result in an improvement of barley yield performance under drought conditions.

Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data

Flowering time is a major determinant of biomass yield in switchgrass (Panicum virgatum), a perennial bioenergy crop, because later flowering allows for an extended period of vegetative growth and increased biomass production. A better understanding of the genetic regulation of flowering time in switchgrass will aid the development of switchgrass varieties with increased biomass yields, particularly at northern latitudes, where late-flowering but southern-adapted varieties have high winter mortality. We use genotypes derived from recently published exome-capture sequencing, which mitigates challenges related to the large, highly repetitive and polyploid switchgrass genome, to perform genome-wide association studies (GWAS) using flowering time data from a switchgrass association panel in an effort to characterize the genetic architecture and genes underlying flowering time regulation in switchgrass. We identify associations with flowering time at multiple loci, including in a homolog of FLOWERING LOCUS T and in a locus containing TIMELESS, a homolog of a key circadian regulator in animals. Our results suggest that flowering time variation in switchgrass is due to variation at many positions across the genome. The relationship of flowering time and geographic origin indicates likely roles for genes in the photoperiod and autonomous pathways in generating switchgrass flowering time variation.

Alternative Splicing of Barley Clock Genes in Response to Low Temperature

Alternative splicing (AS) is a regulated mechanism that generates multiple transcripts from individual genes. It is widespread in eukaryotic genomes and provides an effective way to control gene expression. At low temperatures, AS regulates Arabidopsis clock genes through dynamic changes in the levels of productive mRNAs. We examined AS in barley clock genes to assess whether temperature-dependent AS responses also occur in a monocotyledonous crop species. We identify changes in AS of various barley core clock genes including the barley orthologues of Arabidopsis AtLHY and AtPRR7 which showed the most pronounced AS changes in response to low temperature. The AS events modulate the levels of functional and translatable mRNAs, and potentially protein levels, upon transition to cold. There is some conservation of AS events and/or splicing behaviour of clock genes between Arabidopsis and barley. In addition, novel temperature-dependent AS of the core clock gene HvPPD-H1 (a major determinant of photoperiod response and AtPRR7 orthologue) is conserved in monocots. HvPPD-H1 showed a rapid, temperature-sensitive isoform switch which resulted in changes in abundance of AS variants encoding different protein isoforms. This novel layer of low temperature control of clock gene expression, observed in two very different species, will help our understanding of plant adaptation to different environments and ultimately offer a new range of targets for plant improvement.

Molecular evidence of RNA polymerase II gene reveals the origin of worldwide cultivated barley

The origin and domestication of cultivated barley have long been under debate. A population-based resequencing and phylogenetic analysis of the single copy of RPB2 gene was used to address barley domestication, to explore genetic differentiation of barley populations on the worldwide scale, and to understand gene-pool exchanges during the spread and subsequent development of barley cultivation. Our results revealed significant genetic differentiation among three geographically distinct wild barley populations. Differences in haplotype composition among populations from different geographical regions revealed that modern cultivated barley originated from two major wild barley populations: one from the Near East Fertile Crescent and the other from the Tibetan Plateau, supporting polyphyletic origin of cultivated barley. The results of haplotype frequencies supported multiple domestications coupled with widespread introgression events that generated genetic admixture between divergent barley gene pools. Our results not only provide important insight into the domestication and evolution of cultivated barley, but also enhance our understanding of introgression and distinct selection pressures in different environments on shaping the genetic diversity of worldwide barley populations, thus further facilitating the effective use of the wild barley germplasm.

Flowering time adaption in Swedish landrace pea (Pisum sativum L.)

BACKGROUND

Cultivated crops have repeatedly faced new climatic conditions while spreading from their site of origin. In Sweden, at the northernmost fringe of Europe, extreme conditions with temperature-limited growth seasons and long days require specific adaptation. Pea (Pisum sativum L.) has been cultivated in Sweden for millennia, allowing for adaptation to the local environmental conditions to develop. To study such adaptation, 15 Swedish pea landraces were chosen alongside nine European landraces, seven cultivars and three wild accessions. Number of days to flowering (DTF) and other traits were measured and the diversity of the flowering time genes HIGH RESPONSE TO PHOTOPERIOD (HR), LATE FLOWERING (LF) and STERILE NODES (SN) was assessed. Furthermore, the expression profiles of LF and SN were obtained.

RESULTS

DTF was positively correlated with the length of growing season at the site of origin (GSO) of the Swedish landraces. Alleles at the HR locus were significantly associated with DTF with an average difference of 15.43 days between the two detected haplotypes. LF expression was found to have a significant effect on DTF when analysed on its own, but not when HR haplotype was added to the model. HR haplotype and GSO together explained the most of the detected variation in DTF (49.6 %).

CONCLUSIONS

We show local adaptation of DTF, primarily in the northernmost accessions, and links between genetic diversity and diversity in DTF. The links between GSO and genetic diversity of the genes are less clear-cut and flowering time adaptation seems to have a complex genetic background.

Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation

After domestication, during a process of widespread range extension, barley adapted to a broad spectrum of agricultural environments. To explore how the barley genome responded to the environmental challenges it encountered, we sequenced the exomes of a collection of 267 georeferenced landraces and wild accessions. A combination of genome-wide analyses showed that patterns of variation have been strongly shaped by geography and that variant-by-environment associations for individual genes are prominent in our data set. We observed significant correlations of days to heading (flowering) and height with seasonal temperature and dryness variables in common garden experiments, suggesting that these traits were major drivers of environmental adaptation in the sampled germplasm. A detailed analysis of known flowering-associated genes showed that many contain extensive sequence variation and that patterns of single- and multiple-gene haplotypes exhibit strong geographical structuring. This variation appears to have substantially contributed to range-wide ecogeographical adaptation, but many factors key to regional success remain unidentified.