Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.).

Domestication is considered a model of adaptation that can be used to draw conclusions about the modus operandi of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication-related questions to understand the biological and cultural bases of the domestication process. We employed restriction site-associated DNA sequencing (RAD-seq) of 494 Pisum sativum (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild P. sativum revealed five distinct groups with a notable geographic pattern. Pisum abyssinicum clustered unequivocally within the P. sativum complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in P. sativum ssp. sativum and three in P. abyssinicum. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild P. sativum is structured into well-diverged subgroups. Although Pisum sativum ssp. humile is not supported as a taxonomic entity, the so-called 'southern humile' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.

Advancing Grain Legumes Domestication and Evolution Studies with Genomics.

Grain legumes were domesticated in parallel with cereals in several regions of the world and formed the economic basis of early farming cultures. Since then, legumes have played a vital role in human and animal diets and in fostering agrobiodiversity. Increasing grain legume cultivation will be crucial to safeguard nutritional security and the resilience of agricultural ecosystems across the globe. A better understanding of the molecular underpinnings of domestication and crop evolution of grain legumes may be translated into practical approaches in modern breeding programs to stabilize yield, which is threatened by evolving pathogens and changing climates. During recent decades, domestication research in all crops has greatly benefited from the fast progress in genomic technologies. Yet still, many questions surrounding the domestication and diversification of legumes remain unanswered. In this review, we assess the potential of genomic approaches in grain legume research. We describe the centers of origin and the crucial domestication traits of grain legumes. In addition, we survey the effect of domestication on both above-ground and below-ground traits that have economic importance. Finally, we discuss open questions in grain legume domestication and diversification and outline how to bridge the gap between the preservation of historic crop diversity and their utilization in modern plant breeding.

Identification of a major locus for flowering pattern sheds light on plant architecture diversification in cultivated peanut.

KEY MESSAGE: A major gene controls flowering pattern in peanut, possibly encoding a TFL1-like. It was subjected to gain/loss events of a deletion and changes in mRNA expression levels, partly explaining the evolution of flowering pattern in Arachis. Flowering pattern (FP) is a major characteristic differentiating the two subspecies of cultivated peanut (Arachis hypogaea L.). Subsp. fastigiata possessing flowers on the mainstem (MSF) and a sequential FP, whereas subsp. hypogaea lacks MSF and exhibits an alternate FP. FP is considered the main contributor to plant adaptability, and evidence indicates that its diversification occurred during the several thousand years of domestication. However, the genetic mechanism that controls FP in peanut is unknown. We investigated the genetics of FP in a recombinant inbred population, derivatives of an A. hypogaea by A. fastigiata cross. Lines segregated 1:1 for FP, indicating a single gene effect. Using Axiom_Arachis2 SNP-array, FP was mapped to a small segment in chromosome B02, wherein a Terminal Flowering 1-like (AhTFL1) gene with a 1492 bp deletion was found in the fastigiata line, leading to a truncated protein. Remapping FP in the RIL population with the AhTFL1 indel as a marker increased the LOD score from 53.3 to 158.8 with no recombination in the RIL population. The same indel was found co-segregating with the phenotype in two independent EMS-mutagenized M2 families, suggesting a hotspot for gene conversion. Also, AhTFL1 was significantly less expressed in the fastigiata line compared to hypogaea and in flowering than non-flowering branches. Sequence analysis of the AhTFL1 in peanut world collections indicated significant conservation, supporting the putative role of AhTFL1 in peanut speciation during domestication and modern cultivation.

Limited divergent adaptation despite a substantial environmental cline in wild pea.

Isolation by environment (IBE) is a widespread phenomenon in nature. It is commonly expected that the degree of difference among environments is proportional to the level of divergence between populations in their respective environments. It is therefore assumed that a species' genetic diversity displays a pattern of IBE in the presence of a strong environmental cline if gene flow does not mitigate isolation. We tested this common assumption by analysing the genetic diversity and demographic history of Pisum fulvum, which inhabits contrasting habitats in the southern Levant and is expected to display only minor migration rates between populations, making it an ideal test case. Ecogeographical and subpopulation structure were analysed and compared. The correlation of genetic with environmental distances was calculated to test the effect of isolation by distance and IBE and detect the main drivers of these effects. Historical effective population size was estimated using stairway plot. Limited overlap of ecogeographical and genetic clustering was observed, and correlation between genetic and environmental distances was statistically significant but small. We detected a sharp decline of effective population size during the last glacial period. The low degree of IBE may be the result of genetic drift due to a past bottleneck. Our findings contradict the expectation that strong environmental clines cause IBE in the absence of extensive gene flow.

The Israeli-Palestinian wheat landraces collection: restoration and characterization of lost genetic diversity.

BACKGROUND: For over a century, genetic diversity of wheat worldwide was eroded by continual selection for high yields and industrial demands. Wheat landraces cultivated in Israel and Palestine demonstrate high genetic diversity and a potentially wide repertoire of adaptive alleles. While most Israeli-Palestinian wheat landraces were lost in the transition to 'Green Revolution' semi-dwarf varieties, some germplasm collections made at the beginning of the 20th century survived in gene banks and private collections worldwide. However, fragmentation and poor conservation place this unique genetic resource at a high risk of genetic erosion. Herein, we describe a long-term initiative to restore, conserve, and characterize a collection of Israeli and Palestinian wheat landraces (IPLR). RESULTS: We report on (i) the IPLR construction (n = 932), (ii) the historical and agronomic context to this collection, (iii) the characterization and assessment of the IPLR's genetic diversity, and (iv) a data comparison from two distinct subcollections within IPLR: a collection made by N. Vavilov in 1926 (IPLR-VIR) and a later one (1979-1981) made by Y. Mattatia (IPLR-M). Though conducted in the same eco-geographic space, these two collections were subjected to considerably different conservation pathways. IPLR-M, which underwent only one propagation cycle, demonstrated marked genetic and phenotypic variability (within and between accessions) in comparison with IPLR-VIR, which had been regularly regenerated over ∼90 years. CONCLUSION: We postulate that long-term ex situ conservation involving human and genotype × environment selection may significantly reduce accession heterogeneity and allelic diversity. Results are further discussed in a broader context of pre-breeding and conservation. © 2019 Society of Chemical Industry.

Transcriptome profiling of wheat glumes in wild emmer, hulled landraces and modern cultivars.

BACKGROUND: Wheat domestication is considered as one of the most important events in the development of human civilization. Wheat spikelets have undergone significant changes during evolution under domestication, resulting in soft glumes and larger kernels that are released easily upon threshing. Our main goal was to explore changes in transcriptome expression in glumes that accompanied wheat evolution under domestication. METHODS: A total of six tetraploid wheat accessions were selected for transcriptome profiling based on their rachis brittleness and glumes toughness. RNA pools from glumes of the central spikelet at heading time were used to construct cDNA libraries for sequencing. The trimmed reads from each library were separately aligned to the reference sub-genomes A and B, which were extracted from wheat survey sequence. Differentially expression analysis and functional annotation were performed between wild and domesticated wheat, to identity candidate genes associated with evolution under domestication. Selected candidate genes were validated using real time PCR. RESULTS: Transcriptome profiles of wild emmer wheat, wheat landraces, and wheat cultivars were compared using next generation sequencing (RNA-seq). We have found a total of 194,893 transcripts, of which 73,150 were shared between wild, landraces, and cultivars. From 781 differentially expressed genes (DEGs), 336 were down-regulated and 445 were up-regulated in the domesticated compared to wild wheat genotypes. Gene Ontology (GO) annotation assigned 293 DEGs (37.5 %) to GO term groups, of which 134 (17.1 %) were down-regulated and 159 (20.4 %) up-regulated in the domesticated wheat. Some of the down-regulated DEGs in domesticated wheat are related to the biosynthetic pathways that eventually define the mechanical strength of the glumes, such as cell wall, lignin, pectin and wax biosynthesis. The reduction in gene expression of such genes, may explain the softness of the glumes in the domesticated forms. In addition, we have identified genes involved in nutrient remobilization that may affect grain size and other agronomic traits evolved under domestication. CONCLUSIONS: The comparison of RNA-seq profiles between glumes of wheat groups differing in glumes toughness and rachis brittleness revealed a few DEGs that may be involved in glumes toughness and nutrient remobilization. These genes may be involved in processes of wheat improvement under domestication.

The 'Human Mind' as a common denominator in plant domestication.

The role of conscious versus unconscious selection is a central issue in plant domestication. While some authors hold that domesticated plants arose due to unconscious dynamics driven by selection pressures exerted by the ancient 'cultivation regime', others attribute an indispensable role to conscious and knowledge-based selection as an imperative component of Neolithic Near Eastern plant domestication. Recent experimental work demonstrated that, contrary to commonly held views, deep seed burial as part of the ancient cultivation regime cannot be considered as a general selection pressure underlying the increased seed size of domesticated legumes compared with their wild ancestors. This is a robust conclusion since, in three out of the eight legume species studied from different world regions, there was no association between larger seed size and better seedling emergence from depth. We concur with the authors that these legume crops were most likely under various and multiple (often interacting) selection pressures under domestication, thereby causing the observed parallel/convergent evolution of their larger grain size. However, it is puzzling that these authors did not mention the ever-present common denominator in plant domestication, i.e. conscious human decision-making. In our view, the human 'Mind' and the 'Science of the Concrete' à la Lévi-Strauss deserved to be discussed as an integral component of plant domestication.

The potential use of chickpeas in development of infant follow-on formula.

BACKGROUND: Undernutrition during childhood is a common disorder in the developing countries, however most research has focussed much on its treatment rather than its prevention. OBJECTIVE: We investigated the potential of using chickpeas in infant follow-on formula production against the requirements of WHO/FAO on complementary foods and EU regulations on follow-on formula. METHODS: Chickpeas were germinated for 72 hours followed by boiling, drying and dehulling in order to minimise associated anti-nutrition factors. Saccharifying enzymes were used to hydrolyse starch to maltose and the resulting flours were analysed for their protein content and amino acid profile. RESULTS: The protein content (percentage) increased from 16.66 ± 0.35 and 20.24 ± 0.50 to 20.00 ± 0.15 and 21.98 ± 0.80 for the processed desi and kabuli cultivar compared to raw chickpeas, respectively (P < 0.05). There was insignificant change (P = 0.05) in amino acid profile following processing and the resulting flour was found to meet the amino acid requirements of WHO/FAO protein reference for 0-24 month's children. CONCLUSION: The designed chickpea based infant follow-on formula meets the WHO/FAO requirements on complementary foods and also the EU regulations on follow-on formula with minimal addition of oils, minerals and vitamins. It uses chickpea as a common source of carbohydrate and protein hence making it more economical and affordable for the developing countries without compromising the nutrition quality.

On the 'lost' crops of the neolithic Near East.

The claim that the 'classic' eight 'founder crop' package (einkorn wheat, emmer wheat, barley, lentil, pea, chickpea, bitter vetch, and flax) underlying the emergence of agriculture in the Near East is a relic of a larger number of domesticated species is addressed. The 'lost' crops concept relies on the idea that additional taxa were at certain points in time and in certain locations genuine crops, which were later abandoned. The issue is highly relevant to the debate concerning mono- versus polyphyletic domestication, because if there were numerous 'false starts' that were subsequently lost, this implies that plant domestication occurred over a protracted time period, and across a wide geographic range. Different criteria were used for declaring those taxa as 'lost' crops, including, but not limited to (i) identification in archaeobotanical assemblages of grains from species which are not known as crops at present; (ii) identification of such grains in what is interpreted to have been Neolithic storage facilities; and (iii) recent botanical observations on populations of crop wild relatives in disturbed habitats. The evidence for four presumed 'lost' crops (wild oat, rambling vetch, rye, and wild black lentil) and the broad bean is evaluated, and discussed in light of data on Croatian and Israeli wild pea, and Moroccan wild lentil in disturbed habitats. Based on present knowledge, the broad bean might emerge as a founder crop (without an identified wild progenitor). The same may hold true for rye, which was never lost since its adoption in the Pre-Pottery Neolithic B period in Anatolia. In the remaining three cases, there are alternative, more likely, explanations for the archaeological finds or the recent botanical observations rather than 'lost' domestication episodes.

Threshing efficiency as an incentive for rapid domestication of emmer wheat.

BACKGROUND AND AIMS: The harvesting method of wild and cultivated cereals has long been recognized as an important factor in the emergence of domesticated non-shattering ear genotypes. This study aimed to quantify the effects of spike brittleness and threshability on threshing time and efficiency in emmer wheat, and to evaluate the implications of post-harvest processes on domestication of cereals in the Near East. METHODS: A diverse collection of tetraploid wheat genotypes, consisting of Triticum turgidum ssp. dicoccoides - the wild progenitor of domesticated wheat - traditional landraces, modern cultivars (T. turgidum ssp. durum) and 150 recombinant (wild × modern) inbred lines, was used in replicated controlled threshing experiments to quantify the effects of spike brittleness and threshability on threshing time and efficiency. KEY RESULTS: The transition from a brittle hulled wild phenotype to non-brittle hulled phenotype (landraces) was associated with an approx. 30 % reduction in threshing time, whereas the transition from the latter to non-brittle free-threshing cultivars was associated with an approx. 85 % reduction in threshing time. Similar trends were obtained with groups of recombinant inbred lines showing extreme phenotypes of brittleness and threshability. CONCLUSIONS: In tetraploid wheat, both non-brittle spike and free-threshing are labour-saving traits that increase the efficiency of post-harvest processing, which could have been an incentive for rapid domestication of the Near Eastern cereals, thus refuting the recently proposed hypothesis regarding extra labour associated with the domesticated phenotype (non-brittle spike) and its presumed role in extending the domestication episode time frame.

New flavors from old wheats: exploring the aroma profiles and sensory attributes of local Mediterranean wheat landraces.

Introduction: During the 20th century, the worldwide genetic diversity of wheat was sharply eroded by continual selection for high yields and industry demands for particular standardized qualities. A collection of Israeli and Palestinian landraces (IPLR) was established to represent genetic diversity, accumulated for ten millennia under diverse environments, which was mostly lost in this transition. As our long-term goal is to study this pre- Green Revolution genetic reservoir, herein we focus on its flour and bread quality and sensorial attributes. Methods: Initially, a database was built for the entire IPLR collection (n=901) holding both Triticum durum (durum wheat) and T. aestivum (bread wheat) which included genetic and phenotypic characterization of agronomic traits, grain and flour quality. Then, a representative subset of the IPLR was selected and compared to modern varieties for dough quality, rheology, aroma and taste using both whole and refined flours and breads. The sensory panel used 40 subjects who evaluated common protocol or sourdough breads made by four artisan bakers. Results: Results show modern durum cultivar C-9 had superior rheological properties (gluten index, elasticity, dough development time) as compared with landraces, while bread landrace 'Diar Alla' was markedly preferable for baking in relation to the modern cultivar Gadish. Baking tests and subsequent sensory evaluation clearly demonstrated a preference toward refined breads, apart from whole breads prepared using sourdough starters. In bread wheat, loaves baked using landrace flour were scored higher in several quality parameters, whereas in durum lines, the opposite trend was evident. Loaves baked from landraces 'Diar Alla' and to a lesser extent 'Hittia Soada' presented a markedly different aroma from the control loaves prepared from modern flours, both in terms of overall compositions and individual compounds, including classes such as pyranones, pyrazines, furans and pyrroles (maltol). Modern lines, on the other hand, were consistently richer in terpenes and phenylpropanoids. Further analysis demonstrated a significant association between specific aroma classes and sensory attributes scored by panelists. Discussion: The findings of the study may help advance new niches in the local wheat market aimed at health and nutrition including adapting durum varieties to the bread market and developing flavor-enhanced wholemeal breads.

A critical review of the protracted domestication model for Near-Eastern founder crops: linear regression, long-distance gene flow, archaeological, and archaeobotanical evidence.

The recent review by Fuller et al. (2012a) in this journal is part of a series of papers maintaining that plant domestication in the Near East was a slow process lasting circa 4000 years and occurring independently in different locations across the Fertile Crescent. Their protracted domestication scenario is based entirely on linear regression derived from the percentage of domesticated plant remains at specific archaeological sites and the age of these sites themselves. This paper discusses why estimates like haldanes and darwins cannot be applied to the seven founder crops in the Near East (einkorn and emmer wheat, barley, peas, chickpeas, lentils, and bitter vetch). All of these crops are self-fertilizing plants and for this reason they do not fulfil the requirements for performing calculations of this kind. In addition, the percentage of domesticates at any site may be the result of factors other than those that affect the selection for domesticates growing in the surrounding area. These factors are unlikely to have been similar across prehistoric sites of habitation, societies, and millennia. The conclusion here is that single crop analyses are necessary rather than general reviews drawing on regression analyses based on erroneous assumptions. The fact that all seven of these founder crops are self-fertilizers should be incorporated into a comprehensive domestication scenario for the Near East, as self-fertilization naturally isolates domesticates from their wild progenitors.

When half is more than the whole: Wheat domestication syndrome reconsidered.

Two opposing models currently dominate Near Eastern plant domestication research. The core area-one event model depicts a knowledge-based, conscious, geographically centered, rapid single-event domestication, while the protracted-autonomous model emphasizes a noncentered, millennia-long process based on unconscious dynamics. The latter model relies, in part, on quantitative depictions of diachronic changes (in archaeological remains) in proportions of spikelet shattering to nonshattering, towards full dominance of the nonshattering (domesticated) phenotypes in cultivated cereal populations. Recent wild wheat genome assembly suggests that shattering and nonshattering spikelets may originate from the same (individual) genotype. Therefore, their proportions among archaeobotanical assemblages cannot reliably describe the presumed protracted-selection dynamics underlying wheat domestication. This calls for a reappraisal of the "domestication syndrome" concept associated with cereal domestication.

Seed-Derived Microbial Community of Wild Cicer Seedlings: Composition and Augmentation to Domesticated Cicer.

Seed-borne bacteria are a unique group of microorganisms capable of maintaining stable populations within plant tissues and seeds. These bacteria may benefit their host from germination to maturation and are of great interest for basic and applied plant-microbe interaction studies. Furthermore, many such beneficial bacteria present in wild plant species are missing in their respective congeneric domesticated forms. The objectives of this study were to explore the bacterial communities within the seeds of wild Cicer species and to select beneficial bacteria which could be used to improve production of domesticated chickpea (C. arietinum). We analyzed the composition of seed-borne bacteria of chickpea (Cicer spp.), comparing wild and domesticated species from different geographic locations. Subsequently, we isolated the dominant and prevalent seed-borne bacteria from wild Cicer judaicum and assessed their ability to colonize and affect the growth of domesticated chickpea and other legume crops. The composition and structure of seed-borne bacteria, determined by amplicon sequencing of the 16S rRNA gene, differed between wild and domesticated chickpea and varied among geographic locations. The genus Burkholderia dominated samples from domesticated chickpea at all examined sites, while Bacillus or Sphingomonas dominated cultures isolated from wild C. judaicum, dependent on geographic location. A particular Bacillus strain, Bacillus sp. CJ, representing the most prevalent bacterium in wild C. judaicum, was further isolated. Bacillus sp. CJ, applied by seed coating, successfully inhabited domesticated chickpea plants and improved plant growth parameters. These results demonstrate the potential for reconstructing the microbiota of crop plants using the wild microbiota reservoir. IMPORTANCE Chickpea (garbanzo bean, hummus, Cicer arietinum) representing the third legume crop produced globally. As is the case for many other domesticated crops, the adaptation and resistance of chickpea to biotic and abiotic stresses is inferior compared to that of their wild progenitors and relatives. Re-establishing desirable characteristics from wild to domesticated species may be achieved by reconstructing beneficial microbiota. In this study, we examined the seed-associated microbiota of both wild and domesticated chickpea and applied isolated beneficial bacteria originating from wild Cicer judaicum to domesticated chickpea by seed coating. This isolate, Bacillus sp. CJ, was successfully established in the crop and enhanced its growth, demonstrating effective and efficient manipulation of the chickpea microbiota as a potential model for future application in other crop plants.

Genetic analysis of wheat domestication and evolution under domestication.

Wheat is undoubtedly one of the world's major food sources since the dawn of Near Eastern agriculture and up to the present day. Morphological, physiological, and genetic modifications involved in domestication and subsequent evolution under domestication were investigated in a tetraploid recombinant inbred line population, derived from a cross between durum wheat and its immediate progenitor wild emmer wheat. Experimental data were used to test previous assumptions regarding a protracted domestication process. The brittle rachis (Br) spike, thought to be a primary characteristic of domestication, was mapped to chromosome 2A as a single gene, suggesting, in light of previously reported Br loci (homoeologous group 3), a complex genetic model involved in spike brittleness. Twenty-seven quantitative trait loci (QTLs) conferring threshability and yield components (kernel size and number of kernels per spike) were mapped. The large number of QTLs detected in this and other studies suggests that following domestication, wheat evolutionary processes involved many genomic changes. The Br gene did not show either genetic (co-localization with QTLs) or phenotypic association with threshability or yield components, suggesting independence of the respective loci. It is argued here that changes in spike threshability and agronomic traits (e.g. yield and its components) are the outcome of plant evolution under domestication, rather than the result of a protracted domestication process. Revealing the genomic basis of wheat domestication and evolution under domestication, and clarifying their inter-relationships, will improve our understanding of wheat biology and contribute to further crop improvement.

Prospects for the natural distribution of crop wild-relatives with limited adaptability: The case of the wild pea Pisum fulvum.

Plant breeders and conservationist depend on knowledge about the genetic variation of their species of interest. Pisum fulvum, a wild relative of domesticated pea, has attracted attention as a genetic resource for crop improvement, yet little information about its diversity in the wild has been published hitherto. We sampled 15 populations of P. fulvum from Israeli natural habitats and conducted genotyping by sequencing to analyse their genetic diversity and adaptive state. We also attempted to evaluate the species past demography and the prospects of its future reaction to environmental changes. The results suggest that genetic diversity of P. fulvum is low to medium and is distributed between well diverged populations. Surprisingly, with 56 % in the total population the selfing rate was found to be significantly lower than expected from a species that is commonly assumed to be a predominant selfer. We found a strong genetic bottleneck during the last glacial period and only limited patterns of isolation by distance and environment, which explained 13 %-18 % of the genetic variation. Despite the weak signatures of genome-wide IBE, 1,354 markers were significantly correlated with environmental factors, 1,233 of which were located within known genes with a nonsynonymous to synonymous ratio of 0.382. Species distribution modelling depicted an ongoing fragmentation and decreased habitable area over the next 80 years under two different socio-economic pathways. Our results suggest that complex interactions of substantial drift and selection shaped the genome of P. fulvum. Climate changeis likely to cause further erosion of genetic diversity in P. fulvum. Systematic ex-situ conservation may be advisable to safeguard genetic variability for future utilization of this species.

In-Field Comparative Study of Landraces vs. Modern Wheat Genotypes under a Mediterranean Climate.

The Near East climate ranges from arid to a Mediterranean, under which local wheat landraces have been grown for over millennia, assumingly accumulating a unique repertoire of genetic adaptations. In the current study, we subjected a subset of the Israeli Palestinian Landraces (IPLR) collection (n = 19: durum and bread wheat landraces, modern wheat cultivars, and landraces mixtures) to full-field evaluation. The multifield experiment included a semiarid site (2018-2019, 2019-2020) under low (L) and high (H) supplementary irrigation, and a Mediterranean site (2019-2020). Water availability had a major impact on crop performance. This was reflected in a strong discrimination between environments for biomass productivity and yield components. Compared to landraces, modern cultivars exhibited significantly higher grain yield (GY) across environments (+102%) reflecting the effect of the Green Revolution. However, under the Gilat19 (L) environment, this productivity gap was significantly reduced (only +39%). Five excelling landraces and the durum mix exhibited good agronomic potential across all trails. This was expressed in relatively high GY (2.3-2.85 t ha-1), early phenology (86-96 days to heading) and lodging resistance. Given the growing interest of stakeholders and consumers, these might be considered future candidates for the local artisanal wheat grain market. Yet, this step should be taken only after establishing an adjustable field management protocol.

Assessing adaptive requirements and breeding potential of spelt under Mediterranean environment.

The rising demand for spelt wheat (Triticum aestivum ssp. spelta) as a high-value grain crop has raised interest in its introduction into non-traditional spelt growing areas. This study aimed to assess adaptive constrains of spelt under short Mediterranean season. At first screening of a wide spelt collection for phenology and allelic distribution at the photoperiod (PPD) and vernalization (VRN) loci was done. In addition an in-depth phenotypic evaluation of a selected panel (n = 20) was performed, including agronomically important traits and concentration of grain mineral (GMC) and grain protein (GPC) content. Results from both wide screening and in-depth in panel (group of 18 spelt lines and two bread wheat lines) evaluation shows that the major adaptive constraint for spelt under Mediterranean conditions is late heading, caused by day length sensitivity, as evident from phenology and allelic profile (PPD and VRN). All lines carrying the photoperiod-sensitive allele (PPD-D1b) were late flowering (> 120DH). Based on the panel field evaluations those consequently suffer from low grain yield and poor agronomic performances. As for minerals, GMC for all but Zn, significantly correlated with GPC. In general, GMC negatively correlated with yield which complicated the assessment of GMC per-se and challenge the claim for higher mineral content in spelt grains. The exceptions were, Fe and Zn, which did not correlate with yield. Spelt lines showing high Fe and Zn concentration in a high-yield background illustrate their potential for spelt wheat breeding. Improving spelt adaptation to Mediterranean environments could be mediated by introducing the insensitive-PPD-D1a allele to spelt wheat background. Following this breeding path spelt could better compete with bread wheat under short season with limited and fluctuating rain fall.

A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L.

BACKGROUND: Chickpea (Cicer arietinum L.) is the third most important pulse crop worldwide. Despite its importance, relatively little is known about its genome. The availability of a genome-wide physical map allows rapid fine mapping of QTL, development of high-density genome maps, and sequencing of the entire genome. However, no such a physical map has been developed in chickpea. RESULTS: We present a genome-wide, BAC/BIBAC-based physical map of chickpea developed by fingerprint analysis. Four chickpea BAC and BIBAC libraries, two of which were constructed in this study, were used. A total of 67,584 clones were fingerprinted, and 64,211 (~11.7 x) of the fingerprints validated and used in the physical map assembly. The physical map consists of 1,945 BAC/BIBAC contigs, with each containing an average of 28.3 clones and having an average physical length of 559 kb. The contigs collectively span approximately 1,088 Mb. By using the physical map, we identified the BAC/BIBAC contigs containing or closely linked to QTL4.1 for resistance to Didymella rabiei (RDR) and QTL8 for days to first flower (DTF), thus further verifying the physical map and confirming its utility in fine mapping and cloning of QTL. CONCLUSION: The physical map represents the first genome-wide, BAC/BIBAC-based physical map of chickpea. This map, along with other genomic resources previously developed in the species and the genome sequences of related species (soybean, Medicago and Lotus), will provide a foundation necessary for many areas of advanced genomics research in chickpea and other legume species. The inclusion of transformation-ready BIBACs in the map greatly facilitates its utility in functional analysis of the legume genomes.

Ecological genetic divergence of the fungal pathogen Didymella rabiei on sympatric wild and domesticated Cicer spp. (Chickpea).

For millennia, chickpea (Cicer arietinum) has been grown in the Levant sympatrically with wild Cicer species. Chickpea is traditionally spring-sown, while its wild relatives germinate in the autumn and develop in the winter. It has been hypothesized that the human-directed shift of domesticated chickpea to summer production was an attempt to escape the devastating Ascochyta disease caused by Didymella rabiei. We estimated genetic divergence between D. rabiei isolates sampled from wild Cicer judaicum and domesticated C. arietinum and the potential role of temperature adaptation in this divergence. Neutral genetic markers showed strong differentiation between pathogen samples from the two hosts. Isolates from domesticated chickpea demonstrated increased adaptation to higher temperatures when grown in vitro compared with isolates from the wild host. The distribution of temperature responses among progeny from crosses of isolates from C. judaicum with isolates from C. arietinum was continuous, suggesting polygenic control of this trait. In vivo inoculations of host plants indicated that pathogenic fitness of the native isolates was higher than that of their hybrid progeny. The results indicate that there is a potential for adaptation to higher temperatures; however, the chances for formation of hybrids which are capable of parasitizing both hosts over a broad temperature range are low. We hypothesize that this pathogenic fitness cost is due to breakdown of coadapted gene complexes controlling pathogenic fitness on each host and may be responsible for maintenance of genetic differentiation between the pathogen demes.