A Genome-Wide Association Study Identifying Single-Nucleotide Polymorphisms for Iron and Zinc Biofortification in a Worldwide Barley Collection.

Micronutrient deficiency affects half of the world's population, mostly in developing countries. Severe health issues such as anemia and inadequate growth in children below five years of age and pregnant women have been linked to mineral deficiencies (mostly zinc and iron). Improving the mineral content in staple crops, also known as mineral biofortification, remains the best approach to address mineral malnutrition. Barley is a staple crop in some parts of the world and is a healthy choice since it contains ß-glucan, a high dietary protein. Barley mineral biofortification, especially with zinc and iron, can be beneficial since barley easily adapts to marginalized areas and requires less input than other frequently consumed cereals. In this study, we analyzed zinc and iron content in 496 barley samples. The samples were genotyped with an Illumina 50 K SNP chip. Genome-wide association studies (GWAS) identified 62 SNPs and 68 SNPs (p < 0.001) associated with iron and zinc content in grains, respectively. After a Bonferroni correction (p < 0.005), there were 12 SNPs (single-nucleotide polymorphism) associated with Zn and 6 for iron. SNP annotations revealed proteins involved in membrane transport, Zn and Fe binding, linked to nutrient remobilization in grains. These results can be used to develop biofortified barley via marker-assisted selection (MAS), which could alleviate mineral malnutrition.

Genotypic variation in root architectural traits under contrasting phosphorus levels in Mediterranean and Indian origin lentil genotypes.

The development of phosphorus-efficient crop cultivars boosts productivity while lowering eutrophication in the environment. It is feasible to improve the efficiency of phosphorus (P) absorption in lentils by enhancing phosphorus absorption through root architectural traits. The root architectural traits of 110 diverse lentil genotypes of Indian and Mediterranean origin were assessed, and the relationships between traits were investigated. In a hydroponics experiment, the lentil lines were examined at the seedling stage under two conditions: adequate P supply and deficient P supply. The Pearson correlation coefficients between root architectural traits and genetic diversity among lentil lines were assessed. To estimate variance components, a model (fixed factor) was used. In this experiment, both phosphorus (P) and genotype were fixed variables. Our lentil lines showed significant genetic variability and considerable genetic diversity for all traits under both treatments. The TRL (total root length) and PRL (primary root length) showed strong positive associations with all other characteristics excluding root average diameter (RAD) in both P treatments. In both P treatments, the RAD revealed a negative significant association with Total Root Tips (TRT), as well as total root volume (TRV) and total root forks (TRF) in the deficit conditions of P. Total root volume (TRV), total surface area (TSA), and total root tips had higher coefficient variance values. The first two principal components represented 67.88% and 66.19% of the overall variance in the adequate and deficit P treatments respectively. The Shannon-Weaver diversity index (H') revealed that RAD, PRL, and TSA had more variability than TRT and TRF under both treatments. According to the Comprehensive Phosphorus Efficiency Measure (CPEM), the best five highly efficient genotypes are PLL 18-09, PLS 18-01, PLL 18-25, PLS 18-23, and PLL 18-07, while IG112131, P560206, IG334, L11-231, and PLS18-67 are highly inefficient genotypes. The above contrasting diverse lentil genotypes can be utilized to produce P-efficient lentil cultivars. The lentil germplasm with potentially favorable root traits can be suggested to evaluated for other abiotic stress to use them in crop improvement programme. The scientific breakthroughs in root trait phenotyping have improved the chances of establishing trait-allele relationships. As a result, genotype-to-phenotype connections can be predicted and verified with exceptional accuracy, making it easier to find and incorporate favourable nutrition-related genes/QTLs in to breeding programme.

Co-Inoculation of Mesorhizobium ciceri with Either Bacillus sp. or Enterobacter aerogenes on Chickpea Improves Growth and Productivity in Phosphate-Deficient Soils in Dry Areas of a Mediterranean Region.

Biological nitrogen fixation requires a large amount of phosphorus (P). However, most of the soils are P-deficient and the extensive use of P- chemical fertilizers constitute a serious threat to the environment. In this context, two field experiments were carried out to investigate the effect of co-inoculation of Mesorhizobium ciceri with phosphate solubilizing bacteria (PSB), Bacillus sp., and Enterobacter aerogenes, on chickpea as an alternative to chemical nitrogen (N) and phosphorous fertilizers in P-deficient soils in dry areas of Morocco. The results revealed that combined inoculation of chickpea with rhizobia and PSB showed a significant enhancement of chickpea nodulation, biomass production, yields and N, P, and protein content in grains as compared to single inoculation or single application of N or P. A significantly higher increase was obtained by inoculating chickpea with Mesorhizobium sp. MA72 combined with E. aerogenes P1S6. This combination allowed an enhancement of more than 270% in nodulation, 192% in shoot dry weight and 242% in grain yield. The effect of this combination was equivalent to the effect of combined application of N and P fertilizers. Formulation of biofertilizers based on tasted strains could be used for chickpea co-inoculation in P-deficient soils for an eco-friendly sustainable production of chickpea.

The Global Durum Wheat Panel (GDP): An International Platform to Identify and Exchange Beneficial Alleles.

Representative, broad and diverse collections are a primary resource to dissect genetic diversity and meet pre-breeding and breeding goals through the identification of beneficial alleles for target traits. From 2,500 tetraploid wheat accessions obtained through an international collaborative effort, a Global Durum wheat Panel (GDP) of 1,011 genotypes was assembled that captured 94-97% of the original diversity. The GDP consists of a wide representation of Triticum turgidum ssp. durum modern germplasm and landraces, along with a selection of emmer and primitive tetraploid wheats to maximize diversity. GDP accessions were genotyped using the wheat iSelect 90K SNP array. Among modern durum accessions, breeding programs from Italy, France and Central Asia provided the highest level of genetic diversity, with only a moderate decrease in genetic diversity observed across nearly 50 years of breeding (1970-2018). Further, the breeding programs from Europe had the largest sets of unique alleles. LD was lower in the landraces (0.4 Mbp) than in modern germplasm (1.8 Mbp) at r 2 = 0.5. ADMIXTURE analysis of modern germplasm defined a minimum of 13 distinct genetic clusters (k), which could be traced to the breeding program of origin. Chromosome regions putatively subjected to strong selection pressure were identified from fixation index (F st ) and diversity reduction index (DRI) metrics in pairwise comparisons among decades of release and breeding programs. Clusters of putative selection sweeps (PSW) were identified as co-localized with major loci controlling phenology (Ppd and Vrn), plant height (Rht) and quality (gliadins and glutenins), underlining the role of the corresponding genes as driving elements in modern breeding. Public seed availability and deep genetic characterization of the GDP make this collection a unique and ideal resource to identify and map useful genetic diversity at loci of interest to any breeding program.

Functional Dissection of the Chickpea (Cicer arietinum L.) Stay-Green Phenotype Associated with Molecular Variation at an Ortholog of Mendel's I Gene for Cotyledon Color: Implications for Crop Production and Carotenoid Biofortification.

"Stay-green" crop phenotypes have been shown to impact drought tolerance and nutritional content of several crops. We aimed to genetically describe and functionally dissect the particular stay-green phenomenon found in chickpeas with a green cotyledon color of mature dry seed and investigate its potential use for improvement of chickpea environmental adaptations and nutritional value. We examined 40 stay-green accessions and a set of 29 BC2F4-5 stay-green introgression lines using a stay-green donor parent ICC 16340 and two Indian elite cultivars (KAK2, JGK1) as recurrent parents. Genetic studies of segregating populations indicated that the green cotyledon trait is controlled by a single recessive gene that is invariantly associated with the delayed degreening (extended chlorophyll retention). We found that the chickpea ortholog of Mendel's I locus of garden pea, encoding a SGR protein as very likely to underlie the persistently green cotyledon color phenotype of chickpea. Further sequence characterization of this chickpea ortholog CaStGR1 (CaStGR1, for carietinum stay-green gene 1) revealed the presence of five different molecular variants (alleles), each of which is likely a loss-of-function of the chickpea protein (CaStGR1) involved in chlorophyll catabolism. We tested the wild type and green cotyledon lines for components of adaptations to dry environments and traits linked to agronomic performance in different experimental systems and different levels of water availability. We found that the plant processes linked to disrupted CaStGR1 gene did not functionality affect transpiration efficiency or water usage. Photosynthetic pigments in grains, including provitaminogenic carotenoids important for human nutrition, were 2-3-fold higher in the stay-green type. Agronomic performance did not appear to be correlated with the presence/absence of the stay-green allele. We conclude that allelic variation in chickpea CaStGR1 does not compromise traits linked to environmental adaptation and agronomic performance, and is a promising genetic technology for biofortification of provitaminogenic carotenoids in chickpea.

Phenotypic and Genotypic Diversity Among Symbiotic and Non-symbiotic Bacteria Present in Chickpea Nodules in Morocco.

Environmental pollution problems and increased demand for green technologies in production are forcing farmers to introduce agricultural practices with a lower impact on the environment. Chickpea (Cicer arietinum) in arid and semi-arid environments is frequently affected by harsh environmental stresses such as heat, drought and salinity, which limit its growth and productivity and affect biological nitrogen fixation ability of rhizobia. Climate change had further aggravated these stresses. Inoculation with appropriate stress tolerant rhizobia is necessary for an environmentally friendly and sustainable agricultural production. In this study, endophytic bacteria isolated from chickpea nodules from different soil types and regions in Morocco, were evaluated for their phenotypic and genotypic diversity in order to select the most tolerant ones for further inoculation of this crop. Phenotypic characterization of 135 endophytic bacteria from chickpea nodules showed a wide variability for tolerance to heavy metals and antibiotics, variable response to extreme temperatures, salinity, pH and water stress. 56% of isolates were able to nodulate chickpea. Numerical analysis of rep-PCR results showed that nodulating strains fell into 22 genotypes. Sequencing of 16S rRNA gene of endophytic bacteria from chickpea nodules revealed that 55% of isolated bacteria belong to Mesorhizobium genus. Based on MLSA of core genes (recA, atpD, glnII and dnaK), tasted strains were distributed into six clades and were closely related to Mesorhizobium ciceri, Mesorhizobium opportunistum, Mesorhizobium qingshengii, and Mesorhizobium plurifarium. Most of nodulating strains were belonging to a group genetically distinct from reference Mesorhizobium species. Three isolates belong to genus Burkholderia of the class ß- proteobacteria, and 55 other strains belong to the class γ- proteobacteria. Some of the stress tolerant isolates have great potential for further inoculation of chickpea in the arid and semiarid environments to enhance biological nitrogen fixation and productivity in the context of climate change adaptation and mitigation.

Genetic diversity in algerian durum wheat varieties (Triticum turgidum L var. durum) using microsatellite markers / Diversidade genética em variedades de trigo duro argelino (Triticum turgidum L var. durum) usando marcadores microssatélites

Characterization of germplasm by DNA-markers provides powerful tool to precise germplasm identification. This study aimed to quantify the genetic diversity and to estimate the phylogenetic relationship among genotypes in many crop species. The results of the present study realized between Nov and Dec 2016 in biotechnologie unit (ICARDA, Morocco) which aimed to characterize a subset of 14 Algerian selected durum wheat cultivars (Triticum turgidum L. var. durum), using 13 SSR (Single Sequence Repeat) indicated the presence of a total of 39 alleles. The genetic diversity at the 13 microsatellites loci varied from 0,142 for Xgwm337 to 0.735 for Xgwm213 with a mean of 0.444. Polymorphic information content (PIC) values ranged from 0.13 to 0.70 and the genetic distance among the cultivars from 0.15 to 0.77. Clustering analysis showed that the studied varieties were grouped according to their population of origin, suggesting a provenance effect in their ordination. In fact the most similar varieties were those introduced from CIMMYT-ICARDA breeding program, which may have common parents in their pedigree. Selections from local landraces were more similar to each other and dissimilar to CIMMYT-ICARDA material, showing an agro-ecological adaptation.

A caracterização de germoplasma por marcadores de DNA fornece uma ferramenta poderosa para a identificação precisa de germoplasma, quantificar a diversidade genética e estimar a relação filogenética entre genótipos em muitas espécies de culturas. Os resultados do presente estudo foram realizados entre novembro e dezembro de 2016 na unidade de biotecnologia (ICARDA, Marrocos) que objetivou caracterizar um subconjunto de 14 cultivares de trigo duro argelinos selecionados (Triticum turgidum L. var. durum), utilizando 13 SSR (Single Sequence Repeat ) indicou a presença de um total de 39 alelos. A diversidade genética nos 13 locos de microssatélites variou de 0,142 para Xgwm337 a 0,735 para Xgwm213 com uma média de 0,444. Os valores do conteúdo de informação polimórfica (PIC) variaram de 0,13 a 0,70 e a distância genética entre as cultivares de 0,15 a 0,77. A análise de agrupamento mostrou que as variedades estudadas foram agrupadas de acordo com sua população de origem, sugerindo um efeito de proveniência em sua ordenação. De fato, as variedades mais similares foram aquelas introduzidas no programa de criação CIMMYT-ICARDA, que podem ter pais comuns em seu pedigree. Seleções de variedades locais foram mais similares entre si e diferentes do material CIMMYT-ICARDA, mostrando uma adaptação agroecológica.

Allelic variation at high-molecular weight and low-molecular weight glutenin subunit genes in Moroccan bread wheat and durum wheat cultivars.

Glutenin is a major protein fraction contributing to the functional properties of gluten and dough. The glutenin constitutes 30-40% of the protein in wheat flour and about half of that in gluten. It is essential to identify correct glutenin alleles and to improve wheat quality by selecting alleles that exert favorable effects. Moroccan wheat cultivars are unique in West Asia and North Africa region, since many of them possess resistance to Hessian fly, a pest, which is becoming important in other countries in the region. Hence, these cultivars are being used as donor for the resistance in the breeding program. Here, we determine the allelic variation in high-molecular weight glutenin subunits (HMW-GS) and low-molecular weight glutenin subunits (LMW-GS) in Moroccan cultivars of bread and durum wheat using the gene-specific PCR markers. In 20 cultivars of bread wheat, 9 different allele variants were detected at HMW-GS and 13 different allele variants were detected at LMW-GS, in which the alleles Glu-A1b (2*), Glu-B1i (17 + 18), Glu-B1c (7*/7 + 9), Glu-D1d (5 + 10), Glu-A3c, Glu-B3 h, and Glu-D3b were the most frequents. In 26 cultivars of durum wheat, less allelic variation was found: seven different allele variants at HMW-GS and six different allele variants at LMW-GS were identified, in which the major alleles were Glu-A1c (null), Glu-B1b (7 + 8), Glu-B1e (20), Glu-A3c, and Glu-B3d. The mean value of the genetic diversity for the glutenin loci was 0.502 in bread wheat and 0.449 in durum wheat. Most of the glutenin alleles carried by Moroccan bread wheat cultivars impart good bread-making quality. Most of the durum wheat glutenin alleles were related to low strength dough or poor quality and need to be improved. To improve quality of Moroccan durum wheat, essentially, Glu-A1c and Glu-B3d alleles of the genes should be replaced with the better alleles through breeding.

Identification of Quantitative Trait Loci Controlling Root and Shoot Traits Associated with Drought Tolerance in a Lentil (Lens culinaris Medik.) Recombinant Inbred Line Population.

Drought is one of the major abiotic stresses limiting lentil productivity in rainfed production systems. Specific rooting patterns can be associated with drought avoidance mechanisms that can be used in lentil breeding programs. In all, 252 co-dominant and dominant markers were used for Quantitative Trait Loci (QTL) analysis on 132 lentil recombinant inbred lines based on greenhouse experiments for root and shoot traits during two seasons under progressive drought-stressed conditions. Eighteen QTLs controlling a total of 14 root and shoot traits were identified. A QTL-hotspot genomic region related to a number of root and shoot characteristics associated with drought tolerance such as dry root biomass, root surface area, lateral root number, dry shoot biomass and shoot length was identified. Interestingly, a QTL (QRSratioIX-2.30) related to root-shoot ratio, an important trait for drought avoidance, explaining the highest phenotypic variance of 27.6 and 28.9% for the two consecutive seasons, respectively, was detected. This QTL was closed to the co-dominant SNP marker TP6337 and also flanked by the two SNP TP518 and TP1280. An important QTL (QLRNIII-98.64) related to lateral root number was found close to TP3371 and flanked by TP5093 and TP6072 SNP markers. Also, a QTL (QSRLIV-61.63) associated with specific root length was identified close to TP1873 and flanked by F7XEM6b SRAP marker and TP1035 SNP marker. These two QTLs were detected in both seasons. Our results could be used for marker-assisted selection in lentil breeding programs targeting root and shoot characteristics conferring drought avoidance as an efficient alternative to slow and labor-intensive conventional breeding methods.

Correlation between the Chemical and Genetic Relationships among Thymus saturejoides Genotypes Cultured under in vitro and in vivo Environments.

In this study, the in vitro and in vivo essential oil (EO) composition and genetic variability in six micropropagated genotypes of Thymus saturejoides Coss., a Mediterranean medicinal and aromatic plant, were analyzed by GC/MS and randomly amplified polymorphic DNA (RAPD). Yield and composition of the EO varied between genotypes. Cluster analysis based on RAPD data and EO grouped the six genotypes in three groups in both culture conditions, thus showing considerable intraspecific genetic and chemical variations. Applying the Mantel test, the result showed a significant correlation between the two proximity matrices RAPD and EO obtained from in vitro genotypes, whereas this correlation was not observed when using the EO obtained from the in vivo genotypes.

Genetic characterization of Moroccan and the exotic bread wheat cultivars using functional and random DNA markers linked to the agronomic traits for genomics-assisted improvement.

Genetic characterization, diversity analysis and estimate of the genetic relationship among varieties using functional and random DNA markers linked to agronomic traits can provide relevant guidelines in selecting parents and designing new breeding strategies for marker-assisted wheat cultivar improvement. Here, we characterize 20 Moroccan and 19 exotic bread wheat (Triticum aestivum L.) cultivars using 47 functional and 7 linked random DNA markers associated with 21 loci of the most important traits for wheat breeding. The functional marker analysis revealed that 35, 45, and 10 % of the Moroccan cultivars, respectively have the rust resistance genes (Lr34/Yr18/Pm38), dwarfing genes (Rht1b or Rht2b alleles) and the leaf rust resistance gene (Lr68). The marker alleles for genes Lr37/Yr17/Sr38, Sr24 and Yr36 were present only in the exotic cultivars and absent in Moroccan cultivars. 25 % of cultivars had 1BL.1RS translocation. 70 % of the wheat cultivars had Ppo-D1a and Ppo-A1b associated with low polyphenol oxidase activity. 10 % of cultivars showed presence of a random DNA marker allele (175 bp) linked to Hessian fly resistance gene H22. The majority of the Moroccan cultivars were carrying alleles that impart good bread making quality. Neighbor joining (NJ) and principal coordinate analysis based on the marker data revealed a clear differentiation between elite Moroccan and exotic wheat cultivars. The results of this study are useful for selecting suitable parents for making targeted crosses in marker-assisted wheat breeding and enhancing genetic diversity in the wheat cultivars.

Phenotypic and genetic diversity in Sinorhizobium meliloti and S. medicae from drought and salt affected regions of Morocco.

BACKGROUND: Sinorhizobium meliloti and S. medicae are symbiotic nitrogen fixing bacteria in root nodules of forage legume alfalfa (Medicago sativa L.). In Morocco, alfalfa is usually grown in marginal soils of arid and semi-arid regions frequently affected by drought, extremes of temperature and soil pH, soil salinity and heavy metals, which affect biological nitrogen fixing ability of rhizobia and productivity of the host. This study examines phenotypic diversity for tolerance to the above stresses and genotypic diversity at Repetitive Extragenic Pallindromic DNA regions of Sinorhizobium nodulating alfalfa, sampled from marginal soils of arid and semi-arid regions of Morocco. RESULTS: RsaI digestion of PCR amplified 16S rDNA of the 157 sampled isolates, assigned 136 isolates as S. meliloti and the rest as S. medicae. Further phenotyping of these alfalfa rhizobia for tolerance to the environmental stresses revealed a large degree of variation: 55.41%, 82.16%, 57.96% and 3.18% of the total isolates were tolerant to NaCl (>513 mM), water stress (-1.5 MPa), high temperature (40 degrees C) and low pH (3.5), respectively. Sixty-seven isolates of S. meliloti and thirteen isolates of S. medicae that were tolerant to salinity were also tolerant to water stress. Most of the isolates of the two species showed tolerance to heavy metals (Cd, Mn and Zn) and antibiotics (chloramphenicol, spectinomycin, streptomycin and tetracycline). The phenotypic clusters observed by the cluster analysis clearly showed adaptations of the S. meliloti and S. medicae strains to the multiple stresses. Genotyping with rep-PCR revealed higher genetic diversity within these phenotypic clusters and classified all the 157 isolates into 148 genotypes. No relationship between genotypic profiles and the phenotypes was observed. The Analysis of Molecular Variance revealed that largest proportion of significant (P < 0.01) genetic variation was distributed within regions (89%) than among regions (11%). CONCLUSION: High degree of phenotypic and genotypic diversity is present in S. meliloti and S. medicae populations from marginal soils affected by salt and drought, in arid and semi-arid regions of Morocco. Some of the tolerant strains have a potential for exploitation in salt and drought affected areas for biological nitrogen fixation in alfalfa.

Asymmetric allele-specific expression in relation to developmental variation and drought stress in barley hybrids.

In the present study, we analysed allele-specific expression (ASE) in the selfing species barley to assess the frequency of cis-acting regulatory variation and the effects of genetic background, developmental differences and drought stress on allelic expression levels. We measured ASE ratios in 30 genes putatively involved in stress responses in five hybrids and their reciprocals, namely Hordeum spontaneum 41-1/Alexis (HAl), Hordeum spontaneum 41-1/Arta (HAr), Sloop/WI3408 (SW), Tadmor/Sloop (TS) and Tadmor/WI3408 (TW). In order to detect cis-acting variation related to drought and developmental changes, the barley hybrids were grown under control and water-limited conditions, and leaf tissue was harvested at two developmental stages. The analysis demonstrated that more than half of the genes measured (63%) showed allelic differences in expression of up to 19-fold due to cis-regulatory variation in at least one cross by treatment/stage combination. Drought stress induced changes in allelic expression ratios, indicating differences between drought responsive cis-elements. In addition, ASE differences between developmental stages suggested the presence of cis-acting elements interacting with developmental cues. We were also able to demonstrate that the levels and frequency of allelic imbalance and hence differences in cis-regulatory elements are correlated with the genetic divergence between the parental lines, but may also arise as an adaptation to diverse habitats. Our findings suggest that cis-regulatory variation is a common phenomenon in barley, and may provide a molecular basis of transgression. Differential expression of near-isogenic members of the same gene family could potentially result in hybrid lines out performing their parents in terms of expression level, timing and response to developmental and environmental cues. Identification and targeted manipulation of cis-regulatory elements will assist in breeding improved crops with a better adaptation to changing environments.

SuperSAGE: the drought stress-responsive transcriptome of chickpea roots.

BACKGROUND: Drought is the major constraint to increase yield in chickpea (Cicer arietinum). Improving drought tolerance is therefore of outmost importance for breeding. However, the complexity of the trait allowed only marginal progress. A solution to the current stagnation is expected from innovative molecular tools such as transcriptome analyses providing insight into stress-related gene activity, which combined with molecular markers and expression (e)QTL mapping, may accelerate knowledge-based breeding. SuperSAGE, an improved version of the serial analysis of gene expression (SAGE) technique, generating genome-wide, high-quality transcription profiles from any eukaryote, has been employed in the present study. The method produces 26 bp long fragments (26 bp tags) from defined positions in cDNAs, providing sufficient sequence information to unambiguously characterize the mRNAs. Further, SuperSAGE tags may be immediately used to produce microarrays and probes for real-time-PCR, thereby overcoming the lack of genomic tools in non-model organisms. RESULTS: We applied SuperSAGE to the analysis of gene expression in chickpea roots in response to drought. To this end, we sequenced 80,238 26 bp tags representing 17,493 unique transcripts (UniTags) from drought-stressed and non-stressed control roots. A total of 7,532 (43%) UniTags were more than 2.7-fold differentially expressed, and 880 (5.0%) were regulated more than 8-fold upon stress. Their large size enabled the unambiguous annotation of 3,858 (22%) UniTags to genes or proteins in public data bases and thus to stress-response processes. We designed a microarray carrying 3,000 of these 26 bp tags. The chip data confirmed 79% of the tag-based results, whereas RT-PCR confirmed the SuperSAGE data in all cases. CONCLUSION: This study represents the most comprehensive analysis of the drought-response transcriptome of chickpea available to date. It demonstrates that--inter alias--signal transduction, transcription regulation, osmolyte accumulation, and ROS scavenging undergo strong transcriptional remodelling in chickpea roots already 6 h after drought stress. Certain transcript isoforms characterizing these processes are potential targets for breeding for drought tolerance. We demonstrate that these can be easily accessed by micro-arrays and RT-PCR assays readily produced downstream of SuperSAGE. Our study proves that SuperSAGE owns potential for molecular breeding also in non-model crops.

Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.).

BACKGROUND: Plant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program http://www.generationcp.org conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions. RESULTS: The 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in Mediterranean and West Asia (WA), 117 in South and South East Asia (SSEA), and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild Cicer shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53%) than kabuli (46%), while wild Cicer accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78%) of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents diversity from all directions of the tree diagram of the composite collection. CONCLUSION: The genotype-based reference set, reported here, is an ideal set of germplasm for allele mining, association genetics, mapping and cloning gene(s), and in applied breeding for the development of broad-based elite breeding lines/cultivars with superior yield and enhanced adaptation to diverse environments.