Collection Of Landraces Research Articles

Genome‐Wide Association Mapping of Seedling Net Form Net Blotch Resistance in an Ethiopian and Eritrean Barley Collection

ABSTRACTThe net form of net blotch, caused by Pyrenophora teres f. teres (Ptt), is an economically important disease of barley (Hordeum vulgare L.) that is best managed by breeding for resistance. Previous linkage mapping and genome‐wide association studies (GWAS) have identified many resistance quantitative trait loci (QTL) in barley. Here we report eight novel resistance QTL identified in a unique collection of barley landraces from Ethiopia and Eritrea (EEBC) using a GWAS approach. Lines from the EEBC were genotyped with the Illumina barley iSelect chip and phenotyped with four Ptt isolates. A GWAS was conducted using the efficient mixed model association (EMMA) method with principal components and kinship to control false positives. Using a significance threshold of false discovery rate (FDR) of 0.05, two marker–trait associations (MTAs) were found on chromosomes 6H and 5H, respectively. Since this is a stringent method, markers in the lower 0.1 percentile of the p value distribution were also considered significant, identifying 20 unique MTAs. The 20 MTAs corresponded to 15 unique genomic loci, based on analysis of local linkage disequilibrium. Of the 15 QTL identified, one was identified in chromosome 1H, six in 2H, three each in 3H and 5H, and two in 6H. Eight of these QTL appear to be novel and thus could be of value to barley breeding programs to introgress novel net blotch resistance.

Assessing the Breeding Potential of Thirteen Day‐Neutral Landrace Accessions in an Upland Cotton Breeding Program

ABSTRACTAn untapped genetic resource available to cotton (Gossypium hirsutum L.) breeding programs is represented by the primitive, upland cotton landrace collection. Primarily due to their photoperiodic nature, efforts to utilize these resources have been slow. To complement efforts to develop day‐neutral converted germplasm lines, we identified a number of naturally occurring day neutral landrace genotypes and evaluated their breeding potential when crossed to elite upland germplasm lines and cultivars. The mean performance of parental lines and F2 hybrids along with genetic effect estimates indicate that naturally occurring day‐neutral landrace genotypes provided average agronomic performance while increasing fiber quality performance. Results suggest that crosses derived from naturally occurring day‐neutral genotypes and elite upland lines result in new allelic combinations that interact in both an additive and nonadditive way. However, it appears that several naturally occurring day‐neutral genotypes transmit negatively correlated alleles for agronomic performance and fiber quality that often display opposite additive and nonadditive effects. These negatively correlated allele combinations present a major challenge for cotton breeding programs. Future efforts that determine the percentage of “new” alleles present in the landrace germplasm, along with innovative breeding methods focused on efficiently capturing beneficial alleles, are needed to expand the cotton genetic base.

High-Throughput Genotype, Morphology, and Quality Traits Evaluation for the Assessment of Genetic Diversity of Wheat Landraces from Sicily.

During the XX Century, the widespread use of modern wheat cultivars drastically reduced the cultivation of ancient landraces, which nowadays are confined to niche cultivation areas. Several durum wheat landraces adapted to the extreme environments of the Mediterranean region, are still being cultivated in Sicily, Italy. Detailed knowledge of the genetic diversity of this germplasm could lay the basis for their efficient management in breeding programs, for a wide-range range of traits. The aim of the present study was to characterize a collection of durum wheat landraces from Sicily, using single nucleotide polymorphisms (SNP) markers, together with agro-morphological, phenological and quality-related traits. Two modern cv. Simeto, Claudio, and the hexaploid landrace, Cuccitta, were used as outgroups. Cluster analysis and Principal Coordinates Analysis (PCoA) allowed us to identify four main clusters across the analyzed germplasm, among which a cluster included only historical and modern varieties. Likewise, structure analysis was able to distinguish the ancient varieties from the others, grouping the entries in seven cryptic genetic clusters. Furthermore, a Principal Component Analysis (PCA) was able to separate the modern testers from the ancient germplasm. This approach was useful to classify and evaluate Sicilian ancient wheat germplasm, supporting their safeguard and providing a genetic fingerprint that is necessary for avoiding commercial frauds to sustaining the economic profits of farmers resorting to landraces cultivation.

Sensory and functional quality characterization of protected designation of origin ‘Piennolo del Vesuvio’ cherry tomato landraces from Campania-Italy

Compositional characterization was performed on seven ‘Pomodorino del Piennolo del Vesuvio’ (PPV) tomato landraces, a signature product of Campania (Italy) threatened by genetic erosion. Characterization encompassed determinations of macro-minerals, soluble carbohydrates, starch, acidity, lycopene, polyphenols, anthocyanins, protein and free amino acids. Exceptionally high dry matter (13.0 ± 0.2%) and sugar content (101.3 ± 3.8 μmol g−1 fw) and very low (0.007–0.009) Na/K ratio were invariably obtained across landraces, contrasted by significant variation in acidity (28.5–3.9 g kg−1 dw). Giagiù, Acampora and Riccia San Vito differentiated by high polyphenols content (131.8 ± 2.5 mg 100 g−1) while Acampora, Cozzolino and Fofò by high lycopene content (13.3 ± 10.6 mg 100 g−1 fw). Glutamate, GABA and glutamine represented 65% of the 22 detected amino acids mean total content. Glutamate, linked to umami taste, was highest (19.2 µmol g−1 fw) in Fofò. Our results will contribute towards the systematic documentation of sensory and functional quality profiles of an important collection of tomato landraces.

Effect of cytokinins and auxin on bud burst and direct organogenesis <i>in vitro</i> of some sweet potato landraces (<i>Ipomoea batatas</i> L.) grown in Benin

Objectives: Ipomoea batatas L. is a tuberous root plant of great nutritional and economic importance in Benin. This study aims to analyze the effects of two cytokinins (Benzylaminopurine and kinetin) and a one auxin (Naphthalene Acetic Acid) on direct organogenesis in vitro of six sweet potato landraces in Benin. Methodology and Results: Ten uninodal stems disinfected of each variety are cultivated on a Murashige and Skoog (MS) medium then transplanted onto other MS media with different combinations of Benzylaminopurine, Kinetin and Naphthalene Acetic Acid. Their vitroplants are also acclimatized. Analysis of variance was used for data analysis. The results showed that '' Amitchewin, Vobodouaho and Koidokpon '' have recorded the highest average bud burst (12.67, 12.33 and 11.67 respectively). The media MS + 1 mg.l -1 BAP + 0.1 mg.l -1 NAA and MS + 1 mg.l -1 Kin + 0.1 mg.l -1 NAA were found more effective for the organogenesis of the varieties. Vitroplants of each variety acclimatized well with survival rates ranging from 56.66% to 83.33%. Conclusion: and application of results: The results showed that the combination of 1 mg.l -1 of Benzylaminopurine or kinetin with 0.1 mg.l -1 of Naphthalene Acetic Acid was effective for in vitro organogenesis of sweet potato landraces used with well-acclimated vitroplants. This study paves the way for the establishment of in vitro collection of sweet potato landraces in Benin with a view to their ex situ preservation. Keywords: Ipomoea batatas ; growth regulators; organogenesis in vitro ; Acclimation; Benin

Exploiting Genetic and Genomic Resources to Enhance Heat-Tolerance in Tomatoes

High temperature is one of the most detrimental abiotic stresses in tomatoes. Many studies highlighted that even small increases in temperature can alter the plant reproductive system, causing a significant reduction in tomato yield. The aim of this study was to exploit the phenotypic and genomic variations of a tomato landrace collection grown at high temperatures. Fifteen genotypes were selected as the best performing in two experimental fields. The selection was based on six yield-related traits, including flower earliness, number of flowers per inflorescence, fruit set, number of fruit per plant, fruit weight and yield per plant. In order to identify markers targeting traits that could be highly influenced by adverse climate conditions, such as flowering and fruit setting, an association mapping approach was undertaken exploiting a tomato high-throughput genomic array. The phenotypic variability observed allowed us to identify a total of 15 common markers associated with the studied traits. In particular, the most relevant associations co-localized with genes involved in the floral structure development, such as the style2.1 gene, or with genes directly involved in the response to abiotic stresses. These promising candidate genes will be functionally validated and transferred to a cultivated tomato to improve its performance under high temperatures.

Genetic Diversity of Ethiopian Durum Wheat (Triticum durum Desf.) Landrace Collections as Reveled by SSR Markers

Genetic Diversity of Ethiopian Durum Wheat (Triticum durum Desf.) Landrace Collections as Reveled by SSR Markers

Status of Rice (Oryza sativa L.) Genepool Collected from Western Ghats Region of India: Gap Analysis and Diversity Distribution Mapping using GIS Tools

This paper analyses the genetic resources of cultivated and wild rice in Western Ghats region (WGR) spread in six states of the country. Landraces and wild relatives of rice (Oryza sativa L.) always form a priority germplasm for exploration, collections, conservation, evaluation and utilization. Western Ghats region is one of the 35 biodiversity hot-spots of the world and harbour large diversity of rice under its varied climatic and edaphic conditions. So far, ICAR-NBPGR, New Delhi has collected 2, 758 accessions of cultivated and 49 of wild rice germplasm from 42 districts of WGR of India. Germplasm collecting sites linked with geo-coordinates forms geo-referenced map which showed that Kerala had significant representation (2, 036 accessions), followed by Karnataka (203), Maharashtra (201), Tamil Nadu (153), Gujarat (116) and Goa (49). Highest numbers of landraces were collected from Kerala (386), followed by Tamil Nadu (92), Karnataka (88), Gujarat (56), Goa (30) and Maharashtra (26). GIS-based grid map shows that highest numbers of landraces were collected from north and central regions of Kerala, validated by the highest Shannon-Weaver diversity index (2.1–2.8). Diverse agro-ecosystems as well as selection by farmers for various uses and traits, coupled with extensive exploration efforts might have lead to the assemblage of such landraces collection from Kerala. Collected wild rice germplasm consists six taxa -Oryza meyeriana var. granulata (11), O. nivara (4), O. officinalis (4), O. rufipogon (10), O. sativa f. spontanea (19) and O. officinalis subsp. malampuzhaensis (1). Literature analysis revealed that, out of 678 rice landraces of this region, 43 have been identified/used in crop improvement as source of important traits viz. early and late maturity, aroma, high iron content, medicinal value, drought/cold/salt tolerance, resistance to brown plant hopper, etc. This analysis identified gaps and priority areas for future explorations.

Allelic effects and variations for key bread-making quality genes in bread wheat using high-throughput molecular markers

We developed and validated high-throughput Kompetitive Allele-Specific PCR (KASP) assays for key genes underpinning bread-making quality, including the wbm gene on chromosome 7AL and over-expressed glutenin Bx7OE (Glu-B1al) gene. Additionally, we used pre-existing KASP assay for Sec1 (1B.1R translocation) gene on chromosome 1B. The newly developed KASP assays were compared with gel-based markers for reliability and phenotypically validated in a diversity panel for Mixograph, Rapid Visco Analyzer (RVA) and Mixolab traits. Genotypes carrying the 1B.1R translocation had significantly lower Mixolab parameters than those without the translocation. Similarly, superior effects of the wbm+ and Bx7OE alleles on Mixograph and RVA properties and their extremely low frequencies in global wheat collections supported the idea of using these genes for bread-making quality improvement. The allele frequencies of wbm+ and Bx7OE were extremely low in historical Chinese and CIMMYT wheat germplasm, but were relatively higher in synthetic hexaploid wheats and their breeding derivatives. In both the Vavilov and Watkins global landrace collections, the frequency of wbm+ was 6.4 and 3.5%, and frequency of Bx7OE was 3.2% and 7.0%, respectively. The high-throughput marker resources and large-scale global germplasm screening provided further opportunities to exploit these genes in wheat breeding to enhance bread-making quality.

Agro-morphological diversity of Nepalese naked barley landraces

BackgroundNaked barley is a traditional, climate-resilient and highly nutritious crop of the high mountains of Nepal. Knowledge of agro-morphological diversity among the naked barely genotypes is fundamental for their efficient utilization in plant breeding schemes and effective conservation programs. The primary objective of this study is phenotypic characterization and diversity assessment of naked barley landraces in Nepal for pre-breeding purposes.MethodologyData on quantitative and qualitative traits of 25 naked barley landraces from diversity blocks established across the four mountainous locations of Nepal (Humla, Jumla, Dolakha and Lamjung) were subjected to calculation of descriptive statistics and multivariate analysis (UPGMA cluster analysis/principal component analysis). Frequency distribution of various categories of qualitative traits and Shannon–Weaver diversity indices were computed.ResultsThe UPGMA cluster analysis using both quantitative and qualitative traits individually categorized the 25 naked barley landraces in five clusters in each case with no distinct regional grouping patterns in such a way that the landraces from same or adjacent regions of origin and collection amassed in different clusters. NGRC04894, Lamjung Local, NGRC02306, NPGR1579, NGRC02327 and NPGR1579 exhibited morphoagronomical superiority and potentiality for utilization as genitors in crop improvement programs. Principal component analysis revealed the quantitative traits, viz. grain yield, plant height and earliness, and qualitative traits, viz. grain color, overall phenotypic performance, lemma awn/hood and lemma awn barbs, to be the principal discriminatory characteristics of the Nepalese naked barley landrace collection. The Shannon–Weaver diversity index (H′) ranged from 0.32 to 0.99 with a mean value of 0.73, inferring tremendous diversity in the collection for the qualitative traits.ConclusionThe marked diversity observed among the Nepalese naked barley landraces could be utilized in crop improvement for various traits. The information generated complements the robust breeding program of competitive, stable and climate-resilient varieties of end users’ preferences in different mountainous agro-ecologies and also bolsters the employment of innovative and proven participatory plant breeding approach using diversity kits and informal research and development kits to expand and promote the varietal choice options for expeditious benefits to the farmers in the high mountains, considering that only one naked barley variety, viz. Solu Uwa, has been released in Nepal to date.

Genetic and environmental factors affecting the expression of \u03b1-gliadin canonical epitopes involved in celiac disease in a wide collection of spelt (Triticum aestivum ssp. spelta) cultivars and landraces

BackgroundCeliac disease (CD) is an autoimmune disorder affecting genetically predisposed individuals whose dietary gluten proteins trigger an inflammatory reaction in the small intestine. Gluten is found in the seeds of cereals like bread wheat (Triticum aestivum ssp. aestivum) and spelt (Triticum aestivum ssp. spelta). The development of new varieties lacking immunogenic peptides is one of the strategies currently investigated to address the CD problem. Among gluten proteins, α-gliadins display the strongest immunogenicity with four main T-cell stimulatory epitopes. The objective of this work was to study the expression of α-gliadin epitopes related to CD in a wide collection of 121 spelt accessions (landraces and varieties, spring and winter accessions) from different provenances, and to analyze the correlation between the presence of epitope sequences in gDNA and their expression (cDNA). The effect of environmental factors (harvest year and N fertilization) on the epitope expression was also investigated.ResultsTaqMan probes targeting the canonical form of the epitopes were used to evaluate the epitope expression levels. Significant variations in the amount of epitope transcripts were identified between accessions and according to the provenances. Spring accessions showed a significantly higher immunogenicity than winter ones and no influence of spelt breeding on the epitope expression levels could be assessed when comparing landraces and varieties from Northwestern Europe. No correlation was observed between quantitative PCR results obtained from cDNA and gDNA for 45 accessions tested, stressing the need to use markers focusing on epitope transcripts rather than on genomic sequences. A relative stability of the amount of epitopes expressed by a same accession across four harvest years was detected. The fertilization strategy, evaluated through seven N fertilization modalities applied to two commercial spelt varieties, did not influence the epitope expression of the first variety, whereas it had a slight effect for the second one.ConclusionsThe results obtained in this work showed that the CD-related epitope expression greatly fluctuated among the spelt accessions studied. This expression was not correlated to the epitope genomic occurrence and environmental factors had almost no influence on the amount of epitope transcripts.

A northern Chinese origin of Austronesian agriculture: new evidence on traditional Formosan cereals

BackgroundGenetic data for traditional Taiwanese (Formosan) agriculture is essential for tracing the origins on the East Asian mainland of the Austronesian language family, whose homeland is generally placed in Taiwan. Three main models for the origins of the Taiwanese Neolithic have been proposed: origins in coastal north China (Shandong); in coastal central China (Yangtze Valley), and in coastal south China. A combination of linguistic and agricultural evidence helps resolve this controversial issue.ResultsWe report on botanically informed linguistic fieldwork of the agricultural vocabulary of Formosan aborigines, which converges with earlier findings in archaeology, genetics and historical linguistics to assign a lesser role for rice than was earlier thought, and a more important one for the millets. We next present the results of an investigation of domestication genes in a collection of traditional rice landraces maintained by the Formosan aborigines over a hundred years ago. The genes controlling awn length, shattering, caryopsis color, plant and panicle shapes contain the same mutated sequences as modern rice varieties everywhere else in the world, arguing against an independent domestication in south China or Taiwan. Early and traditional Formosan agriculture was based on foxtail millet, broomcorn millet and rice. We trace this suite of cereals to northeastern China in the period 6000–5000 BCE and argue, following earlier proposals, that the precursors of the Austronesians, expanded south along the coast from Shandong after c. 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BCE. This expansion introduced to Taiwan a mixed farming, fishing and intertidal foraging subsistence strategy; domesticated foxtail millet, broomcorn millet and japonica rice; a belief in the sacredness of foxtail millet; ritual ablation of the upper incisors in adolescents of both sexes; domesticated dogs; and a technological package including inter alia houses, nautical technology, and loom weaving.ConclusionWe suggest that the pre-Austronesians expanded south along the coast from that region after c. 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BCE.

Phenotypic Diversity of Rice Landraces Collected from Goa State for Salinity and Agro-morphological Traits

The present study aimed at the characterization of rice landraces collected from the state of Goa for their utilization in breeding programs. Eighteen landraces of rice were collected from the remote villages of Goa during the survey conducted between 2010 and 2013 along with passport data and traditional knowledge. All the 18 landraces were characterized for 27 qualitative and 16 quantitative characters as per the DUS guidelines. They were also screened for salt tolerance at seedling stage under microplot conditions. Qualitative characters were analyzed using Shannon diversity and Cluster analysis, whereas quantitative characters were subjected to principal component analysis (PCA). Shannon diversity index ranged from 0.00 to 1.00 with a mean of 0.60. Cluster analysis grouped the accessions into two major clusters with three subclusters in each of the main cluster with a Jaccard similarity coefficient varying between 0.38 and 0.87. PCA has revealed four major components (eigenvalue > 1), which altogether explained 80.60% of the total variation. Phenotyping for salt stress at seedling stage grouped the landraces as highly tolerant (Korgut-red), moderately tolerant (Shidde, Korgut-black) and sensitive to highly sensitive. Information generated from this study would be useful in selecting landrace collections as donors in breeding new varieties.

Hidden variation in polyploid wheat drives local adaptation.

Wheat has been domesticated into a large number of agricultural environments and has the ability to adapt to diverse environments. To understand this process, we survey genotype, repeat content, and DNA methylation across a bread wheat landrace collection representing global genetic diversity. We identify independent variation in methylation, genotype, and transposon copy number. We show that these, so far unexploited, sources of variation have had a significant impact on the wheat genome and that ancestral methylation states become preferentially “hard coded” as single nucleotide polymorphisms (SNPs) via 5-methylcytosine deamination. These mechanisms also drive local adaption, impacting important traits such as heading date and salt tolerance. Methylation and transposon diversity could therefore be used alongside SNP-based markers for breeding.

Genetic Diversity and Molecular Characterization of Iranian Durum Wheat Landraces (Triticum turgidum durum (Desf.) Husn.) Using DArT Markers.

Durum wheat is grown mainly in rain-fed regions of Iran and the Mediterranean district under stressful conditions. Different environmental conditions and agricultural practices among ancient communities have led to the development of locally adapted genotypes known as landraces. Landraces are a valued source of genetic variety and show definite adaptation to local environmental conditions according to their home of origin. This study aimed to explore linkage disequilibrium (LD) analysis and the population structure and genetic diversity of Iranian durum wheat landraces. In this study, population structure and genome-wide LD were investigated in 129 durum landrace accessions using 1500 DArT markers. Both structure and discriminant analysis of principal components obviously subdivided the sample collection into seven distinct groups centered on key ancestors and regions of origin of the germplasm. Genetic diversity among the populations was primarily within population (68 vs. 32%). Mean LD values across the entire population sample decayed below r2 of 0.11 after 1cM. LD decay of genomes A and B of Iranian durum wheat landrace is approximately 2-3cM (r2 = 0.11) and approximately 0.5cM (r2 = 0.12), respectively. Altogether, low LD decay, a high number of subpopulations, and the high existence of genetic diversity among and within populations were characteristics of the Iranian durum landrace collection. Hence, the existing genetic diversity within the population can be associated with the very long evolutionary history of plants in Iran. The populations we studied are hence presented as a valuable resource that can be used in basic and applied research in durum wheat breeding.

Genetic variability of faba bean genotypes for chocolate spot (Botrytis fabae) resistance and yield

Faba bean (Vicia faba L.) has high utility as a food and soil fertility improving crop. One of the major fungal pathogens of faba bean is Botrytis fabae, the causative agent of chocolate spot. The disease affects significantly the leaf, stem, pod and seed of faba bean compromise its productivity in the smallholder farming sector. Nonetheless, there are limited resistant/tolerant faba bean varieties available and disease control technology options. Therefore, it was prudent to evaluate faba bean landraces for chocolate spot resistance. Fifty landraces together with ten improved varieties were evaluated both in the field and in the greenhouse under natural and artificial inoculation with previously selected aggressive Botrytis fabae isolate (Iso-016) from West Gojjam, in Ethiopia. There were highly significant differences (p < 0.001) among the landraces for reaction to the disease and agronomic traits. Significant positive correlation was recorded between reaction of genotypes in the field and greenhouse disease data. The overall mean disease epidemics varied from 92.5 to 697.5 for the area under disease progress curve (AUDPC). The highest level of resistance was found in the ICARDA lines, ILB-4726, ILB-938 and BPL-710. Of all 18 landrace collections displayed significantly lower disease reaction than the susceptible check. However the resistance was moderate. The selected eighteen landraces will be recommended for use in breeding for chocolate resistance. Overall, resistance was highly heritable, suggesting that phenotypic selection can be exploited to improve chocolate spot resistance in faba bean varieties.

Genome-Wide Association Mapping for Cold Tolerance in a Core Collection of Rice (Oryza sativa L.) Landraces by Using High-Density Single Nucleotide Polymorphism Markers From Specific-Locus Amplified Fragment Sequencing.

Understanding the genetic mechanism of cold tolerance in rice is important to mine elite genes from rice landraces and breed excellent cultivars for this trait. In this study, a genome-wide association study (GWAS) was performed using high-density single nucleotide polymorphisms (SNPs) obtained using specific-locus amplified fragment sequencing (SLAF-seq) technology from a core collection of landraces of rice. A total of 67,511 SNPs obtained from 116,643 SLAF tags were used for genotyping the 150 accessions of rice landraces in the Ting’s rice core collection. A compressed mixed liner model was used to perform GWAS by using the high-density SNPs for cold tolerance in rice landraces at the seedling stage. A total of 26 SNPs were found to be significantly (P < 1.48 × 10-7) associated with cold tolerance, which could explained phenotypic variations ranging from 26 to 33%. Among them, two quantitative trait loci (QTLs) were mapped closely to the previously cloned/mapped genes or QTLs for cold tolerance. A newly identified QTL for cold tolerance in rice was further characterized by sequencing, real time-polymerase chain reaction, and bioinformatics analyses. One candidate gene, i.e., Os01g0620100, showed different gene expression levels between the cold tolerant and sensitive landraces under cold stress. We found the difference of coding amino acid in Os01g0620100 between cold tolerant and sensitive landraces caused by polymorphism within the coding domain sequence. In addition, the prediction of Os01g0620100 protein revealed a WD40 domain that was frequently found in cold tolerant landraces. Therefore, we speculated that Os01g0620100 was highly important for the response to cold stress in rice. These results indicated that rice landraces are important sources for investigating rice cold tolerance, and the mapping results might provide important information to breed cold-tolerant rice cultivars by using marker-assisted selection.

Genetic diversity in a collection of Italian long storage tomato landraces as revealed by SNP markers array

Tomato (Solanum lycopersicum L.) is one of the most important crops worldwide. In this study, we used 7720 genome-wide SNPs to characterize the genetic diversity within a tomato germplasm collection enriched with 64 accessions from southern Italy of the so called “da serbo” type i.e. drought-tolerant and long storage landraces. Notwithstanding the relatively small collection area, 1575 (20.4%) polymorphic SNPs, mostly on Chr11, detected considerable levels of genetic variation. Maximum parsimony analysis of genetic distance revealed four main clusters and clearly separated most “da serbo” landraces from the outgroups. One of the clusters grouped the landraces from the Mount Vesuvius area, though no further indications of a geographic-specific structure were found. STRUCTURE analysis confirmed the presence of four genetic groups within the collection, with admixture between them. A survey of non-synonymous SNPs highlighted several mutations in genes related to stress tolerance and fruit maturation/quality. Overall, our results suggest possible exchange of “da serbo” genetic material between southern Italy regions and indicate that the long storage “da serbo” germplasm could be a promising reservoir of peculiar alleles for traits of interest.

Integrating phenotypic evaluations with a molecular diversity assessment of an Ethiopian collection of common bean landraces

Understanding the organisation of genetic diversity in a crop species is a key element for both the conservation and utilisation of its genetic resources. In the case of common bean (Phaseolus vulgaris L.), Ethiopia is one of the secondary centers of diversity of this species. Hence, this study sought to improve our understanding of genetic diversity of common bean by integrating morphological and agronomic evaluations with prior molecular diversity data from a collection of landrace accessions from different common bean growing regions of Ethiopia. The samples studied included 115 landraces, four standard varieties, and two control genotypes. Twenty agronomic traits and morphological descriptors were used to evaluate the accessions under field conditions. A Principal Component Analysis clearly separated the accessions into the Andean and Mesoamerican gene pools, with the first two axes explaining most of the variation. Step-wise discriminant and canonical correlation analyses, with all variables or only the morphological variables, enabled the identification of characters distinguishing accessions from the Andean/Mesoamerican gene pools, and their respective ecogeographic races. Data distinguishing racial and morphological traits were used to clarify the identities of five cluster groups, identified at STRUCTURE preset K = 5, in a preceding study. The three Andean cluster groups were shown to belong to two of the races in the gene pool, ‘Nueva Granada’ and ‘Peru’; while the two Mesoamerican groups were from the race ‘Mesoamerica’. By integrating the morphological and agronomic evaluation of an Ethiopian germplasm collection of common bean, initially performed just based on molecular characterisation, we were able to improve our understanding of the organisation of this diversity. Our results suggest extensive hybridisation between the Andean and Mesoamerican gene pools after introduction of common bean germplasm in Ethiopia.Key Words: Canonical discriminant analysis, genetic resources, intra-specific diversity, multivariate analyses, plant breeding, principal component analysis

Landraces of snake melon, an ancient Middle Eastern crop, reveal extensive morphological and DNA diversity for potential genetic improvement

BackgroundSnake melon (Cucumis melo var. flexuosus, “Faqqous”) is a traditional and ancient vegetable in the Mediterranean area. A collection of landraces from 42 grower fields in Israel and Palestinian territories was grown and characterized in a “Common Garden” rain-fed experiment, at the morphological-horticultural and molecular level using seq-DArT markers.ResultsThe different landraces (“populations”) showed extensive variation in morphology and quantitative traits such as yield and femaleness, and clustered into four horticultural varieties. Yield was assessed by five harvests along the season, with middle harvests producing the highest yields. Yield correlated with early vigor, and with femaleness, but not with late vigor. At the molecular level, 2784 SNP were produced and > 90% were mapped to the melon genome. Populations were very polymorphic (46–72% of the markers biallelic in a 4 individuals sample), and observed heterozygosity was higher than the expected, suggesting gene flow among populations and extensive cross pollination among individuals in the field. Genetic distances between landraces were significantly correlated with the geographical distance between collecting sites, and with long term March precipitation average; variation in yield correlated with April temperature maxima.ConclusionsThe extensive variation suggests that selection of local snake melon could result in yield improvement. Correlations between traits and climatic variables could suggest local adaptation of landraces to the diverse environment in which they evolved. This study stresses the importance of preserving this germplasm, and its potential for breeding better snake melons as an heirloom crop in our region.