Although morphological plasticity has been widely known in various cactus genera, few studies have investigated the origin and molecular relationship between morphological variants from cacti. Morphological variants are relevant specimens because atypical, exotic and generally unique forms are preferred by cactus traders and collectors. The current study investigates the molecular relationship between the tortuosus and monstruosus ornamental variants of Cereus peruvianus used in landscapes. Polymorphisms in loci of simple-sequence repeats in DNA were used as molecular markers. The variants tortuosus and monstruosus, and plants with typically columnar and erect shoots cultivated in southern Brazil were retrieved from public parks and home gardens. High polymorphism, an indicative of vegetative propagation, and a moderate genetic divergence were detected at the molecular level in monstruosus and tortuosus plants. Artificial selection and vegetative propagation of the ornamental variants of Cereus may be inducing a moderate genetic divergence and formation of two heterologous groups with conservative genetic diversity. Polymorphism in Cereus variants revealed groups with contrasting genes among the variants tortuosus and monstruosus which may be useful for breeding to generate new and different new variants.

Since the 1600s, a pasta wheat locally known as Sargolla, Saragollio or Saragollo has been cultivated in central and southern regions of Italy, including Abruzzo and Puglia. To identify if distinctive Saragolla landraces are present in Abruzzo and with a view to registering them as Conservation Varieties in the Abruzzo Regional Register of Genetic Resources, a quantitative botanical characterization of 11 farm-saved seed samples from Abruzzo and a previously defined Saragolla landrace from Puglia was performed. All twelve samples were grown for two years at the CREA-CI field station in Foggia, Puglia (Italy), and were morphologically characterized according to the criteria used by the botanist Johan Percival in 1921. In the 12 samples, we identified 9 taxonomically different botanical types, the most frequent of which were the italicum (32%), found in every population from Abruzzo. The leucurum and the affine were the main components of the previously defined Saragolla from Puglia. Results of the multivariate analysis indicated that the samples collected from farms in Abruzzo are more similar to each other than to the landrace of Saragolla from Puglia and support the registration of a specific Saragolla landrace for the Abruzzo region. The diachronic comparison of the botanical diversity of the currently cultivated Saragolla, with that observed in Sicily and Algeria at the beginning of 1900, suggests that a high degree of genetic diversity still exists in the 11 Saragolla populations from the Abruzzo Region.

Date palm is a relatively salt- and drought-tolerant plant and more recent efforts have been focused on recognizing genes and pathways that confer stress tolerance in this species. The cDNA start codon targeted marker (cDNA–SCoT) technique is a novel, simple, fast and effective method for differential gene expression investigation. In the present study, this technique was exploited to identify differentially expressed genes during several stress treatments in date palm. A total of 12 SCoT primers combined with oligo-dT primers amplified differentially expressed fragments among the stress treatments and control samples. Differentially expressed fragments were highly homologous to known genes or encoded unclassified proteins with unknown functions. The expression patterns of the genes that had direct or indirect relationships with salinity and drought stress response were identified and their possible roles were discussed. This study suggests that the cDNA-SCoT differential display method is a useful tool to serve as an initial step for characterizing transcriptional changes induced by abiotic stresses and provide gene information for further study and application in genetic improvement and breeding in date palm.

HMGR, 3-hydroxy-3-methylglutaryl-CoA reductase, is a major rate-limiting enzyme in mevalonate (MVA) pathway for isoprenoids and subsequent tanshinone biosynthesis in the Chinese traditional bulk herbal medicine Danshen, Salvia miltiorrhiza, mainly for cardiovascular disorders. In this paper, the genomic SmHMGR genes of 38 cultivated populations of S. miltiorrhiza collected in China were for the first time sequenced to reveal the genetic diversity and phylogeny. The SmHMGR gene was shown to be intron-free, 1650~1659 bp in complete CDS with the majority being 1656 bp, and two unique populations (W-FJLY-V-1 and W-SCHY-W-1) being 1659 and 1650 bp respectively. A total of 103 SNP variation sites were detected with a variation rate of 6.22%, most of which occurred in S. miltiorrhiza f. alba population W-SCHY-W-1; a total of 25 amino acid variation sites were found, of which 19 was in W-SCHY-W-1. The same four populations, W-SCHY-W-1, V-HBAG-V-1, V-JLCC-V-1 and S-NM-V-1 could be discriminated from the remaining 34 by both the SNP fingerprints and the deduced amino acid variation sites. Other or composite DNA markers are needed for better identification. The SmHMGR gene of white flower S. miltiorrhiza f. alba population W-SCHY-W-1 is especially rich in variations and worthy of further studies. Phylogenetic trees based on both the gene and the deduced amino acid sequences showed a very similar two-clade topological structure. This research enriched the content and the genetic means for the molecular identification, genetic diversity and phylogenetic studies of the cultivated S. miltiorrhiza populations, and laid a solid foundation for further related and in-depth investigations.

Chickpea (Cicer arietinum L.) is one of the most important grain legumes after common bean. In the present study, a total of 35 chickpea genotypes including desi and Kabuli types of cultivated chickpea (C. arietinum) were evaluated for seed physical characteristics that are very important for seed storage, processing and determining seed quality traits. Therefore, it has become imperative to study the seed physical characteristics of chickpea during the present study. The analysis of data revealed that substantial variation is present among the genotypes under study with respect to seed physical characteristics such as seed size, seed volume, seed density, hydration capacity, hydration index, swelling capacity and swelling index. These traits are considered important to determine the seed rate at the time of sowing of the crop, cooking quality, storage and processing and thereby have a direct bearing on the economics of chickpea consumption. Our results indicated that the desi, Kabuli and pea-shaped genotypes differ significantly in seed physical characteristics with overall superior trait performance of the Kabuli type compared to other seed types, making them superior with respect to consumer/market demands.

Teosinte, the wild progenitor of maize, has immense potential for providing unique traits and is more divergent compared to inbred lines and landraces. One hundred and sixty-nine teosinte-introgressed maize backcross inbred lines were developed to widen the genetic base of maize with predomestication alleles. The population was evaluated phenotypically and genotypic data of 76 SSR markers were used to map quantitative trait loci (QTLs) governing the targeted traits. Sixty-six QTLs were detected for eight plant architect-related traits that are spread over 10 different chromosomes with phenotypic variation ranging from 2.29 to 13.97%. Maximum three stable QTLs were recorded for days to anthesis (DA) followed by two for days to silking (DS), plant height (PH) and node bearing first ear (NBE). For rest of three traits namely flag leaf length (FLL), flag leaf width (FLW) and ears per plant (E/P) only one stable QTL was detected. Among the 16 common QTLs, the marker phi328178-linked QTL governed four characters (DA, DS, FLL, FLW) simultaneously, followed by umc1622-linked (ASI, FLW, E/P), umc2341-linked (DA, DS, NBE) and phi075-linked QTLs (ASI, PH, NBE) controlling three traits each. Remaining 12 QTLs controlled two characters. Molecular association between co-localized QTLs for different traits was also validated at the phenotypic level by significant correlation estimates. For eight studied traits, 53 superior lines were identified which along with parents (teosinte and maize inbred DI-103) were grouped into 12 clusters. Therefore, lines clustered independently can be combined to accumulate desirable traits for the improvement of maize.

The use of molecular markers is one of the most sensitive, powerful technologies for genetic purity assessment of seed lots. In this study, we aimed to develop a set of insertion and deletion (InDel) markers, through bioinformatics approaches, that may effectively distinguish three representative japonica rice (Oryza sativa L.) varieties, Nipponbare, Taichung 65 and Zhonghua11. The published whole-genome sequences of these varieties were aligned using BWA-MEM, followed by manual inspection for InDels of more than ten base pairs in size with the tview function of SAMtools. A set of ten InDel markers were thus identified and then validated by PCR in the three japonica rice varieties and their intercross F1 hybrids. Results showed that the InDel markers developed in this study could reliably distinguish these three japonica rice varieties. These molecular markers together with the detection method developed here can be applied to DNA-based genetic purity evaluation in rice breeding.

The members of the Aegilops genus serve as a vast pool of allele discovery for wheat improvement in abiotic and biotic stress responses. Aegilops mutica Boiss (Amblyopyrym muticum (Boiss) Eig) is an unexplored candidate with significant potential. Even though it has been used in cytogenetics applications within the last century, natural population diversity and allele discovery have been neglected. As an endemic species for Anatolia and the lower Caucasian region, it has an unexplored population structure. Here, seventy-five genotypes from five different newly collected populations from central Anatolia were evaluated with 29 polymorphic SSR loci. Significant diversity within (83%) and between (17%) the populations was obtained. Three of the populations were clearly separated, while two had some level of the mixture. Relatively easy cross-species hybridization and introgressions make Ae. mutica a good candidate for novel allele discovery and pre-breeding. Here, for the first time, representative natural populations of Ae. mutica were compared and population structures were revealed with SSR markers which may clear the misty vision that geneticists might have regarding Ae. mutica. This could be exploited in genetic resource conservation and breeding programs and maybe a point for further studies.

A study was conducted to collect and characterize the indigenous Kala zeera (Bunium persicum Boiss. Fedtsch.) accessions from the hills of northwestern Himalayan sates of Jammu and Kashmir, Himachal Pradesh and Uttarakhand. Around 1000 accessions were collected during this exploration mission, out of which diversity of 252 accessions was established through morphological characterization. The morpho-agronomic characterization and the analysis of trait data revealed significant variability in number of branches per plant, number of umbelets per umbel, number of seeds per plant, seed yield per plant and 1000 seed weight. The collection and characterization of these diverse accessions can prove useful in future Kala zeera improvement programmes in the world as this is the first such comprehensive report of the crop from northwestern Himalayan region of India.

The genus Lilium contains a number of ornamental crop species, which are commercially important in many countries. As they are vegetatively propagated, maintaining genetic stability is essential for their efficient conservation. In this study, we investigated the genetic stability of regenerated plants of three cultivars (L. bolanderi ‘Lenora’, L. bolanderi ‘Mount Duckling’ and L. bolanderi ‘Mount Dragon’) and one variety (L. callosum var. flavum) after cryopreservation, compared with fresh (donor) and non-cryopreserved plants using morphological traits and ISSR markers. No differences in morphological parameters including flower, stigma and pollen colour, floral spots, floral direction or polymorphic bands were observed between control (fresh and non-cryopreserved) and cryopreserved plantlets. In addition, based on the resulting UPGMA dendrogram, the four taxa were divided into different clusters. All cryopreserved, non-cryopreserved and fresh plants in each group could be grouped together in a single cluster with more than 97 or 100% similarity. The results suggest a very low level or the absence of genetic variation in terms of morphological and genetic stability among the plants regenerated after cryopreservation.

Being difficult to regenerate and maintain the seeds, the oleaginous bottle gourd was investigated using nine agromorphological traits and 31 amplified fragment length polymorphism (AFLP) markers. Specifically, the study was conducted to determine the intra-specific variability of a total of 173 accessions, which were identified from five agro-ecological regions from Côte d'Ivoire (Centre, East, North and South). Then, the genetic diversity and relationships within accessions were studied using AFLP markers. This characterization using both morphological and AFLP markers was realized in order to ultimately build a reliable core collection. The discriminant analysis, using nine quantitative traits, reveals plant length and seeds number per fruit as discriminating characteristics. From the accessions used for the agromorphological study, 148 were able to be differentiated by the AFLP markers. A range of 52 to 113 bands were amplified per primer combination. As revealed by the analysis of molecular variance (AMOVA), 28% of the total variation resides among accessions and 72% occurs within populations. The AMOVA computed in order to differentiate cultivars, displayed the same trends when no prior grouping of accessions was considered. The differentiation within cultivar (97%) was more than that, among cultivars (3%). Tree topologies inferred by neighbour-joining analysis reflected no clear cut off grouping.

To group accessions, we used a Bayesian clustering analysis which exhibited two clusters. Using the informativeness of the primer combinations analysed in the present study, an orientation was given for the choice of the accessions which would be used to build a core collection.

‘Sikkim Primitive’ (SP) maize locally known as ‘murali makkai’ in Sikkim is a unique genetic resource exhibiting prolificacy and excellent popping capacity. Status of SP has reached extinction level due to its very small population size and neglected conservation efforts in-situ. In an initial effort to conserve and revive this landrace, characterization and documentation was carried out with 31 morphologically assayed traits recorded at different growth stages along with molecular characterization with simple-sequence repeat (SSR) markers. Plants exhibited prolificacy (5–6 cobs/plant) and excellent popping capacity along with other distinct traits. Plants were tall with thin stem, loose drooping tassel with anthocyanin coloration present at the base of glumes and in brace roots. Cobs were medium sized carrying small seeds with low test weight (87.90 g). A total of 22 SSR markers show amplification in murali makkai with markers bnlg1083, umc1353, umc1128, bnlg1017, bnlg2077, umc2298 and umc2373 amplified unique amplicons ranging from 100 to 800 bp. The characterized set of traits and molecular characterization for murali makkai will facilitate in utilization for genetic improvement and maintenance of genetic purity.

Oaks are model species due to their importance in various ecosystems, worldwide distribution, high economic value and emerging genomic resources. As such, knowledge on population differentiation across their distribution range is of high importance for sustainable forest management. As in most angiosperms, chloroplasts are maternally (via seeds) inherited in oak species and acorns are dispersed over comparably short distances. Consequently, chloroplast markers reveal comparatively high differentiation between populations, making them highly viable for the analysis of historic migration patterns and the certification of reproductive material. Despite the existence of various white oak (section: Quercus) chloroplast markers, red oak (section: Lobatae) chloroplast markers remain limited. Northern red oak is one of the most important North American oak species and a widespread non-native plantation tree species in European forests. We took advantage of chloroplast genomes of Q. rubra L. and related oak chloroplast genomes to develop a set of robust and easy-to-use chloroplast microsatellite primers for northern red oak. Furthermore, we tested transferability of those novel red oak primer pairs to Q. robur L. and Q. petraea Matt. Liebl. The new set of fifteen polymorphic chloroplast microsatellite markers revealed three additional northern red oak haplotypes after screening 80 northern red oak individuals representing seven haplotypes, identified based on formerly available markers. Therefore, they provide a higher resolution of haplotypes as compared to currently available markers.

Early elimination of poor crosses based on an objective criterion allows increased allocation of resources only to a few promising crosses for identifying superior recombinant inbred lines (RILs) for use as pure-line cultivars in self-pollinated crops. Early generation (F2:3) prediction of frequency of superior RILs that could be derived from advanced generations of crosses is one such criterion. We predicted the frequency of transgressive RILs from two horse gram crosses (namely HPKM 320 × CRIDA18-R and IC 361290 × Palem 1) for primary branches per plant, pods per plant, pod weight per plant and grain weight per plant based on mid parental value, additive genetic effects and additive genetic variance estimated from trait means of parents, and their F2 and F2:3 generations. The predicted frequency of RILs that transgressed better parent/two checks varied with the cross and the trait within a cross. The frequencies of transgressive RILs predicted from IC 361290 × Palem 1 were higher than those predicted from HPKM 320 × CRIDA 18-R for three of the four traits. As expected, the minimum population size required to recover the transgressive RILs predicted from IC 361290 × Palem 1 was relatively smaller than that from IC 361290 × Palem 1. Increased allocation of resources for handling segregating populations derived from IC 361290 × Palem 1 is expected to result in superior RILs for use as cultivars. We believe that the objective criterion used in our study is handy in identifying superior RILs in early segregating populations derived from a few promising crosses.

In India, the restriction of genetically modified (GM) crops and derived products not approved in the country necessitates surveillance for transgene(s) in plant material/products imported into the country. CDC Triffid expressing acetolactate synthase (ALS) conferring tolerance to sulphonylurea herbicide is the only GM flax event that has got approval in Canada in 1990s and subsequently deregistered in 2001. In spite of deregistration, the unexpected and unauthorized detection of traces of GM flax in the consignments imported from Canada to Europe has further necessitated the stringent monitoring of flax shipments from Canada for suspected GM incidents. This study reports on the detection of transgenic elements being present in GM flax employing polymerase chain reaction assays, in a set of 123 flaxseed accessions imported from Canada for research purpose. Based on the tests conducted, none of the transgenic elements, namely, nos promoter (P-nos), nos terminator (T-nos), nptII marker gene, ALS transgene, as present in the GM flax CDC Triffid were detected in any of the tested accessions. The well-known herbicide tolerance gene cp4-epsps, being employed in Roundup® Ready events of other crops, was also not detected in these samples. This case study has demonstrated the importance of monitoring the presence of transgene(s) in flaxseed imports, and such studies need to be carried out for the imported seeds from the country where GM events of respective crop are being approved whereas they have not been approved in the country of import as a part of precautionary approach.