Melon (Cucumis melo L.) is an economically important vegetable crop worldwide. Karnataka state of southern India is rich in melon landraces and wild relatives, which are potential sources of genetic diversity for crop improvement. Here we report on the collection, characterization and documentation of previously unexplored landrace and wild material to broaden the availability of this genetic diversity for use in melon improvement. Accessions of botanical groups, momordica, kachri, chandalak, reticulatus, acidulus and indicus, intermediate forms of acidulus and momordica, and three melons of an unknown group were sourced directly from farmers of eight agro-ecological regions. Twenty-three representative melon landraces and wild relatives, along with four reference varieties of different botanical groups, were evaluated for agronomic traits during the year 2016. Very wide and distinctive genetic variations were observed among the melon accessions for ovary characters, sex expression, days taken to first fruit maturity, external and internal fruit traits, and fruit cracking (splitting). The remarkable variability displayed among the melon accessions as observed from the study demonstrates the importance of them as a valuable genetic reservoir for melon improvement.

Embryogenic callus induction and regeneration are useful in many aspects of plant biotechnology, especially in the functional characterization of economically important genes. However, in sugarcane, callus induction and regeneration vary across genotypes. Saccharum spontaneum is an important wild germplasm that confers disease resistance and stress tolerance to modern sugarcane cultivars, and its genome has been completely sequenced. The aim of this study was to investigate the effect of genetic variations on embryogenic callus induction and regeneration in S. spontaneum and to screen genotypes having high tissue culture susceptibility. The study was performed using nine genotypes of S. spontaneum and the following five parameters were assessed to determine the response of genotypes to embryogenic callus induction and regeneration: callus induction, embryogenic callus ratio, embryogenic callus induction, embryonic callus regeneration and regeneration capacity. All the genotypes varied significantly (P < 0.01) in all the parameters, except for embryonic callus regeneration, which was high (>80%) for all the genotypes. High broad-sense heritability (86.1–96.8%) indicated that genetic differences are the major source of genotypic variations. Callus induction was found to be strongly positively correlated with embryogenic callus induction (r = 0.890, P < 0.01) and regeneration capacity (r = 0.881, P < 0.01). Among the nine tested genotypes, VN2 was found to be the most responsive to tissue culture and could therefore be used to characterize functional genes in S. spontaneum. We also suggested an approach with potential applications in facilitating the rapid identification of sugarcane genotypes susceptible to tissue culture.

Lepidium latifolium L. (Brassicaceae) grows successfully in a high-altitude cold arid environment. Little molecular data are available for this plant despite its immense ecological importance as a cold- and drought-adapted species. We used a novel approach to identify microsatellite regions using genome walker libraries, called as Random Scans at Microsatellite Regions (RaSMiR), and implemented them on genotypes collected from relatively different topographical conditions within a small geographical area. The success rate of finding a microsatellite sequence using this methodology was 100%, and on developing the RaSMiR technique itself as a molecular marker, 230 electrophoretic bands were obtained using 13 different RaSMiR primers in combination with a microsatellite sequence primer. On an average, 17 bands were obtained for each primer. The electrophoretic profiles generated by RaSMiR markers were distinct from those produced by inter-simple sequence repeat markers. This information has been documented as a dominant marker data, and has been used to construct a neighbour-joining tree that successfully distinguished all genotypes. RaSMiR is an attractive approach for the development of unique and informative microsatellites, or for genome scanning directly as a molecular marker that can potentially be employed for the estimation of genetic diversity or to identify polymorphic loci involved in adaptations particularly in the non-model species, for which sufficient genomic data are not available.

Sweet cherries can be grafted on a wide range of rootstocks belonging to Prunus avium, Prunus cerasus, Prunus mahaleb, Prunus angustifolia or hybrids of different Prunus species. Identification of Prunus rootstocks using morphological traits is almost impossible particularly during the dormant season. However, molecular analysis carried out on actively growing shoot tips, leaves or dormant buds provides good opportunity to reliably distinguish rootstocks. In this study, DNA was extracted from the leaves of a total of 184 sweet cherry rootstock candidates belonging to P. avium L., P. cerasus L., P. mahaleb L. and P. angustifolia L. previously selected from the north-western part of Turkey. The rootstock candidates were tested with ten simple sequence repeat (SSR) primers, developed for the Prunus genus. The primers successfully identified all rootstock candidates. The results showed that the number of alleles per locus ranged from 10 (UDAp-401, UCD-CH21 and CPSCT010) to 20 (UCD-CH31) with an average of 13.3 alleles per locus, indicating that the SSRs were highly informative. Unweighted Pair-Group Method with Arithmetic mean analysis demonstrated that P. avium accessions are closely related to P. cerasus. The reference rootstocks were clustered with their associated botanical species.

Since the immediate wild relatives of Sorghum bicolor (L.) Moench are indigenous to Ethiopia, studying their population biology is timely for undertaking conservation measures. A study was conducted to investigate the occurrence of population bottlenecks and to estimate the long-term effective population size (Ne) in wild relatives of sorghum. For this, 40 samples of wild sorghum were collected from two remotely located populations that were allopatric to the cultivated sorghum. The presence of bottlenecks was investigated using heterozygosity excess/deficiency, mode shift and allelic diversity based on nine polymorphic simple sequence repeat (SSR) loci. We also estimated the Ne of the studied populations using two different methods employing SSR mutation models. The expected heterozygosity was found to be 0.41 and 0.71 and allelic richness was 3.0 and 4.9, in Awash and Gibe populations, respectively. Neither the heterozygosity excess nor the mode-shift methods detected signatures of bottlenecks in the studied populations. The effective size of the two wild sorghum populations studied also showed no risk of population reduction in these regions of Ethiopia. Therefore, these allopatric wild sorghum populations can survive by occupying patches by the roadsides and fences, areas within abandoned farm lands, forests, etc., which shows that their wild characteristics of adaptation have been adequate for them to survive from extinction despite extensive deforestation of their habitat for modern agriculture and frequent grazing by livestock. However, this does not guarantee the survival of these species for the future and ex situ conservation measures or policies could help maintain their diversity.

Focusing on 116 bread wheat landraces, this study investigated high molecular weight glutenin allele polymorphism, gene diversity, genetic variation and linkage disequilibrium (LD) in Glu-1 loci. To identify gluten alleles, sodium dodesyl sulphate-polyacrylamide, gel electrophoresis was used and for statistical analyses POPGENE software was employed. The results indicated that average genetic variation (h) was the highest in Glu-B1 (0.6421) and the lowest in Glu-A1 locus (0.4548); genetic similarity ratio (I) was the highest in Glu-B1 (1.4170); the highest average genetic diversity (Ht) was observed in Glu-B1 (0.6575) and the lowest diversity was observed in Glu-A1 (0.4558). It was also observed that genetic diversity in Glu-1 locus was largely due to intra-population variations. Inter-population gene flow was also calculated as 4.0051. Marmara and Southeastern Anatolia regions, the results further indicated, had the highest (2.8691) and lowest (0.1694) heterozygosity. Genetic erosion risk for Turkish bread wheat landraces was also seen to be high. Considering the mutual analyses of subunits of nationwide wheat landraces, it is possible to speculate about a limited migration between the landraces. LD of the landraces was largely because of this limited migration and/or epistatic natural selection. Since Turkey is known as the gene centre for major cereals including wheat, barley, rye and oat, where they diversified and spread throughout the world, studying the gluten allele diversity of Turkish bread wheat landraces is important. In addition, this study has revealed the applicability of LD, and neutrality tests to gluten protein diversity for the first time.

Germplasm characterization is essential to estimate variation and identify desirable genotypes for crop improvement. The current study was conducted on eight qualitative and 14 quantitative traits related to growth and floral attributes for characterization and grouping of 54 chrysanthemum genotypes. Wide variability was observed among most of the traits and principal component analysis revealed that the first two principal components explained most of the existing variation (>98%) in germplasm. Genotypic coefficient of variation exhibited a wide range from 9.41% (ratio of leaf length/width) to 105.99% (corolla tube length of ray florets), while phenotypic coefficient of variation varied from 10.49% (ratio of leaf length/width) to 106.38% (corolla tube length of ray florets). Broad sense heritability estimates were higher (>96%) for most of the characters, except for traits such as ratio of leaf length/width and peduncle thickness. Forty-four pair-wise inter-trait combinations showed positive genotypic and phenotypic correlations for 91 possible combinations. D2 analysis revealed that genotypes of clusters I and IV to be highly distinct, and hybridization between them might have better chance to obtain desirable types. D2 analysis confirmed that the cultivars in cluster IV namely, Red D Spoon, Tokyo Soldier, Yellow Reflex and hierarchical clustering showed that the cultivar Tokyo Soldier to be highly diverse. It is recommended to use the above genotypes in crossing programme for obtaining better progenies.

Only a little information is available on the genetic association of basic within-boll yield components of segregating populations. A total of 25 genotypes were evaluated for genetic diversity using SSR markers in 2012; of these, eight diverse genotypes were selected to attempt the generation of five crosses. From the progeny of these five crosses, five F3 populations were developed. Data for within-boll yield components were recorded by taking 30 observations (one observation average of five bolls) from each population, and analysed for genotypic and phenotypic correlations followed by the path coefficient analysis from the genotypic correlation. The highest genotypic correlation was observed between seed cotton yield per locule and number of seeds per boll (ranging from 0.654 to 0.972 for different crosses). Except number of seeds per locule and lint percentage, all the other within-boll yield components had a highly significant positive correlation with seed cotton yield, whereas the former two had a negative correlation. Path coefficient analysis revealed that number of seeds per boll had a maximum direct effect on yield (ranging from 0.776 to 0.895 for different crosses), and also had a relatively high magnitude of the indirect effect via other traits. Differences were observed in the magnitude of correlation coefficients and direct/indirect effects for different populations, but the direction of genetic association always remained the same. The present study showed that number of locules per boll, seed cotton yield per locule, number of seeds per boll and seed cotton yield per boll can be used as efficient selection criteria for the improvement in seed cotton yield.

‘Broccolo fiolaro’ (Brassica oleracea L. convar.Italica) is a typical vegetable produced in a restricted hill country area around Creazzo(Vicenza) in north-eastern Italy. The cultivation of this vegetable dates back severalcenturies ago, but a very few farms are still involved in the production.‘Broccolo fiolaro’ is a variety of broccoli highly valued for itsagronomic and organoleptic features.

Four ‘Broccolo fiolaro’ selections were characterized by simplesequence repeats (SSRs) molecular markers and compared with other five cultivatedvarieties of broccoli of the Italica group in order to reconstruct their genetic structureand evaluate the degree of similarity among and within populations. The analysis of 12 SSRpolymorphic loci pointed out a low genetic variability among the four ‘Broccolofiolaro’ selections. Moreover, the whole ‘Fiolaro’ groupshowed significant differentiation from the other broccoli cultivars and could be easilydistinguished by cluster analysis. An assignment test on ~30 genotyped plants randomlychosen from each broccoli population correctly recognized the proper accession 88% of thetime, proving this method to be useful for cultivar identification.

In this study, the genetic variability among 130 accessions of the Portuguese germplasm collection of Cucurbita pepo L. maintained at the Banco Português de Germoplasma Vegetal was assessed using AFLP (amplified fragment length polymorphism) and RAPD (random amplified polymorphic DNA) techniques for the identification of a genetically diverse core group of accessions for field phenotypic analysis. The surprisingly completely different molecular patterns exhibited by multiple accessions was later confirmed in the distribution of the putative C. pepo plants into two clusters drastically separated at a very low level of genetic similarity (DICE coefficient = 0.37). Additional analyses with RAPD and ISSR (inter single sequence repeat) markers and the introduction of standard genotypes of C. maxima L. and C. moschata L. into the analyses allowed the identification of multiple accessions of the last species wrongly included in the C. pepo collection. This study is a good example of the usefulness of DNA markers in the establishment and management of plant germplasm collections.

Chinese Spring (CS) wheat (Triticum aestivum L.) is commonly used in genetic research including cytogenetic analysis, molecular mapping and germplasm development. Aneuploid lines of alien chromosomes in the CS background have been used in studies with diverse objectives. Thousands of genomic and complementary DNA sequences from expressed sequence tag (EST) libraries of biotic- and abiotic-stressed tissues are publicly available from CS. Gene expression analysis of salt-tolerant wheat lines, W4909 and W4910, compared with the CS common wheat background led to the discovery of several expressed sequences that were absent in the CS accession held in our laboratory. A survey of 20 CS accessions from 13 laboratories using the polymerase chain reaction with gene-specific primers for eight salt-responsive genes resulted in amplification success ranging from 15 to 100%. Amplified fragment length polymorphism analysis showed that 99% of the genetic variation was among the accessions while the remaining 1% was within the accessions. A neighbour-joining phylogram showed that four of the five CS accessions from the International Maize and Wheat Improvement Center (CIMMYT) grouped with the salt-tolerant wheat cultivar Yecora Rojo while the remaining 16 CS accessions had limited genetic differences. Thus, variation exists among these highly self-pollinating CS sources, suggesting that appropriate consideration should be taken when using CS accessions to conduct molecular and genetic analyses.

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.

Short duration cotton (Gossypium hirsutum L.) cultivar may be more profitable for the growers, as it will have shortened critical growth window for drought, heat and insect pests. Therefore, in the present research work, two cotton advance lines IUB-71 and IUB-73 along with an approved cotton cultivar IUB-13 were tested under four different sowing dates i.e. S1 (25th April), S2 (10th May), S3 (25th May) and S4 (10th June) in 2017 and 2018 under field condition. Field layout was RCBD factorial with four sowing dates as one factor and three cotton genotypes as another factor with three replications. Data were recorded for plant height, total number of nodes, bolls per plant, seed cotton yield (SCY), above ground fresh biomass (AGFB) and harvest index (HI). An overall decreasing trend with increasing sowing dates was observed in all the traits except HI that relatively increased in all the three genotypes. Within each sowing date, a higher value for each trait was observed for genotype IUB-73 except for AGFB might be due to higher reproductive allocation. It is concluded that IUB-73 due to superior SCY and HI specifically under late planting is best fit for short cotton seasons with reduced critical window for cotton management.

Powdery mildew (PM) is one of the most severe fungal diseases of cucumber that limits its production worldwide. In this study, 140 genotypes of cucumber were screened for disease resistance under field and artificial conditions, and then validated with eight known SSR markers linked to PM resistance. Among these genotypes, genotype GS140 was found resistant (R), whereas GS148, GS16 and GS70 were moderately resistant, and GS169 was found to be tolerant. Of all the eight markers, only C31, C80, C162, SSR16472 and SSR16881 amplified the reported linked allele. The 127 bp allele of SSR16881 was found to be associated with the lowest disease severity of 37.65%. The associated markers could further be verified for their usability using linkage studies and the contrast genotypes in the present study could serve as a tool for selection in future marker-assisted selection breeding strategies for PM resistance.

Improvement in multi-cut forage sorghum varieties that can perform better than SSG 59-3, a sweet Sudan grass released in 1974, has been a challenge. Efforts were made to create variability in SSG 59-3 through mutagenesis using both physical and chemical mutagens. Fifteen such mutants were evaluated for 2 years in different locations in India. Considerable variability was observed for important fodder yield and quality traits. SSG 237 flowered 10 d early than SSG 59-3. SSG 231, SSG 260, SSG 232 and SSG 237 had high protein percentage and in vitro dry matter digestibility (IVDMD) values compared with SSG 59-3. Hydrocyanic acid (HCN), a major anti-nutritional factor, was low in six mutants, the lowest being in SSG 226. This variability can be used in different breeding programmes aimed at improving multi-cut forage sorghum varieties. The lines with improved fodder quality (low HCN, high protein and IVDMD) can be used in the breeding programme for the improvement in multi-cut forage sorghum varieties.

Development of a representative and well-diversified core with minimum duplicate accessions and maximum diversity from a larger population of germplasm is highly essential for breeders involved in crop improvement programmes. Most of the existing methodologies for the identification of a core set are either based on qualitative or quantitative data. In this study, an approach to the identification of a core set of germplasm based on the response from a mixture of qualitative (single nucleotide polymorphism genotyping) and quantitative data was proposed. For this purpose, six different combined distance measures, three for quantitative data and two for qualitative data, were proposed and evaluated. The combined distance matrices were used as inputs to seven different clustering procedures for classifying the population of germplasm into homogeneous groups. Subsequently, an optimum number of clusters based on all clustering methodologies using different combined distance measures were identified on a consensus basis. Average cluster robustness values across all the identified optimum number of clusters under each clustering methodology were calculated. Overall, three different allocation methods were applied to sample the accessions that were selected from the clusters identified under each clustering methodology, with the highest average cluster robustness value being used to formulate a core set. Furthermore, an index was proposed for the evaluation of diversity in the core set. The results reveal that the combined distance measure A 1 B 2 – the distance based on the average of the range-standardized absolute difference for quantitative data with the rescaled distance based on the average absolute difference for qualitative data – from which three clusters that were identified by using the k-means clustering algorithm along with the proportional allocation method was suitable for the identification of a core set from a collection of rice germplasm.

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.

Huauzontle (Chenopodium berlandieri ssp. nuttalliae) is a locally important vegetable crop native to the highland valleys of Central Mexico and a potential source of genes for improving its Andean sister crop, quinoa (Chenopodium quinoa). A previous work involving two huauzontle lines identified one waxy genotype that lacked amylose due to mutations in granule-bound starch synthase I (GBSSI), major amylose-synthesis genes with two constituent subgenomes, A and B. We conducted this study to determine the extent of waxy genotypes and cryptic GBSSI mutations in 11 huauzontle accessions or landrace populations extending from Puebla in the southeast to Jalisco in the northwest. This represents one of the first published studies of genetic variation in C. berlandieri ssp. nuttalliae. Accessions were phenotyped for opaque versus translucent seed morphology and their seed starches were stained with Lugol's Stain. In addition, complete or partial GBSSI genes from their A and B genomes were polymerase chain reaction (PCR)-amplified, cloned and sequenced. Seven accessions were either wholly or partially non-waxy while six were either entirely or partially waxy. All waxy accessions carried the same putatively null alleles, designated gbssIa-tp (A-genome) and gbssIb-del (B-genome). The identification of publicly available genotypes carrying gbssIa-tp and their potential use in breeding waxy grain quinoa is discussed.