Breeding for resistance to biotic stress and higher yield is a continuous process. Thus, the identification of desirable parents with good combining ability and nature of gene action for the target trait is of utmost importance. Hence, in this present investigation, 10 lines and three testers of Okra were crossed in line × tester mating design to generate 30 testcross progenies and their evaluation along with parents and check in a randomized complete block design with three replications. To depict the true picture of genetic variation among the parental genotypes, molecular diversity analysis was also carried out using genomic-simple sequence repeats before crossing to ascertain that sufficient variability is present among the parents. The molecular analysis grouped the parental genotypes into four clusters (I–IV). The analysis of variance revealed that all the treatments were significant for most of the traits. The combining ability analysis suggested Pusa A-4 as the best general combiner for earliness, Pusa Bhindi-5 for high yield, and DOV-92 for fruit length, plant height, yield per plant, and coefficient of infection for Yellow Vein Mosaic Virus Disease resistance. Similarly, the specific combining ability analysis suggested that the cross combinations DOV-92 × Pusa Bhindi-5 followed by DOV-92 × Pusa A-4 and DOV-92 × Pusa Sawani exhibit high economic heterosis for yield per plant as well as for disease resistance. Finally, estimation of the degree of dominance and predictability ratio was also worked out which indicated the prevalence of non-additive gene action for most of the traits pointing towards sufficient scope for heterosis breeding in Okra.

Silverleaf nightshade (Solanum elaeagnifolium Cav.) is an invasive species that has successfully spread outside its native range to become a noxious weed in 21 states in the United States and 42 countries worldwide. The successful establishment of S. elaeagnifolium outside its native habitat indicates its innate ability to adapt to a multitude of environments. Phenotypic plasticity and/or genetic adaptation have been identified as key mechanisms underlying the adaptive success of invasive species. Whereas phenotypic plasticity allows a species to buffer changes in the environment by altering its phenotypic attributes within the short term, genetic adaptation is responsible for the longer-term adaptability of plants to heterogeneous environments and is dependent on the amount of genetic variation present in the species. In this study, we screened DNA markers that are specific to tomato (Solanum lycopersicum L.) and Solanum lycopersicoides Dunal for their interspecific transferability to S. elaeagnifolium and determined the applicability of the transferable DNA markers in assessing the extent of genetic variation in populations from Lubbock, Littlefield, and Blackwell, TX. Of the 187 markers screened, 78 successfully amplified targets in S. elaeagnifolium, indicating the evolutionary conservation of marker loci across S. lycopersicum, S. lycopersicoides, and S. elaeagnifolium, despite their genetic divergence millions of years ago. Genotyping of S. elaeagnifolium populations using 50 DNA markers that consistently amplified clear bands in more than 60% of the plants identified nine polymorphic markers with 0.014 to 0.621 polymorphism information content. Genetic diversity analysis by DNA marker profiling established genetic variation among populations and within individuals of different populations. Unweighted paired group method with arithmetic mean analysis grouped the plants into six clusters that are generally defined by selection pressures unique to each collection site. Results of the study indicate the capacity of S. elaeagnifolium for genetic differentiation in response to variable selection pressures within the same geographic region.

Musa L. was previously separated into five sections (Eumusa, Rhodochlamys, Callimusa, Australimusa and Ingentimusa) based on basic chromosome numbers and morphological characters. However, several molecular analyses currently support restructuring of Musa species into two sections, Musa and Callimusa. The application of simple sequence repeat molecular marker analysis to Musa phylogeny provided valuable, supplemental information about the classification of, and relationships between, Musa species and subspecies. Totally, 28 accessions of Musa acuminata Colla subspecies and varieties and 25 accessions of other Musa species were evaluated; 12 primers produced 91 polymorphic bands, polymorphic information content ranged from 0.4473 to 0.8394 (average = 0.7226), indicating that the primers showed a high level of polymorphism. Our results generally agreed with previous phylogenetic analyses based on molecular data. One clade comprised species of sections Australimusa and Callimusa (X= 10/9); most species of sections Eumusa and Rhodochlamys (X= 11) formed the other clade. The relationships between most species were as expected; however, some species did not conform to findings of previous studies. A wide range of variability was observed in the M. acuminata complex. M. acuminata var. chinensis and M. acuminata subsp. 522 showed the most distant relationships to other subspecies: Musa laterita, Musa ornata and Musa velutina clustered with M. acuminata var. chinensis, suggesting that they may constitute a secondary gene pool for the improvement of cultivated bananas. Molecular data indicated that Musa tongbiguanensis Chen You & Yao-Ting Wu, which was observed and described by our research group in Yunnan, China, was a distinct, new species.

A drought stress panel composed of diverse accessions selected from upland, aerobic, rainfed lowland and irrigated lowland environments, was assembled to serve as germplasm for aerobic adaptation breeding. Aerobic rice requires significant levels of tolerance to drought stress due to intermittent water deficit and high soil impedance caused by aerobic conditions. Genomic information may be utilized to investigate the nature of the panel to guide varietal improvement. Using 153 simple sequence repeat and 384 single nucleotide polymorphism markers, the aim of the study was to compare the allelic properties of the two marker types, infer population structure of the panel, and estimate kinship among the accessions. There was a general agreement between the results derived from the two marker types. Marker alleles were found to occur at low frequencies, as the panel was composed mostly of improved accessions with some landraces. The panel clustered into japonica (JA), aus (AU), upland-adapted indica (UL) and lowland-adapted indica (LL) subpopulations. The AU and JA subpopulations were more divergent from the rest of the subpopulations than were the LL and UL subpopulations. Average marker-based kinship for related accessions was less than 0.20, indicating a low degree of genetic relatedness in the panel. Within the LL and UL subpopulations, the low levels of kinship imply that there is still much genetic gain to be expected from utilizing the accessions in breeding. Thus, an understanding of the genetic variation in the panel suggests focusing on improving the mean in the short term, and tapping into the exotic alleles from the AU and JA subpopulations when genetic gain declines.

Next-generation sequencing technique has been known as a useful tool for de novo transcriptome assembly, functional annotation of genes and identification of molecular markers. This study was carried out to mine molecular markers from de novo assembled transcriptomes of four chilli pepper varieties, the highly pungent ‘Saengryeg 211’ and non-pungent ‘Saengryeg 213’ and variably pigmented ‘Mandarin’ and ‘Blackcluster’. Pyrosequencing of the complementary DNA library resulted in 361,671, 274,269, 279,221, and 316,357 raw reads, which were assembled in 23,607, 19,894, 18,340 and 20,357 contigs, for the four varieties, respectively. Detailed sequence variant analysis identified numerous potential single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for all the varieties for which the primers were designed. The transcriptome information and SNP/SSR markers generated in this study provide valuable resources for high-density molecular genetic mapping in chilli pepper and Quantitative trait loci analysis related to fruit qualities. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.

A chickpea simple sequence repeat (SSR) marker reference kit has been developed based on the genotyping of the global chickpea composite collection (3,000 accessions) with 35 SSR markers. The kit consists of three pools of chickpea accessions along with supporting documentation on the SSR markers, polymerase chain reaction and detection conditions, and the expected allele sizes for each of the 35 SSR loci. These markers were selected based on quality criteria, genome coverage and locus-specific information content. Other important SSR selection criteria were quality of amplification products, locus complexity, polymorphism information content and well-dispersed location on a chickpea genetic map. The developed SSR kit has a wide range of applications, especially for genetic diversity studies in chickpea. Using the markers and reference accessions in the kit, scientists in other laboratories will be able to compare the genotypic data that they obtain for their germplasm with that obtained using the global composite collection.

Studies to quantify genetic variation in cassava germplasm, available within the national breeding programmes in Africa, have been limited. Here, we report on the nature and extent of genetic variation that exists within 1401 cassava varieties from seven countries: Tanzania (270 genotypes); Uganda (268); Kenya (234); Rwanda (184); Democratic Republic of Congo (DRC; 177); Madagascar (186); Mozambique (82). The vast majority of these genotypes do not exist within a formal germplasm conservation initiative and were derived from farmers' fields and National Agricultural Research Systems breeding programmes. Genotypes were assayed using 26 simple sequence repeat markers. Moderate genetic variation was observed with evidence of a genetic bottleneck in the region. Some differentiation was observed among countries in both cultivars and landraces. Euclidean distance revealed the pivotal position of Tanzanian landraces in the region, and STRUCTURE analysis revealed subtle and fairly complex relationships among cultivars and among landraces and cultivars analysed together. This is likely to reflect original germplasm introductions, gene flow including farmer exchanges, disease pandemics, past breeding programmes and the introduction of cultivars from the International Institute of Tropical Agriculture – Nigeria. Information generated from this study will be useful to justify and guide a regional cassava genetic resource conservation strategy, to identify gaps in cassava diversity in the region and to guide breeding strategies.

Triticum urartu, the A-genome donor of tetraploid and hexaploid wheats, is a potential source of novel alleles for crop improvement. A fertile amphiploid between T. urartu (2n = 2x = 14; AuAu) and durum wheat cv ‘Yavaros’ (Triticum turgidum ssp. durum; 2n = 4x = 28, AABB) was obtained as a first step to making the genetic variability of the wild ancestor available to durum wheat breeding. The amphiploid was backcrossed with ‘Yavaros’ and the offspring from this cross was selfed. A plant from this progeny (founder line) with 28 chromosomes and active x and y subunits of the Glu-A1 locus of T. urartu was selfed, which resulted in the obtaining of 98 pre-introgression lines (pre-ILs). In this work, a set of 78 wheat chromosome-specific microsatellite markers (simple sequence repeats, SSR), uniformly distributed over the A genome, was used for marker-assisted selection of T. urartu in a durum wheat background. A total of 57 SSRs allowed a clear discrimination between T. urartu and ‘Yavaros’. This set of markers was further used for characterizing the pre-ILs, identifying and defining the T. urartu introgressed regions. The applicability of these markers is discussed.

Colombia, situated at the northern end of the Andes mountains of South America and in proximity to Central America, is an important centre of diversity for common bean (Phaseolus vulgaris L.) that has a mix of cultivated germplasm from both major gene pools (Andean and Mesoamerican) for the species. Microsatellites are a useful marker system for analyzing genetic diversity of this crop and can be analyzed with manual (silver-stain) or automated (ABI) detection systems and using unlabelled or fluorescently labelled markers, respectively. The objectives of this research were to evaluate the genetic diversity of 92 Colombian landraces and gene pool controls with 36 fluorescent and 30 non-fluorescent microsatellite markers and to determine the extent of introgression between the Andean and Mesoamerican gene pools for this germplasm. A comparison of fluorescent versus non-fluorescent marker systems was performed with 14 loci, which were evaluated with both methods; the fluorescent markers were found to be more precise than the non-fluorescent markers in determining population structure. A combined analysis of 52 microsatellites using the 36 fluorescent markers and 16 non-overlapping, silver-stained markers produced an accurate population structure for the Andean gene pool that separated race Nueva Granada and race Peru genotypes and clearly identified introgression between these races and the gene pools. The results of this research are important for the application of microsatellite markers to diversity analysis in common bean and for the conservation of landraces in Colombia and neighbouring countries of Latin America, where similar germplasm exists and where gene pool or race mixtures also occur.

‘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 order to protect and develop valuable snappers (Lutjanus spp.), genetic diversity and molecular markers of five species (Lutjanus vitta, L. fulvus, L. fulviflamma, L. sebae and L. stellatus) were detected and analysed using random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) techniques. The polymorphic loci ratio (P) (86.00–92.11%), the mean intraspecies genetic distances (D) (0.1775–0.3431) and the intraspecies genetic diversity indexes (Hi) (0.1022–0.1634) were calculated using the RAPD technique. The genetic diversities of L. fulviflamma and L. vitta were richest in terms of P, and D and Hi, respectively. The results of SSR showed that low effective numbers of alleles (1.7893–3.6591), medium average heterozygosities (0.332–0.676) and medium polymorphism information contents (PIC) (0.302–0.641) occurred in five species of snappers, indicating comparatively rich genetic diversity among these fish. Nine molecular markers in the products amplified by primers OPA8 and OPP10, and six molecular markers in 11 microsatellite loci were found to be useful as specific markers to identify five species of snappers. Two neighbour-joining (NJ) dendrograms based on the results of RAPD and SSR suggested that L. stellatus and L. sebae are closely related and clustered in one branch, with L. vitta, L. fulviflamma and L. fulvus in the other.

Two species-specific microsatellite or simple sequence repeat (SSR) markers (UAKLly10a and UAKLla1) were used to distinguish Larix lyallii Parl. (subalpine larch) from L. occidentalis Nutt. (western larch) (Pinaceae). These markers can easily be used for rapid identification of the two species at any stage in the sporophyte phase of the life cycle. In the future, they should prove to be an invaluable tool for determining the possible occurrence and magnitude of introgressive hybridization in overlap zones between the two species. They are also expected to be useful in validating controlled crosses between L. lyallii and L. occidentalis and for certification purposes in reforestation and tree improvement programmes aimed at producing genetically improved hybrid stock.