Maize is among major field crops which provides food, fodder and various byproducts to the industry. Development of better performing varieties is very important to enhance and strengthen the maize production system. In this study ethyl methanesulfonate (EMS) is used to induce genetic variation in maize. Mutant population was derived from two genotypes 100,003 and 100,004. EMS was applied under three different concentrations of 25, 50 and 75 mM. 25 mM was found as an ideal concentration resulting in maximum survival rate. Total 10 SSRs were used in this study, which amplified 28 alleles with average of 2.7 alleles. Analysis of molecular variance showed significant differences present among individuals. Average heterozygosity for mutants derived from 100,003 and 100,004 was 0.58 and 0.53, respectively. UPGMA analysis characterized the mutants into two main and many sub clusters. According to the principal component analysis, PC 1 and 2 contributed to 64.2% variability with eigenvalue greater than 1. Statistics showed maximum coefficients of variance in traits of leaf area, cobb height and plant height. Promising mutants were also identified and recommended for future breeding programme. In conclusion, EMS mutagenesis is an effective technique to develop novel mutants that can be exploited in future breeding programmes.

Seedling vigour is an important indicator of crop establishment, subsequent crop growth and yield. Initial seedling vigour is most vital in case of water-limited conditions and in environments where the crop is exposed to different stresses at the early growth stage. Wild and weedy species are well known for their vigour and survival in adverse environmental conditions. Seedling vigour traits of backcross introgression lines (BILs) derived from Swarna × Oryza nivara IRGC81848(S) (accession from Uttar Pradesh, India) and IRGC81832 (K) (accession from Bihar, India) were studied in wet (Kharif) and dry (Rabi) seasons. Seedling vigour was estimated in terms of plant height and tiller number at 30 and 60 d after transplanting under field conditions. In both the seasons, 148S showed highest seedling vigour for plant height. The highest number of tillers were produced by 7K in Kharif and 248S in Rabi season. 75S showed the highest percentage increase in tiller number consistently. High yielding BILs 166S, 14S and 148S showed higher seedling vigour indices compared with checks Tulasi and Sahbhagidhan. Seedling vigour was also evaluated using paper roll method and shoot length, root length and dry weight were used to estimate vigour index. Season-wise association studies were conducted to determine the relative contribution of seedling vigour to yield traits. Seedling vigour was significantly correlated with yield traits. Markers RM217 and RM253 on chromosome 6 differentiated lines with high seedling vigour from those with low seedling vigour and have the potential for use in marker-assisted breeding.

Germplasm of common beans from the Mesoamerican gene pool races: Durango, Jalisco, Mesoamerica and Guatemala have highest genetic variation for the crop's improvement. The objective was to assign 50 common bean germplasm in Uganda into its gene pool races based on analyses of population structure. Secondly, to estimate heritability and effects of genotype × environment (GXE) interaction on common bean agronomic and yield traits in space and time. Sample genomic DNA was amplified in 2011 with 22 Simple sequence repeat markers (SSRs) and alleles separated using capillary electrophoresis. Field evaluations were conducted in 2010 and 2011 at NaCRRI and 2015 at CIAT – Kawanda. Multivariate analyses of SSRs data identified four subgroups within the germplasm: K4.1–K4.4, with corresponding Wrights fixation indices (FST) as 0.1829 for K4.1, 0.1585 for K4.4, 0.1579 for K4.2 and least for K4.3 at 0.0678. Gene pool race admixtures in the population (14%) were notable and attributed to gene flow. Four superior parents currently used in improving resistance to major diseases grouped as; Jalisco for MLB49-89A; Mesoamerica for MCM5001 and G2333; Durango for MEXICO 54. Heritability values for yield traits estimated using phenotypic data from above fixed parents, was above 0.81. Season and location had significant effect (P < 0.05) on numbers of: flower buds per inflorescence, pod formation and weight of 100 seeds. The findings will improve understanding of co-evolutionary relationships between bean hosts and pathogens for better disease management and will broaden the germplasm base for improving other tropical production constraints.

Microsatellites or simple sequence repeats (SSRs) are useful molecular markers allowing for efficient conservation and sustainable use of genetic resources of plant species. Development of SSR marker system for new species is a very expensive task and time consuming. Cross-species amplification of microsatellite loci is considered as a cost-effective approach for developing microsatellite markers for new species. The aim of this work was to examine the transferability of some SSR markers of two Arecaceae species (Astrocaryum aculeatum and Elaeis oleifera), in Acrocomia aculeata. Out of the total markers analysed 44% of the markers successfully amplified the genomic DNA in A. aculeata, of which 26% were polymorphic detecting a range of three to eight alleles with an average of 4.5 per locus. High average percentage of polymorphic loci (P= 71.2%) per provenance was obtained within a range of 57–100% detecting genetic variation in A. aculeata germplasm collections. The polymorphic markers detected a positive inbreeding coefficient (F>0) per locus revealing heterozygote deficiency in the accessions that were analysed. As the cross-amplification was at family level, in which the taxonomic distance is relatively wider between the sources (A. aculeatum and E. oleifera) and the target (A. aculeata) species, the amplification success was relatively low. However, the results are promising and implicated that high cross-amplification success could be achieved at species or genus level in A. aculeata. The markers will contribute towards the domestication of the potential macaw palm through realizing various studies such as population genetics, germplasm characterization, genetic improvement and conservation.

African yam bean, AYB (Sphenostylis stenocarpa Hochst. ex. A. Rich Harms), is a tuberous legume of tropical Africa. AYB has the potential to significantly boost food security due to its considerable nutritional qualities. However, the crop is underutilized. To efficiently utilize AYB genetic resources for its improvement, it is necessary to understand the crop's diversity. This study investigated the amplification ability of 36 cowpea simple sequence repeat (SSR) primers across AYB genomic DNA, extracted from 67 accessions. Thirteen (36%) of the cowpea SSRs showed transferability in AYB. Eight of these SSRs amplified above 60% of AYB accessions and generated 55 polymorphic fragments with an average of 6.9 per primer. Polymorphic information content ranged from 0.6691 to 0.8857 with an average of 0.7791. This study also assessed the genetic diversity within 67 AYB accessions using eight cowpea (Vigna unguiculata L. Walp)-derived SSR primers. The result revealed a high level of genetic diversity with simple matching coefficient ranging from 0.458 to 1.000. A dendrogram depicting three main clusters was generated based on unweighted pair group method with arithmetic average. Cluster 1 was the most diverse with a dissimilarity range of 0.517–1.000. The level of genetic diversity revealed in this study indicates that the studied AYB germplasm can be exploited for genetic improvement. Additionally, the transferable markers will aid AYB genome research and also make possible the comparative mapping between AYB and cowpea.

Despite widespread mungbean [Vigna radiata (L.) Wilczek] consumption in Indonesia, few molecular studies have been carried out on accessions and available data are minimal. In this study, we used 30 newly developed simple sequence repeat (SSR) markers designed from the mapped sequence scaffolds of the Korean Sunhwanokdu and Gyeonggijaerae 5 mungbean genomes. These markers were used to examine loci in 83 mungbean accessions collected from diverse geographical areas in Indonesia. A total of 107 alleles were detected among the accessions with 29 polymorphic markers. However, the mean of polymorphic information content (0.33) value and diversity index (0.38) value was indicative of low genetic diversity in this germplasm. The mungbean population structure was not clearly differentiated and the number of subpopulations was unclear. Neighbour-joining tree analysis revealed that the genetic cluster did not reflect the geographical origin of the accessions. Interestingly, the most agriculturally improved varieties were genetically similar to some landraces from one of the main mungbean-producing regions. These newly developed SSR markers could be useful for detecting genetic variability as a basis for establishing a conservation strategy for mungbean germplasm with the aim of enhancing Indonesian breeding programmes.

In this study, the genetic constitution of wild grape populations distributed in the Zagros Mountains in the north-west part of Iran was investigated to assess their risk of extinction and to identify the most suitable conservation strategy. A total of 65 wild grapevine samples from five different populations were analysed using 23 SSR loci. Consistent allelic richness was detected in all the analysed populations (from 4.01 to 5.35). The observed heterozygosity and expected heterozygosity were high with mean values of 0.67 and 0.69, respectively. A modest heterozygosity deficiency was detected only in the Piranshahr and Sardasht-Shalmash populations. The neighbour-joining dendrogram clustered the accessions into three groups corresponding to the geographical distribution of the populations. Molecular data combined with field evaluation revealed that an ex situ conservation approach is the most suitable strategy for preserving the genetic richness of Iranian wild grape populations with consistent rare alleles (about 20%). We propose in situ preservation only in the case of the Sardasht-Ghasmarash population to ensure that evolutionary dynamic forces continue to influence plant adaptation and survival in response to environmental alterations.

We present here the first comprehensive genetic characterization of snapmelon landraces from the humid tropics of eastern India. The genetic diversity among 42 snapmelon landraces collected from four agro-ecological regions of eastern India (eight agro-ecological subregions) was assessed by measuring variation at 16 simple sequence repeat (SSR) marker loci, at various traits including plant habit and fruit type, yield (two associated traits), disease resistance and biochemical composition (total soluble solids, ascorbic acid, carotenoids and titrable acidity). Differences between accessions were observed in a number of plant and fruit traits. Snapmelon germplasm with high acidity, elevated carotenoid content and resistance to cucumber mosaic virus were identified in the collection. The SSR analysis indicated that there is a high level of genetic variability within snapmelon germplasm. Comparison of the genetic variability between snapmelons of eastern India and melons from north, south and central regions of India and reference accessions of melon from Spain, France, Japan, Korea, Maldives, Iraq, Zambia, Israel using SSRs showed that Indian snapmelon germplasm is not closely related to melon accessions from other parts of the world and that there are regional differences between Indian melon accessions. Eastern India snapmelon has unique traits, so it is important that more germplasm from this region is sampled and preserved.

Wild relatives of pigeonpea (Cajanus cajan L.) possess many useful genes that can be utilized for crop improvement, most importantly genes for resistance to Helicoverpa armigera, the legume pod borer. The present study aimed at quantifying diversity in a collection of Cajanus scarabaeoides, Cajanus sericeus, Cajanus reticulatus and C. cajan species selected from a wide geographic range using two PCR-based marker systems, amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSRs), and the hybridization-based restriction fragment length polymorphism (RFLP). Polymorphism was higher among the wild accessions than among the cultivated genotypes. Wild and cultivated Cajanus accessions belonging to different species clustered into four distinct major groups largely based on the interspecific differences. C. scarabaeoides accessions derived from same geographical origins formed one group reflecting similar genetic makeup of these accessions. Dendrograms generated using AFLP, RFLP and SSR marker data were comparable with minor clustering differences, which suggests that either method, or a combination of both can be applied to expanded genetic studies in Cajanus. Mantel testing confirmed the congruence between the genetic distances of three markers, indicating that the markers segregated independently, giving similar grouping patterns of all accessions having similar genetic origin.

Quinoa (Chenopodium quinoa Willd.) is a staple food crop for millions of impoverished rural inhabitants of Andean South America where it has been cultivated for millennia. Interest in quinoa, due largely to its superior nutritional characteristics, is fuelling a growing export market and has led to an increased focus on genetic research and the development of quinoa breeding programmes throughout South America. The success of these breeding programmes will rely heavily on the development of core germplasm collections and germplasm conservation. We report the development of a set of fluorescence-tagged microsatellite molecular markers that can be used to characterize genetic diversity within quinoa germplasm and we use this set of 36 microsatellites markers to genetically characterize the diversity of 121 accessions of C. quinoa held in the USDA germplasm bank, 22 accessions from the CIP-FAO international nursery collection and eight accessions representing parents from genetic mapping populations. A total of 420 alleles were detected among the quinoa accessions with an average of 11 alleles detected per microsatellite locus. Genetic heterogeneity was observed in 32% of the quinoa accessions at a given locus and suggests that many of these accessions represent heterogeneous seed lots or landraces. Both unweighted pair-group method with arithmetic averages (UPGMA) and principle components analysis (PCA) analyses partitioned the quinoa accessions into two main clusters. The first major cluster consisted of accessions from the Andean highlands of Peru, Bolivia, Ecuador, Argentina and extreme northeastern Chile. The other main cluster contained accessions from both the lowlands of Chile and a set of USDA accessions with no known passport data, collected by Emigdio Ballón. Using the patterns of genetic diversity detected within the C. quinoa accessions we discuss hypotheses regarding quinoa's centre of diversity, including highland and lowland ecotype clustering patterns, origin of lowland varieties, origin of domestication, and diversity levels in the USDA and CIP-FAO collections.

Groundnut is one of the most important oilseed crops in the world. Bacterial wilt, caused by Ralstonia solanacearum E. F. Smith, is one of the major biotic constraints to groundnut production particularly in South-East Asia and East Africa. Several sources of resistance to bacterial wilt have been identified through field screening of groundnut germplasm. The aim of the present study was to quantify the genetic diversity among selected bacterial wilt-resistant lines, in comparison with the levels of variation observable within the cultivated A. hypogaea gene pool. Thirty-two SSR markers were used to assess the degree of molecular polymorphism between 46 selected genotypes revealing 107 alleles, of which 101 (99.4%) were polymorphic with gene diversity scores ranging from 0.103 to 0.669, averaging 0.386. Cluster and multidimensional scaling analysis revealed two distinct groups within the germplasm broadly corresponding to the two subspecies (hypogaea and fastigiata) of A. hypogaea. However, accessions of varieties peruviana and aequatoriana grouped together with the varieties from subsp. hypogaea, rather than grouping with the other varieties of subsp. fastigiata. Analysis of molecular variance (AMOVA) revealed that 15% of the total observed variation was accounted for by disease response groups. This analysis will be useful in the selection of parental genotypes for mapping populations and breeding programmes attempting to broaden the genetic base of future groundnut cultivars. In particular, this opens up significant opportunities for the development of intraspecific mapping populations that will be highly relevant to modern groundnut breeding programmes.

A regional (Oceania) core collection for taro germplasm has been developed based on phenotypic and molecular characterization. In total, 2199 accessions of taro germplasm have been collected by TaroGen (Taro Genetic Resources: Conservation and Utilisation) from 10 countries in Oceania: Papua New Guinea, Solomon Islands, Vanuatu, New Caledonia, Fiji, Palau, Niue, Tonga, Cook Islands and Samoa. Our objective was to select 10% from each country to contribute to a regional core. The larger collections from Papua New Guinea, Vanuatu and New Caledonia were analysed based on phenotypic characters, and a diverse subset representing 20% of these collections was fingerprinted. A diverse 20% subsample was also taken from the Solomon Islands. All accessions from the other six countries were fingerprinted. In total, 515 accessions were genotyped (23.4% overall) using taro specific simple sequence repeat (SSR) markers. DNA fingerprint data showed that great allelic diversity existed in Papua New Guinea and the Solomon Islands. Interestingly, rare alleles were identified in taros from the Solomon Islands province of Choiseul which were not observed in any of the other collections. Overall, 211 accessions were recommended for inclusion in the final regional core collection based on the phenotypic and molecular characterization.