Cowpea (Vigna unguiculata L. Walp.) is an important grain legume in tropical and subtropical regions. It requires low resource inputs and has a high nutritional value. Therefore, cowpea can play an important role in the development of agriculture. In southern Mexico, Mayan farmers have conserved and developed cowpea landraces for centuries. Nevertheless, information on their genetic diversity, conservation status and potential use is minimal. To generate information toward sustainable use, management and conservation of this species, we evaluated the genetic diversity and structure of 20 cowpea landraces from southeast Mexico using 10 inter-simple sequence repeat (ISSR) molecular markers. These ISSR markers generated 68 loci with a 67.7% polymorphism rate and average polymorphic information content of 0.36. The results of Bayesian assignation and the UPGMA analysis suggest the formation of two main groups defined by their genetic origin in southeast Mexico. High levels of genetic structure were found with a moderate level of genetic diversity distributed mainly between landraces. Low levels of intra-landrace variability were observed. Two landraces (P5 and P12) from Calakmul resulted in the high levels of genetic diversity. The selected markers were efficient at assessing genetic variability among Mexican cowpea landraces, providing valuable information that can be used in local conservation and participatory breeding programmes.

Wheat, a major food crop, faces significant yield constraints due to losses caused by various diseases, especially rusts and powdery mildew. Since the causal organisms are always evolving, there is a never-ending hunt for new genes/quantitative trait loci (QTLs) for resistance to control the damage. For this purpose, Triticum durum–Aegilops speltoides backcross introgression lines (DS-BILs) developed in our wide hybridization programme were screened against stripe rust and powdery mildew at both seedling and adult plant stages. DS-BILs showed complete to moderate resistance at the adult plant stage while varying resistance and susceptibility at the seedling stage. A total of 1095 single-nucleotide polymorphisms (SNPs) identified on 14 chromosomes of T. durum, using genotyping by sequencing, were used for QTL mapping. Eleven unique QTLs, across six chromosomes (chr1B, chr2A, chr2B, chr3B, chr6B and chr7B) were identified for resistance, four QTLs for field mixture of stripe rust pathotypes, two QTLs for stripe rust pathotype 78S84 and five QTLs for field mixture of powdery mildew pathotypes using stepwise regression-based likelihood ratio test for additive effect of markers and single-marker analysis. Eleven DS-BILs carrying multiple QTLs were identified which will serve as a useful resource to transfer the respective resistance to susceptible cultivars to develop all stage resistant elite cultivars where QTL for stripe rust resistance QYrAs.pau-2A.1 (LOD 3.8, PVE 24.51 linked to SNP S2A_16016633) and QTL for powdery mildew resistance QPmAs.pau-6B (logarithm of the odds (LOD) 3.2, phenotypic variation explained (PVE) 17.75 linked to SNP S6B_26793381) are major targets of the transfer.

DNA methylation is known to regulate gene expression when plants are exposed to abiotic stress such as drought. Therefore, insight into DNA methylation pattern would be useful for a better understanding of the expression profile of genes associated with drought adaptation. In the present study, we attempted to analyse the DNA methylation pattern at the whole-genome level and the expression of a few drought-responsive genes in rice under different regimes of soil water status, i.e. puddled, 100 and 60% field capacities (FC). The methylation-sensitive randomly amplified polymorphic DNA analysis was employed to identify DNA methylation pattern. We observed an increase in DNA methylation at 60% FC, and reduced methylation under 100% FC compared to puddled condition. The genes such as protein phosphatases (PP2C) and phenylalanine ammonia-lyase (PAL) having CpG islands in their promoter region had lower expression level under 100 and 60% FC compared to puddled conditions. Heat shock protein 70 (HSP70) and RNA helicase 25 (RH25), with no CpG islands in their promoter region, exhibited enhanced expression compared to puddled plants. In rice, increased DNA methylation seems to be an important mechanism associated with drought responses, which probably regulates the methylation-sensitive gene expression. The drought-induced changes in DNA methylation would contribute for epigenetic mechanism. The study provided evidence to argue that drought-induced increased methylation might be one of the major mechanisms associated with acclimation responses in field crops like rice.

The current study focused on characterization of the underlying genetic divergence in inbred lines developed from local landraces of North Eastern Hill Region of India – a designated Asiatic maize diversity centre – following six generations of inbreeding. Substantial genetic differentiation was indicated based on very high to moderate Fst values for 22 of the 38 simple sequence repeat markers studied. STRUCTURE analysis partitioned the subset into two distinct and one admixture subgroup (Populations I, II and III respectively) accompanied by a significant reduction in heterozygosity. Population II was further subdivided into subpopulations Pop-M9 and Pop-T9. Nei's pairwise genetic distance and population Fst values indicated that Populations I and II were more divergent with neighbour joining clustering analysis clearly defining landraces originating from the states of Tripura (Population II) and Sikkim (Population I) as most divergent. Principal coordinates analysis could explain 31.26% of the variation present in the subgroups wherein Population I was more variable. Analysis of molecular variance and Fst coefficients (P < 0.001) indicated 17% population structuring with 55% variation detected for individuals within populations. These results combined with the presence of phenotypic variability in the subgroups for yield traits supported by results of a preliminary partial diallel analysis strongly suggest the existence of distinct heterotic groups. Divergence studies are crucial for exploiting heterosis, and the current study would go a long way to help establish a germplasm base for developing varieties with improved agronomic performance and surer commercial prospects no reports of which are available thus far.

Andean blackberry (Rubus glaucus Benth.) is an emerging fruit crop with significant commercial potential. Despite its growing popularity, basic research about its genetic resources and breeding remains insufficient. The aim of this study was to assess the genetic diversity of Andean blackberry cultivars and related berries species from the main production areas in Ecuador. We analysed a total of 106 samples and performed DNA screening with different molecular markers: random-amplified polymorphic DNAs (RAPDs), inter-simple sequence repeats (ISSRs) and a set of representative samples with amplified fragment length polymorphisms (AFLPs). The tested RAPD primers did not reveal any differentiation among accessions identified as R. glaucus, however one ISSR primer was useful to find polymorphisms allowing the selection of 29 accessions for the analysis with AFLP markers. AFLP-M13 technology was used for screen genetic variations among these accessions and eight wild Rubus accessions. We scored 203 bands using five primer combinations; out of these 152 were informative in R. glaucus. AFLP markers clearly distinguish R. glaucus from the screened wild Rubus species, also an unexpected genetic structure was revealed among R. glaucus cultivars. This genetic differentiation and detection of admixed genotypes suggest a possible introgression of wild Rubus species in R. glaucus. Our findings are relevant for blackberry genetic breeding and use of these genetic resources.

Cultivated lentil suffers yield loss from stemphylium blight, caused by Stemphylium botryosum Wallr. Identification of sources of stemphylium blight resistance and knowledge of the mode of inheritance of resistance are important for developing resistant cultivars. The interspecific recombinant inbred line (RIL) population developed from a cross between the moderately resistant parent Lens culinaris cv. ‘Eston’ and the resistant parent L. ervoides (Brign.) Grande accession IG 72815 was evaluated for stemphylium blight resistance under controlled conditions at the University of Saskatchewan, Saskatoon, Canada, and under field conditions at the Pulses Research Centre (PRC), Ishurdi, Bangladesh. We hypothesized that resistance from both parents will lead to transgressive segregation indicative of pyramiding of resistance genes from the same. However, no resistant transgressive segregants were observed in the RIL population. A large proportion (50%) of the RILs had disease severity levels similar to the resistant parent IG 72815 in experiments conducted under natural disease pressure in Bangladesh. Under controlled conditions in Saskatoon, 38% of RILs had resistance levels similar to IG 72815. Across all environments, 14 RILs consistently had resistance levels similar to IG 72815. The distribution of disease severity scores for all RILs indicated polygenic inheritance of stemphylium blight resistance in the population. RILs with consistent resistant reactions should prove useful for lentil improvement programmes. This will contribute to increasing the productivity of lentil crops in North America and the Indo-Gangetic region, which account for more than 68% of world lentil production.

Phoebe cooperiana U.N Kanjilal ex A. Das is an indigenous forest tree species yielding fruits consumed widely across the state of Arunachal Pradesh, India. As part of an initiative to domesticate the species, phenotypic variation in fruit and seed morphology as well as the biochemical properties of the pulp were assessed for 14 populations within the state. Nine fruit and seed characters were measured and 12 biochemical parameters of the fruits were analysed. Five trees were selected from each population and a minimum of 30 fruits were collected from each tree. Analysis of variance indicated significant variation in all fruit and seed morphological parameters. The coefficient of variation for fruit weight was reported to be 5.02%, seed weight 5.60%, pulp weight 5.36% and pulp fruit ratio 4.14%. Among biochemical parameters which are of nutritive value, crude protein, vitamin E and A were higher than that found in most common fruits and vegetables. These traits also showed significant variation among the 14 selected populations with crude protein values ranging between 5.99 and 10.76%, vitamin E between 4.80 and 7.33 mg/100 g and vitamin A between 1.88 and 3.13 mg/100 g. The fruits are also high in phenol with a mean value of 22.19 mg/g and displayed promising 2,2-diphenyl-1-picrylhydrazyl radical scavenging properties averaging 56.94% antioxidant activity. However, cyanogen content in the fruits was higher than the permissible amount for human consumption, for which processing is recommended before use. The opportunities for domestication are discussed and some promising traits and populations that can be utilized in the domestication programme are identified.

To identify appropriate genotypes for breeding varieties suitable for semi-arid areas, yield components, as well as morphophonological traits of 127 safflower genotypes, were assessed at the Seed and Plant Improvement Institute, Iran. Cluster analysis revealed four distinct groups. The largest group (third cluster) includes 48 genotypes with characteristics such as mostly yellow-coloured flowers, mostly thorny with few thistle genotypes, relatively early-flowering, relatively high number of heads and grains per plant, highest 1000-grain weight with the highest grain yields. In contrast, the smallest group (second cluster) contains 13 genotypes with characteristics such as yellow florets, semi-dwarf, thorny, moderately late-flowering, low number of heads per plant and number of grains per head, low 1000-grain weight, and low grain yield. Principal component analysis results showed that the three components accounted for 29.5, 15.9 and 11.1% of the total variation, respectively. Graphic representation of the biplots based on the first and second principal components showed that the experimental genotypes were classified into four groups. The results also indicated that stem diameter, the number of branches, heads per plant and grains per head had the highest correlation with the first component, and grain yield, flower colour, flowering initiation and plant height had the highest correlation with the second component. These traits can be considered as an appropriate index for the selection of elite safflower genotypes for breeding varieties suited to cultivation in semi-arid conditions.

In this study, maize landraces, previously collected from different regions of Turkey through a national maize breeding project, were screened for kernel oil content and oil quality. After a seed reproduction in 2017, the screening trial was conducted in 2018, using an Augmented Experimental Design with 192 local maize populations along with seven check hybrids. Data were collected on oil, oleic acid, linoleic acid, monounsaturated (MUFA), polyunsaturated and saturated fatty acids, total carotenoid and total tocopherol contents. The results showed that there was a considerable amount of genetic variation among the Turkish maize landraces for almost all the traits investigated in this study. Some of the evaluated landraces are available that could be considered as high oil variety or special genotypes in terms of certain oil quality traits. Landraces had significantly higher values than checks for oil content, oleic acid, MUFA and tocopherol contents. Genetic analyses suggest that the kernel quality traits could be successfully manipulated using the investigated plant material. Heritability values were found high for all the traits of interest, except for saturated fatty acid and total carotenoid content. The promising landraces detected in this study could be exploited in future breeding programmes upon further evaluations at the population level.

In order to understand rice blast resistance gene patterns in rice landraces from Myanmar and Laos, we analysed the Pita, Pib, Pikh, Pi9 and Pi5 genes in 80 landraces through the use of functional molecular markers and functional fragment sequencing. These landraces were separated into four haplotypes (H1–H4) based upon three mutations identified in the Pita sequence. All four haplotypes were detected among landraces from Myanmar, whereas only the H1 and H2 haplotypes were detected among landraces from Laos. We additionally grouped landraces carrying 0–4 resistance genes into 18 genotypes based upon their resistance-susceptibility patterns and found that 16 of these genotypes were detected among Myanmar landraces at relative frequencies ranging from 2.50–12.50%, while 10 were detected among landraces from Laos at relative frequencies of 2.50–42.50%. The ‘Pib( + ) pikh(−) pi9(−) pi5(−) pita(−)’ genotype was found to be dominant, accounting for 12.5 and 42.5% of landraces from Myanmar and Laos, respectively. The Pib, Pikh, Pi5 and Pita genes were detected in 52.50, 32.50, 37.50 and 30.00% of landraces from Myanmar respectively, whereas they were detected in 52.50, 12.50, 30.00 and 17.50% of landraces from Laos, respectively. The Pi9 gene was rarely detected among analysed landraces and was particularly rare in those from Laos. These findings suggest that rice landraces from Myanmar are more genetically diverse than those from Laos, with clear differences in blast resistance gene patterns between landraces from these two countries.