Association mapping (AM), an alternative method of quantitative trait loci (QTL) discovery, exploits historic linkage disequilibrium (LD) present in natural populations. AM is effective in self-pollinated crops such as Dolichos bean as LD extends over longer genomic distance driven-by low rate of recombination and thereby requiring fewer markers for exploring marker-traits associations. A core set of Dolichos bean germplasm consisting of 64 accessions was evaluated for nine quantitative traits (QTs) during 2014 and 2015 rainy seasons and genotyped using 234 simple sequence repeats (SSR) markers. Substantial diversity was observed among the core set accessions at loci controlling QTs and 95 of the 234 SSR markers were found polymorphic. The structure analysis and low magnitude of fixation indices suggested weak population structure, which in-turn indicated the low possibility of false discovery rates in the marker-QTs association. The marker allele's scores were regressed onto phenotypes at nine QTs following general linear model and mixed linear model for exploring marker-QTs associations. Significantly higher number of SSR markers was found associated with genomic regions controlling nine QTs. A few of the markers such as KT Dolichos (KTD) 200 for days to 50% flowering, KTD 273 for fresh pod yield per plant and KTD 130 for fresh pods per plant explained ≥10% of the trait variations. The study could also identify a few SSR markers such as KTD 273, KTD 271 and KTD 130 linked to multiple traits. These linked SSR markers are suggested for validation for their use in marker-assisted Dolichos bean improvement programmes.

This study was conducted to determine the opinions of the farmers producing dry bean landraces (DBL) at the regional level of Turkey (eight provinces). In total, 140 questionnaire forms were filled by DBL producers. The population and then the sample size were determined according to 2016-year-preliminary-study. The capital structures of the farms according to the production types were evaluated using the Five-Capital-Model approach, and differences were tested by parametric and non-parametric statistical methods. The study showed that 37.86% of the DBL producers produce as the home-garden-type while 62.14% of them as the field-type, which is larger than 0.1 ha. While home-garden-type producers majorly produce for their own family needs, commercial ideas and concerns are at the forefront for field-type producers. While field-type producers have higher values in terms of five capitals, home-garden-type producers move within a more traditional way of production. More than half of the producers indicate that they will continue to produce DBL; this ratio is higher in home-garden-type producers. This indication of approximately 25% of both types of producers wherein their children will continue to produce DBL, there is a need for more human labour, efficiency and profitability concerns, production mostly by the elderly population increasing the risk of future depletion in DBL-genetic resources. This calls for more efforts to increase the awareness among the young population on the importance and protection of genetic resources and to make special policies for the protection of genetic resources by policy makers and develop models based on genetic resources.

Chickpea (Cicer arietinum L.) is an important grain legume nutritionally balanced for human consumption. The physical properties of chickpea seeds are important for processing and storage as well as for assessing seed quality and the hydration properties related to cooking quality. The chickpea mini core collection (211 accessions) and four control cultivars were evaluated for seed morphological (seed colour, shape, dots on seed coat and surface texture); physical (seed moisture content, 100-seed weight, seed coat content, length, width, thickness, geometric mean diameter (GMD), surface area, sphericity, shape aspect, volume, bulk density, true density and porosity); and hydration traits (hydration capacity, hydration index, swelling capacity and swelling index). Highly significant differences were observed for all the seed traits in the mini core collection. Correlation coefficients indicated that accessions with high or more seed weight, GMD, sphericity, seed shape aspect, swelling capacity and swelling index would be useful for utilization in research. The results of this study have refined the seed traits of chickpea and resulted in identifying several desirable accessions in the mini core. Some of these accessions were previously identified as promising sources for important agronomic and nutritional traits and for resistance to biotic and abiotic stresses and will be useful sources to develop high-yielding cultivars with desirable seed physical and hydration quality.

Triticum boeoticum is a valuable gene source for tolerance to drought stress. In order to study the effect of drought stress on this plant, and to understand its adaptive mechanisms at the molecular level, 10 accessions of T. boeoticum were evaluated under non- and drought stress conditions. Evaluation of 31 different phenological, morpho-physiological and root-related traits showed that there were significant differences between accessions. Using the bi-plot resulting from the PCA, the studied traits and accessions were separated in different groups. The most tolerant (B5) and susceptible (B6) accessions to drought stress were identified, so these accessions were used for assessment of changes in the TaNAC2 and TaNAC69-1 transcription factors (TFs) expression. The results showed that in the most tolerant and susceptible accessions, TaNAC2 and TaNAC69-1 expression levels increased between non-stress and stress conditions significantly, but the increased level of these two genes expression in the most tolerant accession was much higher than the most susceptible accession. According to the obtained results, T. boeoticum can be a suitable and promising gene source for improving modern wheat. In addition, the results of TFs expression could improve our understanding about the complex mechanisms associated with drought tolerance in wheat, especially wild wheat.

The grain of modern wheat cultivars has a significantly lower mineral content, including the content of copper, iron, magnesium, manganese, phosphorous, selenium and zinc. For this reason cereal breeders, are constantly searching for new genetic sources of minerals that are essential in human nutrition. Triticum polonicum, which is grown on a small scale in Spain, southern Italy, Algeria, Ethiopia and warm regions of Asia, deserves special attention in this context. The micronutrient and macronutrient content of T. polonicum versus T. durum and T. aestivum was compared in this study. Polish wheat grain was characterized by the significantly highest content of phosphorus (4.55 g/kg), sulphur (1.82 g/kg), magnesium (1.42 g/kg), zinc (49.5 mg/kg), iron (39.1 mg/kg) and boron (0.56 mg/kg) as well as a low content of aluminium (only 1.04 mg/kg). The macronutrient profile of most T. polonicum lines differed completely from that of common wheat and durum wheat. The principal component analysis supported discrimination of seven Polish wheat lines with a particularly beneficial micronutrient profile (P2, P3, P5, P7, P9, P22 and P25). These lines were characterized by the highest content of copper, iron and zinc, as well as the lowest concentrations of strontium, aluminium and barium which are undesirable in food products. The above lines can be potentially applied as source materials for breeding new wheat varieties. The results of this study indicate that Polish wheat could be used in genetic biofortification of durum wheat and common wheat.

Variety selection from locally adapted crops is the major climate change adaptation strategy of farming communities. There are several justifications for re-thinking for the sustainable use of crop biodiversity in our breeding programs. Thirty-one durum wheat farmers' varieties (FVs), together with five improved check varieties, were characterized in Tigray during 2014 and 2015 main cropping seasons. The genotype effect explained most of the variations in measured traits, which enabled us to identify superior and stable genotypes for wider adaptation as well varieties with more local adaptation. The genotypes and test locations imposed a highly significant (P < 0.001) effect on both phenological and quantitative traits. A yield advantage of 14.3% was obtained from top performer FV over top performer improved variety, Asassa. Of the tested FVs, 27.8% were superior for grain yield (GY) than improved varieties and 19.4% of these superior FVs were more stable and adaptable than the improved varieties. Besides giving higher GY with spatial stability, they qualify for industrial requirements with high-grain protein (>13%) and gluten (>33%) contents. FVs such as G10, G16, G21, G22 and G30 have wider adaptability and are suitable for production in all tested areas. As outcome of this study, two superior FVs, G10 (208304) and G30 (8208), were nationally released for commercial production for their productivity, stability and grain quality. Utilizing the diverse durum wheat FVs can effectively improve productivity and adaptability. Wheat breeders need to revisit these resources to improve adaptation of wheat production to the changing climatic conditions.

Trait-specific characterization of rice landraces has significant potential for germplasm management, varietal identification and mining of novel gene/allele for various traits. In the current study, we have characterized 98 unique rice landraces collected from coastal regions of India, affected by submergence and salinity, based on Sub1 and Saltol quantitative trait loci (QTL) linked microsatellite markers. Among these genotypes, four genotypes (IC536558, IC536559, IC536604 and IC536604-1) collected from Kerala and two genotypes (AC34902 and IC324589) collected from West Bengal were identified with tolerance to submergence and salinity stress. A high level of genetic diversity of He = 0.349 and 0.529 at Sub1 and Saltol QTL region was detected by QTL-linked microsatellite markers, respectively. At Sub1 region one genotype, AC34902, was detected with maximum allelic similarity with FR13A, a known submergence tolerant variety. Besides, five genotypes (IC211188-1, IC536604-1, IC536604, IC536558 and IC536559) showed comparatively close genetic relationship with the salt tolerant variety FL478 for Saltol QTL and were clustered together in the neighbour joining dendrogram. Considering the haplotype structure, five genotypes (IC203801, IC203778, IC324584, IC413608 and IC413638) were identified which did not contain any common allele similar to FR13A but were still tolerant to submergence. These individuals need further characterization for identification of new alleles responsible for their tolerance.

Leaf colour characteristics of 730 sweetpotato, Ipomoea batatas (L.) Lam. (Convolvulaceae), plant introduction (PI) accessions from the USDA sweetpotato germplasm collection were evaluated during 2012–2014. Colorimetry data for the abaxial and adaxial leaf surfaces were recorded using a tristimulus colorimeter and the CIE 1976 L*a*b* and CIE L*C*h* colour spaces. Most accessions (725 of 730 PIs) had dark-to-medium green leaves, but two PIs had totally purple leaves, and three PIs had yellow or yellow-green (chartreuse) leaves. For mature, field-grown green leaves, values for the red-green coordinate (a*) averaged −12.4 for the adaxial and −10.4 for the abaxial leaf surface. Values for the blue-yellow coordinate (b*) averaged 17.2 for the adaxial and 17.3 for the abaxial leaf surface. Hue angle (h*) for green leaves averaged 120.9° for the adaxial and 126.2° for the abaxial leaf surface. Colour saturation (Chroma, C*) averaged 21.3 for the adaxial and 20.2 for the abaxial leaf surface. Lightness (L*) averaged 35.4 for the adaxial and 47.2 for the abaxial leaf surface of green leaves. Late in the season, over one-half (53.9%) of the 730 PIs showed some level of purple pigmentation in the leaf lamina. Late-season purple leaves were collected and colour coordinates were recorded for 118 PIs grown in the field. For purple leaves, values for a*, b*, C*, L* and h* averaged 2.3, 6.2, 7.9, 28.2 and 64.4° for the adaxial surface and −1.0, 12.7, 13.9, 43.1 and 87.0° for the abaxial leaf surface, respectively.

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.

Crop wild relatives (CWR) are valuable gene pools for crop improvement and offer unique potential and opportunity for enhancing food security and adaptation to climate change. However, current actions towards conservation of plant genetic resources in Zambia do not adequately cover CWR occurring in the country. The article describes the process leading to the development of a national strategic action plan (NSAP) for the conservation and sustainable use of priority CWR in Zambia. Based on 59 prioritized crops, a partial checklist of 459 CWR taxa was generated from the national flora checklist of 6305 taxa. The generated CWR taxa were prioritized based on the socio-economic value of the related crop, their utilization potential in crop improvement, relative distribution and threat status to produce 30 prioritized CWR taxa. Occurrence data were compiled for all CWR inventory taxa and used in spatial analyses to establish species distribution, species richness, gaps in in situ conservation and genebank collections, and to identify priority sites for in situ conservation and ex situ collecting. Consistent with the national developmental agenda, along with the contribution of national stakeholders, spatial analyses of occurrence data of priority CWR taxa are valuable input for the development of the NSAP for the conservation and sustainable use of the priority CWR.

This research attempts to systematically establish shape descriptor states through elliptic Fourier analysis (EFA) using pili (Canarium ovatum Engl.) kernel as a model. Kernel images of 53 pili accessions from the National Plant Genetic Resources Laboratory (NPGRL), University of the Philippines Los Baños were acquired using VideometerLab 3. Shape features, such as roundness, compactness and elongation, were extracted from the images. Shapes outlines were characterized using elliptic Fourier coefficients calculated from SHAPE version 1.3 software. Principal component analysis and cluster analysis were used to elucidate clusters representing the shape descriptor states. The first principal component accounts for the variation in length to width ratio; whereas, the second and third principal components explain the variation in the location of the widest portion and the truncation of the apex and base of the kernel, respectively. Cluster analysis separated the different accessions into six distinct clusters at 0.04 Euclidian distance. Six descriptor states, narrowly elliptic, elliptic, widely elliptic, ovate, obovate and lance-ovate, were characterized from the shape outlines and visualized through R's shape on r package. The discrimination between clusters was validated through MANOVA and LDA with 95% correct classification. The Fourier coefficients were also able to represent the variation observed from the physical properties of shape. The method may be used in establishing shape descriptors of all plant parts of all crop species.

Sorghum (Sorghum bicolor (L.) Moench) is an important resource to the national economy and it is essential to assess the genetic diversity in existing sorghum germplasm for better conservation, utilization and crop improvement. The aim of this study was to evaluate the level of genetic diversity within and among sorghum germplasms collected from diverse institutes in Nigeria and Mali using Single Nucleotide Polymorphic markers. Genetic diversity among the germplasm was low with an average polymorphism information content value of 0.24. Analysis of Molecular Variation revealed 6% variation among germplasm and 94% within germplasms. Dendrogram revealed three groups of clustering which indicate variations within the germplasms. Private alleles identified in the sorghum accessions from National Center for Genetic Resources and Biotechnology, Ibadan, Nigeria and International Crop Research Institute for the Semi-Arid Tropics, Kano, Nigeria shows their prospect for sorghum improvement and discovery of new agronomic traits. The presence of private alleles and genetic variation within the germplasms indicates that the accessions are valuable resources for future breeding programs.

Heat stress, a regular risk to wheat in the subtropics, is a growing threat in other wheat producing regions as the global temperature rises. This paper reports on three experiments evaluating 49 entries of the 13th High Temperature Wheat Yield Trial (13HTWYT) from the International Centre for Maize and Wheat Improvement (distributed in 2014), with Fang 60 as the local check, at two locations at Chiang Mai, Thailand, a designated representative of the wheat mega-environment 5, in which temperature for the coolest month averages >17.5 °C and the crop is subjected to high temperature for the entire growing season. The wheat was grown in the lowland (elevation 330 m) at Chiang Mai University in (i) sand culture to simulate the condition of non-limiting nutrient and water supply and (ii) in the field and (iii) as an on-farm trial in the highlands (elevation 800 m) at Mae Wang district of Chiang Mai province. Heat tolerance in the wheat germplasm, recently developed for adaptation to high temperature, was indicated by longer pre-heading duration, and the positive correlation between days to heading and grain yield all three experiments. The longer time before heading enabled development of larger spikes that produced more seeds from more and larger spikelets and more competent florets. However, with the number of spikes that was either lower than or similar to Fang 60, none of the recently developed 13HTWYT entries out-yielded the local check from the 1970s.

Landraces (including heritage varieties) are an important agrobiodiversity resource offering considerable value as a buffer against crop failures, as a crop for niche markets, and as a source of diversity for crop genetic improvement activities underpinning future food security. Home gardens are reservoirs of landrace diversity, but some of the accessions held in them are vulnerable or threatened with extinction. Those associated with seed saving networks have added security, for example, ca. 800 varieties are stored in the Heritage Seed Library (HSL) of Garden Organic, UK. In this study, Amplified Fragment Length Polymorphisms-based genetic analysis of accessions held in the HSL was used to (a) demonstrate the range of diversity in the collection, (b) characterize accessions to aid collection management and (c) promote broader use of the collection. In total, 171 accessions were included from six crops: Vicia faba L., Pisum sativum L., Daucus carota L., Cucumis sativus L., Lactuca sativa L. and Brassica oleracea L. var. acephala (DC.) Metzq. Average expected heterozygosity ranged from 0.18 to 0.28 in D. carota; 0.02–0.18 in P. sativum; 0.05–0.18 in L. sativa; 0.15–0.26 in B. oleracea var. acephala; 0.15–0.37 in C. sativus and 0.07–0.36 in V. faba. Genetic diversity and Fst values generally reflected the breeding system and cultivation history of the different crops. Comparisons of the diversity found in heritage varieties with that found in commercial varieties did not show a consistent pattern. Principal coordinates analysis and Unweighted Pair Group Method with Arithmetic Mean cluster analysis were used to identify four potential duplicate accession pairs.

Crop wild relatives (CWR) are wild plant taxa that have broader genetic diversity than crops hence they are an excellent source of genes and traits to improve crops. The potential value of CWR for agriculture and the need to protect these plants in their natural habitats (in situ) have been recognized globally. South Africa has the richest temperate flora globally, and the checklist of food and fodder CWR for the country considers 258 taxa to be high priority for conservation. A systematic conservation planning approach was used for spatial prioritization for in situ conservation actions for CWR. Protected areas were categorized on the basis of their CWR richness. The Kruger National Park has the highest number of CWR (66 taxa), but most of these are widespread and common. Fifty-seven protected areas, most of which are in the Western and Eastern Cape fynbos, are irreplaceable for protecting a number of endemic and threatened CWR. For priority CWR not adequately represented in existing protected areas, a spatial plan was developed to identify the smallest area that aligns with existing targets for the National Protected Areas Expansion Strategy, that are not transformed in terms of habitat, and that are projected to be climate change resilient. Mechanisms for ensuring uptake of the recommendations for the in situ conservation of CWR have been documented in a National Strategy and Action Plan and these include making information and data available and promoting the inclusion of CWR in current management and monitoring activities.

The U genome of Aegilops umbellulata is an important basic genome of genus Aegilops. Direct gene transfer from Ae. umbellulata into wheat is feasible but not easy. Triticum turgidum–Ae. umbellulata amphidiploids can act as bridges to circumvent obstacles involving direct gene transfer. Seven T. turgidum–Ae. umbellulata amphidiploids were produced via unreduced gametes for spontaneous doubling of chromosomes of triploid T. turgidum–Ae. umbellulata F1 hybrid plants. Seven pairs of U chromosomes of Ae. umbellulata were distinguished by fluorescence in situ hybridization (FISH) probes pSc119.2/(AAC)5 and pTa71. Polymorphic FISH signals were detected in three (1U, 6U and 7U) of seven U chromosomes of four Ae. umbellulata accessions. The chromosomes of the tetraploid wheat parents could be differentiated by probes pSc119.2 and pTa535, and identical FISH signals were observed among the three accessions. All the parental chromosomes of the amphidiploids could be precisely identified by probe combinations pSc119.2/pTa535 and pTa71/(AAC)5. The T. turgidum–Ae. umbellulata amphidiploids possess valuable traits for wheat improvement, such as strong tillering ability, stripe rust resistance and seed size-related traits. These materials can be used as media in gene transfers from Ae. umbellulata into wheat.

In this work, 10 processing type Hungarian tomato gene bank accessions were investigated in a 3-year open-field experiment together with three commercial varieties for quantifying the genotype × environment interaction for their total soluble solids, total acid, dry matter, lycopene, total polyphenol content and antioxidant activity. Results showed remarkable differences of accessions in phytonutrient content over the 3 years (environments). Genotype main effect plus genotype × environment interaction biplots were created for the visualization of the best performing samples and of their relation to a theoretical best variety. Obovate fruit-shaped accessions (especially RCAT031257 and RCAT060349) reached outstanding nutritional results in every environment. According to extremities in weather conditions, two landraces (RCAT060348 and RCAT060349) with higher drought tolerance, and two (RCAT031257 and RCAT029837) less prone to excessive rainfalls were identified. The results can contribute to the enrichment of tomato nutritional phenotypic data banks, facilitating the utilization of gene bank accessions in genomic studies.

Soil salinity is a major limitation to legume production in many areas of the world. Identification of the genetic source of salt tolerance is critical in soybean breeding for improving soybean production in salt-affected regions. Vietnam has unique sources of soybean germplasm and varieties are grown in the area where exposure to salinity is frequent. However, there is little research on the identification of salt tolerant sources in the Vietnamese gene pool. The present study compared 18 Vietnamese soybean cultivars for their differences in salt tolerance. Under a range of NaCl stress from 0 to 200 mM NaCl, there was a large variation in salt tolerance among the 18 soybean lines evaluated. The soybean accession PI 675847 A (Vietnamese variety DT2008), was identified as a useful source of salt tolerance. During vegetative growth, PI 675847 A had lower leaf scorch scores, higher cell membrane stability, better photosynthesis and biomass accumulation under NaCl stress than the other 17 strains evaluated. In addition, PI 675847 A maintained better growth and seed yield in salt-affected soils compared with the sensitive lines. Analyses of ion contents in plant leaves under saline conditions showed that PI 675847 A was able to limit uptake and transport of Na+ and Cl−. Because of its higher productivity under saline conditions, PI 675847 A will be a useful germplasm source in soybean improvement programs for salt tolerance.

The complete chloroplast (cp) genome sequences of three Amaranthus species (Amaranthus hypochondriacus, A. cruentus and A. caudatus) were determined by next-generation sequencing. The cp genome sequences of A. hypochondriacus, A. cruentus and A. caudatus were 150,523, 150,757 and 150,523 bp in length, respectively, each containing 84 genes with identical contents and orders. Expansion or contraction of the inverted repeat region was not observed among the three Amaranthus species. The coding regions were highly conserved with 99.3% homology in nucleotide and amino acid sequences. Five genes – matK, accD, ndhJ, ccsA and ndhF – showed relatively high non-synonymous/synonymous values (Ka/Ks > 0.1). Sequence comparison identified two insertion/deletion (InDels) greater than 40 bp in length, and polymerase chain reaction markers that could amplify these InDel regions were applied to diverse Korean Genbank accessions, which could discriminate the three Amaranthus species. Phylogenetic analyses based on 62 protein-coding genes showed that the core Caryophyllales were monophyletic and Amaranthoideae formed a sister group with the Betoideae and Chenopodioideae clade. Comparing each homologous locus among the three Amaranthus species, identified eight regions with high Pi values (>0.03). Seven of these loci, except for rps19-trnH (GUG), were considered to be useful molecular markers for further phylogenetic studies.