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.

Successful conservation strategies require that taxa are prioritized because resources for planning and implementation are always limited. In this study, we created a partial checklist of crop wild relatives (CWR) that occur in the Southern African Development Community (SADC) region and identified the taxa of highest priority for regional conservation planning based on their importance for food and economic security. We found that the region contains over 1900 wild relatives of species cultivated for food, beverages, ornamental, forage/fodder, forestry, medicinal, environmental and other uses. Prioritization of these species was based on two criteria: (i) the value of the related crop for human food and economic security in the region and/or globally, and (ii) the potential or known value of the wild relatives of those crops for crop improvement. The region contains 745 CWR species related to 64 human food and beverage crops that are of high socioeconomic importance and 100 of these are of immediate priority for conservation action. The results of this study show that the SADC region contains a wealth of CWR diversity that is not only of value for food and economic security within the region but also globally. Furthermore, this study represents the first step in developing a CWR conservation and sustainable use strategy for the region, where its implementation would contribute to food security and well-being.

Wild relative of okra, Abelmoschus angulosus Wall. ex Wight & Arn. was identified as a resistant germplasm for Okra Yellow Vein Mosaic Virus (OYVMV) which is the devastating disease for okra cultivation in Sri Lanka. The mode of resistance of OYVMV in A. angulosus was studied with the aim of tagging responsible genes for the disease resistance. Wide hybridization was performed between A. angulosus and highly virus susceptible A. esculentus variety, MI-7. Very poor seed setting was observed in F1 and F2 generations due to post zygotic abortion. Disease screening was carried out using F1 and F2:3 populations along with parents in the field under induced disease pressure. Disease severity index and area under disease progress curve were calculated to measure disease severity. Number of genes segregating for OYVMV disease resistance was calculated for the F2:3 generation. Modified Wright's formula was used to estimate the effective gene number and mode of inheritance by a quantitative method. A χ2 test was performed for qualitative analysis. Plants of A. angulosus were totally free of virus incidence while 100% disease incidence was observed in the variety MI-7. F2:3 population showed between and within progeny segregation for disease incidence. Results indicated that the disease susceptibility was dominant over resistance. χ2 analysis revealed that the segregation of disease severity was significantly fit to the gene model of 9:6:1 (χ2 = 0.1757 at P ≤ 0.05) suggesting the disease resistance in A. angulosus is governing by two recessive genes in an additive manner. Result was confirmed by the quantitative analysis.

Rice blast caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating diseases in rice production worldwide. Information on rice varieties with the blast disease resistance gene is important for rice cultivar development. This study identified rice blast resistant genes in 226 rice cultivars including 203 Thai landrace rice cultivars (19 upland rice cultivars from the North, 99 lowland rice cultivars from the Northeast, 45 floating rice cultivars from the Northeast and 40 cultivars from the South), 21 recommended rice varieties and two susceptible varieties ‘KDML105’ and ‘Nipponbare’ by using gene-specific markers for the blast resistant genes Pid3, Pi54 and Pigm. Results showed that 159 cultivars have at least one resistant gene and four cultivars have all three resistant genes. These results indicate that Thai landrace rice is a valuable source of rice blast resistant genes for rice breeding programmes.

Lentil is now an integral part of prairie cropping systems. Climate forecasts point to variable and increased drought frequency, putting lentil production in jeopardy. Future lentil genotypes will require root systems that can extract more water under drought conditions. This study focuses on root diameter and root tip number, traits known to play an important role in water uptake during drought. We compared the total root length (TRL) in three soil horizons of both wild and cultivated lentil genotypes for three root diameter classes when plants were grown under moderate or severe drought, and when re-watered after exposure to moderate drought conditions. Our study demonstrates that roots of both wild and cultivated lentil genotypes can be categorized into very fine, fine and small diameter classes. Some wild lentil genotypes had significantly higher TRL in the B and C soil horizons when grown under severe or moderate drought and therefore, could act as resources for the transfer of root traits to cultivated lentil genotypes. Further evaluations focused on the root systems of interspecific recombinant inbred lines under drought conditions will be required to determine whether these traits are heritable.

Crop wild relatives (CWR) are valuable resources for crop breeding due to their close genetic relationship to the cultivated plants and their wide genetic variation, allowing the introgression of desirable traits into the crops, such as resistance to plant pests and diseases or adaptability to climate change. Mexico is a centre of agrobiodiversity, including CWR, but climate change, and other factors, are contributing to the loss of important Mexican CWR genetic diversity. The in situ and ex situ conservation status of Mexican priority CWR were assessed through a gap analysis as part of a national CWR conservation strategy for Mexico, to ensure the long-term preservation and improve the availability of these genetic resources. A set of 310 priority CWR taxa, previously identified as part of the national CWR inventory for Mexico, were analysed. Species distribution modelling and ecogeographic diversity analyses were used to detect gaps in in situ and ex situ conservation at taxon and ecogeographic levels. Priority target sites were identified throughout the country for complementary in situ and ex situ conservation of these taxa. The results obtained allow us to make recommendations for immediate conservation actions, thus helping to mitigate the threats to Mexican agrobiodiversity and enhance both national and global food security.

Silphium spp. have garnered interest in Europe as a bioenergy crop and in North America as a perennial oilseed crop. However, very little has been done at this early stage of domestication to characterize wild collections for many key characteristics, including important oilseed traits. The objective of this work was to develop a basic understanding of how biogeography and associated population genetic forces have shaped seed phenotypes in plant collections across the native range of Silphium integrifolium Michx. (Asteraceae: Heliantheae), the primary domestication candidate for oilseed use. A collection of 53 accessions was grown in a common environment in Salina, KS, which is a location well within the native range of the species in central North America. Plants from each collection site were randomly mated by hand to produce seed representative of each accession, and the seeds subjected to seed dimensional trait, oil content and oil composition analyses. Kernel width varied along a latitudinal cline of collection site, while kernel length varied across a longitudinal cline. Palmitic and linoleic acids were inversely correlated with each other and varied along a longitudinal cline of the collection site. The results indicate that accessions collected from more southwesterly sites tended to have larger seed and those from more westerly sites had higher linoleic acid content and lower palmitic and myristic acids, which are all desirable phenotypes for an oilseed Silphium.

Drought stress restricts the production of agricultural crops through morphological, physiological and biochemical changes in plants. This study explored the genetic control of physiological traits related to drought in coriander. In a diallel analysis, all six parents, their 15 F1 hybrids and 15 F2 populations were subjected to different irrigation regimes including well-watered, mild and severe water deficit stress. Drought stress decreased the relative chlorophyll content (RCC), the relative water content (RWC), chlorophyll a (Chla), chlorophyll b (Chlb), total chlorophyll (TChl) content, carotenoids (Car) and essential oil yield (EOY) in F1 and F2 generations. General combining ability (GCA) and specific combining ability effects were highly significant for all traits in F1 and F2 generations. Additive gene action was predominant for Chla, Chlb, TChl and Car under well-watered condition while non-additive gene effects were more important under mild and severe water deficit stresses in F1 and F2 generations for the above traits. Additive gene effects were more important for RCC, RWC and electrolyte leakage (EL) traits in both F1 and F2 generations under mild and severe water deficit stresses. In conclusion, the high narrow-sense heritability and significant genetic correlations between EOY and RCC, RWC and EL suggest that these traits can be used as surrogates to identify superior genotypes for arid and semi-arid regions. Also, the parental lines, P4 and P6 had the best GCA for RCC, RWC, Chla, Chlb, TChl, Car, essential oil content and EOY.

In the USA, western Washington (WWA) and the Alaska (AK) Interior are two regions where maritime and continental climates, high latitude and cropping systems necessitate early maturing spring wheat (Triticum aestivum L.). Both regions aim to increase the production of hard spring bread wheat for human consumption to support regional agriculture and food systems. The Nordic region of Europe has a history of breeding for early maturing spring wheat and also experiences long daylengths with mixed maritime and continental climates. Nordic wheat also carries wildtype (wt) NAM-B1, an allele associated with accelerated senescence and increased grain protein and micronutrient content, at a higher frequency than global germplasm. Time to senescence, yield, protein and mineral content were evaluated on 42 accessions of Nordic hard red spring wheat containing wt NAM-B1 over 2 years on experimental stations in WWA and the AK Interior. Significant variation was found by location and accession for time to senescence, suggesting potential parental lines for breeding programmes targeting early maturity. Additionally, multiple regression analysis showed that decreased time to senescence correlated negatively with grain yield and positively with grain protein, iron and zinc content. Breeding for early maturity in these regions will need to account for this potential trade-off in yield. Nordic wt NAM-B1 accessions with early senescence yet with yields similar to regional checks are reported. Collaboration among alternative wheat regions can aid in germplasm exchange and varietal development as shown here for the early maturing trait.

Drought stress negatively affects the cotton production all over the world. The negative impact of drought varies for different species due to some morphological and root attributes that help some species to better stand under drought. But the extent of disturbance varies for different cotton species. To find out such variation, two cotton species (Gossypium hirsutum and Gossypium arboreum) were studied under normal and drought conditions for 2 years. Two genotypes for each species were included, i.e. PC-1 and COMILLA (G. arboreum) and IUB-13 and IUB-65 (G. hirsutum). The experiment was laid out under a completely randomized design following factorial arrangement. Genotype × treatment × year interaction of cotton genotypes was studied for different root, morphological, physiological and fibre-related traits. Traits such as above ground dry biomass, above ground fresh biomass, chlorophyll contents, leaf area, seed cotton yield, sympodial branches/plant, fibre strength and ginning out-turn were higher in G. hirsutum genotypes as compared to G. arboreum genotypes. However less reduction under drought in all above mentioned traits was recorded for G. arboreum, than G. hirsutum. Furthermore, root traits; primary root length, lateral root numbers, root fresh weight and root dry weight were enriched under drought condition in G. arboreum genotypes than in G. hirsutum genotypes, which is a clear manifestation of higher drought tolerance ability in G. arboreum genotypes transferrable to G. hirsutum genotypes through interspecific crossing or other means.

The aims of the paper are to characterize the ornamental bedding behaviour of selected Glandularia materials, to evaluate breeder and public preferences (PP) of new potential ornamental plants to be introduced in the market and to obtain a ranking with the best-selected materials. After hybrids characterizations through different traits of ornamental interest, a survey was conducted to identify the breeder and PP separately but also with an integrated index. The indices were applied to systematize bedding data considering breeder and public aesthetic preferences using persistent (12-months plants) and new (3-months plants) materials. Similarities were found in the breeder and PP for new materials. The perception of a similar aesthetic value by the breeder and the public was reflected in the scores assigned to Glandularia hybrids materials. For persistent materials, breeder and public perceptions presented some differences that are interesting to be considered at the moment to introduce new ornamental plants into the market.

The rice-based agriculture of the Indian subcontinent has been interwoven in the rich socio-cultural fabric of the country. Of which, bio-culturally diverse North-Eastern states nurture thousands of landraces with poorly tapped agronomic traits. In the present study, 27 standard microsatellite data from 171 rice landraces from six states were analysed to understand their genetic diversity and population structure. Further, combining with a global dataset, we determined subpopulation identity using both model-based and multivariate analyses to uncover their history. We found moderate to high genetic diversity and high differentiation [standardized G”ST = 0.57]. The AMOVA partitioned overall variance into within population (75%) and among population (25%). The landraces from six states remained at various degrees of differentiation (pairwise FST = 0.09–0.41). We have detected a preponderance of aus-type in a majority of aromatic landraces. Rests were japonica and admixed with a little representation of indica. The presence of aromatic aus probably implied assimilation into local culture from the primary aus growing region of Bangladesh and India. Likewise, the arrival of japonica may stem from the exchange of goods among neighbouring dynasties via Southern and Southwestern Silk routes. The shared ancestry may reflect a merger of two ancient cultures. Our analyses also uncovered the existence of aus-type short and medium grain aromatic rice predicting an origin of aroma in aus subpopulation. Collectively, it demonstrated the diversity and divergent history of the rice landraces have been shaped by various socio-cultural interactions operative over time and space.

Soybean [Glycine max (L.) Merr.] is one of the most important legume crops in the world. However, soybean grain yield is extensively affected by environmental stresses such as soil salinity. In this study, we evaluated the germplasm of 51 Indonesian soybean accessions for salt tolerance to identify salt-tolerant germplasms for possible use in breeding for soybean salt tolerance. Based on experiments under hydroponic conditions, adding 100 mM of NaCl to a 1/2 concentration of Hoagland and Arnon solution, several Indonesian soybean germplasms, such as Java 7, Seputih Raman, Tambora, Ringgit (JP 30217), Sinyonya (early) and Sinyonya (late) were identified as salt-tolerant in terms of salt tolerance rate (STR) and leaf chlorophyll content (SPAD value) taken with the Konica Minolta SPAD-502 chlorophyll meter. The selected salt-tolerant germplasms were further evaluated under soil medium cultivation in pots irrigated with 100 mM NaCl for around 5 weeks. The six selected soybean germplasms again showed higher salt tolerance in terms of SPAD, STR and shoot dry weight. Expression analysis of the salt tolerance gene Ncl revealed a significant positive correlation between Ncl expression and salt tolerance, suggesting that Ncl is essential for salt tolerance in the Indonesian soybean germplasms we tested. The salt-tolerant Indonesian soybean germplasms identified in this study could be used in local soybean breeding practices for the improvement of salt tolerance.

Germplasm lines with resistance to the sugarbeet root maggot (SBRM) have been developed and released to the public, providing a means to generate hybrids with resistance against the most devastating insect pest of sugarbeet in North America. Effective use of this germplasm, however, requires knowledge of relative strengths of SBRM resistance between lines and knowledge of the diversity and genetic relationships between germplasm. Therefore, field studies comparing SBRM resistance of four released SBRM-resistant germplasm lines (F1015, F1016, F1024 and F1043), a SBRM-resistant parent (PI 179180) and an unreleased SBRM-resistant population (F1055) were performed, and genetic analysis of the diversity and relationships between SBRM-resistant germplasm and their available parents was conducted using simple sequence repeat (SSR) markers. Under natural SBRM infestations, resistant germplasm exhibited significantly less SBRM damage than a susceptible control, with similar, high levels of resistance in F1016, F1024, F1043, F1055 and PI 179180 and lower resistance in F1015. SSR analysis revealed genetic similarities between F1016, F1024 and F1055, while F1015 and F1043 were genetically distinct from these lines. Among resistant genotypes, F1015 and F1043 exhibited greatest and least within-line genetic diversity, indicating greater and lesser inbreeding for F1043 and F1015, respectively. Similarities in damage ratings and genetics for F1016, F1024 and F1055 indicate that these lines are likely to be equally effective at introducing SBRM resistance into elite populations and in combining ability. In contrast, F1043, with its unique parentage and genetic dissimilarity from other resistant lines, provides a genetically distinct, but similarly effective, source of SBRM resistance.

Yellow mosaic disease (YMD) caused by mungbean yellow mosaic virus (MYMV) is one of the most destructive biotic production constraints in mungbean. Development and introduction of resistant cultivars are considered as the most economical and eco-friendly option to manage YMD, for which availability of stable sources of resistance is a pre-requisite. A set of 14 mungbean genotypes including a susceptible check were evaluated for responses to YMD under natural infection across three seasons and under challenged inoculation in glasshouse for one season. None of the genotypes were immune to YMD and produced different degrees of response to MYMV in terms of yellow mosaic symptoms (YMS). Based on the delayed appearance of initial YMS, and lower estimates of per cent disease index and area under disease progressive curve (AUDPC) in response to natural infection and challenged inoculation, five genotypes namely AVMU 1698, AVMU 1699, AVMU 16100, AVMU 16101 and KPS 2 were identified as resistant to YMD. Failure of detection of MYMV through polymerase chain reaction (PCR) using MYMV coat protein gene-specific primer and successful detection of the same through rolling circle amplification-PCR suggested latent infection of MYMV in resistant genotypes. The resistance response of the five genotypes could be attributed to enhanced activities of enzymes such as peroxidase, polyphenol oxidase and phenylalanine ammonia lyase and increased concentration of total phenols. These results are discussed in relation to strategies to breed mungbean for resistance to YMD.

Significant genetic diversity for sucrose and fibre percentages exists in the species that served as the foundation of present day sugarcane cultivars. However, information is lacking worldwide on the recent contributions of sugarcane crop wild relatives (mainly Saccharum, Erianthus and Miscanthus wild species) in developing new varieties. There is renewed interest in using those relatives for creating new varieties to use as a dedicated bioenergy crop with higher fibre. This study focuses on past data analysis of sugarcane breeding in Mauritius with the objective to assess the efficiency in exploiting sugarcane wild relatives since 1970s to date. Pedigree analyses helped retrace the parentages of elite inter-specific hybrids reaching the final stages of selection. The studies confirmed the high prevalence of a few ‘wonder canes’ (successful hybrids with wild canes produced in the beginning of last century) among the ancestors of Mauritian varieties. Among the wild relatives, eight Saccharum spontaneum, two S. robustum, and one Erianthus clones were involved in generating elite genotypes worth evaluating at the advanced variety trial stages. A few early generation hybrids were released in the past for industrial exploitation, the latest one being M 1002/02 in 2016, with sugar as the primary output. Recent studies on the biomass potential and fibre yield of inter-specific hybrids are giving promising results, which expands the horizon in the use of sugarcane wild relatives for the generation of novel type of sugarcane varieties for multiple end-uses.

Genetic diversity is a valuable asset for crop improvement. In this study, a total of 50 rice genotypes were screened for salinity tolerance at the reproductive stage using gravel-based hydroponics, soil, controlled mini-field and field methods. Different morpho-agronomic, physiological markers and tolerance indices were used to classify tolerant and susceptible genotypes. Our results showed high genetic variability in response of rice genotypes to salinity using different screening methods. The significant effect (P < 0.01) of salinity include increased Na+ sequestration in the flag leaf, increased unfilled grains (except for the field method) and reduced pollen fertility, total yield, panicle length and the average number of filled grains per panicle. Plant height (except for the soil method) and K+ ion concentration in the flag leaf were not significantly affected by salinity (P > 0.05). Genetic diversity analysis indicated that the germplasm evaluated exhibits moderate diversity (PIC ${\overline{\bf X}}$ = 0.2085). Cluster analysis using single nucleotide polymorphisms showed that the genetic make-up of rice germplasm somehow did not necessarily indicate their over-all tolerance or susceptibility to salinity. This study proved that the controlled mini-field method is the most advantageous among the screening methods while geometric mean productivity, stress tolerance index and yield index are the tolerance indices that can be classified as better predictors of salinity tolerance considering the yield potentials of the genotypes. The genotypes Nona Bokra and Mushkan 41 can be used for breeding in the future through low Na+:K+ ratio while Damodar and Bhura Rata 4-10 for breeding salt-tolerant cultivars with higher yield potentials.

Camellia oleifera is an important woody plant producing healthy edible oils. People need a large number of molecular markers, especially microsatellite, in breeding of C. oleifera. In this study, we sequenced the root transcriptomes of C. oleifera, and then designed a novel set of microsatellite markers based on the root-expressed genes. We assembled a total of 57,121 unigenes with a length of 42.63 Mb, which harboured 15,902 microsatellites. Among these microsatellites, di-nucleotide repeat motifs were the most abundant group (56.45%), then followed by tri- (25.20%), mono- (12.12%), hexa- (3.21%), penta- (2.18%) and quad-nucleotide ones (0.84%). In total, 6738 primer pairs were designed successfully to amplify the microsatellite loci. To test these microsatellite markers, 48 primer pairs were randomly selected and synthesized and validated in C. oleifera and its eight relatives. Up to 75% of the primer pairs amplified in C. oleifera and its relatives, and 62.5% displayed polymorphism. The transferability and diverse alleles across its eight relatives were detected for each polymorphic primer pair. The novel set of microsatellites derived from the root transcriptomes here provided a useful resource for future molecular genetics improvement of C. oleifera and its relatives.

Crop wild relatives (CWR) are wild plant taxa relatively closely related to crops that can contribute beneficial traits for crop improvement, such as biotic and abiotic stress resistance. Turkey has a rich flora of approximately 11,000 higher plant taxa, has two Vavilov centres of crop diversity (i.e. the Mediterranean and the Near East), is recognized as the cradle of agriculture providing the northern boundary of the Fertile Crescent, and has recently been identified as the country with the highest concentration of CWR diversity. The objective of this paper is to present the results of a gap analysis of CWR genetic diversity in Turkey using existing data sources of 458 of the 764 priority CWR taxa with available georeferenced data. In total, 27,597 presence points were obtained from the Global Biodiversity Information Facility, Aegean Agricultural Research Institute in Menemen and Field Crops Central Research Institute, Ankara. Geographic Information System (GIS) software was used to identify taxon richness, sampling bias, future ex situ population collection and location where existing protected sites could form the basis of national network of in situ genetic reserves. CWR taxon richness was located along the Aegean Coast, Syrian border and southern Mediterranean coast. Current ex situ representation of CWR taxa is inadequate and further collection across the entire country is required. The highest priority in situ reserve location is found in Izmir, Sanliurfa and Antalya province, which reflects overall CWR richness.

For more than four decades after the introduction of cv. Italia (Vitis vinifera L.) in Brazil, several somatic mutations in the genome of cv. Italia and its somatic mutants gave rise to phenotypes which generated at least five new cultivars of fine table grapes. Since no molecular marker proved to be effective in discriminating cv. Italia (V. vinifera L.) and its coloured mutants (Rubi, Benitaka, Brasil, Black Star), primers for the long terminal repeat (LTR) sequences were developed to analyse Inter Retrotransposon Amplified Polymorphism (IRAP) and Retrotransposon-Microsatellite Amplified Polymorphism (REMAP), and investigate how the coloured cultivars derived from clonal propagations of somatic mutations are genetically structured. Primers for LTR sequences of IRAP and REMAP markers were edited from grape sequence databases available at a GenBank. Twenty-four primers, denominated DKS001–DKS024, were edited. Three hundred and forty-nine DNA segments were amplified by individual DKS primers and DKS/ISSR (Inter Simple Sequence Repeats) primer combinations, at an average of 13.96 amplicons per primer pair. High genetic divergence between the five cultivars was inferred from polymorphism in retrotransposons IRAP and REMAP. The analysis of polymorphism of IRAP and REMAP retrotransposons was crucial to show that clonal propagation of somatic mutations may lead towards the formation of genetically divergent cultivars by the formation of genetically structured vineyards and show the mixture of genomes within each cultivar.