Beachpea (Vigna marina) is a halophytic wild leguminous plant which occurs throughout tropical and subtropical beaches of world. As quantitative trait loci (QTLs) for salt tolerance in V. marina and its crossability with other Vigna species are known, the current study was undertaken to know the presence of these QTLs in the V. marina accessions along with check varieties of pulses. Accordingly, 20 Vigna genotypes (15 accessions of V. marina collected from sea-shore areas of Andaman and Nicobar Islands along with five check varieties of green gram and black gram) were subjected to molecular characterization using seven simple sequence repeat (SSR) markers associated with salt tolerance. Of the markers used, only four SSR markers amplified in the studied germplasm. Number of alleles detected per primer and size of alleles ranged from 1 to 3 and 100 to 325 bp, respectively. Polymorphism information content and heterozygosity values ranged from 0.305 to 0.537 and 0.375 to 0.612, respectively. Three major clusters, cluster I, II and III were obtained at Jaccard's similarity coefficient value of 0.48 through the un-weighted paired group method with arithmetic means method of cluster analysis. It grouped green gram and black gram genotypes in clusters I (04) and II (01), whereas all V. marina genotypes were grouped in cluster III (15). Principal co-ordinate analysis explained 85.9% of genetic variation among genotypes which was further confirmed by cluster analysis. This study indicated the effectiveness of SSR markers in separating cultivated Vigna species from wild V. marina. The findings will be useful for transferring trait of robust salt tolerance of V. marina in cultivated Vigna species using marker-assisted breeding.

African yam bean (AYB) is an affordable protein source capable of diversifying the food base in sub-Saharan Africa. However, research efforts made towards the crop's improvement and in expanding production are limited. This study characterized 169 AYB accessions at Jimma, Ethiopia, using 31 phenotypic characters. The analysis of variance revealed highly significant (P < 0.01) differences for days to 50% flowering, days to first flowering, leaf area, number of seeds per pod, pod length, seed thickness, total seed weight, petiole length and significant (P < 0.05) difference for terminal leaf length. Accession TSs62B produced the highest number of seeds per pod (17.65) and recorded the highest 100 seed weight (25.30 g), while 3A was the earliest to flower at an average of 84.50 d. Principal component analysis (PCA) of qualitative traits attributed 77.6% of observed variations to the first five principal components, of which the first two PC axes accounted for 53.6% of total variations. Cluster analysis and PCA biplot distinctly grouped the accessions into two major groups, cluster I had the highest number of accessions (108). The analytical approaches used confirmed considerable diversity across the germplasm with a distance matrix ranging from 0.37 to 0.85. The extent of diversity reflected in the current study provides breeders the baseline information to design breeding strategies, which might help identify materials for release as variety or parental lines for hybridization programmes.

Seed coat colour is an important quality trait, domestication trait and morphological marker, and is closely associated with flavonoid and anthocyanin metabolism pathways. The seed coat colour of adzuki bean, an important legume crop, influences the processing quality of its paste, the commodity and its nutritional quality. In this study, the genetic relationships of seed coat colour were analysed using 12 hybridized combinations of F2 individuals and four F3 families derived from hybridized combinations between the accessions of eight seed coat colours. The loci of the colour traits were analysed based on phenotypes and using the chi-square test. Ivory colour is recessive to red and is controlled by a single R locus. Black, black mottle on grey, black mottle on red, light brown, golden and brown are all dominant to red. The phenotypes of black mottle on red, light brown, golden and brown are all controlled by a single genetic locus. Black mottle on grey is controlled by two loci. Black is controlled with two loci, and the black locus shows dominant epistasis to another locus. A genetic model of these seed coat colours was predicted. Our results will be important for gene mapping and cloning of seed coat colour characters and for providing further insight into the regulatory network of seed coat colour.

Mexico has a wealth of plant genetic resources, including Capsicum species. In southern Mexico, specifically in the western part of the Yucatan Peninsula, Maya farmers have preserved a great diversity of chilli pepper landraces of C. annuum, C. frutescens and C. chinense. However, the morphological diversity, capsaicinoid content, conservation status and potential use of these species have not been studied. To fill this gap and generate information to support the conservation and use of these species, we characterized the phenotypic diversity and capsaicinoid content for nine chilli pepper landraces from the western Yucatan Peninsula by assessing 15 quantitative and 39 qualitative traits for 10 plants of each landrace. For quantitative variables, two groups of chilli pepper landraces were obtained by principal component analysis and cluster analysis. Group I was formed by Rosita, Bobo, Dulce, Xcat'ik1, Xcat'ik2 and Verde landraces; Group II included the Maax, Bolita and Pico Paloma landraces. For qualitative variables, three groups of chilli pepper landraces were obtained; Group I included Dulce, Bobo, Xcat'ik1, Xcat'ik2 and Verde landraces, Group II only included the Rosita landrace, and Group III included Maax, Bolita and Pico Paloma landraces. Ultra-performance liquid chromatography–photodiode array (UPLC-PDA) quantification of capsaicinoids indicated higher values in landraces Rosita (14,062.3 μg/g D.W), Bolita (5928.1 μg/g D.W), Maax (3438.4 μg/g D.W) and Pico Paloma (3138.9 μg/g D.W). The Yucatan chilli pepper landraces provide valuable diverse germplasm for morphological characteristics and capsaicinoid content that can be used in breeding and conservation programmes.

Acquisition and germination of seeds are the most desired targets for the improvement of vegetatively propagated crops. In the present study, we developed a potential embryo germination protocol for the Red Globe grape cultivar having a low seed germination rate. Three grape berries at different developmental stages, viz. 50, 60 and 70 days after flowering (DAF), were selected for in-vitro embryo germination. Three growth media, namely Emershad and Ramming (ER), Nitsch and Nitsch (NN) and Murashige and Skoog (MS), and plant growth regulators (benzyl amino purine (BA), 0.5, 0.7 and 0.9 mg/l; indole butyric acid (IBA), 1.0, 1.5 and 2.0 mg/l; and gibberellic acid (GA), 0.1, 0.3 and 0.9 mg/l) were screened individually in different combinations with three amino acids, namely cysteine, glutamine and proline (2.0 μmol/l each). The maximum embryos germination percentage recorded at 70 DAF was 63.33, 47.78 and 45.56% in ER, NN and MS media, respectively, supplemented with 0.9 mg/l BA, 2.0 mg/l IBA, 0.9 mg/l GA and 2.0 μmol glutamine. Glutamine was found to have the most significant impact, and it improved the rescued embryos germination. The present study provides a potential recipe for a medium that can facilitate efficient germination of grape embryos.

Soil phosphorus (P) deficiency is one of the major challenges for the cultivation of rice worldwide because it limits the growth and productivity of the crop. Therefore, the ability to grow in P-deficit soils is an important trait for rice cultivation. O . rufipogon Griff., a wild relative of rice, is a source of genetic variation for low phosphorus tolerance. The present study was undertaken to identify low P stress-tolerant introgression lines by analysing stress tolerance indices of 40 introgression lines of O. rufipogon. The populations were screened under low soil P and normal soil P plots for two growing seasons. Based on yield under stress and normal conditions, we computed different stress indices, including stress tolerance index (STI), tolerance index, yield reduction ratio (YR), stress susceptibility index, yield stability index (YSI), yield index, per cent yield reduction and geometric mean productivity (GMP). The studies of correlation analysis, principal component analysis and clustering revealed that STI, YSI and GMP were ideal indices for the selection of genotypes that performed well under both stress and normal conditions. Based on these indices, introgression lines (IL-24, IL-29 and IL-32) were identified as promising low P tolerant lines, which exhibited better grain yield under both stress (YS) and normal (YP) conditions. These pre-breeding lines serve as valuable genetic resources for low P tolerance in rice breeding programmes across the world.

Astronium concinnum Schott ex Spreng. (Anacardiaceae) is a species used in civil construction, naval, luxury furniture, in addition to the potential for recovery and restoration of habitats. The objective of this work was to characterize the diversity and genetic structure of the A. concinnum in the Conservation Units, National Forest of Pacotuba and Private Natural Heritage Reserve of Cafundó, located in the south of the state of Espírito Santo. Eight ISSR primers were used, which produced 121 DNA fragments and 73.55% polymorphism. In the analysis of genetic dissimilarity, seven distinct groups were identified, with the majority of individuals (from both Conservation Units) being brought together into a single group. The genetic diversity of Nei (H*) and the Shannon index (I*), provided values for the species of 0.312 and 0.473, respectively, indicating the genetic diversity conserved in the species and its potential use for collecting genetically diversified seeds. The analysis of molecular variance revealed that most of the diversity (92.54%) is distributed within populations and the value of gene flow (Nm = 10.629) indicates the high rate of genetic exchange between Conservation Units. The results of the genetic structuring indicated the division of individuals into three genetic groups (K = 3), however, it was possible to observe a mixture of genetic material with the sharing of alleles between the three groups. The results indicate that A. concinnum trees maintain genetic diversity for their maintenance. In addition, the potential of the analysed individuals was certified as future matrixes for seed collection.

White Guinea yam (Dioscorea rotundata Poir.) is indigenous to West Africa, a region that harbours the crop's tremendous landrace diversity. The knowledge and understanding of local cultivars’ genetic diversity are essential for properly managing genetic resources, conservation, sustainable use and their improvement through breeding. This study aimed to dissect phenotypic and molecular diversity of white yam cultivars from Benin using agro-morphological and single nucleotide polymorphism (SNP) markers. Eighty-eight Beninese white Guinea yam cultivars collected through a countrywide ethnobotanical survey were phenotyped with 53 traits and genotyped with 9725 DArT-SNP. Multivariate analysis using phenotypic traits revealed 30 traits as most discriminative and explained up to 80.78% of cultivars’ phenotypic variation. Assessment of diversity indices such as Shannon–Wiener (H′), inverse Shannon (H.B.), Simpson's (λ) index and Pilou evenness (J) based molecular and phenotypic data depicted a moderate genetic diversity in Beninese white Guinea yam cultivars. Genetic differentiation of cultivars among country production zones was low due to the high exchange of planting materials among farmers of different regions. However, there was high genetic diversity within regions. Hierarchical clusters (HCs) on phenotypic data revealed the presence of two groups while HCs based on the SNP markers and the combined analysis identified three genetic groups. Our result provided valuable insights into the Beninese white Guinea yam diversity for its proper conservation and improvement through breeding.

Genetically accessible variation to some of the abiotic and biotic stresses are limited in the cultivated lentil (Lens culinaris Medik.) germplasm. Introgression of novel alleles from its wild relative species will be useful for enhancing the genetic improvement of the crop. L. ervoides, one of the wild relatives of lentil, is a proven source of disease resistance for the crop. Here we introduce a lentil advanced backcross (LABC-01) population developed in cultivar ‘CDC Redberry’ background, based on L. ervoides alleles derived from an interspecific recombinant inbred population, LR-59-81. Two-hundred and seventeen individuals of the LABC-01 population at BC2F3:4 generation were screened for the race 0 of anthracnose (Colletotrichum lentis) and stemphylium blight (Stemphylium botryosum) under controlled conditions. The population showed significant variations for both diseases and the transfer of resistance alleles into the elite cultivar was evident. It also segregated for other traits such as days to flowering, seed coat colour, seed coat pattern and flower colour. Overall, we showed that LABC-01 population can be used in breeding programmes worldwide to improve disease resistance and will be available as a valuable genetic resource for future genetic analysis of desired loci introgressed from L. ervoides.

Addressing the impact of heat stress during flowering and grain filling is critical to sustaining wheat productivity to meet a steadily increasing demand from a rapidly growing world population. Crop wild progenitor species of wheat possess a wealth of genetic diversity for several biotic and abiotic stresses, and morphological traits and can serve as valuable donors. The transfer of useful variation from the diploid progenitor, Aegilops tauschii, to hexaploid wheat can be done through the generation of synthetic hexaploid wheat (SHW). The present study targeted the identification of potential primary SHWs to introduce new genetic variability for heat stress tolerance. Selected SHWs were screened for different yield-associated traits along with three advanced breeding lines and durum parents as checks for assessing terminal heat stress tolerance under timely and late sown conditions for two consecutive seasons. Heat tolerance index based on the number of productive tillers and thousand grain weight indicated that three synthetics, syn9809 (64.32, 78.80), syn14128 (50.30, 78.28) and syn14135 (58.16, 76.03), were able to endure terminal heat stress better than other SHWs as well as checks. One of these synthetics, syn14128, recorded a minimum reduction in thousand kernel weight (21%), chlorophyll content (2.56%), grain width (1.07%) despite minimum grain-filling duration (36.15 d) and has been selected as a potential candidate for introducing the terminal heat stress tolerance in wheat breeding programmes. Breeding efforts using these candidate donors will help develop lines with a higher potential to express the desired heat stress-tolerant phenotype under field conditions.

Anthracnose or fruit rot disease caused by Colletotrichum spp. leads to substantial economic losses in chilli (Capsicum annuum L.) production worldwide. In the present study, 24 different Bhut Jolokia chilli landraces and seven Capsicum annuum cultivars have been collected from the northeastern region of India and subsequently screened under in vitro and in vivo conditions against Colletotrichum capsici and C. gloeosporiodes infections. During field evaluation, eight chilli genotypes (CC0164, CC0165, CC0191, CC0192, CC0202, CC0206, CC0209 and CC0218) were highly resistant and 12 genotypes (CC0154, CC0179, CC0181, CC0183, CC0186, CC0189, CC0193, CC0198, CC0205, CC0210, CC0213 and CC0217) were found in resistant category against C. capsici infection. During in-vitro germplasm evaluation, 11 and 12 landraces were found to be highly resistant to C. capsici and C. gloeosporioides infections, respectively. According to the findings, the majority of Bhut Jolokia chilli landraces are resistant to anthracnose. Given the difficulties farmers experience as a result of excessive use of fungicides and pesticides, germplasm screening for host resistance has already begun. The resistant lines identified in the current study offers better choices to tackle anthracnose and could be used effectively in breeding programs to develop anthracnose resistant varieties.

Local cultivars of pearl millet in Saudi Arabia are known to tolerate extreme heat and drought stress. In the current study, the sequences of internal-transcribed spacers (ITSs) of six pearl millet cultivars were sequenced and analysed to investigate the genetic diversity among the local cultivars. The nucleotide polymorphism, secondary structures and phylogenetics were analysed for ITS sequences of the six local cultivars. The obtained sequences were 772–774 base pairs (bp) in length, including complete sequences of the ITS1–5.8S–ITS2 region and partial sequences of 18S and 26S rRNA. The nucleotide diversity among cultivars was higher in ITS2 sequences than ITS1 sequences. The ITS2 had four variable nucleotide sites in three native cultivars, whereas the ITS1 contained one base insertion. The secondary structures of the ITS1 and 5.8S region were highly conserved among the six cultivars and contained some motifs that are conserved across Viridiplantae. However, the ITS2 secondary structure for the two native cultivars, Sayah and Jazan, was distinct from the other cultivars, which confirms the applicability of the ITS2 sequence in distinguishing between genetically close taxa. Additionally, the phylogenetic analysis of the six investigated cultivars and 31 pearl millet accessions from the NCBI database showed close relationships between the local accessions and NCBI accessions from India and France. However, the local cultivar Sayah appeared to be distinct from the other cultivars in the phylogenetic trees. This study provides insights into the polymorphism within local pearl millet cultivars which is important for the identification and conservation of these cultivars.

In order to better understand the molecular mechanisms associated with salinity tolerance, transcriptome analysis of a local salt-tolerant wheat landrace (i.e. Roshan) was performed under salt stress. Transcriptome sequencing yielded 137,508,542 clean reads using the Illumina HiSeq 2000 platform. The results of two alignment programs, i.e. STAR and HISAT2, were used separately to perform the analysis of differentially expressed genes (DEGs) using DESeq2. Finally, a total of 17,897 DEGs were identified by DESeq2. Moreover, gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses identified 108 GO terms and 62 significant KEGG pathways, of which ‘metabolic process’ and ‘metabolic pathways’ were the most abundant enriched term and pathway, respectively. Additionally, key salinity-tolerant genes, including asparagine synthetase, were also identified in the present study. Out of 87 identified families of transcription factors, GAI‐RGA ‐ and ‐SCR (GRAS) was one of the most important, which participates in signal transduction, and meristem maintenance and development. Eventually, to validate the gene expression levels, six DEGs were selected for a quantitative real-time polymerase chain reaction, and the results were in line with those of RNA-Seq. The findings of the current study can guide future genetic and molecular studies and allow a better understanding and improvement of salt tolerance in wheat.

Distant hybridization of cereals is often impaired by fertilization barriers. Haploid induction through intergeneric crossing is well developed in wheat but has not been successful in rice due to incompatibility issues. The present study was thus undertaken to identify fertilization barriers that hinder the compatibility of the rice cultivar Punjab Rice 121 with maize and pearl millet lines as pollinators. A total of 37,357 spikelets were pollinated, yielding 494 caryopses upon supplementation with auxins. The resultant caryopses, arising from true intergeneric crosses, lacked embryos. Imaging of the pollinated pistils at different intervals indicated that intense callose depositions block the release of generative nuclei to the ovule in these wide crosses. Rice spikelets pollinated with rice pollen (cis-generic crosses) exhibited positive indicators of fertilization reaction at the micropyle. While the cis-generic crosses initiated true caryopsis formation after 24 h, no comparative reaction was observed in the intergeneric crosses. The current survey underlines that the rice female gametophyte presents a strong pre-fertilization barrier to foreign pollen. This barrier may be modulated in the future by altering genotype and auxin combinations.

Andrographis paniculata is an Indian medicinal plant with tremendous therapeutic values due to the presence of active diterpenoids in its aerial parts. However, high domestic and export demand has led to overexploitation of wild populations of this species. With a view to bringing A. paniculata into cultivation and to reduce the pressure on wild populations, the present study was undertaken to identify elite germplasm from different locations of eastern India by analysing intraspecific variation in the content of four major active diterpenoids. A total of 166 wild accessions of A. paniculata analysed through high-performance liquid chromatography (HPLC) revealed remarkable variation in the sum of four active diterpenoids in the aerial parts, ranging from 0.41 to 8.55% on a dry weight basis. Three elite accessions (AP-6, AP-8, AP-46) having respectively 8.02, 8.36 & 8.55% of the sum of four major active diterpenoids were identified. These germplasm could be used for commercial cultivation and genetic improvement of A. paniculata.

Epilobium belongs to the family Onagraceae, which consists of approximately 200 species distributed worldwide, and some species have been used as medicinal plants. Epilobium nankotaizanense is an endemic and endangered herb that grows in the high mountains in Taiwan at an elevation of more than 3300 m. Alpine herbs are severely threatened by climate change, which leads to a reduction in their habitats and population sizes. However, only a few studies have addressed genetic diversity and population genetics. In the present study, we developed a new set of microsatellite markers for E. nankotaizanense using high-throughput genome sequencing data. Twenty polymorphic microsatellite markers were developed and tested on 30 individuals collected from three natural populations. These loci were successfully amplified, and polymorphisms were observed in E. nankotaizanense. The number of alleles per locus (A) ranged from 2.000 to 3.000, and the observed (Ho) and expected (He) heterozygosities ranged from 0.000 to 0.929 and from 0.034 to 0.631, respectively. The developed polymorphic microsatellite markers will be useful in future conservation genetic studies of E. nankotaizanense as well as for developing an effective conservation strategy for this species and facilitating germplasm collections and sustainable utilization of other Epilobium species.

In chilli, farmer preferences for fruiting habit traits, namely fruit orientation (pendant erect) and fruits node−1 (solitary cluster), vary from region to region. For increased acceptability by farmers/consumers, cultivars should be bred with preferred fruiting habit traits in high green fruit yielding background. An investigation was carried out to study the influence of fruiting habit traits on green fruit yield and its component traits during the 2016 and 2017 rainy seasons. The F2, backcross populations and near-isogenic lines (NILs) derived from crosses involving parents differing for single or both the fruiting habit traits were grouped into fruiting habit classes (single and cluster fruiting; and clustered erect, clustered pendant, single erect and single pendant). Significance of differences in fruit yield and its component traits between/among different fruiting habit trait classes were examined using ‘t’/‘F’ tests. The significance of ‘t’/‘F’ tests was regarded as pieces of evidence for considerable effects of fruiting habit traits on fruit yield and its component traits. While results-based on F2 and backcross generations indicated a lack of effects, those based on NILs indicated significant effects of fruiting habit traits on fruit yield and its component traits. The plants bearing pendant fruits (irrespective of whether they are clustered or single) produced a large number of heavier and longer fruits than those bearing erect fruits. The results are discussed about the strategies to develop high yielding cultivars with farmer preferred fruiting habit traits.

The Sikkim-Himalaya represents one of the unique reservoirs of rice genetic resources in India owing to the presence of a large number of landraces adapted to extreme climatic and edaphic conditions. This valuable gene pool is now under threat due to the introduction of high-yielding varieties, wanting suitable genetic intervention for enhancing their productivity, and thus economic viability. Development of lodging resistant, high-yielding varieties tolerant to soil acidity through association mapping aided marker-assisted breeding programmes can help achieve this in a fast and efficient manner. But this requires information on genetic diversity, population structure, etc., of the germplasm collection, which is strikingly lacking. We, therefore, characterized a set of 53 rice landraces from Sikkim to address the above issues. The results revealed moderate diversity, poor divergence and high gene flow in our germplasm collection attesting its utility as an association mapping panel. Further, a total of 115 putative marker-trait associations (P < 0.05, R2 ≥ 10%) were obtained using the general linear model and mixed linear models of which 25 were identical in both. Some of the associated markers were positioned in those regions where Qualitative Trait Loci have been previously identified in rice, providing credence to our results. The resources generated from this study will benefit the rice breeders from this region and elsewhere for targeting the yield and related traits, in addition to conservation efforts by the interested researchers.

Drought is a major concern among abiotic stresses in wheat (Triticum aestivum L.) production. Breeding resistant cultivars are the most effective means to manage drought stress. F6 recombinant inbred lines (RIL) derived from the cross of Berkut/Worrakatta were used to identify quantitative trait loci (QTL) for drought tolerance at germination stage under treatment of PEG6000 using the wheat 50 K single nucleotide polymorphism (SNP) array. Twenty-eight linkage groups were constructed, covering a length of 2220.26 cM. Eighteen QTL were detected based on the drought tolerance coefficients and D-value, explaining 2.7–6.5% of the phenotypic variances, in which 15 were likely to be novel. Three QTL, QGR.xjau-5AS, QCL.xjau-5AS and QD.xjau-5AS for GR, CL and D-value, respectively, at physical positions of 11.70–20.61 Mb between markers AX-111258240 and AX-94458300 on chromosome 5AS accounted for 3.4–4.8% of the phenotypic variances. Three QTL, QGP.xjau-5DL, QSH.xjau-5DL and QD.xjau-5DL for GP, SH and D-value, respectively, were flanked by markers AX-94524442 and AX-110998507 at 560.42–567.39 Mb on chromosome 5DL, accounting for 4.4–6.5% of the phenotypic variances. In addition, the candidate genes TraesCS5A02G022100, TraesCS5B02G014200 and TraesCS5D02G563900 were predicted. Based on transcriptional expression data, the results showed that the expression level of TaGATAs-5A, TaUbox-5B and TaGSTP-5D changed with the increase of treatment time under drought stress in tolerant and sensitive varieties. These are interesting targets in mining drought tolerance genes and the improvement of drought tolerance in wheat.