Ocimum gratissimum L. is a well-known medicinal plant with several therapeutic properties, but molecular studies on this species are lacking. Therefore, we have sequenced the whole transcriptome from the leaves of O. gratissimum and assembled 121,651 transcripts. The transcriptome of O. gratissimum was closely related to Sesamum indicum and Erythranthe guttata in congruence with the molecular phylogenetic relationships among these species. Further, 62,194 transcripts were annotated and classified according to the GO terms concerning the biological process, cellular component and metabolic function. In the KEGG pathway analysis, 34,876 transcripts were mapped to 149 pathways and 1410 of them were involved in the biosynthesis of secondary metabolites. In the phenylpropanoid pathway, 101 transcripts were associated with the biosynthesis of eugenol, the principal constituent of the essential oil of O. gratissimum. In the caffeine metabolism pathway, none of the transcripts was related to caffeine biosynthesis, supportive of the caffeine-free nature of Ocimum. Transcripts coding for the metallothionein were abundant in the leaves, supporting the observation that O. gratissimum is an accumulator of heavy metals. We also identified the 930 transcripts coding for 59 transcription factors families with myeloblastosis transcription factors being the most predominant. About 6500 simple sequence repeats were identified, which will be useful in DNA marker-based applications. This is the first report of the leaf transcriptome of O. gratissimum, which will serve as an essential resource for further molecular studies in this important medicinal species.

The flag leaf acts as a functional leaf in rice, Oryza sativa L., primarily supplying photosynthate to the developing grains and influencing yields to a certain extent. Drought stress damages the leaf physiology, severely affecting grain fertility. Autumn rice of northeast India is called locally as ‘ahu’ rice, and is known for its drought tolerance. Exploring diverse germplasm resources at the morphological level using an association mapping approach can aid in identifying the genomic regions influencing leaf shape dynamics. A marker–trait association (MTA) study was carried out using 95 polymorphic SSR markers and a panel of 273 ahu rice germplasm accessions in drought stress and irrigated conditions. The trials suggest that at the vegetative stage, drought stress significantly affects leaf morphology. The leaf physiology of some tolerant accessions was relatively little affected by stress and these can be considered as ideal varieties for drought conditions. The phenotypic coefficient of variance and genotypic coefficient of variance values implied moderate to high variability for the leaf traits studied. Analysis of molecular variance inferred that 11% of variation in the germplasm panel was due to differences between populations, while the remaining 89% may be attributed to a difference within subgroups formed through STRUCTURE analysis. Using the mixed linear model approach revealed 11 MTAs explaining between 4.5 and 20.0% of phenotypic variance at P > 0.001 for all the leaf traits. The study concludes that ahu rice germplasm is extremely diverse and can serve as a valuable resource for mining desirable alleles for drought tolerance.

Existence of genetic divergence, appropriate characterization of breeding lines for economically important traits and determining parents with favourable alleles is the crux of crop genetic improvement programmes. This study is the first report of unravelling genetics and potential of petaloid-type cytoplasmic male sterile (pt-CMS) lines in carrot. Ten pt-CMS lines were crossed with 10 inbreds in line × tester mating fashion to generate 100 testcross progenies. Nutritional profiling of the 100 testcrosses progenies along with 20 parental types was carried out for two consecutive years for eight important traits to identify superior combiners. The pooled analysis revealed that the carotenoid content in root is under the genetic control of major genes (oligogenic). The pooled analysis revealed less than unity value of σ2A/D and σgca2/σsca2 for majority of the traits depicting preponderance of non-additive gene effects. The pt-CMS lines KT-28A, Kt-62A, KT-80A and KT-95A were identified as good combiners for carotenoids. The cross combination, KT-98A × KS-50 identified as the best heterotic combiner for CUPRAC and FRAP content over the years. Similarly, the combinations, KT-62A × KS-21, KT-80A × New Kuroda and KT-62A × KS-59 were found promising across the years for developing nutritionally rich F1 hybrids. The interaction analysis among the different antioxidant traits and plant pigments unveiled the scope of simultaneous improvement.

Powdery mildew (PM) is one of the most severe fungal diseases of cucumber that limits its production worldwide. In this study, 140 genotypes of cucumber were screened for disease resistance under field and artificial conditions, and then validated with eight known SSR markers linked to PM resistance. Among these genotypes, genotype GS140 was found resistant (R), whereas GS148, GS16 and GS70 were moderately resistant, and GS169 was found to be tolerant. Of all the eight markers, only C31, C80, C162, SSR16472 and SSR16881 amplified the reported linked allele. The 127 bp allele of SSR16881 was found to be associated with the lowest disease severity of 37.65%. The associated markers could further be verified for their usability using linkage studies and the contrast genotypes in the present study could serve as a tool for selection in future marker-assisted selection breeding strategies for PM resistance.

Germplasm characterization is essential to estimate variation and identify desirable genotypes for crop improvement. The current study was conducted on eight qualitative and 14 quantitative traits related to growth and floral attributes for characterization and grouping of 54 chrysanthemum genotypes. Wide variability was observed among most of the traits and principal component analysis revealed that the first two principal components explained most of the existing variation (>98%) in germplasm. Genotypic coefficient of variation exhibited a wide range from 9.41% (ratio of leaf length/width) to 105.99% (corolla tube length of ray florets), while phenotypic coefficient of variation varied from 10.49% (ratio of leaf length/width) to 106.38% (corolla tube length of ray florets). Broad sense heritability estimates were higher (>96%) for most of the characters, except for traits such as ratio of leaf length/width and peduncle thickness. Forty-four pair-wise inter-trait combinations showed positive genotypic and phenotypic correlations for 91 possible combinations. D2 analysis revealed that genotypes of clusters I and IV to be highly distinct, and hybridization between them might have better chance to obtain desirable types. D2 analysis confirmed that the cultivars in cluster IV namely, Red D Spoon, Tokyo Soldier, Yellow Reflex and hierarchical clustering showed that the cultivar Tokyo Soldier to be highly diverse. It is recommended to use the above genotypes in crossing programme for obtaining better progenies.

Tomato is a pivotal vegetable crop worldwide concerning human nutrition, economy and in service to biotechnology. Tomato leaf curl virus (ToLCV) is a begomovirus transmitted through the whitefly (Bemisia tabaci) and is responsible for severe losses in tomato production. In this context, the current investigation was carried out to determine heterotic combiners with high yield, resistance to ToLCV and mode of gene action for economically important traits. For this, 11 prescreened inbred lines were crossed in a half diallel fashion to generate 55 F1 hybrids. The 55 crosses with 11 parents and commercial checks were evaluated for different horticultural traits and resistance to ToLCV. The molecular validation with SCAR markers TG0302 and SCAR1 confirmed the presence of ToLCV-resistant genes in parents and their crosses. The hybrid IIHR-2902 × IIHR-2852 showed the presence of both Ty-2 and Ty-3 alleles in the homozygous state. The estimation of σSCA2 and σGCA2 was significant. It also indicated that the genetic control of target traits was under additive and non-additive gene effects. The values of σA/D2 along with σGCA2/σSCA2 found to be less than unity indicates the preponderance of non-additive gene action in the expression of the studied traits except for percent disease incidence. The parental line IIHR-2919 was the best combiner for fruit and yield traits. The cross combinations IIHR-2913 × IIHR-2898 exhibited significantly higher economic heterosis for yield along with the presence of Ty-2 and Ty-3 genes. The study paves the way for breeding high yielding and ToLCV-resistant hybrids in tomato.

Maize and Imperata cylindrica have been utilized globally as a pollen source for induction of haploids in wheat through chromosome elimination technique. Pollen parents with a higher haploid induction rate are desired for recovering the high frequency of haploids in wheat and related species. The present investigation was carried out with the aim to assess haploid induction efficiency of diverse germplasm of maize and I. cylindrica in different generations of intra and intergeneric crosses of hexaploid and tetraploid wheat and triticale-wheat derivatives. Crosses of twenty-six lines (female) with each of two I. cylindrica and twenty-one maize genotypes (testers) were evaluated for four haploid induction parameters viz., pseudoseed formation frequency (PFF), embryo formation frequency (EFF), haploid regeneration frequency (HRF) and haploid formation frequency (HFF). I. cylindrica outperformed maize in haploid induction rate with a frequency of embryos formed with I. cylindrica (18.39%) were significantly higher as compared to maize (4.08%). In the case of I. cylindrica genotype Ic-ye identified best with mean EFF of 30.55, 14.48 and 25.43% for hexaploids, tetraploids and triticale × wheat derivatives, respectively whereas in the case of maize genotype HPMC-60 performed best with EFF of 12.61% for hexaploids, HPMC-58 (12.58%) for tetraploids and HPMC-16 for triticale × wheat derivatives with EFF of 8.91%. I. cylindrica genotype Ic-ye and maize genotypes HPMC-14, HPMC-53, HPMC-60, HPMC-64 with significantly positive GCA for haploid induction parameters may be utilized as efficient pollen parents for recovering higher frequency of haploids in wheat.

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.

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.

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.

Dongxiang wild rice (Oryza rufipogon Griff.) (DXWR) is the northernmost distributed wild rice found in the world. Similar to other populations of O. rufipogon, DXWR contains a large number of agronomically valuable genes, which makes it a natural gene pool for rice breeding. Molecular markers, especially simple repeat sequence (SSR) markers, play important roles in plant breeding. Although a large number of SSR markers have been developed, most of them are derived from the genome coding sequences, rarely from non-coding sequences. Meanwhile, long non-coding RNAs (lncRNAs), which are derived from the transcription of non-coding sequences, play vital roles in plant growth, development and stress responses. In our previous study, we obtained 1655 lncRNA transcripts from DXWR using strand-specific RNA sequencing. In this study, 1878 SSR loci were detected from the lncRNA sequences of DXWR, and 1258 lncRNA-derived-SSR markers were developed on the genome-wide scale. To verify the validity and applicability of these markers, 72 pairs of primers were randomly selected to test 44 rice accessions. The results showed that 42 (58.33%) pairs of primers have abundant polymorphism among these rice materials; the polymorphism information content values ranged from 0.04 to 0.87 with an average of 0.50; the genetic diversity index of SSR loci varied from 0.04 to 0.88 with an average of 0.56; and the number of alleles per marker ranged from 2 to 11 with an average of 4.36. Thus, we concluded that these lncRNA-derived-SSR markers are a very useful source for future basic and applied research.