Tea is popular health beverage consumed by millions of people worldwide. Drought is among the acute abiotic stress severely affecting tea cultivation, globally. In current study, transcriptome sequencing of four diverse tea genotypes with inherent contrasting genetic response to drought (tolerant & sensitive) generated more than 140 million reads.De novoand reference-based assembly and functional annotation of 67,093 transcripts with multifarious public protein databases yielded 54,484 (78.2%) transcripts with significant enrichment of GO and KEGG drought responsive pathways in tolerant genotypes. Comparative DGE and qRT analysis revealed key role of ABA dependent & independent pathways, potassium & ABC membrane transporters (AtABCG22,AtABCG11,AtABCC5 &AtABCC4) and antioxidant defence system against oxidative stress in tolerant genotypes, while seems to be failed in sensitive genotypes. Additionally, highly expressed UPL3HECT E3 ligases and RING E3 ligases possibly enhance drought tolerance by actively regulating functional modification of stress related genes. Further, ascertainment of, 80803 high quality putative SNPs with functional validation of key non-synonymous SNPs suggested their implications for developing high-throughput genotyping platform in tea. Futuristically, functionally relevant genomic resources can be potentially utilized for gene discovery, genetic engineering and marker-assisted genetic improvement for better yield and quality in tea under drought conditions.

This study explicates molecular insights commencing Self-Incompatibility (SI) and CC (cross-compatibility/fertilization) in self (SP) and cross (CP) pollinated pistils of tea. The fluorescence microscopy analysis revealed ceased/deviated pollen tubes in SP, while successful fertilization occurred in CP at 48 HAP. Global transcriptome sequencing of SP and CP pistils generated 109.7 million reads with overall 77.9% mapping rate to draft tea genome. Furthermore, concatenated de novo assembly resulted into 48,163 transcripts. Functional annotations and enrichment analysis (KEGG & GO) resulted into 3793 differentially expressed genes (DEGs). Among these, de novo and reference-based expression analysis identified 195 DEGs involved in pollen-pistil interaction. Interestingly, the presence of 182 genes [PT germination & elongation (67), S-locus (11), fertilization (43), disease resistance protein (30) and abscission (31)] in a major hub of the protein-protein interactome network suggests a complex signaling cascade commencing SI/CC. Furthermore, tissue-specific qRT-PCR analysis affirmed the localized expression of 42 DE putative key candidates in stigma-style and ovary, and suggested that LSI initiated in style and was sustained up to ovary with the active involvement of csRNS, SRKs & SKIPs during SP. Nonetheless, COBL10, RALF, FERONIA-rlk, LLG and MAPKs were possibly facilitating fertilization. The current study comprehensively unravels molecular insights of phase-specific pollen-pistil interaction during SI and fertilization, which can be utilized to enhance breeding efficiency and genetic improvement in tea.

Dactylorhiza hatagirea (D. Don) Soo is medicinally important herb, which is widely used in ayurveda, unani, and folk/traditional medicine system to cure diseases. Due to its immense ethno-botanical properties, the trade of D. hatagirea is estimated to be USD 1 billion/year in India. Unfortunately, due to overexploitation of the herb from the wild, has resulted in dwindling of its populations in their natural habitats, which has led to its critically endangered status. Molecular genetic studies are still scarce in D. hatagirea, therefore, in current study, genetic diversity and population structure analysis was carried out of 10 populations (48 individuals) collected from three cold desert regions (2527 m–3533 m amsl) of Himachal Pradesh. Mean observed heterozygosity (H_o) and expected heterozygosity (H_e) was recorded 0.185 and 0.158. The maximum values for F_st (fixation index) and N_m (gene flow) were recorded 0.945 at locus KSSR14 and 1.547 at locus KSSR 4 respectively. Mean genetic differentiation (F_st) coefficient was estimated to 0.542. Overall, low levels of genetic diversity was recorded in the populations of D. hatagirea, might be due to habitat specificity (alpine meadows ecosystem; humid laden undulating habitat), restricted distribution and high anthropogenic activities. However, two populations viz., Bathad and Rangrik were recorded with high diversity and largest number of private alleles, stipulates that these populations might have high evolutionary significance and response to selection. Dendrogram analysis revealed that the populations of D. hatagirea were clustered into four major clusters, which was supported by Bayesian based STRUCTURE predictions. Clustering pattern of majority individuals of different populations revealed consistency with their geographic origin. Outcomes of current study reveals the status of genetic diversity and population structure of endangered D. hatagirea, which can be futuristically utilised for appropriate planning of conservation strategies.

Root system architecture affects water and mineral uptake and is important for plant adaptation to fluctuating nutrient availability. Small signaling peptides and their receptors influence root traits associated with macronutrient uptake. In this study, genome-wide association analyses were performed using 2D images of agar plate-grown Medicago truncatula accessions to understand the impact of GOLVEN10 peptide (GLV10) treatment on three root traits: root tortuosity, lateral root (LR) branch angle, and the gravity setpoint angle (GSA). Upon GLV10 treatment, roots of wild-type M. truncatula Jemalong A17 and R108 accessions showed increased primary root coiling (or tortuosity), increased LR branch angle, and reduced GSA. We identified 88 significant single nucleotide polymorphisms (SNPs) associated with these traits in GLV10-treated plants, distinct from the 163 SNPs in untreated plants. Importantly, the ethylene regulatory pathway was implicated in root tortuosity and LR emergence relative to the primary root. Application of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid reduced root sensitivity to GLV10, while the ethylene signaling mutant sickle was hypersensitive, indicating that GLV10 and ethylene pathways act antagonistically to control root tortuosity. These findings have implications for root gravitropic responses, and the ability of roots to penetrate deeper soil layers for nutrients and water.

Agriculture is the primary energy source for humans; however, it is facing two major challenges at present -the growing population and rapid climate change causing extreme weather events, which are expected to persist in the future as well. By the end of this century, the global population is expected to grow and reach 10-12 billion, highlights the importance of increasing total food production to feed the rapidly growing population. Therefore, it becomes very important to accelerate agricultural research with a goal to acquire deeper understanding of essential traits for future breeding targets. The advances in genomic technologies in the last two decades have contributed immensely to agricultural research. This issue presents a collection of four original research articles, that have utilized genome-wide identification of potential genes and association studies to investigate and address several challenging biological questions.In the current issue, a study done by Liu et al., 2003 was reported wherein genome-wide association analysis was performed in an economically important crop (rice), targeting traits like panicle length (PL), total grain number per panicle (TGP), filled grain number per panicle (FGP), seed setting rate (SSR) and grain weight per panicle (GWP). Elucidation of underlying genetic players involved in these traits is important for molecular breeding in rice to improve yield. Panicle traits are quantitative in nature and is substantially affected by environment: therefore, these traits require more comprehensive and extensive research to precisely determine their corresponding QTLs (Quantitative Trait Loci) and underlying genes responsible for phenotypic heterogeneity. The authors performed GWAS on data collected over three years and were able to identify four QTLs for PL, three QTLs for FGP and one QTL for TGP, GWP, SSR. These QTLs were detected in both GLM (General Linear Model) and MLM (Mixed Linear Model) analysis and BLUP (Best Linear Unbiased Prediction) was used to improve the accuracy of GWAS via modelling complex interaction between environment and genotypes. Furthermore, two candidate genes viz., LOC_Os01g43700 (Cytochrome P450 protein), and LOC_Os09g25784 (Auxin-induced protein, 5NG4) were also identified that were closely associated with PL; and another, LOC_Os04g47890 (MYB family transcription factor), with FGP, GWP and TGP. In this study, along with mining of excellent alleles related to panicle traits in rice, ten parental lines with favorable alleles associated with yield traits was also recommended for future molecular breeding.Two additional noteworthy studies (Shen et al., 2024 andLi et al.,2024) reported in the current issue were in wild potato (Solanum pinnatisectum) and common potato (Solanum tuberosum L.). Undertaking studies in both wild and cultivated species helps to better understand genetic diversity and to identify beneficial traits which can help in enhancing adaptability and resilience of the crop.This issue includes a study reporting the first draft chromosome-level genome assembly of Solanum pinnatisectum, which has strong resistance against Phytophthora infestans and creates genomic resources fundamental for understanding disease resistance mechanisms. A high-quality genome assembly of 664Mb size with 34,245 genes was reported and a total of 303 NBS-coding disease resistance genes were also identified. Additionally, it was found that S. pinnatisectum harbors a high number of unique genes and its comparative genomic analysis with cultivated species reveals that pathways related to plant-pathogen interaction and phagosomes were highly enriched in wild species, suggest their putative role in plant resistance. An additional 68 genes involved in resistance to late blight in potato were also reported on the basis of RNA seq analysis. This study reported a high quality-reference genome assembly using Oxford Nanopore long read sequencing and Hi-C technologies, which has resulted in creation of a valuable genomic resource of disease resistance genes which can be incorporated in modern breeding programs.Another important investigation on cultivated potato (Solanum tuberosum L.) in this issue (citation?) has presented the genome-wide identification and structural characterization of the FBA (Fructose-1, 6-bisphosphate aldolase) gene family (Li et al.,2024). This gene is involved in photosynthesis and energy metabolism and comprehensive genomic insight into StFBA gene, can be utilized to improve the efficiency of photosynthesis, tuber development and abiotic stress response. Two classes (Eight Class I and one class II) of StFBA genes were reported on the basis of their structure, function and phylogenetic relationship. The evolutionary relationship of the FBA gene family with six other species including Arabidopsis, rice, tomato, eggplant, tobacco and wheat was reported, finding FBA genes of potato and tomato to be closely related. Furthermore, colinearity analyses between potato, tomato and Arabidopsis revealed that segmental duplication is responsible for the expansion of the potato FBA gene family. After performing promoter and expression analysis, the authors concluded that StFBA genes have cis-regulatory elements coupled with light and stress response; and blue light increases StFBA3, StFBA8 and StFBA9 expression in stolon, leaf and tuber. Collectively, the outcome of this study suggests that these genes can be utilized to improve photosynthesis, induction and expansion of tubers, and abiotic stress response.The last and pivotal study published by Kim et al.,2023 in this issue was on Northern red oak (Quercus rubra), which is an economically and ecologically important tree in North America and Southeastern Canada. The strong and durable hardwood of this tree is used as floorboard and building materials and Q. rubra is a key species for woody plant research, as it is one of the most important red oak lumber species. The genome-wide...