Transport mechanism and pharmacology of the human GlyT1.

The glycine transporter 1 (GlyT1) plays a crucial role in the regulation of both inhibitory and excitatory neurotransmission by removing glycine from the synaptic cleft. Given its close association with glutamate/glycine co-activated NMDA receptors (NMDARs), GlyT1 has emerged as a central target for the treatment of schizophrenia, which is often linked to hypofunctional NMDARs. Here, we report the cryo-EM structures of GlyT1 bound with substrate glycine and drugs ALX-5407, SSR504734, and PF-03463275. These structures, captured at three fundamental states of the transport cycle-outward-facing, occluded, and inward-facing-enable us to illustrate a comprehensive blueprint of the conformational change associated with glycine reuptake. Additionally, we identified three specific pockets accommodating drugs, providing clear insights into the structural basis of their inhibitory mechanism and selectivity. Collectively, these structures offer significant insights into the transport mechanism and recognition of substrate and anti-schizophrenia drugs, thus providing a platform to design small molecules to treat schizophrenia.

A comprehensive analysis integrating phenotypic assessment uncovering thornless cultivar lineages in Aralia elata.

Aralia elata is an Araliaceae woody plant species found in Northeastern Asia. To understand how genetic pools are distributed for A.elata clones, we were to analyze the population structure of A.elata cultivars and identify how these are correlated with thorn-related phenotype which determines the utility of A.elata. We found that the de novo assembled genome of 'Yeongchun' shared major genomic compartments with the public A.elata genome assembled from the wild-type from China. To identify the population structure of the 32 Korean and Japanese cultivars, we identified 44 SSR markers and revealed three main sub-clusters using ΔK analysis with one isolated cultivar. Machine-learning based clustering with thorn-related phenotype correlated moderately with population structure based on SSR analysis suggested multi-layered genetic regulation of thorn-related phenotypes. Thus, we revealed genetic lineage of A.elata and uncovered isolated cultivar which can provide new genetic material for further breeding.

Microsatellite marker-assisted backcross breeding for improvement of wheat salt tolerance using Kharchia 65.

BACKGROUND: Salinity is a significant abiotic stress that affects plants from germination through all growth stages. This study was aimed to determine the morpho-physiological and genetic variations in BC1F2, BC2F1 and F3 generations resulting from the cross combination WH1105 × Kharchia 65. RESULTS: A significant reduction in germination percentage was observed under salt stress in BC1F2 and F3 seeds. Correlation, heritability in the broad sense, phenotypic coefficient of variability (PCV) and genotypic coefficient of variability (GCV) were measured for all traits. The presence of both Nax1 and Nax2 loci was confirmed in twenty-nine plants using the marker-assisted selection technique. Genetic relationships among the populations were assessed using twenty-four polymorphic SSR markers. CONCLUSION: Cluster analysis along with two and three-dimensional PCA scaling (Principal Component Analysis) revealed the distinct nature of WH 1105 and Kharchia 65. Six plants closer to the recurrent parent (WH1105) selected through this study can serve as valuable genetic material for salt-tolerant wheat improvement programs.

Genome-wide simple sequence repeat analysis and specific molecular marker development of rye.

BACKGROUND: Rye (Secale cereale L.) is the most widely used related species in wheat genetic breeding, and the introduction of its chromosome fragments into the wheat genome through distant hybridization is essential for enriching the genetic diversity of wheat. Rapid and accurate detection of rye chromatin in the wheat genome is important for distant hybridization. Simple sequence repeats (SSRs) are widely distributed in the genome, and SSRs of different species often exhibit species-specific characteristics. RESULTS: In this study, genome-wide SSRs in rye were identified, and their characteristics were outlined. A total of 997,027 SSRs were selected, with a density of 115.97 SSRs/Mb on average. There was no significant difference in the number of SSRs on each chromosome. The number of SSRs on 2R was the highest (15.29%), and the number of SSRs on 1R was the lowest (13.02%). The number of SSRs on each chromosome is significantly correlated with chromosome length. The types of SSR motifs were abundant, and each type of SSR was distributed on 7 chromosomes of rye. The numbers of mononucleotide simple sequence repeats (MNRs), dinucleotide simple sequence repeats (DNRs), and trinucleotide simple sequence repeats (TNRs) were the greatest, accounting for 46.90%, 18.37%, and 22.64% of the total number, respectively. Among the MNRs, the number of G/C repeats and the number of 10 bp motifs were the greatest, accounting for 26.24% and 31.32% of the MNRs, respectively. Based on the SSR sequences, a total of 657 pairs of primers were designed. The PCR results showed that 119 pairs of these primers were rye-specific and could effectively detect rye chromatin in the wheat genome. Moreover, 86 pairs of the primers could also detect one or more specific rye chromosomes. CONCLUSION: These results lay a foundation for both genomic evolution studies of rye and molecular breeding in wheat.

Genome-wide development of simple sequence repeats markers and genetic diversity analysis of chayote.

BACKGROUND: Chayote is a high economic crop in the Cucurbitaceae family, playing an important role in food production, disease treatment and the production of degradable materials in industries. Due to the harsh environment, such as high temperature, drought and frost, some chayote resources are gradually disappearing. It is crucial to collect, characterize, and conserve chayote resources. However, the genetic diversity of chayote resources in China has not been studied so far. RESULTS: In this study, we collected 35 individuals of chayote from 14 provinces in China. Subsequently, we found 363,156 SSR motifs from the chayote genome and designed 57 pairs of SSR primers for validation. Out of these, 48 primer pairs successfully amplified bands, with 42 of them showing polymorphism. These 42 primer pairs detected a total of 153 alleles, averaging 3.64 alleles per locus. The polymorphic information content ranged from 0.03 to 0.78, with an average value of 0.41, indicating a high level of polymorphism. Based on the analysis using STRUCTURE, PCoA, and UPGMA methods, the 35 chayote individuals were divided into two major clusters. Through further association analysis, 7 significantly associated SSR markers were identified, including four related to peel color and three related to spine. CONCLUSIONS: These molecular markers will contribute to the analysis of genetic diversity and genetic breeding improvement of chayote in the future.

Exploring agro-morphological and fiber traits diversity in cotton (G. barbadense L.).

Cotton (Gossypium barbadense L.) is a leading fiber and oilseed crop globally, but genetic diversity among breeding materials is often limited. This study analyzed genetic variability in 14 cotton genotypes from Egypt and other countries, including both cultivated varieties and wild types, using agro-morphological traits and genomic SSR markers. Field experiments were conducted over two seasons to evaluate 12 key traits related to plant growth, yield components, and fiber quality. Molecular diversity analysis utilized 10 SSR primers to generate DNA profiles. The Molecular diversity analysis utilized 10 SSR primers to generate DNA profiles. Data showed wide variation for the morphological traits, with Egyptian genotypes generally exhibiting higher means for vegetative growth and yield parameters. The top-performing genotypes for yield were Giza 96, Giza 94, and Big Black Boll genotypes, while Giza 96, Giza 92, and Giza 70 ranked highest for fiber length, strength, and fineness. In contrast, molecular profiles were highly polymorphic across all genotypes, including 82.5% polymorphic bands out of 212. Polymorphism information content was high for the SSR markers, ranging from 0.76 to 0.86. Genetic similarity coefficients based on the SSR data varied extensively from 0.58 to 0.91, and cluster analysis separated genotypes into two major groups according to geographical origin. The cotton genotypes displayed high diversity in morphology and genetics, indicating sufficient variability in the germplasm. The combined use of physical traits and molecular markers gave a thorough understanding of the genetic diversity and relationships between Egyptian and global cotton varieties. The SSR markers effectively profiled the genotypes and can help select ideal parents for enhancing cotton through hybridization and marker-assisted breeding.

Genetic diversity analysis and DNA fingerprint construction of Zanthoxylum species based on SSR and iPBS markers.

Zanthoxylum is a versatile economic tree species utilized for its spice, seasoning, oil, medicinal, and industrial raw material applications, and it has a lengthy history of cultivation and domestication in China. This has led to the development of numerous cultivars. However, the phenomenon of mixed cultivars and confusing names has significantly obstructed the effective utilization of Zanthoxylum resources and industrial development. Consequently, conducting genetic diversity studies and cultivar identification on Zanthoxylum are crucial. This research analyzed the genetic traits of 80 Zanthoxylum cultivars using simple sequence repeat (SSR) and inter-Primer Binding Site (iPBS) molecular markers, leading to the creation of a DNA fingerprint. This study identified 206 and 127 alleles with 32 SSR markers and 10 iPBS markers, respectively, yielding an average of 6.4 and 12.7 alleles (Na) per marker. The average polymorphism information content (PIC) for the SSR and iPBS markers was 0.710 and 0.281, respectively. The genetic similarity coefficients for the 80 Zanthoxylum accessions ranged from 0.0947 to 0.9868 and from 0.2206 to 1.0000, with mean values of 0.3864 and 0.5215, respectively, indicating substantial genetic diversity. Cluster analysis, corroborated by principal coordinate analysis (PCoA), categorized these accessions into three primary groups. Analysis of the genetic differentiation among the three Zanthoxylum (Z. bungeanum, Z. armatum, and Z. piperitum) populations using SSR markers revealed a mean genetic differentiation coefficient (Fst) of 0.335 and a gene flow (Nm) of 0.629, suggesting significant genetic divergence among the populations. Molecular variance analysis (AMOVA) indicated that 65% of the genetic variation occurred within individuals, while 35% occurred among populations. Bayesian model-based analysis of population genetic structure divided all materials into two groups. The combined PI and PIsibs value of the 32 SSR markers were 4.265 × 10- 27 and 1.282 × 10- 11, respectively, showing strong fingerprinting power. DNA fingerprints of the 80 cultivars were established using eight pairs of SSR primers, each assigned a unique numerical code. In summary, while both markers were effective at assessing the genetic diversity and relationships of Zanthoxylum species, SSR markers demonstrated superior polymorphism and cultivar discrimination compared to iPBS markers. These findings offer a scientific foundation for the conservation and sustainable use of Zanthoxylum species.

Identification and characterization of functionally relevant SSR markers in natural Dalbergia odorifera populations.

BACKGROUND: Dalbergia odorifera is a rare and precious rosewood specie, which is valued for its amber tones, abstract figural patterns, and impermeability to water and insects. However, the information on genetic diversity and marker-assisted selection breeding of D. odorifera is still limited. Simple sequence repeat (SSR) markers are an ideal tool for genetic diversity analysis and marker-assisted molecular breeding for complex traits. RESULTS: Here, we have developed SSR markers within candidate genes and used them to explore the genetic diversity among D. odorifera germplasm resources. A total of 635 SSR loci were identified. The proportions of mono-, di- and tri-nucleotide repeat motifs were 52.28%, 22.99% and 21.42%, respectively. From these, a total of 114 SSR primers were synthesized, of which 24 SSR markers displayed polymorphism (polymorphic information content (PIC) > 0.25). Subsequently, these polymorphic markers were used for the genetic diversity analysis of 106 D. odorifera individuals from 11 natural populations. According to the genetic diversity analysis of D. odorifera natural populations, the average observed heterozygosity (Ho) was 0.500, the average expected heterozygosity (He) was 0.524, and the average Shannon's information index (I) was 0.946. These indicated that the natural populations had moderate genetic diversity. AMOVA analysis showed that 5% of the total variation was within the individuals of a population, whereas 95% of the variation was among the individuals of the populations, indicating a high degree of genetic variation between populations. On the basis of their genetic structures, these populations could be divided into four groups. CONCLUSIONS: Our study provides important experimental resources for genetic studies and assists in the program of molecular breeding of D. odorifera wood formation.

New simple sequence repeat markers reveal undetected diversity in Spanish and Californian Diplodia sapinea populations.

Diplodia sapinea is the causal agent of Diplodia shoot blight, an emerging disease affecting pine forests worldwide. The range expansion of this pathogen in northern Europe has been suggested to be partially facilitated by recent warmer conditions. Although D. sapinea has been studied extensively, critical aspects of its infection biology and population structure remain unexplored. In this study, we developed nine simple sequence repeat (SSR) markers mined from D. sapinea genomes to assess the genetic diversity at higher resolution. Isolates from northern Spain, an area formerly regarded as having low genetic diversity and samples from a Californian population that was formerly regarded as clonal, were analysed in the study. In Spain, the nine SSR markers identified 56 genotypes in 285 samples. Isolates from symptomatic shoots, cones and asymptomatic tissues collected from different stands, suggested admixture between local populations. The same genotype tended to dominate within a single cone, and the same genotypes were usually found in both symptomatic and asymptomatic shoot tissues. The nine new SSR markers developed in this study revealed a high level of genetic diversity in both the northern Spanish and northern Californian populations than previously anticipated. Analyses using these nine SSR markers should contribute to a better understanding of the epidemiology, evolution and origin of D. sapinea, a pathogen that is gaining prominence in many parts of the world.

Nonunique UPGMA clusterings of microsatellite markers.

Agglomerative hierarchical clustering has become a common tool for the analysis and visualization of data, thus being present in a large amount of scientific research and predating all areas of bioinformatics and computational biology. In this work, we focus on a critical problem, the nonuniqueness of the clustering when there are tied distances, for which several solutions exist but are not implemented in most hierarchical clustering packages. We analyze the magnitude of this problem in one particular setting: the clustering of microsatellite markers using the Unweighted Pair-Group Method with Arithmetic Mean. To do so, we have calculated the fraction of publications at the Scopus database in which more than one hierarchical clustering is possible, showing that about 46% of the articles are affected. Additionally, to show the problem from a practical point of view, we selected two opposite examples of articles that have multiple solutions: one with two possible dendrograms, and the other with more than 2.5 million different possible hierarchical clusterings.

SSR4-CDG, an ultra-rare X-linked congenital disorder of glycosylation affecting the TRAP complex: Review of 22 affected individuals including the first adult patient.

Congenital disorders of glycosylation (CDG) are a group of rare, often multi-systemic genetic disorders that result from disturbed protein and lipid glycosylation. SSR4-CDG is an ultra-rare, comparably mild subtype of CDG, presenting mostly in males. It is caused by pathogenic variants in the SSR4 gene, which is located on the X chromosome. SSR4 (signal sequence receptor protein 4) is a subunit of the translocon-associated protein (TRAP) complex, a structure that is needed for the translocation of proteins across the ER membrane. A deficiency of SSR4 leads to disturbed N-linked glycosylation of proteins in the endoplasmic reticulum. Here, we review the most common clinical, biochemical and genetic features of 18 previously published individuals and report four new cases diagnosed with SSR4-CDG, including the first adult affected by this disorder. Based on our review, developmental delay, speech delay, intellectual disability, muscular hypotonia, microcephaly and distinct facial features are key symptoms of SSR4-CDG that are present in all affected individuals. Although these symptoms overlap with many other neurodevelopmental disorders, their combination with additional clinical features, and a quite distinguishable facial appearance of affected individuals make this disorder a potentially recognizable type of CDG. Additional signs and symptoms include failure to thrive, feeding difficulties, connective tissue involvement, gastrointestinal problems, skeletal abnormalities, seizures and, in some cases, significant behavioral abnormalities. Due to lack of awareness of this rare disorder, and since biochemical testing can be normal in affected individuals, most are diagnosed through genetic studies, such as whole exome sequencing. With this article, we expand the phenotype of SSR4-CDG to include cardiac symptoms, laryngeal abnormalities, and teleangiectasia. We also provide insights into the prognosis into early adulthood and offer recommendations for adequate management and care. We emphasize the great need for causal therapies, as well as effective symptomatic therapies addressing the multitude of symptoms in this disease. In particular, behavioral problems can severely affect quality of life in individuals diagnosed with SSR4-CDG and need special attention. Finally, we aim to improve guidance and education for affected families and treating physicians and create a basis for future research in this disorder.

The chickpea WIP2 gene underlying a major QTL contributes to lateral root development.

Lateral roots are a major component of root system architecture, and lateral root count (LRC) positively contributes to yield under drought in chickpea. To understand the genetic regulation of LRC, a biparental mapping population derived from two chickpea accessions having contrasting LRCs was genotyped by sequencing, and phenotyped to map four major quantitative trait loci (QTLs) contributing to 13-32% of the LRC trait variation. A single- nucleotide polymorphism tightly linked to the locus contributing to highest trait variation was located on the coding region of a gene (CaWIP2), orthologous to NO TRANSMITTING TRACT/WIP domain protein 2 (NTT/WIP2) gene of Arabidopsis thaliana. A polymorphic simple sequence repeat (SSR) in the CaWIP2 promoter showed differentiation between low versus high LRC parents and mapping individuals, suggesting its utility for marker-assisted selection. CaWIP2 promoter showed strong expression in chickpea apical root meristem and lateral root primordia. Expression of CaWIP2 under its native promoter in the Arabidopsis wip2wip4wip5 mutant rescued its rootless phenotype to produce more lateral roots than the wild-type plants, and led to formation of amyloplasts in the columella. CaWIP2 expression also induced the expression of genes that regulate lateral root emergence. Our study identified a gene-based marker for LRC which will be useful for developing drought-tolerant, high-yielding chickpea varieties.

Characterization of field isolates of Fusarium spp. from eggplant in India for species complexity and virulence.

Eggplant wilt, despite emerging as a severe disease in India, the etiology must be better studied for its species' complexity and variability. The identity of fungal isolates associated with eggplants of India was established morphologically followed by sequencing and phylogenetic analysis. Three species, Fusarium falciforme, Fusarium incarnatum and Fusarium proliferatum, were observed for the first time in India. The isolates were tested for pathogenicity. Though all of them were pathogenic, the isolates displayed varying degrees of virulence. In further studies, the genetic relatedness of the isolates for virulence was assessed with candidate avirulent (SIX effectors), virulent (Fow1 and Fow2) and SSR markers. The SIX effector genes could not delineate the virulent isolates and were expressed in some non-F. oxysporum isolates for the first time. Likewise, the virulent genes, Fow1 for expression across the isolates and Fow2 for random expression across the isolates, were unsuitable markers for identifying the virulent groups. Hence, the F. oxysporum and F. solani isolates were genotyped with SSR markers. Though the clustering did not correlate with their virulence levels, the dendrogram grouping revealed variability among the F. oxysporum and F. solani isolates. This study concludes that although multiple species of Fusarium are associated with eggplant wilt in India, only F. oxysporum and F. solani are widespread in the surveyed areas. Though the three markers could not delineate the race specificity of the isolates, only the SSR makers could identify the genetic variability and hence, would help screen eggplant germplasm for fusarium wilt resistance.

Genetic response of a perennial grass to warm and wet environments interacts and is associated with trait means as well as plasticity.

The potential for rapid evolution is an important mechanism allowing species to adapt to changing climatic conditions. Although such potential has been largely studied in various short-lived organisms, to what extent we can observe similar patterns in long-lived plant species, which often dominate natural systems, is largely unexplored. We explored the potential for rapid evolution in Festuca rubra, a long-lived grass with extensive clonal growth dominating in alpine grasslands. We used a field sowing experiment simulating expected climate change in our model region. Specifically, we exposed seeds from five independent seed sources to novel climatic conditions by shifting them along a natural climatic grid and explored the genetic profiles of established seedlings after 3 years. Data on genetic profiles of plants selected under different novel conditions indicate that different climate shifts select significantly different pools of genotypes from common seed pools. Increasing soil moisture was more important than increasing temperature or the interaction of the two climatic factors in selecting pressure. This can indicate negative genetic interaction in response to the combined effects or that the effects of different climates are interactive rather than additive. The selected alleles were found in genomic regions, likely affecting the function of specific genes or their expression. Many of these were also linked to morphological traits (mainly to trait plasticity), suggesting these changes may have a consequence on plant performance. Overall, these data indicate that even long-lived plant species may experience strong selection by climate, and their populations thus have the potential to rapidly adapt to these novel conditions.

Structure and genetic diversity of Canadian Maritimes wild hops.

Studies on the northeastern American native hops (Humulus lupulus ssp. lupuloides) from the Canadian Maritimes are scarce. This study aimed to evaluate the genetic structure and diversity among 25 wild-collected hops from three Canadian Maritime provinces using microsatellite (simple sequence repeat (SSR)) markers. Based on 43 SSR markers, four distinct subgroups were found, with a low molecular variance (19%) between subgroups and a high variance (81%) within subgroups. The Nei's unbiased genetic distance between clusters ranged from 0.01 to 0.08, the genetic distance between clusters 2 and 3 being the farthest and that between clusters 1 and 2 the closest. Cluster 2 captured the highest overall diversity. A total of 18 SSR markers clearly discriminated hop clones by detecting putative subspecies-specific haplotypes, differentiating clones of native-wild H. lupulus ssp. lupuloides from the naturalized old and modern hop cultivars. Seven of the 18 SSR markers also differentiated two clones from the same site from one another. The study is the first, using molecular markers, to identify SSR markers with potential for intellectual property protection in Canadian Maritimes hops. The SSR markers herein used can be prime tools for hop breeders and growers in the region.

Reduced unilateral sweating caused by varicella zoster virus infection: a case report.

BACKGROUND: Herpes zoster is an infectious skin disease caused by the reactivation of the varicella zoster virus (VZV), which has been latent in the posterior root ganglia of the spinal cord or cranial ganglia for an extended period. Neurological complications caused by herpes zoster include aseptic meningitis, white matter disease, peripheral motor neuropathy, and Guillain-Barré syndrome. However, reduced unilateral sweating caused by the VZV is very rare. CASE PRESENTATION: This article reports the case of a 34-year-old woman who was admitted to our hospital with sore throat, dizziness, and reduced sweating on the left side of her body. Physical examination found herpes lesions on the left upper lip and left external ear canal (scabbed) and reduced sweating on the left side of the body. Head magnetic resonance imaging (MRI) with contrast showed no abnormalities. After a lumbar puncture, the patient was diagnosed with viral meningitis by VZV infection. The electromyographic skin sympathetic reflex indicated damage to the left sympathetic nerve. CONCLUSIONS: Secondary unilateral sweating reduction is a rare neurological complication of herpes zoster, caused by damage to the autonomic nervous system. Literature review and comprehensive examination indicated that the reduced unilateral sweating was due to the activation of latent herpes zoster virus in the autonomic ganglia which has damaged the autonomic nervous system. For patients who exhibit acute hemibody sweat reduction, doctors should consider the possibility of secondary autonomic nervous system damage caused by herpes zoster.

Utilization of marker-assisted backcrossing to generate new gynoecious cucumber lines with genetic heritage similar to the indigenous Vietnamese cucumber.

The marker-assisted backcrossing (MAB) can help to transfer an interested allele at a target locus from a donor to a recipient line. Gynoecious is a pivotal trait of cucumber since commercial F1 hybrid seeds produced with gynoecious line as one of the parents are high-yield and affordable. This study aims to transfer the F locus encoded for gynoecious trait to Vietnamese domesticated cucumbers by marker-assisted backcrossing. Two monoecious cucumber lines, A1 (Ha Giang, Vietnam) A2 (Yen Bai, Vietnam), and two gynoecious cucumber lines, B1 (Plantgene, India) and B2 (Hue, Vietnam) were utilized as the starting materials. BCAT marker (located on the F locus) and 52 SSRs (spread across seven chromosomes and tightly linked with some crucial horticultural traits) were used as the foreground and background markers, respectively. With this, phenotype selection for fruit and leaf sizes was also applied. First, using phenotypic screening and foreground marker, A1 (Ha Giang, Vietnam) and B1 (Plantgene, India) were selected as donor and recurrent parents for backcrossing. Then, after two backcrosses followed by two self-pollinations, four gynoecious C cucumber lines were created. These C lines have leaf sizes slightly bigger than the recurrent parent. Importantly, their fruit length is the same or longer than A1 (Ha Giang, Vietnam). These new gynoecious lines could be used as material lines for producing commercial F1 hybrid seeds. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01481-w.

Development of miRNA-SSR and target-SSR markers from yield-associate genes and their applicability in the assessment of genetic diversity and association mapping in rice (Oryza sativa L.).

The gene-derived functional markers are considered effective to use in marker-assisted breeding and genetic diversity analysis. As of now, no functional markers have been identified from miRNAs regulating yield traits. The miRNAs play a key role as regulators in controlling the candidate genes involved in grain yield improvement in rice. In this study, 13 miRNA-SSR and their target gene SSR markers were mined from 29 yield-responsive miRNA along with their 29 target genes in rice. The validation of these markers showed that four miRNA-SSRs and one target gene SSR markers had shown polymorphism among 120 diverse rice genotypes. The PIC values ranged from 0.25 (OsARF18-SSR) to 0.72 (miR408-SSR, miR172b-SSR, and miR396f-SSR) with an average value of 0.57. These polymorphic markers grouped 120 rice genotypes into 3 main clusters based on the levels of high genetic diversity. These markers also showed significant association with key yield traits. Among all, miR172b-SSR showed a strong association with plant height in two seasons. This investigation suggests that this new class of molecular markers has great potential in the characterization of rice germplasm by genetic diversity and population structure and in marker-assisted breeding for the development of high-yielding varieties. Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01462-z.

Development of novel SSR markers and validation by assessing the genetic diversity of endangered Deccan mahseer, Tor khudree.

BACKGROUND: The Deccan mahseer, Tor khudree (Sykes, 1839) is a potential game and food fish species belonging to the family cyprinidae and is categorized as endangered. Its distribution is restricted to southern part of India, specifically to Peninsular Rivers. This study is first to assess the genetic diversity and differentiation in Tor khudree by developing novel simple sequence repeat (SSR) markers. METHODS AND RESULTS: Low depth next generation sequencing followed by sequence analysis in MISA software identified 187,649 SSRs. The novel fourteen validated SSR loci were used for population genetic analysis. All of the SSR loci were highly informative with mean PIC > 0.5. High mean allelic richness (9.29) observed heterozygosity (0.98) and expected heterozygosity (0.79) were observed across the loci. However, genetic differentiation was low but significant (0.052). Negative FIS values were observed in both locus-wise and populations indicating the presence of high heterozygosity. Intrapopulation variation was found to be high (96.29%). The population structure revealed two genetic stocks. CONCLUSIONS: The results from the present study including the highly polymorphic markers developed would be a useful resource for further research on population genetics and conservation genetics of the species.

Screening for drought tolerance and genetic diversity of wheat varieties using agronomic and molecular markers.

BACKGROUND: The future predictions for frequent and severe droughts will represent a significant threat to wheat yield and food security. In this context, breeding has proven to be the most efficient approach to enhance wheat productivity in dry environments. METHODS AND RESULTS: In this study, both agronomic and molecular-based approaches were used to evaluate the response of twenty-eight Tunisian wheat varieties to drought stress. The primary objective was to screen these varieties for drought tolerance using molecular and agro-morphological markers. All varieties were significantly affected by drought stress regarding various traits including total dry matter, straw length, flag leaf area, number of senescent leaves, SPAD value, grain yield and grain number. Furthermore, substantial variability in drought-stress tolerance was observed among wheat genotypes. The cluster analysis and principal component analyses confirmed the existence of genotypic variation in growth and yield impairments induced by drought. The stress susceptibility index (SSI) and tolerance index (TOL) proved to be the most effective indices and were strongly correlated with the varying levels of genotypic tolerance. The genotyping evaluation resulted in the amplification of 101 alleles using highly polymorphic 12 SSR markers, showed an average polymorphism of 74%. CONCLUSIONS: Taken together, the combination of agronomic and molecular approaches revealed that Karim, Td7, D117 and Utique are the most drought-tolerant wheat varieties. These varieties are particularly promising candidates for genetic improvements and can be utilized as potential genitors for future breeding programs in arid and semi-arid regions.