DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing

Addressing Conservation Needs: Genetic Diversity and Population Ecology of the Endemic Tree Spondias tuberosa Arruda

Spondias tuberosa Arruda (Anacardiaceae), popularly known as umbuzeiro or imbuzeiro, is a fruit tree native to the semiarid region of Brazil. The extractive harvesting of its fruits contributes significantly to the economy, generating an annual revenue of approximately $4,2 million. The present study aimed to assess the spatial pattern, allometric variations, fruit measurements, and genetic diversity of trees within a remaining forest of the Caatinga biome, with a focus on intrapopulation analysis. We used intersimple repeated sequence markers and the second-order function density of neighbours to determine the genetic and spatial structure. The density of neighbours was highest within a 10-meter radius. Biometric analyses revealed average fruit lengths of 31.12 mm (±0.22), diameters of 28.68 mm (±0.25), and fresh masses of 15.56 g (±0.33). Diaspores exhibited an average length, diameter, and thickness of 19.27 mm, 13.95 mm, and 11.14 mm, respectively, with a fresh mass of 2.28 g. Notably, the fresh mass demonstrated the highest coefficient of variation. Ten molecular markers were selected, generating 103 highly polymorphic loci (99.03%) with an average informative content of 0.45. Nei's diversity index (0.37) and Shannon's index (0.55) indicated moderate genetic diversity. Furthermore, Bayesian analysis revealed a population structure with two distinct genetic groups. The Infinite Allele and Mutation Step Models suggested a significant historical decline in population size, indicative of a genetic bottleneck. As a result, proactive in situ conservation strategies, including establishing protected natural areas, become essential, considering the socioeconomic significance of the species. Additionally, it is recommended to establish germplasm banks for ex situ conservation and the development of managed cultivation initiatives to reduce the pressure on native populations of S. tuberosa caused by extraction.

Understanding phloem's role in long-distance transport and accumulation of arsenic (As) in rice: toward low-As-accumulating grain development

MAIN CONCLUSION

This review highlights the roles of phloem in the long-distance transport and accumulation of As in rice plants, facilitating the formulation of new strategies to reduce the grain As content. Rice is a staple diet for a significant proportion of the global population. As toxicity is a major issue affecting the rice productivity and quality worldwide. Phloem tissues of rice plants play vital roles in As speciation, long-distance transport, and unloading, thereby controlling the As accumulation in rice grains. Phloem transport accounts for a significant proportion of As transport to grains, ranging from 54 to 100% depending on the species [inorganic arsenate (As(V)), arsenite (As(III)), or organic dimethylarsinic acid (DMA(V)]. However, the specific mechanism of As transport through phloem leading to its accumulation in grains remains unknown. Therefore, understanding the molecular mechanism of phloem-mediated As transport is necessary to determine the roles of phloem in long-distance As transport and subsequently reduce the grain As content via biotechnological interventions. This review discusses the roles of phloem tissues in the long-distance transport and accumulation of As in rice grains. This review also highlights the biotechnological approaches using critical genetic factors involved in nodal accumulation, vacuolar sequestration, and cellular efflux of As in phloem- or phloem-associated tissues. Furthermore, the limitations of existing transgenic techniques are outlined to facilitate the formulation of novel strategies for the development of rice with reduced grain As content.

Potential probiotic Lactobacillus delbrueckii subsp. lactis KUMS-Y33 suppresses adipogenesis and promotes osteogenesis in human adipose-derived mesenchymal stem cell

Today, probiotics are considered to be living microorganisms whose consumption has a certain number of beneficial effects on the consumer. The present study aimed to investigate the effect of a new probiotic extract (Lactobacillus delbrueckii subsp. lactis KUMS Y33) on the differentiation process of human adipose-derived stem cells (hADSCs) into adipocytes and osteocytes and, as a result, clarify its role in the prevention and treatment of bone age disease. Several bacteria were isolated from traditional yogurt. They were evaluated to characterize the probiotic's activity. Then, the isolated hADSCs were treated with the probiotic extract, and then osteogenesis and adipogenesis were induced. To evaluate the differentiation process, oil red O and alizarin red staining, a triglyceride content assay, an alkaline phosphatase (ALP) activity assay, as well as real-time PCR and western blot analysis of osteocyte- and adipocyte-specific genes, were performed. Ultimately, the new strain was sequenced and registered on NBCI. In the probiotic-treated group, the triglyceride content and the gene expression and protein levels of C/EBP-α and PPAR-γ2 (adipocyte-specific markers) were significantly decreased compared to the control group (P < 0.05), indicating an inhibited adipogenesis process. Furthermore, the probiotic extract caused a significant increase in the ALP activity, the expression levels of RUNX2 and osteocalcin, and the protein levels of collagen I and FGF-23 (osteocyte-specific markers) in comparison to the control group (P < 0.05), indicating an enhanced osteogenesis process. According to the results of the present study, the probiotic extract inhibits adipogenesis and significantly increases osteogenesis, suggesting a positive role in the prevention and treatment of osteoporosis and opening a new aspect for future in-vivo study.

Analysis of volatile organic compounds in Korean-bred strawberries: insights for improving fruit flavor

Introduction

The strawberry industry in South Korea has witnessed a significant 65% growth over the past decade, surpassing other fruits and vegetables in production value. While sweetness and acidity are well-recognized flavor determinants, the role of volatile organic compounds (VOCs) in defining the desirable flavor profiles of strawberries is also crucial. However, existing research has predominantly concentrated on a limited range of commercial cultivars, neglecting the broader spectrum of strawberry varieties.

Methods

This study embarked on developing a comprehensive VOC database for a diverse array of strawberry cultivars sourced both domestically and internationally. A total of 61 different strawberry cultivars from Korea (45), the USA (7), Japan (8), and France (1) were analyzed for their VOC content using Tenax TA Thermo Desorption tubes and Gas Chromatography-Mass Spectrometry (GC-MS). In addition to VOC profiling, heritability was assessed using one-way ANOVA to compare means among multiple groups, providing insights into the genetic basis of flavor differences.

Results and discussion

The analysis identified 122 compounds categorized into esters, alcohols, terpenes, and lactones, with esters constituting the majority (46.5%) of total VOCs in Korean cultivars. 'Arihyang', 'Sunnyberry', and 'Kingsberry' exhibited the highest diversity of VOCs detected (97 types), whereas 'Seolhong' showed the highest overall concentration (57.5mg·kg-1 FW). Compared to the USA cultivars, which were abundant in γ-decalactone (a peach-like fruity aroma), most domestic cultivars lacked this compound. Notably, 'Misohyang' displayed a high γ-decalactone content, highlighting its potential as breeding germplasm to improve flavor in Korean strawberries. The findings underscore the importance of a comprehensive VOC analysis across different strawberry cultivars to understand flavor composition. The significant variation in VOC content among the cultivars examined opens avenues for targeted breeding strategies. By leveraging the distinct VOC profiles, particularly the presence of γ-decalactone, breeders can develop new strawberry varieties with enhanced flavor profiles, catering to consumer preferences for both domestic and international markets.

Genetic diversities in wild and cultivated populations of the two closely-related medical plants species, Tripterygium Wilfordii and T. Hypoglaucum (Celastraceae)

BACKGROUND

The sustainable supply of medicinal plants is important, and cultivating and domesticating them has been suggested as an optimal strategy. However, this can lead to a loss of genetic diversity. Tripterygium wilfordii Hook. f. is a medicinal plant commonly used in traditional Chinese medicine, but its wild populations are dwindling due to excessive harvesting. To protect the species and meet the increasing demand, it is urgent to cultivate it on a large scale. However, distinguishing between T. wilfordii and T. hypoglaucum, two similar species with different medicinal properties, is challenging. Therefore, it is crucial to understand the genetic diversity and population structure of these species for their sustainable utilization.

RESULTS

In this study, we investigated the genetic diversity and population structure of the two traditional medicinal semiwoody vines plant species, Tripterygium wilfordii and T. hypoglaucum, including wild and cultivated populations using chloroplast DNA (cpDNA) sequences and microsatellite loci. Our results indicated that the two species maintain a high level of genetic divergence, indicating possible genetic bases for the different contents of bioactive compounds of the two species. T. wilfordii showed lower genetic diversity and less subdivided population structures of both markers than T. hypoglaucum. The potential factors in shaping these interesting differences might be differentiated pollen-to-seed migration rates, interbreeding, and history of population divergence. Analyses of cpDNA and microsatellite loci supported that the two species are genetically distinct entities. In addition, a significant reduction of genetic diversity was observed for cultivated populations of the two species, which mainly resulted from the small initial population size and propagated vegetative practice during their cultivation.

CONCLUSION

Our findings indicate significant genetic divergence between T. wilfordii and T. hypoglaucum. The genetic diversity and population structure analyses provide important insights into the sustainable cultivation and utilization of these medicinal plants. Accurate identification and conservation efforts are necessary for both species to ensure the safety and effectiveness of crude drug use. Our study also highlighted the importance of combined analyses of different DNA markers in addressing population genetics of medicinal plants because of the contrasts of inheritance and rates of gene flow. Large-scale cultivation programs should consider preserving genetic diversity to enhance the long-term sustainability of T. wilfordii and T. hypoglaucum. Our study proposed that some populations showed higher genetic diversity and distinctness, which can be considered with priority for conservation and as the sources for future breeding and genetic improvement.

Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding

Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.

A systematic review of ginsenoside biosynthesis, spatiotemporal distribution, and response to biotic and abiotic factors in American ginseng

American ginseng (Panax quinquefolius) has gained recognition as a medicinal and functional food homologous product with several pharmaceutical, nutritional, and industrial applications. However, the key regulators involved in ginsenoside biosynthesis, the spatiotemporal distribution characteristics of ginsenosides, and factors influencing ginsenosides are largely unknown, which make it challenging to enhance the quality and chemical extraction processes of the cultivated American ginseng. This review presents an overview of the pharmacological effects, biosynthesis and spatiotemporal distribution of ginsenosides, with emphasis on the impacts of biotic and abiotic factors on ginsenosides in American ginseng. Modern pharmacological studies have demonstrated that American ginseng has neuroprotective, cardioprotective, antitumor, antidiabetic, and anti-obesity effects. Additionally, most genes involved in the upregulation of ginsenoside biosynthesis have been identified, while downstream regulators (OSCs, CYP450, and UGTs) require further investigation. Futhermore, limited knowledge exists regarding the molecular mechanisms of the impact of biotic and abiotic factors on ginsenosides. Notably, the nonmedicinal parts of American ginseng, particularly its flowers, fibrous roots, and leaves, exhibit higher ginsenoside content than its main roots and account for a considerable amount of weight in the whole plant, representing promising resources for ginsenosides. Herein, the prospects of molecular breeding and metabolic engineering based on multi-omics to improve the unstable quality of cultivated American ginseng and the shortage of ginsenosides are proposed. This review highlights the gaps in the current research on American ginseng and proposes solutions to address these limitations, providing a guide for future investigations into American ginseng ginsenosides.

Hybrid Rice Production: A Worldwide Review of Floral Traits and Breeding Technology, with Special Emphasis on China

Rice is an important diet source for the majority of the world's population, and meeting the growing need for rice requires significant improvements at the production level. Hybrid rice production has been a significant breakthrough in this regard, and the floral traits play a major role in the development of hybrid rice. In grass species, rice has structural units called florets and spikelets and contains different floret organs such as lemma, palea, style length, anther, and stigma exsertion. These floral organs are crucial in enhancing rice production and uplifting rice cultivation at a broader level. Recent advances in breeding techniques also provide knowledge about different floral organs and how they can be improved by using biotechnological techniques for better production of rice. The rice flower holds immense significance and is the primary focal point for researchers working on rice molecular biology. Furthermore, the unique genetics of rice play a significant role in maintaining its floral structure. However, to improve rice varieties further, we need to identify the genomic regions through mapping of QTLs (quantitative trait loci) or by using GWAS (genome-wide association studies) and their validation should be performed by developing user-friendly molecular markers, such as Kompetitive allele-specific PCR (KASP). This review outlines the role of different floral traits and the benefits of using modern biotechnological approaches to improve hybrid rice production. It focuses on how floral traits are interrelated and their possible contribution to hybrid rice production to satisfy future rice demand. We discuss the significance of different floral traits, techniques, and breeding approaches in hybrid rice production. We provide a historical perspective of hybrid rice production and its current status and outline the challenges and opportunities in this field.

Complete Chloroplast Genomes of Four Oaks from the Section Cyclobalanopsis Improve the Phylogenetic Analysis and Understanding of Evolutionary Processes in the Genus Quercus

Quercus is a valuable genus ecologically, economically, and culturally. They are keystone species in many ecosystems. Species delimitation and phylogenetic studies of this genus are difficult owing to frequent hybridization. With an increasing number of genetic resources, we will gain a deeper understanding of this genus. In the present study, we collected four Quercus section Cyclobalanopsis species (Q. poilanei, Q. helferiana, Q. camusiae, and Q. semiserrata) distributed in Southeast Asia and sequenced their complete genomes. Following analysis, we compared the results with those of other species in the genus Quercus. These four chloroplast genomes ranged from 160,784 bp (Q. poilanei) to 161,632 bp (Q. camusiae) in length, with an overall guanine and cytosine (GC) content of 36.9%. Their chloroplast genomic organization and order, as well as their GC content, were similar to those of other Quercus species. We identified seven regions with relatively high variability (rps16, ndhk, accD, ycf1, psbZ-trnG-GCC, rbcL-accD, and rpl32-trnL-UAG) which could potentially serve as plastid markers for further taxonomic and phylogenetic studies within Quercus. Our phylogenetic tree supported the idea that the genus Quercus forms two well-differentiated lineages (corresponding to the subgenera Quercus and Cerris). Of the three sections in the subgenus Cerris, the section Ilex was split into two clusters, each nested in the other two sections. Moreover, Q. camusiae and Q. semiserrata detected in this study diverged first in the section Cyclobalanopsis and mixed with Q. engleriana in the section Ilex. In particular, 11 protein coding genes (atpF, ndhA, ndhD, ndhF, ndhK, petB, petD, rbcL, rpl22, ycf1, and ycf3) were subjected to positive selection pressure. Overall, this study enriches the chloroplast genome resources of Quercus, which will facilitate further analyses of phylogenetic relationships in this ecologically important tree genus.

Genetic Diversity and Structure of Terminalia bellerica (Gaertn. Roxb.) Population in India as Revealed by Genetic Analysis

In this study, an extensive exploration survey of wild progeny was conducted which yielded 18 candidate plus trees (CPTs) of Terminalia bellerica. Seeds of these CPTs were collected from diverse locations between 10°54' and 28°07' E longitude, and 76°27' and 95°32' N latitude, covering 18 different locations across 5 states of the Indian subcontinent. The objective of the progeny trial was to assess genetic associations and variability in growth and physio-chemical characteristics. Significant variations (p < 0.05) were observed among the growth traits, encompassing plant height, basal diameter, girth at breast height and volume, as well as physio-chemical characteristics such as leaf length, width, area and chlorophyll content, carotenoids, and protein in the progeny trial. Broad-sense heritability (h2b) estimates were consistently high, exceeding 80% for all growth and physiological related traits under investigation except for plant height, leaf length, and girth at breast height. A correlation study revealed that selecting based on plant height, leaf area, and girth at breast height effectively enhances T. bellerica volume. A moderate genetic advance in percent of the mean (GAM) was observed for most traits, except leaf length, leaf width, girth at breast height, and plant height. Across all 13 traits, phenotypic coefficient of variation (PCV) surpassed genotypic coefficient of variation (GCV). Utilizing principal component analysis (PCA) and dendrogram construction categorized the genotypes into seven distinct groups. In conclusion, the study has demonstrated that targeting girth at breast height and plant height would be a highly effective strategy for the establishment of elite seedling nurseries and clonal seed nurseries for varietal and hybridization programs in the future.

Construction of SNP fingerprints and genetic diversity analysis of radish (Raphanus sativus L.)

Radish (Raphanus sativus L.) is a vegetable crop with economic value and ecological significance in the genus Radish, family Brassicaceae. In recent years, developed countries have attached great importance to the collection and conservation of radish germplasm resources and their research and utilization, but the lack of population genetic information and molecular markers has hindered the development of the genetic breeding of radish. In this study, we integrated the radish genomic data published in databases for the development of single-nucleotide polymorphism (SNP) markers, and obtained a dataset of 308 high-quality SNPs under strict selection criteria. With the support of Kompetitive Allele-Specific PCR (KASP) technology, we screened a set of 32 candidate core SNP marker sets to analyse the genetic diversity of the collected 356 radish varieties. The results showed that the mean values of polymorphism information content (PIC), minor allele frequency (MAF), gene diversity and heterozygosity of the 32 candidate core SNP markers were 0.32, 0.30, 0.40 and 0.25, respectively. Population structural analysis, principal component analysis and genetic evolutionary tree analysis indicated that the 356 radish materials were best classified into two taxa, and that the two taxa of the material were closely genetically exchanged. Finally, on the basis of 32 candidate core SNP markers we calculated 15 core markers using a computer algorithm to construct a fingerprint map of 356 radish varieties. Furthermore, we constructed a core germplasm population consisting of 71 radish materials using 32 candidate core markers. In this study, we developed SNP markers for radish cultivar identification and genetic diversity analysis, and constructed DNA fingerprints, providing a basis for the identification of radish germplasm resources and molecular marker-assisted breeding as well as genetic research.

Genome assembly and microsatellite marker development using Illumina and PacBio sequencing in Persicaria maackiana (Polygonaceae) from Korea

BACKGROUND

Persicaria maackiana (Regel) is a potential medicinal plant that exerts anti-diabetic effects. However, the lack of genomic information on P. maackiana hinders research at the molecular level.

OBJECTIVE

Herein, we aimed to construct a draft genome assembly and obtain comprehensive genomic information on P. maackiana using high-throughput sequencing tools PacBio Sequel II and Illumina.

METHODS

Persicaria maackiana samples from three natural populations in Gaecheon, Gichi, and Uiryeong reservoirs in South Korea were used to generate genomic DNA libraries, perform genome de novo assembly, gene ontology analysis, phylogenetic tree analysis, genotyping, and identify microsatellite markers.

RESULTS

The assembled P. maackiana genome yielded 32,179 contigs. Assessment of assembly integrity revealed 1503 (93.12%) complete Benchmarking Universal Single-Copy Orthologs. A total of 64,712 protein-coding genes were predicted and annotated successfully in the protein database. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs, 13,778 genes were annotated into 18 categories. Genes that activated AMPK were identified in the KEGG pathway. A total of 316,992 microsatellite loci were identified, and primers targeting the flanking regions were developed for 292,059 microsatellite loci. Of these, 150 primer sets were randomly selected for amplification, and 30 of these primer sets were identified as polymorphic. These primers amplified 3-9 alleles. The mean observed and expected heterozygosity were 0.189 and 0.593, respectively. Polymorphism information content values of the markers were 0.361-0.754.

CONCLUSION

Collectively, our study provides a valuable resource for future comparative genomics, phylogeny, and population studies of P. maackiana.

Newly Developed Restorer Lines of Sorghum [Sorghum bicolor (L.) Moench] Resistant to Greenbug

Eight lines of grain sorghum [Sorghum bicolor (L.) Moench], which can be used as a promising source material in heterotic hybrid breeding as pollen fertility restorers and donors of resistance to the greenbug (Schizaphis graminum Rondani), are characterized. The new restorer lines (R-lines) were developed by crossing the maternal sterile line Nizkorosloe 81s (CMS A1) with two lines selected from the grain sorghum collection accessions VIR-928 and VIR-929 as the paternal forms. The R-lines were genotyped using PCR markers, and also characterized by height, duration of the seedling-flowering period, and some of the technological properties of flour. With the use of microsatellite markers linked to the Rf genes and by hybridological analysis, it was shown that the new lines carry the dominant allele of the gene Rf2. The PCoA analysis demonstrated clear differences of each R-line from the parents. The genotypes of the new lines and their parental forms for the Rf2 locus were confirmed by applying three allele-specific codominant CAPS markers which detected SNPs in the candidate Rf2 gene. All new lines were highly fertile, as demonstrated by cytological analysis of acetocarmine-stained pollen preparations. A high resistance to the greenbug was demonstrated for each new R-line both in the laboratory and field conditions against a severe aphid infestation. Grain quality parameters such as protein content and dough rheological properties varied widely and were quite satisfactory in some R-lines. Characteristics common to all eight sorghum lines studied, such as the ability to restore pollen fertility in the F1 generation, good pollen quality, greenbug resistance, early ripening, spreading panicle, and low stature, allow us to recommend them for producing commercial F1 hybrids with satisfactory grain quality for both fodder and food purposes.

Gender specific SNP markers in Coscinium fenestratum (Gaertn.) Colebr. for resource augmentation

BACKGROUND

Unregulated extraction of highly traded medicinal plant species results in drastic decline of the natural resources and alters viable sex ratio of populations. Conservation and long-term survival of such species, require gender specific restoration programs to ensure reproductive success. However, it is often difficult to differentiate sex of individuals before reaching reproductive maturity. C. fenestratum is one of the medicinally important and overexploited dioecious woody liana, with a reproductive maturity of 15 years. Currently, no information is available to identify sex of C. fenestratum in seedling stage while augmenting the resources. Thus, the current study envisages to utilize transcriptomics approach for gender differentiation which is imperative for undertaking viable resource augmentation programmes.

METHODS AND RESULTS

Gender specific SNPs with probable role in sexual reproduction/sex determination was located using comparative transcriptomics approach (sampling male and female individuals), alongside gene ontology and annotation. Nine sets of primers were synthesized from 7 transcripts (involved in sexual reproduction/other biological process) containing multiple SNP variants. Out of the nine primer pairs, only one SNP locus with no available information of its role in reproduction, showed consistent and accurate results (males-heterozygous and females-homozygous), in the analyzed 40 matured individuals of known sexes. Thus validated the efficiency of this SNP marker in differentiating male and female individuals.

CONCLUSIONS

The study could identify SNPs linked to the loci with apparent role in gender differentiation. This SNP marker can be used for early sexing of seedlings for in-situ conservation and resource augmentation of C. fenestratum in Kerala, India.

Cationic and anionic detergent buffers in sequence yield high-quality genomic DNA from diverse plant species

Because of the heterogeneity among seedlings of outbreeding species, the use of seedling tissues as a source of DNA is unsuitable for the genomic characterization of elite germplasms. High-quality DNA, free of RNA, proteins, polysaccharides, secondary metabolites, and shearing, is mandatory for downstream molecular biology applications, especially for next-generation genome sequencing and pangenome analysis aiming to capture the complete genetic diversity within a species. The study aimed to accomplish an efficient protocol for the extraction of high-quality DNA suitable for diverse plant species/tissues. We describe a reliable, and consistent protocol suitable for the extraction of DNA from 42 difficult-to-extract plant species belonging to 33 angiosperm (monocot and dicot) families, including tissues such as seeds, roots, endosperm, and flower/fruit tissues. The protocol was first optimized for the outbreeding recalcitrant trees viz., Prosopis cineraria, Conocarpus erectus, and Phoenix dactylifera, which are rich in proteins, polysaccharides, and secondary metabolites, and the quality of the extracted DNA was confirmed by downstream applications. Nine procedures were attempted to extract high-quality, impurities-free DNA from these three plant species. Extraction of the ethanol-precipitated DNA from cetyltrimethylammonium bromide (CTAB) protocol using sodium dodecyl sulfate (SDS) buffer, i.e., the extraction using a cationic (CTAB) detergent followed by an anionic (SDS) detergent was the key for high yield and high purity (1.75-1.85 against A260/280 and an A260/230 ratio of >2) DNA. A vice versa extraction procedure, i.e., SDS buffer followed by CTAB buffer, and also CTAB buffer followed by CTAB, did not yield good-quality DNA. PCR (using different primers) and restriction endonuclease digestion of the DNA extracted from these three plants validated the protocol. The accomplishment of the genome of P. cineraria using the DNA extracted using the modified protocol confirmed its applicability to genomic studies. The optimized protocol successful in extracting high-quality DNA from diverse plant species/tissues extends its applicability and is useful for accomplishing genome sequences of elite germplasm of recalcitrant plant species with quality reads.

Identification of QTLs and allelic effect controlling lignan content in sesame (Sesamum indicum L.) using QTL-seq approach

Sesame (Sesamum indicum L.), an oilseed crop, is gaining worldwide recognition for its healthy functional ingredients as consumption increases. The content of lignans, known for their antioxidant and anti-inflammatory effects, is a key agronomic trait that determines the industrialization of sesame. However, the study of the genetics and physiology of lignans in sesame is challenging, as they are influenced by multiple genes and environmental factors, therefore, the understanding of gene function and synthetic pathways related to lignan in sesame is still limited. To address these knowledge gaps, we conducted genetic analyses using F7 recombinant inbred line (RIL) populations derived from Goenbaek and Gomazou as low and high lignin content variants, respectively. Using the QTL-seq approach, we identified three loci, qLignan1-1, qLignan6-1, and qLignan11-1, that control lignan content, specifically sesamin and sesamolin. The allelic effect between loci was evaluated using the RIL population. qLignan6-1 had an additive effect that increased lignan content when combined with the other two loci, suggesting that it could be an important factor in gene pyramiding for the development of high-lignan varieties. This study not only highlights the value of sesame lignan, but also provides valuable insights for the development of high-lignan varieties through the use of DNA markers in breeding strategies. Overall, this research contributes to our understanding of the importance of sesame oil and facilitates progress in sesame breeding for improved lignan content.

Use of retrotransposon based iPBS markers for determination of genetic relationship among some Chestnut Cultivars (Castanea sativa Mill.) in Türkiye

BACKGROUND

The aim of this study was to reveal the genetic relationships among some economically important chestnut cultivars for Türkiye by using retrotransposon-based inter primer binding site (iPBS) markers.

METHODS AND RESULTS

In this study, a total of 19 iPBS markers were used to determine the genetic relationships among 11 chestnut cultivars (Castanea sativa Mill.). In the study, chestnut cultivars named Hacıömer, Osmanoğlu, Sarıaşlama, Erfelek, Kemer, Işıklar, Şekerci, Siyah Bursa, Tülü, Bouche De Betizac and Marigoule were the preferred cultivars utilised. Using the online marker efficiency calculator (iMEC), some indices of polymorphism, such as the mean heterozygosity, polymorphism information content, marker index and discriminating power, were determined. In addition, the size ranges of alleles, number of average alleles, number of total alleles, number of polymorphic alleles, and polymorphism rate were determined at a successful level. The chestnut cultivars of Hacıömer and Şekerci were determined to be the most similar cultivars with a similarity coefficient value of 0.924, and they formed a subgroup together with the chestnut cultivars Osmanoğlu and Erfelek, showing close similarity with these two cultivars.

CONCLUSIONS

The use of iPBS markers in chestnuts in Türkiye was carried out for the first time in this study. The power of iPBS markers to evaluate the genetic relationship for our preferred chestnut cultivars was revealed. For this reason, it has emerged that it will be useful in the molecular characterization of both genotypes in natural chestnut populations and chestnut breeding materials such as varieties and cultivars in chestnut breeding programs.

A simulation study comparing advanced marker-assisted selection with genomic selection in tree breeding programs

Advances in DNA sequencing technologies allow the sequencing of whole genomes of thousands of individuals and provide several million single nucleotide polymorphisms (SNPs) per individual. These data combined with precise and high-throughput phenotyping enable genome-wide association studies (GWAS) and the identification of SNPs underlying traits with complex genetic architectures. The identified causal SNPs and estimated allelic effects could then be used for advanced marker-assisted selection (MAS) in breeding programs. But could such MAS compete with the broadly used genomic selection (GS)? This question is of particular interest for the lengthy tree breeding strategies. Here, with our new software "SNPscan breeder," we simulated a simple tree breeding program and compared the impact of different selection criteria on genetic gain and inbreeding. Further, we assessed different genetic architectures and different levels of kinship among individuals of the breeding population. Interestingly, apart from progeny testing, GS using gBLUP performed best under almost all simulated scenarios. MAS based on GWAS results outperformed GS only if the allelic effects were estimated in large populations (ca. 10,000 individuals) of unrelated individuals. Notably, GWAS using 3,000 extreme phenotypes performed as good as the use of 10,000 phenotypes. GS increased inbreeding and thus reduced genetic diversity more strongly compared to progeny testing and GWAS-based selection. We discuss the practical implications for tree breeding programs. In conclusion, our analyses further support the potential of GS for forest tree breeding and improvement, although MAS may gain relevance with decreasing sequencing costs in the future.

Available cloned genes and markers for genetic improvement of biotic stress resistance in rice

Biotic stress is one of the major threats to stable rice production. Climate change affects the shifting of pest outbreaks in time and space. Genetic improvement of biotic stress resistance in rice is a cost-effective and environment-friendly way to control diseases and pests compared to other methods such as chemical spraying. Fast deployment of the available and suitable genes/alleles in local elite varieties through marker-assisted selection (MAS) is crucial for stable high-yield rice production. In this review, we focused on consolidating all the available cloned genes/alleles conferring resistance against rice pathogens (virus, bacteria, and fungus) and insect pests, the corresponding donor materials, and the DNA markers linked to the identified genes. To date, 48 genes (independent loci) have been cloned for only major biotic stresses: seven genes for brown planthopper (BPH), 23 for blast, 13 for bacterial blight, and five for viruses. Physical locations of the 48 genes were graphically mapped on the 12 rice chromosomes so that breeders can easily find the locations of the target genes and distances among all the biotic stress resistance genes and any other target trait genes. For efficient use of the cloned genes, we collected all the publically available DNA markers (~500 markers) linked to the identified genes. In case of no available cloned genes yet for the other biotic stresses, we provided brief information such as donor germplasm, quantitative trait loci (QTLs), and the related papers. All the information described in this review can contribute to the fast genetic improvement of biotic stress resistance in rice for stable high-yield rice production.

Genome-wide association study as a powerful tool for dissecting competitive traits in legumes

Legumes are extremely valuable because of their high protein content and several other nutritional components. The major challenge lies in maintaining the quantity and quality of protein and other nutritional compounds in view of climate change conditions. The global need for plant-based proteins has increased the demand for seeds with a high protein content that includes essential amino acids. Genome-wide association studies (GWAS) have evolved as a standard approach in agricultural genetics for examining such intricate characters. Recent development in machine learning methods shows promising applications for dimensionality reduction, which is a major challenge in GWAS. With the advancement in biotechnology, sequencing, and bioinformatics tools, estimation of linkage disequilibrium (LD) based associations between a genome-wide collection of single-nucleotide polymorphisms (SNPs) and desired phenotypic traits has become accessible. The markers from GWAS could be utilized for genomic selection (GS) to predict superior lines by calculating genomic estimated breeding values (GEBVs). For prediction accuracy, an assortment of statistical models could be utilized, such as ridge regression best linear unbiased prediction (rrBLUP), genomic best linear unbiased predictor (gBLUP), Bayesian, and random forest (RF). Both naturally diverse germplasm panels and family-based breeding populations can be used for association mapping based on the nature of the breeding system (inbred or outbred) in the plant species. MAGIC, MCILs, RIAILs, NAM, and ROAM are being used for association mapping in several crops. Several modifications of NAM, such as doubled haploid NAM (DH-NAM), backcross NAM (BC-NAM), and advanced backcross NAM (AB-NAM), have also been used in crops like rice, wheat, maize, barley mustard, etc. for reliable marker-trait associations (MTAs), phenotyping accuracy is equally important as genotyping. Highthroughput genotyping, phenomics, and computational techniques have advanced during the past few years, making it possible to explore such enormous datasets. Each population has unique virtues and flaws at the genomics and phenomics levels, which will be covered in more detail in this review study. The current investigation includes utilizing elite breeding lines as association mapping population, optimizing the choice of GWAS selection, population size, and hurdles in phenotyping, and statistical methods which will analyze competitive traits in legume breeding.

Integrated Genomic Selection for Accelerating Breeding Programs of Climate-Smart Cereals

Rapidly rising population and climate changes are two critical issues that require immediate action to achieve sustainable development goals. The rising population is posing increased demand for food, thereby pushing for an acceleration in agricultural production. Furthermore, increased anthropogenic activities have resulted in environmental pollution such as water pollution and soil degradation as well as alterations in the composition and concentration of environmental gases. These changes are affecting not only biodiversity loss but also affecting the physio-biochemical processes of crop plants, resulting in a stress-induced decline in crop yield. To overcome such problems and ensure the supply of food material, consistent efforts are being made to develop strategies and techniques to increase crop yield and to enhance tolerance toward climate-induced stress. Plant breeding evolved after domestication and initially remained dependent on phenotype-based selection for crop improvement. But it has grown through cytological and biochemical methods, and the newer contemporary methods are based on DNA-marker-based strategies that help in the selection of agronomically useful traits. These are now supported by high-end molecular biology tools like PCR, high-throughput genotyping and phenotyping, data from crop morpho-physiology, statistical tools, bioinformatics, and machine learning. After establishing its worth in animal breeding, genomic selection (GS), an improved variant of marker-assisted selection (MAS), has made its way into crop-breeding programs as a powerful selection tool. To develop novel breeding programs as well as innovative marker-based models for genetic evaluation, GS makes use of molecular genetic markers. GS can amend complex traits like yield as well as shorten the breeding period, making it advantageous over pedigree breeding and marker-assisted selection (MAS). It reduces the time and resources that are required for plant breeding while allowing for an increased genetic gain of complex attributes. It has been taken to new heights by integrating innovative and advanced technologies such as speed breeding, machine learning, and environmental/weather data to further harness the GS potential, an approach known as integrated genomic selection (IGS). This review highlights the IGS strategies, procedures, integrated approaches, and associated emerging issues, with a special emphasis on cereal crops. In this domain, efforts have been taken to highlight the potential of this cutting-edge innovation to develop climate-smart crops that can endure abiotic stresses with the motive of keeping production and quality at par with the global food demand.

Drought stress in rice: morpho-physiological and molecular responses and marker-assisted breeding

Rice (Oryza Sativa L.) is an essential constituent of the global food chain. Drought stress significantly diminished its productivity and threatened global food security. This review concisely discussed how drought stress negatively influenced the rice's optimal growth cycle and altered its morpho-physiological, biochemical, and molecular responses. To withstand adverse drought conditions, plants activate their inherent drought resistance mechanism (escape, avoidance, tolerance, and recovery). Drought acclimation response is characterized by many notable responses, including redox homeostasis, osmotic modifications, balanced water relations, and restored metabolic activity. Drought tolerance is a complicated phenomenon, and conventional breeding strategies have only shown limited success. The application of molecular markers is a pragmatic technique to accelerate the ongoing breeding process, known as marker-assisted breeding. This review study compiled information about quantitative trait loci (QTLs) and genes associated with agronomic yield-related traits (grain size, grain yield, harvest index, etc.) under drought stress. It emphasized the significance of modern breeding techniques and marker-assisted selection (MAS) tools for introgressing the known QTLs/genes into elite rice lines to develop drought-tolerant rice varieties. Hence, this study will provide a solid foundation for understanding the complex phenomenon of drought stress and its utilization in future crop development programs. Though modern genetic markers are expensive, future crop development programs combined with conventional and MAS tools will help the breeders produce high-yielding and drought-tolerant rice varieties.

mtDNA CR Evidence Indicates High Genetic Diversity of Captive Forest Musk Deer in Shaanxi Province, China

Forest musk deer (Moschus berezovskii) are endangered ruminants whose adult males secrete musk. China has been breeding forest musk deer artificially since the 1950s in an effort to restore wild populations, with Shaanxi and Sichuan provinces as the two main sites for captive breeding. Genetic diversity is a significant indicator that determines the long-term viability and status of a population, particularly for species at risk of extinction. In this study, we analyzed the current genetic makeup of seven captive forest musk deer populations in the Shaanxi province, using the mitochondrial DNA (mtDNA) control region (CR) as the molecular marker. We sequenced 604 bp of mtDNA CR, with an average content of A+T higher than G+C. We observed 111 variable sites and 39 different haplotypes from 338 sequences. The nucleotide diversity (Pi) and haplotype diversity (Hd) were 0.02887 and 0.908, respectively. Genetic differentiation between these populations was not significant, and the populations might not have experienced rapid growth. By combining our sequences with previous ones, we identified 65 unique haplotypes with 26 rare haplotypes and estimated a total of 90 haplotypes in Shaanxi province captive populations. The Shaanxi province and Sichuan province obtained 88 haplotypes, the haplotypes from the two populations were mixed together, and the two populations showed moderate genetic differentiation. Our findings suggested that captive forest musk deer populations in the Shaanxi province had high genetic diversity, with a rich founder population of about 90 maternal lines. Additionally, managers could develop genetic management plans for forest musk deer based on the haplotype database. Overall, our study will provide insights and guidelines for the conservation of genetic diversity in captive forest musk deer populations in the Shaanxi province.

DBALM: A novel method for identifying ornamental flowering plants based on DNA barcodes-leaf morphology

Whereas the presence of flowers on ornamental flowering plants is essential for their identification via traditional methods, ornamental flowering plants cannot be reliably identified in non-flowering stages likewise. Here, DBALM (DNA Barcodes-Leaf Morphology), a new approach that combines DNA barcoding data with micromorphological features of the leaf epidermis and that is not limited by the flowering stage, was used to identify 16 evergreen rhododendron cultivars. First, the sequences of DNA barcodes, ITS, matK, psbA-trnH, and rbcL, were obtained from the DNA of leaves. Phylogenetic analysis was conducted to clarify the groupings among all the samples based on the four markers. Then, microscopic features of the leaf epidermis were used to further distinguish individuals from the same clade. DNA barcoding permitted the 16 cultivars to be divided into eight groups. The microscopic features of the leaf epidermis permitted cultivars within the same clade to be distinguished. The matK + psbA-trnH combination was the most effective barcode combination in this study. In addition, the new primer matK-Rh_R was designed, and it increased the amplification rate of evergreen rhododendron cultivars to 100%. In sum, DBALM was capable of accurately identifying the 16 evergreen rhododendron cultivars using data collected from a single leaf in the vegetative growth stage. This method can greatly facilitate the identification and breeding of ornamental flowering plants.

Identification of SNPs Related to Salmonella Resistance in Chickens Using RNA-Seq and Integrated Bioinformatics Approach

Potential single nucleotide polymorphisms (SNPs) were detected between two chicken breeds (Kashmir favorella and broiler) using deep RNA sequencing. This was carried out to comprehend the coding area alterations, which cause variances in the immunological response to Salmonella infection. In the present study, we identified high impact SNPs from both chicken breeds in order to delineate different pathways that mediate disease resistant/susceptibility traits. Samples (liver and spleen) were collected from Salmonella resistant (K. favorella) and susceptible (broiler) chicken breeds. Salmonella resistance and susceptibility were checked by different pathological parameters post infection. To explore possible polymorphisms in genes linked with disease resistance, SNP identification analysis was performed utilizing RNA seq data from nine K. favorella and ten broiler chickens. A total of 1778 (1070 SNPs and 708 INDELs) and 1459 (859 SNPs and 600 INDELs) were found to be specific to K. favorella and broiler, respectively. Based on our results, we conclude that in broiler chickens the enriched pathways mostly included metabolic pathways like fatty acid metabolism, carbon metabolism and amino acid metabolism (Arginine and proline metabolism), while as in K. favorella genes with high impact SNPs were enriched in most of the immune-related pathways like MAPK signaling pathway, Wnt signaling pathway, NOD-like receptor signaling pathway, etc., which could be a possible resistance mechanism against salmonella infection. In K. favorella, protein-protein interaction analysis also shows some important hub nodes, which are important in providing defense against different infectious diseases. Phylogenomic analysis revealed that indigenous poultry breeds (resistant) are clearly separated from commercial breeds (susceptible). These findings will offer fresh perspectives on the genetic diversity in chicken breeds and will aid in the genomic selection of poultry birds.

An Overview of Mapping Quantitative Trait Loci in Peanut (Arachis hypogaea L.)

Quantitative Trait Loci (QTL) mapping has been thoroughly used in peanut genetics and breeding in spite of the narrow genetic diversity and the segmental tetraploid nature of the cultivated species. QTL mapping is helpful for identifying the genomic regions that contribute to traits, for estimating the extent of variation and the genetic action (i.e., additive, dominant, or epistatic) underlying this variation, and for pinpointing genetic correlations between traits. The aim of this paper is to review the recently published studies on QTL mapping with a particular emphasis on mapping populations used as well as traits related to kernel quality. We found that several populations have been used for QTL mapping including interspecific populations developed from crosses between synthetic tetraploids and elite varieties. Those populations allowed the broadening of the genetic base of cultivated peanut and helped with the mapping of QTL and identifying beneficial wild alleles for economically important traits. Furthermore, only a few studies reported QTL related to kernel quality. The main quality traits for which QTL have been mapped include oil and protein content as well as fatty acid compositions. QTL for other agronomic traits have also been reported. Among the 1261 QTL reported in this review, and extracted from the most relevant studies on QTL mapping in peanut, 413 (~33%) were related to kernel quality showing the importance of quality in peanut genetics and breeding. Exploiting the QTL information could accelerate breeding to develop highly nutritious superior cultivars in the face of climate change.

Genetic resources and breeding of maize for Striga resistance: a review

The potential yield of maize (Zea mays L.) and other major crops is curtailed by several biotic, abiotic, and socio-economic constraints. Parasitic weeds, Striga spp., are major constraints to cereal and legume crop production in sub-Saharan Africa (SSA). Yield losses reaching 100% are reported in maize under severe Striga infestation. Breeding for Striga resistance has been shown to be the most economical, feasible, and sustainable approach for resource-poor farmers and for being environmentally friendly. Knowledge of the genetic and genomic resources and components of Striga resistance is vital to guide genetic analysis and precision breeding of maize varieties with desirable product profiles under Striga infestation. This review aims to present the genetic and genomic resources, research progress, and opportunities in the genetic analysis of Striga resistance and yield components in maize for breeding. The paper outlines the vital genetic resources of maize for Striga resistance, including landraces, wild relatives, mutants, and synthetic varieties, followed by breeding technologies and genomic resources. Integrating conventional breeding, mutation breeding, and genomic-assisted breeding [i.e., marker-assisted selection, quantitative trait loci (QTL) analysis, next-generation sequencing, and genome editing] will enhance genetic gains in Striga resistance breeding programs. This review may guide new variety designs for Striga-resistance and desirable product profiles in maize.

Genetic Diversity and Population Structure of Sorghum (Sorghum bicolor (L.) Moench) Landraces Using DArTseq-Derived Single-Nucleotide Polymorphism (SNP) Markers

Genetic integrity of an accession should be preserved in the conservation of germplasm. Characterization of diverse germplasm based on a molecular basis enhances its conservation and use in breeding programs. The aim of this study was to assess the genetic diversity of 169 sorghum accessions using a total of 6977 SNP markers. The polymorphic information content of the markers was 0.31 which is considered to be moderately high. Structure analysis using ADMIXTURE program revealed a total of 10 subpopulations. Neighbor-joining tree revealed the presence of six main clusters among these subpopulations whereas in principal component analysis, seven clusters were identified. Cluster analysis grouped most populations depending on source of collection although other accessions originating from the same source were grouped under different clusters. Analysis of molecular variance (AMOVA) revealed 30% and 70% of the variation occurred within and among accessions, respectively. Gene flow within the populations was, however, limited indicating high differentiation within the subpopulation. Observed heterozygosity among accessions varied from 0.03 to 0.06 with a mean of 0.05 since sorghum is a self-pollinating crop. High genetic diversity among the subpopulations can be further explored for superior genes to develop new sorghum varieties.

Development of Molecular Marker Linked to Seed Hardness in Pomegranate Using Bulked Segregant Analysis

The pomegranate (Punica granatum L.) is one of the fruit species with the oldest cultural history. There are many traits to determine the quality of pomegranate fruits. Among them, soft-seeded feature of pomegranate fruit is important trait for the market value of the fruit. For this reason, the demand for pomegranate varieties with soft seeds has been increasing, especially in recent years. In this study, molecular markers associated with seed hardness were developed to distinguish pomegranate cultivars with soft-seeded feature based on genomic DNA at the early stages of the pomegranate breeding process. For this purpose, pomegranate genotypes and/or cultivars from the population involved in reciprocal crosses of hard-seeded Ernar, medium-hard-seeded Hicaznar, and soft-seeded Fellahyemez cultivars were grouped as soft-seeded or hard-seeded. Further, leaf samples were collected from individuals belonging to each group. Then, the genomic DNA was isolated from each plant separately, and equal amount of genomic DNA from individuals with the similar seed hardness were mixed for bulked segregant analysis (BSA). The bulked genomic DNAs of opposite characters were analyzed by polymerase chain reaction (PCR) using random decamer primers to develop random amplified polymorphic DNA (RAPD) markers associated with soft-seeded or hard-seeded pomegranates. A total of three RAPD markers were determined to distinguish the individuals having soft- or hard-seeded pomegranate genotypes and/or cultivars. As a result of the comparison of the DNA sequences of these RAPD markers, insertion-deletions (inDels) primers were designed to developed and validate a PCR assay to distinguish the soft- and hard-seeded pomegranate genotypes/cultivars from each other. The molecular markers developed in this study will enable us to distinguish soft-seeded pomegranate types easily in a short time at the early stages of the pomegranate breeding programs.

Vitis vinifera genotyping toolbox to highlight diversity and germplasm identification

The contribution of vine cultivation to human welfare as well as the stimulation of basic social and cultural features of civilization has been great. The wide temporal and regional distribution created a wide array of genetic variants that have been used as propagating material to promote cultivation. Information on the origin and relationships among cultivars is of great interest from a phylogenetics and biotechnology perspective. Fingerprinting and exploration of the complicated genetic background of varieties may contribute to future breeding programs. In this review, we present the most frequently used molecular markers, which have been used on Vitis germplasm. We discuss the scientific progress that led to the new strategies being implemented utilizing state-of-the-art next generation sequencing technologies. Additionally, we attempted to delimit the discussion on the algorithms used in phylogenetic analyses and differentiation of grape varieties. Lastly, the contribution of epigenetics is highlighted to tackle future roadmaps for breeding and exploitation of Vitis germplasm. The latter will remain in the top of the edge for future breeding and cultivation and the molecular tools presented herein, will serve as a reference point in the challenging years to come.

Creation of New Oregano Genotypes with Different Terpene Chemotypes via Inter- and Intraspecific Hybridization

Oregano is a medicinal and aromatic plant of value in the pharmaceutical, food, feed additive, and cosmetic industries. Oregano breeding is still in its infancy compared with traditional crops. In this study, we evaluated the phenotypes of 12 oregano genotypes and generated F₁ progenies by hybridization. The density of leaf glandular secretory trichomes and the essential oil yield in the 12 oregano genotypes varied from 97-1017 per cm² and 0.17-1.67%, respectively. These genotypes were divided into four terpene chemotypes: carvacrol-, thymol-, germacrene D/β-caryophyllene-, and linalool/β-ocimene-type. Based on phenotypic data and considering terpene chemotypes as the main breeding goal, six oregano hybrid combinations were performed. Simple sequence repeat (SSR) markers were developed based on unpublished whole-genome sequencing data of Origanum vulgare, and 64 codominant SSR primers were screened on the parents of the six oregano combinations. These codominant primers were used to determine the authenticity of 40 F₁ lines, and 37 true hybrids were identified. These 37 F₁ lines were divided into six terpene chemotypes: sabinene-, β-ocimene-, γ-terpinene-, thymol-, carvacrol-, and p-cymene-type, four of which (sabinene-, β-ocimene-, γ-terpinene-, and p-cymene-type) were novel (i.e., different from the chemotypes of parents). The terpene contents of 18 of the 37 F₁ lines were higher than those of their parents. The above results lay a strong foundation for the creating of new germplasm resources, constructing of genetic linkage map, and mapping quantitative trait loci (QTLs) of key horticultural traits, and provide insights into the mechanism of terpenoid biosynthesis in oregano.

Breeding and Genomic Approaches towards Development of Fusarium Wilt Resistance in Chickpea

Chickpea is an important leguminous crop with potential to provide dietary proteins to both humans and animals. It also ameliorates soil nitrogen through biological nitrogen fixation. The crop is affected by an array of biotic and abiotic factors. Among different biotic stresses, a major fungal disease called Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceris (FOC), is responsible for low productivity in chickpea. To date, eight pathogenic races of FOC (race 0, 1A, and 1B/C, 2-6) have been reported worldwide. The development of resistant cultivars using different conventional breeding methods is very time consuming and depends upon the environment. Modern technologies can improve conventional methods to solve these major constraints. Understanding the molecular response of chickpea to Fusarium wilt can help to provide effective management strategies. The identification of molecular markers closely linked to genes/QTLs has provided great potential for chickpea improvement programs. Moreover, omics approaches, including transcriptomics, metabolomics, and proteomics give scientists a vast viewpoint of functional genomics. In this review, we will discuss the integration of all available strategies and provide comprehensive knowledge about chickpea plant defense against Fusarium wilt.

Exploring the genetic diversity and population structure of upland cotton germplasm by iPBS-retrotransposons markers

BACKGROUND

Upland cotton is one of the utmost significant strategic fiber crops, and play a vital role in the global textile industry.

METHODS AND RESULTS

A total of 128 genotypes comprised Gossypium hirsutum L, Gossypium barbadense L., and pure lines were used to examine genetic diversity using iPBS-retrotransposon markers system. Eleven highly polymorphic primers yielded 287 bands and 99.65% polymorphism was recorded. The mean polymorphism information content was estimated at 0.297 and the average diversity indices for the effective number of alleles, Shannon's information index, and overall gene diversity were 1.481, 0.443, and 0.265, respectively. The analysis of molecular variance (AMOVA) revealed that 69% of the genetic variation was within the population. A model-based STRUCTURE algorithm divided the entire germplasm into four populations and one un-classified population, the genotypes G42 (originating in Egypt) and G128 (originating in the United States), showed the highest genetic distance (0.996) so these genotypes could be suggested for breeding programs as parental lines.

CONCLUSIONS

This is the first investigation using an iPBS-retrotransposon marker system to examine the genetic diversity and population structure of upland cotton germplasm. The rich diversity found in upland cotton germplasm could be exploited as a genetic resource when developing breeding programs and could also help with efforts to breed cotton around the world. These findings also show the applicability and effectiveness of iPBS-retrotransposons for the molecular characterization of cotton germplasm.

Genome survey sequencing-based SSR marker development and their validation in Dendrocalamus longispathus

Bamboo is an important genetic resource in India, supporting rural livelihood and industries. Unfortunately, most Indian bamboo taxa are devoid of basic genomic or marker information required to comprehend the genetic processes for further conservation and management. In this study, we perform genome survey sequencing for development of de novo genomic SSRs in Dendrocalamus longispathus, a socioeconomically important bamboo species of northeast India. Using Illumina platform, 69.49 million raw reads were generated and assembled into 1,145,321 contig with GC content 43% and N50 1228 bp. In total, 46,984 microsatellite repeats were mined-out wherein di-nucleotide repeats were most abundant (54.71%) followed by mono- (31.91%) and tri-repeats (9.85%). Overall, AT-rich repeats were predominant in the genome, but GC-rich motifs were more frequent in tri-repeats. Afterwards, 21,596 SSR loci were successfully tagged with the primer pairs, and a subset of 50 were validated through polymerase chain reaction amplification. Of these, 36 SSR loci were successfully amplified, and 16 demonstrated polymorphism. Using 13 polymorphic SSRs, a moderate level of gene diversity (He = 0.480; Ar = 3.52) was recorded in the analysed populations of D. longispathus. Despite the high gene flow (Nm = 4.928) and low genetic differentiation (F_ST = 0.119), severe inbreeding (F_IS = 0.407) was detected. Further, genetic clustering and STRUCTURE analysis revealed that the entire genetic variability is captured under two major gene pools. Conclusively, we present a comprehensive set of novel SSR markers in D. longispathus as well as other taxa of tropical woody bamboos.

Investigating the geographical, phenotypic and genetic diversity of Sickleweed populations by bioclimatic parameters, morphological traits and SCoT molecular markers

Sickleweed (Falcaria vulgaris) is important due to its nutritional value and medicinal effects on the human body. The 15 different Sickleweed populations were collected based on an unbalanced nest design with 10 replications and nine morphological traits were measured on them. The diversity was investigated with 15 primers of SCoT marker. The genetic diversity was investigated by ANOVA, cluster analysis and Bayesian statistical model based on morphological traits, bioclimatic and SCoT. Grouping the study areas based on bioclimatic parameters by UPGMA method showed that these areas were divided into two groups and were similar in terms of climatic similarities and bioclimatic information. The results of analysis of variance showed that there was a significant difference between populations at the level of one percent for the studied traits. The cluster analysis based traits by the UPGMA method divided these populations into two groups. The phenotypic diversity of these populations was largely consistent with the geographical diversity. The primers used for SCoT marker produced 137 polymorphic bands on the populations, The UPGMA cluster analysis with molecular data placed the studied populations into three groups and four subgroups. Grouping based on the Bayesian method placed the populations into nine groups, although the populations were not differentiated and were a mixture of all nine groups. High genetic diversity for the studied Sickleweed populations have showed valuable insights into the evolution of this plant and provides basic data for designing appropriate management practices for breeding Sickleweed populations.

Forward genetic studies reveal LsAPRR2 as a key gene in regulating the green color of pericarp in bottle gourd (Lagenaria siceraria)

The fruit peel color is an important factor that affects its quality. However, genes involved in regulating pericarp color in bottle gourd (Lagenaria siceraria) have not been explored to date. Genetic analysis of color traits in bottle gourd peel through a genetic population of six generations demonstrated that the green color of peels is inherited as a single gene dominant trait. Combined phenotype-genotype analysis of recombinant plants using BSA-seq mapped the candidate gene to a 22.645 Kb interval at the head end of chromosome 1. We observed that the final interval contained only one gene, LsAPRR2 (HG_GLEAN_10010973). Sequence and spatiotemporal expression analyses of LsAPRR2 unraveled two nonsynonymous mutations (A→G) and (G→C) in the parental CDS sequences. Further, LsAPRR2 expression was higher in all green-skinned bottle gourds (H16) at various stages of fruit development than in white-skinned bottle gourds (H06). Cloning and sequence comparison of the two parental LsAPRR2 promoter regions indicated 11 bases insertion and 8 SNPs mutations in the region -991~-1033, upstream of the start codon in white bottle gourd. Proof of GUS reporting system, Genetic variation in this fragment significantly reduced the expression of LsAPRR2 in the pericarp of white bottle gourd. In addition, we developed a tightly linked (accuracy 93.88%) InDel marker for the promoter variant segment. Overall, the current study provides a theoretical basis for comprehensive elucidation of the regulatory mechanisms underlying the determination of bottle gourd pericarp color. This would further help in the directed molecular design breeding of bottle gourd pericarp.

Whole Genome Wide SSR Markers Identification Based on ddRADseq Data

The advent of advanced NGS technologies have led to the generation of enormous amount of sequence data which further aid in the discovery of the various type of markers such as SSRs, SNPs, InDels, etc. Among all these markers, microsatellite SSR markers can be mined from the ddRADseq data as certain properties of SSR markers make them ideal markers for study. These assist researchers and breeders in diversity analysis and producing new varieties with desired traits. To extract the markers, first, the ddRADseq data is assembled into consensus sequences using STACKS program which are further assembled for mining microsatellites using QDD along with MISA tool.

Response Surface Methodology for Optimization of Multiplex-PCR Protocols for Detection of TYLCV, TSWV and Fol Molecular Markers: Analytical Performance Evaluation

Molecular markers linked to disease resistance genes which affect economically important crops are of great interest. In the case of tomato, a major focus on resistance breeding to multiple fungal and viral pathogens such as Tomato yellow leaf curl virus (TYLCV), Tomato spotted wilt virus (TSWV) and Fusarium oxysporum f. sp. lycopersici (Fol), have led to the introgression of several resistance genes; therefore, molecular markers have become important in molecular-assisted selection (MAS) of tomato varieties resistant to those pathogens. However, assays that allow simultaneous evaluation of resistant genotypes, such as multiplex PCR, need to be optimized and evaluated to demonstrate their analytical performance, as many factors can affect them. This work aimed to generate multiplex PCR protocols for the joint detection of the molecular markers associated with pathogen resistance genes in tomato plants that are sensitive, specific and repeatable. For the optimization a central composite design of a response surface methodology (RSM-CCD) was used. For analytical performance evaluation, specificity/selectivity and sensibility (limit of detection and dynamic range) were analyzed. Two protocols were optimized: the first one with a desirability of 1.00, contained two markers (At-2 and P7-43) linked to I- and I-3-resistant genes. The second one with a desirability of 0.99, contained markers (SSR-67, SW5 and P6-25) linked to I-, Sw-5-, and Ty-3-resistant genes. For protocol 1, all the commercial hybrids (7/7) were resistant to Fol, and for protocol 2, two hybrids were resistant to Fol, one to TSWV and one to TYLCV with good analytical performance. In both protocols, the varieties considered susceptible to the pathogens, no-amplicon or susceptible amplicons, were observed. The optimized multiplex PCR protocols showed dynamic ranges from 5.97 up to 161.3 ng DNA. The limit of detection was 17.92 ng and 53.76 ng DNA for protocols 1 and 2, respectively, giving 100% positive results in the test replicates. This method allowed to develop optimized multiplex PCR protocols with few assays which translates into less time and resources, without sacrificing method performance.

Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta

Tropical rainforests in Southeast Asia are enriched by multifarious biota dominated by Dipterocarpaceae. In this family, Shorea robusta is an ecologically sensitive and economically important timber species whose genomic diversity and phylogeny remain understudied due to lack of datasets on genetic resources. Smattering availability of molecular markers impedes population genetic studies indicating a necessity to develop genomic databases and species-specific markers in S. robusta. Accordingly, the present study focused on fostering de novo low-depth genome sequencing, identification of reliable microsatellites markers, and their validation in various populations of S. robusta in Uttarakhand Himalayas. With 69.88 million raw reads assembled into 1,97,489 contigs (read mapped to 93.2%) and a genome size of 357.11 Mb (29 × coverage), Illumina paired-end sequencing technology arranged a library of sequence data of ~ 10 gigabases (Gb). From 57,702 microsatellite repeats, a total of 35,049 simple sequence repeat (SSR) primer pairs were developed. Afterward, among randomly selected 60 primer pairs, 50 showed successful amplification and 24 were found as polymorphic. Out of which, nine polymorphic loci were further used for genetic analysis in 16 genotypes each from three different geographical locations of Uttarakhand (India). Prominently, the average number of alleles per locus (Na), observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) were recorded as 2.44, 0.324, 0.277 and 0.252, respectively. The accessibility of sequence information and novel SSR markers potentially enriches the current knowledge of the genomic background for S. robusta and to be utilized in various genetic studies in species under tribe Shoreae.

Breeding techniques to dispense higher genetic gains

Plant breeding techniques encompass all the processes aimed at improving the genetic characteristics of a crop. It helps in achieving desirable characteristics like resistance to diseases and pests, tolerance to environmental stresses, higher yield and improved quality of the crop. This review article aims to describe and evaluate the current plant breeding techniques and novel methods. This qualitative review employs a comparative approach in exploring the different plant breeding techniques. Conventional plant breeding techniques were compared with modern ones to understand the advancements in plant biotechnology. Backcross breeding, mass selection, and pure-line selection were all discussed in conventional plant breeding for self-pollination and recurrent selection and hybridisation were employed for cross-pollinated crops. Modern techniques comprise of CRISPR Cas-9, high-throughput phenotyping, marker-assisted selection and genomic selection. Further, novel techniques were reviewed to gain more insight. An in-depth analysis of conventional and modern plant breeding has helped gain insight on the advantages and disadvantages of the two. Modern breeding techniques have an upper hand as they are more reliable and less time consuming. It is also more accurate as it is a genotype-based method. However, conventional breeding techniques are cost effective and require less expertise. Modern plant breeding has an upper hand as it uses genomics techniques. Techniques like QTL mapping, marker assisted breeding aid in selection of superior plants right at the seedling stage, which is impossible with conventional breeding. Unlike the conventional method, modern methods are capable of selecting recessive alleles by using different markers. Modern plant breeding is a science and therefore more reliable and accurate.

Advances in genomics for diversity studies and trait improvement in temperate fruit and nut crops under changing climatic scenarios

Genetic improvement of temperate fruit and nut crops through conventional breeding methods is not sufficient alone due to its extreme time-consuming, cost-intensive, and hard-to-handle approach. Again, few other constraints that are associated with these species, viz., their long juvenile period, high heterozygosity, sterility, presence of sexual incompatibility, polyploidy, etc., make their selection and improvement process more complicated. Therefore, to promote precise and accurate selection of plants based on their genotypes, supplement of advanced biotechnological tools, viz., molecular marker approaches along with traditional breeding methods, is highly required in these species. Different markers, especially the molecular ones, enable direct selection of genomic regions governing the trait of interest such as high quality, yield, and resistance to abiotic and biotic stresses instead of the trait itself, thus saving the overall time and space and helping screen fruit quality and other related desired traits at early stages. The availability of molecular markers like SNP (single-nucleotide polymorphism), DArT (Diversity Arrays Technology) markers, and dense molecular genetic maps in crop plants, including fruit and nut crops, led to a revelation of facts from genetic markers, thus assisting in precise line selection. This review highlighted several aspects of the molecular marker approach that opens up tremendous possibilities to reveal valuable information about genetic diversity and phylogeny to boost the efficacy of selection in temperate fruit crops through genome sequencing and thus cultivar improvement with respect to adaptability and biotic and abiotic stress resistance in temperate fruit and nut species.

Digitalizing breeding in plants: A new trend of next-generation breeding based on genomic prediction

As the world's population grows and food needs diversification, the demand for cereals and horticultural crops with beneficial traits increases. In order to meet a variety of demands, suitable cultivars and innovative breeding methods need to be developed. Breeding methods have changed over time following the advance of genetics. With the advent of new sequencing technology in the early 21st century, predictive breeding, such as genomic selection (GS), emerged when large-scale genomic information became available. GS shows good predictive ability for the selection of individuals with traits of interest even for quantitative traits by using various types of the whole genome-scanning markers, breaking away from the limitations of marker-assisted selection (MAS). In the current review, we briefly describe the history of breeding techniques, each breeding method, various statistical models applied to GS and methods to increase the GS efficiency. Consequently, we intend to propose and define the term digital breeding through this review article. Digital breeding is to develop a predictive breeding methods such as GS at a higher level, aiming to minimize human intervention by automatically proceeding breeding design, propagating breeding populations, and to make selections in consideration of various environments, climates, and topography during the breeding process. We also classified the phases of digital breeding based on the technologies and methods applied to each phase. This review paper will provide an understanding and a direction for the final evolution of plant breeding in the future.

Wheat end-use quality: State of art, genetics, genomics-assisted improvement, future challenges, and opportunities

Wheat is the most important source of food, feed, and nutrition for humans and livestock around the world. The expanding population has increasing demands for various wheat products with different quality attributes requiring the development of wheat cultivars that fulfills specific demands of end-users including millers and bakers in the international market. Therefore, wheat breeding programs continually strive to meet these quality standards by screening their improved breeding lines every year. However, the direct measurement of various end-use quality traits such as milling and baking qualities requires a large quantity of grain, traits-specific expensive instruments, time, and an expert workforce which limits the screening process. With the advancement of sequencing technologies, the study of the entire plant genome is possible, and genetic mapping techniques such as quantitative trait locus mapping and genome-wide association studies have enabled researchers to identify loci/genes associated with various end-use quality traits in wheat. Modern breeding techniques such as marker-assisted selection and genomic selection allow the utilization of these genomic resources for the prediction of quality attributes with high accuracy and efficiency which speeds up crop improvement and cultivar development endeavors. In addition, the candidate gene approach through functional as well as comparative genomics has facilitated the translation of the genomic information from several crop species including wild relatives to wheat. This review discusses the various end-use quality traits of wheat, their genetic control mechanisms, the use of genetics and genomics approaches for their improvement, and future challenges and opportunities for wheat breeding.

Distinctive origin and evolution of endemic thistle of Korean volcanic island: Structural organization and phylogenetic relationships with complete chloroplast genome

Unlike other Cirsium in Korea, Cirsium nipponicum (Island thistle) is distributed only on Ulleung Island, a volcanic island off the east coast of the Korean Peninsula, and a unique thistle with none or very small thorns. Although many researchers have questioned the origin and evolution of C. nipponicum, there is not much genomic information to estimate it. We thus assembled the complete chloroplast of C. nipponicum and reconstructed the phylogenetic relationships within the genus Cirsium. The chloroplast genome was 152,586 bp, encoding 133 genes consisting of 8 rRNA genes, 37 tRNA genes, and 88 protein-coding genes. We found 833 polymorphic sites and eight highly variable regions in chloroplast genomes of six Cirsium species by calculating nucleotide diversity, as well as 18 specific variable regions distinguished C. nipponicum from other Cirsium. As a result of phylogenetic analysis, C. nipponicum was closer to C. arvense and C. vulgare than native Cirsium in Korea: C. rhinoceros and C. japonicum. These results indicate that C. nipponicum is likely introduced through the north Eurasian root, not the mainland, and evolved independently in Ulleung Island. This study contributes to further understanding the evolutionary process and the biodiversity conservation of C. nipponicum on Ulleung Island.

Detection and distribution of two dominant alleles associated with the sweet kernel phenotype in almond cultivated germplasm

Almond [Prunus dulcis Miller (D. A. Webb), syn. Prunus amygdalus L.)] is the major tree nut crop worldwide in terms of production and cultivated area. Almond domestication was enabled by the selection of individuals bearing sweet kernels, which do not accumulate high levels of the toxic cyanogenic glucoside amygdalin. Previously, we showed that the Sweet kernel (Sk) gene, controlling the kernel taste in almond, encodes a basic helix loop helix (bHLH) transcription factor regulating the amygdalin biosynthetic pathway. In addition, we characterized a dominant allele of this gene, further referred to as Sk-1, which originates from a C¹⁰³⁶→T missense mutation and confers the sweet kernel phenotype. Here we provide evidence indicating that the allele further referred to as Sk-2, originally detected in the cultivar "Atocha" and arising from a T⁹⁸⁹→G missense mutation, is also dominantly inherited and confers the sweet kernel phenotype in almond cultivated germplasm. The use of single nucleotide polymorphism (SNP) data from genotyping by sequencing (GBS) for population structure and hierarchical clustering analyses indicated that Sk-2 occurs in a group of related genotypes, including the widespread cultivar "Texas", descending from the same ancestral population. KASP and dual label functional markers were developed for the accurate and high-throughput selection of the Sk-1 and Sk-2 alleles, and the genotyping of a panel of 134 almond cultivars. Overall, our results provide further insights on the understanding of the almond cultivation history. In addition, molecular marker assays and genotypic data presented in this study are expected to be of major interest for the conduction of almond breeding programs, which often need to select sweet kernel individuals in segregant populations.

The impact of environmental and climatic variables on genetic diversity and plant functional traits of the endangered tuberous orchid (Orchis mascula L.)

Understanding how environmental factors shape patterns of genetic and phenotypic variations in a species is necessary for conservation and plant breeding. However, these factors have not yet been completely understood in tuberous orchid species used to make 'Salep', an important ingredient in traditional medicine and beverages in middle eastern countries and India. In many areas, increasing demand has pushed species to the brink of extinction. In this study, 198 genotypes from 18 populations of the endangered species Orchis mascula L. spanning a large-scale climatic gradient in northern Iran were used to investigate patterns of genetic diversity and plant functional traits. Populations were sampled from three land cover types (woodland, shrubland, and pastureland/grassland). Plant height, stem length, number of flowers, bulb fresh and dry weight, glucomannan, and starch concentrations showed high variation among populations and were significantly related to land cover type. In general, genetic diversity was high, particularly in those from eastern Hyrcanian; additionally, populations showed a high level of genetic differentiation (G'_st = 0.35) with low gene flow (Nm = 0.46). The majority of genetic differentiation occurred within populations (49%) and land cover types (20%). The population structural analysis using the AFLP marker data in K = 4 showed a high geographical affinity for 198 O. mascula genotypes, with some genotypes having mixed ancestry. Temperature and precipitation were found to shape genetic and phenotypic variation profoundly. Significant isolation by the environment was observed, confirming the strong effect of environmental variables on phenotypic and genetic variation. Marker-trait association studies based on MLM1 and MLM2 models revealed significant associations of P-TGG + M-CTT-33 and E-AGG + M-CGT-22 markers with plant height and glucomannan content. Overall, a combination of large-scale climatic variables and land cover types significantly shaped genetic diversity and functional trait variation in O. mascula populations.

Miracle Tree Moringa oleifera: Status of the Genetic Diversity, Breeding, In Vitro Propagation, and a Cogent Source of Commercial Functional Food and Non-Food Products

Moringa oleifera Lam. (MO) is a fast-growing drought-resistant tree belonging to the family Moringaceae and native to the Indian subcontinent and cultivated and/or naturalized worldwide with a semi-arid climate. MO is also popularly known as a miracle tree for its repertoire of nutraceutical, pharmacological, and phytochemical properties. The MO germplasm is collected, conserved, and maintained by various institutions across the globe. Various morphological, biochemical, and molecular markers are used for determining the genetic diversity in MO accessions. A higher yield of leaves and pods is often desirable for making various products with commercial viability and amenable for trade in the international market. Therefore, breeding elite varieties adapted to local agroclimatic conditions and in vitro propagation are viable and sustainable approaches. Here, we provide a comprehensive overview of MO germplasm conservation and various markers that are employed for assessing the genetic diversity among them. Further, breeding and in vitro propagation of MO for various desirable agronomic traits are discussed. Finally, trade and commerce of various functional and biofortified foods and non-food products are enumerated albeit with a need for a rigorous and stringent toxicity evaluation.

RNA Editing in Chloroplast: Advancements and Opportunities

Many eukaryotic and prokaryotic organisms employ RNA editing (insertion, deletion, or conversion) as a post-transcriptional modification mechanism. RNA editing events are common in these organelles of plants and have gained particular attention due to their role in the development and growth of plants, as well as their ability to cope with abiotic stress. Owing to rapid developments in sequencing technologies and data analysis methods, such editing sites are being accurately predicted, and many factors that influence RNA editing are being discovered. The mechanism and role of the pentatricopeptide repeat protein family of proteins in RNA editing are being uncovered with the growing realization of accessory proteins that might help these proteins. This review will discuss the role and type of RNA editing events in plants with an emphasis on chloroplast RNA editing, involved factors, gaps in knowledge, and future outlooks.

A divide-and-conquer approach for genomic prediction in rubber tree using machine learning

Rubber tree (Hevea brasiliensis) is the main feedstock for commercial rubber; however, its long vegetative cycle has hindered the development of more productive varieties via breeding programs. With the availability of H. brasiliensis genomic data, several linkage maps with associated quantitative trait loci have been constructed and suggested as a tool for marker-assisted selection. Nonetheless, novel genomic strategies are still needed, and genomic selection (GS) may facilitate rubber tree breeding programs aimed at reducing the required cycles for performance assessment. Even though such a methodology has already been shown to be a promising tool for rubber tree breeding, increased model predictive capabilities and practical application are still needed. Here, we developed a novel machine learning-based approach for predicting rubber tree stem circumference based on molecular markers. Through a divide-and-conquer strategy, we propose a neural network prediction system with two stages: (1) subpopulation prediction and (2) phenotype estimation. This approach yielded higher accuracies than traditional statistical models in a single-environment scenario. By delivering large accuracy improvements, our methodology represents a powerful tool for use in Hevea GS strategies. Therefore, the incorporation of machine learning techniques into rubber tree GS represents an opportunity to build more robust models and optimize Hevea breeding programs.