Breeding Efforts Research Articles

Integrated analysis of the gonadal methylome and transcriptome provides new insights into the expression regulation of sex determination and differentiation genes in spotted scat (Scatophagus argus)

The spotted scat (Scatophagus argus) is an economically important mariculture fish. There have been no studies of gonadal DNA methylation at the genomic level in S. argus. Here, the gonadal methylome profiles of male and female S. argus were constructed and a link between DNA methylation and transcriptional regulation was identified. The gonads at stage IV of three male and female S. argus individuals were subjected to whole-genome bisulfite sequencing (WGBS), generating an average of 17.76 Gb of clean data for each sample. Analysis of methylation levels in different genomic regions revealed that both male and female S. argus gonads exhibited low methylation levels in the promoters and first exons, but high levels in the inner exons and introns. In general, DNA methylation levels were higher in the testes than in the ovaries. A total of 234,482 differentially methylated regions (DMRs) were identified between testes and ovaries, including 234,245, 26 and 211 DMRs in the CpG, CHG, and CHH backgrounds, respectively. Combined methylation and transcriptome analysis revealed that the relationship between methylation patterns and gene expression was generally negatively correlated. The male-specific Dmrt1Y, which is the candidate sex-determining gene of S. argus, was lowly modified by DNA methylation at its promoter region in the testis. While its allele on the X chromosome, Dmrt1ΔX, was highly modified by DNA methylation in both the testis and ovary. The expression levels of some other genes involved in sex differentiation and sex steroid synthesis were also regulated by DNA methylation. This study sheds light on the divergent methylation patterns in the gonadal genomes of male and female S. argus. These findings laid the foundation for subsequent analysis of differentially expressed sex determination and differentiation genes between male and female S. argus, providing a crucial theoretical basis for sex-control breeding efforts in S. argus.

An SNP based genotyping assay for genes associated with drought tolerance in bread wheat.

SnRK2 plays vital role in responding to adverse abiotic stimuli. The applicability of TaSnRK2.4 and TaSnRK2.9 was investigated to leverage the potential of these genes in indigenous wheat breeding programs. Genetic diversity was assessed using pre-existing markers for TaSnRK2.4 and TaSnRK2.9. Furthermore, new markers were also developed to enhance their broader applicability. KASP markers were designed for TaSnRK2.4, while CAPS-based markers were tailored for TaSnRK2.9. Analysis revealed lack of polymorphism in TaSnRK2.4 among Pakistani wheat germplasm under study. To validate this finding, available gel-based markers for TaSnRK2.4 were employed, producing consistent results and offering limited potential for application in marker-assisted wheat breeding with Pakistani wheat material. For TaSnRK2.9-5A, CAPS2.9-5A-1 and CAPS2.9-5A-2 markers were designed to target SNP positions at 308 nt and 1700 nt revealing four distinct haplotypes. Association analysis highlighted the significance of Hap-5A-1 of TaSnRK2.9-5A, which exhibited association with an increased number of productive tillers (NPT), grains per spike (GPS), and reduced plant height (PH) under well-watered (WW) conditions. Moreover, it showed positive influence on NPT under WW conditions, GPS under water-limited (WL) conditions, and PH under both WW and WL conditions. High selection intensity observed for Hap-5A-1 underscores the valuable role it has played in Pakistani wheat breeding programs. Gene expression studies of TaSnRK2.9-5A revealed the involvement of this gene in response to PEG, NaCl, low temperature and ABA treatments. These findings propose that TaSnRK2.9 can be effectively employed for improving wheat through marker-assisted selection in wheat breeding efforts.

Advances in Okra (Abelmoschus esculentus L.) Breeding: Integrating Genomics for Enhanced Crop Improvement

Okra (Abelmoschus esculentus L.) holds significant importance as a vegetable crop, thriving in tropical and subtropical regions globally, especially in the warmer areas of temperate zones. Traditional breeding approaches tailored for self-pollinated crops have been utilized to enhance the genetic diversity of okra. These methods encompass various techniques such as plant introduction, pure line selection, hybridization combined with selection, mutation breeding, and heterosis breeding. Particularly in countries like India, pedigree selection and heterosis breeding have led to the development of numerous okra varieties and hybrids, significantly impacting local agricultural practices. Contemporary okra breeding focuses on traits crucial for optimal performance, including high yield potential, resistance to prevalent diseases like Yellow Vein Mosaic Virus (YVMV) and Okra Enation Leaf Curl Virus (OELCV), tolerance to sucking pests and borers, ease of harvest, deep green fruit coloration, and desirable plant architecture. Public sector institutions have played a pivotal role in introducing and disseminating improved okra varieties and hybrids, with more than 33 cultivars introduced in recent decades. Some of these varieties have demonstrated substantial improvements in okra production across India. This review offers an overview of the current state of okra breeding, encompassing genetic resources, cytogenetic relationships, breeding goals, varietal development processes, efforts in resistance breeding, biotechnological interventions, and future improvement strategies. By consolidating existing knowledge and highlighting ongoing research initiatives, this article aims to provide guidance and inspiration for further advancements in okra breeding and genomics, ultimately contributing to the sustainability and productivity of this essential vegetable crop.

Gonadal transcriptome sequencing reveals sexual dimorphism in expression profiling of sex-related genes in Asian arowana (Scleropages formosus).

Asia arowana (Scleropages formosus) is an ornamental fish with high economic value, while its sex determination mechanism is still poorly understood. By far, no morphological evidence or molecular marker has been developed for effective distinguishment of genders, which poses a critical challenge to our captive breeding efforts. In this study, we sequenced gonadal transcriptomes of adult Asian arowanas and revealed differential expression profiling of sex-related genes. Based on the comparative transcriptomics analysis of testes (n = 3) and ovaries (n = 3), we identified a total of 8,872 differentially expressed genes (DEGs) and 18,490 differentially expressed transposable elements (TEs) between male and female individuals. Interestingly, the expression of TEs usually has been more significantly testis-biased than related coding genes. As expected, several genes related to females (such as foxl2 and cyp19a1a) are significantly transcribed in the ovary, and some genes related to male gonad development (such as dmrt1, gsdf and amh) are highly expressed in the testis. This sexual dimorphism is valuable for ascertaining the differential expression patterns of sex-related genes and enriching the genetic resources of this economically important species. These valuable genetic materials thereby provide instructive references for gender identification and one-to-one breeding practices so as to expand fish numbers for a rapid elevation of economic value.

Physico-Chemical and Rheological Trait-Based Identification of Indian Wheat Varieties Suitable for Different End-Uses.

India has increased its wheat production phenomenally in the last two decades and it now has a buffer stock of 9.7 million tonnes. However, despite the release of several wheat cultivars, the end-use quality traits of Indian wheat varieties have not been explored in-depth to determine the increasing demand of the domestic processing industry as well as export. In this study, 55 wheat genotypes including 47 released varieties, and 8 genetic stocks were grown along with 10 Australian varieties grown during cropping seasons: 2019-2020 and 2020-2021 and diversity in different physiochemical and rheological traits was evaluated. They showed considerable diversity in all the quality traits studied. However, very few genotypes could be found suitable for any one end-use. Five genotypes were found to possess four to five traits for superior bread-making quality. Two varieties and three advanced breeding lines had up to four good chapati quality traits. None of the released varieties investigated had suitable traits for biscuit making; however, two breeding lines possessed requisite quality traits suitable for biscuit making. It is, therefore, concluded that systematic breeding efforts are required to develop genotypes that bring together the most important quality traits in a single genotype to be suitable for domestic industry as well as for export.

Advances in Genetic Enhancement of Nutritional Quality of Tropical Maize in West and Central Africa

Micronutrient deficiencies are pervasive in the diets of millions of people in developing countries, calling for effective mitigation measures. The development of biofortified cultivars through breeding holds promise for sustainable and affordable solutions to combat micronutrient deficiencies. Breeding efforts in the past decade have resulted in dozens of biofortified open-pollinated varieties and hybrids adapted to diverse agroecological zones. Advances in genomics and molecular tools enabled rapid identification of maize cultivars enriched with essential micronutrients such as pro vitamin A (PVA), iron (Fe), and zinc (Zn). Leveraging Multi-omics-driven discovery of the genetic factors underlying the vast array of nutritional traits is paramount to mainstreaming breeding for quality traits in the product profile. Molecular breeding schemes, and integrating emerging Omics tools at every stage of the breeding pipeline, are vital to enhancing genetic gain. The recent momentum in elucidating the metabolism of micronutrients should be expanded to novel breeding targets as well as to the simultaneous enhancement of nutritional qualities while curtailing anti-nutritional factors in staple food crops. Harnessing new technologies to establish comprehensive and integrated breeding approaches involving nutrigenomics, genome editing, and agronomic biofortification is crucial in tackling nutritional insecurity. This review highlights the prospect of integrating modern tools in hastening the genetic improvement of nutritionally enriched maize.

Induction and characterization of induced tetraploid, mixoploid and control diploid teak seedlings (Tectona grandis L.f.) from shoot cultures treated with oryzalin*

Teak, known for its high-quality timber and economic value, holds significant potential as the major component of an agroforestry system to combat climate change and support sustainable development goals. The challenge of slow teak growth can be addressed by introducing fast-growing teak varieties amenable to vegetative propagation. Furthermore, the improvement of teak through somatic cell genetics, such as inducing polyploidy, can result in more vigorous, faster-growing, and drought-tolerant trees. While a report exists on a tetraploid teak accession with enhanced less water tolerance, information on the induction and characterization of tetraploid teak is lacking. In this study, we report the induction of polyploid teak by immersing 1 – 1.5 cm nodal stem segments and shoot tips obtained from teak shoot cultures in a modified MS liquid medium containing 5 − 30 µM oryzalin for one week, followed by subculture for 6 passages. The resulting shoots were acclimatized and grown in the nursery for 10 months. Based on flow cytometry for ploidy analysis of pre-selected plants having morphologies typical of polyploid followed by chromosome counting, we identified two tetraploid plants from one accession and 18 mixoploid teak plants from four accessions. Chromosome counting analysis confirmed that a diploid plant had a chromosome number of 2n = 2x = 36, tetraploid plant had a chromosome number of 2n = 4x = 72, and mixoploid plant exhibited both chromosome number of 2n = 2x = 36 and 2n = 4x = 72 in root tip cells. Morphological characterization revealed that tetraploid and mixoploid teak plants displayed typical polyploid characteristics, such as larger, thicker, and greener leaves, increased root diameter, increased cell size in root tip region, and larger stomata size but with reduced density. The development of tetraploid teak holds the potential to provide faster-growing and more drought-tolerant varieties, facilitating breeding efforts, including the development of triploid varieties.

Combining Ability Analysis and Association of Yield and Yield Components among Selected Rajmash (Phaseolus vulgaris L.) Lines

Background: Rajmash (Phaseolus vulgaris L.) is a significant leguminous crop known for its high protein content and dietary value. As global demand for nutritious food sources rises, enhancing the productivity and nutritional quality of Rajmash has become imperative. This research paper aims to investigate the combining ability and character associations in rajmash to facilitate the development of improved varieties with superior agronomic traits. Methods: An experiment was carried out in Rajmash using line × tester mating design to estimate the gca effect of parents and sca effect of 21 hybrids for yield and its traits using 7 lines and 3 testers. Hybrids along with ten parents were studied for combining ability and phenotypic correlations for seed yield and nine yield related traits. Result: The result indicated that the general combining ability (GCA) and specific combining ability (SCA) were significant for most characters indicating the importance of both additive and non-additive genetic components. This implies that a comprehensive understanding of both types of genetic effects is crucial for effective breeding programs. Among parent TRCR 3, SKAU-R-19, RR-21-01 and RKR 1033 were found to be good general combiners for seed yield per plant. This indicates their potential to consistently impart favorable traits to their progeny. The identification of such strong general combiners is valuable information for breeders aiming to enhance overall seed yield. The most promising specific combiners for seed yield were from crosses including SKAU-R-19 × RKR 1033, IPR-205-19 × HUR, RR-21-01 × RKR 1033, RR-21-12 × GR 1 and RR-21-01 × HUR. Significant desirable phenotypic correlations were observed between seed yield with days to flowering, days maturity, number of pods per plant, pod length and 100 seed weight these characters can act as indirect selection criteria in yield that could be used in rajmash breeding programs. The identification of strong general combiners, promising specific crosses and meaningful phenotypic correlations offers practical guidance for future breeding efforts, contributing to the development of improved varieties with enhanced yield potential and desirable agronomic traits.

The Physiological Response of Apricot Flowers to Low-Temperature Stress.

The growth and development of apricot flower organs are severely impacted by spring frosts. To better understand this process, apricot flowers were exposed to temperatures ranging from 0 °C to -8 °C, including a control at 18 °C, in artificial incubators to mimic diverse low-temperature environments. We aimed to examine their physiological reactions to cold stress, with an emphasis on changes in phenotype, membrane stability, osmotic substance levels, and antioxidant enzyme performance. Results reveal that cold stress induces significant browning and cellular damage, with a sharp increase in browning rate and membrane permeability below -5 °C. Soluble sugars and proteins initially rise as osmoprotectants, but their content decreases at lower temperatures. Proline content consistently increases, suggesting a protective role. Antioxidant enzyme activities, including catalase (CAT), peroxidase (POD), superoxide dismutase (SOD), and ascorbate peroxidase (APX), exhibit a complex pattern, with initial increases followed by declines at more severe cold conditions. Correlation and principal component analyses highlight the interplay between these responses, indicating a multifaceted adaptation strategy. The findings contribute to the understanding of apricot cold tolerance and inform breeding efforts for improved crop resilience.

Rapid Determination of Taraxacum kok-saghyz Rubber Content Using a Pyrolyzer Hyphenated with a Miniaturized Mass Spectrometer

Taraxacum kok-saghyz (TKS), a rubber-producing plant with excellent potential, emerges as a viable substitute for rubber tree (Hevea brasiliensis). While natural rubber is a desirable material, conventional techniques for assessing rubber content have faced challenges in meeting practical production requirements. To address this issue, we have developed a pyrolysis–mass spectrometry (PY-MS) instrument for the quantitative evaluation of natural rubber (NR) content in rubber-producing plants. The derived standard curve equation, established for the detection of TKS dry weight through external standard calibration, demonstrates a correlation coefficient (R2) surpassing 0.99. The method exhibits commendable recovery rates (93.27–107.83%), relative standard deviations (RSD ≤ 3.93%), and a swift analysis time of merely 10 min per sample, thereby enabling accurate and efficient quantification of NR dry weight. Additionally, the PY-MS system we designed can be modified for vehicular use, enabling on-site, in situ analysis, and it provides substantial support for TKS breeding and propagation efforts. This approach possesses significant potential for extensive utilization in the assessment of rubber content in rubber-producing plants other than TKS. The integration of pyrolysis–mass spectrometry for the identification of polymers with high molecular weight offers a valuable pathway for the examination of diverse polymers.

Genetic Variability and Clustering Patterns of Sugarcane (Saccharum spp.) Germplasms with Respect to Sucrose-Related Traits

Fifty-five sugarcane genotypes from around the world were collected and evaluated for potential use as parental material in the USDA ARS Canal Point (CP) sugarcane breeding program in Florida, USA. The genotypes were planted in a trial with four check cultivars on organic soils with four replications, and data were collected for two years [i.e., plant cane (PC) and first ratoon (FR) crops] to assess sucrose-yield-related traits and the cane-yield-related traits in PC. Using a multivariate analysis, variation was observed in all cane—[i.e., stalk weight, stalk population and cane yield] and sugar-yield-related traits [i.e., Brix, Pol, sucrose content and commercial recoverable sucrose (CRS)]. The mean CRS content was greater in the FR crop than the PC crop. Significant variations were attributed to genotype (G), crop cycles (C) and G × C effects. Variations between crop cycles were highly significant for all sucrose yield components, which could complicate the downstream selection of genotypes for sucrose yield. Based on CRS content, genotypes could be grouped into six distinct clusters. Based on plant cane data, cane yield traits (stalk weight, stalk population and cane yield) were used to estimate the breeding values of parents. Of the 55 genotypes, 8 had significantly greater t-BLUP values for cane yield, along with CP 00-1101. Combined sucrose yield traits, (Brix, Pol and sucrose content) from the two crops were used to estimate the breeding values of parents. Of the 55 genotypes, 10 genotypes had significantly greater t-BLUP values for CRS, along with CP 00-1101, CP 96-1252 and CP 01-2390, and can be considered as elite parents in future breeding efforts. These results provide a foundation for the efficient integration of genetic diversity in developing commercial cultivars, with improved sucrose yields, into the CP sugarcane breeding program.

Unveiling the Genetic Mechanism of Meat Color in Pigs through GWAS, Multi-Tissue, and Single-Cell Transcriptome Signatures Exploration.

Meat color traits directly influence consumer acceptability and purchasing decisions. Nevertheless, there is a paucity of comprehensive investigation into the genetic mechanisms underlying meat color traits in pigs. Utilizing genome-wide association studies (GWAS) on five meat color traits and the detection of selection signatures in pig breeds exhibiting distinct meat color characteristics, we identified a promising candidate SNP, 6_69103754, exhibiting varying allele frequencies among pigs with different meat color characteristics. This SNP has the potential to affect the redness and chroma index values of pork. Moreover, transcriptome-wide association studies (TWAS) analysis revealed the expression of candidate genes associated with meat color traits in specific tissues. Notably, the largest number of candidate genes were observed from transcripts derived from adipose, liver, lung, spleen tissues, and macrophage cell type, indicating their crucial role in meat color development. Several shared genes associated with redness, yellowness, and chroma indices traits were identified, including RINL in adipose tissue, ENSSSCG00000034844 and ITIH1 in liver tissue, TPX2 and MFAP2 in lung tissue, and ZBTB17, FAM131C, KIFC3, NTPCR, and ENGSSSCG00000045605 in spleen tissue. Furthermore, single-cell enrichment analysis revealed a significant association between the immune system and meat color. This finding underscores the significance of the immune system associated with meat color. Overall, our study provides a comprehensive analysis of the genetic mechanisms underlying meat color traits, offering valuable insights for future breeding efforts aimed at improving meat quality.

Unraveling root and rhizosphere traits in temperate maize landraces and modern cultivars: Implications for soil resource acquisition and drought adaptation.

A holistic understanding of plant strategies to acquire soil resources is pivotal in achieving sustainable food security. However, we lack knowledge about variety-specific root and rhizosphere traits for resource acquisition, their plasticity and adaptation to drought. We conducted a greenhouse experiment to phenotype root and rhizosphere traits (mean root diameter [Root D], specific root length [SRL], root tissue density, root nitrogen content, specific rhizosheath mass [SRM], arbuscular mycorrhizal fungi [AMF] colonization) of 16 landraces and 22 modern cultivars of temperate maize (Zea mays L.). Our results demonstrate that landraces and modern cultivars diverge in their root and rhizosphere traits. Although landraces follow a 'do-it-yourself' strategy with high SRLs, modern cultivars exhibit an 'outsourcing' strategy with increased mean Root Ds and a tendency towards increased root colonization by AMF. We further identified that SRM indicates an 'outsourcing' strategy. Additionally, landraces were more drought-responsive compared to modern cultivars based on multitrait response indices. We suggest that breeding leads to distinct resource acquisition strategies between temperate maize varieties. Future breeding efforts should increasingly target root and rhizosphere economics, with SRM serving as a valuable proxy for identifying varieties employing an outsourcing resource acquisition strategy.

Genetic Insights into the Extremely Dwarf Hibiscus syriacus var. micranthus: Complete Chloroplast Genome Analysis and Development of a Novel dCAPS Marker.

This study explored the chloroplast (cp) genomes of three Hibiscus syriacus (HS) specimens endemic to Korea possessing unique ornamental and conservation values: the dwarf H. syriacus var. micranthus (HSVM), renowned for its small stature and breeding potential; HS 'Tamra', a cultivar from Korea's southernmost islands, noteworthy for its distinctive beauty; and HS Natural Monument no. 521 (N.M.521), a specimen of significant lifespan and height. Given the scarcity of evolutionary studies on these specimens, we assembled and analyzed their cp genomes. We successfully assembled genomes spanning 160,000 to 160,100 bp and identified intraspecific variants. Among these, a unique ATA 3-mer insertion in the trnL-UAA region was identified in HSVM, highlighting its value as a genetic resource. Leveraging this finding, we developed a novel InDel dCAPS marker, which was validated across 43 cultivars, enhancing our ability to distinguish HSVM and its derivatives from other HS cultivars. Phylogenetic analysis involving 23 Malvaceae species revealed that HSVM forms a clade with woody Hibiscus species, closely associating with N.M.520, which may suggest a shared ancestry or parallel evolutionary paths. This investigation advances our understanding of the genetic diversity in Korean HS and offers robust tools for accurate cultivar identification, aiding conservation and breeding efforts.

Determination of essential oil and chemical composition of St. John’s Wort

Abstract Considering it contains a variety of physiologically active compounds, including flavonoids, common phenols, and essential oils (EOs), St. John’s wort (Hypericum perforatum L.) is a common plant in Bulgaria that is predominantly used in folk medicine to cure various disorders. Determining the chemical makeup of St. John’s wort inflorescences that were gathered from northern Bulgaria was the purpose of this investigation. The antioxidant activity of H. perforatum L. extracts was assessed using 1,1-diphenyl-2-picrilhydrazyl (DPPH), ferric reducing antioxidant power (FRAP), and Trolox equivalent antioxidant capacity (TEAC) tests on methanol extract. The amount of EO obtained by water distillation was 0.08%, with its main components (over 3%) being n-nonane (27.46%), β-sesquiphellandrene (11.17%), heptanal dimethyl acetal (5.94%), ethyl hexyl ketone (5.93%), undecane (3.75%), sabinene (3.3%), and tridecyl alcohol (3.1%). Methanol extracts were obtained from the inflorescences, with the total flavonoid content determined as 8.66 mg quercetin equivalents (QE)/mg and total phenolic content as 271.33 mg Gallic acid equivalent/g. The FRAP assay yielded 493.07 µmol/L of antioxidant activity, while the TEAC assay yielded 106.39 µmol/L, respectively. Our findings enable a comprehensive characterization of H. perforatum from Bulgaria and an assessment of its oil suitability for potential industrial applications. Additionally, the results could guide the selection of specimens for future targeted breeding efforts.

Chromosome-level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean.

Adzuki bean (Vigna angularis) is an important legume crop cultivated in over 30 countries worldwide. We developed a high-quality chromosome-level reference genome of adzuki bean cultivar Jingnong6 by combining PacBio Sequel long-read sequencing with short-read and Hi-C technologies. The assembled genome covers 97.8% of the adzuki bean genome with a contig N50 of approximately 16 Mb and a total of 32 738 protein-coding genes. We also generated a comprehensive genome variation map of adzuki bean by whole-genome resequencing (WGRS) of 322 diverse adzuki beans accessions including both wild and cultivated. Furthermore, we have conducted comparative genomics and a genome-wide association study (GWAS) on key agricultural traits to investigate the evolution and domestication. GWAS identified several candidate genes, including VaCycA3;1, VaHB15, VaANR1 and VaBm, that exhibited significant associations with domestication traits. Furthermore, we conducted functional analyses on the roles of VaANR1 and VaBm in regulating seed coat colour. We provided evidence for the highest genetic diversity of wild adzuki (Vigna angularis var. nipponensis) in China with the presence of the most original wild adzuki bean, and the occurrence of domestication process facilitating transition from wild to cultigen. The present study elucidates the genetic basis of adzuki bean domestication traits and provides crucial genomic resources to support future breeding efforts in adzuki bean.

Genetic diversity of grain yield traits and identification of a grain weight gene SiTGW6 in foxtail millet.

Agronomic traits were evaluated in 1250 foxtail millet accessions, and a crucial gene SiTGW6 governing grain yield was identified. Elite haplotypes and dCAPS markers developed for SiTGW6 facilitate molecular breeding. A comprehensive evaluation of phenotypic characteristics and genetic diversity in germplasm resources are important for gene discovery and breeding improvements. In this study, we conducted a comprehensive evaluation of 1250 foxtail millet varieties, assessing seven grain yield-related traits and fourteen common agronomic traits over two years. Principal component analysis, correlation analysis, and cluster analysis revealed a strong positive correlation between 1000-grain weight and grain width with grain yield, emphasizing their importance in foxtail millet breeding. Additionally, we found that panicle weight positively correlated with 1000-grain weight but negatively correlated with branch and tiller numbers, indicating selection factors during domestication and breeding. Using this information, we identified 27 germplasm resources suitable for high-yield foxtail millet breeding. Furthermore, through an integration of haplotype variations and phenotype association analysis, we pinpointed a crucial gene, SiTGW6, responsible for governing grain yield in foxtail millet. SiTGW6 encodes an IAA-glucose hydrolase, primarily localized in the cytoplasm and predominantly expressed in flowering panicles. Employing RNAseq analysis, we identified 1439 differentially expressed genes across various SiTGW6 haplotypes. Functional enrichment analysis indicating that SiTGW6 regulates grain yield through the orchestration of auxin and glucan metabolism, as well as plant hormone signaling pathways. Additionally, we have identified elite haplotypes and developed dCAPS markers for SiTGW6, providing valuable technical tools to facilitate molecular breeding efforts in foxtail millet.

Advancements in Enhancing Oil Quality in Rapeseed and Mustard: A Comprehensive Review

Rapeseed and mustard are important oilseed crops cultivated worldwide for their high oil content and versatile applications in food, feed, and industrial sectors. The quality of oil derived from these crops is influenced by various genetic, environmental, and agronomic factors. Breeding efforts aimed at improving oil quality traits in rapeseed and mustard have garnered significant attention in recent years due to their impact on market value, nutritional attributes, and industrial utility. In this review, we provide a comprehensive overview of breeding strategies and methodologies employed to enhance oil quality traits in rapeseed and mustard. We explore the genetic basis of oil quality traits, including fatty acid composition, erucic acid content, glucosinolate content, and tocopherol content, and discuss the importance of these traits for different end-uses. Furthermore, we highlight the role of molecular markers, genomics-assisted breeding, and biotechnological approaches in accelerating the breeding process and achieving targeted improvements in oil quality. The review also addresses the challenges and constraints associated with breeding for oil quality in rapeseed and mustard, including genotype-environment interactions, trait stability, and regulatory considerations. Additionally, we discuss emerging trends and future prospects in oil quality breeding, such as genome editing, metabolic engineering, and precision breeding, which offer novel avenues for achieving desired oil quality profiles while addressing sustainability and consumer preferences. Overall, this review underscores the significance of breeding for oil quality in rapeseed and mustard and provides insights into the latest advancements, challenges, and opportunities in this field. By integrating multidisciplinary approaches and harnessing the power of modern breeding tools and technologies, rapeseed and mustard breeders can continue to drive innovation and deliver oilseed crops with enhanced nutritional value, functional properties, and market competitiveness.

Elucidating the genomic regions through genome-wide association study (GWAS) for root traits in cowpea (Vigna unguiculata (L) Walp) mini-core collection

Enhancing the root traits through selection and breeding efforts can significantly improve the acquisition of soil resources, consequently boosting crop production in marginal environments. Cowpea is one of the important legume crops in arid and semi-arid regions, grown mostly in marginal environments under drought conditions. The roots play a crucial role in plant's ability to survive and adapt under such water stressed conditions. The understanding of cowpea genetic architecture related to root system architecture (RSA) remains limited due to difficulties in accurately measuring root traits. In the present study, a set 110 diverse mini-core collection of cowpea from IITA, Nigeria was evaluated for thirteen (13) different root-shoot traits under controlled conditions in the green house. Significant variation was recorded for all the root traits in the mini-core set. Most promising genotype for most of the root traits, viz., root volume, dry root weight, root biomass density and tap root diameter were identified. The correlation analysis revealed significant positive association (p < 0.001) of root weight with shoot weight (0.85), root volume (r = 0.61), and tap root diameter (0.56). In the principal component analysis (PCA), first three principal components explained the variance of 64.31%, with PC1 contributing 44.43%, PC2 10% and PC3 9.88%. All the root-shoot traits contribute positive variation to PC1especially dry root weight and dry shoot weight that had high component loading and in PC2 root shoot ratio had high loading. The root-shoot trait data was used with 6,574 good quality SNP data for discovery of genes/QTLs/marker-trait associations for root traits. The analysis of results of genome wide association study (GWAS) led to the identification of 52 unique SNPs associated significantly (p < 10−4) with thirteen root-shoot traits. Highest number of SNPs was found associated with root weight and chromosome 5 was identified as SNP hotspot for harboring majority of significant SNPs. We further delve candidate genes within 50 kb around the identified SNP that led to the identification of several important candidate genes underlying genomic regions responsible for root-shoot traits in cowpea. The promising cowpea genotypes for root traits and promising MTAs/candidate genes will prove useful in cowpea improvement programs including improvement of drought tolerance in cowpea.

Relative Discriminatory Ability of AMMI and GGE Biplot in Analysis of GxE Interaction for Yield and Seed Index in Chickpea (Cicer arietinum L.)

Background: The research focused on investigating the impact of genotype-environment interaction on the yield stability and performance of eight chickpea genotypes across three different locations (Bhatapara, Kawardha and Raipur). Method: The study employed a randomized block design with two replications in each environment in Rabi season during 2021-22. Analysis of variance (ANOVA) revealed significant variations between environments and genotype-environment interaction (G x E) based on AMMI and GGE biplot. Results: To visualize the genotype-environment relationship, a two-dimensional GGE biplot was created using the first two principal components, which accounted for 87.8% and 11.5% of the interaction’s variation. The GGE biplot indicated that genotype g4 (ICCX 161100-B-B-B-B) in environment e2 (Kawardha) and g8 (JG-24) in environment e1 (Bhatapara) exhibited high yield. Genotype g3 (ICCV 201112) in environment e3 (Raipur) also showed high yield, while genotype g5 (JG 2020-10) demonstrated stability across all three environments. Furthermore, the AMMI analysis identified genotype g2 (ICCV 201103) as a superior performer in terms of yield stability across environments. By employing the GGE biplot and AMMI analysis, the study categorized the genotypes into three groups, facilitating simplified visual evaluations. The GGE biplot highlighted that genotype g8 (JG-24) exhibited better seed index in environment e3 (Raipur), while genotype g1 (ICCV 201210) performed well in environment e1 (Bhatapara). Genotype g2 (ICCV 201103) demonstrated a good seed index in all three environments. The AMMI analysis indicated that genotype g3 (ICCV 201112) had a slightly lower seed index but maintained stability across all environments. Overall, the findings of this investigation, as represented by the GGE and AMMI biplots, visually illustrated the relationship between genotypes and environments. The identified genotypes hold potential for improving yield production and further research and breeding efforts can be based on these findings.