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TAG. Theoretical and Applied Genetics.... Mar 2024Integrating GAB methods with high-throughput phenotyping, genome editing, and speed breeding hold great potential in designing future smart peanut cultivars to meet... (Review)
Review
Integrating GAB methods with high-throughput phenotyping, genome editing, and speed breeding hold great potential in designing future smart peanut cultivars to meet market and food supply demands. Cultivated peanut (Arachis hypogaea L.), a legume crop greatly valued for its nourishing food, cooking oil, and fodder, is extensively grown worldwide. Despite decades of classical breeding efforts, the actual on-farm yield of peanut remains below its potential productivity due to the complicated interplay of genotype, environment, and management factors, as well as their intricate interactions. Integrating modern genomics tools into crop breeding is necessary to fast-track breeding efficiency and rapid progress. When combined with speed breeding methods, this integration can substantially accelerate the breeding process, leading to faster access of improved varieties to farmers. Availability of high-quality reference genomes for wild diploid progenitors and cultivated peanuts has accelerated the process of gene/quantitative locus discovery, developing markers and genotyping assays as well as a few molecular breeding products with improved resistance and oil quality. The use of new breeding tools, e.g., genomic selection, haplotype-based breeding, speed breeding, high-throughput phenotyping, and genome editing, is probable to boost genetic gains in peanut. Moreover, renewed attention to efficient selection and exploitation of targeted genetic resources is also needed to design high-quality and high-yielding peanut cultivars with main adaptation attributes. In this context, the combination of genomics-assisted breeding (GAB), genome editing, and speed breeding hold great potential in designing future improved peanut cultivars to meet market and food supply demands.
Topics: Arachis; Plant Breeding; Fabaceae; Genomics; Vegetables
PubMed: 38438591
DOI: 10.1007/s00122-024-04575-3 -
Plant Physiology and Biochemistry : PPB Mar 2024Sucrose content is a key factor for the flavor of edible peanut, which determines the sweet taste of fresh peanut and also attribute to pleasant flavor of roasted...
Sucrose content is a key factor for the flavor of edible peanut, which determines the sweet taste of fresh peanut and also attribute to pleasant flavor of roasted peanut. To explore the genetic mechanism of the sucrose content in peanut, an F population was created by crossing the sweet cultivar Zhonghuatian 1 (ZHT1) with Nanyangbaipi (NYBP). A genomic region spanning 28.26 kb on chromosome A06 was identified for the sucrose content through genetic mapping, elucidating 47.5% phenotypic variance explained. As the sucrose content had a significantly negative correlation with the oil content, this region was also found to be related to the oil content explaining 37.2% of phenotype variation. In this region, Arahy.42CAD1 was characterized as the most likely candidate gene through a comprehensive analysis. The nuclear localization of Arahy.42CAD1 suggests its potential involvement in the regulation of gene expression for sucrose and oil contents in peanut. Transcriptome analysis of the developing seeds in both parents revealed that genes involved in glycolysis and triacylglycerol biosynthesis pathways were not significantly down-regulated in ZHT1, indicating that the sucrose accumulation was not attributed to the suppression of triacylglycerol biosynthesis. Based on the WGCNA analysis, Arahy.42CAD1 was co-expressed with the genes involved in vesicle transport and oil body assembly, suggesting that the sucrose accumulation may be caused by disruptions in TAG transportation or storage mechanisms. These findings offer new insights into the molecular mechanisms governing sucrose accumulation in peanut, and also provide a potential gene target for enhancing peanut flavor.
Topics: Arachis; Sucrose; Gene Expression Profiling; Chromosome Mapping; Triglycerides; Transcriptome; Seeds
PubMed: 38422578
DOI: 10.1016/j.plaphy.2024.108448 -
TAG. Theoretical and Applied Genetics.... Feb 2024We identified two stable and homologous major QTLs for sucrose content in peanut, and developed breeder-friendly molecular markers for marker-assisted selection...
We identified two stable and homologous major QTLs for sucrose content in peanut, and developed breeder-friendly molecular markers for marker-assisted selection breeding. Sucrose content is a crucial quality trait for edible peanuts, and increasing sucrose content is a key breeding objective. However, the genetic basis of sucrose content in peanut remains unclear, and major quantitative trait loci (QTLs) for sucrose content have yet to be identified. In this study, a high-density genetic map was constructed based on whole-genome re-sequencing data from a peanut RIL population. This map consisted of 2,042 bins and 24,142 SNP markers, making it one of the most comprehensive maps to date in terms of marker density. Two major QTLs (qSCA06.2 and qSCB06.2) were identified, explaining 31.41% and 24.13% of the phenotypic variance, respectively. Notably, these two QTLs were located in homologous genomic regions between the A and B subgenomes. The elite allele of qSCA06.2 was exclusive to Valencia-type, while the elite allele of qSCB06.2 existed in other peanut types. Importantly, the distribution of alleles from two homologous QTLs in the RIL population and diverse germplasm accessions consistently demonstrated that only the combination of elite allelic genotypes from both QTLs/genes resulted in a significantly dominant phenotype, accompanied by a substantial increase in sucrose content. The newly developed diagnostic markers for these QTLs were confirmed to be reliable and could facilitate future breeding efforts to enhance sucrose content using marker-assisted selection techniques. Overall, this study highlights the co-regulation of sucrose content by two major homologous QTLs/genes and provides valuable insights into the genetic basis of sucrose in peanuts.
Topics: Arachis; Quantitative Trait Loci; Plant Breeding; Alleles; Sucrose
PubMed: 38411751
DOI: 10.1007/s00122-024-04549-5 -
Microscopy Research and Technique Jul 2024The present study was conducted to investigate the biochemical and histological changes of liver tissue in Siberian sturgeon (Acipenser baerii) exposed to different...
The present study was conducted to investigate the biochemical and histological changes of liver tissue in Siberian sturgeon (Acipenser baerii) exposed to different doses of bisphenol A (BPA). One hundred and eighty pieces of 1-year-old A. baerii with an average weight of 200-250 g bought and randomly distributed in 18 tanks (n = 10). After 2 weeks of adaptation, the fish received intraperitoneal injections of 1, 10, and 100 μg/g/week BPA and μg/g/week of 17β-estradiol intraperitoneally. The solvent control group received only peanut oil, while the control group did not receive any injections. In order to investigate histological changes of the liver, after 2 weeks the liver samples were taken, fixed in 10% formalin solution and slides prepared by routine histological methods. For assaying antioxidant defense status, the liver tissue from three fish of each replicates was captured and after homogenization, activity of catalase, superoxide dismutase, and glutathione peroxidase and malondialdehyde measured. The most important histological changes observed in the liver tissue were: vacuolation of hepatocytes, nuclear hypertrophy, necrosis of liver cells, expansion of sinusoids, and accumulation of fat cells. In the highest dose, the intensity of tissue changes increased. Activity of antioxidant enzymes and malondialdehyde content increased in fish exposed to 100 μg/g/week BPA in compare with other groups (p < .05). According to our findings, it could be concluded that liver histology was affected by BPA and tissue damage had occurred, which had led to changes in blood parameters. Also, the obtained results showed that the high concentrations of BPA used in this study stimulate the antioxidant defense. RESEARCH HIGHLIGHTS: BPA evoke oxidative stress in Siberian sturgeons in high dose of exposure. Severity of liver histologic lesions was dose dependent.
Topics: Animals; Phenols; Liver; Benzhydryl Compounds; Fishes; Antioxidants; Superoxide Dismutase; Catalase; Glutathione Peroxidase; Malondialdehyde; Oxidative Stress; Hepatocytes
PubMed: 38400640
DOI: 10.1002/jemt.24527 -
Genes Jan 2024The capability of embryogenic callus induction is a prerequisite for in vitro plant regeneration. However, embryogenic callus induction is strongly genotype-dependent,...
The capability of embryogenic callus induction is a prerequisite for in vitro plant regeneration. However, embryogenic callus induction is strongly genotype-dependent, thus hindering the development of in vitro plant genetic engineering technology. In this study, to examine the genetic variation in embryogenic callus induction rate (CIR) in peanut ( L.) at the seventh, eighth, and ninth subcultures (T7, T8, and T9, respectively), we performed genome-wide association studies (GWAS) for CIR in a population of 353 peanut accessions. The coefficient of variation of CIR among the genotypes was high in the T7, T8, and T9 subcultures (33.06%, 34.18%, and 35.54%, respectively), and the average CIR ranged from 1.58 to 1.66. A total of 53 significant single-nucleotide polymorphisms (SNPs) were detected (based on the threshold value -log() = 4.5). Among these SNPs, SNPB03-83801701 showed high phenotypic variance and neared a gene that encodes a peroxisomal ABC transporter 1. SNPA05-94095749, representing a nonsynonymous mutation, was located in the locus (encoding an auxin response factor 19 protein) at T8, which was associated with callus formation. These results provide guidance for future elucidation of the regulatory mechanism of embryogenic callus induction in peanut.
Topics: Arachis; Genome-Wide Association Study; Polymorphism, Single Nucleotide; Genotype; Genetic Engineering
PubMed: 38397150
DOI: 10.3390/genes15020160 -
Genes Jan 2024Peanuts ( L.) are important high-protein and oil-containing legume crops adapted to arid to semi-arid regions. The yield and quality of peanuts are complex quantitative...
Peanuts ( L.) are important high-protein and oil-containing legume crops adapted to arid to semi-arid regions. The yield and quality of peanuts are complex quantitative traits that show high environmental influence. In this study, a recombinant inbred line population (RIL) (Valencia-C × JUG-03) was developed and phenotyped for nine traits under two environments. A genetic map was constructed using 1323 SNP markers spanning a map distance of 2003.13 cM. Quantitative trait loci (QTL) analysis using this genetic map and phenotyping data identified seventeen QTLs for nine traits. Intriguingly, a total of four QTLs, two each for 100-seed weight (HSW) and shelling percentage (SP), showed major and consistent effects, explaining 10.98% to 14.65% phenotypic variation. The major QTLs for HSW and SP harbored genes associated with seed and pod development such as the gene, gene, gene, gene, -encoding gene, gene, -encoding gene and superfamily gene. Additionally, the identification of 76 major epistatic QTLs, with PVE ranging from 11.63% to 72.61%, highlighted their significant role in determining the yield- and quality-related traits. The significant G × E interaction revealed the existence of the major role of the environment in determining the phenotype of yield-attributing traits. Notably, the gene in the vicinity of major QTLs for HSW can be further investigated to develop a diagnostic marker for HSW in peanut breeding. This study provides understanding of the genetic factor governing peanut traits and valuable insights for future breeding efforts aimed at improving yield and quality.
Topics: Quantitative Trait Loci; Arachis; Plant Breeding; Chromosome Mapping; Phenotype
PubMed: 38397130
DOI: 10.3390/genes15020140 -
Genome Jun 2024For peanut, the lack of stable cytological markers is a barrier to tracking specific chromosomes, elucidating the genetic relationships between genomes and identifying...
For peanut, the lack of stable cytological markers is a barrier to tracking specific chromosomes, elucidating the genetic relationships between genomes and identifying chromosomal variations. Chromosome mapping using single-copy oligonucleotide (oligo) probe libraries has unique advantages for identifying homologous chromosomes and chromosomal rearrangements. In this study, we developed two whole-chromosome single-copy oligo probe libraries, LS-7A and LS-8A, based on the reference genome sequences of chromosomes 7A and 8A of . Fluorescence in situ hybridization (FISH) analysis confirmed that the libraries could specifically paint chromosomes 7 and 8. In addition, sequential FISH and electronic localization of LS-7A and LS-8A in AA) and (BB) showed that chromosomes 7A and 8A contained translocations and inversions relative to chromosomes 7B and 8B. Analysis of the chromosomes of wild species using LS-8A confirmed that this library could accurately and effectively identify A genome species. Finally, LS-7A and LS-8A were used to paint the chromosomes of interspecific hybrids and their progenies, which verified the authenticity of the interspecific hybrids and identified a disomic addition line. This study provides a model for developing specific oligo probes to identify the structural variations of other chromosomes in and demonstrates the practical utility of LS-7A and LS-8A.
Topics: Chromosome Painting; In Situ Hybridization, Fluorescence; Chromosomes, Plant; Arachis; Chromosome Mapping; Oligonucleotides; Translocation, Genetic
PubMed: 38394647
DOI: 10.1139/gen-2023-0116 -
Chemistry & Biodiversity Apr 2024Peanut is rich in oil and protein and has a large content of bioactive constituents consisting of tocopherols, phytosterols, and so on. Generally, Virginia, Spanish,...
Peanut is rich in oil and protein and has a large content of bioactive constituents consisting of tocopherols, phytosterols, and so on. Generally, Virginia, Spanish, Valencia and Runner market types are grown of peanut. In this study, it is aimed to determine the antioxidant activity, total phenolic content and total flavonoid content of peanuts from four different market types, for the first time, and group them with principal component analysis (PCA) and hierarchical cluster analysis (HCA). For PCA, PC1 and PC2 explained 87.655 % of the total variation and, according to the HCA of peanut samples, two main groups were determined. The total phenolic content changed 1.556 to 2.899 mg GAE/g. The lowest value have seen at Spanish merket type to determine the antioxidant activities of peanut samples were maked FRAP and DPPH assay, the lowest FRAP value (8.136 μmol FeSO7HO/g sample) was seen at Valencia market type, the highest (14.004 μmol FeSO7HO/g sample) was seen at Virginia market type. It was determined that the total flavonoid, total phenolic content, and antioxidant activities of the Virginia, Valencia, Spanish, and Runner market types included in the study were different from each other, and the Virginia market type showed superior characteristics compared to the others. The results obtained suggest that Virginia market type may be preferred more especially in peanut cultivation for food uses. It is thought that this study can be a source for future studies by eliminating a deficiency in the literature.
Topics: Antioxidants; Arachis; Chemometrics; Phenols; Flavonoids
PubMed: 38380875
DOI: 10.1002/cbdv.202301419 -
Nature Genetics Mar 2024Peanut (Arachis hypogaea L.) is an important allotetraploid oil and food legume crop. China is one of the world's largest peanut producers and consumers. However,...
Peanut (Arachis hypogaea L.) is an important allotetraploid oil and food legume crop. China is one of the world's largest peanut producers and consumers. However, genomic variations underlying the migration and divergence of peanuts in China remain unclear. Here we reported a genome-wide variation map based on the resequencing of 390 peanut accessions, suggesting that peanuts might have been introduced into southern and northern China separately, forming two cultivation centers. Selective sweep analysis highlights asymmetric selection between the two subgenomes during peanut improvement. A classical pedigree from South China offers a context for the examination of the impact of artificial selection on peanut genome. Genome-wide association studies identified 22,309 significant associations with 28 agronomic traits, including candidate genes for plant architecture and oil biosynthesis. Our findings shed light on peanut migration and diversity in China and provide valuable genomic resources for peanut improvement.
Topics: Arachis; Genome-Wide Association Study; Chromosome Mapping; Phenotype; Genomics; Genome, Plant
PubMed: 38378864
DOI: 10.1038/s41588-024-01660-7 -
Environmental Technology Feb 2024A significantly high protease enzyme yield of 617 U/ml was achieved with as the microorganism and peanut oil meal as the substrate. Peanut oil meal, which consists of...
A significantly high protease enzyme yield of 617 U/ml was achieved with as the microorganism and peanut oil meal as the substrate. Peanut oil meal, which consists of proteins (40-60%) and carbohydrates (22-30%), serves as a sufficient source of nitrogen and carbon necessary for microbial growth and production of enzymes. Moreover, peanut meal offers the advantages of being affordable and available in large quantities, making the meal suitable for cost-effective enzyme production. In the present study, two bacterial strains and one fungal strain were selected to produce proteases utilizing peanut oil meal as the substrate. The experimental conditions during the enzyme production, including pH and temperature, were optimized. In addition, the substrate was enriched with various carbon and nitrogen sources. The microbial strains were streaked on nutritional agar (for bacteria) and potato dextrose agar (for fungus). Following an incubation period, the plates were stored at 4°C for further studies. The molecular weight of partially purified proteases of was found to be ≅ 95.5 kDa. Potassium nitrate was the most ideal nitrogen source (up to 411% increase in activity) and fructose was the best carbon source (425% increase). These enzymes exhibited excellent temperature tolerance and were capable of functioning over a wide pH range. Furthermore, the obtained proteases demonstrated ability to coagulate milk effectively, indicating their potential for various food-related applications.
PubMed: 38312074
DOI: 10.1080/09593330.2024.2309471