Search Results (57)

The improvement in yield in cultivar mixtures has been well established. Despite increasing knowledge of the improvement involving within-species diversification and resource use efficiency, little is known about the benefits arising from relatedness-mediated intraspecific interactions in cultivar mixtures. This study used a relatedness gradient of rice cultivars to test whether neighbor relatedness contributes to improvements in grain yields in cultivar mixtures. We experimentally demonstrated the grain yield of rice cultivar mixtures with varying genetic relatedness under both field and controlled conditions. As a result, a closely related cultivar mixture had increased grain yield compared to monoculture and distantly related mixtures by optimizing the root-to-shoot ratio and accelerating flowering. The benefits over monoculture were most pronounced when compared to the significant yield reductions observed in distantly related mixtures. The relatedness-mediated improvement in yields depended on soil volume and nitrogen use level, with effects attenuating under larger soil volumes or nitrogen deficiency. Furthermore, neighbor relatedness enhanced the richness and diversity of both bacterial and fungal communities in the rhizosphere soil, leading to a significant restructuring of the microbial community composition. These findings suggest that neighbor relatedness may improve the grain yield of rice cultivar mixtures. Beneficial plant–plant interactions may be generated by manipulating cultivar kinship within a crop species. A thorough understanding of kinship strategies in cultivar mixtures offers promising prospects for increasing crop production. Full article

The molecular identification of valuable genotypes is an important problem of germplasm management. In this study, we evaluated the potential of 11 universal primer pairs for the DNA barcoding of locally derived cultivars of subtropical crops (actinidia, feijoa, citrus, and tea). A total of 47 accessions (elite cultivars, forms, and breeding lines) of these four genera were included in the study. The efficiency of the following universal primers was assessed using Sanger sequencing: ITS-p5/ITS-u4, ITS-p5/ITS-u2, ITS-p3/ITS-u4, 23S,4.5S&5S, 16S, petB/petD, rpl23/rpl2.l, rpl2 intron, rpoC1 intron, trnK intron, and trnE-UUC/trnT-GUU. Among these primers, trnE-UUC/trnT-GUU showed greater intraspecific polymorphisms, while rpl2 intron and 16S displayed the lowest polymorphism levels in all crops. In addition, the 23S,4.5S & 5S, and rpoC1 intron were efficient for intraspecific analysis of tea and actinidia species. Using five efficient chloroplast primers, a total of 22/6 SNPs/InDels were observed in tea accessions, 45/17 SNPs/InDels in actinidia, 23/3 SNPs/InDels in mandarins, and 5/4 SNPs/InDels in feijoa. These results will be useful for the further development of DNA barcodes of related accessions. Full article

DNA barcoding of intraspecific diversity of agricultural crops is important to develop the genetic passports of valuable genotypes and cultivars. The advantage of DNA-barcoding as compared to traditional genotyping of cultivars is that the procedure can be unified and applied for the broad range of accessions. This not only makes it cost efficient, but also allows to develop open access genetic databases to accumulate information of the world’s germplasm collections of different crops. In this regard, the aim of the review was to analyze the latest research in this field, including the selection of loci, universal primers, strategies of amplicons analysis, bioinformatic tools, and the development of databases. We reviewed the advantages and disadvantages of each strategy with the focus of cultivars identification. The data indicates that following chloroplast loci are the most prominent for the intraspecific diversity analysis: (trnE-UUC/trnT-GUU, rpl23/rpl2.l, psbA-trnH, trnL-trnF, trnK, rpoC1, ycf1-a, rpl32-trnL, trnH-psbA and matK). We suggest that the combination of three or four of these loci can be a sufficient DNA barcode for cultivar-level identification. This combination has to be selected for each crop. Advantages and disadvantages of different approaches of amplicons analysis are discussed. The bioinformatic tools and databases for the plant barcoding are reviewed. This review will be useful for selecting appropriate strategies for barcoding of intraspecific diversity of agricultural crops to develop genetic passports of valuable cultivars in germplasm collections worldwide. Full article

Climate change challenges existing strawberry cultivars, requiring adaptation and the introduction of new varieties better suited to new climate conditions. This research evaluated the response over time of new advanced breeding selections (AN15,07,53, AN16,53,54 and AN12,44,60) derived from intraspecific crosses, proposed for the Mediterranean environment and organic greenhouse cultivation, by comparing plant yield and fruit quality at each harvest stage against five commercial strawberry cultivars (Dina, Arwen, Melissa, Marimbella, and Elide). Results showed that Dina, AN15,07,53, and AN16,53,54 had higher levels of soluble sugars, organic acids, and anthocyanins than the other cultivars evaluated. In addition, AN16,53,54 showed anticipated peak production and plant yield similar to that of commercial cultivars. Elide showed on average the highest total yield (632 g plant⁻¹), while Dina, AN15,07,53 and AN12,44,60 showed lower yields. The lowest and highest percentages of discarded fruits were recorded in Arwen (10%) and AN 12,44,60 (27.7%), respectively. Two genotypes, AN16,53,54 and AN15,07,53 are susceptible to further evaluation; AN16,53,54 showed appropriate features for organic systems management. An important feature related to the environmental conditions of the Mediterranean area is the precocity of production, combined with good quality properties. The genotype AN15,07,53 derived from two parents with high and low chilling requirements, would need to be evaluated for its performance under very different climatic conditions. Full article

Leaves are the most ubiquitous plant organs, whose macrostructures exhibit close correlations with environmental factors while simultaneously reflecting inherent genetic and evolutionary patterns. These characteristics render them highly significant for plant taxonomy, ecology, and related disciplines. Therefore, this study presents the first comprehensive evaluation of Malus leaf macrostructures for infraspecific classification. By establishing a trait-screening system, we conducted a numerical taxonomic analysis of leaf phenotypic variation across 73 Malus germplasm (34 species and 39 cultivars). Through ancestor-inclined distribution characteristic analysis, we investigated phylogenetic relationships at both the genus level and infraspecific ranks within Malus. A total of 21 leaf phenotypic traits were selected from 50 candidate traits based on the following criteria: high diversity, abundance, and evenness (D ≥ 0.50, H ≥ 0.80, and E ≥ 0.60); significant intraspecific uniformity and interspecific distinctness ($\overline{CV}$ ≤ 10% and $CV$ ≥ 15%). Notably, the selected traits with low intraspecific variability ($\overline{CV}$ ≤ 10%) exhibit environmental robustness, likely reflecting low phenotypic plasticity of these specific traits under varying conditions. This stability enhances their taxonomic utility. It was found that the highest ancestor-inclined distribution probability reached 90% for 10 traceable cultivars, demonstrating reliable breeding lines. Based on morphological evidence, there was a highly significant correlation between the evolutionary orders of (Sect. Docyniopsis → Sect. Sorbomalus → Sect. Malus) and group/sub-groups (B₁ → B₂ → A). This study demonstrates that phenotypic variation in leaf macrostructures can effectively explore the affinities among Malus germplasm, exhibiting taxonomic significance at the infraspecific level, thereby providing references for variety selection. However, hybrid offspring may exhibit mixed parental characteristics, leading to blurred species boundaries. And convergent evolution may create false homologies, potentially misleading morphology-based taxonomic inferences. The inferred taxonomic relationships present certain limitations that warrant further investigation. Full article

Blueberry breeding requires a significant commitment of time, skilled labour, and financial resources, but it is essential to develop new cultivars that can meet challenges such as climate change, disease resistance, and changing market preferences. Intraspecific hybridisationis a widely used breeding strategy to increase genetic diversity, broaden the selection base, and develop new cultivars. By crossing different varieties and making advanced selections, breeders can introduce desirable traits such as improved fruit quality, increased yield, improved disease resistance and greater adaptability to environmental conditions. The present study aimed to evaluate the heritability of some key biometric and biochemical parameters inblueberry hybrids derived from intraspecific crosses to assess their inheritance patterns. The results can guide breeders in selecting parent combinations that maximise genetic gain, ultimately supporting the advancement of commercial blueberry production. The ‘Delicia × 4/6’ hybrid combination showed excellent performance for total polyphenol content, flavonoids, tannins, and ascorbic acid, with high genetic gain and near complete heritability, making it a promising candidate for improving antioxidant activity. The ‘Azur × Northblue’ hybrid had favourable total anthocyanin and tannin content, but an unfavourable sugar and ascorbic acid profile.The ‘Simultan × Duke’ hybrid combination showed the highest genetic gain for total soluble solids and firmness, together with high positive heterosis and heterotic progress, highlighting its potential for high-quality cultivars suitable for mechanical harvesting and storage. This research provides valuable insights into the efficiency of intraspecific hybridisationin the development of new blueberry cultivars with improved agronomic and nutritional qualities. Full article

Litchi chinensis, a crucial tropical and subtropical fruit tree in southern China, is widely appreciated for its distinctive flavor, high nutritional value, and significant economic impact. The bZIP (basic leucine zipper) gene family plays an essential role in regulating key biological functions during plant growth and development. In this study, we performed a comprehensive bioinformatics analysis of the bZIP gene family in litchi to systematically elucidate its molecular characteristics and functional properties. A total of 55 bZIP gene family members were identified, with the encoded proteins containing between 129 and 845 amino acid residues and theoretical isoelectric points (pI) ranging from 4.85 to 10.23. Protein–protein interaction network analysis revealed that 46 proteins exhibited interaction relationships. Phylogenetic analysis classified these genes into 13 distinct subgroups (A–K, M, and S). Chromosomal localization analysis indicated that bZIP gene family members were successfully mapped to 15 chromosomes. Intraspecific collinearity analysis identified 39 segmental duplication events, while interspecific and single-gene collinearity analyses suggested evolutionary conservation, with only a few genes exhibiting duplication or loss events. Cis-acting element analysis revealed a total of 213 elements associated with growth and development, which may play an important role in fruit development regulation. The results of differential gene expression, related to fruit development across different litchi cultivars, tissues, and flowering stages, combined with qRT-PCR validation, suggest that LITCHI017015.m1 and LITCHI004463.m1 may be involved in the early regulation of fruit development, while LITCHI018843.m1 may play a regulatory role during the later stages of fruit development. These findings provide a strong theoretical foundation for understanding the roles of bZIP genes in litchi fruit growth and development, and lay the groundwork for further functional studies. This study has potential application value in litchi fruit development and genetic improvement. Full article

A novel primer (FaSt-R) targeting the Prunus-specific Falling Stone (FaSt) non-autonomous transposon was combined with start-codon-targeted (SCoT) primers to assess genetic diversity in 12 cultivars from six Prunus species and 28 cultivars of European plum. Compared to SCoT-only analyses, the SCoT–FaSt combination produced fewer total bands but a higher percentage of polymorphic bands, while maintaining comparable values for polymorphism information content, resolving power, gene diversity, and Shannon’s index. SCoT–FaSt markers generated bands across a broader size range, which made gel patterns less dense, enabling the more accurate detection of differentially amplified fragments. Neighbor-joining and principal component analyses confirmed that SCoT–FaSt markers provided sufficient phylogenetic resolution at both interspecific and intraspecific levels. The sequencing of 32 SCoT–FaSt amplicons revealed FaSt elements in 26 fragments, with SCoT primers preferentially annealing to GC-rich exonic and intergenic regions. Seventeen protein-coding and one RNA-coding gene were partially identified, with FaSt elements localized in UTRs and introns of genes with key physiological functions. Comparative analysis indicated a biased distribution of FaSt elements between the Cerasus and Prunus subgenera. In silico findings suggest that FaSt elements are more fragmented in cherry species, potentially contributing to subgeneric divergence. Overall, the SCoT–FaSt marker system is effective for evaluating Prunus genetic diversity, reconstructing phylogenetic relationships, and elucidating the genomic impact of an active Mutator-like transposon. Full article

Intraspecific diversity is often introduced in orchards to promote cross-pollination, which is essential for self-incompatible crops and beneficial for many self-compatible crops. In lychee, orchards are often planted with multiple cultivars to increase the availability of male flowers, enhancing pollen transfer to female flowers. Typically, this diversity is arranged in single-cultivar blocks, requiring pollinators to transport cross-pollen across rows to reach trees in the middle of each block. We aimed to determine the levels of outcrossing at the edge and in the middle of blocks of Fay Zee Siu, Kaimana, Kwai Mai Pink, Sah Keng, Souey Tung and Wai Chee in a multi-cultivar lychee orchard. We also aimed to determine whether outcrossed fruit have different mass, skin colour and flavour attributes from selfed fruit. All cultivars produced a mixture of outcrossed and selfed fruit. Fay Zee Siu and Kaimana fruit were predominantly outcrossed, Kwai Mai Pink produced slightly more selfed than outcrossed fruit, and Souey Tung displayed high selfing. Outcrossing levels did not differ significantly between the edge and middle rows of these four cultivars. In contrast, Sah Keng and Wai Chee produced more outcrossed fruit in their edge row but more selfed fruit in their middle row. These two cultivars were at the orchard periphery, with another cultivar planted on only one side. Pollinators transported cross-pollen 56–60 m into the middle of blocks when different cultivars were planted on both sides, but this distance decreased to 42–56 m into the blocks when another cultivar was planted on only one side. Cross-pollination had few effects on fruit mass or quality, although pollination by Souey Tung sometimes increased fruit mass or Brix. These findings suggest that interplanting different cultivars of lychee can make effective use of its mixed-mating system, providing additional pollen sources in the orchard, supporting fruitlet retention, and sustaining tree productivity, without contributing greatly to quality variation in each cultivar. Full article

Pollen carries extensive genetic information, which may provide clues regarding the kinship of Malus, whose genetic relationships are complex. In this study, the phenotypic variation of pollen from 107 Malus taxa was investigated using combined methods of intraspecific/interspecific uniformity testing, cluster analysis, and Pearson correlation analysis. The family aggregation distributions in Malus sections, species, and cultivars were analyzed to infer their pedigree relationships. The results showed that (1) compared with pollen size and morphology, aberrant pollen rate and ornamentation were highly interspecifically differentiated, but ornamentation was also intraspecifically unstable, especially perforation densities ($\overline{c.v.}$ > 15%). (2) The pollen alteration direction from the original to the evolutionary population of Malus was large to small, with elliptic to rectangular morphologies, large and compact to small and sparse ridges, and low to high perforation densities. However, there was no significant change in pollen size. (3) The 107 studied taxa were divided into four groups. Malus species were relatively clustered in the same section, while homologous cultivars showed evidence of family aggregation distribution characteristics (92.60% of cultivars were clustered with their parents). (4) M. baccata and M. pumilar var. neidzwetzkyana were high-frequency parents, participating in 38.7% and 20.7% of cross-breeding, respectively. Overall, this study provides a reference for identifying Malus’ pedigree relationship. Full article

Roses (genus Rosa), renowned for their economic significance and aesthetic appeal, face multifaceted challenges in cultivation due to biotic and abiotic stressors. To address these challenges, this study explores the role of osmolytes, particularly polyamines, proline and glycine betaine, as well as antioxidant capacities and condensed tannins, in enhancing stress tolerance in roses. Despite the genetic diversity inherent in roses, the metabolic aspect of stress tolerance has been underexplored in breeding programs. This paper investigates the intraspecific variability among 22 rose cultivars, focusing on osmolyte content (proline and glycine betaine), individual polyamines (putrescine, spermine and spermidine), as well as antioxidant activities, measuring radical scavenging capacity against 2,2′-azinobis(3-ethylbenzothiozoline-6-sulfonic acid (ABTS^•+) and NO^• radicals. Employing a targeted metabolomic approach, we quantified the levels of individual polyamines in both the petals and leaves of rose cultivars. This was achieved through high-performance liquid chromatography coupled with fluorescent detection following a derivatization pretreatment process. Within the evaluated cultivars, “Unique Aroma”, “Andre Rieu”, “Aroma 3”, “Frayla Marija” and “Trendy Fashion” stood out for their significantly elevated levels of total foliar polyamines. The predominant polyamine detected at both petal and leaf levels was putrescine, with concentrations ranging from 335.81 (“Zora Frayla”) to 2063.81 nmol g⁻¹ DW (“Unique Aroma”) at the leaf level. Following putrescine, foliar spermidine levels varied from 245.08 (“Olivera Frayla”) to 1527.16 nmol g⁻¹ DW (“Andre Rieu”). Regarding antioxidant capacity, the leaf extracts of rose cultivars “Zora Frayla” and “Natalija Frayla” were prominent by showing 68.08 and 59.24 mmol Trolox equivalents (TE) g⁻¹ DW, respectively. The results highlight the intricate biochemical variability across rose cultivars and show that osmolytes, such as glycine betaine, proline and polyamines, and other biochemical markers can be used as reliable criteria for the selection of rose cultivars that are more resilient to biotic stress factors, especially powdery and downy mildew. Bridging fundamental research with practical applications, this study aims to contribute to the development of stress-tolerant rose cultivars adaptable to dynamic environmental conditions. Full article

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. Full article

Variations between fruit cultivars can significantly impact their biochemical composition. The present research examined the variability in the qualitative and quantitative content of phenolic compounds in berry extracts of Actinidia kolomikta and Actinidia arguta cultivars. Additionally, antioxidant activities of berry extracts were evaluated. The total phenolic, flavonoid, proanthocyanidin contents and hydroxycinnamic acid derivatives were determined using the appropriate methodologies. The average amount of phenolic compounds in A. kolomikta berries (177.80 mg/g) was three times higher than that of A. arguta (54.45 mg/g). Our findings revealed that berries of A. kolomikta and A. arguta accumulated, on average, 1.58 RE/g DW (rutin equivalent/g dry weight) and 0.615 mg RE/g DW of total flavonoids, 1439.31 mg EE/g DW (epicatechin equivalent/g dry weight) and 439.97 mg EE/g DW of proanthocyanidins, and 23.51 mg CAE/g DW (chlorogenic acid equivalent/g dry weight) and 5.65 mg CAE/g DW of hydroxycinnamic acid derivatives, respectively. The cultivars of both species were characterized by higher antioxidant activity of total phenolic compounds determined using CUPRAC and FRAP methods compared to the ABTS^•+ method. The variability in phenolic compounds’ qualitative and quantitative content in tested berry extracts was evaluated by applying ultra-high performance liquid chromatography (UHPLC) coupled to mass spectrometry in tandem with electrospray ionization. Significant intraspecific differences in the amounts of total phenolic compounds, total flavonoid compounds, proanthocyanidins, and hydroxycinnamic acid derivatives were determined among cultivars. Four phenolic acids, eight flavonols, two flavones, and five flavon-3-ols were identified in the berry extracts. Full article

Interplanting is an efficient method of improving nutrient utilization. However, the impact of intraspecific interplanting on rhizosphere microbial nitrogen cycling needs to be studied further. In this study, two corn cultivars were selected as the materials: Zhengdan958 (ZD958, high nitrogen use efficiency) and Denghai3622 (DH3622, low nitrogen use efficiency). Three planting patterns (interplanting, ZD958 monocropping, and DH3622 monocropping) were set up to study the effects of interplanting on crop growth and rhizosphere microbial nitrogen cycle function under two nitrogen levels: low nitrogen (140 kg N ha⁻¹) and normal nitrogen (280 kg N ha⁻¹). The results showed that the grain yield and nitrogen content in interplanting were significantly increased due to an enhanced leaf area index and root dry weight. The nitrogen accumulation and nitrogen use efficiency were enhanced by 8.14% and 19.38% in interplanting, which resulted in reductions in NH₄⁺ and NO₃⁻ content in the rhizosphere. Interplanting enhanced rhizosphere nitrogen cycling processes; nitrification, denitrification, and nitrate reduction were increased. This study demonstrated that interplanting promotes corn nitrogen acquisition from the soil and indirectly regulates rhizosphere microbial function. These findings imply that the intraspecific interplanting of crops with appropriate functional traits is a promising approach to establishing diversified, productive, and efficient resource utilization ecosystems. Full article

In the face of climate change, bringing more useful alleles and genes from wild relatives of wheat is crucial to develop climate-resilient varieties. We used two populations of backcrossed recombinant inbred lines (BIL1 and BIL2), developed by crossing and backcrossing two intra-specifically diverse Aegilops tauschii accessions from lineage 1 and lineage 2, respectively, with the common wheat cultivar ‘Norin 61′. This study aimed to identify quantitative trait loci (QTLs) associated with heat stress (HS) tolerance. The two BILs were evaluated under heat stress environments in Sudan for phenology, plant height (PH), grain yield (GY), biomass (BIO), harvest index (HI), and thousand-kernel weight (TKW). Grain yield was significantly correlated with BIO and TKW under HS; therefore, the stress tolerance index (STI) was calculated for these traits as well as for GY. A total of 16 heat-tolerant lines were identified based on GY and STI-GY. The QTL analysis performed using inclusive composite interval mapping identified a total of 40 QTLs in BIL1 and 153 QTLs in BIL2 across all environments. We detected 39 QTLs associated with GY-STI, BIO-STI, and TKW-STI in both populations (14 in BIL1 and 25 in BIL2). The QTLs associated with STI were detected on chromosomes 1A, 3A, 5A, 2B, 4B, and all the D-subgenomes. We found that QTLs were detected only under HS for GY on chromosome 5A, TKW on 3B and 5B, PH on 3B and 4B, and grain filling duration on 2B. The higher number of QTLs identified in BIL2 for heat stress tolerance suggests the importance of assessing the effects of intraspecific variation of Ae. tauschii in wheat breeding as it could modulate the heat stress responses/adaptation. Our study provides useful genetic resources for uncovering heat-tolerant QTLs for wheat improvement for heat stress environments. Full article