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Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 20 December 2025 | Viewed by 10328

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Dr. Luigi De Masi

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National Research Council (CNR), Institute of Biosciences and BioResources (IBBR), Via Università n. 133, 80055 Portici, Italy
Interests: plant agrobiodiversity; genetic and chemical variability; plant genetic resources; molecular characterization; biomolecular resources; DNA-based molecular markers; biosequences; DNA polymorphisms; bioinformatics; protein function prediction; nutrition and health; natural products; secondary metabolites; bioactive molecules; functional foods and nutraceuticals
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Dear Colleagues,

Molecular marker technology (MMT) comprises a keystone for modern geneticists and molecular biologists. Since its introduction, MMT has been commonly used for the analysis of genome architecture and polymorphisms in plants, greatly improving our ability to characterize genetic variation. MMT has also revolutionized plant breeding, leading to gene mapping and marker-assisted selection (MAS). MMT can allow for the identification of specific chromosomal regions associated with genes for traits of interest. Then, this information is exploited to transfer quality traits to improved varieties via MAS programs.

DNA polymorphisms have huge potential to detect evolutionary and genetic relationships between and within plant species, and can be useful in conserving biodiversity in natural and domesticated plant populations. Today more than ever, plant biodiversity has a key role in maintaining ecosystemic services and sustainable productions, guaranteeing food security, and increasing resistance and resilience to the global climate change and to invasive/native biotic stresses. In the near future, MMT represents a powerful tool available to perform molecular characterization of natural populations and germplasm collections so that potentially useful genes, new alleles, and genotypes (above all if endangered and rare) can be properly preserved from genetic erosion and exploited by the next generations.

Therefore, DNA polymorphism detection is of paramount importance for conducting natural variation studies and breeding. MMT offers a robust characterization system to increase our knowledge about plant biodiversity, the strength of which comes from the fact it is not influenced by environmental or developmental factors. MMT is mainly based on PCR applications for the detection of polymorphic DNA in plant species of agricultural or ecological interest. Nowadays, there is a wide availability of different types of DNA markers. However, with the aim of accelerating the discovery of DNA polymorphisms, more research should be carried out through the latest technologies, such as next-generation sequencing (NGS), to thoroughly analyse the genetic diversity of natural and cultivated plant species at the highest resolution possible. Indeed, bioinformatic analysis of genome sequences is revealing the impact of DNA polymorphisms on gene function, on the phenotype, and on evolutionary processes in plants.

All this considered, we would like to focus on the discovery, current methodologies, advantages, challenges, and applications of DNA polymorphisms as molecular markers. Reports on bioinformatics tools and biosequence databases are also welcomed. Thus, the aim of this Special Issue is to present relevant studies and recent progress across all aspects of plant biodiversity as seen through the lens of MMT.

Dr. Luigi De Masi
Guest Editor

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Keywords

plant biodiversity
plant genetic resources
genetic variability
molecular characterization
biomolecular resources
DNA-based molecular markers
DNA sequencing
next generation sequencing
biosequences
DNA polymorphisms
bioinformatics

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Published Papers (12 papers)

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18 pages, 2524 KiB

Open AccessArticle

Rapid Specific PCR Detection Based on THCAS and CBDAS for the Prediction of Cannabis sativa Chemotypes: Drug, Fiber, and Intermediate

by Patwira Boonjing, Worakorn Wiwatcharakornkul, Chayapol Tungphatthong, Taksina Chuanasa, Somchai Keawwangchai, Tae-Jin Yang, Wanchai De-Eknamkul and Suchada Sukrong

Int. J. Mol. Sci. 2025, 26(11), 5077; https://doi.org/10.3390/ijms26115077 - 24 May 2025

Viewed by 185

Abstract

Cannabis sativa L. is divided into three main groups: drug-type, intermediate-type, and fiber-type. The presence of tetrahydrocannabinol (THC) exceeding 0.2–0.3% in drug-type and intermediate Cannabis that utilized for recreational and medicinal purposes renders them illegal due to potential mental health implications. Fiber-type contains high cannabidiol (CBD) and low THC, making it suitable for household use such as textiles and animal feed. Accurate classification is essential to prevent misuse of the plant. High-performance thin-layer chromatography (HPTLC) and ultra-performance liquid chromatography (UPLC), used respectively for the qualitative and quantitative analyses of THC and CBD particularly in female inflorescences, categorized 85 samples of 46 cultivars used in this study into three distinct chemotypes. While chemotype analysis of a very specific organ of the plants accurately identifies Cannabis groups, it requires time-consuming plant development to maturity. Genotype analysis targeting tetrahydrocannabinolic acid synthase (THCAS) and cannabidiolic acid synthase (CBDAS) genes offers a faster alternative for classifying Cannabis types, allowing for sample determination from any part at any developmental stage of the plant. DNA sequencing allowed a phylogenetic analysis based on these genes, classifying all 85 samples of 46 cultivars into the same three groups identified by chemotype analysis. This study is the first to successfully examine the relationship between chemotype and genotype in 85 samples of 46 cultivars. Rapid identification of Cannabis types through genotype analysis lays the groundwork for future development of detection kits. Full article

(This article belongs to the Special Issue Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms)

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20 pages, 3276 KiB

Open AccessArticle

Harnessing Genomics for Breeding Lantana camara L.: Genotyping and Ploidy Testing of Clonal Lines Through ddRADseq Applications

by Angelo Betto, Fabio Palumbo, Damiano Riommi, Alessandro Vannozzi and Gianni Barcaccia

Int. J. Mol. Sci. 2025, 26(10), 4898; https://doi.org/10.3390/ijms26104898 - 20 May 2025

Viewed by 127

Abstract

Lantana camara L. is sold worldwide for ornamental purposes, although it is also characterized by high invasiveness potential. Genetic and molecular data available for L. camara are still poor, and breeding is performed through conventional methods. This study focused on a molecular genotyping analysis through the ddRADseq method on an experimental collection of lantana clonal lines to evaluate the potential of molecular techniques in performing marker-assisted breeding, in favour of variety registration and in guaranteeing plant variety protection for the species. Although high genetic uniformity was observed in the population, a unique molecular profile was assigned to every line, indicating the effectiveness of the approach used. Interestingly, low degrees of heterozygosity were observed. In addition, the possibility of inferring ploidy levels through SNP profiles was assessed since it would avoid the necessity of previous biological knowledge and the use of fresh materials. Ploidy analysis is of high interest for lantana breeding to obtain less invasive triploids. Flow cytometry and chromosome counting were used for inference assessment. An nQuack framework provided correct results for the majority of the clonal lines, confirming its effectiveness. These findings encourage the adoption of molecular systems to help breed minor species such as L. camara. Full article

(This article belongs to the Special Issue Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms)

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23 pages, 6786 KiB

Open AccessArticle

P-Type Pentatricopeptide Repeat Proteins YS1 and YS2 Function in Splicing of petB Intron to Maintain Chloroplast Homeostasis During Rice Seedling Development

by Hui Sun, Yanshen Nie, Li Yu, Xiaohong Yue, Xin Hou and Jie Zhao

Int. J. Mol. Sci. 2025, 26(9), 4459; https://doi.org/10.3390/ijms26094459 - 7 May 2025

Viewed by 213

Abstract

Regulating chloroplast gene expression is crucial for maintaining chloroplast function and plant development. Pentatricopeptide repeat (PPR) proteins form a vast protein family that regulates organelle genes and has multiple functions during plant development. Here, we found that two P-type PPR proteins, YS1 (yellow-green seedling 1) and YS2, jointly regulated seedling development in rice. The loss of YS1 and YS2 exhibited the collapsed chloroplast thylakoids and decreased photosynthetic activity, leading to the yellowing and death of rice seedlings. YS1 and YS2 could directly bind to the transcript of the psbH-petB intergenic region to facilitate the splicing of petB intron, thereby affecting the splicing efficiency of petD, which is located downstream of petB in the five-cistronic transcription unit psbB-psbT-psbH-petB-petD. The mutations in YS1 and YS2 led to decreased mature transcripts of petB and petD after splicing, significantly reducing the protein levels of PetB and PetD. This further led to deficiencies in the cytochrome b6/f and photosystem I complexes of the electron transport chain (ETC), ultimately resulting in decreased ETC-produced NADPH and reduced contents of carbohydrates in ys mutants. Moreover, transcriptome sequencing analysis revealed that YS1 and YS2 were vital for chloroplast organization and carbohydrate metabolism, as well as chloroplast RNA processing. In previous studies, the mechanism of petB intron splicing in the five-cistronic transcription unit psbB-psbT-psbH-petB-petD of rice is unclear. Our study revealed that the two highly conserved proteins YS1 and YS2 were functionally redundant and played critical roles in photosynthesis and seedling development through their involvement in petB intron splicing to maintain chloroplast homeostasis in rice. This work broadened the perspective on PPR-mediated chloroplast development and laid a foundation for exploring the biofunctions of duplicated genes in higher plants. Full article

(This article belongs to the Special Issue Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms)

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20 pages, 2710 KiB

Open AccessArticle

Elite Cacao Clonal Cultivars with Diverse Genetic Structure, High Potential of Production, and Good Organoleptic Quality Are Helping to Rebuild the Cocoa Industry in Brazil

by Lívia Souza Freitas, Gonçalo Santos Silva, Ivanildes Conceição dos Santos, Adriana C. Reis Ferreira, Laysa Evelin Silva Santos, Pathmanthan Umaharan, Lambert A. Motilal, Juan Calle-Bellido, Dapeng Zhang, Ronan Xavier Corrêa and Dário Ahnert

Int. J. Mol. Sci. 2025, 26(7), 3386; https://doi.org/10.3390/ijms26073386 - 4 Apr 2025

Viewed by 1387

Abstract

In the Americas’ leading cocoa-producing countries, more productive clonal cultivars than traditional biclonal hybrids have been created. In Brazil, several disease-resistant and self-compatible clones such as PS 1319, FA 13, and SJ 02 have been selected on producer farms. The CCN 51 clone from Ecuador is also significant in Brazil. This study aimed to analyze these clones concerning their genetic structures using single-nucleotide polymorphisms, productive potential, disease resistance, and the physico-chemical and organoleptic characteristics of the beans. Clone SJ 02 has ancestry from Contamana (40.7%), Iquitos (34.5%), and Amelonado (23.5%). PS 1319 is primarily Amelonado (67.9%), with Criollo (15.7%) and Contamana (15.6%). FA 13 mainly consists of Amelonado (53.5%) and Iquitos (44.1%). Local cultivars of Bahia are mostly Amelonado, with 99.8% in Comum and Parazinho, 97.4% in Maranhão, and 95.5% in Pará. PS 1319, SJ 02, and FA 13 clones were significantly more productive than CCN 51 but did not differ in disease resistance levels. Significant differences were noted among the cultivars in physicochemical traits (fat, caffeine, and theobromine content). Sensorially, SJ 02 outperformed the other cultivars and was comparable to the reference clone BN 34. The findings indicate that Brazil’s elite clones, derived from complex crosses involving Amelonado, Contamana, Iquitos, and Criollo groups, are productive, resistant, and exhibit favorable physico-chemical and organoleptic qualities, making them valuable for future clonal breeding programs. Full article

(This article belongs to the Special Issue Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms)

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17 pages, 2056 KiB

Open AccessArticle

Screening and Application of DNA Markers for Novel Quality Consistency Evaluation in Panax ginseng

by Siyuan Cai, Xuejiao Liao, Yidan Xi, Yang Chu, Shuang Liu, Hang Su, Deqiang Dou, Jiang Xu and Shuiming Xiao

Int. J. Mol. Sci. 2025, 26(6), 2701; https://doi.org/10.3390/ijms26062701 - 17 Mar 2025

Cited by 1 | Viewed by 340

Abstract

Quality control remains a challenge in traditional Chinese medicine (TCM). This study introduced a novel genetic-based quality control method for TCM. Genetic variations in ginseng were evaluated across whole-genome, chloroplast genome, and ITS2 DNA barcode dimensions. Significant genetic variations were found in whole-genome comparison, leading to the use of inter-simple sequence repeat markers to assess the genetic diversity of ginseng decoction pieces (PG), garden ginseng (GG), and ginseng under forest (FG). Fingerprints of ginseng samples revealed instability within some batches. These evaluations were transformed into information entropy to calculate the size of Hardy–Weinberg equilibrium population (HWEP). FG had significantly higher genetic and chemical minimum HWEP than GG (p < 0.05). Notably, a significant positive correlation was observed between the minimum HWEP for genetics and for chemistry (r = 0.857, p = 0.014). Genetic polymorphism analysis of ginseng has the potential to evaluate chemical quality consistency, offering a new method to ensure quality consistency in TCM. Full article

(This article belongs to the Special Issue Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms)

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19 pages, 4831 KiB

Open AccessArticle

Rapid Identification of Alien Chromosome Fragments and Tracing of Bioactive Compound Genes in Intergeneric Hybrid Offspring Between Brassica napus and Isatis indigotica Based on AMAC Method

by Yanhong Guo, Yutian Han, Jinxiang Gao, Xianhong Ge, Yanqing Luo, Kaiqin Zhao, Genze Li, Feng Zu and Xiaomao Cheng

Int. J. Mol. Sci. 2025, 26(5), 2091; https://doi.org/10.3390/ijms26052091 - 27 Feb 2025

Viewed by 402

Abstract

Distant hybridization between Brassica napus and related genera serves as an effective approach for rapeseed germplasm innovation. Isatis indigotica, a wild relative of Brassica, has emerged as a valuable genetic resource for rapeseed improvement due to its medicinal properties. This study employed anchor mapping of alien chromosomal fragment localization (AMAC) method to efficiently identify alien chromosomal fragments in the progeny derived from distant hybridization between I. indigotica and Brassica napus, ‘Songyou No. 1’. Based on the AMAC method, we developed 193,101 IP and SSR markers utilizing the I. indigotica reference genome (Woad-v1.0). Through Electronic-PCR analysis against the Brassica and I. indigotica pan-genome, 27,820 specific single-locus (SSL) IP and SSR markers were obtained. Subsequently, 205 pairs of IP primers and 50 pairs of SSR primers were synthesized randomly, among which 148 pairs of IP markers (72.20%) and 45 pairs of SSR markers (90%) were verified as SSL molecular markers for the I. indigotica genome with no amplification product in four Brassica crops. These 193 SSL markers enable precise identification of one complete I6 chromosome and three chromosomal fragments (I1:1.17 Mb, I5:2.61 Mb, I7:1.11 Mb) in ‘Songyou No. 1’. Furthermore, we traced 32 genes involved in bioactive compound biosynthesis within/near these alien segments in ‘Songyou No. 1’ and developed seven functional markers. This study not only validates the efficacy of SSL markers for detecting exogenous chromatin in intergeneric hybrids but also provides valuable insights for the precise identification and mapping of desired chromosomal fragments or genes embedded in the derivatives from distant hybridization and potential applications in marker-assisted breeding for medicinal plant via distant hybridization strategy between I. indigotica and Brassica crops. Full article

(This article belongs to the Special Issue Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms)

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14 pages, 3347 KiB

Open AccessArticle

Fine Mapping and Candidate Genes Analysis for Regulatory Gene of Anthocyanin Synthesis in the Corolla, Shedding Light on Wild Potato Evolution

by Zewei Zhang, Hongjun Li, Lingkui Zhang, Shaoguang Duan, Guangcun Li and Yanfeng Duan

Int. J. Mol. Sci. 2025, 26(5), 1966; https://doi.org/10.3390/ijms26051966 - 25 Feb 2025

Viewed by 382

Abstract

Petota includes more than 100 species (wild and cultivated), presenting a rich variety of corolla colors and associated traits. This variability provides important opportunities for investigating the differentiation of orthologous genes’ functions and their evolutionary pathways. However, the genetic underpinnings of this diversity in corolla colors are still to be further explored. In our previous study, a locus responsible for corolla color in potato was mapped to a 740 kb region on chromosome 10, which contains the AN2 gene previously identified as a regulation gene for corolla color. In the present study, this locus was further refined to a 380 kb interval through recombinant analysis. Targeted analysis of anthocyanidins and carotenoids revealed that purple corollas exhibit significantly higher levels of petunidin and delphinidin, while showing significantly lower levels of lutein and β-carotene compared to yellow corollas. Transcriptome and qRT-PCR analysis indicated that StMYB180, rather than AN2, is the candidate gene responsible for regulating coloration, specifically on the abaxial side of the corolla in potato. Expression analysis revealed that StMYB180 is exclusively highly expressed in corolla and leaf tissues, with purple coloration on the abaxial side of both corollas and leaves. Phylogenetic analysis further suggests that corolla color-regulatory genes may be closely tied to the origin and evolutionary trajectory of potato species. This study provides valuable insights into the regulation of tissue-specific expression of anthocyanin biosynthesis in potato and lays the groundwork for understanding the evolution of orthologous genes in the Petota section. Full article

(This article belongs to the Special Issue Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms)

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19 pages, 4765 KiB

Open AccessArticle

Unraveling the Ancient Introgression History of Xanthoceras (Sapindaceae): Insights from Phylogenomic Analysis

by Jian He, Mingyang Li, Huanyu Wu, Jin Cheng and Lei Xie

Int. J. Mol. Sci. 2025, 26(4), 1581; https://doi.org/10.3390/ijms26041581 - 13 Feb 2025

Viewed by 662

Abstract

Ancient introgression is an infrequent evolutionary process often associated with conflicts between nuclear and organellar phylogenies. Determining whether such conflicts arise from introgression, incomplete lineage sorting (ILS), or other processes is essential to understanding plant diversification. Previous studies have reported phylogenetic discordance in the placement of Xanthoceras, but its causes remain unclear. Here, we analyzed transcriptome data from 41 Sapindaceae samples to reconstruct phylogenies and investigate this discordance. While nuclear phylogenies consistently placed Xanthoceras as sister to subfam. Hippocastanoideae, plastid data positioned it as the earliest-diverging lineage within Sapindaceae. Our coalescent simulations suggest that this cyto-nuclear discordance is unlikely to be explained by ILS alone. HyDe and PhyloNet analyses provided strong evidence that Xanthoceras experienced ancient introgression, incorporating approximately 16% of its genetic material from ancestral subfam. Sapindoideae lineages. Morphological traits further support this evolutionary history, reflecting characteristics of both contributing subfamilies. Likely occurring during the Paleogene, this introgression represents a rare instance of cross-subfamily gene flow shaping the evolutionary trajectory of a major plant lineage. Our findings clarify the evolutionary history of Xanthoceras and underscore the role of ancient introgression in driving phylogenetic conflicts, offering a rare example of introgression-driven diversification in angiosperms. Full article

(This article belongs to the Special Issue Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms)

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18 pages, 4663 KiB

Open AccessArticle

Development of Genome-Wide SSR Markers in Leymus chinensis with Genetic Diversity Analysis and DNA Fingerprints

by Taiyou Ou, Zinian Wu, Chunyu Tian, Yanting Yang, Wenlong Gong, Jianjiang Niu and Zhiyong Li

Int. J. Mol. Sci. 2025, 26(3), 918; https://doi.org/10.3390/ijms26030918 - 22 Jan 2025

Viewed by 986

Abstract

Leymus chinensis, a major component of the plant community in the eastern Eurasian grasslands with a wide distribution, provides stability to grassland ecosystems and supports animal husbandry. This study aimed to bridge the gap between the molecular breeding and industrial application of L. chinensis by conducting a comprehensive simple sequence repeat (SSR) analysis. A total of 973,129 SSRs were identified in the L. chinensis whole genome, which was used to design 20 polymorphic pairs of SSR primers to further assess 105 L. chinensis accessions. On average, 33.55 alleles were detected per locus, with an average Shannon index of 2.939 and a polymorphic information content value of 0.910. Principal coordinate, maximum likelihood, and structure analyses consistently showed that all samples were coincidentally divided into four subclasses. In addition, Mantel test data indicated a weak correlation between genetic and geographical distances in L. chinensis, whose variability may be related to the pollination mode and natural selection pressures. Finally, we used the 20 pairs of selected markers to scan 105 accessions, constructing a fingerprint for them. These findings provide new foundations for identifying superior varieties, improving the management of genetic resources, and constructing a germplasm resource database for L. chinensis. Full article

(This article belongs to the Special Issue Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms)

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18 pages, 2372 KiB

Open AccessArticle

Exploring Taxonomic and Genetic Relationships in the Pinus mugo Complex Using Genome Skimming Data

by Joanna Sikora and Konrad Celiński

Int. J. Mol. Sci. 2024, 25(18), 10178; https://doi.org/10.3390/ijms251810178 - 22 Sep 2024

Viewed by 1283

Abstract

Genome skimming is a novel approach that enables obtaining large-scale genomic information based on high-copy DNA fractions from shallow whole-genome sequencing. The simplicity of this method, low analysis costs, and large amounts of generated data have made it widely used in plant research, including species identification, especially in the case of protected or endangered taxa. This task is particularly difficult in the case of closely related taxa. The Pinus mugo complex includes several dozen closely related taxa occurring in the most important mountain ranges in Europe. The taxonomic rank, origin, or distribution of many of these taxa have been debated for years. In this study, we used genome skimming and multilocus DNA barcoding approaches to obtain different sequence data sets and also to determine their genetic diversity and suitability for distinguishing closely related taxa in the Pinus mugo complex. We generated seven different data sets, which were then analyzed using three discrimination methods, i.e., tree based, distance based, and assembling species by automatic partitioning. Genetic diversity among populations and taxa was also investigated using haplotype network analysis and principal coordinate analysis. The proposed data set based on divergence hotspots is even twenty-times more variable than the other analyzed sets and improves the phylogenetic resolution of the Pinus mugo complex. In light of the obtained results, Pinus × rhaetica does not belong to the Pinus mugo complex and should not be identified with either Pinus uliginosa or Pinus rotundata. It seems to represent a fixed hybrid or introgressant between Pinus sylvestris and Pinus mugo. In turn, Pinus mugo and Pinus uncinata apparently played an important role in the origins of Pinus uliginosa and Pinus rotundata. Full article

(This article belongs to the Special Issue Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms)

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16 pages, 1678 KiB

Open AccessArticle

MassARRAY and SABER Analyses of SNPs in Embryo DNA Reveal the Abscission of Self-Fertilised Progeny during Fruit Development of Macadamia (Macadamia integrifolia Maiden & Betche)

by Anushika L. De Silva, Wiebke Kämper, Steven M. Ogbourne, Joel Nichols, Jack W. L. Royle, Trent Peters, David Hawkes, Shahla Hosseini Bai, Helen M. Wallace and Stephen J. Trueman

Int. J. Mol. Sci. 2024, 25(12), 6419; https://doi.org/10.3390/ijms25126419 - 11 Jun 2024

Cited by 3 | Viewed by 1255

Abstract

Yield in many crops is affected by abscission during the early stages of fruitlet development. The reasons for fruitlet abscission are often unclear but they may include genetic factors because, in some crops, self-pollinated fruitlets are more likely to abscise than cross-pollinated fruitlets. Pollen parentage can also affect final fruit size and fruit quality. Here, we aimed to understand the effects of pollen parentage on fruitlet retention and nut quality in orchards of macadamia (Macadamia integrifolia Maiden & Betche). We identified the pollen parent of macadamia ‘cultivar ‘816’ embryos by analysing single nucleotide polymorphisms (SNPs) in their DNA using customised MassARRAY and Single Allele Base Extension Reaction (SABER) methods. This allowed us to determine the proportions of self-fertilised and cross-fertilised progeny during premature fruit drop at 6 weeks and 10 weeks after peak anthesis, as well as at nut maturity. We determined how pollen parentage affected nut-in-shell (NIS) mass, kernel mass, kernel recovery, and oil concentration. Macadamia trees retained cross-fertilised fruitlets rather than self-fertilised fruitlets. The percentage of progeny that were cross-fertilised increased from 6% at 6 weeks after peak anthesis to 97% at nut maturity, with each tree producing on average 22 self-fertilised nuts and 881 cross-fertilised nuts. Three of the four cross-pollen parents provided fruit with significantly higher NIS mass, kernel mass, or kernel recovery than the few remaining self-fertilised fruit. Fruit that were cross-fertilised by ‘842’, ‘A4’, or ‘A203’ had 16–29% higher NIS mass and 24–44% higher kernel mass than self-fertilised fruit. Nuts that were cross-fertilised by ‘A4’ or ‘A203’ also had 5% or 6% higher kernel recovery, worth approximately $US460–540 more per ton for growers than self-fertilised nuts. The highly selective abscission of self-fertilised fruitlets and the lower nut quality of self-fertilised fruit highlight the critical importance of cross-pollination for macadamia productivity. Full article

(This article belongs to the Special Issue Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms)

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18 pages, 3646 KiB

Open AccessArticle

Development of Genome-Wide Intron Length Polymorphism (ILP) Markers in Tea Plant (Camellia sinensis) and Related Applications for Genetics Research

by Yuan Shen, Xiaoying He, Feng Zu, Xiaoxia Huang, Shihua Yin, Lifei Wang, Fang Geng and Xiaomao Cheng

Int. J. Mol. Sci. 2024, 25(6), 3241; https://doi.org/10.3390/ijms25063241 - 13 Mar 2024

Cited by 4 | Viewed by 1607

Abstract

The market value of tea is largely dependent on the tea species and cultivar. Therefore, it is important to develop efficient molecular markers covering the entire tea genome that can be used for the identification of tea varieties, marker-assisted breeding, and mapping important quantitative trait loci for beneficial traits. In this study, genome-wide molecular markers based on intron length polymorphism (ILP) were developed for tea trees. A total of 479, 1393, and 1342 tea ILP markers were identified using the PCR method in silico from the ‘Shuchazao’ scaffold genome, the chromosome-level genome of ‘Longjing 43’, and the ancient tea DASZ chromosome-level genome, respectively. A total of 230 tea ILP markers were used to amplify six tea tree species. Among these, 213 pairs of primers successfully characterize products in all six species, with 112 primer pairs exhibiting polymorphism. The polymorphism rate of primer pairs increased with the improvement in reference genome assembly quality level. The cross-species transferability analysis of 35 primer pairs of tea ILP markers showed an average amplification rate of 85.17% through 11 species in 6 families, with high transferability in Camellia reticulata and tobacco. We also used 40 pairs of tea ILP primers to evaluate the genetic diversity and population structure of C. tetracocca with 176 plants from Puan County, Guizhou Province, China. These genome-wide markers will be a valuable resource for genetic diversity analysis, marker-assisted breeding, and variety identification in tea, providing important information for the tea industry. Full article

(This article belongs to the Special Issue Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms)

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