Special Issue "Analysis of Crop Genetic and Germplasm Diversity"

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: 10 October 2020.

Special Issue Editors

Prof. Dr. Antonio M. De Ron
Website
Guest Editor
Misión Biológica de Galicia (MBG), CSIC, 36143 Pontevedra, Spain
Interests: agronomy; crop genetics and breeding; genetic resources; legumes; agrosystems; cropping systems
Dr. A. Paula Rodiño
Website
Guest Editor
Misión Biológica de Galicia (MBG), CSIC, 36143 Pontevedra, Spain
Interests: agronomy; crop genetics and breeding; genetic resources; legumes; interaction plant–soil microbiota

Special Issue Information

Dear Colleagues,

This Special Issue of Agronomy dedicated to the Analysis of Crop Genetic and Germplasm Diversity is aimed at publishing original research or review papers dedicated to the study of the diversity of crop genetic resources and genetics of cultivated plant species. Genetic resources are the basic element of the genetic study of crops and allow their genetic improvement. Likewise, the interactions of the plants with their agrosystem, the relevance of the different cropping systems, the resistance of crops to biotic and abiotic stresses, and the interactions with the soil microbiota are relevant aspects, as well as the adaptation of the plants to different environmental conditions under the current changing conditions.

These aspects will be included in the Special Issue, although not exclusively, since other aspects related to the Analysis of Crop Genetic and Germplasm Diversity will also be welcome in this volume.

Prof. Antonio M. De Ron
Dr. A. Paula Rodiño
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • crop genetics
  • agrobiodiversity
  • biology of agrosystems
  • germplams diversity
  • genetic improvement of crops
  • adaptation of crops
  • cropping systems

Published Papers (18 papers)

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Research

Open AccessArticle
Assessment of Agro-Morphologic Performance, Genetic Parameters and Clustering Pattern of Newly Developed Blast Resistant Rice Lines Tested in Four Environments
Agronomy 2020, 10(8), 1098; https://doi.org/10.3390/agronomy10081098 - 29 Jul 2020
Abstract
Multi-environmental yield trial is very vital in assessing newly developed rice lines for its adaptability and stability across environments especially prior to release of the newly developed variety for commercial cultivation. The growth performance and phenotypic variability of these genotypes are the combination [...] Read more.
Multi-environmental yield trial is very vital in assessing newly developed rice lines for its adaptability and stability across environments especially prior to release of the newly developed variety for commercial cultivation. The growth performance and phenotypic variability of these genotypes are the combination of environment, genotype and genotype by environment (G×E) interaction factors. Thus, evaluation creates an opportunity for effective selection of superior genotypes. The objectives of this study were to evaluate the newly developed blast resistant rice lines in varied environmental conditions, precisely measure the response of the advanced lines in multiple environments and classify the genotypes into groups that could serve as varieties for commercial cultivation. Genetic materials included 18 improved blast resistant rice lines and the recipient parent MR219. The total of 19 newly developed genotypes was evaluated under four varied environments in Peninsular Malaysia. The experiments were carried out using randomized complete block design (RCBD) with three replications at each environment. Data were collected on the vegetative, yield and yield component traits. Descriptive statistics (mean performance) and analysis of variance were conducted using SAS Software version 9.4. Genotypic and phenotypic coefficients, phenotypic variance component, heritability and genetic advance were also determined. Analysis of variance revealed that all traits were significantly different for genotypes except days to maturity, number of filled grains and total number of grains. Meanwhile, all the traits differed significantly for genotype × environment (G×E) except number of tillers per hill and number of panicles per hill. Low heritability (<30%) was found for all the traits. Similarly, low genetic advance was also observed for all the traits except for number of tillers per hill and number of panicles per hill. yield per hectare had significant and positive correlation with most evaluated traits except for days to flowering, days to maturity, plant height and number of unfilled grains. Cluster analysis classified the 19 evaluated genotypes into six groups. Therefore, the six clusters/groups of genotypes were recommended as varieties for commercial cultivation in Malaysia and other rice growing regions. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
Isolate-Dependent Inheritance of Resistance Against Pseudoperonospora cubensis in Cucumber
Agronomy 2020, 10(8), 1086; https://doi.org/10.3390/agronomy10081086 - 27 Jul 2020
Abstract
Six wild accessions of Cucumis sativum were evaluated for resistance against each of the 23 isolates of the downy mildew oomycete Pseudoperonospora cubensis. The isolates originated from Israel, Europe, USA, and Asia. C. sativum PI 197088 (India) and PI 330628 (Pakistan) exhibited [...] Read more.
Six wild accessions of Cucumis sativum were evaluated for resistance against each of the 23 isolates of the downy mildew oomycete Pseudoperonospora cubensis. The isolates originated from Israel, Europe, USA, and Asia. C. sativum PI 197088 (India) and PI 330628 (Pakistan) exhibited the highest level of resistance against multiple isolates of P. cubensis. Resistance was manifested as reduced lesion number, lesion size, sporangiophores and sporangia per lesion and enhanced encasement of haustoria with callose and intensive accumulation of lignin in lesions of both Plant Introductions (PIs) compared to the susceptible C. sativum SMR-18. In the field, much smaller AUDPC (Area Under Disease Progress Curve) values were recorded in PI 197088 or PI 330628 as compared to SMR-18. Each PI was crossed with SMR-18 and offspring progeny plants were exposed to inoculation with each of several isolates of P. cubensis in growth chambers and the field during six growing seasons. F1 plants showed partial resistance. F2 plants showed multiple phenotypes ranging from highly susceptible (S) to highly resistant (R, no symptoms) including moderately resistant (MR) phenotypes. The segregation ratio between phenotypes in growth chambers ranged from 3:1 to 1:15, depending on the isolate used for inoculation, suggesting that the number of genes, dominant, partially dominant, or recessive are responsible for resistance. In the field, the segregation ratio of 1:15, 1:14:1, or 1:9:6 was observed. F2 progeny plants of the cross between the two resistant PI’s were resistant, except for a few plants that were partially susceptible, suggesting that some of the resistance genes in PI 197088 and PI 330328 are not allelic. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
The Variability of Puroindoline-Encoding Alleles and Their Influence on Grain Hardness in Modern Wheat Cultivars Cultivated in Poland, Breeding Lines and Polish Old Landraces (Triticum aestivum L.)
Agronomy 2020, 10(8), 1075; https://doi.org/10.3390/agronomy10081075 - 25 Jul 2020
Abstract
Wheat (Triticum aestivum L.) grain hardness is determined mainly by variations in puroindoline genes (Pina-D1 and Pinb-D1), which are located on the short arm of chromosome 5D. This trait has a direct effect on the technological properties of the flour [...] Read more.
Wheat (Triticum aestivum L.) grain hardness is determined mainly by variations in puroindoline genes (Pina-D1 and Pinb-D1), which are located on the short arm of chromosome 5D. This trait has a direct effect on the technological properties of the flour and the final product quality. The objective of the study was to analyze the mutation frequency in both Pin genes and their influence on grain hardness in 118 modern bread wheat cultivars and breeding lines cultivated in Poland, and 80 landraces from Poland. The PCR products containing the Pin gene coding sequences were sequenced by the Sanger method. Based on detected the SNPs (single-nucleotide polymorphisms) we designed CAPS (cleaved amplified polymorphic sequence) markers for the fast screening of Pinb alleles in a large number of genotypes. All analyzed cultivars, breeding lines, and landraces possess the wild-type Pina-D1a allele. Allelic variation was observed within the Pinb gene. The most frequently occurring allele in modern wheat cultivars and breeding lines (over 50%) was Pinb-D1b. The contribution of the remaining alleles (Pinb-D1a, Pinb-D1c, and Pinb-D1d) was much less (approx. 15% each). In landraces, the most frequent allele was Pinb-D1a (over 70%), followed by Pinb-D1b (21% frequency). Pinb-D1c and Pinb-D1g were found in individual varieties. SKCS (single-kernel characterization system) analysis revealed that grain hardness was strictly connected with Pinb gene allelic variation in most tested cultivars. The mean grain hardness values were significantly greater in cultivars with mutant Pinb variants as compared to those with the wild-type Pinb-D1a allele. Based on grain hardness measured by SKCS, we classified the analyzed cultivars and lines into different classes according to a previously proposed classification system. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
Analysis of Proteomic Profile of Contrasting Phosphorus Responsive Rice Cultivars Grown under Phosphorus Deficiency
Agronomy 2020, 10(7), 1028; https://doi.org/10.3390/agronomy10071028 - 16 Jul 2020
Abstract
Phosphorus (P) deficiency is one of the major limiting factors for crop productivity. The yield of rice (Oryza sativa L.) is severely limited by phosphorus deficiency. An attempt has been made in this study to identify P deficiency responsive differentially expressed proteins [...] Read more.
Phosphorus (P) deficiency is one of the major limiting factors for crop productivity. The yield of rice (Oryza sativa L.) is severely limited by phosphorus deficiency. An attempt has been made in this study to identify P deficiency responsive differentially expressed proteins of rice through analysis of leaf proteome of contrasting P-responsive rice cultivars under P deficiency conditions because genetic variability has been found in the rice cultivars for adaptive response to P deficiency and a controlled regulatory system is involved in the P deficiency adaptation response. Phosphorus-efficient (cv. Panvel) and P-inefficient (cv. Nagina 22) rice cultivars were hydroponically grown in the nutrient medium under control environmental conditions at low-P level (2.0 µM) and optimum-P level (320 µM) treatments. Expression patterns of the proteins of the leaves of both the cultivars were analyzed in 30-day-old plants. The identification of these proteins through mass spectrometry and MASCOT software (Matrix Science Inc., Boston, USA) revealed that these differentially expressed proteins were homologous to known functional proteins involved in energy metabolism, biosynthesis, photosynthesis, signaling, protein synthesis, protein folding, phospholipid metabolism, oxidative stress, transcription factors, and phosphorus metabolism. It has been observed that rice cultivars responded differently to low-P treatment through modification in protein expressions pattern to maintain the growth of the plants. Therefore, the expression patterns of proteins were different in both of the cultivars under low-P treatment. Higher potential of protein stability, stress tolerance, osmo-protection, and regulation of phosphorus uptake was observed in cv. Panvel than cv. Nagina 22. This study could help to unravel the complex regulatory process that is involved in adaptation to P deficiency in rice. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
Genetic Variation and Sequence Diversity of Starch Biosynthesis and Sucrose Metabolism Genes in Sweet Potato
Agronomy 2020, 10(5), 627; https://doi.org/10.3390/agronomy10050627 - 29 Apr 2020
Abstract
Knowledge of genetic variations can provide clues into the molecular mechanisms regulating key crop traits. Sweet potato (Ipomoea batatas (L.) Lam.) is an important starch-producing crop, but little is known about the genetic variations in starch biosynthesis and sucrose metabolism genes. Here, [...] Read more.
Knowledge of genetic variations can provide clues into the molecular mechanisms regulating key crop traits. Sweet potato (Ipomoea batatas (L.) Lam.) is an important starch-producing crop, but little is known about the genetic variations in starch biosynthesis and sucrose metabolism genes. Here, we used high-throughput sequencing of pooled amplicons of target genes to identify sequence variations in 20 genes encoding key enzymes involved in starch biosynthesis and sucrose metabolism in 507 sweet potato germplasms. After filtering potential variations between gene copies within the genome, we identified 622 potential allelic single nucleotide polymorphisms (SNPs) and 85 insertions/deletions (InDels), including 50 non-synonymous SNPs (nsSNPs) and 12 frameshift InDels. Three nsSNPs were confirmed to be present in eight sweet potato varieties with various starch properties using cleaved amplified polymorphic sequence (CAPS) markers. Gene copy with loss of the fifth intron was detected in IbAGPb3 genes, and loss of multiple introns were observed in IbGBSS1-1 genes and various among germplasms based on intron length polymorphism (ILP) markers. Thus, we identified sequence variations between germplasms in 20 genes involved in starch biosynthesis and sucrose metabolism, and demonstrated the diversity in intron-loss alleles among sweet potato germplasms. These findings provide critical genetic information and useful molecular markers for revealing regulatory mechanism of starch properties. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
Development of a Multipurpose Core Collection of Bread Wheat Based on High-Throughput Genotyping Data
Agronomy 2020, 10(4), 534; https://doi.org/10.3390/agronomy10040534 - 08 Apr 2020
Abstract
Modern plant breeding practices have narrowed the genetic base of wheat throughout the world, increasing crop vulnerability. Therefore, there is clearly a need for introducing new germplasm in breeding programs to search for variability related to traits of agronomic interest for wheat improvement. [...] Read more.
Modern plant breeding practices have narrowed the genetic base of wheat throughout the world, increasing crop vulnerability. Therefore, there is clearly a need for introducing new germplasm in breeding programs to search for variability related to traits of agronomic interest for wheat improvement. The existence of subsets of accessions (core collections) that represent the diversity conserved in germplasm collections is a favored approach for breeders to explore novel variation and enhance the use of germplasm. In this study, a core collection of Spanish landraces of bread wheat has been created using high-throughput genotyping technologies (DArTseq), which yielded more than 50 K molecular markers. This marker system not only provides a robust estimate of the diversity, but also information about its distribution in the genome. Two core collections of 94 entries were created by using two common sampling strategies: the maximization strategy and the population structure-based method. Both core collections showed high geographic, phenotypic and genetic representativeness, but the collection obtained with the maximization strategy captured better the diversity displayed by the initial collection. This core collection, which includes a broad range of adapted genotypes, can be efficiently utilized for mining new alleles for useful traits in wheat breeding. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
Biomorphological Characterization of Brazilian Capsicum Chinense Jacq. Germplasm
Agronomy 2020, 10(3), 447; https://doi.org/10.3390/agronomy10030447 - 24 Mar 2020
Abstract
Loss of biodiversity and ecosystem degradation become major concerns worldwide, making the conservation process an important strategy for maintaining biodiversity. Capsicum chinense Jacq. is the most Brazilian species of the genus, with representatives in different biomes. Anthropic pressure, such as burns, real estate [...] Read more.
Loss of biodiversity and ecosystem degradation become major concerns worldwide, making the conservation process an important strategy for maintaining biodiversity. Capsicum chinense Jacq. is the most Brazilian species of the genus, with representatives in different biomes. Anthropic pressure, such as burns, real estate speculation, and changing cultivation habit has led to risks of genetic erosion. Conservation and characterization of conserved accessions are paramount to ensure genetic diversity, useful for the bioeconomy and for genetic improvement. We report the characterization of 55 C. chinense accessions from four different regions of Brazil and one accession from Peru. The accessions were characterized based on 37 morpho-agronomic variables, Inter Simple Sequence Repeats—ISSR and Simple Sequence Repeat—SSR. Qualitative descriptors were analyzed using a descriptive statistical, while the quantitative descriptors were analyzed via F test and significant differences in mean values were separated using Scott-Knott test. The relative contribution of each quantitative trait was determined. A correlation between morphological and molecular distances was calculated. Color of ripe fruit and fruit shape had the largest number of observed classes. Six distinct groups and the joint analysis presented an entanglement rate of 0.58, evidencing the divergence of accessions between the groups of both dendrograms. Bayesian analysis allowed the distinction of two clusters for SSR. A significant variability was observed among accession with potential to integrate several breeding programs. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
Genetic Variability of Eggplant Germplasm Evaluated under Open Field and Glasshouse Cropping Conditions
Agronomy 2020, 10(3), 436; https://doi.org/10.3390/agronomy10030436 - 23 Mar 2020
Abstract
Knowledge of agro-morphological genetic variation and cropping conditions on vegetative and yield-related traits plays a significant role in varietal improvement and production of eggplant (Solanum melongena L.). Following this premise, the current study was conducted to critically asses the genetic variation of [...] Read more.
Knowledge of agro-morphological genetic variation and cropping conditions on vegetative and yield-related traits plays a significant role in varietal improvement and production of eggplant (Solanum melongena L.). Following this premise, the current study was conducted to critically asses the genetic variation of 29 eggplant accessions by using agro-morphological characterization evaluated under two cropping conditions, namely, glasshouse and open field. The experiments were laid out in randomized complete block design (RCBD) with three replications. Data on vegetative and yield characteristics were collected and subjected to analysis of variance (ANOVA) using SAS 9.4, while variance components were estimated manually. The results obtained from the analysis of variance indicated a highly significant difference (p ≤ 0.01) for all characteristics studied in both cropping conditions. The evaluated accessions were grouped into six major clusters based on agro-morphological traits using Unweighted Pair Group Method with Arithmetic mean (UPGMA) dendrogram. Hence, crosses between group I with VI or V could be used to attain higher heterosis and vigor among the accessions. Also, this evaluation could be used as a selection criterion for important yield agronomic traits in eggplant. The methodology and the approaches used may provide a model for the enhancement of other vegetable crop diversity towards adaptability to the cropping condition decision. This result displayed importance for preserving eggplant germplasm for future varietal development and revealed that open field cropping condition is more suitable under Malaysia’s agroecology. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
Genetic Basis Dissection for Eating and Cooking Qualities of Japonica Rice in Northeast China
Agronomy 2020, 10(3), 423; https://doi.org/10.3390/agronomy10030423 - 20 Mar 2020
Abstract
The japonica rice in Northeast China is famous because of its high quality. Eating and cooking qualities (ECQs) are the most important factors that determine cooked rice quality. However, the genetic basis of ECQ of japonica varieties in Northeast China needs further study. [...] Read more.
The japonica rice in Northeast China is famous because of its high quality. Eating and cooking qualities (ECQs) are the most important factors that determine cooked rice quality. However, the genetic basis of ECQ of japonica varieties in Northeast China needs further study. In this study, 200 japonica varieties that are widely distributed in Northeast China were collected to evaluate the physicochemical indices of grain ECQs. The distribution of each trait was concentrated without large variations. Correlation analysis indicated that gel consistency (GC) had a significantly negative correlation with gelatinization temperature (GT). By integrating various analyses including kinship calculation, principal component analysis (PCA), linkage disequilibrium (LD) analysis, and original parent investigation, we found that the japonica varieties in Northeast China exhibited a narrow genetic basis. An association study for grain ECQs was performed and eight quantitative trait loci (QTLs) were detected. ALK was the major locus that regulated GT and also significantly affecting GC. Through the linkage disequilibrium (LD) and expression pattern analysis, one possible candidate gene (LOC_Os02g29980) was predicted and required further research for validation. Additionally, a different allele of Wx was identified in the variety CH4126, and ALK was not fixed in these japonica varieties. These results further elucidate the genetic basis of ECQs of japonica varieties in Northeast China and provide local breeders some assistance for improving ECQs of rice grain in rice breeding. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
Nucleotide Diversity and Association Analysis of ZmMADS60 with Root Length in the Maize Seedling Stage
Agronomy 2020, 10(3), 342; https://doi.org/10.3390/agronomy10030342 - 02 Mar 2020
Abstract
Root length is a determining factor of the root system architecture, which is essential for the uptake of water, nutrients and plant anchorage. In this study, ZmMADS60 was resequenced in 285 inbred lines, 68 landraces and 32 teosintes to detect the nucleotide diversity [...] Read more.
Root length is a determining factor of the root system architecture, which is essential for the uptake of water, nutrients and plant anchorage. In this study, ZmMADS60 was resequenced in 285 inbred lines, 68 landraces and 32 teosintes to detect the nucleotide diversity and natural variations associated with root length. Nucleotide diversity and neutral tests revealed that ZmMADS60 might be selected in domestication and improvement processes. ZmMADS60 in maize retained only 40.1% and 66.9% of the nucleotide diversity found in teosinte and landrace, respectively. Gene-based association analysis of inbred lines identified nine variants that were significantly associated with primary root length (PRL), lateral root length (LRL), root length between 0 mm and 0.5 mm in diameter (RL005) and total root length (TRL). One single-nucleotide polymorphism SNP1357 with pleiotropic effects was significantly associated with LRL, RL005 and TRL. The frequency of the increased allele T decreased from 68.8% in teosintes to 52.9% and 38.9% in the landrace and inbred lines, respectively. The frequency of the increased allele of another significant SNP723 associated with PRL also decreased during the maize domestication and improvement processes. The results of this study reveal that ZmMADS60 may be involved in the elongation of primary and lateral roots in the seedling stage and that significant variants can be used to develop functional markers to improve root length in maize. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
A 1Ns Disomic Addition from Psathyrostachys Huashanica Keng Confers Resistance to Powdery Mildew in Wheat
Agronomy 2020, 10(2), 312; https://doi.org/10.3390/agronomy10020312 - 24 Feb 2020
Abstract
Powdery mildew is a fungal disease that threatens wheat production throughout the world. Breeding resistant cultivars is an effective way to reduce harm caused by powdery mildew. In this study, 35 wheat-Psathyrostachys huashanica-derived lines were developed by crossing common wheat and [...] Read more.
Powdery mildew is a fungal disease that threatens wheat production throughout the world. Breeding resistant cultivars is an effective way to reduce harm caused by powdery mildew. In this study, 35 wheat-Psathyrostachys huashanica-derived lines were developed by crossing common wheat and P. huashanica Keng (2n = 2x = 14, NsNs) using embryo culture. Resistance to powdery mildew in the derived lines was identified at the seedling and adult stages. Line H5-5-4-2 was selected with immunity to powdery mildew at both growth stages. The chromosome structure of this line was characterized by cytology, genomic in situ hybridization (GISH), and expressed sequence tag-sequence-tagged site (EST-STS) analysis. The chromosome configuration was 2n = 44 = 22II. Two P. huashanica chromosomes with strong hybridization signals were detected by GISH analysis. Among 83 EST-STS markers that covered all seven homologous groups in wheat, three pairs of STS markers, BE497584, BF202643, and BG262410, located in wheat homologous group 1 amplified clear specific bands related to P. huashanica. The results indicated that resistant line H5-5-4-2 was a wheat-P. huashanica 1Ns disomic addition line. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
Estimation of Genetic Diversity in Seven Races of Native Maize from the Highlands of Mexico
Agronomy 2020, 10(2), 309; https://doi.org/10.3390/agronomy10020309 - 22 Feb 2020
Abstract
Characterizing the genetic diversity of maize (Zea mays L.) populations by their morphological and molecular attributes makes it possible to place populations into specific groups; thus, facilitating the design of procedures for their optimum and sustainable use. In this study, data from [...] Read more.
Characterizing the genetic diversity of maize (Zea mays L.) populations by their morphological and molecular attributes makes it possible to place populations into specific groups; thus, facilitating the design of procedures for their optimum and sustainable use. In this study, data from two lines of evidence were analyzed simultaneously to robustly classify maize populations and to determine their genetic relationships. Seven maize races of the central high plateau of Mexico were characterized using a combined analysis of 13 morphological traits and 31 microsatellite loci. The germplasm assessed included samples of 119 accessions held at Mexican germplasm banks. Cluster and principal component analyses were performed. Also, genetic and geographic relationships among the accessions were determined. Principal component analysis separated the different accessions into well-defined groups using first three principal components. The accessions of Arrocillo Amarillo and Elotes Cónicos races did not exhibit a grouping pattern, indicating greater genetic complexity. Better grounded grouping and phylogenetic relationships were obtained when traits of both lines of evidence were used simultaneously. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
Allelic Variation for Prolamins in Spanish Durum Wheat Landraces and Its Relationship with Quality Traits
Agronomy 2020, 10(1), 136; https://doi.org/10.3390/agronomy10010136 - 16 Jan 2020
Cited by 1
Abstract
Wheat landraces are currently being explored mainly as a source of allelic variation related to crop resilience and low-input adaptation. Characterization of their high- and low-molecular weight glutenin subunits can aid breeders to select as donor local materials those ensuring good end-use properties [...] Read more.
Wheat landraces are currently being explored mainly as a source of allelic variation related to crop resilience and low-input adaptation. Characterization of their high- and low-molecular weight glutenin subunits can aid breeders to select as donor local materials those ensuring good end-use properties in the derived elite cultivars. By using protein electrophoretic methods, we have determined the prolamin allelic profile of 116 Spanish durum wheat landraces. Their quality properties (as defined by grain protein content, sodium dodecyl sulfate (SDS) sedimentation volume and mixograph behavior) have also been assessed. The study has identified six novel glutenin alleles plus some other rare alleles some of which have been associated with improved durum wheat quality. Most of the novel variation detected needs to be characterized in a wider sample of varieties to establish any eventual beneficial effect on functional quality. Further analysis of the quality properties associated to specific allele combinations of Glu-A3, Glu-B3, and Glu-A1 has disclosed some clues on the influence on quality of certain non-allelic interactions between these main prolamin-encoding loci. Some of the landraces, showing outstanding values for the gluten quality parameters analyzed, might be directly used by farmers interested in the cultivation of traditional varieties for specialized food markets. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
Molecular Genetic Diversity and Population Structure of Ginseng Germplasm in RDA-Genebank: Implications for Breeding and Conservation
Agronomy 2020, 10(1), 68; https://doi.org/10.3390/agronomy10010068 - 03 Jan 2020
Abstract
Ginseng (Panax ginseng C.A. Meyer), commonly known as Korean or Asian ginseng, is a perennial herb native to Korea and China. There has been limited research effort to analyze the genetic diversity and population structure of ginseng germplasm because of its growth [...] Read more.
Ginseng (Panax ginseng C.A. Meyer), commonly known as Korean or Asian ginseng, is a perennial herb native to Korea and China. There has been limited research effort to analyze the genetic diversity and population structure of ginseng germplasm because of its growth habits. In the present study, genetic diversity and population structure of ginseng germplasm conserved in the National Agrobiodiversity Center (NAC) of South Korea were analyzed to provide basic data for future preservation and breeding of ginseng genetic resources. Seventeen simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 1109 ginseng accessions. Among 1109 ginseng accessions, 1042 (94.0%) accessions were landraces and 66 (6.0%) accessions were breeding lines (61 accessions, 5.5%) or cultivars (5 accessions, 0.5%). SSR markers revealed 56 different alleles with an average of 3.29 alleles per locus. The average gene diversity was 0.49. Analysis of molecular variance showed that 91% of allelic diversity was attributed to individual accessions within clusters while only 9% was distributed among clusters. Using discriminant analysis of principal components, 12 clusters were detected in 1109 ginseng accessions. The results of this study provide molecular evidence for the narrow genetic base of ginseng germplasm in NAC. For the broad understanding and efficient use of ginseng germplasm, it is necessary to analyze functional factors and to evaluate morphological traits. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
Multi-Level Characterization of Eggplant Accessions from Greek Islands and the Mainland Contributes to the Enhancement and Conservation of this Germplasm and Reveals a Large Diversity and Signatures of Differentiation between both Origins
Agronomy 2019, 9(12), 887; https://doi.org/10.3390/agronomy9120887 - 13 Dec 2019
Cited by 2
Abstract
Crop landraces are found in many inhabited islands of Greece. Due to the particularity of environment and isolation from the mainland, Greek islands represent a natural laboratory for comparing the diversity of landraces from the islands with those of the Greek mainland. A [...] Read more.
Crop landraces are found in many inhabited islands of Greece. Due to the particularity of environment and isolation from the mainland, Greek islands represent a natural laboratory for comparing the diversity of landraces from the islands with those of the Greek mainland. A collection of 36 Greek eggplant landraces and traditional cultivars from the mainland and the islands has been phenotypically and genetically characterized using 22 morphological descriptors and 5 SSR markers. The mineral composition (K, Mg, Cu, Fe, Mn, Zn) of fruits was also determined. The objectives of this study include the multi-level characterization of eggplant local landraces and the comparison of diversity among accessions from the Greek mainland and the islands. Characterization of eggplant landraces will contribute to the enhancement and prevention of genetic erosion in this local group and will provide a resource for future investigation and breeding. PCA analysis of morphological traits explained 45.4% of the total variance revealing the formation of two clusters, one with most of the island accessions, and another with most of the mainland ones. The SSR markers used exhibited high average values for the number of alleles/locus (4.6), expected heterozygosity (0.60) and PIC (0.55), while the observed heterozygosity was low (0.13). Both STRUCTURE and PCoA analyses based on SSR data revealed two genetic clusters, one made up mainly by the mainland accessions, while the other one was mainly made up by the island accessions. Although there was considerable variation among the landraces for the concentration of minerals studied, only average Mg concentration was significantly different between mainland and island accessions. Based on our data, the Greek eggplant landraces present considerable morphological and genetic diversity with some differentiation signatures between the island and the mainland accessions. Our results have implications for conservation of Greek landraces and suggest that Greece might be considered as part of a secondary center of diversity for eggplant in the Mediterranean basin. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
Variability in Nutraceutical Lipid Content of Selected Rice (Oryza sativa L. spp. indica) Germplasms
Agronomy 2019, 9(12), 823; https://doi.org/10.3390/agronomy9120823 - 30 Nov 2019
Cited by 1
Abstract
Rice (Oryza sativa L.) contains many high-value nutritional compounds, including nutraceutical lipid compounds that offer health benefits. An understanding of the genetic variability in the lipid contents of different rice germplasms is necessary to support breeding programs. The goals of this study [...] Read more.
Rice (Oryza sativa L.) contains many high-value nutritional compounds, including nutraceutical lipid compounds that offer health benefits. An understanding of the genetic variability in the lipid contents of different rice germplasms is necessary to support breeding programs. The goals of this study were: i) to investigate varietal differences in levels of the nutraceutical lipid α-tocopherol, γ-oryzanol, campesterol, β-sitosterol, octacosanol, and squalene and ii) to identify clusters of rice germplasms based on their lipid contents. Eighty-three indica rice subspecies were evaluated using a randomized complete block design with three replications. Research was conducted in Thailand during the 2016 rice-growing season. Significant differences were found among genotypes across all traits. The largest variation was found for β-sitosterol, followed by campesterol, octacosanol, and α-tocopherol. Variation in squalene content was small. Four principal components were found that accounted for 93.47% of overall variability. β-sitosterol, campesterol, and squalene were the principal discriminatory constituents. No significant correlation was found between color parameters and levels of these compounds, suggesting that former are of little use as an indirect marker for selection of fat-soluble nutraceuticals. Cluster analysis sorted the germplasm into nine clusters, based on their nutraceutical lipid content. TU-010, TU-027, TU-093, and TU-244 genotypes had the highest levels, making them a potentially useful genetic resource in breeding programs for nutraceutically-improved rice. The findings of this study can support the introduction of novel rice varieties with high added-value bioactive properties. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
Genetic Diversity of Sweet Potato (Ipomoea batatas L. Lam) Germplasms Collected Worldwide Using Chloroplast SSR Markers
Agronomy 2019, 9(11), 752; https://doi.org/10.3390/agronomy9110752 - 13 Nov 2019
Cited by 1
Abstract
Sweet potato (Ipomoea batatas L. Lam) is an important food crop widely cultivated in the world. In this study, nine chloroplast simple sequence repeat (cpSSR) markers were used to analyze the genetic diversity and relationships of 558 sweet potato accessions in the [...] Read more.
Sweet potato (Ipomoea batatas L. Lam) is an important food crop widely cultivated in the world. In this study, nine chloroplast simple sequence repeat (cpSSR) markers were used to analyze the genetic diversity and relationships of 558 sweet potato accessions in the germplasm collection of the National Agrobiodiversity Center (NAC). Eight of the nine cpSSR showed polymorphisms, while Ibcp31 did not. The number of alleles per locus ranged from two to four. In general, the Shannon index for each cpSSR ranged from 0.280 to 1.123 and the diversity indices and unbiased diversity ranged from 0.148 to 0.626, and 0.210 to 0.627, respectively. Results of the median-joining network showed 33 chlorotypes in 558 sweet potato accessions. In factor analysis, 558 sweet potato accessions were divided into four clusters, with clusters I and II composed only of the sweet potato accessions from Korea, Japan, Taiwan, and the USA. The results of this study confirmed that the genetic diversity of the female parents of sweet potato accessions conserved at the NAC is low and therefore more sweet potato accessions need to be collected. These results will help to establish an efficient management plan for sweet potato genetic germplasms at the NAC. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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Open AccessArticle
Exploring the Genetic Diversity and Population Structure of Turkish Laurel Germplasm by the iPBS-Retrotransposon Marker System
Agronomy 2019, 9(10), 647; https://doi.org/10.3390/agronomy9100647 - 17 Oct 2019
Cited by 1
Abstract
Laurel is a medicinally important plant and is known to the world for its essential oil. Turkey is the main market in the laurel leaf trade by sharing about 90% of the world trade. Here we made an effort to elucidate genetic diversity [...] Read more.
Laurel is a medicinally important plant and is known to the world for its essential oil. Turkey is the main market in the laurel leaf trade by sharing about 90% of the world trade. Here we made an effort to elucidate genetic diversity and population structure of 94 Turkish laurel genotypes collected from 26 provinces and four geographical regions using inter-primer binding site (iPBS) retrotransposon markers. A total of 13 most polymorphic primers were selected which yielded 195 total bands, of which 84.10% were found polymorphic. Mean polymorphism information content (PIC) was (0.361) and diversity indices including mean effective number of alleles (1.36), mean Shannon’s information index (0.35) and overall gene diversity (0.22) revealed the existence of sufficient amount of genetic diversity in the studied plant material. Most diversity was found in genotypes collected from the Mediterranean region. Analysis of molecular variance (AMOVA) revealed that most of the variation (85%) in Turkish laurel germplasm is due to differences within populations. Model-based structure, principal coordinate analysis (PCoA) and neighbor-joining algorithms were found in agreement and clustered the studied germplasm according to their collection provinces and regions. This is a very first study exploring the genetic diversity and population structure of laurel germplasm using iPBS-retrotransposon marker system. We believe that information provided in this work will be helpful for the scientific community to take more interest in this forgotten but the medicinally important plant. Full article
(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)
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