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Harnessing Crop Diversity through Genetics, Genomics and Phenomics Approaches

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (10 February 2023) | Viewed by 25616

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Special Issue Editor

Dr. Pasquale Tripodi

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Guest Editor

CREA Research Center for Vegetable and Ornamental Crops, 84098 Salerno, Italy
Interests: molecular breeding; genomics; GWAS; QTL mapping
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Feeding the world is the main challenge that agriculture will have to address in the next decades for ensuring food security in the scenario of climate change and global demographic growth. In the past 50 years, tremendous efforts have been undertaken toward the establishment of strategies for crop conservation and management. This has led to the establishment of germplasm repositories able to maintain and reproduce, ex situ and in situ, millions of accessions for thousands of existing plant species. This largely untapped biodiversity represents one of the key elements for accelerating the identification of new sources of variation able to enhance the productivity and resilience ability of crops. Several technologies in the field of biology provide the opportunity for deep investigation of genetic resources at different depth scales, facilitating an understanding of mechanisms regulating the complex basis of traits and discovering of novel alleles for breeding programs.

This Special Issue will positively consider original research, reviews, communications, opinions, perspectives, and technology reports, based on advances in the exploration of germplasm diversity through genetic (molecular markers), genomics (cutting edge sequencing-based platforms), and phenomics (metabolomics, sensors, phenotyping platforms) approaches. Research focusing on genome wide association studies and QTL mapping, as well as the exploitation of primary, secondary, and tertiary genetic pool by development and phenotyping of: i) interspecific and intergeneric hybrids (using different techniques, e.g., sexual crosses, embryo rescue, bridge crosses); ii) bi-parental mapping populations such as introgression lines, backcross inbred lines, and recombinant inbred lines; and iii) multi-parental mapping populations such as MAGIC or NAM will be welcome. Phenotyping of core collection, miscellaneous stocks, etc., across multilocation trials towards an understanding of genotypic and environmental factors underlying the variation of traits will be within the general scope of this Special Issue.

Dr. Pasquale Tripodi
Guest Editor

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Keywords

genetic resources
germplasm enhancement
breeding
genomic assisted breeding
genetic diversity
sequencing; transcriptomics
core collection
GWAS
QTL mapping
introgression libraries
local varieties
genotype x environment
phenomics
metabolomics
sensing technologies
phenotyping platforms
digital phenotyping

Published Papers (12 papers)

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Editorial

Jump to: Research

4 pages, 210 KiB

Open AccessEditorial

Harnessing Crop Diversity through Genetics, Genomics and Phenomics Approaches

by Pasquale Tripodi and Annalisa Cocozza

Plants 2023, 12(8), 1685; https://doi.org/10.3390/plants12081685 - 17 Apr 2023

Cited by 1 | Viewed by 1014

Abstract

Developing resilient cultivars ensuring adequate productions will be the agriculture industry’s primary challenge in the coming decades to ensure food security, especially with climate change and a growing global population [...] Full article

(This article belongs to the Special Issue Harnessing Crop Diversity through Genetics, Genomics and Phenomics Approaches)

Research

Jump to: Editorial

23 pages, 2305 KiB

Open AccessArticle

High-Density Linkage Maps from Japanese Rice japonica Recombinant Inbred Lines Using Genotyping by Random Amplicon Sequencing-Direct (GRAS-Di)

by Rym Fekih, Yohei Ishimaru, Satoshi Okada, Michihiro Maeda, Ryutaro Miyagi, Takahiro Obana, Kazuyo Suzuki, Minoru Inamori, Hiroyuki Enoki and Masanori Yamasaki

Plants 2023, 12(4), 929; https://doi.org/10.3390/plants12040929 - 17 Feb 2023

Cited by 2 | Viewed by 1817

Abstract

The genetic dissection of agronomically important traits in closely related Japanese rice cultivars is still in its infancy mainly because of the narrow genetic diversity within japonica rice cultivars. In an attempt to unveil potential polymorphism between closely related Japanese rice cultivars, we used a next-generation-sequencing-based genotyping method: genotyping by random amplicon sequencing-direct (GRAS-Di) to develop genetic linkage maps. In this study, four recombinant inbred line (RIL) populations and their parents were used. A final RIL number of 190 for RIL71, 96 for RIL98, 95 for RIL16, and 94 for RIL91 derived from crosses between a common leading Japanese rice cultivar Koshihikari and Yamadanishiki, Taichung 65, Fujisaka 5, and Futaba, respectively, and the parent plants were subjected to GRAS-Di library construction and sequencing. Approximately 438.7 Mbp, 440 Mbp, 403.1 Mbp, and 392 Mbp called bases covering 97.5%, 97.3%, 98.3%, and 96.1%, respectively, of the estimated rice genome sequence at average depth of 1× were generated. Analysis of genotypic data identified 1050, 1285, 1708, and 1704 markers for each of the above RIL populations, respectively. Markers generated by GRAS-Di were organized into linkage maps and compared with those generated by GoldenGate SNP assay of the same RIL populations; the average genetic distance between markers showed a clear decrease in the four RIL populations when we integrated markers of both linkage maps. Genetic studies using these markers successfully localized five QTLs associated with heading date on chromosomes 3, 6, and 7 and which previously were identified as Hd1, Hd2, Hd6, Hd16, and Hd17. Therefore, GRAS-Di technology provided a low cost and efficient genotyping to overcome the narrow genetic diversity in closely related Japanese rice cultivars and enabled us to generate a high density linkage map in this germplasm. Full article

(This article belongs to the Special Issue Harnessing Crop Diversity through Genetics, Genomics and Phenomics Approaches)

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19 pages, 6491 KiB

Open AccessArticle

Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata (L.) Walp.) Landraces from Portugal and Mozambique

by Joana Bagoin Guimarães, Cátia Nunes, Graça Pereira, Ana Gomes, Nascimento Nhantumbo, Paula Cabrita, José Matos, Fernanda Simões and Maria Manuela Veloso

Plants 2023, 12(4), 846; https://doi.org/10.3390/plants12040846 - 13 Feb 2023

Cited by 3 | Viewed by 1720

Abstract

Cowpea (Vigna unguiculata (L.) Walp.) is currently a legume crop of minor importance in Europe but a highly relevant staple crop in Africa and the second most cultivated legume in Mozambique. In Portugal and Mozambique, cowpea’s phenotypic and genetic variation has been maintained locally by farmers in some areas. We used the molecular markers SSR, SilicoDArT and SNP to analyze the genetic diversity and population structure of 97 cowpea accessions, mainly from Portugal (Southern Europe) and Mozambique (Southern Africa). As far as we know, this is the first time that the genetic variation and the relationship between cowpea landraces collected in Portugal with those originated in Mozambique is reported. Despite the shared historical past, the Portuguese landraces did not share a common genetic background with those from Mozambique, and two different gene pools were revealed. Knowledge of the genetic structure of cowpea landraces offers an opportunity for individual selection within landraces adapted to particular eco-physiological conditions and suggests the existence of a valuable gene pool for exploitation in future Portugal-PALOP (Portuguese-speaking African countries) cowpea breeding programs. Full article

(This article belongs to the Special Issue Harnessing Crop Diversity through Genetics, Genomics and Phenomics Approaches)

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17 pages, 1658 KiB

Open AccessArticle

Genetic Variation of Zinc and Iron Concentration in Normal, Provitamin A and Quality Protein Maize under Stress and Non-Stress Conditions

by Nakai Goredema-Matongera, Thokozile Ndhlela, Angeline van Biljon, Casper N. Kamutando, Jill E. Cairns, Frederic Baudron and Maryke Labuschagne

Plants 2023, 12(2), 270; https://doi.org/10.3390/plants12020270 - 6 Jan 2023

Cited by 4 | Viewed by 1476

Abstract

The negative impacts of zinc (Zn) and iron (Fe) deficiency due to over-reliance on monotonous cereal-based diets are well-documented. Increasing micronutrient densities in maize is currently among top breeders’ priorities. Here, 77 single-cross Zn-enhanced hybrids with normal, provitamin A and quality protein maize genetic backgrounds were evaluated together with seven checks for grain Zn and Fe concentration and agronomic traits under optimum, low nitrogen (N) and managed drought conditions. Results showed a fairly wide variability for grain Zn (10.7–57.8 mg kg⁻¹) and Fe (7.1–58.4 mg kg⁻¹) concentration amongst the hybrids, across management conditions. Notable differences in Zn concentration were observed between the Zn-enhanced quality protein maize (QPM) (31.5 mg kg⁻¹), Zn-enhanced provitamin A maize (28.5 mg kg⁻¹), Zn-enhanced normal maize (26.0 mg kg⁻¹) and checks (22.9 mg kg⁻¹). Although checks showed the lowest micronutrient concentration, they were superior in grain yield (GY) performance, followed by Zn-enhanced normal hybrids. Genotypes grown optimally had higher micronutrient concentrations than those grown under stress. Genotype × environment interaction (G × E) was significant (p ≤ 0.01) for GY, grain Zn and Fe concentration, hence micronutrient-rich varieties could be developed for specific environments. Furthermore, correlation between grain Zn and Fe was positive and highly significant (r = 0.97; p ≤ 0.01) suggesting the possibility of improving these traits simultaneously. However, the negative correlation between GY and grain Zn (r = −0.44; p ≤ 0.01) and between GY and grain Fe concentration (r = −0.43; p ≤ 0.01) was significant but of moderate magnitude, suggesting slight dilution effects. Therefore, development of high yielding and micronutrient-dense maize cultivars is possible, which could reduce the highly prevalent micronutrient deficiency in sub-Saharan Africa (SSA). Full article

(This article belongs to the Special Issue Harnessing Crop Diversity through Genetics, Genomics and Phenomics Approaches)

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21 pages, 3135 KiB

Open AccessArticle

Genetic and Pomological Determination of the Trueness-to-Type of Sweet Cherry Cultivars in the German National Fruit Genebank

by Stefanie Reim, Juliane Schiffler, Annette Braun-Lüllemann, Mirko Schuster, Henryk Flachowsky and Monika Höfer

Plants 2023, 12(1), 205; https://doi.org/10.3390/plants12010205 - 3 Jan 2023

Cited by 4 | Viewed by 1805

Abstract

Genebank collections preserve many old cultivars with ancient breeding history. However, often, cultivars with synonymous or incorrect names are maintained in multiple collections. Therefore, pomological and genetic characterization is an essential prerequisite for confirming trueness-to-type of cultivars in gene bank collections. In our study, 1442 single sweet cherry (Prunus avium L.) trees of the German Fruit Genebank were evaluated according to their trueness-to-type. For this purpose, pomological analysis was performed, in which the accessions were assigned totheir historical cultivar names. The pomological identifications were based on several historical reference sources, such as fruit references from historical cherry cultivar and fruit-stone collections, as well as historical pomological literature sources. In addition, the cherry trees were genetically analyzed for cultivar identity using 16 SSR markers. Based on pomological characterization and genetic analysis for the majority of the trees (86%), cultivar authenticity could be confirmed. Most markers were highly discriminating and powerful for cultivar identification. The cherry collection showed a high degree of genetic diversity, with an expected heterozygosity He = 0.67. Generally, high genetic admixture between cultivars of different geographic origin and year of origin was obtained after STRUCTURE analysis, demonstrating the extensive exchange of genetic information between cherry cultivars in the collection over time. However, the phylogenetic tree calculated by DARwin reflected the geographic origin of selected cherry cultivars. After parentage analysis with CERVUS, paternity could not be confirmed for three cultivars, indicating the necessity of further pedigree analysis for these cultivars. The results of our study underlined the general importance of evaluating the authenticity of cultivars in genebank collections based on genetic and pomological characterization. Full article

(This article belongs to the Special Issue Harnessing Crop Diversity through Genetics, Genomics and Phenomics Approaches)

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13 pages, 2077 KiB

Open AccessArticle

Assessment of Wild Rocket (Diplotaxis tenuifolia (L.) DC.) Germplasm Accessions by NGS Identified SSR and SNP Markers

by João M. Reis, Ricardo J. Pereira, Paula S. Coelho and José M. Leitão

Plants 2022, 11(24), 3482; https://doi.org/10.3390/plants11243482 - 12 Dec 2022

Cited by 1 | Viewed by 1943

Abstract

Rocket is the common designation for two baby-leaf salad crops of the Brassicaceae family: Eruca sativa (L.) Cav., usually referred to as annual garden rocket, and Diplotaxis tenuifolia (L.) DC. commonly named to as perennial wild rocket. E. sativa is used for human consumption since antiquity. However, the growing consumer preference for D. tenuifolia is being accompanied by the fast increase in its production area and commercialization of new cultivars. Nevertheless, the worldwide number of wild rocket accessions maintained in germplasm collections is very reduced, the solution for which situation the project “REMIRucula” intends to contribute, establishing a germplasm collection at the INIAV, Oeiras, Portugal. Herein, we report on the establishment via next generation sequencing (NGS) of the first genome assembly of D. tenuifolia and the identification of specific single sequence repeat (SSR) and single nucleotide polymorphisms (SNP) loci for the establishment of specific DNA-markers for this species. A representative set of 87 D. tenuifolia and 3 E. sativa accessions were assessed by 5 SSR and 9 SNP-CAPS markers, allowing a drastic discrimination between both species and the establishment of unequivocal molecular fingerprints for the analyzed accessions. The non-discrimination within six pairs and one trio of D. tenuifolia accessions is discussed. Full article

(This article belongs to the Special Issue Harnessing Crop Diversity through Genetics, Genomics and Phenomics Approaches)

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13 pages, 1145 KiB

Open AccessEditor’s ChoiceArticle

Analysis of Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata (L.) Walp) Genotypes Using Single Nucleotide Polymorphism Markers

by Mbali Thembi Gumede, Abe Shegro Gerrano, Assefa Beyene Amelework and Albert Thembinkosi Modi

Plants 2022, 11(24), 3480; https://doi.org/10.3390/plants11243480 - 12 Dec 2022

Cited by 5 | Viewed by 1566

Abstract

Cowpea (Vigna unguiculata (L.) Walp) is an important legume crop with immense potential for nutritional and food security, income generation, and livestock feed in Sub-Saharan Africa. The crop is highly tolerant to heat and drought stresses which makes it an extremely important crop for improving resilience in crop production in the face of climate change. This study was carried out to assess the genetic diversity and population structure of 90 cowpea accessions using single nucleotide polymorphism (SNP) markers. Out of 11,940 SNPs used, 5864 SNPs were polymorphic and maintained for genome diversity analysis. Polymorphic information content (PIC) values ranged from 0.22 to 0.32 with a mean value of 0.27. The model-based Bayesian STRUCTURE analysis classified 90 cowpea accessions into four subpopulations at K = 4, while the distance-based cluster analysis grouped the accessions into three distinct clusters. The analysis of molecular variance (AMOVA) revealed that 59% and 69% of the total molecular variation was attributed to among individual variation for model-based and distance-based populations, respectively, and 18% was attributed to within individual variations. Furthermore, the low heterozygosity among cowpea accessions and the high inbreeding coefficient observed in this study suggests that the accessions reached an acceptable level of homozygosity. This study would serve as a reference for future selection and breeding programs of cowpea with desirable traits and systematic conservation of these plant genetic resources. Full article

(This article belongs to the Special Issue Harnessing Crop Diversity through Genetics, Genomics and Phenomics Approaches)

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9 pages, 4356 KiB

Open AccessCommunication

Genotyping-by-Sequencing Defines Genetic Structure within the “Acquaviva” Red Onion Landrace

by Chiara Delvento, Stefano Pavan, Monica Marilena Miazzi, Angelo Raffaele Marcotrigiano, Francesca Ricciardi, Luigi Ricciardi and Concetta Lotti

Plants 2022, 11(18), 2388; https://doi.org/10.3390/plants11182388 - 13 Sep 2022

Cited by 1 | Viewed by 1282

Abstract

Genetic structure and distinctive features of landraces, such as adaptability to local agro-ecosystems and specific qualitative profiles, can be substantially altered by the massive introduction of allochthonous germplasm. The landrace known as “Cipolla rossa di Acquaviva” (Acquaviva red onion, further referred to as ARO) is traditionally cultivated and propagated in a small area of the Apulia region (southern Italy). However, the recent rise of its market value and cultivation area is possibly causing genetic contamination with foreign propagating material. In this work, genotyping-by-sequencing (GBS) was used to characterize genetic variation of seven onion populations commercialized as ARO, as well as one population of the landrace “Montoro” (M), which is phenotypically similar, but originates from another cultivation area and displays different qualitative features. A panel of 5011 SNP markers was used to perform parametric and non-parametric genetic structure analyses, which supported the hypothesis of genetic contamination of germplasm commercialized as ARO with a gene pool including the M landrace. Four ARO populations formed a core genetic group, homogeneous and clearly distinct from the other ARO and M populations. Conversely, the remaining three ARO populations did not display significant differences with the M population. A set of private alleles for the ARO core genetic group was identified, indicating the possibility to trace the ARO landrace by means of a SNP-based molecular barcode. Overall, the results of this study provide a framework for further breeding activities and the traceability of the ARO landrace. Full article

(This article belongs to the Special Issue Harnessing Crop Diversity through Genetics, Genomics and Phenomics Approaches)

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15 pages, 2379 KiB

Open AccessFeature PaperArticle

Genetic Variability Assessment of Tropical Indica Rice (Oryza sativa L.) Seedlings for Drought Stress Tolerance

by Naqeebullah Kakar, Salah H. Jumaa, Saroj Kumar Sah, Edilberto D. Redoña, Marilyn L. Warburton and Kambham R. Reddy

Plants 2022, 11(18), 2332; https://doi.org/10.3390/plants11182332 - 6 Sep 2022

Cited by 2 | Viewed by 2096

Abstract

Drought stress is one of the most devastating abiotic factors limiting plant growth and development. Devising an efficient and rapid screening method at the seedling stage is vital in identifying genotypes best suited under drought conditions. An experiment was conducted to assess 74 rice genotypes for drought tolerance using specially designed mini-hoop structures. Two treatments were imposed on rice seedlings, including 100% moisture and a 50% moisture regime. Several shoot morpho-physiological traits and root traits were measured and analyzed. The genotypes exhibited a wide range of variability for the measured traits, with the leaf area showing the most significant variation, followed by plant height, tiller number, and shoot dry weight. In contrast, the drought did not significantly affect most root traits. The germplasm was classified into different categories using cumulative drought stress response indices (CDSRI); 19 genotypes (26%) were identified as drought sensitive, and 33 (45%), 15 (20%), and 7 (9%) were determined as low, moderately, and highly drought-tolerant, respectively. Genotypes IR86638 and IR49830 were the most and least drought-tolerant, respectively. Overall, a poor correlation was observed between CDSRI, total shoot traits (R² = 0.36), and physiological parameters (R² = 0.10). A strong linear correlation was found between CDSRI and root traits (R² = 0.81), suggesting that root traits are more crucial and better descriptors in screening for drought tolerance. This study can help rice breeders and scientists to accelerate breeding by adopting a mini-hoop rapid screening method. The tolerant genotypes could serve as appropriate donor parents, progenies, and potential genotypes for developing drought-tolerant commercial cultivars. Full article

(This article belongs to the Special Issue Harnessing Crop Diversity through Genetics, Genomics and Phenomics Approaches)

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16 pages, 2420 KiB

Open AccessEditor’s ChoiceArticle

Genomic Insights into Cultivated Mexican Vanilla planifolia Reveal High Levels of Heterozygosity Stemming from Hybridization

by Paige Ellestad, Miguel Angel Pérez-Farrera and Sven Buerki

Plants 2022, 11(16), 2090; https://doi.org/10.3390/plants11162090 - 11 Aug 2022

Cited by 7 | Viewed by 1906

Abstract

Although vanilla is one of the most valuable spices, there is a lack of understanding of the genomic variability of the main vanilla producing species, Vanilla planifolia, within its cultivated origin, Mexico. High genomic heterozygosity levels within the globally cultivated ‘Daphna’ genome have raised questions on the possibility of a hybrid origin and analogous genomic signatures of vanilla cultivated within its origin. This study investigated these questions by assessing whether the genomic structure of Mexican V. planifolia reflected domestication events. Whole genome re-sequencing was used to compare genome complexity between 15 cultivated accessions from different regions and gene pools. Results showed high levels of heterozygosity, ranging from 2.48% to 2.85%, in all but one accession, which exhibited a low level (0.403%). Chromosome-level comparative analyses revealed genomic variability among samples, but no signals of chromosome rearrangements. These findings support the hypotheses that cultivated vanilla resulted from hybridization and that multiple domestication events have shaped cultivated vanilla leading to the formation of landraces. High cultural diversity within this region further supports the occurrence of multiple domestication processes. These results may help to improve breeding and conservation efforts aiming to preserve the genetic diversity of this beloved spice threatened by climate change. Full article

(This article belongs to the Special Issue Harnessing Crop Diversity through Genetics, Genomics and Phenomics Approaches)

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14 pages, 2020 KiB

Open AccessArticle

Exploration of the Genetic Diversity of Solina Wheat and Its Implication for Grain Quality

by Riccardo De Flaviis, Giorgio Tumino, Valeria Terzi, Caterina Morcia, Veronica Santarelli, Giampiero Sacchetti and Dino Mastrocola

Plants 2022, 11(9), 1170; https://doi.org/10.3390/plants11091170 - 26 Apr 2022

Cited by 4 | Viewed by 4852

Abstract

Different Solina wheat accessions (n = 24) collected in the Abruzzo region (Italy) were studied using 45,000 SNP markers generated from the DarTseq platform. The structure of genetic data was analyzed by Principal Component Analysis and Hierarchical Cluster analysis that revealed the existence of two main clusters (Clu1 and Clu2) characterized by samples with different geographical origin. The Solina genetic dataset was further merged and analyzed with a public genetic one provided by CIMMYT containing 25,963 genotypes from all over the world. The Solina accessions occupied a vast space, thus confirming a high heterogeneity of this landrace that, nevertheless, is considerably unique and placed quite far from other clusters. Clu1 and Clu2 divergence were clearly visible. Solina clusters were genetically closer to landraces from Turkey and the central fertile crescent than to the Italian genotypes present in the dataset. Selected commercial quality traits of accessions of the two Solina clusters were analyzed (yield, thousand kernel weight, test weight, and protein content), and significant differences were found between clusters. The results of this investigation did not highlight any relationships of Solina with Italian genotypes, and confirmed its wide genetic diversity by permitting to identify two genetic groups with distinct origin and quality traits. Full article

(This article belongs to the Special Issue Harnessing Crop Diversity through Genetics, Genomics and Phenomics Approaches)

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13 pages, 1175 KiB

Open AccessArticle

A Core Set of Snap Bean Genotypes Established by Phenotyping a Large Panel Collected in Europe

by Carmen García-Fernández, Maria Jurado, Ana Campa, Creola Brezeanu, Valérie Geffroy, Elena Bitocchi, Roberto Papa and Juan Jose Ferreira

Plants 2022, 11(5), 577; https://doi.org/10.3390/plants11050577 - 22 Feb 2022

Cited by 5 | Viewed by 3022

Abstract

Snap beans are a group of bean cultivars grown for their edible immature pods. The objective of this work was to characterize the diversity of pod phenotypes in a snap bean panel (SBP), comprising 311 lines collected in Europe, and establish a core set (Core-SBP) with the maximum diversity of pod phenotypes. Phenotyping of the SBP was carried out over two seasons based on 14 quantitative pod dimension traits along with three qualitative traits: pod color, seed coat color, and growth habit. Phenotypes were grouped into 54 classes using a hierarchical method, and a Core-SBP with one line per phenotype class was established. A further field-based evaluation of the Core-SBP revealed higher diversity index values than those obtained for the SBP. The Core-SBP was also genotyped using 24 breeder-friendly DNA markers tagging 21 genomic regions previously associated with pod trait control. Significant marker-trait associations were found for 11 of the 21 analyzed regions as well as the locus fin. The established Core-SBP was a first attempt to classify snap bean cultivars based on pod morphology and constituted a valuable source of characteristics for future breeding programs and genetic analysis. Full article

(This article belongs to the Special Issue Harnessing Crop Diversity through Genetics, Genomics and Phenomics Approaches)

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