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Genetic Identification, Exploration, Evaluation and Breeding of Plant Genetic Resources

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A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Genotype Evaluation and Breeding".

Deadline for manuscript submissions: closed (15 November 2023) | Viewed by 14687

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Prof. Dr. Penelope Bebeli

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Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, 11855 Athens, Greece
Interests: plant genetic resources; crop landraces; crop wild relatives; plant breeding; gene banks; genetic and phenotypic diversity; experimental design in agriculture

Prof. Dr. Vasileios Papasotiropoulos

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Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, 11855 Athens, Greece
Interests: plant genetic resources; horticultural and medicinal plants; molecular fingerprinting; genetic and phenotypic diversity; gene expression

Prof. Dr. Jaime Prohens

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Institute for Conservation and Improvement of Valencian Agrodiversity, Universitat Politècnica de València, Camí de Vera 14, 46022 Valencia, Spain
Interests: genetic resources; breeding; genomics; crop wild relatives; landraces; gene banks; phenotyping
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Special Issue Information

Dear Colleagues,

As new uniform, distinct and genetically homogeneous improved varieties are being bred to satisfy the market needs, less uniform landraces of annual species, traditional varieties, farmer’s varieties, indigenous varieties of perennial species, crop wild relatives, wild harvested plants and other wild plant species are being lost, and their diversity eroded. Plant genetic resources have an important role to play to ensure food security but also in the production of other valuable materials such as fiber, fuel, chemical substances, etc. Under the effect of the upcoming climate change, which is increasing the occurrence of abiotic and biotic stresses, landraces and similar types of genetically diverse heterogeneous resources are important due to their specific adaptive traits.

Genetic erosion is continuously endangering plant genetic resources. Additionally, landraces’ and indigenous varieties’ names, cultivation practices and uses are important components of cultural heritage and therefore need to be preserved. The exploration, evaluation and genetic identification of plant genetic resources are also important for their ex situ conservation in gene banks as well as in situ/on-farm in their place of origin, which allows their uninterrupted adaptation to specific microclimates under the forces of both natural and human selection.

Until today, many plant genetic resources have been collected; however, many regions of the planet remain unexplored, and even though many accessions are conserved in gene banks, their on-farm conservation shows a decline. Moreover, the vast collections in gene banks have many duplicates, and there is uncertainty whether they are different accessions or different samples that belong to the same population. Moreover, the collections of plant genetic resources should be evaluated for biotic and abiotic tolerances such as drought, salinity stress or resistance to pests, which could rise due to the upcoming climate change. Therefore, their characterization and genetic identification are of the utmost importance to ensure that the maximum possible genetic diversity is maintained and available for utilization for breeding.

Crop wild relatives (CWRs) and wild plant species are considered valuable resources for crop improvement since they represent a large pool of genetic diversity. This genetic diversity is well recognized for its value in enhancing crop resilience to stresses and also for increasing yield and nutritional value.

The objective of this Special Issue is to provide new research and review articles on plant genetic resources worldwide. The scope of this Special Issue will include plant genetic resources’ exploration, evaluation, and genetic identification to reduce the risk of genetic erosion and the loss of important alleles and genetic stocks, as well as to utilize the useful genes in crop breeding to increase yield stability in newly bred cultivars and to meet the growing environmental challenges and climate change.

Prof. Dr. Penelope Bebeli
Prof. Dr. Vasileios Papasotiropoulos
Prof. Dr. Jaime Prohens
Guest Editors

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Keywords

plant genetic resources
crop wild relatives
landraces
gene banks
indigenous species
traditional varieties
characterization
conservation
genetic improvement
molecular fingerprinting
genetic erosion
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Published Papers (10 papers)

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Research

18 pages, 2233 KiB

Open AccessArticle

Participatory On-Farm Evaluation of Improved Groundnut Genotypes in the Guinea Savannah Agro-Ecological Zone of Ghana

by Ophelia Asirifi Amoako, Richard Oteng-Frimpong, Julius Yirzagla, Yussif Baba Kassim, Theophilus Kwabla Tengey, Desmond Sunday Adogoba, Mercy Mingle, Ramatu Alhassan and Abdul Aleem Ibrahim

Agriculture 2023, 13(12), 2249; https://doi.org/10.3390/agriculture13122249 - 07 Dec 2023

Viewed by 755

Abstract

The on-farm mother–baby trial experimental approach was employed to evaluate the performance of elite groundnut genotypes on farmers’ fields in the Guinea savannah agroecology of Ghana in the 2020 and 2021 cropping seasons. Analysis of the data from the mother trial revealed significant (p < 0.05) genotypic differences for the traits measured over the two years. The genotype ICGV-IS 13842 reached physiological maturity in 88 days and was identified as the genotype with the shortest maturity period. However, in terms of pod yield and its associated components, genotype ICGV-IS 13864 emerged as the best from the mother trial. During farmer evaluation of the materials, genotype ICGV-IS 13979 was selected as the most preferred in addition to genotypes ICGV-IS 13864 and ICGV-IS 131090. The genotypes ICGV-IS 13864 and ICGV-IS 131090 were observed to combine both high pod yield and high haulm yield. These two traits were identified as very important by the farmers who participated in the study as the haulms serve as fodder for their animals and fetch additional household income when sold with the pods harvested. The preference for genotype ICGV-IS 13842, an early maturing genotype, can be seen as an indication of farmers responding to the changing growing season due to erratic rainfall. However, if genotypes ICGV-IS 13864 and ICGV-IS 131090 are combined with some water management practices in the future, they could potentially withstand the changing growing season. Economic analysis showed that the improved genotypes had a greater net return on investment and higher cost–benefit ratio ranging from 2.74 to 4.84 across both years. Full article

(This article belongs to the Special Issue Genetic Identification, Exploration, Evaluation and Breeding of Plant Genetic Resources)

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18 pages, 6770 KiB

Open AccessArticle

Traditional Olive Tree Varieties in Alto Aragón (NE Spain): Molecular Characterization, Single-Varietal Oils, and Monumental Trees

by Alfredo Serreta-Oliván, Rubén Sancho-Cohen, Ana Cristina Sánchez-Gimeno, Pablo Martín-Ramos, José Antonio Cuchí-Oterino and José Casanova-Gascón

Agriculture 2023, 13(12), 2204; https://doi.org/10.3390/agriculture13122204 - 27 Nov 2023

Viewed by 1044

Abstract

Recovering minority olive tree varieties helps preserve genetic diversity and contributes to sustainable agriculture practices. The International Olive Council has recognized the importance of conserving olive tree genetic resources and the European Union’s Horizon Europe program has identified the preservation of crop diversity as a priority for sustainable food systems. In the work presented herein, old olive groves in the province of Huesca (NE Spain), managed according to the traditional model, were surveyed, sampled, and analyzed using molecular characterization techniques (based on EST-SNPs markers). Twenty-nine new varieties were identified and deposited in IFAPA’s World Germplasm Bank of Olive Varieties. In the first step towards their valorization, eight single-varietal oils from Alto Aragon varieties were produced and characterized, and their organoleptic properties were evaluated, paving the way for the production of differentiated quality oils. Furthermore, ancient olive trees were selected and 3D scanned to promote their protection as singular or monumental trees and for oleo-tourism purposes. The reported findings highlight the rich olive-growing heritage of this northernmost frontier of olive tree cultivation in Spain. Full article

(This article belongs to the Special Issue Genetic Identification, Exploration, Evaluation and Breeding of Plant Genetic Resources)

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11 pages, 6554 KiB

Open AccessArticle

Deletion of the OsLA1 Gene Leads to Multi-Tillering and Lazy Phenotypes in Rice

by Zhanglun Sun, Tianrun Mei, Tingting Feng, Hao Ai, Yafeng Ye, Sumei Duan, Binmei Liu and Xianzhong Huang

Agriculture 2023, 13(11), 2166; https://doi.org/10.3390/agriculture13112166 - 17 Nov 2023

Cited by 1 | Viewed by 1017

Abstract

Plant architecture, one of the key factors that determine grain yield in rice, is mainly affected by components such as plant height, tiller number, and panicle morphology. For this paper, we obtained a multi-tillering and lazy mutant from a japonica rice cultivar, Wuyunjing 7 (WYJ7), via treatment with a heavy ion beam. Compared to WYJ7, the mutant showed a significant increase in tiller angle, tiller number, number of primary and secondary branches, and number of grains; however, the plant height and grain thickness of the mutant was significantly decreased. Phenotypic analysis of the F₁ hybrids revealed that the multi-tillering and lazy mutant phenotypes were regulated by a recessive gene. The segregation ratio of 1׃3 of the mutant phenotype and the wild-type plant in the F₂ population indicated that the former was controlled by a single gene named Multi-Tillering and Lazy 1 (MTL1). Bulked segregant analysis was performed using the individual plants with extremely typical tiller angles in the F₂ population. The MTL1 gene was initially mapped within a region of 5.58–17.64 Mb on chromosome 11. By using the F₂ segregated population for fine mapping, the MTL1 gene was ultimately fine mapped within the range of 66.67 kb on chromosome 11. The analysis of genes in this region revealed the presence of the previously identified LAZY1 (LA1) gene. Genomic PCR amplification and semi-quantitative RT-PCR assays showed that the LA1 gene could not be amplified and was not expressed, thus indicating that the MTL1 gene might be identical to the LA1 gene. This study suggests that the multi-tillering and lazy mutant phenotypes might be caused by the deletion of LA1 function. This finding can guide further investigations on the functional mechanisms of the LA1 gene, thus enriching the theoretical knowledge of plant architecture in relation to rice. Full article

(This article belongs to the Special Issue Genetic Identification, Exploration, Evaluation and Breeding of Plant Genetic Resources)

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26 pages, 18228 KiB

Open AccessArticle

Pollen Development and Stainability in Vicia faba L. and Lupinus angustifolius L.

by Wiktor Skrzypkowski, Renata Galek, Adela Adamus and Agnieszka Kiełkowska

Agriculture 2023, 13(11), 2065; https://doi.org/10.3390/agriculture13112065 - 27 Oct 2023

Viewed by 1217

Abstract

Commercially, leguminous crops (Fabaceae) are the second most important group of cultivated plants, just after grasses (Poaceae). This study focuses on the analysis of pollen development and stainability in two species belonging to the Fabaceae family: Vicia faba L. and Lupinus angustifolius L. Morphological analysis of the anthers at various stages of flower development allowed us to trace the processes of microsporogenesis and microgametogenesis. Nine different cell staining protocols with diverse mechanisms of action, including acetocarmine, Alexander’s dye, aniline blue in lactophenol, Calcein AM, FDA, MTT, TTC, Lugol’s iodine, and aceto-orcein, were tested for their suitability in assessing the viability of microspores as well as pollen grains in both species. Among the applied dyes, four allowed for the discrimination between viable and nonviable microspores in V. faba, and six dyes allowed for this in L. angustifolius. For mature pollen grains, all dyes enabled differentiation between viable and nonviable cells in both species. The highest viability indications for V. faba microspores were obtained with acetocarmine (94.6%), while for mature pollen, aniline blue in lactophenol, MTT, and aceto-orcein yielded the highest viability indications (90.8–96.3%). In L. angustifolius, the highest percentages of viable microspores (64.9–66.5%) were obtained with the acetocarmine, aniline blue in lactophenol, and TTC dyes. For mature pollen, the highest viability indications (83.4%–92.9%) were obtained with acetocarmine, aniline blue in lactophenol, Lugol’s iodine, and aceto-orcein. The viability of V. faba pollen grains in an in vitro germination test showed that the highest pollen germination (61.3%) was observed on the BK medium (rich in minerals with 10% sucrose). In L. angustifolius, the highest pollen germination was observed on the media containing boric acid and 5% sucrose (70.5%) and on the medium containing 10% sucrose only (74.2%). Full article

(This article belongs to the Special Issue Genetic Identification, Exploration, Evaluation and Breeding of Plant Genetic Resources)

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16 pages, 931 KiB

Open AccessArticle

Evaluation of the Genetic Diversity of Greek Garlic (Allium sativum L.) Accessions Using DNA Markers and Association with Phenotypic and Chemical Variation

by Charikleia Papaioannou, Georgia Fassou, Spyridon A. Petropoulos, Fotini N. Lamari, Penelope J. Bebeli and Vasileios Papasotiropoulos

Agriculture 2023, 13(7), 1408; https://doi.org/10.3390/agriculture13071408 - 15 Jul 2023

Cited by 3 | Viewed by 1220

Abstract

The genetic diversity of 27 garlic accessions (local varieties/landraces) was investigated using five simple sequence repeat (SSR) and six inter-simple sequence repeat (ISSR) markers. The SSR genotyping revealed 26 different alleles, while 84 polymorphic bands were produced using the ISSR markers. The average polymorphism information content (PIC) was 0.471 and 0.465 for the SSR and the ISSR markers, respectively. Compared to ISSRs, SSR markers revealed a higher level of redundancy, indicating potential duplicates among the accessions. The analysis of molecular variance (AMOVA) based on both marker systems showed that most of the molecular diversity was attributable to differences within accessions, rather than among them. UPGMA, STRUCTURE, and Principal Coordinate Analysis (PCoA) based on the SSRs produced similar clustering results, although not in agreement with those produced by the ISSR markers. Fisher’s exact tests and multinomial logistic regression analyses identified significant associations between the chemical compounds, the morphological traits of the bulb, and specific SSR and ISSR loci. Our results provide a molecular basis for understanding the genetic diversity of Greek garlic landraces, which could be useful for the conservation and sustainable management of this crop. Potential markers fostering the selection of genotypes in garlic breeding have also been revealed. Full article

(This article belongs to the Special Issue Genetic Identification, Exploration, Evaluation and Breeding of Plant Genetic Resources)

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16 pages, 5373 KiB

Open AccessArticle

Characteristics of Schisandra chinensis (Turcz.) Baillon Collected in Habitats of South Korea

by Beung Sung Kim, Jong Soo Kim, Young Jin Seo, Tae Young Oh and Jeong-Dong Lee

Agriculture 2023, 13(6), 1256; https://doi.org/10.3390/agriculture13061256 - 16 Jun 2023

Cited by 1 | Viewed by 1081

Abstract

Schisandra chinensis (Turcz.) Baill. has been traditionally used as a medicine for bronchial tube ailments in Northeast Asia. Recently, the demand for S. chinensis has increased for use as food and medicine because of the lignans found in its fruits. However, the species germplasm collection has rarely been studied to evaluate their phenotypic traits in Korea. In this study, 96 accessions of S. chinensis were collected in South Korea for two years to evaluate their phenotypes, and principal component analysis (PCA) and cluster analysis were conducted. Significant variations among the measured phenotypic traits were observed. The total bunch weight produced from a single tree ranged from 109 to 5844 g; the contents in schizandrin, gomisin A, and gomisin N—three types of lignan—were 2.2–14.5, 0.9–9.8, and 2.1–12.2 mg/g, respectively. Gomisin N positively correlated with flowering traits (flowering start, period, and peduncle length) and leaf characteristics (leaf width and length). PCA and cluster analyses revealed four clusters among the 96 S. chinensis accessions. These results provide valuable information for systematic characterization of species germplasm collections and tools for further research. Full article

(This article belongs to the Special Issue Genetic Identification, Exploration, Evaluation and Breeding of Plant Genetic Resources)

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20 pages, 2759 KiB

Open AccessArticle

Exploring the Genetic and Morphological Variation and Disease Resistance in Local and Foreign Prunus persica (L.) Batsch Cultivars

by Pavlina Drogoudi, Georgios Pantelidis, Lefkothea Karapetsi, Konstantina Ziakou, Konstantinos Kazantzis, Panagiotis Madesis and Thomas Thomidis

Agriculture 2023, 13(4), 800; https://doi.org/10.3390/agriculture13040800 - 30 Mar 2023

Cited by 1 | Viewed by 1408

Abstract

Local germplasm may be the basis for genetic improvement for sustainability and resilience, yet little is known about Greek peach [Prunus persica (L.) Batsch] local genetic resources. The aims of the present study were to entail a prospection in the mainland and islands of Greece for local traditional and underutilized germplasm and study their genetic and morphological variation and susceptibility to shoot blight from Cylindrocarpon destructans and Monilinia laxa. A total of 32 peach cultivars/accessions were prospected from the mainland (Imathia and Magnesia) and islands (Andros, Ikaria, Kythira, Lesvos and Samos) of Greece. Leaf and fruit morphological characterization was made in situ and ex situ using 42 qualitative and quantitative morphological descriptors. Nine clones of ‘Lemonato’, isolated in Magnesia, with differing ripening times, were found to vary in leaf and fruit phenotypic traits. The local peach genotypes were separated from 12 old foreign cultivars, in 8 out of the 42 leaf and fruit phenotypic traits studied. We observed greater lesion damages from C. destructans than M. laxa. Local cultivars had greater resistance to Cylindrocarpon destructans than foreign cultivars, with ‘Lemonato Andrea’, ‘Daggalakou’ and ‘Papagianni’ exhibiting the greatest resistance. Genetic characterization was performed in the studied local and foreign peach cultivars/accessions, using eight Inter Simple Sequence Repeats (ISSRs), resulting in a total of 404 bands. Analysis of molecular variance and principal coordinates analysis revealed moderate to low genetic diversity among the peach cultivars, and three distinct clusters were formed. Furthermore, multiple regression analysis was implemented for the association study between morphological traits and the ISSR markers, revealing several markers that are statistically and significantly correlated with fruits’ traits. The obtained results could be valuable for breeding programs and future research on peach. Full article

(This article belongs to the Special Issue Genetic Identification, Exploration, Evaluation and Breeding of Plant Genetic Resources)

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19 pages, 1296 KiB

Open AccessArticle

Genetic Diversity of Black Amaranth (Amaranthus quitensis Kunth) Landraces of Ecuadorian Highlands: Association Genotypes—Color Morphotypes

by Hipatia Delgado and Juan Pedro Martín

Agriculture 2023, 13(1), 34; https://doi.org/10.3390/agriculture13010034 - 22 Dec 2022

Cited by 1 | Viewed by 1589

Abstract

Black amaranth (Amarantus quitensis Kunth) is an ancestral crop of the Ecuadorian Andean region, where traditionally it is called ataco or sangorache. Nowadays, there is some information about the phenotypic diversity of black amaranth landraces, but there are no data about their genetic diversity. In this study, we evaluated the genetic diversity of 139 black amaranth accessions collected twice (1981–1986 and 2014–2015) in three representative Ecuadorian Andean provinces for this crop (Imbabura, Tungurahua, and Cañar) using nine simple sequence repeats (SSR) markers. We detected low genetic diversity levels; only a total of 36 alleles were amplified in 139 accessions, with a mean allelic richness of 4.0 per marker, observed heterozygosity of 0.014, expected heterozygosity of 0.134, and Shannon’s information index of 0.297. In addition, only 17 genotypes were found, with a predominant genotype (83.6%) and up to 12 accession-unique genotypes. Moreover, a certain genetic diversity decrease was observed over the last decades, especially in Tungurahua and Cañar, where today practically only the predominant genotype exists. The ataco germplasm is genetically structured into two well-defined genotype clusters and could constitute two different genetic lineages. Furthermore, a clear association of each genotype group with a different color morphotype defined in a previous agromorphological characterization was observed. The accessions of the majority group of genotypes showed purple pigmentation in stems, leaves, and inflorescences, whereas those of the other genotype group showed less intense pigmentation (pink stems, inflorescences, and green leaves). Molecular information obtained in this study may be useful for the suitable management and conservation of this underutilized genetic plant resource that is of great food and cultural significance for indigenous farming communities of the Ecuadorian highlands. Full article

(This article belongs to the Special Issue Genetic Identification, Exploration, Evaluation and Breeding of Plant Genetic Resources)

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26 pages, 1614 KiB

Open AccessArticle

Genome-Wide Association Study of Leaf Rust Resistance at Seedling and Adult Plant Stages in a Global Barley Panel

by Mariam Amouzoune, Sajid Rehman, Rachid Benkirane, Swati Verma, Sanjaya Gyawali, Muamar Al-Jaboobi, Ramesh Pal Singh Verma, Zakaria Kehel and Ahmed Amri

Agriculture 2022, 12(11), 1829; https://doi.org/10.3390/agriculture12111829 - 01 Nov 2022

Cited by 2 | Viewed by 2136

Abstract

Barley leaf rust caused by Puccinia hordei (Ph) is one of the major limiting biotic stresses of barley production worldwide and causes yield losses of up to 60%. A diversity panel of 316 barley genotypes (AM2017) composed of released cultivars, advanced breeding lines and landraces was screened for Ph resistance at the seedling stage using two isolates (SRT-SAT and SRT-MRC), while the adult plant stage resistance screening was conducted at the disease hotspot location of Sidi Allal Tazi (SAT) for the cropping seasons of 2017 and 2019. The phenotypic responses were combined with 36,793 single nucleotide polymorphism (SNP) markers in a genome-wide association study (GWAS) using the general linear model (GLM), mixed linear model (MLM), settlement of MLM under progressively exclusive relationship (SUPER), multiple-locus MLM (MLMM), fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) in GAPIT3, and MLM (K+Q), MLM (K+PCA), and GLM (Q) models in TASSEL to identify genomic regions linked to Ph resistance. Fourteen barley genotypes were resistant (R) at the seedling stage to both Ph isolates, SRT-SAT and SRT-MRC, and twelve genotypes were either resistant (R) or moderately resistant (MR) at the adult plant stage, whereas only one genotype was resistant at the seedling stage, and moderately resistant at the adult plant stage. The genome scan revealed 58 significant marker trait associations (MTA) among which 34 were associated with seedling resistance (SR) and 24 with adult plant resistance (APR). Common genomic regions conferring resistance to Ph were identified at both stages on chromosome 2H (106.53 cM and at 107.37 cM), and on chromosome 7H (126.7 cM). Among the 58 MTA identified, 26 loci had been reported in previous studies, while the remaining 32 loci were regarded as novel. Furthermore, the functional annotation of candidate genes (CGs) adjacent to 36 SNP markers with proteins involved in disease resistance further confirms that some of the SNP markers from our study could be associated with Ph resistance in barley. The resistant barley genotypes and some of the SNP markers from this study with high R² and additive effects can be converted into high-throughput functional markers for accelerated selection and pyramiding of leaf rust resistance genes in North African barley germplasm. Full article

(This article belongs to the Special Issue Genetic Identification, Exploration, Evaluation and Breeding of Plant Genetic Resources)

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13 pages, 3603 KiB

Open AccessArticle

High-Throughput Phenotyping of Cross-Sectional Morphology to Assess Stalk Mechanical Properties in Sorghum

by Hongzeng Fan, Jibin Wang, Songhao Shen, Mingchong Yang, Suli Li, Bihong Feng, Ruimin Zhong, Chongjian Ma, Jihong Wang, Ruohan Xie and Lingqiang Wang

Agriculture 2022, 12(10), 1696; https://doi.org/10.3390/agriculture12101696 - 15 Oct 2022

Cited by 2 | Viewed by 1639

Abstract

Lodging is one of the major constraints in attaining high yield in crop production. Major factors associated with stalk lodging involve morphological traits and anatomical features along with the chemical composition of the stem. However, little relevant research has been carried out in sorghum, particularly on the anatomical aspects. In this study, with a high-throughput procedure newly developed by our research group, the nine parameters related to stem regions and vascular bundles were generated in 58 sorghum germplasm accessions grown in two successive seasons. Correlation analysis and principal component analysis were conducted to investigate the relationship between anatomical aspects and stalk mechanical traits (breaking force, stalk strength and lodging index). It was found that most vascular parameters were positively associated with breaking force and lodging index with the correlation coefficient r varying from −0.46 to 0.64, whereas stalk strength was only associated with rind area with the r = 0.38. The germplasm resources can be divided into two contrasting categories (classes I with 23 accessions and II with 30 accessions). Compared to class II, the class I was characterized by a larger number (+40.7%) and bigger vascular bundle (+30%), thicker stem (+19.6%) and thicker rind (+36.0%) but shorter internode (plant) (−91.0%). This study provides the methodology and information for the studies of the stem anatomical parameters in crops and facilitates the selective breeding of sorghum. Full article

(This article belongs to the Special Issue Genetic Identification, Exploration, Evaluation and Breeding of Plant Genetic Resources)

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