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A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Crop Genetics, Genomics and Breeding".

Deadline for manuscript submissions: closed (15 May 2021) | Viewed by 51480

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Dr. Panagiotis Madesis

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Guest Editor

School of Agricultural Sciences, Department of Agriculture Crop Production and Rural Environment, University of Thessaly, 38446 Volos, Greece
Interests: genomics; plant breeding; CRISP/R; stress tolerance; molecular genetics; population genetics molecular species identification and authentication
Special Issues, Collections and Topics in MDPI journals

Dr. Irini Nianiou-Obeidat

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Co-Guest Editor

Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, 54124 Thessaloniki, Greece
Interests: tissue culture; stress tolerance; molecular plant breeding; genetic resources; seed breeding omics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The global nature of food security becomes more important due to increased population, demand for products and climate change. These problems suggest we need a new “green revolution” As the ultimate goal of plant breeding is to improve crop performance for traits or defined characteristics and to address the problems arising and due to the nature of the changes we should exploit all available methods in our hands. We live in the era of omics technologies. Next generation sequencing techniques now allow the massive sequencing of whole genomes and all the varieties in a species, coupled with phenotyping and conventional plant breeding allows us to identify the mechanisms underling different plant functions and the corresponding genes. While metagenomic analysis offers new insights on soil microbiota – plant interactions very important for plant breeding. Finally, novel techniques such as CRISPR/cas9 systems could revolutionise both our understanding of gene function as well plant breeding.

In this Special Issue we welcome research papers and reviews (a reduced number) dealing with topics related to the Crop Breeding and Genetics The integration of -omics technologies is promising to revolutionize plant breeding, providing an exceptional opportunity to identify genetic variations that can be employed in durum wheat breeding programs. For these reasons, contributions highlighting the usefulness of new genotyping, phenotyping and modelling techniques to improve the understanding and prediction of complex traits (e.g. yield, protein content, interaction with weeds and soil micro-organisms, etc.), are welcome.

Dr. Panagiotis Madesis
Guest Editor

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Keywords

Stress tolerance
Genomics
Phenotyping
Metagenomics
Marker assisted breeding
Yield potential
Conventional breeding
Molecular breeding

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Published Papers (12 papers)

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Research

16 pages, 731 KiB

Open AccessArticle

Estimations on Trait Stability of Maize Genotypes

by Vasileios Greveniotis, Elisavet Bouloumpasi, Stylianos Zotis, Athanasios Korkovelos and Constantinos G. Ipsilandis

Agriculture 2021, 11(10), 952; https://doi.org/10.3390/agriculture11100952 - 30 Sep 2021

Cited by 8 | Viewed by 2823

Abstract

The purposes of this study were to define the kind of trait inheritance through stability estimations of various traits in maize, to define the relationship between different environments and maize hybrids, and to propose the best environments and hybrids for farmers. Field experiments were conducted in two years (2011 and 2012) at four different locations in Greece: Florina, Trikala, Kalambaka and Giannitsa which were selected as they represent different environments. The genetic materials tested in a Randomized Complete Block (RCB) design, were 15 F1 commercial maize hybrids and 15 open-pollination lines developed from 4-cycle Honeycomb evaluation. Materials were sown and harvested by hand at different dates according to local conditions. Trait stability index

{(\bar{x} ∕ s)}^{2}

across environments was computed for each maize trait studied: yield, specific weight, 1000-kernel weight, axis (spindle) weight, spike weight, number of kernels per spike, spike length and diameter, number of kernel rows, spindle diameter, main spike and plant height, prolificacy and number of kernels per row. The findings showed great differences in stability index between traits and also for the same trait across environments or between maize genotypes. GGE biplot for yield distributed genotypes in a different way for Florina on the basis of one main factor and managed to depict Trikala’s differential response on the basis of two factors. Almost the same trend was found for 1000-kernel weight and specific weight, where there was a wide core for similar responding genotypes. Basic conclusions of this research are summarized in great differences of various traits, indicating qualitative, medium or quantitative inheritance. Estimations for trait stability can be easily performed in a multi-genotype experiment using trait stability index. The most stable hybrids were proved to be 31Y43, COSTANZA and FACTOR. The environment favouring a general stable performance proved to be Florina. Full article

(This article belongs to the Special Issue Crop Breeding and Genetics)

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14 pages, 554 KiB

Open AccessArticle

Introgression of QTLs for Drought Tolerance into Farmers’ Preferred Sorghum Varieties

by Andekelile Mwamahonje, John Saviour Yaw Eleblu, Kwadwo Ofori, Tileye Feyissa, Santosh Deshpande, Ana Luísa Garcia-Oliveira, Rajaguru Bohar, Milcah Kigoni and Pangirayi Tongoona

Agriculture 2021, 11(9), 883; https://doi.org/10.3390/agriculture11090883 - 15 Sep 2021

Cited by 10 | Viewed by 3366

Abstract

Sorghum is a major staple food crop for the people in semi-arid areas of Africa and Asia. Post-flowering drought is a global constraint of sorghum production. The study aimed to improve stay-green (STG) characteristics of farmer-preferred sorghum varieties in Tanzania using marker-assisted backcrossing. A total of 752 individuals representing five BC₂F₁ populations and their parents were genotyped using previously reported KASP markers linked with STG 3A and STG 3B quantitative trait loci (QTL). In the BC₂F₁ populations, the maximum number of individuals with heterozygous alleles were observed in S35*Pato background (37) whereas only seven individuals derived from the B35*Wahi parents’ background contained heterozygous alleles. Of the 30 single nucleotide polymorphism (SNP) markers, favourable alleles were observed at 18 loci in BC₂F₁ populations. In the BC₂F₁ generation, the highest (0.127 kg/panicle) grain yield was observed in the B35*NACO Mtama 1 background population. The genotypic analysis revealed the presence of favourable alleles in homozygous conditions at markers loci associated with STG 3A and STG 3B QTLs in BC₂F₃ populations, suggesting successful introgression of STG QTLs from the donor parents to the recurrent parents. Across water irrigation regimes, the highest (0.068 kg/panicle) mean grain weight was observed in the genotype NA316C. Therefore, our study demonstrated the utility of marker-assisted backcrossing for drought tolerance improvement of locally adapted sorghum varieties in Africa. Full article

(This article belongs to the Special Issue Crop Breeding and Genetics)

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22 pages, 4858 KiB

Open AccessEditor’s ChoiceArticle

Yield Components Stability Assessment of Peas in Conventional and Low-Input Cultivation Systems

by Vasileios Greveniotis, Elisavet Bouloumpasi, Stylianos Zotis, Athanasios Korkovelos and Constantinos G. Ipsilandis

Agriculture 2021, 11(9), 805; https://doi.org/10.3390/agriculture11090805 - 24 Aug 2021

Cited by 14 | Viewed by 3132

Abstract

The primary purpose of this study was to explore yield stability of pea (Pisum sativum L.) cultivars based on stability index, with specific aim at studying cultivar behavior regarding yield of peas under both conventional and low-input cultivation systems. Five cultivars of peas were used in a strip-plot design. Correlations showed a significant positive relation between seed yield and some other traits. Indirect seed yield improvement may be implemented by improving pod length, which generally showed high stability indices in Greek mega-environment. Comparisons between conventional and low-input farming systems generally did not affect stability estimations, but revealed cultivars that exhibited stable performance, even in low-input farming systems. The additive main effects and multiplicative interaction (AMMI) biplot analysis, genotype by environment interaction (GGE) biplot analysis and analysis of variance (ANOVA) showed statistically significant differences between genotypes and environments, and also the farming system. This way, we have certain cultivars of peas to recommend for specific areas and farming system, in order to achieve the most stable performance. Vermio proved to be a stable cultivar for seed yield performance, in Giannitsa, Trikala and Kalambaka area, in low-inputs farming systems, while Olympos was the best in Florina area and low-input farming. Full article

(This article belongs to the Special Issue Crop Breeding and Genetics)

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20 pages, 1983 KiB

Open AccessArticle

Protoplast Isolation, Fusion, Culture and Transformation in the Woody Plant Jasminum spp.

by Mohamed A. A. Ahmed, Miao Miao, Emmanouil D. Pratsinakis, Hongliang Zhang, Wei Wang, Yuan Yuan, Meiling Lyu, Junaid Iftikhar, Ahmed F. Yousef, Panagiotis Madesis and Binghua Wu

Agriculture 2021, 11(8), 699; https://doi.org/10.3390/agriculture11080699 - 26 Jul 2021

Cited by 17 | Viewed by 10590

Abstract

Plant protoplasts are significant for plant cell culture, somatic cell fusion, genetics, and breeding studies. In addition, in vitro plant regeneration has great importance for developmental biology, manifesting potential applications in agriculture and biotechnology. In this regard, we present a well-established protocol regarding protoplast isolation, cell culture and protoplast fusion of Jasminum spp. In particular, different tissues of Jasminum samab L. and Jasminum mesnyi were employed for protoplast isolation, and stem explants provided a high callus induction rate in a short period of time. The best source for protoplast isolation was calli tissues. The optimized isolation protocol consisted of digesting callus in an enzyme solution containing 0.4 M mannitol, 0.2 M MES, 1 M CaCl₂, 0.2 M KCL and 1 M NaH₂PO_4, 1.5% Cellulases onozuka R-10, 0.4% Macerozyme R-10 and 0.8% Pectinase for 4 h at 26 °C in the dark, providing a yield of 23.8 × 10⁶ Protoplast/gFW with 88% viability. Protoplasts were cultured both in liquid and agarose medium under optimum conditions, leading to microcalli formation after eight weeks. A 5% protoplast-fusion rate can be achieved when cultured in 40% (w/v) PEG-MW6000 supplemented with 0.1 M CaCl₂, 0.1 M sorbitol and 1 M Tris for 20 min. Furthermore, we developed an efficient PEG-mediated transformation protocol for jasmine protoplasts. The best results regarding protoplast transformation were obtained when the protoplast concentration was 4 × 10⁵ cells/mL and the exogenous plasmid DNA added had a concentration of 10 µg DNA/100 µL protoplast solution, followed by the application of 40% PEG-4000 for 10 min. Full article

(This article belongs to the Special Issue Crop Breeding and Genetics)

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23 pages, 3298 KiB

Open AccessArticle

A Stability Analysis Using AΜΜΙ and GGE Biplot Approach on Forage Yield Assessment of Common Vetch in Both Conventional and Low-Input Cultivation Systems

by Vasileios Greveniotis, Elisavet Bouloumpasi, Stylianos Zotis, Athanasios Korkovelos and Constantinos G. Ipsilandis

Agriculture 2021, 11(6), 567; https://doi.org/10.3390/agriculture11060567 - 20 Jun 2021

Cited by 10 | Viewed by 3247

Abstract

Common vetch (Vicia sativa L.) is a widespread legume crop in the Mediterranean mega-environment, due to its versatile uses and its compatibility with organic and low-input farming systems. However, its adaptation to various such environments should be studied and varieties suitable for forage yield must be selected. This study aimed to explore forage yield stability of common vetch varieties based on the stability index, with a specific target to explore common vetch variety behavior in various environments. Six Greek varieties of common vetch were used over four environments for two years. The cultivation was conducted using a strip plot with the varieties randomized within each plot in both conventional and low-input cultivation systems. (Alexandros) and (Tempi) varieties showed stability for days to 50% of flowering (index >4000), while (Pigasos) and (Zefyros) for fresh forage yield (>200) across environments. Combined estimations, also showed stability of (Pigasos) and (Zefyros) for fresh forage yield. Comparisons between the conventional and low-input farming systems generally showed minor differences but revealed varieties that exhibit stable performance even in the low-input farming systems, where stability is generally a little higher. The AMMI and GGE biplot analysis depicted the stability performance of the varieties regarding the traits under experimentation. As far as the fresh forage and dry matter yield, (Zefyros) was the most stable and productive variety over all others. Correlations between traits displayed the positive relation of fresh forage yield with days for 50% flowering and dry forage yield. Positive correlations may be proved useful for indirect breeding through traits with high stability leading to the selection of traits that show low stability. Full article

(This article belongs to the Special Issue Crop Breeding and Genetics)

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15 pages, 1700 KiB

Open AccessFeature PaperArticle

Genetic Variability, Correlation among Agronomic Traits, and Genetic Progress in a Sugarcane Diversity Panel

by Fernanda Zatti Barreto, Thiago Willian Almeida Balsalobre, Roberto Giacomini Chapola, Antonio Augusto Franco Garcia, Anete Pereira Souza, Hermann Paulo Hoffmann, Rodrigo Gazaffi and Monalisa Sampaio Carneiro

Agriculture 2021, 11(6), 533; https://doi.org/10.3390/agriculture11060533 - 9 Jun 2021

Cited by 15 | Viewed by 3964

Abstract

Sugarcane breeding programs require 15 years of experimentation to create more productive cultivars, and estimates of genetic progress can indicate the efficiency of breeding programs. In this study, we used a diversity panel, the Brazilian Panel of Sugarcane Genotypes (BPSG), with the following objectives: (i) to estimate, through a mixed model, the adjusted means and genetic parameters of ten traits evaluated over three harvest years; (ii) to estimate genotypic correlation among those traits; and (iii) to estimate genetic progress over six decades of breeding. The heritabilities ranged from 0.43 to 0.88, and we detected 42 significant correlations, 9 negative and 33 positive. Over six decades, the sucrose-related traits BRIX, POL%C, and POL%J showed an average increase per decade of 0.27 °Brix, 0.26% and 0.31%, respectively. Stalk number, height, and weight of the plot, and cane and sucrose yields revealed average increases per decade of 3.27 stalks, 0.06 m, 9.42 kg, 11.22 t/ha, and 2.08 t/ha, respectively. The genetic progress of the main agronomic traits is discussed through a historical series of sugarcane genotypes present in the BPSG. The findings of this study could contribute to the management of new breeding strategies and allow for future studies of associative mapping. Full article

(This article belongs to the Special Issue Crop Breeding and Genetics)

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17 pages, 1131 KiB

Open AccessArticle

Winter Wheat Cultivar Recommendation Based on Expected Environment Productivity

by Marzena Iwańska, Jakub Paderewski, Michał Stępień and Paulo Canas Rodrigues

Agriculture 2021, 11(6), 522; https://doi.org/10.3390/agriculture11060522 - 4 Jun 2021

Cited by 3 | Viewed by 2569

Abstract

We used 5 years of data from multi-environmental trials conducted in Poland to assess average winter wheat yield based on selected environmental factors to recommend cultivars depending on their performance in environments of different productivity. Average expected yields in particular environments were calculated using a model based on analysis of covariance (ANCOVA), which describes the relationship between winter wheat yield and environmental factors of soil suitability and pH, drought length and Selyaninov’s Hydrothermal Coefficient (HTC) in 10-day periods. The cultivar performance was evaluated using linear regression. The cultivar yield estimated by the mixed model was considered the dependent variable, whereas the environmental mean yields, estimated by ANCOVA, were considered independent variables. The cultivars were ranked according to the estimated yield in environments of determined average wheat productivity. Higher yielding cultivars were divided into two groups: widely and narrowly adapted cultivars, which were then recommended. The novelty of this study stems from the consideration of the environmental productivity in the recommendation process, the indication of widely adapted cultivars to be grown in a broad range of productivity sites and the selection of cultivars with narrow adaptation, which may outperform cultivars of wide adaptation in homogeneous fields. This study confirmed the importance of soil suitability and HTC for winter wheat yield. Direct application of our results is possible in Poland and in other countries with similar conditions. Full article

(This article belongs to the Special Issue Crop Breeding and Genetics)

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21 pages, 3432 KiB

Open AccessArticle

Fruit Quality Traits and Genotypic Characterization in a Pomegranate Ex Situ (Punica granatum L.) Collection in Greece

by Lefkothea Karapetsi, Georgios Pantelidis, Emmanouil D. Pratsinakis, Pavlina Drogoudi and Panagiotis Madesis

Agriculture 2021, 11(6), 482; https://doi.org/10.3390/agriculture11060482 - 24 May 2021

Cited by 14 | Viewed by 3213

Abstract

Pomegranate is one of the oldest known fruit crops, well adapted to hot and dry areas and successfully grown in Mediterranean countries. During the last two decades, numerous publications have revealed the traditionally known associations between pomegranate consumption and health benefits, which led to increased demand by consumers and expansion in cultivation areas. Pomegranate is well adapted to areas with diverse pedoclimatic conditions and local cultivars could provide an essential source of genes for breeding. In this study, fruit phenotypic and genetic variability, and relationships, were studied in 26 Greek and foreign pomegranate cultivars/accessions grown in an ex situ collection located in Naoussa Greece, using Inter Simple Sequence Repeat (ISSR) and Start Codon Targeted (SCoT) molecular markers. Results from the principal component analysis made on fruit phenotypic characters revealed five components that accounted for 74.8% of the total variance, the first being related to skin color parameters and the second to juice antioxidant contents and aril color. Clustering from phenotypic data allocated individuals into four clusters. A total of 184 bands were generated for all markers applied across the 26 pomegranate cultivars/accessions, with an average of 77 bands per ISSR markers and 82 bands for SCoT markers. Low variability in the phenotypic and genotypic level was indicated; nevertheless, results from the association study between phenotypic traits and molecular markers that were obtained using Multiple Regression Analysis (MRA) could prove valuable for marker-assisted breeding programs, especially from SCoT markers that were found to be strongly or averagely associated with the morphological traits and chemical components. Full article

(This article belongs to the Special Issue Crop Breeding and Genetics)

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10 pages, 1236 KiB

Open AccessArticle

Development of a Simple and Low-Resource Regeneration System of Two Greek Tomato Varieties

by Vaia Styliani Titeli, Ioannis Zafeiriou, Angeliki Laskaridou, Georgios Menexes, Panagiotis Madesis, Evangelia Stavridou and Irini Nianiou-Obeidat

Agriculture 2021, 11(5), 412; https://doi.org/10.3390/agriculture11050412 - 3 May 2021

Cited by 4 | Viewed by 3379

Abstract

Native tomato landrace varieties (Solanum lycopersicum L.) are sources of high genetic diversity and are adaptable to local environmental conditions. The in vitro propagation system can be used as a tool to produce disease-free, high-quality propagation material and preserve the unique characteristics of commercial Greek tomato varieties, such as the variety Areti and the traditional landrace variety Makedonia, both of exceptional quality and economic importance. Twenty- and 27-day-old cotyledon and leaf explants were cultivated in 4 regeneration media supplemented with 0 or 0.1 mg∙L⁻¹ indole-3-acetic acid and 0.5 or 1 mg∙L⁻¹ zeatin. Regeneration efficiency was dependent on variety, explant type and age, and regeneration media. Areti was a more appropriate target genetic material, exhibiting a six-fold greater response to regeneration compared to Makedonia, regardless of media and explant age. The regenerated shoots of both varieties were successfully rooted (60%) and acclimatized (98%). This regeneration protocol would be valuable in the production of propagation material for commercial and conservation practices and in breeding programs for genetic improvement. Full article

(This article belongs to the Special Issue Crop Breeding and Genetics)

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18 pages, 1941 KiB

Open AccessEditor’s ChoiceArticle

Assessment of Interactions between Yield Components of Common Vetch Cultivars in Both Conventional and Low-Input Cultivation Systems

by Vasileios Greveniotis, Elisavet Bouloumpasi, Stylianos Zotis, Athanasios Korkovelos and Constantinos G. Ipsilandis

Agriculture 2021, 11(4), 369; https://doi.org/10.3390/agriculture11040369 - 19 Apr 2021

Cited by 12 | Viewed by 3044

Abstract

The primary purpose of this study was to explore yield stability of common vetch varieties based on the stability index, with a specific aim of exploring common vetch variety behavior regarding the yield of legumes under both conventional and low-input cultivation systems. Six varieties of common vetch (Vicia sativa L.), namely, cv. Filippos, cv. Omiros, cv. Alexandros, cv. Tempi, cv. Zefyros and cv. Pigasos, were used. The cultivation was conducted using a strip-plot design with the six varieties randomized within each plot in two farming systems (conventional and low-input). Filippos was the best variety in conventional farming for seed yield, followed by Omiros. Omiros was the best variety in the low-input farming system for seed yield. Comparisons between conventional and low-input farming systems generally did not display any effect on stability estimations, but revealed the varieties that exhibit stable performance even in low-input farming systems. Stability analysis via the AMMI1 and GxE biplot analysis for one main factor showed two groups of varieties for seed yield with similar behavior. Genotype and environment distribution were used to group varieties that showed better performance in certain environments for seed yield but with differences in comparison to other traits. Correlations between traits showed the positive relation of seed yield to the number of pods per plant, the number of seeds per pod, the pod length, the mean weight of pods and, especially, the hay weight (r = 0.771), a useful finding for indirect selection for breeders. The results provide valuable data regarding the genetic material, its adaptability and stability in varied environments and suitability for low-input cultivation systems. Full article

(This article belongs to the Special Issue Crop Breeding and Genetics)

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19 pages, 5220 KiB

Open AccessArticle

Effect of Genotype × Environment Interaction for Seed Traits in Winter Oilseed Rape (Brassica napus L.)

by Alina Liersch, Jan Bocianowski, Kamila Nowosad, Katarzyna Mikołajczyk, Stanisław Spasibionek, Franciszek Wielebski, Marcin Matuszczak, Laurencja Szała, Teresa Cegielska-Taras, Katarzyna Sosnowska and Iwona Bartkowiak-Broda

Agriculture 2020, 10(12), 607; https://doi.org/10.3390/agriculture10120607 - 8 Dec 2020

Cited by 25 | Viewed by 3805

Abstract

Brassica napus (L.), winter oilseed rape (WOSR) or canola, is one of the most important oilseed crop species of the moderate climate zone. Improving the seed quality and yield makes the main target in breeding programs worldwide. In this study, we examined the genotype-by-environment (G×E) interaction with respect to six seed traits among 25 WOSR genotypes. The plant material included the registered canola cultivars, our newly developed mutant breeding lines and the Ogura F1 hybrids and their parental components, in addition to our domestic breeding lines including two semi-resynthesized (semi-RS) lines. The 25 genotypes were examined in field trials at two locations, in three growing seasons. Seed oil and protein content, total glucosinolates (GLS) content in seed meal and C18 unsaturated fatty acid (oleic, linoleic and linolenic) composition in seed oil were examined. The additive main effects and multiplicative interaction (AMMI) analyses revealed significant effects of both, genotype (G) and environment (E) as well as the G×E interaction regarding the analyzed seed traits. In our study, two Ogura F1 hybrids, a CMS line and a new high oleic mutant breeding line revealed high stability and good average values for most of the analyzed seed traits, thus making a valuable source of starting materials for further improvement. Full article

(This article belongs to the Special Issue Crop Breeding and Genetics)

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18 pages, 4267 KiB

Open AccessArticle

Selection of Habanero Pepper F1 Hybrids (Capsicum chinense Jacq.) at the Yucatan Peninsula, Mexico with a High Potential for Different Markets

by Liliana S. Muñoz-Ramírez, Laura P. Peña-Yam, Martha A. Álvarez-Gil, Lourdes G. Iglesias-Andreu, Susana A. Avilés-Viñas, Adriana Canto-Flick, Adolfo Guzmán-Antonio and Nancy Santana-Buzzy

Agriculture 2020, 10(10), 478; https://doi.org/10.3390/agriculture10100478 - 15 Oct 2020

Cited by 10 | Viewed by 6397

Abstract

This study evaluated 29 F1 lines and the 11 genotypes of habanero peppers used in the crossbreeding program developed by the Scientific Research Center of Yucatan, México. A randomized complete block design with four repetitions was used. Eight plants of each of the genotypes were studied per block. A total of 22 qualitative and 18 quantitative descriptors established in the manuals of the International Plant Genetic Resources Institute (IPGRI) and the National Service for Seed Inspection and Certification (SNICS) was used. The multiple correspondence analysis of the qualitative traits explained 38.2% of the total variability. The trait that contributed the most to the qualitative variability identified was the presence of anthocyanins in the node. Principal component analysis showed that the first two axes explained 85.1% of the total variability and that capsaicin content and fruit pericarp thickness were the major contributors to the variation recorded. Based on these results, four F1 hybrids of habanero pepper were selected because of their promising traits for the different markets, i.e., high productive potential and/or high pungency. These traits are described in the section on Results. Full article

(This article belongs to the Special Issue Crop Breeding and Genetics)

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