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Identification and Evaluation of Plant Genetic Resources for Eco-Friendly Agriculture

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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 22457

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Special Issue Editors

Dr. Francesco Mercati

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Institute of Biosciences and BioResources, Division of Palermo, National Research Council, Corso Calatafimi, 414, I-90129 Palermo, Italy
Interests: plant genetics; plant nutrition; breeding; molecular markers; NGS (next-generation sequencing); PGPR
Special Issues, Collections and Topics in MDPI journals

Dr. Gabriella De Lorenzis

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Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, 20122 Milano MI, Italy
Interests: molecular markers; SNP; SSR; genetic structure; genetic diversity; fingerprinting; heterozygosity; pedigree; QTL; GWAS

Special Issue Information

Dear Colleagues,

During the last few decades, we witnessed a progressive loss of genetic resources of crop plants. Future progress in developing sustainable agriculture depends, to a great extent, on the conservation and preservation of crop genetic resources and on promoting their effective utilization in plant breeding. In this context, a great deal has been accomplished to safeguard plant genetic richness thanks to the establishment of germplasm collections.

Molecular markers have become routine to study crop genetic diversity, to investigate the genetic structure of germplasm resources, to establish parentage analysis, and to identify loci associated with agronomical traits.

Due to rapid developments in the field of molecular genetics, a variety of different techniques have emerged to analyze genetic variation. The most commonly used are SSR (simple sequence repeats) and SNP (single nucleotide polymorphism). Their success lies in (i) the medium–high polymorphic information content, (ii) the medium–high power of multiplexing, (iii) high level of automation, (iv) medium–high level of assay throughput, and (v) high reproducibility. Moreover, SSR and SNP markers are suitable for all purposes related to the study of genetic variability, from diversity to mapping and association studies.

This Special Issue will promote works performed for the genetic characterization of germplasm collections of horticultural crops using informative and co-dominant markers (SSR and SNP), as well as studies on the use of molecular markers to support breeding programs for eco-friendly agriculture.

We welcome excellent original research and review articles that address, but should not be restricted to, the following topics:

Genetic characterization of germplasm collections;
Mapping study (QTL – quantitative trait loci)
Association study (GWAS – genome-wide association Analysis)
Marker-assisted selection (MAS)

Dr. Francesco Mercati
Dr. Gabriella De Lorenzis
Guest Editors

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 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

horticultural crops
population structure
synonymies
homonymies
QTL
GWAS
MAS

Published Papers (10 papers)

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Research

24 pages, 2336 KiB

Open AccessArticle

Morphological, Molecular, and Nutritional Characterisation of the Globe Artichoke Landrace “Carciofo Ortano”

by Enrica Alicandri, Anna Rita Paolacci, Giulio Catarcione, Alberto Del Lungo, Valentina Iacoponi, Francesco Pati, Giuseppe Scarascia Mugnozza and Mario Ciaffi

Plants 2023, 12(9), 1844; https://doi.org/10.3390/plants12091844 - 29 Apr 2023

Cited by 1 | Viewed by 1553

Abstract

The present study focused on the molecular, morphological, and nutritional characterisation of a globe artichoke landrace at risk of genetic erosion still cultivated in the municipality of Orte (Lazio Region, Central Italy) and therefore named “Carciofo Ortano”. Molecular analysis based on SSR and ISSR markers was carried out on 73 genotypes selected at random from 20 smallholdings located in the Orte countryside and 17 accessions of landraces/clones belonging to the main varietal types cultivated in Italy. The results confirmed that “Carciofo Ortano” belongs to the “Romanesco” varietal typology and revealed the presence within the landrace of two distinct genetic populations named Orte 1 and Orte 2. Despite the high level of within-population genetic variation detected, the two populations were genetically differentiated from each other and from the landraces/clones of the main varietal types cultivated in Italy. Morphological and nutritional characterisation was performed on representative genotypes for each of the two populations of the “Carciofo Ortano” and the four landraces/clones included in the varietal platform of the PGI “CARCIOFO ROMANESCO DEL LAZIO” used as reference genotypes (“Campagnano”, “Castellammare”, “C3”, and “Grato 1”). Principal component analysis showed that, of the 43 morphological descriptors considered, 12, including plant height, head shape index, head yield, and earliness, allowed a clear grouping of genotypes, distinguishing Orte 1 and Orte 2 populations from the reference genotypes. Regarding the nutritional composition of heads, particular attention should be devoted to the Orte 2 genotypes for their high dietary fibre, inulin, flavonoid, and phenol content, a feature that could be highly appreciated by the market. Full article

(This article belongs to the Special Issue Identification and Evaluation of Plant Genetic Resources for Eco-Friendly Agriculture)

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23 pages, 5219 KiB

Open AccessArticle

Genetic Diversity and Population Structure of Common Bean (Phaseolus vulgaris L.) Landraces in the Lazio Region of Italy

by Giulio Catarcione, Anna Rita Paolacci, Enrica Alicandri, Elena Gramiccia, Paola Taviani, Roberto Rea, Maria Teresa Costanza, Gabriella De Lorenzis, Guglielmo Puccio, Francesco Mercati and Mario Ciaffi

Plants 2023, 12(4), 744; https://doi.org/10.3390/plants12040744 - 07 Feb 2023

Cited by 7 | Viewed by 2059

Abstract

Common bean cultivation has historically been a typical component of rural economies in Italy, particularly in mountainous and hilly zones along the Apennine ridge of the central and southern regions, where the production is focused on local landraces cultivated by small-scale farmers using low-input production systems. Such landraces are at risk of genetic erosion because of the recent socioeconomic changes in rural communities. One hundred fourteen accessions belonging to 66 landraces still being grown in the Lazio region were characterized using a multidisciplinary approach. This approach included morphological (seed traits), biochemical (phaseolin and phytohemagglutinin patterns), and molecular (microsatellite loci) analyses to investigate their genetic variation, structure, and distinctiveness, which will be essential for the implementation of adequate ex situ and in situ conservation strategies. Another objective of this study was to determine the original gene pool (Andean and Mesoamerican) of the investigated landraces and to evaluate the cross-hybridization events between the two ancestral gene pools in the P. vulgaris germplasm in the Lazio region. Molecular analyses on 456 samples (four for each of the 114 accessions) revealed that the P. vulgaris germplasm in the Lazio region exhibited a high level of genetic diversity (He = 0.622) and that the Mesoamerican and Andean gene pools were clearly differentiated, with the Andean gene pool prevailing (77%) and 12% of landraces representing putative hybrids between the two gene pools. A model-based cluster analysis based on the molecular markers highlighted three main groups in agreement with the phaseolin patterns and growth habit of landraces. The combined utilisation of morphological, biochemical, and molecular data allowed for the differentiation of all landraces and the resolution of certain instances of homonymy and synonymy. Furthermore, although a high level of homozygosity was found across all landraces, 32 of the 66 examined (49%) exhibited genetic variability, indicating that the analysis based on a single or few plants per landrace, as usually carried out, may provide incomplete information. Full article

(This article belongs to the Special Issue Identification and Evaluation of Plant Genetic Resources for Eco-Friendly Agriculture)

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17 pages, 6921 KiB

Open AccessArticle

ADH Gene Cloning and Identification of Flooding-Responsive Genes in Taxodium distichum (L.) Rich

by Rui Zhang, Lei Xuan, Longjie Ni, Ying Yang, Ya Zhang, Zhiquan Wang, Yunlong Yin and Jianfeng Hua

Plants 2023, 12(3), 678; https://doi.org/10.3390/plants12030678 - 03 Feb 2023

Cited by 2 | Viewed by 1696

Abstract

As a flooding-tolerant tree species, Taxodium distichum has been utilized in afforestation projects and proven to have important value in flooding areas. Alcohol dehydrogenase (ADH), which participates in ethanol fermentation, is essential for tolerance to the anaerobic conditions caused by flooding. In a comprehensive analysis of the ADH gene family in T. distichum, TdADHs were cloned on the basis of whole-genome sequencing, and then bioinformatic analysis, subcellular localization, and gene expression level analysis under flooding were conducted. The results show that the putative protein sequences of 15 cloned genes contained seven TdADHs and eight TdADH-like genes (one Class III ADH included) that were divided into five clades. All the sequences had an ADH_N domain, and except for TdADH-likeE2, all the other genes had an ADH_zinc_N domain. Moreover, the TdADHs in clades A, B, C, and D had a similar motif composition. Additionally, the number of TdADH amino acids ranged from 277 to 403, with an average of 370.13. Subcellular localization showed that, except for TdADH-likeD3, which was not expressed in the nucleus, the other genes were predominantly expressed in both the nucleus and cytosol. TdADH-likeC2 was significantly upregulated in all three organs (roots, stems, and leaves), and TdADHA3 was also highly upregulated under 24 h flooding treatment; the two genes might play key roles in ethanol fermentation and flooding tolerance. These findings offer a comprehensive understanding of TdADHs and could provide a foundation for the molecular breeding of T. distichum and current research on the molecular mechanisms driving flooding tolerance. Full article

(This article belongs to the Special Issue Identification and Evaluation of Plant Genetic Resources for Eco-Friendly Agriculture)

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16 pages, 3766 KiB

Open AccessArticle

Transcriptomic and iTRAQ-Based Quantitative Proteomic Analyses of inap CMS in Brassica napus L.

by Aifan Wang, Lei Kang, Guangsheng Yang and Zaiyun Li

Plants 2022, 11(19), 2460; https://doi.org/10.3390/plants11192460 - 21 Sep 2022

Cited by 1 | Viewed by 1387

Abstract

Brassica napus inap cytoplasmic male sterility (CMS) is a novel sterile line with potential application in rapeseed hybrid breeding. Sterile cytoplasm was obtained from Isatis indigotica through somatic fusion and then recurrent backcrossing with B. napus. Previous studies have shown that inap CMS abortion occurred before the stamen primordia (stage 4–5), but the genetic mechanism of sterility needs to be studied. RNA-seq analyses were performed on the floral buds at two stages (0–5 and 6–8), before and after the formation of stamen primordium. As a result, a total of 1769 and 594 differentially expressed genes (DEGs) were detected in the CMS line compared to its maintainer line at the two stages, respectively. In accordance with the CMS phenotype, the up- and downstream regulators of the stamen identity genes AP3 and PI were up- and downregulated in the CMS line, respectively. Furthermore, isobaric tags for relative and absolute quantitation (iTRAQ) analysis showed that a total of 760 differentially abundant proteins (DAPs) were identified in flower buds at stages 0–8, and most of the proteins related to the anther development, oxidative phosphorylation, and programmed cell death (PCD) were downregulated in inap CMS. In combined transcriptomic and proteomic analysis, a total of 32 DEGs/DAPs were identified, of which 7 common DEGs/DAPs had the same expression trend at stage 0–8 of flower development. The downregulation of genes related to the energy deficiency, hormone signal transduction, and the maintenance of mitochondrial metabolic homeostasis at stage 0–5 might disturb the normal differentiation of stamen primordium, resulting in carpelloid stamen of inap CMS. The study will help provide insights into the molecular mechanism of this new male sterility. Full article

(This article belongs to the Special Issue Identification and Evaluation of Plant Genetic Resources for Eco-Friendly Agriculture)

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14 pages, 1753 KiB

Open AccessArticle

A Novel Strategy to Reveal the Landscape of Crossovers in an F1 Hybrid Population of Populus deltoides and Populus simonii

by Zhiting Li, Wei Zhao, Jinpeng Zhang, Zhiliang Pan, Shengjun Bai and Chunfa Tong

Plants 2022, 11(8), 1046; https://doi.org/10.3390/plants11081046 - 12 Apr 2022

Viewed by 1423

Abstract

Although the crossover (CO) patterns of different species have been extensively investigated, little is known about the landscape of CO patterns in Populus because of its high heterozygosity and long-time generation. A novel strategy was proposed to reveal the difference of CO rate and interference between Populus deltoides and Populus simonii using their F1 hybrid population. We chose restriction site-associated DNA (RAD) tags that contained two SNPs, one only receiving the CO information from the female P. deltoides and the other from the male P. simonii. These RAD tags allowed us to investigate the CO patterns between the two outbred species, instead of using the traditional backcross populations in inbred lines. We found that the CO rate in P. deltoides was generally greater than that in P. simonii, and that the CO interference was a common phenomenon across the two genomes. The COs landscape of the different Populus species facilitates not only to understand the evolutionary mechanism for adaptability but also to rebuild the statistical model for precisely constructing genetic linkage maps that are critical in genome assembly in Populus. Additionally, the novel strategy could be applied in other outbred species for investigating the CO patterns. Full article

(This article belongs to the Special Issue Identification and Evaluation of Plant Genetic Resources for Eco-Friendly Agriculture)

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21 pages, 3147 KiB

Open AccessArticle

Multiparent-Derived, Marker-Assisted Introgression Lines of the Elite Indian Rice Cultivar, ‘Krishna Hamsa’ Show Resistance against Bacterial Blight and Blast and Tolerance to Drought

by Jyothi Badri, Gandhudi Lakshmidevi, L. R. K. JaiVidhya, Madamsetty Srinivasa Prasad, Gouri Shankar Laha, Vattikutti Jhansi Lakshmi, Subhakara Rao Isetty, Revadi Padmashree, Divya Balakrishnan, Yasaswini Vishnu Priya Varanasi, Aravind Kumar Jukanti, Uma Maheshwar Singh, Vikas Kumar Singh, Arvind Kumar, T. Ram, Lella Venkata Subba Rao and Raman Meenakshi Sundaram

Plants 2022, 11(5), 622; https://doi.org/10.3390/plants11050622 - 25 Feb 2022

Cited by 3 | Viewed by 2788

Abstract

Major biotic stresses viz., bacterial blight (BB) and blast and brown plant hopper (BPH) coupled with abiotic stresses like drought stress, significantly affect rice yields. To address this, marker-assisted intercross (IC) breeding involving multiple donors was used to combine three BB resistance genes—xa5, xa13 and Xa21, two blast resistance genes—Pi9 and Pi54, two BPH resistance genes—Bph20 and Bph21, and four drought tolerant quantitative trait loci (QTL)—qDTY1.1, qDTY2.1, qDTY3.1 and qDTY12.1—in the genetic background of the elite Indian rice cultivar ‘Krishna Hamsa’. Three cycles of selective intercrossing followed by selfing coupled with foreground selection and phenotyping for the target traits resulted in the development of 196 introgression lines (ILs) with a myriad of gene/QTL combinations. Based on the phenotypic reaction, the ILs were classified into seven phenotypic classes of resistance/tolerance to the following: (1) BB, blast and drought—5 ILs; (2) BB and blast—10 ILs; (3) BB and drought—9 ILs; (4) blast and drought—42 ILs; (5) BB—3 ILs; (6) blast—84 ILs; and (7) drought—43 ILs; none of the ILs were resistant to BPH. Positive phenotypic response (resistance) was observed to both BB and blast in 2 ILs, BB in 9 ILs and blast in 64 ILs despite the absence of corresponding R genes. Inheritance of resistance to BB and/or blast in such ILs could be due to the unknown genes from other parents used in the breeding scheme. Negative phenotypic response (susceptibility) was observed in 67 ILs possessing BB-R genes, 9 ILs with blast-R genes and 9 ILs harboring QTLs for drought tolerance. Complex genic interactions and recombination events due to the involvement of multiple donors explain susceptibility in some of the marker positive ILs. The present investigation successfully demonstrates the possibility of rapid development of multiple stress-tolerant/resistant ILs in the elite cultivar background involving multiple donors through selective intercrossing and stringent phenotyping. The 196 ILs in seven phenotypic classes with myriad of gene/QTL combinations will serve as a useful genetic resource in combining multiple biotic and abiotic stress resistance in future breeding programs. Full article

(This article belongs to the Special Issue Identification and Evaluation of Plant Genetic Resources for Eco-Friendly Agriculture)

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20 pages, 3458 KiB

Open AccessArticle

Genetic and Molecular Characterization of a Self-Compatible Brassica rapa Line Possessing a New Class II S Haplotype

by Bing Li, Xueli Zhang, Zhiquan Liu, Lulin Wang, Liping Song, Xiaomei Liang, Shengwei Dou, Jinxing Tu, Jinxiong Shen, Bin Yi, Jing Wen, Tingdong Fu, Cheng Dai, Changbin Gao, Aihua Wang and Chaozhi Ma

Plants 2021, 10(12), 2815; https://doi.org/10.3390/plants10122815 - 20 Dec 2021

Cited by 6 | Viewed by 3264

Abstract

Most flowering plants have evolved a self-incompatibility (SI) system to maintain genetic diversity by preventing self-pollination. The Brassica species possesses sporophytic self-incompatibility (SSI), which is controlled by the pollen- and stigma-determinant factors SP11/SCR and SRK. However, the mysterious molecular mechanism of SI remains largely unknown. Here, a new class II S haplotype, named BrS-325, was identified in a pak choi line ‘325’, which was responsible for the completely self-compatible phenotype. To obtain the entire S locus sequences, a complete pak choi genome was gained through Nanopore sequencing and de novo assembly, which provided a good reference genome for breeding and molecular research in B. rapa. S locus comparative analysis showed that the closest relatives to BrS-325 was BrS-60, and high sequence polymorphism existed in the S locus. Meanwhile, two duplicated SRKs (BrSRK-325a and BrSRK-325b) were distributed in the BrS-325 locus with opposite transcription directions. BrSRK-325b and BrSCR-325 were expressed normally at the transcriptional level. The multiple sequence alignment of SCRs and SRKs in class II S haplotypes showed that a number of amino acid variations were present in the contact regions (CR II and CR III) of BrSCR-325 and the hypervariable regions (HV I and HV II) of BrSRK-325s, which may influence the binding and interaction between the ligand and the receptor. Thus, these results suggested that amino acid variations in contact sites may lead to the SI destruction of a new class II S haplotype BrS-325 in B. rapa. The complete SC phenotype of ‘325’ showed the potential for practical breeding application value in B. rapa. Full article

(This article belongs to the Special Issue Identification and Evaluation of Plant Genetic Resources for Eco-Friendly Agriculture)

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24 pages, 2863 KiB

Open AccessArticle

Grapevine Diversity and Genetic Relationships in Northeast Portugal Old Vineyards

by Diana Augusto, Javier Ibáñez, Ana Lúcia Pinto-Sintra, Virgílio Falco, Fernanda Leal, José Miguel Martínez-Zapater, Ana Alexandra Oliveira and Isaura Castro

Plants 2021, 10(12), 2755; https://doi.org/10.3390/plants10122755 - 14 Dec 2021

Cited by 10 | Viewed by 3031

Abstract

More than 100 grapevine varieties are registered as suitable for wine production in “Douro” and “Trás-os-Montes” Protected Designations of Origin regions; however, only a few are actually used for winemaking. The identification of varieties cultivated in past times can be an important step to take advantage of all the potential of these regions grape biodiversity. The conservation of the vanishing genetic resources boosts greater product diversification, and it can be considered strategic in the valorisation of these wine regions. Hence, one goal of the present study was to prospect and characterise, through molecular markers, 310 plants of 11 old vineyards that constitute a broad representation of the grape genetic patrimony of “Douro” and “Trás-os-Montes” wine regions; 280 samples, grouped into 52 distinct known varieties, were identified through comparison of their genetic profiles generated via 6 nuclear SSR and 43 informative SNP loci amplification; the remaining 30 samples, accounting for 13 different genotypes, did not match with any profile in the consulted databases and were considered as new genotypes. This study also aimed at evaluating the population structure among the 65 non-redundant genotypes identified, which were grouped into two ancestral genetic groups. The mean probability of identity values of 0.072 and 0.510 (for the 6 SSR and 226 SNP sets, respectively) were determined. Minor differences were observed between frequencies of chlorotypes A and D within the non-redundant genotypes studied. Twenty-seven pedigrees were confirmed and nine new trios were established. Ancestors of eight genotypes remain unknown. Full article

(This article belongs to the Special Issue Identification and Evaluation of Plant Genetic Resources for Eco-Friendly Agriculture)

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14 pages, 2199 KiB

Open AccessArticle

Characterization of a Common S Haplotype BnS-6 in the Self-Incompatibility of Brassica napus

by Zhiquan Liu, Bing Li, Yong Yang, Changbin Gao, Bin Yi, Jing Wen, Jinxiong Shen, Jinxing Tu, Tingdong Fu, Cheng Dai and Chaozhi Ma

Plants 2021, 10(10), 2186; https://doi.org/10.3390/plants10102186 - 15 Oct 2021

Cited by 3 | Viewed by 1665

Abstract

Self-incompatibility (SI) is a pollen-stigma recognition system controlled by a single and highly polymorphic genetic locus known as the S-locus. The S-locus exists in all Brassica napus (B. napus, AACC), but natural B. napus accessions are self-compatible. About 100 and 50 S haplotypes exist in Brassica rapa (AA) and Brassica oleracea (CC), respectively. However, S haplotypes have not been detected in B. napus populations. In this study, we detected the S haplotype distribution in B. napus and ascertained the function of a common S haplotype BnS-6 through genetic transformation. BnS-1/BnS-6 and BnS-7/BnS-6 were the main S haplotypes in 523 B. napus cultivars and inbred lines. The expression of SRK in different S haplotypes was normal (the expression of SCR in the A subgenome affected the SI phenotype) while the expression of BnSCR-6 in the C subgenome had no correlation with the SI phenotype in B. napus. The BnSCR-6 protein in BnSCR-6 overexpressed lines was functional, but the self-compatibility of overexpressed lines did not change. The low expression of BnSCR-6 could be a reason for the inactivation of BnS-6 in the SI response of B. napus. This study lays a foundation for research on the self-compatibility mechanism and the SI-related breeding in B. napus. Full article

(This article belongs to the Special Issue Identification and Evaluation of Plant Genetic Resources for Eco-Friendly Agriculture)

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19 pages, 3445 KiB

Open AccessArticle

The Divergent Roles of the Rice bcl-2 Associated Athanogene (BAG) Genes in Plant Development and Environmental Responses

by Hailian Zhou, Jiaying Li, Xueyuan Liu, Xiaoshuang Wei, Ziwei He, Lihua Hu, Jibin Wang, Mingzheng Duan, Guosheng Xie, Jihong Wang and Lingqiang Wang

Plants 2021, 10(10), 2169; https://doi.org/10.3390/plants10102169 - 13 Oct 2021

Cited by 6 | Viewed by 2234

Abstract

Bcl-2-associated athanogene (BAG), a group of proteins evolutionarily conserved and functioned as co-chaperones in plants and animals, is involved in various cell activities and diverse physiological processes. However, the biological functions of this gene family in rice are largely unknown. In this study, we identified a total of six BAG members in rice. These genes were classified into two groups, OsBAG1, -2, -3, and -4 are in group I with a conserved ubiquitin-like structure and OsBAG5 and -6 are in group Ⅱ with a calmodulin-binding domain, in addition to a common BAG domain. The BAG genes exhibited diverse expression patterns, with OsBAG4 showing the highest expression level, followed by OsBAG1 and OsBAG3, and OsBAG6 preferentially expressed in the panicle, endosperm, and calli. The co-expression analysis and the hierarchical cluster analysis indicated that the OsBAG1 and OsBAG3 were co-expressed with primary cell wall-biosynthesizing genes, OsBAG4 was co-expressed with phytohormone and transcriptional factors, and OsBAG6 was co-expressed with disease and shock-associated genes. β-glucuronidase (GUS) staining further indicated that OsBAG3 is mainly involved in primary young tissues under both primary and secondary growth. In addition, the expression of the BAG genes under brown planthopper (BPH) feeding, N, P, and K deficiency, heat, drought and plant hormones treatments was investigated. Our results clearly showed that OsBAGs are multifunctional molecules as inferred by their protein structures, subcellular localizations, and expression profiles. BAGs in group I are mainly involved in plant development, whereas BAGs in group II are reactive in gene regulations and stress responses. Our results provide a solid basis for the further elucidation of the biological functions of plant BAG genes. Full article

(This article belongs to the Special Issue Identification and Evaluation of Plant Genetic Resources for Eco-Friendly Agriculture)

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