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Genetic Diversity, Conservation, and Innovative Plant Breeding Strategies

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetic Resources".

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 46413

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Special Issue Editors

Dr. Shri Mohan Jain

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Guest Editor

Department of Agricultural Sciences, University of Helsinki, PL-27, Helsinki, Finland
Interests: germplasm conservation; molecular breeding; mutagenesis; plant biotechnology; plant tissue culture
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Jameel M. Al-Khayri

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Department of Plant Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
Interests: date palm biotechnology; plant secondary metabolites; plant tissue culture
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Global climate has continuously been changing and will continue to change in the impending future. Erratic and rapid climate change is being recorded worldwide and is adversely impacting agriculture and threatening food security and economy worldwide. The rapidly changing climate and ever-growing human population have caused a loss of genetic resources, arable land destruction, soil erosion, and water shortage. Small changes in global temperature may influence the development of new pests and diseases, which could devastate agricultural sustainability. The preceding factors threaten plant productivity and diversity. Genetic diversity is important for adaptation to a changing environment. The conservation of genetic variation within a species is the key for survivability and adaptation to variable environmental conditions. Genetic variation constitutes the raw material for genetic improvement. Plant breeding—the art and science of improving the genetic potential of crop plants—has evolved over decades of continued practices of selection, hybridization, and recombination. Despite significant development in achieving sustainable food production, there is a persistent demand for increased food security for the growing human population, and food availability is gradually becoming a serious concern. The erosion of genetic diversity and the dependence on only 30 major crop species for global food supply increase pressure on food security. Plant breeders and geneticists are under constant pressure to sustain food production by using conventional and innovative breeding strategies. Recently, there has been a growing interest to introduce novel, minor crops that are well adapted to the marginal lands, are nutritionally rich, and have better tolerance to abiotic and biotic stresses. Advances in biotechnological tools have facilitated the rapid introgression of transgenes in addition to the creation, analysis, and manipulation of plant genetic variation for developing new improved crop varieties. This Special Issue of Plants will focus on recent research progress on the development of a multi-disciplinary approach to traditional plant breeding where plant biotechnology, molecular tools, and their applications would be strategically ideal in developing new improved varieties for sustainable food security and economy. It will address precision agriculture and plant domestication under different environmental conditions, germplasm genetic diversity and conservation, functional genomics, mutagenesis, gene editing, transgenics, bioinformatics, molecular markers, and in vitro techniques in plant breeding.

Prof. Dr. Shri Mohan Jain
Prof. Dr. Jameel M. Al-Khayri
Guest Editors

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Keywords

biotechnology
food security
gene editing
genetic diversity
genetic transformation
genomics
germplasm conservation
in vitro techniques
molecular breeding
mutagenesis
plant breeding

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Published Papers (12 papers)

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22 pages, 1625 KiB

Open AccessArticle

DNA Barcoding Medicinal Plant Species from Indonesia

by Ria Cahyaningsih, Lindsey Jane Compton, Sri Rahayu, Joana Magos Brehm and Nigel Maxted

Plants 2022, 11(10), 1375; https://doi.org/10.3390/plants11101375 - 21 May 2022

Cited by 17 | Viewed by 5139

Abstract

Over the past decade, plant DNA barcoding has emerged as a scientific breakthrough and is often used to help with species identification or as a taxonomical tool. DNA barcoding is very important in medicinal plant use, not only for identification purposes but also for the authentication of medicinal products. Here, a total of 61 Indonesian medicinal plant species from 30 families and a pair of ITS2, matK, rbcL, and trnL primers were used for a DNA barcoding study consisting of molecular and sequence analyses. This study aimed to analyze how the four identified DNA barcoding regions (ITS2, matK, rbcL, and trnL) aid identification and conservation and to investigate their effectiveness for DNA barcoding for the studied species. This study resulted in 212 DNA barcoding sequences and identified new ones for the studied medicinal plant species. Though there is no ideal or perfect region for DNA barcoding of the target species, we recommend matK as the main region for Indonesian medicinal plant identification, with ITS2 and rbcL as alternative or complementary regions. These findings will be useful for forensic studies that support the conservation of medicinal plants and their national and global use. Full article

(This article belongs to the Special Issue Genetic Diversity, Conservation, and Innovative Plant Breeding Strategies)

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15 pages, 2310 KiB

Open AccessArticle

An Analysis of Genetic Variability and Population Structure in Wheat Germplasm Using Microsatellite and Gene-Based Markers

by Alireza Pour-Aboughadareh, Peter Poczai, Alireza Etminan, Omid Jadidi, Farzad Kianersi and Lia Shooshtari

Plants 2022, 11(9), 1205; https://doi.org/10.3390/plants11091205 - 29 Apr 2022

Cited by 20 | Viewed by 2657

Abstract

Knowledge of the natural patterns of genetic variation and their evolutionary basis is required for sustainable management and conservation of wheat germplasm. In the current study, the genetic diversity and population structure of 100 individuals from four Triticum and Aegilops species (including T. aestivum, Ae. tauschii, Ae. cylindrica, and Ae. crassa) were investigated using two gene-based markers (start codon targeted (SCoT) polymorphism and CAAT-box derived polymorphism (CBDP)) and simple-sequence repeats (SSRs). The SCoT, CBDP, and SSR markers yielded 76, 116, and 48 polymorphism fragments, respectively. The CBDP marker had greater efficiency than the SCoT and SSR markers due to its higher polymorphism content information (PIC), resolving power (Rp), and marker index (MI). Based on an analysis of molecular variance (AMOVA) performed using all marker systems and combined data, there was a higher distribution of genetic variation within species than among them. Ae. cylindrica and Ae. tauschii had the highest values for all genetic variation parameters. A cluster analysis using each marker system and combined data showed that the SSR marker had greater efficiency in grouping of tested accessions, such that the results of principal coordinate analysis (PCoA) and population structure confirmed the obtained clustering patterns. Hence, combining the SCoT and CBDP markers with polymorphic SSR markers may be useful in genetic fingerprinting and fine mapping and for association analysis in wheat and its germplasm for various agronomic traits or tolerance mechanisms to environmental stresses. Full article

(This article belongs to the Special Issue Genetic Diversity, Conservation, and Innovative Plant Breeding Strategies)

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18 pages, 2090 KiB

Open AccessArticle

Elucidating Genetic Diversity in Apricot (Prunus armeniaca L.) Cultivated in the North-Western Himalayan Provinces of India Using SSR Markers

by Zahid Nabi Sheikh, Vikas Sharma, Rafiq Ahmad Shah, Shilpa Raina, Maha Aljabri, Javid Iqbal Mir, Naser AlKenani and Khalid Rehman Hakeem

Plants 2021, 10(12), 2668; https://doi.org/10.3390/plants10122668 - 4 Dec 2021

Cited by 11 | Viewed by 2994

Abstract

Apricot (Prunus armeniaca L.) is an important temperate fruit crop worldwide. The availability of wild apricot germplasm and its characterization through genomic studies can guide us towards its conservation, increasing productivity and nutritional composition. Therefore, in this study, we carried out the genomic characterization of 50 phenotypically variable accessions by using SSR markers in the erstwhile States of Jammu and Kashmir to reveal genetic variability among accessions and their genetic associations. The genetic parameter results revealed that the number of alleles per locus (Na) ranged from 1 to 6 with a mean Na value of 3.89 and the mean effective number of alleles (Ne) per locus 1.882 with a range of 1.22 to 2. Similarly, the polymorphic information content (PIC) values ranged from 0.464 to 0.104. The observed heterozygosity (Ho) (0.547) was found to have higher than expected heterozygosity (He) (0.453) with average heterozygosity of 0.4483. The dendrogram clustered genotypes into three main clades based on their pedigree. The population structure revealed IV sub-populations with all admixtures except the III sub-population, which was mainly formed of exotic cultivars. The average expected heterozygosity (He) and population differentiation within four sub-populations was 1.78 and 0.04, respectively, and explained 95.0% of the total genetic variance in the population. The results revealed that the SSR marker studies could easily decrypt the genetic variability present within the germplasm, which may form the base for the establishment of good gene banks by reducing redundancy of germplasm, selection of parents for any breeding program. Full article

(This article belongs to the Special Issue Genetic Diversity, Conservation, and Innovative Plant Breeding Strategies)

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18 pages, 1584 KiB

Open AccessArticle

Diversity of Water Yam (Dioscorea alata L.) Accessions from Côte d’Ivoire Based on SNP Markers and Agronomic Traits

by Lassana Bakayoko, Désiré N’Da Pokou, Abou Bakari Kouassi, Paterne A. Agre, Amani Michel Kouakou, Konan Evrard Brice Dibi, Boni Nzue, Jean M. Mondo, Patrick Adebola, Oluyemi T. Akintayo, Asrat Asfaw and Assanvo Simon Pierre N’Guetta

Plants 2021, 10(12), 2562; https://doi.org/10.3390/plants10122562 - 24 Nov 2021

Cited by 5 | Viewed by 2993

Abstract

Dioscorea alata (L.), also referred to as water, winged, or greater yam, is one of the most economically important staple food crops in tropical and subtropical areas. In Côte d’Ivoire, it represents, along with other yam species, the largest food crop and significantly contributes to food security. However, studies focusing on better understanding the structure and extent of genetic diversity among D. alata accessions, using molecular and phenotypic traits, are limited. This study was, therefore, conducted to assess the pattern of genetic variability in a set of 188 D. alata accessions from the National Agronomic Research Centre (CNRA) genebank using 11,722 SNP markers (generated by the Diversity Arrays Technology) and nine agronomic traits. Phylogenetic analyses using hierarchical clustering, admixture, kinship, and Discriminant analysis of principal component (DAPC) all assigned the accessions into four main clusters. Genetic diversity assessment using molecular-based SNP markers showed a high proportion of polymorphic SNPs (87.81%). The analysis of molecular variance (AMOVA) showed low molecular variability within genetic groups. In addition, the agronomic traits evaluated for two years in field conditions showed a high heritability and high variability among D. alata accessions. This study provides insights into the genetic diversity among accessions in the CNRA genebank and opens an avenue for sustainable resource management and the identification of promising parental clones for water yam breeding programs in Côte d’Ivoire. Full article

(This article belongs to the Special Issue Genetic Diversity, Conservation, and Innovative Plant Breeding Strategies)

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17 pages, 1982 KiB

Open AccessArticle

Analysis of Genetic Diversity and Population Structure in Bitter Gourd (Momordica charantia L.) Using Morphological and SSR Markers

by Ahmad Alhariri, Tusar Kanti Behera, Gograj Singh Jat, Mayanglambam Bilashini Devi, G. Boopalakrishnan, Nada F. Hemeda, Ayaat A. Teleb, E. Ismail and Ahmed Elkordy

Plants 2021, 10(9), 1860; https://doi.org/10.3390/plants10091860 - 8 Sep 2021

Cited by 17 | Viewed by 3978

Abstract

The present investigation was carried out using 51 diverse bitter gourd accessions as material for studying genetic diversity and relatedness using morphological and SSR markers. A wide variation was observed for morphological traits like the number of days to the first female flower anthesis (37.33–60.67), the number of days to the first fruit harvest (47.67–72.00), the number of fruits/plant (12.00–46.67), fruit length (5.00–22.23 cm), fruit diameter (1.05–6.38 cm), average fruit weight (20.71–77.67 g) and yield per plant (513.3–1976 g). Cluster analysis for 10 quantitative traits grouped the 51 accessions into 6 clusters. Out of 61 SSR primers screened, 30 were polymorphic and highly informative as a means to differentiate these accessions. Based on genotyping, a high level of genetic diversity was observed, with a total of 99 alleles. The polymorphic information content (PIC) values ranged from 0.038 for marker BG_SSR-8 to 0.721 for S-24, with an average of 0.429. The numbers of alleles ranged from 2 to 5, with an average of 3.3 alleles per locus. Gene diversity ranged from 0.04 for BG_SSR-8 to 0.76 for S-24, showing a wide variation among 51 accessions. The UPGMA cluster analysis grouped these accessions into 3 major clusters. Cluster I comprised 4 small, fruited accessions that are commercially cultivated in central and eastern India. Cluster II comprised 35 medium- to long-sized fruited accessions, which made up an abundant and diverse group. Cluster III comprised 11 long and extra-long fruited accessions. The polymorphic SSR markers of the study will be highly useful in genetic fingerprinting and mapping, and for association analysis in Momordica regarding several economic traits. Full article

(This article belongs to the Special Issue Genetic Diversity, Conservation, and Innovative Plant Breeding Strategies)

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11 pages, 4632 KiB

Open AccessArticle

Applying Biotechnology in the Propagation and Further Selection of Vaccinium uliginosum × (V. corymbosum × V. angustifolium) Hybrids

by Anna A. Erst, Aleksey B. Gorbunov, Sergey V. Asbaganov, Maria A. Tomoshevich, Evgeny V. Banaev and Andrey S. Erst

Plants 2021, 10(9), 1831; https://doi.org/10.3390/plants10091831 - 3 Sep 2021

Cited by 3 | Viewed by 2814

Abstract

The most serious problem of intergeneric and interspecific hybridization is related to overcoming the reproductive isolation of different species. We assessed the efficiency of reproduction under in vitro conditions and the ex vitro growth capacity of interspecific hybrids of Vaccinium uliginosum × (V. corymbosum × V. angustifolium). The percentage of seed germination in in vitro culture was 88% for V. uliginosum, form No. 8 × (V. corymbosum × V. angustifolium), SC5-8, while it was 42% for V. uliginosum, form No. 8 × (V. corymbosum × V. angustifolium), ‘Northcountry’. The analysis of mean value showed that the multiplication rate increased and the shoot height decreased as the 2-isopentenyl adenine (2iP) concentration was increased in the nutrient medium of the studied hybrids. The maximum rate was achieved using 15 μM 2iP. A detailed analysis of the hybrids indicated that the hybrid variant reliably affected growth and development indicators. Inter simple sequence repeat analysis demonstrated that all analyzed hybrids inherited DNA fragments of the parent plants in various combinations, confirming their hybrid nature. Thus, the use of in vitro methods for the propagation and further selection of genotypes is demonstrated as being an effective approach for developing interspecific hybrids of V. uliginosum × (V. corymbosum × V. angustifolium). Full article

(This article belongs to the Special Issue Genetic Diversity, Conservation, and Innovative Plant Breeding Strategies)

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15 pages, 7620 KiB

Open AccessArticle

Patterns of Genetic Variation in a Soybean Germplasm Collection as Characterized with Genotyping-by-Sequencing

by Yong-Bi Fu, Elroy R. Cober, Malcolm J. Morrison, Frédéric Marsolais, Gregory W. Peterson and Carolee Horbach

Plants 2021, 10(8), 1611; https://doi.org/10.3390/plants10081611 - 5 Aug 2021

Cited by 7 | Viewed by 2482

Abstract

Genomic characterization is playing an increasing role in plant germplasm conservation and utilization, as it can provide higher resolution with genome-wide SNP markers than before to identify and analyze genetic variation. A genotyping-by-sequencing technique was applied to genotype 541 soybean accessions conserved at Plant Gene Resources of Canada and 30 soybean cultivars and breeding lines developed by the Ottawa soybean breeding program of Agriculture and Agri-Food Canada. The sequencing generated an average of 952,074 raw sequence reads per sample. SNP calling identified 43,891 SNPs across 20 soybean chromosomes and 69 scaffolds with variable levels of missing values. Based on 19,898 SNPs with up to 50% missing values, three distinct genetic groups were found in the assayed samples. These groups were a mixture of the samples that originated from different countries and the samples of known maturity groups. The samples that originated from Canada were clustered into all three distinct groups, but 30 Ottawa breeding lines fell into two groups only. Based on the average pairwise dissimilarity estimates, 40 samples with the most genetic distinctness were identified from three genetic groups with diverse sample origin and known maturity. Additionally, 40 samples with the highest genetic redundancy were detected and they consisted of different sample origins and maturity groups, largely from one genetic group. Moreover, some genetically duplicated samples were identified, but the overall level of genetic duplication was relatively low in the collection. These findings are useful for soybean germplasm management and utilization. Full article

(This article belongs to the Special Issue Genetic Diversity, Conservation, and Innovative Plant Breeding Strategies)

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19 pages, 41218 KiB

Open AccessArticle

Diversity Assessment of the Montenegrin Maize Landrace Gene Pool Maintained in Two Gene Banks

by Vojka Babić, Violeta Andjelkovic, Zoran Jovovic, Milosav Babic, Vladimir Vasic and Natalija Kravic

Plants 2021, 10(8), 1503; https://doi.org/10.3390/plants10081503 - 22 Jul 2021

Cited by 2 | Viewed by 2269

Abstract

Due to the loss of agro-biodiversity, there is a strong effort to find apparent and efficient mechanisms for the conservation and sustainable use of genetic diversity. A joint monitoring of the diversity and collections structure of the Montenegrin maize landraces conserved in the Serbian (MRIZPGB) and Montenegrin (MGB) gene banks has been conducted in order to improve the composition of the collections and to identify and eliminate possible redundancy. Based on a separate analysis of white- and yellow-orange maize landraces, it can be concluded that the diversity and evolution of distinct maize landraces grown and collected in Montenegro have been simultaneously shaped by both environmental (i.e., natural selection) and socially driven factors (farmers’ selection, migration and colonization processes of the human population). Although it has been determined that the authenticity and variability of the Montenegrin maize landraces gene pool have largely been preserved in the MRIZPGB collection, a significant amount of redundancy was observed. The obtained results will contribute to the cost-efficient conservation of the maize gene pool in the Montenegrin and Serbian gene banks. The recognized and well-preserved original variability of the MRIZPGB and MGB Montenegrin gene pool represents a valuable source for pre-breeding activities on broadening the white and flint maize breeding programmes under temperate conditions. Full article

(This article belongs to the Special Issue Genetic Diversity, Conservation, and Innovative Plant Breeding Strategies)

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20 pages, 3417 KiB

Open AccessArticle

Genetic Diversity, Linkage Disequilibrium and Population Structure of Bulgarian Bread Wheat Assessed by Genome-Wide Distributed SNP Markers: From Old Germplasm to Semi-Dwarf Cultivars

by Vladimir Aleksandrov, Tania Kartseva, Ahmad M. Alqudah, Konstantina Kocheva, Krasimira Tasheva, Andreas Börner and Svetlana Misheva

Plants 2021, 10(6), 1116; https://doi.org/10.3390/plants10061116 - 31 May 2021

Cited by 19 | Viewed by 3961

Abstract

Genetic diversity and population structure are key resources for breeding purposes and genetic studies of important agronomic traits in crops. In this study, we described SNP-based genetic diversity, linkage disequilibrium and population structure in a panel of 179 bread wheat advanced cultivars and old accessions from Bulgaria, using an optimized wheat 25K Infinium iSelect array. Out of 19,019 polymorphic SNPs, 17,968 had a known chromosome position on the A (41%), B (42%) and D (11%) genome, and 6% were not assigned to any chromosome. Homoeologous group 4, in particular chromosome 4D, was the least polymorphic. In the total population, the Nei’s gene diversity was within the range 0.1–0.5, and the polymorphism information content ranged from 0.1 to 0.4. Significant differences between the old and modern collections were revealed with respect to the linkage disequilibrium (LD): the average values for LD (r²), the percentage of the locus pairs in LD and the LD decay were 0.64, 16% and 3.3 for the old germplasm, and 0.43, 30% and 4.1 for the modern releases, respectively. Structure and k-means clustering algorithm divided the panel into three groups. The old accessions formed a distinct subpopulation. The cluster analysis further distinguished the modern releases according to the geographic region and genealogy. Gene exchange was evidenced mainly between the subpopulations of contemporary cultivars. The achieved understanding of the genetic diversity and structure of the Bulgarian wheat population and distinctiveness of the old germplasm could be of interest for breeders developing cultivars with improved characteristics. The obtained knowledge about SNP informativeness and the LD estimation are worthwhile for selecting markers and for considering the composition of a population in association mapping studies of traits of interest. Full article

(This article belongs to the Special Issue Genetic Diversity, Conservation, and Innovative Plant Breeding Strategies)

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13 pages, 2293 KiB

Open AccessArticle

Genome-Wide Association Study Reveals the QTLs for Seed Storability in World Rice Core Collections

by Fangxi Wu, Xi Luo, Lingqiang Wang, Yidong Wei, Jianguo Li, Huaan Xie, Jianfu Zhang and Guosheng Xie

Plants 2021, 10(4), 812; https://doi.org/10.3390/plants10040812 - 20 Apr 2021

Cited by 12 | Viewed by 2885

Abstract

Seed storability is a main agronomically important trait to assure storage safety of grain and seeds in rice. Although many quantitative trait loci (QTLs) and associated genes for rice seed storability have been identified, the detailed genetic mechanisms of seed storability remain unclear in rice. In this study, a genome-wide association study (GWAS) was performed in 456 diverse rice core collections from the 3K rice genome. We discovered the new nine QTLs designated as qSS1-1, qSS1-2, qSS2-1, qSS3-1, qSS5-1, qSS5-2, qSS7-1, qSS8-1, and qSS11-1. According to the analysis of the new nine QTLs, our results could well explain the reason why seed storability of indica subspecies was superior to japonica subspecies in rice. Among them, qSS1-2 and qSS8-1 were potentially co-localized with a known associated qSS1/OsGH3-2 and OsPIMT1, respectively. Our results also suggest that pyramiding breeding of superior alleles of these associated genes will lead to new varieties with improved seed storability in the future. Full article

(This article belongs to the Special Issue Genetic Diversity, Conservation, and Innovative Plant Breeding Strategies)

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13 pages, 1120 KiB

Open AccessEditor’s ChoiceReview

Integrative Pre-Breeding for Biotic Resistance in Forest Trees

by Melisa Guevara-Escudero, Angy N. Osorio and Andrés J. Cortés

Plants 2021, 10(10), 2022; https://doi.org/10.3390/plants10102022 - 26 Sep 2021

Cited by 20 | Viewed by 4680

Abstract

Climate change is unleashing novel biotic antagonistic interactions for forest trees that may jeopardize populations’ persistence. Therefore, this review article envisions highlighting major opportunities from ecological evolutionary genomics to assist the identification, conservation, and breeding of biotic resistance in forest tree species. Specifically, we first discuss how assessing the genomic architecture of biotic stress resistance enables us to recognize a more polygenic nature for a trait typically regarded Mendelian, an expectation from the Fisherian runaway pathogen–host concerted arms-race evolutionary model. Secondly, we outline innovative pipelines to capture and harness natural tree pre-adaptations to biotic stresses by merging tools from the ecology, phylo-geography, and omnigenetics fields within a predictive breeding platform. Promoting integrative ecological genomic studies promises a better understanding of antagonistic co-evolutionary interactions, as well as more efficient breeding utilization of resistant phenotypes. Full article

(This article belongs to the Special Issue Genetic Diversity, Conservation, and Innovative Plant Breeding Strategies)

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36 pages, 5260 KiB

Open AccessReview

Induced Genetic Variations in Fruit Trees Using New Breeding Tools: Food Security and Climate Resilience

by Muhammad Naeem Sattar, Zafar Iqbal, Jameel M. Al-Khayri and S. Mohan Jain

Plants 2021, 10(7), 1347; https://doi.org/10.3390/plants10071347 - 1 Jul 2021

Cited by 14 | Viewed by 5865

Abstract

Fruit trees provide essential nutrients to humans by contributing to major agricultural outputs and economic growth globally. However, major constraints to sustainable agricultural productivity are the uncontrolled proliferation of the population, and biotic and abiotic stresses. Tree mutation breeding has been substantially improved using different physical and chemical mutagens. Nonetheless, tree plant breeding has certain crucial bottlenecks including a long life cycle, ploidy level, occurrence of sequence polymorphisms, nature of parthenocarpic fruit development and linkage. Genetic engineering of trees has focused on boosting quality traits such as productivity, wood quality, and resistance to biotic and abiotic stresses. Recent technological advances in genome editing provide a unique opportunity for the genetic improvement of woody plants. This review examines application of the CRISPR-Cas system to reduce disease susceptibility, alter plant architecture, enhance fruit quality, and improve yields. Examples are discussed of the contemporary CRISPR-Cas system to engineer easily scorable PDS genes, modify lignin, and to alter the flowering onset, fertility, tree architecture and certain biotic stresses. Full article

(This article belongs to the Special Issue Genetic Diversity, Conservation, and Innovative Plant Breeding Strategies)

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