Importance of Genetic Diversity Assessment in Crop Plants and Its Recent Advances: An Overview of Its Analytical Perspectives

The importance of plant genetic diversity (PGD) is now being recognized as a specific area since exploding population with urbanization and decreasing cultivable lands are the critical factors contributing to food insecurity in developing world. Agricultural scientists realized that PGD can be captured and stored in the form of plant genetic resources (PGR) such as gene bank, DNA library, and so forth, in the biorepository which preserve genetic material for long period. However, conserved PGR must be utilized for crop improvement in order to meet future global challenges in relation to food and nutritional security. This paper comprehensively reviews four important areas; (i) the significance of plant genetic diversity (PGD) and PGR especially on agriculturally important crops (mostly field crops); (ii) risk associated with narrowing the genetic base of current commercial cultivars and climate change; (iii) analysis of existing PGD analytical methods in pregenomic and genomic era; and (iv) modern tools available for PGD analysis in postgenomic era. This discussion benefits the plant scientist community in order to use the new methods and technology for better and rapid assessment, for utilization of germplasm from gene banks to their applied breeding programs. With the advent of new biotechnological techniques, this process of genetic manipulation is now being accelerated and carried out with more precision (neglecting environmental effects) and fast-track manner than the classical breeding techniques. It is also to note that gene banks look into several issues in order to improve levels of germplasm distribution and its utilization, duplication of plant identity, and access to database, for prebreeding activities. Since plant breeding research and cultivar development are integral components of improving food production, therefore, availability of and access to diverse genetic sources will ensure that the global food production network becomes more sustainable. The pros and cons of the basic and advanced statistical tools available for measuring genetic diversity are briefly discussed and their source links (mostly) were provided to get easy access; thus, it improves the understanding of tools and its practical applicability to the researchers.

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Genetic Diversity Assessment and its Importance on Crop improvement in Ethiopia: Potentials and challenges

Journal of Commercial Biotechnology ◽

10.5912/jcb779 ◽

2017 ◽

Vol 23 (1) ◽

Author(s):

Obssi Dessalegn Hora ◽

Abebaw Misganaw Amebaw

Keyword(s):

Genetic Diversity ◽

Food Production ◽

Crop Production ◽

Plant Genetic Resources ◽

Crop Improvement ◽

Genetic Material ◽

Germplasm Conservation ◽

Global Perspective ◽

Easy Access ◽

Diversity Assessment

Genetic diversity assessments of plant play a great role in a predictable area to improve agricultural production and productivity, to solve food uncertainty in developing world. Many breeders has tried to realized that crop with diverge genetic diversity can be assessed , evaluated ,captured and stored in the form of superior plant genetic resources such as gene bank, DNA library to preserve genetic material for long period. However, the conserved genetically diversified plant must be utilized to improve crop production in order to solve future food and nutritional challenges. This paper reviews eight important areas; (i) Gaps in Developing Taxonomy of Ethiopian crops (ii) Monitoring diversity for crop improvement, (iii) Alterations in landscape features, (iv) Significance of Germplasm Conservation of crops, (v) Gap in morphological characterization, (vi) Global perspective of agro biodiversity and molecular evolution, (vii) Emergence of tissue culture technology in Ethiopia (viii) Germplasm improvement. It provides basic enlightenment for plant breeders for better understanding and rapid diversity assessment of crop, for better understanding and utilization of germplasm from gene banks to their applied breeding programs. With the advent of new biotechnological techniques, this process of conventional breeding is now being accelerated and carried out with more precision and speedy manner than the classical breeding techniques by using molecular markers to avoid taxonomic confusion. For sustainable food production, conventional plant breeding research should have integration with molecular marker assisted evaluation of crops genetic diversity and/or cultivar improvement will be achieved. As a result, availability and access to diverse genetic sources will ensure that the global food production network becomes more sustainable. The merit and demerit of the basic morphological characterizations are briefly discussed and their source links were provided to get easy access; thus, it improves the understanding of modern molecular tools and its practical applicability to the breeders.

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Genetic diversity assessment of sorghum (Sorghum bicolor (L.) Moench) accessions using single nucleotide polymorphism markers

Plant Genetic Resources ◽

10.1017/s1479262119000212 ◽

2019 ◽

Vol 17 (5) ◽

pp. 412-420

Author(s):

G. Afolayan ◽

S. P. Deshpande ◽

S. E. Aladele ◽

A. O. Kolawole ◽

I. Angarawai ◽

...

Keyword(s):

Genetic Diversity ◽

Sorghum Bicolor ◽

Agronomic Traits ◽

Crop Improvement ◽

Single Nucleotide ◽

Breeding Programs ◽

Diversity Assessment ◽

Crop Research ◽

International Crop Research Institute ◽

Private Alleles

AbstractSorghum (Sorghum bicolor (L.) Moench) is an important resource to the national economy and it is essential to assess the genetic diversity in existing sorghum germplasm for better conservation, utilization and crop improvement. The aim of this study was to evaluate the level of genetic diversity within and among sorghum germplasms collected from diverse institutes in Nigeria and Mali using Single Nucleotide Polymorphic markers. Genetic diversity among the germplasm was low with an average polymorphism information content value of 0.24. Analysis of Molecular Variation revealed 6% variation among germplasm and 94% within germplasms. Dendrogram revealed three groups of clustering which indicate variations within the germplasms. Private alleles identified in the sorghum accessions from National Center for Genetic Resources and Biotechnology, Ibadan, Nigeria and International Crop Research Institute for the Semi-Arid Tropics, Kano, Nigeria shows their prospect for sorghum improvement and discovery of new agronomic traits. The presence of private alleles and genetic variation within the germplasms indicates that the accessions are valuable resources for future breeding programs.

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Genomic Analysis of Spanish Wheat Landraces Reveals Their Huge Potential for Breeding

10.21203/rs.2.9775/v1 ◽

2019 ◽

Author(s):

Laura Pascual ◽

Magdalena Ruiz ◽

Matilde López-Fernández ◽

Helena Pérez-Peña ◽

Elena Benavente ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Durum Wheat ◽

Bread Wheat ◽

Plant Genetic Resources ◽

Crop Improvement ◽

Geographic Origin ◽

Local Conditions ◽

Reference Set ◽

Wheat Landraces

Abstract Background One of the main goals for the XXI century breeding is the development of crop cultivars that can maintain current yields under unfavorable environments. Landraces that have been grown under varied local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research (CRF-INIA) holds a wide collection of wheat landraces. These accessions, locally adapted to a really wide diversity of eco-climatic conditions, represent a highly valuable material for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping. Results DArTseq GBS approach generated 10K SNPs and 40K DArT high-quality markers that were mapped against the currently available bread wheat reference genome. The markers with known location were distributed in all the chromosomes, having a relatively well-balanced genome-wide coverage. The genetic analysis showed that Spanish wheat landraces are clustered in different groups, thus representing genetic pools capable to provide different allelic variation. The subspecies had a major impact on the population structure of durum wheat landraces, identifying three different clusters that corresponded to subsps. durum, turgidum and dicoccon. The population structure of bread wheat landraces was more biased by geographic origin. Conclusions The results showed a wider genetic diversity in landraces when compared to a reference set that included commercial varieties, and a higher divergence between landraces and the reference set in durum wheat than in bread wheat. Some genomic regions with patterns of variation that differ between landraces and reference varieties could be detected, pointing out loci under selection during crop improvement that could help to target breeding efforts. The results obtained from this work will be highly valuable for future GWAS analysis.

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654 The Role of Plant Genetic Resources in Safeguarding Global Carrying Capacity

HortScience ◽

10.21273/hortsci.35.3.511a ◽

2000 ◽

Vol 35 (3) ◽

pp. 511A-511

Author(s):

Peter Bretting

Keyword(s):

Genetic Resources ◽

Carrying Capacity ◽

Plant Genetic Resources ◽

Crop Improvement ◽

Genetic Material ◽

Basic Knowledge ◽

Timber Species ◽

Minor Crops ◽

Minor Crop ◽

Improvement Programs

Plants provide humans with food, fiber, feed, ornamentals, industrial products, medicine, shelter, and fuel. As vegetation, they maintain global environmental integrity and the carrying capacity for all life. From an anthropocentric perspective, plants serve as genetic resources (PGR) for sustaining the growing human population. Research on PGR can provide basic knowledge for crop improvement or environmental management that enables renewable, sustainable production of the preceding necessities. PGR also provide the raw material for increasing yield and end product's quality, while requiring fewer inputs (water, nutrients, agrichemicals, etc.). The staples of life—30 or so major grain, oilseed, fiber, and timber species—comprise the “thin green line” vital to human survival, either directly, or through trade and income generation. Many crop genebanks worldwide focus on conserving germplasm of these staples as a shield against genetic vulnerability that may endanger economies and humanity on an international scale. Fewer genebanks and crop improvement programs conserve and develop “minor crops,” so called because of their lesser economic value or restricted cultivation globally. Yet, these minor crops, many categorized as horticultural, may be key to human carrying capacity—especially in geographically or economically marginal zones. The USDA/ARS National Plant Germplasm System (NPGS) contains a great number and diversity of minor crop germplasm. The NPGS, other genebanks, and minor crop breeding programs scattered throughout the world, help safeguard human global carrying capacity by providing the raw genetic material and genetic improvement infrastructure requisite for producing superior minor crops. The latter may represent the best hope for developing new varieties and crops, new crop rotations, and new renewable products that in the future may enhance producer profitability or even ensure producer and consumer survival.

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Genomic Analysis Of Spanish Wheat Landraces Reveals Their Variability And Potential For Breeding

10.21203/rs.2.9775/v3 ◽

2020 ◽

Author(s):

Laura Pascual ◽

Magdalena Ruiz ◽

Matilde López-Fernández ◽

Helena Pérez-Peña ◽

Elena Benavente ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Durum Wheat ◽

Bread Wheat ◽

Plant Genetic Resources ◽

Crop Improvement ◽

Genome Wide Association Studies ◽

Reference Set ◽

Genome Wide ◽

Wheat Landraces

Abstract Background One of the main goals of the plant breeding in the 21 st century is the development of crop cultivars that can maintain current yields in unfavorable environments. Landraces that have been grown under varying local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research maintains a broad collection of wheat landraces. These accessions, which are locally adapted to diverse eco-climatic conditions, represent highly valuable materials for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping. Results The DArTseq GBS approach generated 10K SNPs and 40K high-quality DArT markers, which were located against the currently available bread and durum wheat reference genomes. The markers with known locations were distributed across all chromosomes with relatively well-balanced genome-wide coverage. The genetic analysis showed that the Spanish wheat landraces were clustered in different groups, thus representing genetic pools providing a range of allelic variation. The subspecies had a major impact on the population structure of the durum wheat landraces, with three distinct clusters that corresponded to subsps. durum , turgidum and dicoccon being identified. The population structure of bread wheat landraces was mainly biased by geographic origin. Conclusions The results showed broader genetic diversity in the landraces compared to a reference set that included commercial varieties and higher divergence between the landraces and the reference set in durum wheat than in bread wheat. The analyses revealed genomic regions whose patterns of variation were markedly different in the landraces and reference varieties, indicating loci that have been under selection during crop improvement, which could help to target breeding efforts. The results obtained from this work will provide a basis for future genome-wide association studies.

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Maximizing genetic representation in seed collections from populations of self and cross-pollinated banana wild relatives

BMC Plant Biology ◽

10.1186/s12870-021-03142-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Simon Kallow ◽

Bart Panis ◽

Dang Toan Vu ◽

Tuong Dang Vu ◽

Janet Paofa ◽

...

Keyword(s):

Genetic Diversity ◽

Papua New Guinea ◽

Mating Systems ◽

Plant Genetic Resources ◽

Genetic Material ◽

New Guinea ◽

Wild Relatives ◽

Ex Situ ◽

Conservation Targets ◽

Seed Collections

Abstract Background Conservation of plant genetic resources, including the wild relatives of crops, plays an important and well recognised role in addressing some of the key challenges faced by humanity and the planet including ending hunger and biodiversity loss. However, the genetic diversity and representativeness of ex situ collections, especially that contained in seed collections, is often unknown. This limits meaningful assessments against conservation targets, impairs targeting of future collecting and limits their use. We assessed genetic representation of seed collections compared to source populations for three wild relatives of bananas and plantains. Focal species and sampling regions were M. acuminata subsp. banksii (Papua New Guinea), M. balbisiana (Viet Nam) and M. maclayi s.l. (Bougainville, Papua New Guinea). We sequenced 445 samples using suites of 16–20 existing and newly developed taxon-specific polymorphic microsatellite markers. Samples of each species were from five populations in a region; 15 leaf samples from different individuals and 16 seed samples from one infructescence (‘bunch’) were analysed for each population. Results Allelic richness of seeds compared to populations was 51, 81 and 93% (M. acuminata, M. balbisiana and M. maclayi respectively). Seed samples represented all common alleles in populations but omitted some rarer alleles. The number of collections required to achieve the 70% target of the Global Strategy for Plant Conservation was species dependent, relating to mating systems. Musa acuminata populations had low heterozygosity and diversity, indicating self-fertilization; many bunches were needed (> 15) to represent regional alleles to 70%; over 90% of the alleles from a bunch are included in only two seeds. Musa maclayi was characteristically cross-fertilizing; only three bunches were needed to represent regional alleles; within a bunch, 16 seeds represent alleles. Musa balbisiana, considered cross-fertilized, had low genetic diversity; seeds of four bunches are needed to represent regional alleles; only two seeds represent alleles in a bunch. Conclusions We demonstrate empirical measurement of representation of genetic material in seeds collections in ex situ conservation towards conservation targets. Species mating systems profoundly affected genetic representation in seed collections and therefore should be a primary consideration to maximize genetic representation. Results are applicable to sampling strategies for other wild species.

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Genetic diversity and GWAS of agronomic traits using an ICARDA lentil (Lens culinaris Medik.) Reference Plus collection

Plant Genetic Resources ◽

10.1017/s147926212100006x ◽

2021 ◽

pp. 1-10

Author(s):

Karthika Rajendran ◽

Clarice J. Coyne ◽

Ping Zheng ◽

Gopesh Saha ◽

Dorrie Main ◽

...

Keyword(s):

Genetic Diversity ◽

Lens Culinaris ◽

Agronomic Traits ◽

Plant Genetic Resources ◽

Crop Improvement ◽

Principal Component ◽

Genotyping By Sequencing ◽

Phenotypic Data ◽

Reference Set ◽

Genome Wide

Abstract Genotyping of lentil plant genetic resources holds the promise to increase the identification and utilization of useful genetic diversity for crop improvement. The International Center for Agriculture Research in the Dry Areas (ICARDA) lentil reference set plus collection of 176 accessions was genotyped using genotyping-by-sequencing (GBS) and 22,555 SNPs were identified. The population structure was investigated using Bayesian analysis (STRUCTURE, k = 3) and principal component analysis. The two methods are in concordance. Genome-wide association analysis (GWAS) using the filtered SNP set and ICARDA historical phenotypic data discovered putative markers for several agronomic traits including days to first flower, seeds per pod, seed weight and days to maturity. The genetic and genomic resources developed and utilized in this study are available to the research community interested in exploring the ICARDA reference set plus collection using GWAS.

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Genomic Analysis Of Spanish Wheat Landraces Reveals Their Variability And Potential For Breeding

10.21203/rs.2.9775/v2 ◽

2019 ◽

Author(s):

Laura Pascual ◽

Magdalena Ruiz ◽

Matilde López-Fernández ◽

Helena Pérez-Peña ◽

Elena Benavente ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Durum Wheat ◽

Bread Wheat ◽

Plant Genetic Resources ◽

Crop Improvement ◽

Genome Wide Association Studies ◽

Reference Set ◽

Genome Wide ◽

Wheat Landraces

Abstract Background One of the main goals of the plant breeding in the 21 st century is the development of crop cultivars that can maintain current yields in unfavorable environments. Landraces that have been grown under varying local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research maintains a broad collection of wheat landraces. These accessions, which are locally adapted to diverse eco-climatic conditions, represent highly valuable materials for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping. Results The DArTseq GBS approach generated 10K SNPs and 40K high-quality DArT markers, which were mapped against the currently available bread and durum wheat reference genomes. The markers with known locations were distributed across all chromosomes with relatively well-balanced genome-wide coverage. The genetic analysis showed that the Spanish wheat landraces were clustered in different groups, thus representing genetic pools providing a range of allelic variation. The subspecies had a major impact on the population structure of the durum wheat landraces, with three distinct clusters that corresponded to subsps. durum , turgidum and dicoccon being identified. The population structure of bread wheat landraces was mainly biased by geographic origin. Conclusions The results showed broader genetic diversity in the landraces compared to a reference set that included commercial varieties and higher divergence between the landraces and the reference set in durum wheat than in bread wheat. The analyses revealed genomic regions whose patterns of variation were markedly different in the landraces and reference varieties, indicating loci that have been under selection during crop improvement, which could help to target breeding efforts. The results obtained from this work will provide a basis for future genome-wide association studies.

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Genetic diversity assessment of ancient mulberry (Morus spp.) in Lebanon using morphological, chemical and molecular markers (SSR and ISSR)

Advances in Horticultural Science ◽

10.36253/ahsc-8376 ◽

2021 ◽

Vol 35 (3) ◽

pp. 243-253

Author(s):

Aline Kadri ◽

Shoaib Saleh ◽

Ahmad Elbitar ◽

Ali Chehade

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Crop Improvement ◽

Germplasm Management ◽

Diversity Assessment ◽

Geographical Regions ◽

Relative Separation ◽

Morus Spp ◽

High Level ◽

Issr Primers

Lebanon has ancient mulberry trees which are the remnants of the abundant orchards that dominated its lands during the nineteenth century. Lebanese mulberry germplasm has not been assessed yet. This study aims to collect local old rainfed mulberry accessions from different geographical regions and assess their diversity by using morphological and molecular markers (SSR and ISSR). Genetic diversity of 70 accessions of mulberry were evaluated by using 27 morphological traits. The dendrogram based on the morphological attributes showed a relative separation of the different accessions based on fruits color and taste. Molecular analysis was performed for the accessions by using selected SSR and ISSR primers. The primers marked a high discriminating power (0.7 to 0.89). The dendrogram constructed on the base of UPGMA method showed 13 different groups. The clustering patterns indicated no location nor local name specificity among mulberry accessions. The combination of SSR and ISSR primers was informative for estimating the extent of mulberry genetic diversity. It can be concluded that there is a high level of genetic diversity within mulberry trees in Lebanon. These results will be useful for mulberry germplasm management in terms of biodiversity protection and as a valuable source of gene pool for crop improvement.

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