Ecogeographical studies identify diversity and potential gaps in the largest germplasm collection of bladder clover (Trifolium spumosum L.)

Plant germplasm collections are important reservoirs of diversity for plant breeders and adding to the knowledge of the diversity among and within germplasm accessions helps plant breeders to use them more efficiently. The annual legume, bladder clover (Trifolium spumosum L.), was the model plant in this study. The hypothesis that ecogeographical variables are important sources of diversity in the germplasm collection of bladder clover and some variables are more important than others has been studied. Three themes have been addressed here: firstly, analysis of the existing passport data to determine a minimum set of ecogeographical descriptors required for capturing ecological aspects of each collection site; secondly, illustration of the ecogeographical regions and subregions using GIS techniques to identify areas with the greatest likelihood of filling gaps in the collection; thirdly, development of an approach for the evaluation of genetic diversity by grouping accessions with a focus on outliers within the collection using principal component and cluster analyses. In this paper the importance of longitude as a geographical factor has been documented and the overall ecogeographical diversity in the germplasm collection of bladder clover has been screened.

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Harnessing genetic diversity in the USDA pea (Pisum sativum L.) germplasm collection through genomic prediction

10.1101/2021.05.07.443173 ◽

2021 ◽

Author(s):

Md Abdullah Al Bari ◽

Ping Zheng ◽

Indalecio Viera ◽

Hannah Worral ◽

Stephen Szwiec ◽

...

Keyword(s):

Genetic Diversity ◽

Seed Yield ◽

Genomic Prediction ◽

Prediction Models ◽

Germplasm Collection ◽

Predictive Ability ◽

Germplasm Collections ◽

Pisum Sativum L ◽

Generation Sequencing ◽

Germplasm Accessions

Phenotypic evaluation and efficient utilization of germplasm collections can be time-intensive, laborious, and expensive. However, with the plummeting costs of next-generation sequencing and the addition of genomic selection to the plant breeder's toolbox, we now can more efficiently tap the genetic diversity within large germplasm collections. In this study, we applied and evaluated genomic selection's potential to a set of 482 pea accessions, genotyped with 30,600 SNP markers and phenotyped for seed yield and yield-related components, for enhancing selection of accessions from the USDA Pea Germplasm Collection. Genomic prediction models and several factors affecting predictive ability were evaluated in a series of cross-validation schemes across complex traits. Different genomic prediction models gave similar results, with predictive ability across traits ranging from 0.23 to 0.60, with no model working best across all traits. Increasing the training population size improved the predictive ability of most traits, including seed yield. An increasing trend in predictive ability was also observed with an increasing number of SNPs. Accounting for population structure effects did not significantly boost predictive ability, but we observed a slight improvement in seed yield. By applying the genomic prediction model from this study, we then examined the distribution of nonphenotyped accessions, and the reliability of genomic estimated breeding values (GEBV) of the USDA Pea accessions genotyped but not phenotyped. The distribution of GEBV suggested that none of the nonphenotyped accessions were expected to perform outside the range of the phenotyped accessions. Desirable breeding values with higher reliability can be used to identify and screen favorable germplasm accessions. Expanding the training set and incorporating additional orthogonal information into the genomic prediction framework could enhance prediction accuracy. Keywords: genomic selection, genomic prediction, reliability criteria, germplasm accessions, pea (Pisum sativum L.), next-generation sequencing

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Managing self-pollinated germplasm collections to maximize utilization

Plant Genetic Resources ◽

10.1017/s147926211000047x ◽

2011 ◽

Vol 9 (01) ◽

pp. 123-133 ◽

Cited By ~ 11

Author(s):

Randall L. Nelson

Keyword(s):

Genetic Diversity ◽

Dna Markers ◽

Germplasm Collection ◽

Whole Genome ◽

Germplasm Collections ◽

Seed Distribution ◽

Future Potential ◽

Primary Mission ◽

Germplasm Accessions ◽

Current Potential

The primary mission of germplasm collections is to preserve genetic diversity, but germplasm is preserved so that it can be used. Historically, the standard practice is that all germplasm accessions should be maintained as collected, so that even self-pollinated accessions are maintained as heterogeneous seed lots. In theory, this seems like an ideal strategy for preserving genetic diversity, but in practice, it is simply not workable. Heterogeneous accessions are in constant risk of change and loss. It is possible to mitigate the risk factors, but they can only be lessened and not eliminated. Maintaining pure-lined accessions for self-pollinated species not only eliminates the problems associated with genetic drift and natural selection, but also enhances the accuracy of the evaluations and fosters effective germplasm utilization. Neither the current potential to characterize entire germplasm collections with tens of thousands of DNA markers nor the future potential of whole genome sequencing to completely characterize the diversity of all accessions in collections can be fully realized for self-pollinated species unless accessions are homogeneous and homozygous. In this manuscript, the case is made for pure-lining self-pollinated germplasm accessions using the USDA Soybean Germplasm Collection, which has maintained pure-lined accessions for over 50 years, as an example. There is also an analysis of the extensive seed distribution from this collection to indicate the value of a diverse collection of genotypes.

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Genetic Analysis of Chinese Cucumber Collections in the U.S. National Germplasm Collection

HortScience ◽

10.21273/hortsci.33.3.534e ◽

1998 ◽

Vol 33 (3) ◽

pp. 534e-534 ◽

Cited By ~ 1

Author(s):

J. Staub ◽

Felix Sequen ◽

Tom Horejsi ◽

Jin Feng Chen

Keyword(s):

Genetic Diversity ◽

Principal Component Analysis ◽

Genetic Variation ◽

Genetic Analysis ◽

Allelic Variation ◽

Germplasm Collection ◽

Principal Component ◽

Isozyme Loci ◽

National Plant Germplasm System ◽

The U.S

Genetic variation in cucumber accessions from China was assessed by examining variation at 21 polymorphic isozyme loci. Principal component analysis of allelic variation allowed for the depiction of two distinct groupings of Chinese accessions collected in 1994 and 1996 (67 accessions). Six isozyme loci (Gpi, Gr, Mdh-2, Mpi-2, Pep-gl, and Pep-la) were important in elucidating these major groups. These groupings were different from a single grouping of Chinese 146 accessions acquired before 1994. Allelic variation in Chinese accessions allowed for comparisons with other accessions in the U.S. National Plant Germplasm System (U.S. NPGS) collection grouped by continent and sub-continent. When Chinese accessions taken collectively were compared with an array of 853 C. sativus U.S. NPGS accessions examined previously, relationships differed between accessions grouped by country or subcontinent. Data indicate that acquisition of additional Chinese and Indian cucumber accessions would be strategically important for increasing genetic diversity in the U.S. NPGS cucumber collection.

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Genetic Diversity and Geographic Differentiation in Pawpaw [Asimina triloba (L.) Dunal] Populations from Nine States as Revealed by Allozyme Analysis

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.123.4.635 ◽

1998 ◽

Vol 123 (4) ◽

pp. 635-641 ◽

Cited By ~ 6

Author(s):

Hongwen Huang ◽

Desmond R. Layne ◽

Don E. Riemenschneider

Keyword(s):

Genetic Diversity ◽

New York ◽

Germplasm Collection ◽

Principal Component ◽

Major Group ◽

State University ◽

Allozyme Diversity ◽

Woody Perennial ◽

Asimina Triloba ◽

Hardy Weinberg Equilibrium

As a new National Clonal Germplasm Repository for Asimina species at Kentucky State University (KSU), of major concern to us is the genetic variation within our germplasm collection. The present study investigated the extent of genetic diversity for the pawpaw germplasm in our collection and the geographical pattern of genetic diversity among populations using isozyme markers. Allozyme diversity was high in Asimina triloba (L.) Dunal (Annonaceae) collected from all nine different states, as is typical for temperate woody perennial, widespread and outcrossing plant species. Averaged across populations, mean number of alleles per locus (A), percent polymorphic loci (P), effective number of alleles per locus (Ae), and expected heterozygosity (He) were 1.54, 43.5, 1.209, and 0.172, respectively. Significant deviations from Hardy-Weinberg equilibrium were found in nine populations at an average of 4.8 loci. Observed heterozygosity was higher than expected. Partitioning of genetic diversity showed that 88.2% resided within populations. The proportion of genetic diversity among populations (Gst = 0.118; FST = 0.085) was either lower than or within the range of those species with similar ecological and life-history traits. The mean genetic identity among populations was high (I = 0.988). An analysis using UPGMA clustered most populations as one major group, with the southernmost (Georgia) and the westernmost (Illinois) populations readily separated from the main group. The relationships discovered by principal component analysis (PCA) were similar to those revealed by UPGMA. In addition, PCA separated the northernmost population (New York) from the major group. Sampling strategies for future germplasm collection of A. triloba are also discussed.

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Harnessing Genetic Diversity in the USDA Pea Germplasm Collection Through Genomic Prediction

Frontiers in Genetics ◽

10.3389/fgene.2021.707754 ◽

2021 ◽

Vol 12 ◽

Author(s):

Md. Abdullah Al Bari ◽

Ping Zheng ◽

Indalecio Viera ◽

Hannah Worral ◽

Stephen Szwiec ◽

...

Keyword(s):

Genetic Diversity ◽

Seed Yield ◽

Genomic Prediction ◽

Complex Traits ◽

Prediction Models ◽

Germplasm Collection ◽

Predictive Ability ◽

Snp Markers ◽

Breeding Values ◽

Germplasm Collections

Phenotypic evaluation and efficient utilization of germplasm collections can be time-intensive, laborious, and expensive. However, with the plummeting costs of next-generation sequencing and the addition of genomic selection to the plant breeder’s toolbox, we now can more efficiently tap the genetic diversity within large germplasm collections. In this study, we applied and evaluated genomic prediction’s potential to a set of 482 pea (Pisum sativum L.) accessions—genotyped with 30,600 single nucleotide polymorphic (SNP) markers and phenotyped for seed yield and yield-related components—for enhancing selection of accessions from the USDA Pea Germplasm Collection. Genomic prediction models and several factors affecting predictive ability were evaluated in a series of cross-validation schemes across complex traits. Different genomic prediction models gave similar results, with predictive ability across traits ranging from 0.23 to 0.60, with no model working best across all traits. Increasing the training population size improved the predictive ability of most traits, including seed yield. Predictive abilities increased and reached a plateau with increasing number of markers presumably due to extensive linkage disequilibrium in the pea genome. Accounting for population structure effects did not significantly boost predictive ability, but we observed a slight improvement in seed yield. By applying the best genomic prediction model (e.g., RR-BLUP), we then examined the distribution of genotyped but nonphenotyped accessions and the reliability of genomic estimated breeding values (GEBV). The distribution of GEBV suggested that none of the nonphenotyped accessions were expected to perform outside the range of the phenotyped accessions. Desirable breeding values with higher reliability can be used to identify and screen favorable germplasm accessions. Expanding the training set and incorporating additional orthogonal information (e.g., transcriptomics, metabolomics, physiological traits, etc.) into the genomic prediction framework can enhance prediction accuracy.

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Genetic diversity of Cuban pineapple germplasm assessed by AFLP Markers

Cropp Breeding and Applied Biotechnology ◽

10.1590/s1984-70332012000200002 ◽

2012 ◽

Vol 12 (2) ◽

pp. 104-110 ◽

Cited By ~ 8

Author(s):

Ermis Yanes Paz ◽

Katia Gil ◽

Laureano Rebolledo ◽

Andrés Rebolledo ◽

Daniel Uriza ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Characterization ◽

Genetic Relationships ◽

Germplasm Collection ◽

Morphological Characterization ◽

Aflp Markers ◽

Ananas Comosus ◽

Morphological Descriptors ◽

Low Level ◽

Germplasm Collections

The Cuban pineapple germplasm collection represents the genetic diversity of pineapple cultivated in that country and includes other important genotypes obtained from the germplasm collections in Brazil and Martinique. The collection has previously been characterized with morphological descriptors but a molecular characterization has been lacking. With this aim, 56 six genotypes of A. comosus and one of Bromelia pinguin were analyzed with a total of 191 AFLP markers. A dendrogram that represents the genetic relationships between these samples based on the AFLP results showed a low level of diversity in the Cuban pineapple collection. All Ananas comosus accessions, being the majority obtained from farmers in different regions in Cuba, are grouped at distances lower than 0.20. Molecular characterization was in line with morphological characterization. These results are useful for breeding and conservation purposes.

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Geographical patterns of diversity for qualitative and quantitative traits in the pigeonpea germplasm collection

Plant Genetic Resources ◽

10.1079/pgr200587 ◽

2005 ◽

Vol 3 (3) ◽

pp. 331-352 ◽

Cited By ~ 13

Author(s):

Hari D. Upadhyaya ◽

R.P.S. Pundir ◽

C.L.L. Gowda ◽

K.N. Reddy ◽

Sube Singh

Keyword(s):

Quantitative Traits ◽

Diversity Index ◽

Germplasm Collection ◽

Flower Colour ◽

Principal Component ◽

The Philippines ◽

Growth Duration ◽

Flowering Pattern ◽

Stem Colour ◽

Germplasm Accessions

We analysed the patterns of variation for 14 qualitative and 12 quantitative traits in 11,402 pigeonpea germplasm accessions from 54 countries, which were grouped into 11 regions. Semi-spreading growth habit, green stem colour, indeterminate flowering pattern and yellow flower colour were predominant among qualitative traits. Primary seed colour had maximum variability and orange colour followed by cream were the two most frequent seed colours in the collection. Variances for all the traits were heterogeneous among regions. The germplasm accessions from Oceania were conspicuous by short growth duration, short height, fewer branches, pods with fewer seeds, smaller seed size and lower seed yields. The accessions from Africa were of longer duration, taller, with multi-seeded pods and larger seeds. The germplasm diversity indicated by Shannon–Weaver diversity index (H′) pooled over all traits, was highest for Africa (0.464±0.039) and lowest for Oceania (0.337±0.037). The cluster analysis based on three principal component scores using 12 quantitative traits revealed formation of three clusters: cluster 1 includes accessions from Oceania; cluster 2 from India and adjacent countries; and cluster 3 from Indonesia, Thailand, the Philippines, Europe, Africa, America and the Caribbean countries. Pigeonpea-rich countries such as Myanmar, Uganda, and others like Bahamas, Burundi, Comoros, Haiti and Panama are not adequately represented in the collection, and need priority attention for germplasm exploration.

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Relationship between seed traits and pasting and cooking behaviour in a pulse germplasm collection

Crop and Pasture Science ◽

10.1071/cp18205 ◽

2018 ◽

Vol 69 (9) ◽

pp. 892 ◽

Cited By ~ 3

Author(s):

Carla S. Santos ◽

Bruna Carbas ◽

Ana Castanho ◽

Maria Rosário Bronze ◽

Carmo Serrano ◽

...

Keyword(s):

Faba Bean ◽

Seed Weight ◽

Germplasm Collection ◽

Principal Component ◽

Cooking Time ◽

Seed Traits ◽

Germplasm Collections ◽

Physico Chemical ◽

Selection Of ◽

Hydration Capacity

Development of food products from legume flours is increasing. Seed and flour characteristics must be analysed for selection of the best screening quality traits. With this purpose, germplasm collections of faba bean (Vicia faba), chickpea (Cicer arietinum), lentil (Lens culinaris) and grass pea (Lathyrus sativus) were evaluated for their physico-chemical, pasting and cooking characteristics. The accessions were grouped accordingly to several seed traits (size, shape, colour, variety and surface) that affected final viscosity, cooking time, hydration capacity and seed weight. In general, seed weight was correlated with hydration capacity. Among species, faba bean revealed higher values of pasting parameters. Cooking time was significantly negatively correlated with final viscosity (–0.298) and positively correlated with seed weight (0.601). The general variance was analysed by using principal component analysis, which allowed identification of specific accessions with important traits such as higher protein or fibre content, hydration capacity or seed weight.

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A perfect storm: ploidy and preadaptation facilitate Saccharum spontaneum escape and invasion in the Republic of Panama

Biological Invasions ◽

10.1007/s10530-020-02421-3 ◽

2020 ◽

Author(s):

Kristin Saltonstall ◽

Graham D. Bonnett ◽

Karen S. Aitken

Keyword(s):

Genetic Diversity ◽

Perennial Grass ◽

Germplasm Collection ◽

High Survival ◽

Saccharum Spontaneum ◽

Local Conditions ◽

Ploidy Levels ◽

Germplasm Collections ◽

High Ploidy ◽

Sugarcane Germplasm

AbstractPolyploidy may contribute to invasive ability as it can lead to high survival and fitness during establishment and enhance the processes of adaptation to novel environments by increasing genetic diversity in invading propagules. Many grasses are polyploid and many are aggressive invaders, making them persistent problems in disturbed environments worldwide. Today, vast areas of central Panama are dominated by Saccharum spontaneum, a perennial grass that originates from Asia. While widely regarded as invasive, it is not known when or how it arrived in Panama. We explore hypotheses regarding the timing and origins of this invasion through literature review and comparisons of genetic diversity in Panama with accessions from available sugarcane germplasm collections, highlighting historical accessions that were likely brought to Panama in 1939 as part of a USDA sugarcane germplasm collection. Samples were haplotyped at two chloroplast loci and genotyped using eight microsatellite markers. All sequenced individuals from Panama belong to a single chloroplast lineage which is common worldwide and was common in the Historic germplasm collection. Although genotypic diversity was extremely high in all samples due to high ploidy, samples from Panama had reduced diversity and clustered with several accessions in the Historic collection which had the same haplotype and high ploidy levels. Our results suggest that accidental escape from the historical sugarcane germplasm collection is the likely origin of the S. spontaneum invasion in Panama. Intraspecific hybridization among several historical accessions and pre-adaptation to local conditions may have facilitated its rapid spread and persistence. We discuss the implications of our findings for biosecurity of germplasm collections.

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Identification of gaps in pearl millet germplasm from East and Southern Africa conserved at the ICRISAT genebank

Plant Genetic Resources ◽

10.1017/s1479262112000275 ◽

2012 ◽

Vol 10 (3) ◽

pp. 202-213 ◽

Cited By ~ 8

Author(s):

H. D. Upadhyaya ◽

K. N. Reddy ◽

M. Irshad Ahmed ◽

C. L. L. Gowda

Keyword(s):

Pearl Millet ◽

Southern Africa ◽

Gap Analysis ◽

Germplasm Collection ◽

Geographic Area ◽

East African ◽

African Countries ◽

Passport Data ◽

Gis Software ◽

Germplasm Accessions

The International Crops Research Institute for the semi-Arid Tropics Genebank at Patancheru, India holds the world's largest collection of 22,211 pearl millet germplasm accessions from 50 countries including 4488 landraces from 16 East and Southern African (ESA) countries. Gap analysis using FloraMap software and 3750 georeferenced pearl millet germplasm accessions from ESA countries revealed 34 districts located in 18 provinces of four East African countries and 76 districts located in 34 provinces of seven Southern African countries as geographical gaps. Analysis of characterization data using DIVA-GIS software showed 11 districts of seven provinces in Sudan and Uganda and 58 districts of 20 provinces of seven countries in Southern Africa as gaps in diversity for important morphoagronomic traits. The following districts were identified as gaps common to geographic area and diversity for some or the other traits: Amuria district in Soroti province of Uganda; Mpwapwa in Dodoma province of Tanzania; Mahalapye in Centre province and Kgatleng in Kgatleng province of Botswana; Lalomo in Southern province of Zambia; and Motoko, Mudzi and Wedza in the province of Mashonaland East; Makoni in Manikaland; Gutu and Chivi in Masvingo; Gwanda and Bulalimamangwe in Metabeland south; Hwange and Nkayi in Metabeland north; and Kwe Kwe in Midlands of Zimbabwe. For a successful germplasm collection mission to fill the gaps identified, planning should be made in advance of collaboration and consultation with National Agricultural Systems, local government officials and extension officers. It is suggested to collect the complete passport data including georeference information while collecting the germplasm.

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